https://reading.michaelmvh.com/feeds/protein-nanopores/ Protein Nanopores & Protein Sequencing. Recent publications parsed from OpenAlex. en-US 1440 Thu, 29 Oct 2026 23:02:51 GMT https://reading.michaelmvh.com/article/a1359cd457119b7ce262375d674a39d2e3d04c22dcdf6eb1ccc80929ac2a4b17/ urn:sha256:a1359cd457119b7ce262375d674a39d2e3d04c22dcdf6eb1ccc80929ac2a4b17 <p>The early detection of disabling or life-threatening diseases remains a major challenge in healthcare and relies on the direct identification of disease-specific protein and peptide biomarkers in biological fluids. Here, we establish a polymer-engineered solid-state nanopore platform for the direct electrical identification and quantification of peptide biomarkers in 20% human serum. A semidilute polyethylene glycol network generates an osmotic driving force that promotes peptide capture while screening nonspecific interactions responsible for nanopore clogging. We combine this strategy based on polymer physics with machine-learning-assisted digital serum cleaning to overcome the complexity of biological samples. This method thus allows for the extraction of peptide-specific electrical fingerprints from the serum background. As a proof of concept, we investigate three closely related kinin biomarkers: bradykinin (BK), des-Arg9-bradykinin (DABK), and Lys-bradykinin (LBK), which differ by only one or two terminal amino acids. Despite their high structural similarity, each peptide generates a distinct electrical signature, allowing reliable single-molecule discrimination in both buffer and serum. The platform further identifies and quantifies these biomarkers in mixtures of varying composition in 20% serum. More broadly, this work establishes a general strategy for the direct electrical decoding of closely related peptide biomarkers in clinically relevant biofluids.</p><p class="metadata"><time datetime="2026-10-28" title="Source date; precision not specified">October 28, 2026</time> <span aria-hidden="true"> · </span> Journal of the American Chemical Society</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/jacs.6c17884">Original publication</a></p> Wed, 28 Oct 2026 00:00:00 GMT Yuhua Cai Yuhan Liu Ismahane Khaled Benjamin Cressiot Laurent Bacri Juan Pelta OpenAlex https://reading.michaelmvh.com/article/2efb12c7625bc3bc2b6b87b75381e9a2d80295a177900611628658930faae236/ urn:sha256:2efb12c7625bc3bc2b6b87b75381e9a2d80295a177900611628658930faae236 <p>Initial Research Code Release This release contains the original Python code developed for nanopore-based amino acid analysis and classification using ADIC-AA and γ-cyclodextrin (γ-CD). The repository includes code for nanopore signal processing, feature extraction, data analysis, and machine-learning-based amino acid classification.</p><p class="metadata"><time datetime="2026-10-27" title="Source date; precision not specified">October 27, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.23702455">Original publication</a></p> Tue, 27 Oct 2026 00:00:00 GMT jaeoncho OpenAlex https://reading.michaelmvh.com/article/aa6a0b9446c006566985f175b118908a7faf08321968afe63cf74b7e17ee981f/ urn:sha256:aa6a0b9446c006566985f175b118908a7faf08321968afe63cf74b7e17ee981f <p>Nanoviruses have a multipartite circular ssDNA genome and are transmitted by aphids in a circulative manner. Although generally considered non-propagative within their vectors, direct experimental evidence supporting the absence of viral replication remains limited. This question is particularly relevant for multipartite viruses because replication within vectors could theoretically help maintain genome integrity during transmission, decreasing dilution effects and the probability of genome segment loss. Here, we investigated whether faba bean necrotic stunt virus (FBNSV, genus Nanovirus , family Nanoviridae ) replicates in aphids using several independent approaches. Viral load dynamics were quantitative PCR-monitored after virus acquisition, the replication-associated protein M-Rep was searched for within gut and salivary gland cells by immunofluorescence, viral DNA localization and strand specificity were analysed using HCR-DNA-FISH (hybridization chain reaction fluorescence in situ hybridization) and confocal microscopy, viral transcription was investigated by Illumina mRNA sequencing, and viral DNA replication was analysed by Nanopore sequencing. All approaches converged towards the same conclusion. Viral loads did not increase after acquisition, M-Rep was undetectable in aphid tissues, viral DNA accumulated outside nuclei, no negative-strand viral DNA was detected, and only negligible quantities of viral transcripts and dsDNA molecules were detected in RNA-seq and Nanopore-seq datasets from viruliferous aphids, although these molecules were readily detected in FBNSV-infected plants used as the acquisition source. While none of these approaches could alone suffice to definitely exclude a weak, localized and/or transient replication, they together strongly support the conclusion that FBNSV is transmitted in a genuinely circulative non-propagative manner.</p><p class="metadata"><time datetime="2026-10-27" title="Source date; precision not specified">October 27, 2026</time> <span aria-hidden="true"> · </span> Journal of General Virology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1099/jgv.0.002354">Original publication</a></p> Tue, 27 Oct 2026 00:00:00 GMT Laura Di Pietro Mathilde Villegas Auguste Rajot Nina I. Lukhovitskaya Valentin Guyot François Hoh Yasmine Tiberbache Jean-Louis Zeddam Yannis Michalakis Mikhail M. Pooggin Stéphane Blanc OpenAlex https://reading.michaelmvh.com/article/da434a837270cc182751007dbb9387480fffbba4d89c8cd78e830abcc1510561/ urn:sha256:da434a837270cc182751007dbb9387480fffbba4d89c8cd78e830abcc1510561 <p>midgut, we identified a posttranscriptional regulatory layer that supervises enterocyte (EC) identity and fails upon aging. Combining single-cell RNA-seq with lineage tracing in aging ECs and classical genetics, we found that aging ECs express genes that unlock the differentiated state. Upon aging, the protein Rogue (CG13928), a translational repressor, along with its partner, Orb2, orchestrates reactivation of a stem cell-related translational repression machinery involving P-body-associated RNA-binding proteins canceling the differentiated state. In young ECs, this machinery is continuously suppressed by the deubiquitinase nonstop (dUSP22) and the ubiquitin E2 dUbcH8/Kdo and E3 CTLH complex, mediating the degradation of the stem cell-related RNA binding proteins safeguarding EC identity. Upon aging, levels of dUSP22 decline and Rogue is ectopically expressed. RNA immunoprecipitation followed by nanopore-based direct RNA sequencing identified that Rogue binds to the RNA transcripts of dUbcH8/Kdo and eEF2, shortening their poly(A) tail and suppressing Kdo protein, resulting in accelerated proteasomal clearance of the CTLH complex. Subsequently, the stem cell-related P-bodies are reactivated, leading to decline in EC gene signatures and unlocking EC identity.</p><p class="metadata"><time datetime="2026-10-27" title="Source date; precision not specified">October 27, 2026</time> <span aria-hidden="true"> · </span> Genes &amp; Development</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1101/gad.353786.126">Original publication</a></p> Tue, 27 Oct 2026 00:00:00 GMT Salwa Danial Raya Ghanim Muhammad Makhzumy Avital Oknin Vaisman Eliya Bitman-Lotan Fabian Glaser Jelly HM Soffers Jesslyn C. Henriksen Avital Sarusi-Portuguez Olivia S. Rissland Ryan D. Mohan Ayala Shiber Amir Orian OpenAlex https://reading.michaelmvh.com/article/4f67e8beeb98f450479366afa973411a2570eac10047d9ef3e68b8fbd5e84c37/ urn:sha256:4f67e8beeb98f450479366afa973411a2570eac10047d9ef3e68b8fbd5e84c37 <p>Protein fingerprinting with nanopores enables single-molecule proteoform analysis but is often limited by conformational heterogeneity of flexible polypeptides. Here, we reduce this stochasticity through a geometric relocalization strategy by engineering dual hydrophobic anchoring sites (T83F/R118F) in the vestibule of the Mycobacterium smegmatis porin A (M2MspA) nanopore. These substitutions are proposed to create localized aromatic interaction sites that alter the docking geometry of the folded Smt3 domain and improve the reproducibility of sensing-segment presentation near the constriction. We demonstrated that this reconfiguration could convert stochastic, tail-dominated signals into regulated, segment-resolved readouts. Analysis of the single-site mutants suggests that R118F makes the predominant contribution to the observed reporter-positioning phenotype, enabling discrimination of peptide sequences unresolved in M2MspA. Using this spatial control, we achieve single-molecule detection of lysine acetylation in a tau-derived peptide via distinct noise signatures. These results support a nanopore design strategy that emphasizes spatial alignment for high-fidelity proteoform analysis.</p><p class="metadata"><time datetime="2026-10-25" title="Source date; precision not specified">October 25, 2026</time> <span aria-hidden="true"> · </span> ACS Sensors</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acssensors.6c01784">Original publication</a></p> Sun, 25 Oct 2026 00:00:00 GMT Jiadun Liu Ronghui Liu Meilin Zhu Xinlei Sheng Shujun He Jiajia Guo Yi Li OpenAlex https://reading.michaelmvh.com/article/ce87ba1d679cf7970d3c4da8d65bcf2d67af9872c71a59445167c3aefa99dccc/ urn:sha256:ce87ba1d679cf7970d3c4da8d65bcf2d67af9872c71a59445167c3aefa99dccc <p>Abstract Accurate characterization of bioactive peptides and proteins is needed to fully understand the origin of their activity. Nanopore reading enables polypeptide characterization at the single-molecule level. Here we describe a digestion-ligation method based on readily available reagents and benchtop equipment to convert peptides and proteins into DNA-peptide-DNA conjugates that can be analyzed by nanopores. Chymotrypsin digestion yields peptide fragments with C-terminal tyrosine residues suitable for oxidation-induced click chemistry. Subsequent selective installation of an azide on the N terminus enables installation of a template DNA strand needed for nanopore reading. The findings provide a facile approach to prepare DNA-peptide-DNA conjugates that has great potential for applicability to nanopore reading of many proteins.</p><p class="metadata"><time datetime="2026-10-23" title="Source date; precision not specified">October 23, 2026</time> <span aria-hidden="true"> · </span> Bioconjugate Chemistry</p><p><a href="https://doi.org/10.1021/acs.bioconjchem.6c00355">Original publication</a></p><p><a href="https://pubs.acs.org/bcches/article-pdf/doi/10.1021/acs.bioconjchem.6c00355/68969091/bc6c00355.pdf">Open PDF</a></p> Fri, 23 Oct 2026 00:00:00 GMT Jasper W. van de Sande Xiuqi Chen Cees Dekker Bauke Albada OpenAlex https://reading.michaelmvh.com/article/ce1f1f20079156351e0ae1946f84c24e8dbaeef2bf89bfd5dd3a4a4a44762215/ urn:sha256:ce1f1f20079156351e0ae1946f84c24e8dbaeef2bf89bfd5dd3a4a4a44762215 <p>Abstract Rapid, cost-efficient and miniaturized protein analysis is essential for point-of-care clinical diagnostics. Nanopores offer a promising alternative to mass spectrometry, offering high-resolution, single-molecule sensing with a minimal footprint. However, peptide-level protein identification remains challenging due to difficulties in assigning nanopore signals to peptide sequences and the incompatibility of conventional proteolysis workflows with nanopore sensing. Here we integrate a single-pot, solid-phase-enhanced sample preparation (SP3) workflow with nanopore sensing. The SP3 protocol decouples proteolysis from interfering components via magnetic bead cleanup, yielding a digest compatible with nanopore sensing. As a proof of concept, tryptic digests of myelin basic protein measured with an engineered aerolysin variant (AeL-R220S) generated a reproducible five-peak peptide fingerprint. Cross-validation against a synthetic peptide library and LC-MS/MS enabled reference-based assignment of blockade signatures to four MBP-derived peptides. This approach establishes SP3 as a sample-preparation workflow for nanopore sensing, paving the way for label-free identification and characterization of protein targets.</p><p class="metadata"><time datetime="2026-10-23" title="Source date; precision not specified">October 23, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.10.21.760613">Original publication</a></p> Fri, 23 Oct 2026 00:00:00 GMT Carolin Hensel Carolin Kleber Ida Suppanz Atefeh Akbari Sebastian Gutsch Tobias Hutzenlaub Tobias Ensslen Jan Claas Behrends Felix von Stetten Gerhard Mittler Jan-Niklas Klatt Andreas W. Schreiber OpenAlex https://reading.michaelmvh.com/article/391b1ae0d904e8567f7d5c41f94f75b48ae45e3277622eaab575b9bbe45c9eac/ urn:sha256:391b1ae0d904e8567f7d5c41f94f75b48ae45e3277622eaab575b9bbe45c9eac <p>Epigenetic regulation involves multiple molecular layers, including DNA and RNA modifications, histone post-translational modifications (PTMs), and chromatin accessibility. These processes contribute to cell identity, development, and disease, but their measurement remains technically challenging because sequence context, molecular modification, chromatin state, and transcript structure are often assayed separately. As a representative third-generation sequencing technology, nanopore sequencing is profoundly reshaping the interpretation of the epigenetic code through its distinctive capabilities, including long-read sequencing, direct single-molecule signal detection, and the identification of nucleic acid modifications without bisulfite conversion or PCR in appropriate workflows. This review summarizes applications of nanopore sequencing in epigenomics and epitranscriptomics and evaluates emerging nanopore-based approaches for protein and histone sensing. We focus on what can currently be measured, the experimental and computational requirements for reliable decoding, and the limitations that must be addressed before broader multi-omic and clinical use.</p><p class="metadata"><time datetime="2026-10-16" title="Source date; precision not specified">October 16, 2026</time> <span aria-hidden="true"> · </span> International Journal of Molecular Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/ijms27209175">Original publication</a></p> Fri, 16 Oct 2026 00:00:00 GMT Jiachao Xin Jiaxuan Liu Yichao Liu Xinru Liu Mengke Ma An Huang Zijie Ye Pengfan Zhang Xue Wang Tao Zeng Xiumei Lin Chengwei Liu Liang Lu Liang Chen OpenAlex https://reading.michaelmvh.com/article/e367ce14a28859115b98d3796f9d884130ee6618d6baaee1583e3d170d25ab3b/ urn:sha256:e367ce14a28859115b98d3796f9d884130ee6618d6baaee1583e3d170d25ab3b <p>Abstract Bottom-up synthetic biology aims not only to build individual artificial cells but also to connect them into higher-order systems that communicate with each other. Reported artificial cells communicate through partner recognition, physical connection, and chemical signaling that are typically implemented by separate molecular species. Here, we engineer the pore-forming protein α-hemolysin (AH) with the SpyTag–SpyCatcher (ST-SC) pair to integrate partner recognition, covalent linkage between cells, and nanopore-mediated connection of their lumens into a single protein system. Fusion of ST or SC to AH preserved heptamer assembly and pore formation, and allowed the two heptamers (AH-ST and AH-SC) to be covalently joined. Cryo-electron microscopy resolved the resulting head-to-head 14-mer assembly at 2.20 Å. Calcein leakage and single-channel recordings confirmed that the engineered pores remain functional. Mixing ST- and SC-displaying giant unilamellar vesicles (GUVs) resulted in partner-specific association between the two vesicle populations. Finally, photo-triggered release of a newly synthesized caged ethidium bromide (EtBr) in sender GUVs produced EtBr accumulation in receiver GUVs that required direct physical linkage between the two GUVs. This platform provides a modular route toward artificial-cell assemblies in which both connectivity and cargo exchange are programmable.</p><p class="metadata"><time datetime="2026-10-16" title="Source date; precision not specified">October 16, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.10.16.759538">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/10/16/2026.10.16.759538.full.pdf">Open PDF</a></p> Fri, 16 Oct 2026 00:00:00 GMT Xu Han Ishii Yuta Kota Naito Ayako Ijuin Takayoshi Watanabe Wancheng Zhang Ako Kagawa Asako Narita Takeshi Yokoyama Toshihisa Osaki Shoji Takeuchi Ryuji Kawano Yoshikazu Tanaka Tomoaki Matsuura OpenAlex https://reading.michaelmvh.com/article/7588571b4c8047144b6294081f836cf2571f3a636cdc24500f6f2c8d81613ec3/ urn:sha256:7588571b4c8047144b6294081f836cf2571f3a636cdc24500f6f2c8d81613ec3 <p>Resolving cancer-associated protein variants remains difficult when variants share similar molecular masses and folded structures. Conventional assays often require labels or provide ensemble-averaged readouts, limiting their ability to resolve subtle variant differences. Here, a YaxAB nanopore workflow is presented for label-free single-molecule current fingerprinting of wild-type Bcl-xL and the cancer-associated single-residue variants N136K and R165W. Individual Bcl-xL proteins were electro-osmotically trapped within the funnel-shaped YaxAB lumen, where they generated characteristic ionic-current events. These events formed reproducible, analyte-specific event populations in normalized current blockade and current noise space, resolving wild-type Bcl-xL, N136K, and R165W as distinct single-molecule current fingerprints. Wild-type Bcl-xL and N136K remained distinct despite a mass difference of only 14 Da, and the fingerprint separation was consistent with combined differences in excluded volume, net charge, and dipole moment. Concentration-dependent capture-rate analysis further supported sub-nanomolar to low-nanomolar detection corresponding to protein amounts in the sub-picomole to low-picomole range, while capture-rate normalization brought the estimated concentrations closer to the nominal concentrations. These results present YaxAB nanopore sensing as a label-free single-molecule workflow for the current fingerprinting of cancer-associated single-residue Bcl-xL variants, with low-concentration detection as a supporting analytical capability.</p><p class="metadata"><time datetime="2026-10-14" title="Source date; precision not specified">October 14, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.71126">Original publication</a></p><p><a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/smtd.71126">Open PDF</a></p> Wed, 14 Oct 2026 00:00:00 GMT Minji Chung Sohee Oh Jin‐Sik Kim 황성보 Ki‐Baek Jeong Seung‐Wook Chi OpenAlex https://reading.michaelmvh.com/article/8cc3d42b27ff79f9d48a56975107089cf246478c0687aad3619513867a1be8d6/ urn:sha256:8cc3d42b27ff79f9d48a56975107089cf246478c0687aad3619513867a1be8d6 <p>split–merge plateau detector + browser demo for nanopore peptide current</p><p class="metadata"><time datetime="2026-10-10" title="Source date; precision not specified">October 10, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.23272874">Original publication</a></p> Sat, 10 Oct 2026 00:00:00 GMT Shizhe Jiang OpenAlex https://reading.michaelmvh.com/article/7818ebd4e25a143d6552df600de928a929a24928caa3ae78dff3b9253dce794b/ urn:sha256:7818ebd4e25a143d6552df600de928a929a24928caa3ae78dff3b9253dce794b <p>The objective of this work was to identify and characterise the causative agent(s) of an atypical septicaemic syndrome in 3- to 6-month-old calves. Nine cattle from three Scottish dairy farms were subject to post-mortem in 2020 and 2021, and tissue samples were screened via routine bacteriology. Escherichia coli was isolated from all sampled tissues and a representative isolate from each calf was taken forward for whole-genome sequencing for strain typing, identification of putative virulence factors and antimicrobial resistance genes, and assessment of phylogenetic relationships with other sequenced strains. The nine E. coli isolates were highly-related, being separated by a maximum of 5 single nucleotide polymorphisms. The isolates were serotyped in silico as O78, H9 and were multilocus sequence typed as ST23. Further analysis revealed 13 virulence genes, with the most frequent being associated with serum survival, cytotoxic protein and haemolysin production, and iron transport. These strains encode a novel fimH variant - designated fimH-1571 - which has a mutation potentially linked to increased adherence and invasion. Phylogeny and virulence gene profile indicate an avian pathogenic-like E. coli within a poultry lineage, however there were no poultry units in the vicinity of these farms. Ampicillin, amoxicillin, streptomycin and tetracycline resistance was predicted from their genome sequences, which agreed with phenotypic antimicrobial susceptibility testing. In conclusion, while not demonstrated here, these data are consistent with a transmission event between cattle units (or a common source) and suggest the possible emergence of virulent avian pathogenic-like E. coli in cattle for which future surveillance is merited.</p><p class="metadata"><time datetime="2026-10-09" title="Source date; precision not specified">October 9, 2026</time> <span aria-hidden="true"> · </span> PLoS ONE</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1371/journal.pone.0359646">Original publication</a></p><p><a href="https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0359646&amp;type=printable">Open PDF</a></p> Fri, 09 Oct 2026 00:00:00 GMT Jolinda Pollock Geoffrey Foster Jordan Maliska Katrina Henderson Colin Mason Cici Corbett Gavin K. Paterson OpenAlex https://reading.michaelmvh.com/article/b311f71a431d542bd7322c80ab9e918f1a8d9dcbaea8c5d0e789f303309cbb65/ urn:sha256:b311f71a431d542bd7322c80ab9e918f1a8d9dcbaea8c5d0e789f303309cbb65 <p>The aim of the study was to perform a comprehensive phenotypic and genetic study of clinical strains of Vibrio paracholerae isolated in the Russian Federation and neighboring countries. Materials and methods. We used 210 nucleotide sequences of complete genomes of V. cholerae nonO1/nonO139 and 12 strains of V. paracholerae that caused acute intestinal infections in 1975–2014. Motility, production of soluble hemagglutinin/protease, phospholipase, and hemolysin were determined using specialized media; antibiotic sensitivity - applying the disk diffusion method. BLAST, BioEdit (v.7.7.1), ABRicate, and the VFDB and CARD databases were used for bioinformatics analysis; fastANI v.1.34 – to calculate ANI. Results and discussion. The analysis of 210 V. cholerae nonO1/nonO139 genomes has revealed 12 genomes containing specific markers of V. paracholerae and lacking the loci characteristic of V. cholerae . Determination of the average nucleotide identity of the genomes confirmed their relationship to V. paracholerae . It has been established that paracholera vibrios, like cholera vibrios, are motile and produce pathogenic enzymes and hemolysin. All strains are sensitive to tetracycline, azithromycin, aminoglycosides, cephalosporins, and third-generation fluoroquinolones, but resistant to rifampicin (100 %), ampicillin (58.3 %), trimethoprime/sulfamethaxazole (25 %), and second-generation fluoroquinolones (16.7 %). Genomic analysis has revealed the absence of the CTXφ prophage and the VPI-1 pathogenicity island. A number of strains possesses isolated genes for the VSP-I and VSP-II pandemicity islands. Loci encoding additional pathogenicity determinants have been identified: hemolysin HlyA, soluble hemagglutinin protease HapA, MARTX toxin, type VI secretion system proteins, and cholyx toxin ChxA (in 75 % of isolates). All strains have RND-type efflux system loci, and 85.7 % of ampicillin-resistant isolates harbored carb β-lactamase genes. Thus, in terms of phenotypic characteristics and genetic structure, clinical isolates of V. paracholerae are similar to aquatic vibrios; pathogenicity factors specific to this group could not be identified. Despite the presence of multidrug-resistant isolates, sensitivity to most antibiotics used in the treatment of intestinal infections was noted.</p><p class="metadata"><time datetime="2026-10-08" title="Source date; precision not specified">October 8, 2026</time> <span aria-hidden="true"> · </span> Problems of Particularly Dangerous Infections</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.21055/0370-1069-2026-3-104-112">Original publication</a></p><p><a href="https://journal.microbe.ru/jour/article/download/2398/1703">Open PDF</a></p> Thu, 08 Oct 2026 00:00:00 GMT Daria L. Kusmartseva Челдышова Надежда Борисовна M. V. Proskuryakova Т.В. Валова A. V. Osin Федоров Андрей Витальевич Портенко Светлана Анатольевна Заднова Светлана Петровна OpenAlex https://reading.michaelmvh.com/article/d046e4b33fa23d85a7ccd16310ee6a0cdaea98d82cafb2c27f14a1195911b975/ urn:sha256:d046e4b33fa23d85a7ccd16310ee6a0cdaea98d82cafb2c27f14a1195911b975 <p>Nanopore sensors have demonstrated single-molecule resolution for nucleic acids and small molecules, yet the discrimination and detection of folded proteins in complex biological matrices remains a challenge. Insulin is a demanding test case: it circulates in blood at picomolar concentrations, differs from clinically used pharmaceutical analogues by as little as a single amino acid, and its continuous monitoring would close the remaining open loop in artificial pancreas systems. Here, we show targeted mutations near MspA nanopore&#39;s constriction-enabled discrimination of insulin from the pharmaceutical analogues insulin aspart─differing by one amino acids, and insulin glargine. Furthermore, we reported on insulin degradation by interstrand disulfide reduction and deamidation, a ubiquitous degradation pathway in protein pharmaceuticals that compromises both potency and safety. A machine-learning classifier built on 16 single-event features separated insulin from the blood background with a per-pore limit of detection of 16 nM in 25% v/v blood, suggesting that an array of ∼1000 pores could reach physiologically relevant concentrations. A single-molecule electrical readout for insulin is a requirement for wearable sensors for making an artificial pancreas and could be used for preadministration quality control of insulin pharmaceuticals.</p><p class="metadata"><time datetime="2026-10-07" title="Source date; precision not specified">October 7, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p><a href="https://doi.org/10.1021/acsnano.6c10533">Original publication</a></p> Wed, 07 Oct 2026 00:00:00 GMT Sabine Straathof Matthijs Jonathan Tadema Lijian Zhan Giovanni Maglia OpenAlex https://reading.michaelmvh.com/article/c8a7836fbc42a23946f1fc9726369ceb80f1f7251edb3fb2461d6cb15b89ae77/ urn:sha256:c8a7836fbc42a23946f1fc9726369ceb80f1f7251edb3fb2461d6cb15b89ae77 <p>Abstract Background Nanopore-based protein reading holds promise for single-molecule proteomics, but analyzing the resulting ionic current signals presents substantial computational challenges. Unlike nucleic acids, peptide-associated ionic signals exhibit complex patterns with subtle transitions between amino acids that can be obscured by noise. We developed an integrated computational strategy for processing nanopore protein ionic current signals from synthetic protein constructs containing all 20 amino acids in controlled sequence contexts. We started with denoising to remove artifacts, followed by change point detection using variable-number and fixed-number segmentation methods. Results We employed dynamic time warping barycenter averaging to generate amino acid-specific reference templates. In parallel, we performed classification of amino acid regions using bidirectional LSTM networks trained on segment-level statistical features. Accuracy for 20-way amino acid classification remained limited, while charge-based binary classification reached 93.3% accuracy. Pairwise classification revealed that certain amino acids, particularly negatively charged residues, generate distinctive signatures. We used a profile hidden Markov model to capture sequential structure of protein translocation. Conclusion This approach provides computational strategies for automated segmentation, classification, and modeling of nanopore peptide translocation ionic current data.</p><p class="metadata"><time datetime="2026-10-02" title="Source date; precision not specified">October 2, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/bioinformatics" rel="external">bioRxiv: Bioinformatics</a></p><p><a href="https://doi.org/10.64898/2026.09.28.755023">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/10/02/2026.09.28.755023.full.pdf">Open PDF</a></p> Fri, 02 Oct 2026 00:00:00 GMT Andrew J. Stein Neda Ghohabi Esfahani Stuart Akeson Pooria Daneshvar Kakhaki Daphne Kontogiorgos-Heintz Jeff Nivala Miten Jain OpenAlex bioRxiv: Bioinformatics https://reading.michaelmvh.com/article/3836269c6a11a7f18aea848ec694425fb4997563abf06db6310da2090c380b18/ urn:sha256:3836269c6a11a7f18aea848ec694425fb4997563abf06db6310da2090c380b18 <p>Post-transcriptional transfer RNA (tRNA) modifications dynamically regulate translational capacity, yet whether the tRNA epitranscriptome is temporally coordinated with gene expression programs during bacterial growth remains unknown. Here, we combine time-resolved nanopore tRNA sequencing, liquid chromatography–tandem mass spectrometry modification profiling, transcriptomics, and proteomics across the Pseudomonas aeruginosa PA14 growth cycle to show that tRNA-modifying enzymes, the corresponding tRNA modifications, and modification-dependent genes are expressed in a coordinated temporal cascade. GidA-dependent 5-methylaminomethyl-2-thiouridine (mnm 5 s 2 U) modifications exemplify this program: GidA expression peaks during early growth, followed by rising mnm 5 s 2 U levels coinciding with maximal expression of genes enriched in rare AGA and UUA codons, with a concomitant enrichment of virulence-associated functions. This sequential pattern is consistent with a feedforward architecture in which the modification machinery acts in advance of translational demands. This mechanism is especially relevant for a set of horizontally acquired genes, suggesting that temporally programmed tRNA epitranscriptomic remodeling may help bridge local codon usage deviations between horizontally acquired genes and the core translational context.</p><p class="metadata"><time datetime="2026-10-02" title="Source date; precision not specified">October 2, 2026</time> <span aria-hidden="true"> · </span> Proceedings of the National Academy of Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1073/pnas.2615985123">Original publication</a></p> Fri, 02 Oct 2026 00:00:00 GMT Yannick Noah Frommeyer Jingjing Sun Junzhou Wu Benedikt Kennepohl Julius Witte Nicolas Oswaldo Gomez Jana Battermann Leon Becker Pierina Cetraro Ruth Verstraten Jürgen Tomasch Andreas Pich Daniel Pearce Depledge Peter C. Dedon Susanne Häußler OpenAlex https://reading.michaelmvh.com/article/7f2a695e64514d9c6262489fd68abb3ece51b9e9c192d95a710fba011720f465/ urn:sha256:7f2a695e64514d9c6262489fd68abb3ece51b9e9c192d95a710fba011720f465 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-10-01" title="Source date; precision not specified">October 1, 2026</time> <span aria-hidden="true"> · </span> Nature Nanotechnology</p><p><a href="https://doi.org/10.1038/s41565-026-02302-1">Original publication</a></p> Thu, 01 Oct 2026 00:00:00 GMT Giovanni Maglia OpenAlex https://reading.michaelmvh.com/article/c365b31becc2b9a0b2454b5ef8e3c7ad340b92f5529042d827da9b4e4beee035/ urn:sha256:c365b31becc2b9a0b2454b5ef8e3c7ad340b92f5529042d827da9b4e4beee035 <p>Staphylococcus aureus is a major opportunistic pathogen responsible for a wide range of infections, and its pathogenicity is tightly controlled by regulatory networks linking metabolism and virulence. ArcR, a member of the Crp/Fnr family that regulates the arginine deiminase (ADI) pathway, has an unclear role in coordinating metabolism with virulence. In this study, we investigated the function of ArcR in the clinically relevant USA300 LAC strain. Deletion of arcR significantly enhanced hemolytic activity and altered the expression of toxin-associated genes, with upregulation of hla, hld, and psmα, downregulation of psmβ, and increased transcription of components of the Agr quorum-sensing system and the effector RNAIII. Mechanistically, ArcR directly repressed hlgC transcription, as demonstrated by promoter activity analysis and DNA-protein interaction assays, indicating a direct regulatory role in controlling γ-hemolysin expression. In a murine subcutaneous abscess model, the ΔarcR mutant exhibited increased virulence, characterized by larger abscesses, higher bacterial loads, and more severe tissue damage, whereas deletion of hlgC attenuated these phenotypes. In addition, disruption of ArcR altered host inflammatory responses, suggesting a role in modulating host-pathogen interactions. Collectively, these findings identify ArcR as a negative regulator of toxin production and virulence that links metabolic adaptation to toxin expression in S. aureus, at least in part through direct repression of hlgC. This study provides new insight into the regulatory mechanisms underlying staphylococcal pathogenesis and highlights ArcR as a potential target for anti-virulence strategies.</p><p class="metadata"><time datetime="2026-10-01" title="Source date; precision not specified">October 1, 2026</time> <span aria-hidden="true"> · </span> International Journal of Medical Microbiology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.ijmm.2026.151744">Original publication</a></p><p><a href="https://www.sciencedirect.com/science/article/pii/S1438422126000470/pdf">Open PDF</a></p> Thu, 01 Oct 2026 00:00:00 GMT Ayesha Serwat Samira Khodi Aghmiuni Mujahid Hussain Shihui Yuan Ping Yan Huang Yi Jinglong Guo Yujie Li Ting Xue Baolin Sun OpenAlex https://reading.michaelmvh.com/article/33917f9b47ab409047078d47420a16cd642bd78c2ab0c7f6d301b07db4ff3b9b/ urn:sha256:33917f9b47ab409047078d47420a16cd642bd78c2ab0c7f6d301b07db4ff3b9b <p>We previously found that, among three biotinylated heptapeptides (Peptide 1, Peptide 2, and Peptide 3) derived from the amino acid sequence of Asp-hemolysin, a protein toxin produced by Aspergillus fumigatus, Peptide 2, which contains a d-amino acid, exhibits potent anti-allergic activity in vitro and in vivo. In this study, we evaluated the effects of Peptide 2 on immunoglobulin E (IgE)-dependent allergic edema induced by ovalbumin (OVA) in OVA-specific IgE transgenic mice, IgE-independent allergic edema induced by compound 48/80 (C48/80), and nonallergic inflammatory edema induced by histamine, serotonin, bradykinin, zymosan A, and λ-carrageenan. Peptide 2 significantly suppressed both OVA-IgE- and C48/80-induced paw edema, indicating inhibitory effects on both IgE-dependent and -independent allergic responses. Peptide 2 also dose-dependently inhibited histamine-induced edema but did not affect serotonin-, bradykinin-, zymosan A-, or λ-carrageenan-induced edema. These findings indicate that Peptide 2 modulates IgE-dependent and -independent allergic responses involving mast cell activation and histamine-related pathways and may be a candidate for the development of selective anti-allergic agents.</p><p class="metadata"><time datetime="2026-10-01" title="Source date; precision not specified">October 1, 2026</time> <span aria-hidden="true"> · </span> Biological and Pharmaceutical Bulletin</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1248/bpb.b26-00370">Original publication</a></p><p><a href="https://www.jstage.jst.go.jp/article/bpb/49/10/49_b26-00370/_pdf">Open PDF</a></p> Thu, 01 Oct 2026 00:00:00 GMT Makoto Ohira Hana Yuki Miu Tsumuraya Erika Nozaki Ryoka Nukimizu Tadahiro Etoh Daisuke Uta Tsukasa Matsumoto Akira Sato OpenAlex https://reading.michaelmvh.com/article/c63e2c8f0a3c53cf8760e762f1dc5ef73b0f93d47282e792cca91c63a2263f51/ urn:sha256:c63e2c8f0a3c53cf8760e762f1dc5ef73b0f93d47282e792cca91c63a2263f51 <p>Solid-state nanopore sensors consist of a nanoscopic hole in a thin free-standing dielectric film (a membrane) bridging independent reservoirs of salt solution to interrogate the analytes present therein. Nanopores have demonstrated promising results in applications spanning DNA sequencing, biomarker detection, information storage and energy harvesting. Recently, researchers in the field have aimed to interrogate proteins with enough precision to extract their sequences. Despite their versatility, solid-state nanopores have advanced slowly experimentally due to obstacles and knowledge gaps that need to be explored. A few challenges are addressed in this thesis, attempting to provide insight for future steps in this direction, namely: 1) extracting surface charge density is key to studying the effect of membrane material properties on nanopore transport, fabrication conditions and subsequent chemical functionalization, 2) unwanted adsorption between the biomolecules and the sensor’s surface during the electrophoretic capture and translocation process hinders sensing performance and results in clog events, 3) small proteins or DNA nanostructures can be challenging to fully resolve, leading to missed or attenuated molecular event signatures, and 4) reducing membrane thickness to enhance the signal-to-noise ratio and the spatial resolution leads to faster sensor degradation over time for SiN. For the first objective, I present an experimental characterization platform capable of measuring the surface charge density of silicon nitride as a membrane material. The platform allows high-pressure streaming current measurements in the picoampere range, providing enough resolution to extract the zeta potential and surface charge density of new materials. Next, I explore an alternative anti-fouling protocol for the possibility of increasing sensing time while interrogating long and flexible single-stranded DNA (ssDNA). This analyte clogs the sensor in less than 15 seconds, while after surface modification, we collect relevant data for ⁓45–60 minutes before the first clog event. This improved protocol preserves noise performance comparable to pristine nanopores, even after surface modification. Furthermore, I evaluate the surface properties of these modified nanopores to confirm the successful binding of the polymer on the surface through zeta potential measurements. Moreover, I develop a trapping procedure that takes advantage of the surface characterization platform to reduce the translocation velocity of complex analytes, thus investigating pressure-voltage actuation for analytes of known velocity while determining the impact of this mode of translocation on dwell time. This actuation approach provides an up to 6× reduction in translocation velocity for DNA nanostructures and proteins respectively, facilitating the extraction of high-fidelity event signatures. Finally, I perform an exploration of nanopore membrane microfabrication processes and materials to improve signal amplitude while reducing noise limitations. Here, I present an alternative deposition approach for SiN thin films with a lower thermal budget, namely ion beam deposition (IBD) compared to the traditional Low-Pressure Chemical Vapor Deposition (LPCVD). Independently, I explore the properties of a sub-5 nm annealed Hafnium oxide (HfO2) membrane deposited by Atomic Layer Deposition (ALD), supported by an LPCVD SiN, in terms of film stability and sensing performance. Future work involves combining the lower thermal budget SiN deposition as a mechanical support for a sub-3 nm ALD HfO2 membrane. This approach will offer an ultra-thin solid-state nanopore architecture with reduced degradation, enhanced signal-to-noise ratio, and bypass the annealing step due to the temperature mismatch between depositions. Ultimately, my goal is to pave the way for more efficient and sensitive nanopore-based technologies, contributing to the fields of genomics, proteomics, and beyond.</p><p class="metadata"><time datetime="2026-10-01" title="Source date; precision not specified">October 1, 2026</time> <span aria-hidden="true"> · </span> uO Research (University of Ottawa)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.20381/ruor-32287">Original publication</a></p><p><a href="https://ruor.uottawa.ca/bitstreams/d9d1fda9-44b2-4da3-93bd-a0a404c997cc/download">Open PDF</a></p> Thu, 01 Oct 2026 00:00:00 GMT Mohamed Yassine Bouhamidi OpenAlex https://reading.michaelmvh.com/article/599060d2d2ef0c1a4629a07f2e589c1cfa2b0ca398e99e033b0819dcbc1e47a3/ urn:sha256:599060d2d2ef0c1a4629a07f2e589c1cfa2b0ca398e99e033b0819dcbc1e47a3 <p>《Nanomedicine &amp; Biointerfaces at the Limit: Precision Delivery, Diagnostics, Sequencing, Regeneration, and Safe Human Interfaces》 is a flagship-scale research volume exploring what happens when nanoscale engineering begins to interact directly with living systems. The central question is not simply: Can nanoparticles deliver medicine? It is: Can nanoscale systems safely sense, enter, communicate with, modify, support, and eventually integrate with living matter? This book approaches nanomedicine as a complete systems problem. Its central pathway is: Nanoparticle → Body → Target → Cell → Payload → Clearance. Every stage matters. A therapeutic nanoparticle that reaches the bloodstream but not the target may fail. A carrier that reaches the target but cannot enter the appropriate cell may fail. A system that enters the cell but cannot release its payload may fail. A therapy that performs its intended function but accumulates indefinitely or triggers unacceptable immune responses may also fail. Nanomedicine therefore cannot be evaluated through delivery efficiency alone. The entire biological journey must be engineered. The book develops the Nano Therapeutic Systems Index: NTSI = (Targeting_n × Payload_n × Control_n × Clearance_n) / (1 + OffTarget_n + Immunogenicity_n + Toxicity_n) The NTSI is introduced as a research comparison framework rather than a universal medical law. Its purpose is to force therapeutic performance, biological control, clearance, immune response, toxicity, and off-target effects into the same analytical frame. A nanosystem is not successful merely because it performs one task extremely well. It must function within a living system. This leads to one of the central principles of the book: Performance without biological compatibility is not successful engineering. The research begins with nanoscale delivery systems. Lipid nanoparticles, polymeric nanoparticles, inorganic nanoparticles, protein-based carriers, hybrid structures, vesicles, and responsive nanomaterials are examined through size, surface chemistry, charge, morphology, stability, payload loading, release kinetics, circulation, biodistribution, and clearance. The book emphasizes that the biological identity of a nanoparticle may differ from its manufactured identity. Once introduced into biological fluids, proteins, lipids, metabolites, and other molecules may adsorb onto its surface and form a biological corona. This can change targeting, uptake, circulation, immune recognition, and toxicity. Surface engineering therefore becomes a biological design problem. Targeting forms another major research domain. Passive accumulation, ligand-mediated targeting, receptor recognition, microenvironment-responsive systems, cell-specific delivery, organ targeting, and barrier crossing are studied as part of a broader targeting architecture. The book distinguishes between reaching a region and reaching the correct biological compartment. Tumor tissue is not the same as a tumor cell. A cell membrane is not the same as the cytoplasm. The cytoplasm is not the same as the nucleus. The bloodstream is not the same as the brain. Targeting therefore becomes hierarchical: Organ → Tissue → Cell → Organelle → Molecular Target. Endosomal escape is treated as a major engineering bottleneck. A delivery system may enter a cell successfully and still fail if its payload remains trapped inside intracellular compartments. The book therefore examines membrane disruption, pH-responsive systems, ionizable materials, fusogenic mechanisms, carrier degradation, trafficking pathways, and intracellular release. Gene and RNA delivery form an important technological layer. Nucleic-acid medicines require protection, transport, cellular entry, release, expression, and eventual clearance. The research examines mRNA, siRNA, gene-editing payloads, oligonucleotides, and other programmable molecular therapies through the broader framework of controlled intracellular delivery. Nanopores create another major branch of the book. Biological and solid-state nanopores may enable single-molecule sensing, nucleic-acid analysis, protein characterization, molecular identification, and highly sensitive diagnostics. At these scales, individual molecules can become measurable events. The book explores pore geometry, ionic transport, translocation dynamics, signal-to-noise ratio, surface chemistry, molecular capture, temporal resolution, and signal interpretation. This leads naturally into sequencing. DNA and RNA sequencing are only part of the future molecular readout landscape. Protein sequencing, post-translational modification analysis, molecular fingerprinting, nanopore sensing, zero-mode waveguides, atomic-force methods, and hybrid single-molecule techniques could expand biological measurement far beyond current genomic information. The research therefore asks: How much of biology can eventually become readable at the level of individual molecules? Diagnostics form another major section. Lab-on-chip systems, microfluidics, nanosensors, optical probes, electrochemical detection, plasmonic sensors, magnetic nanoparticles, molecular assays, and point-of-care platforms are examined as integrated diagnostic systems. The goal is not merely higher sensitivity. Useful diagnostics must combine: Sensitivity Specificity Speed Robustness Interpretability Manufacturability Clinical usefulness A sensor capable of detecting extremely small signals may still be clinically weak if false positives, sample preparation, calibration, device variability, or data interpretation remain unresolved. Biosensors therefore become coupled measurement systems rather than isolated detectors. Nanoelectrodes and bioelectronic interfaces extend the field from chemical measurement into electrical interaction with living systems. Nanoscale electrodes, neural interfaces, flexible electronics, tissue-integrated sensors, electrochemical interfaces, and implantable devices may support recording, stimulation, closed-loop regulation, prosthetic control, and long-term physiological monitoring. Here, the engineering problem changes again. The interface must survive both worlds. It must satisfy the requirements of electronics and biology simultaneously. Electrical performance alone is insufficient. Mechanical compliance, inflammation, encapsulation, tissue motion, corrosion, charge transfer, long-term stability, sterilization, and removal or replacement all become central. This leads to a broader principle: The biointerface is not simply where the device touches the body. It is where two engineering regimes negotiate coexistence. Regenerative nanomaterials form another major research direction. Nanofibers, hydrogels, extracellular-matrix-inspired structures, bioactive surfaces, porous scaffolds, conductive materials, and responsive systems may help guide cell adhesion, differentiation, tissue organization, vascularization, nerve growth, and repair. At this level, a material is no longer merely supporting tissue. It may begin to communicate information to cells through chemistry, stiffness, topology, electrical signals, and spatial organization. The research therefore explores how nanoscale structure can influence biological regeneration. Bioelectronics extends this concept further. Future interfaces may combine sensing, computation, stimulation, drug delivery, adaptive control, and communication. A system may sense a biological state, interpret it, respond to it, and continue learning from subsequent measurements. This creates the possibility of closed-loop biological systems: Sense → Interpret → Decide → Act → Measure Again. Artificial intelligence may become deeply involved in this loop. AI can support signal interpretation, molecular pattern recognition, imaging, biosensor analysis, sequencing, pharmacokinetics, individualized dosing, device calibration, digital twins, and predictive models. However, the book emphasizes that biological AI systems must remain uncertainty-aware, interpretable, verifiable, and constrained by safety. High predictive accuracy does not eliminate the need for biological validation. Pharmacokinetics and biodistribution therefore remain central. Absorption, distribution, metabolism, degradation, retention, excretion, immune recognition, organ accumulation, and long-term persistence determine whether nanoscale systems can become clinically viable. The book examines how size, shape, surface chemistry, elasticity, charge, protein corona, and material composition influence these processes. Clearance is treated as a design variable rather than an afterthought. A nanosystem should not merely arrive correctly. It must also leave correctly. This leads to a broader engineering objective: Designed Entry → Controlled Function → Predictable Exit. Safety is embedded throughout the entire research architecture. NanoEHS is not reserved for the final chapter. Toxicity, immunogenicity, environmental release, occupational exposure, persistence, degradation products, reproductive effects, lifecycle behavior, manufacturing residues, and ethical implications are treated as design constraints from the beginning. This creates the principle of Safer-by-Design Nanomedicine. The research asks not only whether a system works, but whether unnecessary hazards can be removed before large-scale deployment. Clinical</p><p class="metadata"><time datetime="2026-09-26" title="Source date; precision not specified">September 26, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.22969186">Original publication</a></p> Sat, 26 Sep 2026 00:00:00 GMT 33 OpenAlex https://reading.michaelmvh.com/article/7533ae7209f3170c6b553dea36a9b96e83db292012cdff06d3e5253a12fc5a93/ urn:sha256:7533ae7209f3170c6b553dea36a9b96e83db292012cdff06d3e5253a12fc5a93 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-09-25" title="Source date; precision not specified">September 25, 2026</time> <span aria-hidden="true"> · </span> Microchemical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.microc.2026.119790">Original publication</a></p> Fri, 25 Sep 2026 00:00:00 GMT Ying Wang Shanshan Wang Lei Ma OpenAlex https://reading.michaelmvh.com/article/4d4f5d35209b7698f56625c86f0a587dcadd86896e4c9e69cd148b9d3539a22d/ urn:sha256:4d4f5d35209b7698f56625c86f0a587dcadd86896e4c9e69cd148b9d3539a22d <p>Exosomes contain abundant molecular information derived from parental cells and represent promising biomarkers for liquid biopsy. However, current exosome detection methods often suffer from complicated procedures, insufficient sensitivity, and limited applicability in complex biological samples. Herein, we developed a nanopore-based enzyme-linked immunosorbent assay (NELISA) for sensitive exosome analysis. This strategy employs exosomal surface antigens to construct alkaline phosphatase (ALP)-labelled sandwich immunocomplexes, followed by enzymatic conversion of the phosphorylated peptide probe FGpYD8 (where “p” denotes phosphorylation modification). The substrate and product peptides generate distinct current signatures during translocation through a protein nanopore, enabling quantitative analysis through statistical evaluation of nanopore events. By rational selection of capture antibodies, the proposed method enables differential analysis of exosomes from distinct cellular origins and achieves a broad dynamic range of 102–109 particles/mL with a detection limit of 102 particles/mL for HeLa cell-derived exosomes, while maintaining reliable performance in complex biological matrices. This work provides a sensitive and versatile platform for exosome analysis and highlights its potential for exosome-based liquid biopsy applications.</p><p class="metadata"><time datetime="2026-09-24" title="Source date; precision not specified">September 24, 2026</time> <span aria-hidden="true"> · </span> Life Analysis</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.55092/la20260011">Original publication</a></p><p><a href="https://pdf.elspublishing.com/paper/journal/open/LA/2026/la20260011.pdf">Open PDF</a></p> Thu, 24 Sep 2026 00:00:00 GMT Xinyao Liu Yakun Yi Lei Liu Haichen Wu OpenAlex https://reading.michaelmvh.com/article/9481d1725223c3e68684da8a875ee59e679c10df51439e10b0a6839570affb6d/ urn:sha256:9481d1725223c3e68684da8a875ee59e679c10df51439e10b0a6839570affb6d <p>Chiral discrimination of amino acids and short peptides remains challenging due to their subtle stereochemical differences and the limited resolution of conventional analytical techniques. Here, we report a single-molecule nanopore sensing strategy in which noncovalent-interaction-driven molecular exchange enables robust discrimination of specific amino acid enantiomers and diastereomeric peptides. By integrating cucurbit[7]uril with an engineered α-hemolysin nanopore, transient molecular pairs are formed and undergo configuration-dependent exchange, converting enantiomeric analytes into pseudo-diastereomeric complexes that generate distinct ionic current signatures. We demonstrate enantiomeric discrimination for selected proteinogenic, and unnatural amino acids bearing aromatic or aliphatic side chains and provide mechanistic insight through symmetry analysis and density functional theory calculations. Beyond amino acids, this platform resolves enzymatically cleaved diastereomeric peptides and enables quantitative monitoring of enzymatic conversion via enantiomeric excess measurements. This work establishes a mechanistic framework for stereochemical recognition under nanoscale confinement and offers a rational design principle for next-generation nanopore sensors targeting chiral biomolecules.</p><p class="metadata"><time datetime="2026-09-23" title="Source date; precision not specified">September 23, 2026</time> <span aria-hidden="true"> · </span> Angewandte Chemie International Edition</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/anie.6314537">Original publication</a></p><p><a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/anie.6314537">Open PDF</a></p> Wed, 23 Sep 2026 00:00:00 GMT Wenying Hao Jing Zhan Jianchuan Liu Mingqian Zhang Xiaobin Huang Ke Zhou Dongmei Xi Lei Liu Hai‐Chen Wu OpenAlex https://reading.michaelmvh.com/article/89b6484fafdaa031a8658d8c7bcce9e7b37918b9b73019c259a0844b5440b123/ urn:sha256:89b6484fafdaa031a8658d8c7bcce9e7b37918b9b73019c259a0844b5440b123 <p>Glycopeptide antibiotics (GPAs) are a critical class of last-resort therapeutics for treating severe infections caused by multidrug-resistant Gram-positive bacteria. However, their highly similar molecular structures and binding mechanisms make accurate discrimination and mechanistic analysis challenging. Here, we report a peptidoglycan-mimetic nanopore receptor (PGP-αHL) for single-molecule fingerprinting of GPA-target interactions. The receptor incorporates a biomimetic peptide that can be stably immobilized within an αHL nanopore, thereby creating a well-defined single-molecule interface at which antibiotic binding events can be monitored in real time. Single-channel recordings reveal transient binding and unbinding events that follow a bimolecular association and unimolecular dissociation model, with kinetic parameters consistent with those obtained from isothermal titration calorimetry. Substitution of the terminal D-Ala residue with D-Ser in the peptide leads to reduced binding affinity, enabling direct observation of resistance-associated effects at the single-molecule level. In addition, the PGP-αHL platform enables reliable discrimination of structurally similar GPAs, including vancomycin, teicoplanin, and dalbavancin, achieving approximately 99% overall classification accuracy when combined with machine learning. The applicability of this approach is further demonstrated by the detection of GPA residues in spiked milk samples. This work establishes a target-mimetic nanopore receptor strategy that integrates single-molecule analysis of antibiotic-target recognition, resistance-associated binding alterations, and discrimination of structurally similar antibiotics within a unified sensing platform.</p><p class="metadata"><time datetime="2026-09-22" title="Source date; precision not specified">September 22, 2026</time> <span aria-hidden="true"> · </span> ACS Sensors</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acssensors.6c03381">Original publication</a></p> Tue, 22 Sep 2026 00:00:00 GMT Zhuoqun Su Liuxin Jiao Jingxian Hou Yirong Wang Jianing Chen Wanxiao Wang Di Wu Yongning Wu Guoliang Li OpenAlex https://reading.michaelmvh.com/article/53fe818a5c9c30d2ab86bc6d8cfa8d3e3cf5708647a35b01b86aeb9a90342d33/ urn:sha256:53fe818a5c9c30d2ab86bc6d8cfa8d3e3cf5708647a35b01b86aeb9a90342d33 <p>Peptide sensing and sequencing are essential for elucidating sequence-function relationships and evaluating the peptide drug quality. Nanopore electrochemistry enables label-free characterization of peptide composition, structure, and interactions at the single-molecule level through ionic-current fingerprints. However, efficient capture remains challenging for low-abundance peptides with heterogeneous charge and conformational properties. Herein, we study peptide capture by the asymmetric OmpF nanopore and examine the relative contributions of electroosmotic flow (EOF), electrophoretic force (EPF), peptide conformation, and field-gradient-mediated interactions. The laterally heterogeneous charge distribution within OmpF modulates the salt dependence of ionic screening and electroosmotic transport, supporting an efficient EOF-associated peptide capture under high-salt conditions. Atomistic molecular dynamics simulations reveal salt-dependent changes in ionic conductance, water flux, and counterion accumulation within the constriction zone, suggesting that the local counterion accumulation approaches saturation at high ionic strength. This behavior enables OmpF to combine high signal-to-noise ratio with low-concentration peptide detection across net charges from -2 e to +6 e. This OmpF sensor provides a linear detection range spanning more than four orders of magnitude, nanomolar concentration limits, and femtogram-level sample consumption. Furthermore, by utilizing the stereoselective recognition capability of OmpF&#39;s asymmetric constriction zone, this approach was further applied to the identification of chiral impurities in near-neutral peptide drugs. The OmpF-based nanopore sensor provides a sensitive and label-free platform with a broad dynamic range for single-molecule peptide analysis, paving the way for versatile nanopore applications.</p><p class="metadata"><time datetime="2026-09-18" title="Source date; precision not specified">September 18, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.6c16303">Original publication</a></p> Fri, 18 Sep 2026 00:00:00 GMT Fan Gao Abhishek Acharya Lin-Lin Zhang Pratik Kumar Behera Mathias Winterhalter Ulrich Kleinekathöfer Yi‐Tao Long Yi‐Lun Ying OpenAlex https://reading.michaelmvh.com/article/51ea63c749fa7e931f37010cd8f35e66416f6d75ee7b7da07c7d6b85b99fdd78/ urn:sha256:51ea63c749fa7e931f37010cd8f35e66416f6d75ee7b7da07c7d6b85b99fdd78 <p>The pore forming toxins pneumolysin and а-hemolysin play a key role in the pathogenicity of Streptocoocus pneumonia and staphylococcus aureus respectively. We used the phage display platform at BicycleTx Ltd to screen these toxins for potential bicyclic peptide inhibitors. Despite multiple efforts with multiple different versions of target protein no bicyclic peptide binders to pneumolysin could be identified. Selections against а-hemolysin were more successful with bicyclic peptides which bound to and inhibited the pore forming activity of а-hemolysin being identified. An extensive optimisation procedure was undertaken including the production of affinity maturation libraries as well as testing non-canonical amino acids. A 1.98Å co-crystal structure gave useful insights into the epitope and mechanism of binding as well as interesting similarities to a previous α-hemolysin antibody. The final optimised hit of BCY00034709 was produced and its mechanism of inhibition characterised. We were able to show that this novel bacterial-anti-toxin is capable of protecting red blood cells as well as human lung cells from the toxic effects of а-hemolysin in vitro. We also describe the discovery of novel bicyclic peptide inhibitors of the type 1 signal peptidase of staphylococcus aureus produced by bicyclic peptide phage display selections. We show that these bicyclic peptides are capable of inhibiting SpsB in a FRET assay which mimics the proteins endogenous function. Through the process of affinity maturation this produced our most potent hit which had an IC50 of 22nM. Computational modelling and assay data provided insights into the mechanism of action of BCY00041582 as well as the potential role of crucial residues. Despite this potent inhibition in vitro no activity against a clinical S. aureus strain was seen that could be attributed to SpsB inhibition and we explore potential reasons for this asymmetry as well as a possible strategy to bridge this gap. The limitations of phage display selections against SpsB and detergent solubilised membrane proteins as a whole are also discussed. Focusing on the production of the false positives we observed that show S. aureus growth inhibition whilst not displaying any inhibition of SpsB, along with the potential mechanism and strategies for overcoming this. Keywords: Graph limit theory, Complex networks, Machine learning, Deep learning, Persistent homology, Topological data analysis, Statistical mechanics, Condensed matter physics, Soft matter, Molecular dynamics simulations.</p><p class="metadata"><time datetime="2026-09-17" title="Source date; precision not specified">September 17, 2026</time> <span aria-hidden="true"> · </span> Warwick Research Archive Portal (University of Warwick)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.82444/warw.33911530">Original publication</a></p><p><a href="https://wrap.warwick.ac.uk/id/eprint/197866/1/WRAP_Theses_Whiteside_2024.pdf">Open PDF</a></p> Thu, 17 Sep 2026 00:00:00 GMT Jonathan Whiteside OpenAlex https://reading.michaelmvh.com/article/92ae2d57b953370f431b6544ef14f2541c2ce2013ee09ef72c236c62f2e6715b/ urn:sha256:92ae2d57b953370f431b6544ef14f2541c2ce2013ee09ef72c236c62f2e6715b <p>The global burden of infectious disease is on the rise, driven by antibiotic resistance, emerging pathogens, and gaps in accessible, decentralized diagnostics. To address these demands, there is a need for the development of diagnostic platforms for detection, surveillance, or monitoring assays with quick turnaround times. Oxford Nanopore sequencing, a platform for real-time long-read third-generation sequencing, has emerged as a promising tool in this space, with the ability to detect a wide range of molecular targets, including DNA, RNA, proteins, and base modifications. Its unique advantages, including portability, scalability, and the capacity for culture-independent workflows, combined with the depth of sequencing data produced, make it especially well-suited for infectious disease diagnostics and surveillance in both clinical and field settings. In this review, we aim to critically examine recent advances in the application of nanopore sequencing for diagnosing infectious diseases caused by bacterial, viral, fungal, and parasitic agents, as well as for detecting antimicrobial resistance genes. We also compare its potential advantages over conventional diagnostic methods and explore its expanding role in tracking outbreaks, monitoring pathogens in the environment, and detecting spillover events from animals to humans. Together, these applications highlight the relevance and position of this novel technology as a tool of choice for translational medical research and clinicians in the fight against infectious diseases and for global health preparedness.</p><p class="metadata"><time datetime="2026-09-17" title="Source date; precision not specified">September 17, 2026</time> <span aria-hidden="true"> · </span> Journal of Clinical Microbiology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1128/jcm.00083-26">Original publication</a></p> Thu, 17 Sep 2026 00:00:00 GMT Adithi Somayaji Piyas Mukherjee Caroline Koch Clarissa Prazeres da Costa Youssef Hamway OpenAlex https://reading.michaelmvh.com/article/0fd350c9d8ec07f52f3f49688deb3c8d52b63f15f60a32b6f69425686e76631b/ urn:sha256:0fd350c9d8ec07f52f3f49688deb3c8d52b63f15f60a32b6f69425686e76631b <p>Abstract Existing biological nanopores are often too narrow to accommodate large proteins and biomolecular complexes in their native folded states, precluding the analysis of megadalton assemblies. Here, we report the self-assembly of the cholesterol-dependent cytolysin Perfringolysin O (PFO) into stable transmembrane nanopores composed of 46 ± 9 monomers, with an inner pore diameter of 28.5 ± 5.6 nm and a length of 9.8 nm. We demonstrate that despite the large size of the pore assembly, PFO pores exhibit a stable open-pore current with a high signal-to-noise ratio, making them suitable for resistive-pulse recordings. Moreover, PFO nanopores enable accurate, calibration-free, and label-free sizing of individual proteins, multi-protein complexes, and viral particles across a large molecular-weight range spanning 50 kDa to 3.4 MDa. The exceptionally large diameter of these pores enables, for the first time, resistive-pulse-based characterization of intact virus particles and ribosomes with a biological nanopore. Specifically, we determined the volume, shape, and diameter of complete capsids of recombinant adeno-associated virus serotype 2 (rAAV2) as well as capsid fragments. Finally, simultaneous analysis of molecular volume and shape resolved intact 70S ribosomes from their dissociated 30S and 50S subunits in a mixture. By extending biological nanopore sensing to single-particle characterization of large protein complexes well beyond the reach of existing pores, this approach introduces PFO nanopores as a versatile platform for label-free, single-particle analysis in solution.</p><p class="metadata"><time datetime="2026-09-17" title="Source date; precision not specified">September 17, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.09.16.752082">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/09/17/2026.09.16.752082.full.pdf">Open PDF</a></p> Thu, 17 Sep 2026 00:00:00 GMT Andela Vracar Veneta Salyahetdinova Sandor Balog Alessandro Ianiro Anasua Mukhopadhyay Michael Mayer OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/881db2385c7edd5fa960c5f31f1869f4432ddeddd52e87bca6d1513bf23a7946/ urn:sha256:881db2385c7edd5fa960c5f31f1869f4432ddeddd52e87bca6d1513bf23a7946 <p>We report a thermoplastic nanofluidic device that combines an extended immobilized nanoscale enzymatic reactor (eINER) with a dual in‐plane nanopore time‐of‐flight (DNP‐ToF) reader for label‐free peptide fingerprinting of single protein molecules. As opposed to traditional membrane‐based nanopores, the DNP‐ToF reader uses two sub‐10 nm pores placed in series and are made from plastic to allow securing the resistive pulse sensing (RPS) independent ToF variable as well as the traditional RPS variables. The device enables on‐chip proteolytic digestion with downstream identification of peptide fragments. Using amyloid‐β (Aβ) as a model system, we demonstrate efficient digestion under nanoscale confinement consistent with a reaction‐limited regime and convection‐dominated transport. The device achieved robust event detection with &gt;95% successful pairing of dual nanopore RPS signals enabling extraction of five key features (ΔI 1 /I 0 , ΔI 2 /I 0 , t D1 , t D2 , and ToF) from individual peptide events. Machine learning provided high‐confidence peptide identification with a random forest (RF) classifier achieving 100% accuracy and a cross‐validated accuracy of 99.6% ± 0.9%. Digestion efficiency was tunable through occupancy‐controlled conditions with RF‐assigned intact Aβ events decreasing from ∼9.5% at 1 nM to ∼0.33% at 100 pM. These results establish a scalable, high‐sensitivity platform for integrated single molecule analysis to secure proteomic data from mass‐limited samples.</p><p class="metadata"><time datetime="2026-09-16" title="Source date; precision not specified">September 16, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.71044">Original publication</a></p> Wed, 16 Sep 2026 00:00:00 GMT Suresh Shivanka Randy F. Espinal Cabrera Maximillian I. Chibuike Pramodi Vithanage Indu A. Chandrasoma Pubudu Premarathne Matthew Verber Steven A. Soper OpenAlex https://reading.michaelmvh.com/article/36f5956b886e79dae576cde7f8fe8ea26d342a754287f51da34af8a5d2a2ae49/ urn:sha256:36f5956b886e79dae576cde7f8fe8ea26d342a754287f51da34af8a5d2a2ae49 <p>Versioned HURDLER data deposition containing repeat-protein fragment designs, assembled plasmid constructs, Nanopore sequencing outputs, a deterministic Supplementary Information file tree, and validation records.</p><p class="metadata"><time datetime="2026-09-16" title="Source date; precision not specified">September 16, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.22787559">Original publication</a></p> Wed, 16 Sep 2026 00:00:00 GMT Wenzhao Dai OpenAlex https://reading.michaelmvh.com/article/f488021a2e2e70e336447b21a8239c00c2def242ccb90e524070aea8a606add2/ urn:sha256:f488021a2e2e70e336447b21a8239c00c2def242ccb90e524070aea8a606add2 <p>Rational design of nanopore-forming proteins and peptides is a promising approach for single-molecule analysis by using custom-designed nanopores tailored to specific target molecules. One challenge in this approach is the expression or synthesis of the designed nanopores, due to their high hydrophobicity. We sought to streamline the synthesis of an artificial and highly aggregative nanopore-forming peptide using liposome-supplemented cell-free protein synthesis. By optimizing the liposomal lipid composition, we recovered yields of the expressed aggregative peptide that were suitable for functional measurements. Channel current measurements involving peptide-embedded liposome fusion to a planar lipid bilayer confirmed the pore formation and single-molecule detection capabilities of the expressed peptide nanopore. Through the exploration of various lipid compositions, it was found that the incorporation of anionic lipids and a sufficient acyl chain length were crucial for efficient peptide insertion and the reproduction of native oligomeric states. Such modulation of liposomal lipid composition alongside cell-free protein synthesis has the capacity to alleviate the aggregation propensity constraints in the design of nanopores and other membranous peptides.</p><p class="metadata"><time datetime="2026-09-15" title="Source date; precision not specified">September 15, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.5c15163">Original publication</a></p><p><a href="https://pubs.acs.org/ancac3/article-pdf/doi/10.1021/acsnano.5c15163/68522408/acsnano.5c15163.pdf">Open PDF</a></p> Tue, 15 Sep 2026 00:00:00 GMT Shoko Fujita Mana Sato Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/79906c393be38ada602bcf1f079d77a301f11c3ae3cfa6ef23f11a0a9d261fb6/ urn:sha256:79906c393be38ada602bcf1f079d77a301f11c3ae3cfa6ef23f11a0a9d261fb6 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-09-14" title="Source date; precision not specified">September 14, 2026</time> <span aria-hidden="true"> · </span> Nature Biotechnology</p><p><a href="https://doi.org/10.1038/s41587-026-03308-9">Original publication</a></p> Mon, 14 Sep 2026 00:00:00 GMT Lang Yao Zixuan Wang Jialu Chen Wen SUN Kefan Wang Yunqi Xiao Hanhan Zhang Wenzheng Li Yifan Wang Lulu Zhao Xinyi Dai Qian Lu Panke Zhang Shuo Huang OpenAlex https://reading.michaelmvh.com/article/d2f450c555aaacfcabc879f86ce706d94a99cb1f6f8b98034383b0bb809bcf31/ urn:sha256:d2f450c555aaacfcabc879f86ce706d94a99cb1f6f8b98034383b0bb809bcf31 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-09-12" title="Source date; precision not specified">September 12, 2026</time> <span aria-hidden="true"> · </span> Chemical Engineering Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.cej.2026.181871">Original publication</a></p> Sat, 12 Sep 2026 00:00:00 GMT Yanru Ding Cai Gao Zhong Wang Jie Chen Xing‐Hua Xia Li-Na Ji Kang Wang OpenAlex https://reading.michaelmvh.com/article/0b90d717f5ef9d81b749a0792b880fa7407f63cda3f5d0b6fcdd7956634e46e4/ urn:sha256:0b90d717f5ef9d81b749a0792b880fa7407f63cda3f5d0b6fcdd7956634e46e4 <p>Solid-state nanopores have become a fast-rising technique in single-molecule sensing, especially in DNA and protein sensing. Carbohydrates, as one of the most important biomacromolecules for human life, have posed challenges in related research and analysis due to their complexities, and solid-state nanopores have shown great potential in glycan sensing and analysis because of their stability, cost-effectiveness, fast results and high sensitivity. The kinetics, conformation, and identification of heparin molecules were investigated. Heparin is a widely used anticoagulant in medical practices, and a large-scale contamination scandal in 2008 has attracted more attention, as a quick and effective method to differentiate heparin and OSCS (oversulphated chondroitin sulphate) needs to be developed. A series of experiments was done in different salts and salt concentrations, at different pH levels, to find an optimized sensing condition for maximum capture. By a simulation tool developed in the lab and the experimental results, we also investigated conformations of heparin as they pass through a solid-state nanopore. However, the negatively charged small particles pass through the nanopores too fast for the state-of-the-art instruments to fully resolve. An attempt was also made to differentiate heparin and OSCS, but no significant differences were seen. In an effort to slow down the molecules, a specialized flow cell that incorporates a pressure system was adopted. However, under a small counterpressure, heparin molecules were not seen to slow down. Lectin, a human protein that has proved to be heparin-binding, was also experimented with. It was shown that at 3.6 M LiCl, pH 4, heparin and lectin molecules could bind and form a compound that translocates through the nanopore as one, which produces significantly slower and deeper signals.</p><p class="metadata"><time datetime="2026-09-10" title="Source date; precision not specified">September 10, 2026</time> <span aria-hidden="true"> · </span> uO Research (University of Ottawa)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.20381/ruor-32222">Original publication</a></p><p><a href="https://ruor.uottawa.ca/bitstreams/75092a1b-fade-44af-aa6b-ae0f30527081/download">Open PDF</a></p> Thu, 10 Sep 2026 00:00:00 GMT Kexin Zhao OpenAlex https://reading.michaelmvh.com/article/762350dbe44b4103b37af5bf054fd180dd859125a7b7f6061631da0fabfec7f1/ urn:sha256:762350dbe44b4103b37af5bf054fd180dd859125a7b7f6061631da0fabfec7f1 <p>Abstract Hydrophobic pores are generally expected to exclude ions because the large desolvation penalty associated with ion transfer cannot be compensated within a nonpolar environment. The envelope (E) protein of Middle East Respiratory Syndrome coronavirus (MERS-CoV) presents a striking exception, conducting cations with high efficiency despite forming a predominantly hydrophobic pore. To resolve this apparent paradox, we combine finite-temperature string simulations with additive and polarizable force fields to determine the minimum free-energy pathways for ion permeation through the MERS E channel. The simulations reveal a cooperative permeation mechanism in which transient counterion association, localized pore hydration, and electronic polarization jointly reduce the desolvation penalty. Rather than acting as passive spectators, counterions transiently chaperone the permeating cation before dissociating within the channel, thereby lowering the energetic cost of charge desolvation while preserving net ionic conductance. Explicit electronic polarization further reshapes the pore hydration landscape and cation– π interactions, leading to substantially reduced free-energy barriers and a permeation mechanism in substantially better agreement with experiment. These results suggest that efficient ion transport through hydrophobic pores arises from the cooperative interplay between electrostatics, polarization and hydration rather than complete pore wetting, providing both a mechanistic framework for MERS E protein function and a general physical principle for ion transport through biological and synthetic hydrophobic nanopores.</p><p class="metadata"><time datetime="2026-09-08" title="Source date; precision not specified">September 8, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.09.03.749198">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/09/08/2026.09.03.749198.full.pdf">Open PDF</a></p> Tue, 08 Sep 2026 00:00:00 GMT Zhongyi Wan Mei Hong Qiang Cui OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/58840e433e1fdc95b085b274699573ee67b249996bd2f95866e6bcab0e93928a/ urn:sha256:58840e433e1fdc95b085b274699573ee67b249996bd2f95866e6bcab0e93928a <p>Protein oxidation generates diverse chemical states that regulate cellular signaling yet progressively accumulate as molecular damage during aging. However, characterizing oxidation-state heterogeneity of individual proteins or peptides remains challenging, as conventional ensemble methods average over coexisting species. Here, we report a nanopore strategy based on a confined hydrogen-bond network to decode oxidation states within individual native peptides. By engineering a constricted recognition region enriched with hydrogen-bond interactions, the changes induced by diverse oxidation states were specifically recognized. This enables discrimination of closely related oxidative modifications, including proline hydroxylation, methionine oxidation, and tryptophan oxidation, even at ultra-low abundance. We show that the reversible and regulated oxidation state could be clearly distinguished from irreversible and damaged oxidation with the same mass without separation or purification. Furthermore, we quantified heterogeneous oxidation distributions generated under controlled oxidative conditions. This approach provides a molecular-level strategy for characterizing oxidation-state heterogeneity in individual peptides, with potential applications in studying oxidative modifications associated with aging and disease in future biological investigations.</p><p class="metadata"><time datetime="2026-09-08" title="Source date; precision not specified">September 8, 2026</time> <span aria-hidden="true"> · </span> Angewandte Chemie International Edition</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/anie.9376050">Original publication</a></p><p><a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/anie.9376050">Open PDF</a></p> Tue, 08 Sep 2026 00:00:00 GMT Jun‐Ge Li Jie Jiang Yan Gao Xia Zhou Yi‐Tao Long Meng‐Yin Li OpenAlex https://reading.michaelmvh.com/article/b5a4ad28128b2f72da242050263f2689d1cea61255729c899556fe59d8d2a2fa/ urn:sha256:b5a4ad28128b2f72da242050263f2689d1cea61255729c899556fe59d8d2a2fa <p>1. Overview This dataset contains all configuration files, input structures, force field parameters, and trajectory outputs from all-atom molecular dynamics (MD) simulations and Adaptive Biasing Force (ABF) free energy calculations. The study investigates the single-molecule translocation dynamics and discrimination of two sequence-similar peptide hormones: Ex-4/pl14a (Exendin-4 analog, PDB ID: 2NAV, 30 residues, net charge: -1e) Thymosin-α1 (PDB ID: 2L9I, 28 residues, net charge: -4e) The peptides were modeled translocating through four geometrically distinct silicon nitride (Si3N4 solid-state nanopores (Circular, Rhombic, Square, and Triangular) with an identical cross-sectional area under an external electric field in 2 M KCl solution. 2. Archive Contents &amp; File Hierarchy The dataset is organized into three primary zip archives: Archive 1: 1_2nav-nanopore_All-Atom_MD_namd.zip Contains all-atom MD simulation files for Ex-4/pl14a (PDB: 2NAV) under a 300 mV bias across 4 pore geometries and 4 initial translocation orientations: 1_namd_configuration_files/: NAMD configuration scripts for minimization, multi-stage equilibration (eq0.namd, eq1.namd, eq2.namd), and production runs (run0_pore-2nav_0.3v.namd through run3_...). 2_namd_input_files/: Organized by pore shape (01-pore-cir, 02-pore-rho, 03-pore-squ, 04-pore-tri) and orientation (01-orient1 to 04-orient4): Coordinate files (.pdb) and protein structure files (.psf). Harmonic restraint definition files for the Si3N4 membrane (siliconRest_1.0.pdb, siliconRest_2.0.pdb). Langevin temperature coupling definition files (*_all_langevin.pdb). 3_namd_output_files/: Stripped production trajectories (.dcd) and structure templates: No_water+SiN_*: 40 ns trajectories excluding water and pore atoms for peptide conformational analysis. No_water+ion_*: 40 ns trajectories including ions for calculating local ionic currents and free ion distributions. toppar/: Force field parameter and topology files (CHARMM36 protein, lipid, nucleic acid, CGenFF, TIP3P water/ions, and Resulting trajectories and free energy output files along the reaction coordinate (-25 Å ≤ z ≤ 25 Å). parameters: par_silicon_ions_NEW5.inp). Archive 2: 2_2l9i-nanopore_All-Atom_MD_namd.zip Contains all-atom MD simulation files for Thymosin-α1 (PDB: 2L9I) under identical conditions (300 mV, 2 M KCl, 4 geometries, 4 orientations): 1_namd_configuration_files/: Equilibration and production NAMD scripts. 2_namd_input_files/: Geometric configurations (01-pore-cir, 02-pore-rho, 03-pore-squ, 04-pore-tri) and orientation setups (01-orient1 to 04-orient4). 3_namd_output_files/: 40 ns stripped trajectory snapshots and .dcd files for analysis. toppar/: CHARMM36 and modified silicon nitride force field parameters. Archive 3: 3_ABF_simulation_namd.zip Contains free energy profile (Potential of Mean Force, PMF) calculations using the Adaptive Biasing Force (ABF) module implemented in NAMD: 001-2nav-nanopore/ (Ex-4/pl14a) &amp; 002-2l9i-nanopore/ (Thymosin-α1): 1_namd_configuration_files/: Colvars collective variables configuration (abf.colvars), equilibration files, and ABF production scripts (e.g., run0_pore-2nav_0.45v.namd, run0_pore-2l9i_0.45v.namd). 2_namd_input_files/: Structural and constraint files for all 4 pore shapes oriented toward pore corners. 3_namd_output_files/: Resulting 10 ns trajectories along the reaction coordinate (-25 Å ≤ z ≤ 25 Å). toppar/: Corresponding force field libraries. 3. Simulation Parameters &amp; Software Specifications MD Engine: NAMD3.0 (CUDA-accelerated) Colvars Module: Used for ABF free energy calculations along the translocation axis (z) Force Field: CHARMM36 all-atom additive force field (for peptides and ions); Customized parameters (par_silicon_ions_NEW5.inp) for Si3N4 membranes (Si: +0.76e, N: -0.57e). Water Model: Solvated with TIP3P water molecules; 2 M KCl neutral electrolyte. Thermostat/Barostat: Langevin dynamics (298 K) and Nosé-Hoover Langevin piston barostat (1 atm). Applied Transmembrane Voltage: 300 mV for standard translocation runs; 450 mV for ABF free energy profiling. 4. File Naming Conventions Pore Shapes: cir: Circular pore (d = 6.0 nm) rho: Rhombic pore (150°/30°) squ: Square pore (90°) tri: Triangular pore (60°) Orientations: orient1: 0° (aligned with pore axis) orient2: 45° clockwise tilt orient3: 90° clockwise tilt orient4: 135° clockwise tilt</p><p class="metadata"><time datetime="2026-09-06" title="Source date; precision not specified">September 6, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.22231130">Original publication</a></p> Sun, 06 Sep 2026 00:00:00 GMT Gang Hu Tingwang Jiang Jing Tu OpenAlex https://reading.michaelmvh.com/article/06bc205610a4913da3e88a3b9f089aeada2cb0cda223528cd910e9be2923f090/ urn:sha256:06bc205610a4913da3e88a3b9f089aeada2cb0cda223528cd910e9be2923f090 <p>Abstract Background There is a critical need to change the treatment paradigm for mental disorders by developing interventions that are able to target specific clinical components, alter the disease course and are not merely palliative in intent. A key strategy towards this goal is to focus research on causal pathways in mental disordersPMID:35026139. However, despite considerable advancesPMID:27144355, 38104575, 36801618, connecting associational findings with causal pathways remains elusive. This is largely attributable to the absence of clinically useful biomarkers, assayable structural pathology and the technology to directly investigate putative molecular pathologies in the human brain. Moreover, disorder heterogeneity with considerable inter- and intra-individual variation of symptom profile across the disease course suggests diverse underlying disease processes. These challenges have forced attention on preclinical models but there is widespread recognition of major unmet translational needs which stymie drug target identification and validation for mental disorders. These gaps have prompted calls to integrate and synthesis information from diverse preclinical modelsPMID: 39245692and that to address this requires a collaborative multi-disciplinary approach uniting preclinical and clinical research and lived experience. We describe here the creation of an international collaborative network of preclinical psychiatric research, the Consortium of Preclinical Psychiatric Research (CPPR)PMID: 41315813. We then describe how the CPPR will use a multimodal multiomics pipeline to probe schizophrenia by synthesising information from diverse preclinical models and integrating this with clinical data to build a data commons globally accessible and interrogable through AI and machine learning approaches. We propose this will accelerate understanding of causal pathways leading to schizophrenia and subsequently other mental illness and identification of putative biomarkers and novel treatment targets. Aims &amp; Objectives 1. To establish an international consortium of preclinical psychiatric research incorporating the full spectrum of preclinical psychiatric models including animal, cell and stem cell, clinical biological samples, imaging data and human post-mortem brain tissue. 2. With schizophrenia as an exemplar to use a multimodal multiomics pipeline to generate putative biomarkers and novel drug targets. 3. To create a globally accessible data commons of harmonised &quot;omics&quot; data integrated with clinical data sets. Method Animal prefrontal cortex and hippocampus samples from 544 animals from 17 models, 34 cell lines, 705 human post-mortem dorsolateral prefrontal cortex and hippocampus tissue samples and 200 clinical plasma samples covering schizophrenia and healthy controls will undergo proteomic (Orbitrap Astral mass spectrophotometry / Seer Proteograph XT) and direct RNA long-read transcriptomics (Oxford Nanopore Technologies ONT) for epigenomic and transcriptomic data. Analysis and synthesis of data will be undertaken with Australian Biocommons through the open-source Gen3 platform. Results The CPPR was established in 20246 with over 50 researchers and 14 institutions. Deep phenotyping of &gt;1450 distinct preclinical and clinical samples relevant to schizophrenia is being undertaken to create a comprehensive and detailed map of putative pathways involved in schizophrenia. Discussion &amp; Conclusions The CPPR presents a novel approach to bridge the translational gap in psychiatric disorders. It will create a template using schizophrenia that can be applied across mental disorders and herald a new path for fast-tracking putative biomarker and drug target identification.</p><p class="metadata"><time datetime="2026-09-01" title="Source date; precision not specified">September 1, 2026</time> <span aria-hidden="true"> · </span> The International Journal of Neuropsychopharmacology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1093/ijnp/pyag040.090">Original publication</a></p><p><a href="https://academic.oup.com/ijnp/article-pdf/29/Supplement_1/i48/71009437/pyag040.090.pdf">Open PDF</a></p> Tue, 01 Sep 2026 00:00:00 GMT Suresh Sundram OpenAlex https://reading.michaelmvh.com/article/d094b2ad612e7d55e951d1bee677fe28d01143ab10722ad4932c4a5e23a8ce20/ urn:sha256:d094b2ad612e7d55e951d1bee677fe28d01143ab10722ad4932c4a5e23a8ce20 <p>Mass mortality due to hemorrhagic ulcerative lesions in Indian Minor Carp (Labeo bata) has been reported in the East Kolkata Wetland, Kolkata, West Bengal, India. Enterobacter cloacae as the etiological agent responsible for the infection in L. bata was characterised. The study identified the Haemolysin III superfamily protein in E.cloacae. The expression levels of immune-related genes Interleukin-10 (IL-10), Complement factor 3a (C3a), and Heat Shock Proteins 70 (Hsp70) were found to be up-regulated in the kidney’s and liver of experimentally challenged fish after 12h of post injection. This is the first report of L. bata infection by E. cloacae. Key words Enterobacter cloacae, Gene expression, hlyIII gene, Labeo bata</p><p class="metadata"><time datetime="2026-09-01" title="Source date; precision not specified">September 1, 2026</time> <span aria-hidden="true"> · </span> Journal of the Inland Fisheries Society of India</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.56093/jifsi.v56i4.2024.167577">Original publication</a></p> Tue, 01 Sep 2026 00:00:00 GMT Tanuja Abdulla Prasenjit Paria A. K. BERA R K Manna Madonna T. Thachil B. K. DAS OpenAlex https://reading.michaelmvh.com/article/c460a7972622aef793bdf9798b71cbf4495792597390e6b171f44554b388e34a/ urn:sha256:c460a7972622aef793bdf9798b71cbf4495792597390e6b171f44554b388e34a <p>Objective The pathogenesis of metabolic dysfunction-associated fatty liver disease (MAFLD) is very complex, which has not been fully revealed as so far. This study aimed to identify differentially expressed genes involved in the pathogenesis of MAFLD using Oxford Nanopore Technologies (ONT) transcriptomic sequencing and to investigate the potential role of fatty acid-binding protein 5 (FABP5) in hepatic lipid accumulation. Methods Male C57/BL6N mice with fed either a high-fat, high-fructose (HFHF) diet for 19 weeks to induce MAFLD or a standard chow diet. Liver tissues were subjected to histological examination and ONT transcriptomic analysis and selected differentially expressed genes involved in lipid transport and metabolism were validated by quantitative reverse-transcription PCR (RT-qPCR). Serum FABP5 concentrations were measured in HFHF-fed mice and patients with MAFLD using enzyme-linked immunosorbent assay (ELISA). In vitro , Huh-7 cells were treated with different concentrations of palmitic acid (PA) to induce lipid accumulation. FABP5 was subsequently overexpressed in PA-treated cells, followed by assessment of intracellular lipid accumulation and the expression of genes involved in fatty acid oxidation. Result HFHF-fed mice exhibited marked hepatic steatosis, hepatocyte ballooning, and lobular inflammation. ONT transcriptomic analysis identified 400 differentially expressed genes between the HFHF and chow groups, including 12 genes involved in lipid transport and metabolism. RT-qPCR validation showed that hepatic Fabp5 expression was significantly decreased in HFHF-fed mice, consistent with the ONT sequencing results. Serum FABP5 concentrations were significantly lower in HFHF-fed mice and patients with MAFLD than in their respective controls. PA treatment induced intracellular lipid accumulation in Huh-7 cells in a concentration-dependent manner. FABP5 overexpression attenuated PA-induced lipid accumulation and increased PPARα expression, together with changes in other genes associated with fatty acid oxidation. Conclusion Hepatic Fabp5 expression and circulating FABP5 concentrations are reduced in experimental and human MAFLD. Restoration of FABP5 attenuates PA-induced lipid accumulation in hepatocyte-derived cells and is accompanied by increased expression of PPARα and other fatty acid oxidation-related genes. These findings suggest that FABP5 is a candidate regulator of hepatic lipid metabolism and warrants further investigation as a potential therapeutic target for MAFLD. Additional inhibition and rescue experiments are required to determine whether PPARα is a necessary mediator of the lipid-lowering effect of FABP5.</p><p class="metadata"><time datetime="2026-08-31" title="Source date; precision not specified">August 31, 2026</time> <span aria-hidden="true"> · </span> Frontiers in Endocrinology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3389/fendo.2026.1883460">Original publication</a></p> Mon, 31 Aug 2026 00:00:00 GMT Kaishuo Lv Shuhang Zhong Xiaoqing Liu Junru Zhou Di Lu Xiaoying Luo Liqun Tu Bingxi Zhou Shuangyin Han Bingyong Zhang Xiuling Li Jiayu Ye Zhiyu Yang OpenAlex https://reading.michaelmvh.com/article/b7a8fb876391451cf5e912717a345e881e96ca8171f823133066d47968440140/ urn:sha256:b7a8fb876391451cf5e912717a345e881e96ca8171f823133066d47968440140 <p>SUMMARY Methods for installing synthetic functions on living cell surfaces provide powerful approaches for imaging, sensing, and manipulating cell behavior, but many require genetic modification of the target cell or chemical modification of the plasma membrane. Here, we repurpose the glycosylphosphatidylinositol-anchored protein (GPI-AP)-binding toxin aerolysin as a modular chassis for non-genetic cell-surface functionalization. We show that a non-cytotoxic, monomeric aerolysin mutant retains high-affinity and GPI-AP-dependent cell binding when genetically fused to diverse protein cargos. Fluorescent protein-aerolysin fusions robustly label multiple cell types and remain predominantly associated with the cell surface for at least 24 h, in contrast to wheat germ agglutinin, which is extensively internalized. Aerolysin can also be equipped with SpyTag/SpyCatcher to enable simple and modular assembly with independently expressed protein cargos. Importantly, aerolysin supports functional rather than solely optical modification of the cell surface: fusion to the proximity-labeling enzyme APEX2 enables cell surface protein biotinylation, while fusion to HUH endonuclease tags enables covalent attachment of synthetic DNA to living cells. Using this latter architecture, we developed a DNA hairpin sensor that converts cell-surface nuclease activity into a fluorescent signal and distinguishes cells with different levels of extracellular nuclease activity. Together, these results establish a non-cytotoxic and monomeric aerolysin mutant as a soluble adapter for installing proteins, enzymes, and programmable nucleic acids onto living cells without modification of the target-cell genome.</p><p class="metadata"><time datetime="2026-08-31" title="Source date; precision not specified">August 31, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.08.28.746739">Original publication</a></p> Mon, 31 Aug 2026 00:00:00 GMT Andrew C.D. Lemmex Matthew R. Pawlak Wendy Ryan Gordon OpenAlex https://reading.michaelmvh.com/article/ecf7439dd12e6d96f2011d24a51fae3a5886ca4db2e43c2730c1f860cae78662/ urn:sha256:ecf7439dd12e6d96f2011d24a51fae3a5886ca4db2e43c2730c1f860cae78662 <p>Staphylococcus aureus (S. aureus) is a major human pathogen associated with diverse infections due to its array of virulence factors. This study aimed to isolate S. aureus from clinical samples at Madonna University Teaching Hospital (MUTH), Elele, Nigeria, and molecularly detect the virulence genes fibronectin-binding protein A (fnbA), collagen adhesin (cna), and alpha-haemolysin (hla). A total of 106 clinical samples (mainly urine, high vaginal swab, endocervical swab, wound swab, sputum, and skin swab) were collected from patients. S. aureus was isolated using standard bacteriological methods (blood agar, mannitol salt agar, Gram staining, catalase, and coagulase tests) and confirmed molecularly. Antimicrobial susceptibility was determined by the Kirby-Bauer disk diffusion method. Genomic DNA was extracted by the boiling method, and the target virulence genes were detected by polymerase chain reaction (PCR) followed by agarose gel electrophoresis. Out of 106 samples, 26 (24.5%) yielded S. aureus, with higher prevalence among females (69.2%) and in the 31–40 years age group (46.2%). Among 18 isolates tested, fnbA was detected in 13 (72.2%), hla in 5 (27.8%), while cna was absent in all isolates. No statistically significant associations were observed between the genes and demographic/clinical variables (p&gt;0.05). This study provides the first molecular characterization of S. aureus virulence genes at MUTH and in the south-south geopolitical zone of Nigeria. The findings highlight the predominance of fnbA-mediated adhesion in local strains and the absence of the cna gene, suggesting regional clonal variations. Routine molecular surveillance is recommended for better management of S. aureus infections.</p><p class="metadata"><time datetime="2026-08-31" title="Source date; precision not specified">August 31, 2026</time> <span aria-hidden="true"> · </span> Iconic Research and Engineering Journals</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64388/irev10i2-1722626">Original publication</a></p><p><a href="https://www.irejournals.com/formatedpaper/1722626.pdf">Open PDF</a></p> Mon, 31 Aug 2026 00:00:00 GMT Chidinma C Nwanesindu Mirabeau Tatfeng Silas Goodluck OpenAlex https://reading.michaelmvh.com/article/722ef37d3686bec844c8ea6f4970a02bd087138d117259805c6113ba1ea7f308/ urn:sha256:722ef37d3686bec844c8ea6f4970a02bd087138d117259805c6113ba1ea7f308 <p>The anthrax protective antigen forms a heptameric transmembrane channel under acidic conditions and serves as a biological nanopore. Its use in nanopore sensing is limited by stability and signal quality under conventional electrolytes containing potassium or sodium ions. A stable anthrax protective antigen nanopore was constructed using a pH-asymmetric organic ionic liquid electrolyte, operated under a proton-driven gating mechanism. The resulting nanopore was evaluated for electrochemical performance, chemical stability, and capacity to distinguish levorotatory and dextrorotatory amino acid enantiomers. The system operated without the need for enzymes, chemical reactions, or machine-learning algorithms. The anthrax nanopore exhibited a single-channel open current of-approximately 5 pA, whereas commonly used protein nanopores display current amplitudes of tens to hundreds of picoamperes. This architecture provides a basis for chiral molecule identification via direct nanopore current readout.</p><p class="metadata"><time datetime="2026-08-31" title="Source date; precision not specified">August 31, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.6c12067">Original publication</a></p> Mon, 31 Aug 2026 00:00:00 GMT Yan Wang Zhirui Zhang Shilong Liu Yunjiao Wang Yao Li Mingdong Dong Liang Wang OpenAlex https://reading.michaelmvh.com/article/a13674fde94b13229bb254f04210eb28291b2759f0c3514a1992ae9afb6d09e3/ urn:sha256:a13674fde94b13229bb254f04210eb28291b2759f0c3514a1992ae9afb6d09e3 <p>Formaldehyde (HCHO) is a reactive electrophile that covalently modifies diverse amino acid residues in proteins. Although ensemble studies have characterized reactions between HCHO and amino acids, the reaction dynamics at individual residue sites have yet to be resolved at the single-molecule level. Here, we engineer a Mycobacterium smegmatis porin A (MspA) nanopore by positioning a single lysine residue at its constriction, enabling real-time single-molecule monitoring of HCHO-lysine chemistry. Distinct current blockade states and reversible transitions between them are observed, consistent with multistep HCHO-lysine reactions involving monoadducts, bisadducts, and Schiff bases under nanoconfinement. The reactions exhibited concentration- and pH-dependent kinetics and generated characteristic electrical signatures that differentiate HCHO from potential interferents, supporting label-free detection of airborne HCHO via aqueous trapping, as well as identification of HCHO in food matrices. This work establishes a residue-confined nanopore platform for real-time probing of HCHO-amino acid chemistry and selective detection of HCHO.</p><p class="metadata"><time datetime="2026-08-30" title="Source date; precision not specified">August 30, 2026</time> <span aria-hidden="true"> · </span> Nano Letters</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.nanolett.6c02512">Original publication</a></p> Sun, 30 Aug 2026 00:00:00 GMT Xiaoyu Du Qianqian Cao Na Fan Yuqin Wang OpenAlex https://reading.michaelmvh.com/article/1ecc89fc8278a46038b306c66826c9ba9d41ff13575de23c820646811d12f4f4/ urn:sha256:1ecc89fc8278a46038b306c66826c9ba9d41ff13575de23c820646811d12f4f4 <p>α-Helical nanopores are attractive molecular sensors, yet their rational design and assembly remain challenging. Here we show that the single peptide pPorA, derived from porin PorACj, self-assembles into flexible α-helical nanopores, inserts in lipid membranes and exists in distinct small- and large-conductance states. By strategically incorporating unnatural amino acids, we engineered small- and large-diameter pores exhibiting single-channel conductances of 2.4 nS and 3.5 nS in 1 M KCl, respectively, while retaining a common octameric architecture. These nanopores enabled the detection of sugars, peptide enantiomers and intrinsically disordered disease proteins that form dynamic, heterogeneous assemblies. The large pores detected multiple α-synuclein (α-syn) variants, including a pathogenic Parkinson’s disease-associated C-terminal deletion mutant with nanomolar affinity (KD ≈ 20 nM). Selective electrostatic trapping of the α-syn N-terminus enabled charge-resolved identification of individual α-syn species within heterogeneous mixtures. The nanopores further resolved time-dependent and inhibitor-modulated α-syn aggregation pathways from monomers to toxic oligomers and fibrils. The small pores detected humanin and superoxide dismutase peptides associated with apoptosis and amyotrophic lateral sclerosis, demonstrating tunable sensing through pore-size control. These conformationally programmable α-helical nanopores provide a versatile platform for ultrasensitive profiling of disease biomarkers. An engineered peptide self-assembles into α-helical octameric flexible nanopores with tunable diameters and conductances, enabling conformationally programmable biomolecular sensing.</p><p class="metadata"><time datetime="2026-08-28" title="Source date; precision not specified">August 28, 2026</time> <span aria-hidden="true"> · </span> Nature Nanotechnology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41565-026-02265-3">Original publication</a></p> Fri, 28 Aug 2026 00:00:00 GMT Varsha Shaji Rajeev Jain Neethu Puthumadathil Kalyanashis Jana Vedasmiritha T S Ulrich Kleinekathöfer Krishnananda Chattopadhyay Kozhinjampara R. Mahendran OpenAlex https://reading.michaelmvh.com/article/d7eaa165c35db1fe12ddf7b8307971cb7ef71c5a7450d435f616dca57d6517b9/ urn:sha256:d7eaa165c35db1fe12ddf7b8307971cb7ef71c5a7450d435f616dca57d6517b9 <p>Single-molecule nanopore sensing provides a high-resolution, label-free platform to probe biomolecular dynamics and transport phenomena. Here, we investigate the biophysical response of proteins to low-powered (~160 mW) near-infrared (NIR) radiation (1050 nm) — a spectral region traditionally considered silent due to minimal absorption by water and biomolecules. Using nanopore sensors, we record single-molecule translocation events under varying electrolyte conditions. In control conditions with 2 M LiCl as the electrolyte, proteins translocate in the electroosmotic flow (EOF) direction. However, after 1050 nm NIR exposure, single-molecule recordings reveal a distinct switch in the transport mechanism, marked by the emergence of events in the electrophoretic (EPF) direction. This behavioral shift is observed across five distinct proteins, demonstrating a generalized phenomenon. Furthermore, in EPF-favoring electrolytes (KCl, NaCl, and CsCl), NIR illumination leads to a clear increase in current blockade depth (). Together, these direct single-molecule observations suggest that 1050 nm NIR radiation can potentially induce non-covalent protein aggregation, fundamentally altering transport behavior despite operating within an optically silent window.</p><p class="metadata"><time datetime="2026-08-26" title="Source date; precision not specified">August 26, 2026</time> <span aria-hidden="true"> · </span> ChemRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26434/chemrxiv.15007913/v1">Original publication</a></p> Wed, 26 Aug 2026 00:00:00 GMT Tithi Lai Jayamini Hewage Teesha Pathirage Y. M. Nuwan D. Y. Bandara OpenAlex https://reading.michaelmvh.com/article/333251ec4f05089945f783745690b7af30711c06c1bc094803471c764a5c06fc/ urn:sha256:333251ec4f05089945f783745690b7af30711c06c1bc094803471c764a5c06fc <p>Repeated observations of one physical object need not constitute independent channel uses. We model partial nanopore protein rereads as a finite-alphabet channel with canonical content, persistent readout, and pass-local coverage and synchronization. For exact compound-pass data, matched inference approaches the equivalence-class canonical posterior, and sitewise excess Bayes risk admits an action-aware achievable exponent. In an aligned specialization, observation-local redraw can cause linear-in-$K$ growth in true-label negative log-likelihood (NLL). We derive order-$b$ projection-stability bounds and an exact passwise-fusion diagnostic. On a PASTOR-informed semi-synthetic hard-symbol channel, label-blind deterministic-mixture importance sampling (LB-IS) agrees with exact enumeration at $L=7$. At $L=24, K=10$, LB-IS meets every prespecified aggregate absolute marginal-posterior and score-agreement criterion against a fixed high-allocation reference in three selected conditions. Joint agreement holds for the representative and high-NLL conditions, while the near-zero condition remains inconclusive. Exact $L \leq 6$ benchmarks identify order 4 as the smallest tested common cap. At target scale, the reference supports selected unprojected functionals, while neither order 4 nor 5 attains joint agreement, defining a tested finite-memory boundary. Across 16 cells, the order-4 shared branch lowers NLL by 0.033-0.224 nats per residue relative to pass-local.</p><p class="metadata"><time datetime="2026-08-25" title="Source date; precision not specified">August 25, 2026</time> <span aria-hidden="true"> · </span> arXiv (Cornell University)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.48550/arxiv.2608.24819">Original publication</a></p><p><a href="https://arxiv.org/pdf/2608.24819">Open PDF</a></p> Tue, 25 Aug 2026 00:00:00 GMT H. Ni Haofan Dong Ozgur B. Akan OpenAlex https://reading.michaelmvh.com/article/ab588dfeefee88eb8184f648a36106fe1887e213dfecf4394be3d4b6275aa63c/ urn:sha256:ab588dfeefee88eb8184f648a36106fe1887e213dfecf4394be3d4b6275aa63c <p>Nanopore sensing, first conceived more than three decades ago, has seen rapid advancements in recent years in its capability in single-molecule sensing. Following immense success in nucleic acid sequencing, increased efforts have been directed to probing other biomolecules such as proteins. In recent years, our group has investigated the enhancement of nanopore sensing of peptide signals by introducing gold clusters to the pore. Gold clusters have been shown to prolong peptide occupation times in the pore, permitting the observation of unique characteristic signals related to the peptide’s kinetics that are not otherwise observable. While the ability to sense peptide biomarkers of diseases such as diabetes, neurodegeneracy, and ovarian cancer has been demonstrated, the challenge of achieving biomarker detection at clinical concentrations remains. In this work, we sought to reduce the limit of detection of this approach through the modification of the gold clusters and the consideration of non-cluster methods of enhancing peptide dwell times, such as the introduction of small thiol dimers. By achieving a lower detection limit, a wider range of critical diagnostic applications become practically possible using nanopore sensing.</p><p class="metadata"><time datetime="2026-08-21" title="Source date; precision not specified">August 21, 2026</time> <span aria-hidden="true"> · </span> VCU Scholars Compass (Virginia Commonwealth University)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.25772/xvmb-m074">Original publication</a></p> Fri, 21 Aug 2026 00:00:00 GMT Bella Bitner OpenAlex https://reading.michaelmvh.com/article/2b59d62e2eccf6a773e9936faa245335e58030adff7ac6c7afd267bb87fa681a/ urn:sha256:2b59d62e2eccf6a773e9936faa245335e58030adff7ac6c7afd267bb87fa681a <p>Abstract Single-molecule protein sequencing promises to democratize clinical proteomics, but platforms retrofitting static DNA-sequencing nanopores face a fundamental biophysical bottleneck: they only measure one-dimensional excluded volume. Consequently, these static calipers struggle to resolve isobaric residues, requiring complex DNA-handle chemistries and target concentrations that exceed clinically relevant abundance ranges. Here, we introduce a dynamical, target-docking translocase engine – the anthrax toxin protective antigen (PA) – as a label-free single-molecule peptide sensor. By extracting the multi-state thermodynamic friction generated as the pore’s active site dynamically “breathes” around translocating analytes, we trained a physics-informed machine learning (PIML) architecture to classify a 20-member guest-host peptide library panel representing all 20 canonical amino acids at the single-event level. Operating at low nanomolar concentrations under a 35-millisecond thermodynamic read constraint, the translocase resolved isobaric variants (leucine and isoleucine). Furthermore, we achieved 98.02 (±0.05)% classification accuracy on a panel of five un-tagged, native clinical biomarkers (e.g., KRAS G12D, angiotensin, bradykinin). Transitioning from static volumetric measurement to time-domain thermodynamic fingerprinting establishes the requisite protein nanopore hardware for de novo proteomics.</p><p class="metadata"><time datetime="2026-08-20" title="Source date; precision not specified">August 20, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.08.17.745284">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/08/20/2026.08.17.745284.full.pdf">Open PDF</a></p> Thu, 20 Aug 2026 00:00:00 GMT Jaylen E. Taylor Parichit Sharma Bryan A. Krantz OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/4917beaa9afdbae87d2d94f9f18dfbb3dedf4e7c87adc65b78aa656c17a741e1/ urn:sha256:4917beaa9afdbae87d2d94f9f18dfbb3dedf4e7c87adc65b78aa656c17a741e1 <p>An important group of proteins to design are membrane proteins, and a specific type of membrane protein is the transmembrane β-barrel (TMB), commonly used as nanopores. Nanopores are used for analysis and sequencing of DNA molecules. To analyze specific targets, the chemical properties of the TMB need to be compatible with the target, otherwise the nanopore will be unable to detect change in current. De novo design would allow for making these versatile and functional nanopores. With current methods, it is difficult to design these nanopores de novo due to the lack of PDB representations. Our goal is to computationally design sequences for membrane embedded nanopores by combining the structure-based protein design model ProteinMPNN with the membrane protein language model MemDLM. We expect that using a combination of embeddings from sequence-based language models and weights of structure-based design models will improve membrane protein design. Our hypothesis is that integrating explicit physical 3D-geometric principles with evolutionary language models produces proteins that are both highly stable and biologically functional, overcoming limitations of relying on just one approach. After training MemDLM, an adapter was added to it. This adapter is a layer that can accept structural information from ProteinMPNN and feed it to the pre-trained MemDLM with frozen parameters. The system was then tested on a blind dataset of both designed and naturally occurring beta barrels, and its ability to create effective TMBs will be further tested through sequence identity, hydropathy of the barrel core, and propensity for beta sheet formation.</p><p class="metadata"><time datetime="2026-08-18" title="Source date; precision not specified">August 18, 2026</time> <span aria-hidden="true"> · </span> Digital Commons - University of South Florida (University of South Florida)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://digitalcommons.usf.edu/usf_summer_urs/2026/college_engineering/9">Original publication</a></p> Tue, 18 Aug 2026 00:00:00 GMT Keagan Hitt OpenAlex https://reading.michaelmvh.com/article/d82e2d75ea587e317f7c2cde923faf417ca731c3a76ff4e3da2a1bec28965bed/ urn:sha256:d82e2d75ea587e317f7c2cde923faf417ca731c3a76ff4e3da2a1bec28965bed <p>Single-molecule protein sequencing promises to democratize clinical proteomics, but platforms retrofitting static DNA-sequencing nanopores face a fundamental biophysical bottleneck: they only measure one-dimensional excluded volume. Consequently, these static calipers struggle to resolve isobaric residues, requiring complex DNA-handle chemistries and target concentrations that exceed clinically relevant abundance ranges. Here, we introduce a dynamical, target-docking translocase engine – the anthrax toxin protective antigen (PA) – as a label-free single-molecule peptide sensor. By extracting the multi-state thermodynamic friction generated as the pore’s active site dynamically “breathes” around translocating analytes, we trained a physics-informed machine learning (PIML) architecture to classify a 20-member guest-host peptide library panel representing all 20 canonical amino acids at the single-event level. Operating at low nanomolar concentrations under a 35-millisecond thermodynamic read constraint, the translocase resolved isobaric variants (leucine and isoleucine). Furthermore, we achieved 98.02 (±0.05)% classification accuracy on a panel of five un-tagged, native clinical biomarkers (e.g., KRAS G12D, angiotensin, bradykinin). Transitioning from static volumetric measurement to time-domain thermodynamic fingerprinting establishes the requisite protein nanopore hardware for de novo proteomics.</p><p class="metadata"><time datetime="2026-08-17" title="Source date; precision not specified">August 17, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21982623">Original publication</a></p> Mon, 17 Aug 2026 00:00:00 GMT Bryan A. Krantz OpenAlex https://reading.michaelmvh.com/article/59e2660071ae0ce4678948fe42f0e295879395e12ff9ddfa2a78aa868fc9996d/ urn:sha256:59e2660071ae0ce4678948fe42f0e295879395e12ff9ddfa2a78aa868fc9996d <p>This study reviews the detection, antimicrobial resistance patterns, and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) in a tertiary-care hospital setting. The review synthesizes findings from 274 clinical specimens collected over a five-month period, yielding 106 confirmed S. aureus isolates identified using conventional microbiological methods and the Vitek 2 automated system. Phenotypic antimicrobial susceptibility testing against 18 antimicrobial agents demonstrated substantial multidrug resistance, with resistance to oxacillin and cefoxitin detected in 93.4% and 87.7% of isolates, respectively. Molecular analysis using polymerase chain reaction (PCR) investigated key genetic determinants, particularly mecA, which encodes the altered penicillin-binding protein PBP2a responsible for beta-lactam resistance, and hlg, a gene associated with gamma-haemolysin production and virulence. The study highlights the importance of combining phenotypic susceptibility testing with molecular surveillance for accurate MRSA detection and characterization. It also emphasizes the need for strengthened hospital infection-control practices, continuous antimicrobial-resistance surveillance, and responsible antimicrobial stewardship to limit the spread and clinical impact of multidrug-resistant MRSA.</p><p class="metadata"><time datetime="2026-08-16" title="Source date; precision not specified">August 16, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21965008">Original publication</a></p> Sun, 16 Aug 2026 00:00:00 GMT Satwinder Singh Manita Paneri Showkat Hussain Dr. Praveen Kumar OpenAlex https://reading.michaelmvh.com/article/bb73a36c343417cfab7995a2d315c1c9570f07a2e79a38d3f0c27962b89d1519/ urn:sha256:bb73a36c343417cfab7995a2d315c1c9570f07a2e79a38d3f0c27962b89d1519 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-08-14" title="Source date; precision not specified">August 14, 2026</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.6c02289">Original publication</a></p> Fri, 14 Aug 2026 00:00:00 GMT Yingying Jiang 郑多楷 Huan Fang Xinyi Li Yong Hu OpenAlex https://reading.michaelmvh.com/article/d7734dab0666f83736ef8ec155b38c049d92527f992354b82f84d14d2b429a98/ urn:sha256:d7734dab0666f83736ef8ec155b38c049d92527f992354b82f84d14d2b429a98 <p>Single-molecule protein analysis is crucial for elucidating biological processes and enabling early disease diagnosis. Nanopore sensing technology, owing to its label-free operation, high throughput, and direct electrical readout, has emerged as a highly promising platform for protein analysis. This review summarizes recent advances in nanopore-based protein analysis, with an emphasis on the detection of both folded and unfolded proteins. We discuss protein size and shape analysis based on ionic-current blockade signals, the monitoring of conformational changes, the characterization of protein unfolding and unfolded proteins, the detection of posttranslational modifications (PTMs), and highly sensitive quantitative analysis. We further highlight the integration of machine learning to improve signal classification and analytical performance. In addition, we review recent applications in complex biological samples, including serum and urine, and discuss the challenges that currently limit practical implementation. Finally, we outline key future directions, including the integration of nanopore arrays, optical readout, and machine-learning-assisted analysis, which may synergistically enhance throughput, signal quality, and data-processing capabilities and thereby accelerate clinical translation.</p><p class="metadata"><time datetime="2026-08-13" title="Source date; precision not specified">August 13, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.70936">Original publication</a></p> Thu, 13 Aug 2026 00:00:00 GMT 史银岭 Ziyi Wang Yueming Zhai OpenAlex https://reading.michaelmvh.com/article/dbfeab24e8404d7713bd593c60865014b04011fe102ec5e9738b7df1d4772fda/ urn:sha256:dbfeab24e8404d7713bd593c60865014b04011fe102ec5e9738b7df1d4772fda <p>Determination of the concentration of a biomolecule in a sample is a fundamental measurement in analytical chemistry and central to many diagnostic applications. Solid-state nanopores (ssNPs) stand out as leading candidates to quantify biomolecules due to their capacity to achieve label-free electrical detection with single-molecule resolution. Often, the concentration of a biomolecular sample is estimated in relation to the ssNP capture rate, that is, the number of molecules translocated by the nanopore per unit time. However, this method poses challenges due to variability in capture rates, which have proven difficult to control experimentally. In this work, we introduce a microtrap, that is, a microfluidic device with an integrated nanopore sensor, that leverages sample compartmentalization in known pL volumes allowing direct molecule counting and eliminating the need for capture rate calibration. We demonstrate direct quantification of pico- to nanomolar concentrations of double-stranded DNA (dsDNA) and green fluorescent protein (GFP) molecules in minutes and without the need for calibration of the nanopore sensor capture rate. Moreover, we demonstrate the ability to preconcentrate the biomolecular sample by real-time tuning of the microtrap volume, which can be used to reduce the measurement time and to lower the detection limit.</p><p class="metadata"><time datetime="2026-08-11" title="Source date; precision not specified">August 11, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.70924">Original publication</a></p><p><a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/smtd.70924">Open PDF</a></p> Tue, 11 Aug 2026 00:00:00 GMT Morteza Safari Juliana Chawich Ali Najafi Sohi Martin Charron Vincent Tabard‐Cossa Michel Godin OpenAlex https://reading.michaelmvh.com/article/fbb46dc95cf843005cab0a5cd22956a1771b1081e40365fd4364605f4c8df387/ urn:sha256:fbb46dc95cf843005cab0a5cd22956a1771b1081e40365fd4364605f4c8df387 <p>Symmetric histone recycling is vital for maintaining epigenetic inheritance upon eukaryotic DNA replication. Recent genome-wide studies have uncovered key determinants of this process, but how these factors collectively support parental histone transfer remains incompletely understood. Here, we successfully reconstitute histone recycling with 24 purified proteins and analyze the products digested by Micrococcal nuclease with Repli-pore-seq, the newly developed pipeline combining nanopore sequencing and deep-learning-based classification. As a result, we identify histones symmetrically recycled as tetrasomes or hexasomes on nucleosome-favorable sequences. We also observe the discordance of the recycled position between lagging and leading strands on the GC-rich DNA sequences. Moreover, removal of Pol δ, Pol32, Dpb3/4, Ctf4, Csm3/Tof1, or Mrc1 disrupts the balance of histone recycling between the two daughter strands, whereas removal of Ctf4, Csm3/Tof1, or Mrc1 additionally alters the positions at which histones were recycled. Furthermore, addition of the lagging-strand maturation factors Fen1 and Cdc9 enhances histone recycling to the lagging strand. These findings provide critical insights into the molecular players and mechanisms underlying symmetric histone recycling.</p><p class="metadata"><time datetime="2026-08-11" title="Source date; precision not specified">August 11, 2026</time> <span aria-hidden="true"> · </span> Nature Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41467-026-76520-5">Original publication</a></p> Tue, 11 Aug 2026 00:00:00 GMT Fritz Nagae Shizuko Endo Yasuto Murayama Tsuyoshi Terakawa OpenAlex https://reading.michaelmvh.com/article/c16bbe766e14c478ac0789377d08fbba674e5544b7ede47d7869585a49c64c5e/ urn:sha256:c16bbe766e14c478ac0789377d08fbba674e5544b7ede47d7869585a49c64c5e <p>The recent repurposing of nanopore arrays for proteomics generates extensive high-throughput datasets, but stochastic molecular translocations and sensor heterogeneity inevitably introduce massive non-informative signal artifacts. Therefore, an automated and unbiased data curation method is essential. Here, we present NanoCurator, an iterative, self-supervised CNN-LSTM autoencoder that automatically extracts high-fidelity translocation fingerprints from complex raw data. By evaluating reconstruction error and Lempel-Ziv complexity via adaptive thresholding, NanoCurator effectively segregates genuine signals from diverse noise profiles in both simulated and empirical datasets. Crucially, this curation significantly elevates classification accuracy by 1.8% for a 15-peptide panel, 2.3% for post-translational modifications, and 1.5% for heterogeneous mixtures, while reducing data volume requirements, thereby establishing a robust, highly generalizable paradigm for automated signal quality control. Ultimately, this versatile framework accelerates precise peptide identification and enables the reliable, large-scale application of massively parallel nanopore sensing in proteomics.</p><p class="metadata"><time datetime="2026-08-11" title="Source date; precision not specified">August 11, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.70949">Original publication</a></p> Tue, 11 Aug 2026 00:00:00 GMT Hailin Pan Fengqin Luo Yishuo Zhang Shizhe Jiang Wenzhi Wang Huixian Zeng Yunfeng Zhang Ou Wang Wenbing Qin Lingxuan Zhang Dapeng Wang Junyi Chen Ji Wang OpenAlex https://reading.michaelmvh.com/article/4b42bebb5bd1120fe756b1fd3a5208213db7805f4c6334dca1abd2eef5b211f7/ urn:sha256:4b42bebb5bd1120fe756b1fd3a5208213db7805f4c6334dca1abd2eef5b211f7 <p>Despite substantial progress in nanopore sensing, residue-by-residue peptide sequencing remains a major challenge. Herein, we present EANPSeq, an exopeptidase-assisted nanopore peptide identification strategy based on peptide libraries to decode the peptide sequence. By continuously recognizing the resulting fragments from digesting peptides stepwise through a nanopore, this approach could achieve the identification of peptide sequence based on the comparison of fragment data with libraries of shortened and mutated peptides, with the assistance of machine learning. Notably, compared with previously reported nanopore peptide sensing strategies, EANPSeq shows sufficient resolution to recognize the continuous sequence of peptides containing adjacent identical residues and to precisely localize post-translational modification (PTM) sites within consecutive residues. These proof-of-concept results highlight our nanopore-based strategy as a new avenue for single-molecule protein sequencing. There is significant interest in developing nanopore-based methods for peptide sensing and sequencing. Here the authors report, EANPSeq, a method which enables residue-by-residue peptide sequencing using an exopeptidase-assisted approach, decoding stepwise digestion fragments with machine-learning to achieve single-molecule sequence identification and PTM localization.</p><p class="metadata"><time datetime="2026-08-06" title="Source date; precision not specified">August 6, 2026</time> <span aria-hidden="true"> · </span> Nature Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41467-026-75942-5">Original publication</a></p><p><a href="https://www.nature.com/articles/s41467-026-75942-5_reference.pdf">Open PDF</a></p> Thu, 06 Aug 2026 00:00:00 GMT Ying-Huan FU Nannan Wei Kai‐Li Xin Xinyi Li Li-Min Zhang Cheng Yang Feng Yan Yi‐Tao Long Yi‐Lun Ying OpenAlex https://reading.michaelmvh.com/article/22c19cdd363de9c0d52ffef3559eccc2ff24f3ef21532b99525ec15725f4b3aa/ urn:sha256:22c19cdd363de9c0d52ffef3559eccc2ff24f3ef21532b99525ec15725f4b3aa <p>Adipogenic differentiation is essential for adipose tissue development, fat deposition, and metabolic regulation in livestock, but the role of RNA-binding proteins in sheep preadipocyte differentiation remains unclear. This study investigated whether Quaking (QKI) regulates sheep preadipocyte adipogenesis and explored its downstream regulatory mechanism. QKI expression was examined in sheep adipose tissues, and QKI knockdown was performed in sheep preadipocytes. Adipogenic marker expression, lipid accumulation, glucose consumption, Oxford Nanopore Technologies (ONT) full-length transcriptome sequencing, RNA immunoprecipitation coupled with quantitative real-time PCR (RIP-qPCR), actinomycin D assay, caveolae-associated protein 3 (Cavin3) knockdown, and simultaneous QKI and Cavin3 knockdown were used to evaluate the function and mechanism of QKI. QKI was expressed in different sheep adipose tissues, with relatively higher expression in tail fat. QKI knockdown reduced adipogenic marker expression, Oil Red O staining, and glucose consumption after adipogenic induction. ONT full-length transcriptome sequencing identified Cavin3 as a markedly upregulated candidate downstream target after QKI knockdown. RIP-qPCR showed enrichment of Cavin3 mRNA in QKI immunoprecipitates, and actinomycin D assays indicated that QKI knockdown delayed Cavin3 mRNA degradation. Cavin3 knockdown enhanced adipogenic marker expression, Oil Red O staining, and glucose consumption. Simultaneous QKI and Cavin3 knockdown increased adiponectin, fatty-acid-binding protein 4, and peroxisome proliferator-activated receptor gamma mRNA abundance and Oil Red O staining relative to the matched control, whereas glucose consumption was not significantly different. These findings suggest that QKI promotes sheep preadipocyte differentiation, at least in part, by reducing Cavin3 mRNA stability, providing insight into RNA-binding protein-mediated regulation of livestock adipogenesis.</p><p class="metadata"><time datetime="2026-08-06" title="Source date; precision not specified">August 6, 2026</time> <span aria-hidden="true"> · </span> Animals</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/ani16152441">Original publication</a></p><p><a href="https://www.mdpi.com/2076-2615/16/15/2441/pdf?version=1786018617">Open PDF</a></p> Thu, 06 Aug 2026 00:00:00 GMT Zicheng Li Changsong Xu Bokang Shan Yuan Wang Wangyang Qin Lei Xia Liying Qiao Wenzhong Liu Yangyang Pan OpenAlex https://reading.michaelmvh.com/article/b3a642042b7be852b298892b9f231ef9a4ad8c95e64474bc77c311a3096de150/ urn:sha256:b3a642042b7be852b298892b9f231ef9a4ad8c95e64474bc77c311a3096de150 <p>ABSTRACT Solid-state nanopores offer a versatile platform for single-molecule sensing owing to their mechanical robustness, tuneable geometry, and compatibility with scalable fabrication. Here, we present a pyramidal silicon nanopore with a 40 nm sensing aperture for label-free characterisation of protein molecules by resistive pulse sensing. The nanopore operates stably over transmembrane voltages ranging from −2 to +2 V and across a broad range of electrolyte concentrations, enabling analysis under diverse experimental conditions. As molecules traverse the confined sensing region, transient ionic current modulations are generated that reflect their excluded volume and molecular geometry. Using this approach, we characterise unlabelled Tau species spanning monomeric proteins, intermediate aggregates, and mature fibrillar assemblies. Analysis of the resulting current signatures, together with simplified geometrical models, enables reconstruction of molecular dimensions and discrimination of distinct Tau populations based on their electrical fingerprints. These results demonstrate that pyramidal silicon nanopores provide a sensitive and scalable platform for label-free monitoring of structurally heterogeneous protein aggregation and establish a framework for investigating protein aggregation using solid-state nanopore sensing.</p><p class="metadata"><time datetime="2026-08-04" title="Source date; precision not specified">August 4, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.08.04.742667">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/08/04/2026.08.04.742667.full.pdf">Open PDF</a></p> Tue, 04 Aug 2026 00:00:00 GMT Hoi Lam Cheung Dehua Hu Jianxin Yang Ho Pui Ho OpenAlex https://reading.michaelmvh.com/article/efaa9782968a477d71ca23a6536e7a34e82bdadac5f0828f50d779bcfff00194/ urn:sha256:efaa9782968a477d71ca23a6536e7a34e82bdadac5f0828f50d779bcfff00194 <p>Nanopore technology has revolutionized single-molecule science by enabling ultrasensitive characterization of biomolecular structure and interactions via accessible, physics-based tabletop measurements. In a typical experiment, the chemical structure of a biomolecule is determined by measuring a transient blockade of the nanopore ionic current produced by the nanopore passage of the molecule. Nanopore sensing can now deliver a telomere-to-telomere sequence of a human chromosome and is poised to unravel the vast complexity of the proteome. Notwithstanding the three decades of development, a fundamental interpretive bottleneck remains: the method cannot independently determine the 3D structure of a biomolecule as it passes through the nanopore. All-atom molecular dynamics has emerged as a go-to method for determining the structure of the translocating molecules and its relationship with the nanopore current. Here, we review molecular dynamics methods used to simulate the transport through biological, solid-state, and DNA origami nanopores. We highlight how advances in high-performance computing and enhanced sampling are dismantling historical timescale barriers, allowing the simulations to achieve unprecedented experimental relevance. By detailing the path from system construction to the extraction of experimental observables, we illustrate how computational insights are transitioning from providing post-hoc signal interpretation to enabling predictive, rational design of next-generation biosensors.</p><p class="metadata"><time datetime="2026-08-03" title="Source date; precision not specified">August 3, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p><a href="https://doi.org/10.1002/smtd.70904">Original publication</a></p> Mon, 03 Aug 2026 00:00:00 GMT Behzad Mehrafrooz Xavier Mleziva Meng Xu Melika Shekari Christopher Maffeo Aleksei Aksimentiev OpenAlex https://reading.michaelmvh.com/article/bcae8df28a70ecd29d5a1227519bced751364b450c59b5a656892686d0bca249/ urn:sha256:bcae8df28a70ecd29d5a1227519bced751364b450c59b5a656892686d0bca249 <p>Antibiotic resistance is a global health threat, driving the need for new molecules that kill bacteria via nontraditional mechanisms. Here, we present a computational de novo design strategy for α-helical peptides that self-assemble into large, stable and membrane-spanning nanopores with antimicrobial activity, including in vivo efficacy against drug-resistant pathogens. Molecular dynamics simulations guided the selection of sequences for transmembrane barrel-stave pore formation, which were validated by microscopy, electrophysiology and fluorescence assays. Using computational and experimental analyses, including negative design controls, we developed general design guidelines and 52 modular sequence templates with tunable antimicrobial, pore-forming properties. Mechanistic studies confirmed bacterial cytoplasmic membrane disruption via designed nanopore formation. A tuned lead peptide selectively killed drug-resistant ESKAPEE bacteria, including Acinetobacter baumannii, without harming human cells, and showed anti-infective efficacy in preclinical mouse infection models. The framework presented here enables the design of synthetic peptide nanopores for precision antimicrobials, anticancer agents, molecular sensors and delivery systems.</p><p class="metadata"><time datetime="2026-08-03" title="Source date; precision not specified">August 3, 2026</time> <span aria-hidden="true"> · </span> Nature Chemical Biology</p><p><a href="https://doi.org/10.1038/s41589-026-02269-z">Original publication</a></p><p><a href="https://www.nature.com/articles/s41589-026-02269-z.pdf">Open PDF</a></p> Mon, 03 Aug 2026 00:00:00 GMT Rahul Deb Marcelo D. T. Torres Ivo Kabelka Jan Přibyl Kateřina Dvořáková Bendová Edo Vreeker Markéta Koběrská Gabriela Balikova Novotna Miloš Petřík Giovanni Maglia César de la Fuente‐Núñez Robert Vácha OpenAlex https://reading.michaelmvh.com/article/95c8a0b873091232f47b65548af238f53fe6a976dc300948dee27539c2bfbef6/ urn:sha256:95c8a0b873091232f47b65548af238f53fe6a976dc300948dee27539c2bfbef6 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-08-01" title="Source date; precision not specified">August 1, 2026</time> <span aria-hidden="true"> · </span> Molecular Cell</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.molcel.2026.07.019">Original publication</a></p> Sat, 01 Aug 2026 00:00:00 GMT Zhirui Zhang Xihao Yang Yifan Sun Yi Hao Yao Li Yunjiao Wang Chunyang Xie Pinghui Peng Shilong Liu Xinyan Jiang Zhonghao Zhang Eryan Kong Liang Wang Aimin Yang OpenAlex https://reading.michaelmvh.com/article/1c488dac23f963888d3787d7e2ca901d9d2e6d54148e209df6bc94feed8960c5/ urn:sha256:1c488dac23f963888d3787d7e2ca901d9d2e6d54148e209df6bc94feed8960c5 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-07-31" title="Source date; precision not specified">July 31, 2026</time> <span aria-hidden="true"> · </span> Chemical Engineering Science</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.ces.2026.124829">Original publication</a></p> Fri, 31 Jul 2026 00:00:00 GMT Daiwen Li Mingjie Wei Shi-Peng Sun Yong Wang OpenAlex https://reading.michaelmvh.com/article/01f28340f3fca0e132bebbab9dedee1eb2fdd5efbdd19babd1c8c8934b88731a/ urn:sha256:01f28340f3fca0e132bebbab9dedee1eb2fdd5efbdd19babd1c8c8934b88731a <p>No abstract is available.</p><p class="metadata"><time datetime="2026-07-29" title="Source date; precision not specified">July 29, 2026</time> <span aria-hidden="true"> · </span> Nature</p><p class="provenance">Curated by <a href="https://github.com/Michaelmvh/scholarly-rss-feed/blob/main/src/curated/nanopore-foundations.json" rel="external">Nanopore Foundations &amp; Signal Analysis</a> · Protein analysis · Rereading · Sequential cleavage · Transient pore analyte looping</p><p><a href="https://doi.org/10.1038/s41586-026-10881-1">Original publication</a></p> Wed, 29 Jul 2026 00:00:00 GMT Jialu Chen Hanhan Zhang Kefan Wang Tian Li Wen SUN Zixuan Wang Xinmeng Gao Zhenyuan Cao Yusheng Ouyang Lang Yao Yifan Wang Yunqi Xiao Ruidong Li Xingwang An Xinyi Dai Lulu Zhao Qian Lu Panke Zhang Shuo Huang OpenAlex Nanopore Foundations & Signal Analysis https://reading.michaelmvh.com/article/b11eec751f0053f3d01edd2b11ce7922fd7c62a6dab18976ff40bf462e9b3df5/ urn:sha256:b11eec751f0053f3d01edd2b11ce7922fd7c62a6dab18976ff40bf462e9b3df5 <p>Environmental exposures are known to contribute to the development and progression of human diseases. For example, air pollution is a modifiable risk factor for dementia, but the underlying biological pathways linking inhaled pollutants to amyloid-beta accumulation and neuroinflammation are not well defined. The lung-brain axis has been proposed as a route whereby toxins, inflammatory mediators, and immune cells may enter the circulation and access the brain through a compromised blood-brain barrier, but empirical evidence remains limited. The transcription factor Nrf2 regulates antioxidant defence pathways that counteract environmentally induced oxidative stress, though its broader regulatory functions require further characterisation. In addition, the genomic occurrence of DNA methylation, which is a repressive epigenetic mark occurring at cytosine-phosphate-guanine (CpG) sites, can be altered by air pollution exposures, however, the impacts on cell function and health remain unclear. This PhD study aims to define molecular pathways altered by environmental pollutants in mouse models and to evaluate their translational relevance to human disease. Heme oxygenase (HO)-based oxidative-stress reporter mice carrying either Nrf2-wildtype or Nrf2-knockout genotypes were exposed in vivo to polychlorinated biphenyl (PCB) compounds, which are long-lasting industrial chemical pollutants. Two Alzheimer’s disease (AD) mouse models carrying humanized amyloid-beta-precursor protein (APP)-mutations were subjected to in vivo inhalation exposures to either woodsmoke or propane-derived ultrafine particles. Multi-omic approaches were performed following these exposure experiments, including bulk-RNA sequencing, Infinium DNA methylation BeadChip profiling, and validation by Nanopore long-read sequencing for DNA methylation, and mass spectrometry-based proteomics. In the transcriptomic analysis, differentially expressed genes (DEG) were filtered (|log2 fold change| &gt; 1.5 &amp; FDR &lt; 0.05), followed by over-representation analysis using Gene Ontology and KEGG databases. Weighted gene correlational network analysis (WGCNA), an unsupervised learning algorithm, was employed to cluster co-expressed genes related to exposure conditions, and then identify putative pathway regulators. Gene set enrichment analyses (GSEA) were applied to assess cross-species consistency with human datasets. Differentially methylated regions (DMRs) were identified as the genomic segments with consistent methylation changes spanning adjacent CpGs. To examine their relationship with gene expression, DMRs were mapped to genomic regulatory features, including enhancers, promoters, and gene bodies. Random forest method was further used to select key CpG loci most discriminative of exposure conditions. In addition, analogous to WGCNA, co-methylated CpG clusters were identified, which may reflect coordinated pathway-level responses. Key findings of this PhD study: (1)Using the oxidative stress reporter mouse model, we identified a previously unrecognised Nrf2-dependent cell-cycle response in the liver following PCB exposure. (2)Building on the emerging concept of the lung-brain axis in neurodegeneration, we demonstrated that woodsmoke exposure in Alzheimer’s disease (AD) model mice induces markedly exacerbated pulmonary immune responses and suppresses hippocampal ion-channel activity. Notably, reduced hippocampal ion-channel activity was also observed in a separate familial AD mouse model exposed to propane-derived ultrafine particles. (3)Although direct relationship between DNA methylation and gene expression were limited across these exposure experiments, methylation alterations were highly enriched within open-chromatin regions, suggesting that these domains are susceptible to environmental insults. Together, these findings demonstrate how controlled exposure models can uncover novel molecular pathways and highlight potential neurotoxic effects of inhaled pollutants. The identified gene sets show strong correspondence with human molecular signatures, underscoring the translational potential of this work in contributing understanding to human diseases.</p><p class="metadata"><time datetime="2026-07-28" title="Source date; precision not specified">July 28, 2026</time> <span aria-hidden="true"> · </span> ERA</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7488/era/7490">Original publication</a></p> Tue, 28 Jul 2026 00:00:00 GMT Wenduo Qi OpenAlex https://reading.michaelmvh.com/article/504a62d85ddac4ac88fffe9ee6fd8427f5a728d6e553737c9038fb59e1ae8989/ urn:sha256:504a62d85ddac4ac88fffe9ee6fd8427f5a728d6e553737c9038fb59e1ae8989 <p>Solid-state nanopores are established tools for single-molecule analysis, yet their sensing performance is often constrained by the limited temporal resolution of ionic current recordings. This is particularly challenging given the short residence times of proteins, nanostructured barcodes, and targets bound to molecular carriers. To overcome this limitation, we report a platform utilizing a controllable pressure gradient to generate a hydrodynamic fluid flow that opposes the electrokinetic forces acting on the analyte, thereby decoupling molecular transport speed from the sensing voltage. Here, we systematically investigate the dynamics of passage under these voltage-pressure conditions for diverse analytes, ranging from linear DNA and DNA origami nanostructures to proteins. Crucially, we show that polymer folding probability is reduced and the instantaneous velocity profile throughout the translocation process is uniformly attenuated. Furthermore, the effective slowing down of low molecular weight proteins improves the detection rate and yields rich event signatures required for accurate fingerprinting. This platform also provides novel insights into the origin of enhanced current blockages and enables an independent measurement of the effective charge of DNA under our operating conditions. Ultimately, this technique transforms solid-state nanopores into highly tunable devices, unveiling complex protein signatures and barcoded DNA substructures often obscured by translocation speed.</p><p class="metadata"><time datetime="2026-07-28" title="Source date; precision not specified">July 28, 2026</time> <span aria-hidden="true"> · </span> ChemRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26434/chemrxiv.15006642/v1">Original publication</a></p> Tue, 28 Jul 2026 00:00:00 GMT Mohamed Yassine Bouhamidi Martin Charron Vincent Tabard‐Cossa OpenAlex https://reading.michaelmvh.com/article/96b313477aa08d2df61012c4c3fea0c2330bd487931dce650a6f20d2ff8cdb14/ urn:sha256:96b313477aa08d2df61012c4c3fea0c2330bd487931dce650a6f20d2ff8cdb14 <p>The concept of single-entity electrochemistry (SEE) emerged as a transformative framework for studying individual particles, molecules, and cells, distinct from traditional ensemble approaches, following its formal introduction during the 2016 Faraday Discussion in York, UK. Within the repertoire of techniques available under SEE, nanopore sensing has distinguished itself as a highly precise and versatile method for single-entity analysis of individual nanoparticles, cells, viruses, and (bio)molecules. Its ability to probe and characterize individual entities at nanoscale resolution has made it a cornerstone technology in this field. This review examines the foundational principles of nanopore sensing, its inherent advantages, and the technical challenges associated with its implementation. Strategies to overcome these challenges, including the incorporation of hydrogel and polymer enhancements, are presented as effective solutions for improving the reliability and efficiency of nanopore-based experiments. An exploration of the two primary types of nanopores—solid-state nanopores and biological nanopores—follows, with a focus on their respective fabrication techniques, material properties, and functional advantages. Solid-state nanopores, known for their robustness and customizability, are compared with biological nanopores, which offer unparalleled molecular specificity due to their naturally evolved structures. The integration of computational tools is discussed as a critical component of nanopore sensing. Computational modeling and simulation methods are shown to play a pivotal role in interpreting complex nanopore data by providing insights into dynamic molecular interactions and enhancing experimental accuracy. These tools allow for the prediction and analysis of ion flux, molecular trajectories, and conformational changes, thereby broadening the scope and precision of nanopore-based studies. Applications of nanopore technology are highlighted, particularly in the detection and characterization of nanoparticles, biomolecules, and genetic material. Nanopore sensing has been successfully employed to study properties such as size, shape, and surface charge, as well as to identify specific biomolecules such as DNA and proteins. Its utility in both fundamental research and proof-of-concept studies demonstrates its adaptability across diverse fields, including material science, molecular biology, and chemical engineering. The review concludes by exploring the transformative potential of integrating artificial intelligence (AI) with nanopore technology. AI algorithms have shown remarkable promise in automating data acquisition and analysis, significantly enhancing the throughput and precision of nanopore experiments. Through machine learning and self-optimization techniques, AI streamlines the identification of patterns in complex datasets, enabling rapid and reliable single-entity characterization. This fusion of nanopore technology with AI not only reduces experimental burdens but also accelerates innovation in the field, paving the way for autonomous experimentation and high-throughput diagnostics.</p><p class="metadata"><time datetime="2026-07-27" title="Source date; precision not specified">July 27, 2026</time> <span aria-hidden="true"> · </span> CRC Press eBooks</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1201/9781003506348-9">Original publication</a></p> Mon, 27 Jul 2026 00:00:00 GMT Eugene Gyasi Agyemang OpenAlex https://reading.michaelmvh.com/article/4d0468af1a9e642f83f71a590081299131ec26c9c3505ebe71f8c1de80554154/ urn:sha256:4d0468af1a9e642f83f71a590081299131ec26c9c3505ebe71f8c1de80554154 <p>A Nextflow DSL2 pipeline for metagenomic pathogen detection, host profiling, antimicrobial resistance (AMR) gene detection, and targeted SNP/amino-acid variant profiling, supporting both Illumina/Element short reads and Oxford Nanopore long reads.</p><p class="metadata"><time datetime="2026-07-27" title="Source date; precision not specified">July 27, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21632291">Original publication</a></p> Mon, 27 Jul 2026 00:00:00 GMT Edward Bird OpenAlex https://reading.michaelmvh.com/article/8a16f037db6e249b6cb3d665bf1722269f6c587173b3cc766662fb914409849f/ urn:sha256:8a16f037db6e249b6cb3d665bf1722269f6c587173b3cc766662fb914409849f <p>Data for &quot;A single peptide self-assembles into flexible nanopores for ultrasensitive disease protein profiling&quot;</p><p class="metadata"><time datetime="2026-07-25" title="Source date; precision not specified">July 25, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21564511">Original publication</a></p> Sat, 25 Jul 2026 00:00:00 GMT Varsha Shaji Neethu Puthumadathil Renu Jain Kalyanashis Jana Vedasmiritha T S Ulrich Kleinekathöfer Krishnananda Chattopadhyay Kozhinjampara R. Mahendran OpenAlex https://reading.michaelmvh.com/article/f1a5d98619f983aaa2c990ef3bfb32809d9a2d5e53660854bacb9068ef629844/ urn:sha256:f1a5d98619f983aaa2c990ef3bfb32809d9a2d5e53660854bacb9068ef629844 <p>ABSTRACT Localized measurements of electric fields offer a promising route to expand the information content of nanopore-based single-molecule sensing beyond conventional ionic-current blockade. Here, using all-atom molecular dynamics simulations with virtual electric-field probes placed around a graphene nanopore, we show that the local electric-field captures the presence, and distribution of charged amino acids as the peptides translocate through the pore. These field signatures create reproducible peptide-specific fingerprints across independent translocation events and enable substantially improved discrimination between peptides compared with ionic-current traces obtained under the same simulation conditions. Our results suggest that localized nanopore electrometry can provide a complementary, information-rich readout of peptide charge order that is largely inaccessible to conventional current blockade-based measurement. This study establishes a simulation-guided framework for integrating nanoscale electrometry with nanopore platforms for future peptide and protein analysis.</p><p class="metadata"><time datetime="2026-07-23" title="Source date; precision not specified">July 23, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.07.20.739564">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/07/23/2026.07.20.739564.full.pdf">Open PDF</a></p> Thu, 23 Jul 2026 00:00:00 GMT Pranjal Sur Prabal Kumar Maiti Manoj M. Varma OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/462fdcb05eefe98c16369d9806c4927efe0094279dbbe81a477789bd4b9794e5/ urn:sha256:462fdcb05eefe98c16369d9806c4927efe0094279dbbe81a477789bd4b9794e5 <p>The advent of single-molecule nanopore sequencing established a powerful platform for modern genomics by using static biological pores to report the translocation of canonical nucleic acids, enabling rapid, accessible nucleic acid analysis. However, extending this strategy to single-molecule proteomics has stalled against a fundamental biophysical bottleneck. Current efforts in nanopore proteomics attempt to retrofit these static, spatial “caliper” biological nanopores (e.g., α-hemolysin, MspA, CsgG, aerolysin) for protein sequencing despite the immense steric, charge, and conformational heterogeneity of proteins. Unlike the chemically uniform, polyanionic phosphodiester backbone of DNA, the proteome contains isosteric and isobaric variants that confound purely volumetric measurements made by static pores. To address this bottleneck, we propose the application of dynamical translocases – naturally evolved, protein-handling nanomachines (e.g., the anthrax toxin protective antigen). Unlike static pores that rely on passive diffusion, dynamical translocases employ target-docking clamp architectures that achieve low nanomolar sensitivity. Active-site conformational dynamics generate high-dimensional kinetic fingerprints that enable molecular discrimination during translocation. By coupling dynamical translocases with Physics-Informed Machine Learning (PIML), we demonstrate that amino-acid side-chain-dependent thermodynamic friction can be mathematically decoded, enabling &gt;90% accurate classification of chemically distinct amino acid classes and doing so label-free without the artificial DNA-handles required by legacy platforms.</p><p class="metadata"><time datetime="2026-07-23" title="Source date; precision not specified">July 23, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.07.20.739629">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/07/23/2026.07.20.739629.full.pdf">Open PDF</a></p> Thu, 23 Jul 2026 00:00:00 GMT Jaylen E. Taylor Parichit Sharma Bryan A. Krantz OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/947aa4c85f5c86e6294533268e1a90967c048ca3f62b5f672b064401c00e81a8/ urn:sha256:947aa4c85f5c86e6294533268e1a90967c048ca3f62b5f672b064401c00e81a8 <p>Soil salinization is a major abiotic stress limiting wheat production. Although transcriptional responses to salt stress are well-studied, the role of posttranscriptional regulation, particularly through RNA modifications, remains unclear in wheat (Triticum aestivum L.). Here, we present an integrated analysis of the early salt stress response using Nanopore direct RNA sequencing and quantitative proteomics. We generated genome-wide maps of N6-methyladenosine (m6A) modifications, concurrently profiling alternative polyadenylation events and poly(A) tail length dynamics. This multiomics approach characterizes coordinated epitranscriptomic reprogramming and enabled the construction of a regulatory network linking m6A marks to proteomic changes. Furthermore, we identified and functionally validated the putative m6A reader protein EVOLUTIONARILY CONSERVED C-TERMINAL REGION 5 (TaECT5) as a positive regulator of wheat salt tolerance. Our study provides a systems-level view of posttranscriptional regulation during salt stress in wheat and identifies potential targets for enhancing salt tolerance.</p><p class="metadata"><time datetime="2026-07-22" title="Source date; precision not specified">July 22, 2026</time> <span aria-hidden="true"> · </span> PLANT PHYSIOLOGY</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1093/plphys/kiag540">Original publication</a></p> Wed, 22 Jul 2026 00:00:00 GMT Jie Zang Qian Zhang Yuyu Zhang Zheng Wang Yuxiu Dong Yongming Chen Xian Sheng Zhang Yifeng Hou OpenAlex https://reading.michaelmvh.com/article/1c410197194828e20cd6e780a461998de1255b7eeabd469d05ac192b77384d41/ urn:sha256:1c410197194828e20cd6e780a461998de1255b7eeabd469d05ac192b77384d41 <p>Proteins derive their biological identity from an amino acid sequence, and even subtle sequence variations can mark disease states, therapeutic response, and cancer progression. Although solid-state nanopores offer single-molecule sensitivity, protein analysis with conventional nanopores remains limited by stochastic capture, rapid translocation, and the need for sub-nanometer control over pore dimensions. Here, we report that this size-matching requirement can be bypassed by converting sequence-dependent protein surface chemistry into amplified particle-scale transport signatures through leveraging chaotropic chemistry for surface charge modulation. We immobilized monoclonal anti-prostate-specific antigen antibody variants, differing only in partial amino acid sequence, on polymeric microparticles and measured their passage through readily fabricated SiNx micropores. In the presence of guanidine hydrochloride, chaotropic perturbation of hydration shells and compression of the electric double layer reshaped the electrokinetic landscape around the particle-protein complexes in a variant-dependent manner. These chemically amplified differences generated distinct resistive pulse waveforms, allowing near-perfect discrimination of antibody variants by machine learning. This approach shifts protein sensing from geometrical confinement in nanoscale pores to chemically tuned amplification in micrometer-scale pores, providing a scalable route to sequence-sensitive biomarker profiling without advanced nanofabrication.</p><p class="metadata"><time datetime="2026-07-21" title="Source date; precision not specified">July 21, 2026</time> <span aria-hidden="true"> · </span> ACS Sensors</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acssensors.6c02297">Original publication</a></p> Tue, 21 Jul 2026 00:00:00 GMT Shoji Kashiwabara Md Sifat Islam Makusu Tsutsui Masateru Taniguchi OpenAlex https://reading.michaelmvh.com/article/4b913f26062c8b65156193b33f9f2bf7f3913226ea523d441dc43e97a9e151d1/ urn:sha256:4b913f26062c8b65156193b33f9f2bf7f3913226ea523d441dc43e97a9e151d1 <p>Effective and precise detection of peptides and their post-translational modifications (PTMs) is crucial for biomedical research but remains technically challenging. Here, we present a nanopore sensing strategy that enables label-free analysis of negatively charged peptides. By introducing arginine residues into the nanopore and using amino-cyclodextrin as a molecular adaptor, the system enables unambiguous discrimination of short negatively charged homopeptides differing by only a single residue. Building on this capability, the platform further demonstrates high sensitivity for detecting representative PTMs, including acetylation, lactylation, and phosphorylation, introduced on a negatively charged peptide scaffold. Notably, the system could also analyze fragments generated by proteolytic digestion of full-length proteins, underscoring its potential for accurate protein identification. This work offers an accessible and reliable strategy to characterize peptide variants with single-amino acid differences and PTMs, which may facilitate future applications in peptide biomarker detection and protein sequence analysis.</p><p class="metadata"><time datetime="2026-07-21" title="Source date; precision not specified">July 21, 2026</time> <span aria-hidden="true"> · </span> Journal of Nanobiotechnology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1186/s12951-026-04818-z">Original publication</a></p> Tue, 21 Jul 2026 00:00:00 GMT Liting Kang Linting Wang Xuefei Fan Lingfang Xu Han Yang Chenxin Wu Tongxin Zhu Xiangyi Zhao Linming Zhang Jianhuang Xue Shuanghong Yan OpenAlex https://reading.michaelmvh.com/article/9a5ec7450c99618eb570c30a4bcc70a409eaef3e63df86b3ad3df56ca05b4e10/ urn:sha256:9a5ec7450c99618eb570c30a4bcc70a409eaef3e63df86b3ad3df56ca05b4e10 <p>Supplementary material 1.</p><p class="metadata"><time datetime="2026-07-21" title="Source date; precision not specified">July 21, 2026</time> <span aria-hidden="true"> · </span> Figshare</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.6084/m9.figshare.34516847">Original publication</a></p> Tue, 21 Jul 2026 00:00:00 GMT Liting Kang Linting Wang Xuefei Fan Lingfang Xu Yang Han Chenxin Wu Tongxin Zhu Xiangyi Zhao Linming Zhang Jianhuang Xue Shuanghong Yan OpenAlex https://reading.michaelmvh.com/article/9a2aa19bcfd13353759c3a2bd93364ed768a732e04421b0bfcc56ad9326089a2/ urn:sha256:9a2aa19bcfd13353759c3a2bd93364ed768a732e04421b0bfcc56ad9326089a2 <p>The Asian green mussel Perna viridis is expanding across coastal systems of the Americas, creating demand for curated molecular references to support biosecurity, aquaculture monitoring, and comparative invasion studies. Here, we report the first complete mitochondrial genomes of invasive P. viridis from Brazil and the southwestern Atlantic, generated from two specimens collected in Santa Catarina, at the current southern Brazilian invasion front. Long-range PCR, Oxford Nanopore sequencing, read-supported assembly, manual annotation, comparative mitogenomics, nucleotide-diversity analysis, protein-level divergence, and phylogenomic inference were used to generate and evaluate complete mitochondrial references. The two circular assemblies were 16,015 bp and 16,011 bp and contained 38 annotated features, including 13 protein-coding genes, 23 tRNAs, and two rRNAs, all on the H strand, with an identical A+T content of 67.5%. Pairwise comparisons among complete P. viridis mitogenomes showed high overall similarity but retained 20-125 SNPs/mismatches and one to 12 indel events. Gene order was conserved within P. viridis but differed from P. canaliculus and P. perna, and phylogenomics placed the Brazilian assemblies within the P. viridis clade. These curated mitogenomes establish a genomic baseline for molecular surveillance and future invasion-focused studies of P. viridis in the southwestern Atlantic.</p><p class="metadata"><time datetime="2026-07-20" title="Source date; precision not specified">July 20, 2026</time> <span aria-hidden="true"> · </span> Biology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/biology15141199">Original publication</a></p><p><a href="https://www.mdpi.com/2079-7737/15/14/1199/pdf?version=1784534521">Open PDF</a></p> Mon, 20 Jul 2026 00:00:00 GMT André Oliveira de Souza Lima Rafael Schroeder Gabriela Scholante Delabary Gilberto Caetano Manzoni Mayara Carneiro Beltrão OpenAlex https://reading.michaelmvh.com/article/443a158c87df846d2333f5149dcde0b514423d716b8683b1a7cd71980d37a51f/ urn:sha256:443a158c87df846d2333f5149dcde0b514423d716b8683b1a7cd71980d37a51f <p>The advent of single-molecule nanopore sequencing established a powerful platform for modern genomics by using static biological pores to report the translocation of canonical nucleic acids, enabling rapid, accessible nucleic acid analysis. However, extending this strategy to single-molecule proteomics has stalled against a fundamental biophysical bottleneck. Current efforts in nanopore proteomics attempt to retrofit these static, spatial “caliper” biological nanopores (e.g., α-hemolysin, MspA, CsgG, aerolysin) for protein sequencing despite the immense steric, charge, and conformational heterogeneity of proteins. Unlike the chemically uniform, polyanionic phosphodiester backbone of DNA, the proteome contains isosteric and isobaric variants that confound purely volumetric measurements made by static pores. To address this bottleneck, we propose the application of dynamical translocases – naturally evolved, protein-handling nanomachines (e.g., the anthrax toxin protective antigen). Unlike static pores that rely on passive diffusion, dynamical translocases employ target-docking clamp architectures that achieve low nanomolar sensitivity. Active-site conformational dynamics generate high-dimensional kinetic fingerprints that enable molecular discrimination during translocation. By coupling dynamical translocases with Physics-Informed Machine Learning (PIML), we demonstrate that amino-acid side-chain-dependent thermodynamic friction can be mathematically decoded, enabling &gt;90% accurate classification of chemically distinct amino acid classes and doing so label-free without the artificial DNA-handles required by legacy platforms.</p><p class="metadata"><time datetime="2026-07-20" title="Source date; precision not specified">July 20, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21453989">Original publication</a></p> Mon, 20 Jul 2026 00:00:00 GMT Bryan A. Krantz OpenAlex https://reading.michaelmvh.com/article/7cd65c7e8de0363f8d03dc8135881f49f245ce8312def1e25330c5749873a6ce/ urn:sha256:7cd65c7e8de0363f8d03dc8135881f49f245ce8312def1e25330c5749873a6ce <p>Abstract Animal venoms are a rich source of bioactive molecules, yet their diversity remains incompletely characterized in many species. Here we present the first long-read transcriptomic analysis of venom glands from Philippine tarantulas (Theraphosidae), a highly endemic but understudied group. Using Oxford Nanopore sequencing, we reconstructed near full-length venom gland transcriptomes across multiple species and identified extensive repertoires of toxin-encoding peptides. Venom glands were enriched in cysteine-rich inhibitor cystine knot (ICK) peptides, which dominated the toxin landscape and are known modulators of ion channels. Cross-species comparative analyses revealed a distinct transcriptional signature separating venom from non-venom tissues, driven by coordinated expression of toxin-associated and regulatory gene families. Phylogenomic reconstruction based on orthologous peptides recovered expected taxonomic relationships while revealing potential lineage-specific diversification and potential cryptic taxa. Despite a conserved core set of toxin families, substantial variation in toxin composition was observed among species, consistent with rapid evolution driven by gene duplication and functional divergence. Analysis of highly expressed ICK peptides showed a conserved cysteine framework alongside marked sequence variability in inter-cysteine regions, supporting a model in which structural stability is maintained while functional diversification proceeds. Together, these findings establish the first long-read transcriptomic resource for Philippine theraphosid spiders, reveal a conserved molecular signature underlying venom gland specialization, and provide new insights into the diversification of ICK toxin repertoires that may facilitate future evolutionary and functional studies, including the discovery and characterization of bioactive venom peptides.</p><p class="metadata"><time datetime="2026-07-18" title="Source date; precision not specified">July 18, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/bioinformatics" rel="external">bioRxiv: Bioinformatics</a></p><p><a href="https://doi.org/10.64898/2026.07.14.737467">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/07/18/2026.07.14.737467.full.pdf">Open PDF</a></p> Sat, 18 Jul 2026 00:00:00 GMT Lorenz Rhuel P. Ragasa Maria Mikaela U. Dumbrique Sid Alfred S. Gamboa Anj Guillan M. Baile Darrell C. Acuña Heidie Frisco Cabanos Ricardo C.H. del Rosario Leonardo A. Guevarra Myla R. Santiago-Bautista OpenAlex bioRxiv: Bioinformatics https://reading.michaelmvh.com/article/a00671c108280ddb31d1c1e91a9570154ef0880cab812f88d02a445305806061/ urn:sha256:a00671c108280ddb31d1c1e91a9570154ef0880cab812f88d02a445305806061 <p>Transfer RNA (tRNA)-modifying enzymes are emerging as key regulators of bacterial physiology. MiaA, a tRNA isopentenyltransferase, is well studied in model organisms, but its role in the opportunistic pathogen Pseudomonas aeruginosa remains unclear. Using LC-MS, nanopore tRNA sequencing, as well as transcriptional, translational, and proteomic profiling, we mapped MiaA-dependent tRNA modifications and revealed unexpected effects of MiaA loss. Impaired translation of MiaA-sensitive codons reduced quorum-sensing-controlled virulence gene expression and attenuated pathogenicity in Galleria mellonella. Ribosome stalling at trp codons in miaA mutants overrides the attenuation-controlled repression of tryptophan biosynthesis, causing overproduction of tryptophan, along with upregulation of cognate tRNAs, thereby linking translation to global metabolic adaptation. MiaA is tightly regulated and is so central to bacterial physiology that its expression level correlates directly to virulence in clinical isolates, highlighting its role as a hub connecting translation, transcription, metabolism, and pathogenicity. These findings position MiaA as a key integrator of cellular processes critical for pathogen fitness and host interactions.</p><p class="metadata"><time datetime="2026-07-17" title="Source date; precision not specified">July 17, 2026</time> <span aria-hidden="true"> · </span> Nucleic Acids Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1093/nar/gkag755">Original publication</a></p> Fri, 17 Jul 2026 00:00:00 GMT Yannick Noah Frommeyer Janne Gesine Thöming Nicolas O Gomez Svenja Grobe Matthias Preuße Alejandro Arce‐Rodríguez Kerstin Neubauer Benedikt Kennepohl Tim Kirk Raimo Franke Mark Brönstrup Meina Neumann‐Schaal Mathias Müsken Daniel Pearce Depledge Heike Bähre Andreas Pich Susanne Häußler OpenAlex https://reading.michaelmvh.com/article/3546ab2ee709aa81e2bb6101322827b74cb0af4f549b0943cf202e7df41bdfd6/ urn:sha256:3546ab2ee709aa81e2bb6101322827b74cb0af4f549b0943cf202e7df41bdfd6 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-07-17" title="Source date; precision not specified">July 17, 2026</time> <span aria-hidden="true"> · </span> UNC Libraries</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.17615/90bz-6a65">Original publication</a></p> Fri, 17 Jul 2026 00:00:00 GMT Steven A. Soper Suresh Shivanka Adam R. Hall Collin McKinney Maximillian I. Chibuike Matthew Verber Sunggook Park Junseo Choi Farhad Shiri OpenAlex https://reading.michaelmvh.com/article/3f0b3ac0350a9f59b67e2f36b489a63859cec928f76412913e10231e45602a0b/ urn:sha256:3f0b3ac0350a9f59b67e2f36b489a63859cec928f76412913e10231e45602a0b <p>Po uspešni uporabi nanopor za določanje zaporedja nukleinskih kislin se raziskave na tem področju usmerjajo v zaznavanje proteinov in določanje njihovega aminokislinskega zaporedja. Metoda temelji na zaznavi električnih tokov in njihovih sprememb ob prehajanju ionov in analitov skozi nanometrsko proteinsko poro, vstavljeno v električno neprevodno lipidno ali polimerno membrano. Med najpogosteje uporabljenimi biološkimi porami so porotvorni proteini, pri čemer je FraC edini aktinoporin, že uporabljen v ta namen. V okviru doktorskega raziskovalnega dela smo proučevali in za zaznavanje optimizirali pore aktinoporinom podobnega proteina iz morske korale Orbicella faveolata (Fav). Mutant RN1-Fav je kljub manj stabilnemu α-vijačnemu transmembranskemu delu v primerjavami z β-porotvornimi proteini izkazoval stabilno vgradnjo v polimerne planarne membrane in omogočil razločevanje histonov. Zunajcelične histone se namreč vse pogosteje omenja kot potencialne biomarkerje, katerih hitra, natančna zaznava v realnem času bi lahko nadomestila dosedanji tehniki zaznavanja s protitelesi in masno spektrometrijo. Naši rezultati kažejo, da so za opažene spremembe električnih tokov ob dodatku histonov H4, H3.1, H3K9ac, H3K23ac in H3Cit ključne elektrostatske interakcije med pozitivno nabitimi histoni in negativnim neto nabojem lumna pore. Dodatno smo s pomočjo modelnega učenja uspešno ločili blokade, pripadajoče histonom v mešanicah H4/H3Cit, H4/H3.1 in H4/H3Cit/H3K9ac. V primeru najpogosteje prisotnih serumskih histonov H3Cit in H4 smo pokazali, da je na podlagi frekvence dogodkov mogoče določiti tudi njihovo koncentracijo in razmerje v mešanici. Kljub nezmožnosti sočasnega zaznavanja vseh petih uporabljenih histonov pa robustnost pore na spremembe aminokislinskega zaporedja v lumnu pore predstavlja dobro izhodišče za nadaljnjo optimizacijo pore in zaznavanje histonov v veliko bolj kompleksnejših bioloških vzorcih, kot je serum.</p><p class="metadata"><time datetime="2026-07-17" title="Source date; precision not specified">July 17, 2026</time> <span aria-hidden="true"> · </span> Repository of the University of Ljubljana (University of Ljubljana)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://repozitorij.uni-lj.si/IzpisGradiva.php?id=184905">Original publication</a></p><p><a href="https://repozitorij.uni-lj.si/Dokument.php?lang=slv&amp;id=240302&amp;dn=">Open PDF</a></p> Fri, 17 Jul 2026 00:00:00 GMT Marija Srnko OpenAlex https://reading.michaelmvh.com/article/b40679b75836ae054d75e3602a5c201263e7add63473645f62510e1622c64938/ urn:sha256:b40679b75836ae054d75e3602a5c201263e7add63473645f62510e1622c64938 <p>Accurate and timely sequencing of poliovirus is critical for global eradication efforts, particularly for molecular epidemiology based on the typing region of the genome, viral protein 1 (VP1). While Oxford Nanopore Technologies (ONT) sequencing has expanded capabilities for poliovirus surveillance, the relative performance of different ONT library preparation methods, including ligation-based (Native Barcoding) and transposase-based (Rapid Barcoding) approaches, has not been systematically evaluated. In this study, we compared rapid barcoding and native barcoding workflows for sequencing VP1 amplicons from 17 type 2 poliovirus-positive samples, each processed in triplicate. Native barcoding generated significantly more sequencing output, producing approximately 2.3-fold greater total read yield than rapid barcoding, and demonstrated higher run-to-run reproducibility (R 2 = 0.979-0.998 vs. 0.847-0.929, respectively; p &lt; 0.001). In addition, native barcoding generated 80% of the total yield achieved by rapid barcoding within approximately 7 hours, whereas rapid barcoding required approximately 40 hours to reach the same output. Despite these differences, both methods produced identical VP1 consensus sequences across all samples, with comparable read quality (median per-base Q-scores of approximately Q17-Q18). Rapid barcoding provided substantial practical advantages, reducing hands-on library preparation time (55 vs. 200 minutes) and per-sample cost ($12.82 vs. $16.54), while simplifying workflow and reducing technical complexity. These findings indicate that sequencing yield may not be a determinant of downstream analytical outcomes for poliovirus VP1 ONT sequencing. Rapid barcoding therefore represents a cost-effective and efficient approach for routine poliovirus surveillance, whereas native barcoding remains advantageous in applications requiring rapid data generation or maximal sequencing depth.</p><p class="metadata"><time datetime="2026-07-16" title="Source date; precision not specified">July 16, 2026</time> <span aria-hidden="true"> · </span> Journal of Virological Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.jviromet.2026.115436">Original publication</a></p><p><a href="https://www.sciencedirect.com/science/article/pii/S0166093426001011/pdf">Open PDF</a></p> Thu, 16 Jul 2026 00:00:00 GMT James E. Bullows Christina J. Castro Caeden Meade Katherine D. Poston Jaume C. Jorba OpenAlex https://reading.michaelmvh.com/article/2c48116ff1f2a35aea83371ee99d9d46be4316a8138292922f82debd0b4515a1/ urn:sha256:2c48116ff1f2a35aea83371ee99d9d46be4316a8138292922f82debd0b4515a1 <p>Résumé FRCe document, produit avec l’assistance de Gemini 3 Raisonnement, est publié sous Licence Apache 2.0. Il constitue une publication défensive (antériorité) volontaire et entre de ce fait dans l’état de la technique au sens des législations applicables : (EPC Art. 54(2); French IPC Art. L 611-11; cf. 35 U.S.C. §102(a)). Ce rapport technique décrit de manière exhaustive une plateforme décentralisée de thérapie génique. Il présente 32 inventions actionnables incluant le séquençage au point de soin, la synthèse microfluidique d&#39;ARNm, la formulation de nanoparticules lipidiques (LNP), le DRM biologique cryptographique sur blockchain et la gestion verte des effluents. Chaque proposition est documentée de façon à permettre sa reproduction, associée à des codes CIB/CPC, et horodatée afin d&#39;empêcher tout blocage par brevet ultérieur. Abstract ENThis document, produced with the assistance of Gemini 3 Reasoning, is released under the Apache 2.0 licence. It is a voluntary defensive publication (prior art) and therefore enters the prior art upon release under the applicable patent statutes: (art. L 611-11 CPI / art. 54(2) CBE). This publication describes an exhaustive, end-to-end decentralized genetic therapy platform. It discloses 32 enabling inventions spanning point-of-care sequencing, automated microfluidic synthesis, lipid nanoparticle (LNP) formulation, cryptographic biological DRM via TPM 2.0/blockchain, and green disposal units. Each innovation is described with detailed specifications to enable reproduction, designated with plausible IPC/CPC codes, and timestamped (RFC 3161) to preempt subsequent offensive patent filings by third parties globally, securing a shared open-access commons for personalized mRNA medicine. Timestamp: 2026-07-16T19:23:26ZSHA-256: 83c64589fce322d8c32e5ff9fbcf93506c38f5e9d0b5eff49add04a886be9706 Liste des innovations &amp; classification (IPC ; CPC)#1 Integrated microfluidic nanopore sequencer (IPC B01L 3/00 ; CPC B01L 3/5027)#2 Multiplexed MHC haplotyping kit (IPC C12Q 1/6886 ; CPC C12Q 1/6886)#3 Hybrid cloud-edge MHC docking pipeline (IPC G16H 50/20 ; CPC G16H 50/20)#4 Closed-loop mRNA dosing scheduler (IPC G16H 20/17 ; CPC G16H 20/17)#5 Optimized SM-102 LNP formulation (IPC A61K 9/127 ; CPC A61K 9/1272)#6 Automated microfluidic chip clean-in-place (IPC B01L 99/00 ; CPC B01L 2200/10)#7 LNP biodistribution imaging reconstruction (IPC A61B 5/00 ; CPC A61B 5/4848)#8 Dissolvable microneedle patch for LNPs (IPC A61K 9/00 ; CPC A61K 9/0021)#9 Synchronized mRNA and anti-PD-1 co-therapy (IPC A61K 39/00 ; CPC A61K 39/0011)#10 Privacy-preserving federated antigen learning (IPC G06F 21/62 ; CPC G06F 21/6245)#11 Cryptographic DRM biological synthesizer (IPC G06F 21/44 ; CPC G06F 21/44)#12 Smart IoT cold chain container (IPC F25D 29/00 ; CPC F25D 29/003)#13 Cloud-based microfluidic calibration service (IPC G05B 19/418 ; CPC G05B 19/4183)#14 Segmented Poly(A) expression cassette (IPC C12N 15/67 ; CPC C12N 15/67)#15 On-chip chromatographic dsRNA purification (IPC B01D 15/34 ; CPC B01D 15/345)#16 Multi-species dynamic codon optimizer (IPC G16B 25/10 ; CPC G16B 25/10)#17 Smart sensor-enabled reagent cartridge (IPC G01N 27/02 ; CPC G01N 27/02)#18 LAMP1 lysosomal-targeting mRNA chimera (IPC C12N 15/62 ; CPC C12N 15/62)#19 Automated lipid effluent inactivation module (IPC B01D 21/00 ; CPC C02F 1/02)#20 Function-based biosecurity screening AI (IPC G16B 40/00 ; CPC G06N 3/08)#21 Direct RNA-pore sequencing for haplotyping (IPC C12Q 1/6869 ; CPC C12Q 1/6869)#22 Enzymatic long DNA template assembly (IPC C12N 15/10 ; CPC C12N 15/10)#23 Microfluidic full-substitution IVT bioreactor (IPC C12P 19/34 ; CPC C12P 19/34)#24 Asymmetric staggered herringbone mixer (IPC B01F 33/30 ; CPC B01F 33/30)#25 Refractometer-controlled active micro-dialyser (IPC B01D 61/14 ; CPC B01D 61/14)#26 Edge-distributed semantic genomic cache (IPC G16B 50/00 ; CPC G16B 50/00)#27 Unified memory CUDA orchestration for AF3 (IPC G06F 12/02 ; CPC G06F 12/02)#28 Coordinated structural neoantigen selector (IPC G16B 15/00 ; CPC G16B 15/30)#29 Blockchain biosecurity validation consensus (IPC H04L 9/32 ; CPC H04L 9/3239)#30 Clinical MLOps regulatory continuous auditor (IPC G06N 20/00 ; CPC G06N 20/00)#31 Lyophilized multi-lipid argon-sealed mix (IPC A61K 47/54 ; CPC A61K 47/54)#32 Benchtop microwave pyrolysis waste neutralizer (IPC A61L 11/00 ; CPC A61L 11/00) Keywordsnanopore sequencing, microfluidic cartridge, point-of-care diagnostics, MHC haplotyping, long-read sequencing, cancer neoantigens, hybrid cloud-edge, structural biology, neoantigen prediction, closed-loop dosing, ctDNA monitoring, personalized immunotherapy, lipid nanoparticles, SM-102, messenger RNA delivery, clean-in-place, microfluidic chip, cross-contamination prevention, fluorescence imaging, deep learning reconstruction, LNP biodistribution, microneedle patch, transdermal delivery, mRNA vaccine, combination immunotherapy, neoantigen vaccine, anti-PD-1 antibody, federated learning, homomorphic encryption, genomic privacy, biological DRM, blockchain consensus, hardware-bound security, cold chain logistics, IoT thermal monitoring, self-destruct security, calibration-as-a-service, dynamic light scattering, microfluidic tuning, segmented polyA, enzymatic synthesis, mRNA stability, dsRNA purification, microfluidic chromatography, in vitro transcription, codon optimization, expression cassette, comparative oncology, reagent cartridge, lipid stability, quality control sensor, lysosomal targeting, tPA signal peptide, MHC class II presentation, waste inactivation, lipid nanoparticle disposal, ecotoxicity prevention, functional biosecurity, deep learning screening, sequence evasion, direct RNA sequencing, nanopore basecalling, enzymatic DNA synthesis, template assembly, plasmid-free IVT, staggered herringbone mixer, microfluidic shear, lipid nanoparticle formulation, tangential flow filtration, solvent extraction, closed-loop dialysis, genomic sequence cache, sequence alignment, edge computing, unified memory CUDA, structural inference, edge hardware optimization, neoantigen selection, pLDDT score, molecular docking filter, biosecurity consensus, smart contract, DNA synthesis authorization, MLOps, software certification, clinical AI drift, lipid mix cartridge, SM-102 stability, clinical reagents, waste neutralizer, microwave pyrolysis, biohazardous waste disposal</p><p class="metadata"><time datetime="2026-07-16" title="Source date; precision not specified">July 16, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21400987">Original publication</a></p> Thu, 16 Jul 2026 00:00:00 GMT Xavier Pillet OpenAlex https://reading.michaelmvh.com/article/ce6db50e91a0a97659d731e4c9700c4c947c9ae5d7849d50b0f6b8a2c9911774/ urn:sha256:ce6db50e91a0a97659d731e4c9700c4c947c9ae5d7849d50b0f6b8a2c9911774 <p>A physical device to aid post-synthetic modification of specific single residues in a peptide at the single molecule level is proposed; it is similar to a structure that was recently proposed for peptide synthesis without side-chain protection (doi: 10.26434/chemrxiv-2025-gsw8x-v5). An electrolytic cell with cis and trans chambers bridged by a nanopore is combined with a mechanical positioning system in which peptides with a homopeptide header or header and trailer are anchored to a platform at one or both ends. A peptide can be moved electrophoretically through the pore with an applied voltage and positioned electromechanically by moving the platform(s) in sub-nm steps with piezo-electric sensors and actuators. A specific residue can be targeted for shielding inside the pore and movement thereafter into trans for targeted protection before it is exposed to reactants (catalyst, linker, conjugate) for modification. Peptides can be modified at the free N- or C- end (single platform) or at arbitrary internal positions (single or dual platform) by cyclization (including overlapping and nested cycles), stapling, linking, or conjugation with a desired cargo for drug delivery/tracking while allowing for diffusion effects. Modification procedures are outlined in theory and illustrated with examples. In many cases successful modification can be detected from the blockade current level in the pore. The results of coarse-grained probabilistic computational simulations showing target, catalyst, and conjugate converging in space, a pre-condition for target-conjugate binding while diffusing in trans, are presented; they suggest that with a trans chamber height of 1 micron-1 mm, the molar catalyst/conjugate-to-target ratio required for convergence in under a minute with probability 1 is 103-106. Although this appears excessive virtually all of the former can be recovered and recycled. The method may be implemented in parallel with an array of pores in a synthetic membrane; with a pore separation of 20 nm on a 2 cm × 2 cm chip, the theoretical maximum yield is ~1.6 picomoles, the actual yield can be estimated from the blockade current. In its present form the proposed system does not scale to the bulk level so its potential use is limited to research and preclinical studies.</p><p class="metadata"><time datetime="2026-07-14" title="Source date; precision not specified">July 14, 2026</time> <span aria-hidden="true"> · </span> ChemRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26434/chemrxiv.15006068/v1">Original publication</a></p> Tue, 14 Jul 2026 00:00:00 GMT G Sampath OpenAlex https://reading.michaelmvh.com/article/b811538750b64ef650d3cade4371feaacb167e1f7a90154a3068e22ecf092b05/ urn:sha256:b811538750b64ef650d3cade4371feaacb167e1f7a90154a3068e22ecf092b05 <p>Methicillin-resistant Staphylococcus aureus (MRSA) is a major multidrug-resistant human pathogen. Vancomycin has long been the cornerstone therapy for invasive MRSA infections. Although nearly all MRSA isolates are susceptible to vancomycin in standard antimicrobial susceptibility testing, vancomycin treatment failure in MRSA bloodstream infections approaches 30%, and the underlying mechanisms remain poorly defined. Here, we show that subinhibitory concentrations of vancomycin promote MRSA survival within macrophages by hijacking host macroautophagy/autophagy. Using in vitro and in vivo models, we demonstrate that vancomycin exacerbates S. aureus-induced autophagic flux blockade, facilitating bacterial persistence. Mechanistically, this effect is not caused directly by vancomycin but by extracellular vesicles (EVs) secreted by S. aureus under conditions of vancomycin stress. These EVs exhibit a potent capacity to disrupt autophagosome-lysosome fusion, leading to the accumulation of autophagosomes. Proteomic profiling revealed a significant enrichment of the toxin α-hemolysin (Hla) in EVs derived from vancomycin-stressed bacteria. Deletion of the hla gene in S. aureus substantially attenuates the autophagy-disrupting capacity of vancomycin-induced EVs. Furthermore, recombinant α-hemolysin directly impaired autophagic flux in macrophages. RNA-sequencing and mechanistic analyses identified the PI3K-AKT pathway as a key signaling axis downstream of Hla, and this mechanism was further confirmed to mediate the autophagic degradation blockade induced by EVs from vancomycin-stressed S. aureus. Collectively, vancomycin triggers S. aureus to secrete EVs enriched with α-hemolysin, which potently inhibit autophagosome-lysosome fusion and promote intracellular MRSA survival. These findings provide critical insights into vancomycin treatment failure and identify bacterial EVs and α-hemolysin as potential therapeutic targets.</p><p class="metadata"><time datetime="2026-07-12" title="Source date; precision not specified">July 12, 2026</time> <span aria-hidden="true"> · </span> Autophagy</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1080/15548627.2026.2702841">Original publication</a></p> Sun, 12 Jul 2026 00:00:00 GMT Bing Lu Wenjiao Chang Xueer Liu Shanshan Zhang Pengsheng Ding Zhengchao Nie Lan Shi Gan Liu Wenjin Wang Wei Y Chenggong Guo Yuanyuan Dai Xiaoling Ma OpenAlex https://reading.michaelmvh.com/article/06003fbf66913412f8b27235545cdc9df64e03e68d407c9d4157603d7003fd3d/ urn:sha256:06003fbf66913412f8b27235545cdc9df64e03e68d407c9d4157603d7003fd3d <p>## 🔄 ALTERNATIVE TITLES ### Option 1: Comprehensive/Scholarly**The Generalized Universal Mass Balance Framework (GUMBF): Mathematical Foundations, Cross-Disciplinary Applications, and Cosmological Implications** ### Option 2: Systems Theory Focus**A Universal Systems Theory of Matter Flow: From Cellular Metabolism to Cosmic Evolution Through Transfer, Transformation, Storage, and Sequestration** ### Option 3: Validation-Focused**The GUMBF Proposition: Mathematical Validation, Observational Confirmation, and Unified Interpretation of Conservation Principles Across All Scales** ### Option 4: Cosmological Focus**Reinterpreting Stars and Black Holes: A Generalized Mass Balance Framework for Understanding Cosmic Matter Flow and Observable Universe Radius** ### Option 5: Short/Journal-Friendly**The Generalized Universal Mass Balance Framework (GUMBF): A Unified Systems Approach to Matter Conservation Across All Scales** ### Option 6: Process-Focused**Transfer, Transformation, Storage, and Sequestration: A Universal Framework for Understanding Matter Flow in Natural and Engineered Systems** ### Option 7: Interdisciplinary Focus**Bridging Disciplines Through Conservation: A Mathematically Rigorous Universal Mass Balance Framework with Applications Across Science and Engineering** ### Option 8: Sustainability Focus**A Universal Systems Framework for Sustainable Resource Management: From Human Physiology to Planetary Stewardship and Cosmic Evolution** ### Option 9: Mathematical/Physical Focus**A Generalized Universal Balance Framework: Mathematical Derivation, Theorems, and Applications Spanning Cells to Galaxies** ### Option 10: Comprehensive Title**The Generalized Universal Mass Balance Framework (GUMBF): A Unified Mathematical and Conceptual Framework for Matter Conservation Across All Scales of Reality, with Validation Against Established Physical Laws and Cosmological Confirmation** --- ## 📝 SUBTITLES ### Formal Academic Subtitle*A Systems-Theoretic Approach to Mass Conservation with Mathematical Validation and Cross-Disciplinary Applications Across Physics, Biology, Ecology, Engineering, and Cosmology* ### Descriptive Subtitle*Understanding Matter Flow Through the Universal Processes of Transfer, Transformation, Storage, and Sequestration from Subatomic Particles to the Observable Universe* ### Validation-Focused Subtitle*Mathematical Validation, Observational Confirmation, and Consistency with Established Conservation Laws in Thermodynamics, Continuum Mechanics, and Systems Theory* ### Applications-Focused Subtitle*Applications in Human Physiology, Drug Kinetics, Ecosystem Dynamics, Industrial Ecology, Planetary Geochemistry, Stellar Evolution, Black Hole Physics, and Cosmology* ### Philosophical Subtitle*From the First Law of Thermodynamics to a Unified Theory of Material Organization, Transformation, and Sequestration in the Universe* ### Comprehensive Subtitle*Integrating Conservation Principles with Novel Mathematical Constructs Including the Universal Organization Number, Stability Index, and Coupled Radius Evolution Equation* ### Sustainability-Focused Subtitle*Foundations for Circular Economy, Resource Management, and Planetary Stewardship Through a Unified Understanding of Matter Flow* ### Cosmological Subtitle*Reinterpreting Stars as Transformation Centers, Black Holes as Sequestration Centers, and Deriving the Observable Universe Radius from First Principles* ### Interdisciplinary Subtitle*Bridging Engineering, Biology, Ecology, Geology, Astrophysics, and Systems Science Through a Common Mathematical Language* ### Practical Applications Subtitle*From Cellular Metabolism to Galactic Evolution: A Unified Framework for Understanding and Managing Matter Flow Across All Systems* --- ## 📚 DETAILED DESCRIPTION --- ### Abstract (Extended) The **Generalized Universal Mass Balance Framework (GUMBF)** represents a paradigm-shifting synthesis of conservation principles across all known scales of reality. This comprehensive framework proposes that the fundamental equation governing matter flow in any system—whether a living cell, a human body, an ecosystem, an industrial process, a star, or the universe itself—can be expressed through four universal processes: **Transfer (T)**, **Transformation (F)**, **Storage (S)**, and **Sequestration (Q)** . At its core, the framework posits: $$\boxed{\frac{dM}{dt} = T + F + S - Q}$$ This equation, while mathematically simple, carries profound implications for how we understand organization, evolution, and sustainability across all domains of knowledge. The framework is built on **two fundamental axioms** derived from established physical principles: **Axiom 1 (Conservation):** For every open system, total mass is conserved. The classical mass balance equation holds, and the total of all generation and consumption terms is zero. **Axiom 2 (Universal System Partition):** The universe of material processes can be partitioned into four mutually exclusive and exhaustive categories: Transfer (T), Transformation (F), Storage (S), and Sequestration (Q). From these axioms, the framework derives **six major theorems**, introduces **two novel dimensionless parameters**, and provides a **unified interpretation** of matter flow across all scales. --- ### The Four Universal Processes #### 1. TRANSFER (T): Matter Crossing Boundaries Transfer represents the movement of matter across defined system boundaries. This is the most familiar process, corresponding to the classical input and output terms in mass balance equations. **Key Characteristics:**- Matter moves in and out of the system- Reversible (matter can flow both directions)- Conservative (total mass conserved across the boundary)- Scale-invariant (applies from cells to galaxies) **Examples:**- Biological: Ingestion of food, inhalation of oxygen, excretion of waste- Ecological: Immigration and emigration of species- Engineering: Material inputs to a reactor, product outputs- Astrophysical: Accretion onto a star, ejection of stellar material **Mathematical Formulation:**$$T = \sum \dot{m}_{in} - \sum \dot{m}_{out}$$ --- #### 2. TRANSFORMATION (F): Matter Changing Form Transformation represents the conversion of matter from one form to another through physical, chemical, biological, geological, or nuclear processes. This replaces the traditional concepts of &quot;generation&quot; and &quot;consumption&quot; with a unified process of transformation. **Key Characteristics:**- Matter changes form but is conserved- Total mass is conserved ($\sum \dot{r}_k = 0$)- Represents the creative/organizing aspect of the framework- Stars are interpreted as large-scale transformation centers **Examples:**- Chemical: Combustion, oxidation, reduction- Biological: Metabolism, photosynthesis, cellular respiration- Nuclear: Stellar fusion, nucleosynthesis, radioactive decay- Geological: Weathering, metamorphism, diagenesis **Mathematical Formulation:**$$F = \sum \dot{M}_{gen} - \sum \dot{M}_{cons}$$ --- #### 3. STORAGE (S): Matter Accumulation in Organized Structures Storage represents the accumulation of matter within the system in organized structures. This is the concept of &quot;positive accumulation&quot; that represents growth, development, and organization. **Key Characteristics:**- Matter is retained within the system- May be temporary or long-term- Represents organized or potentially usable matter- Can be mobilized for future transformation or transfer **Examples:**- Biological: Adipose tissue, glycogen, protein stores- Ecological: Biomass accumulation, carbon storage- Engineering: Inventory, raw material stockpiles- Astrophysical: Stellar structure, planetary formation **Mathematical Formulation:**$$S = \frac{dM_{organized}}{dt}$$ --- #### 4. SEQUESTRATION (Q): Long-Term Isolation from Active Circulation Sequestration represents the removal of matter from active circulation for extended periods, often on geological or cosmological timescales. This is the novel contribution of the framework, representing &quot;negative accumulation&quot; that removes matter from the active system. **Key Characteristics:**- Matter is removed from active cycling- Effectively irreversible on human timescales- Includes carbonates, fossil fuels, and black holes- Represents the ultimate sink in the universal balance **Examples:**- Biological: Bone mineralization- Ecological: Soil organic carbon, peat formation- Industrial: Landfill disposal, nuclear waste storage- Astrophysical: Black holes, stellar remnants **Mathematical Formulation:**$$Q = \frac{dM_{sequestered}}{dt}$$ --- ### The Six Major Theorems #### Theorem 1: Isolated Universe **Statement:** For an isolated system such as the universe as a whole, $T = 0$ because no matter crosses the boundary. **Mathematical Expression:**$$\frac{dM}{dt} = F + S - Q$$ If total mass-energy is conserved:$$\boxed{F + S = Q}$$ **Interpretation:** In a closed universe, transformations and storage must be balanced by sequestration to maintain constant total mass. This is the cosmological steady-state condition. --- #### Theorem 2: Observable Matter Evolution **Statement:** For observable matter ($M_o$), the evolution equation differs from the total mass equation. **Mathematical Expression:**$$\boxed{\frac{dM_o}{dt} = F_o - Q_o}$$ **Interpretation:** Black holes remove observable matter from circulation ($Q_o &gt; 0$), while stars transform and redistribute observable matter ($F_o \neq 0$). This equation describes the evolution of visible matter in the universe. --- #### Theorem 3: Universal Organization Number **Definition:**$$\boxed{\eta = \frac{S}{Q}}$$ **Interpretation:**- $\eta &gt; 1$: Organization dominates over sequestration- $\eta &lt; 1$: Sequestration dominates over organization- $\eta = 1$: Organization and sequestration are balanced **Applications:** This dimensionless number can be used to compare the organizational state of different systems across scales. --- #### Theorem 4: Radius Identity</p><p class="metadata"><time datetime="2026-07-11" title="Source date; precision not specified">July 11, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.21309314">Original publication</a></p> Sat, 11 Jul 2026 00:00:00 GMT Sudhakar Geruganti OpenAlex https://reading.michaelmvh.com/article/5d9eda51f89efee21acbf4f284a51b249a45abda28cb620a8533bfd3674fd5b7/ urn:sha256:5d9eda51f89efee21acbf4f284a51b249a45abda28cb620a8533bfd3674fd5b7 <p>ABSTRACT Infections by Aeromonas can rapidly progress from mucosal colonization to invasive disease, but how these bacteria efficiently breach epithelial barriers is unclear. Here, we define a coordinated two-component virulence strategy in Aeromonas veronii biotype sobria ( A. veronii sobria) involving a secreted serine protease (ASP) and aerolysin. In polarized T84 monolayers, wild-type infection caused rapid transepithelial electrical resistance (TEER) loss and degradation of junctional/adhesion proteins. An ASP-deficient strain exhibited delayed barrier collapse with reduced cleavage of ZO-1/2/3 and EpCAM, and purified ASP restored these effects, indicating ASP is required but alone insufficient for full disruption. A transposon screen identified aerolysin and secretion-related genes as key contributors to junctional damage. Mechanistically, ASP directly converted recombinant pro-aerolysin into a hemolytically active toxin in vitro , linking protease activity to toxin maturation. Functionally, ASP and aerolysin synergized to promote bacterial translocation across epithelial monolayers with marked sequence dependence; pro-aerolysin pretreatment enhanced ASP-mediated degradation of ZO proteins, claudin-7, and EpCAM. ASP further cleaved EpCAM at multiple extracellular sites, compromising adhesion and junctional homeostasis. Together, these findings establish an ASP–aerolysin pathway that couples toxin activation with junctional proteolysis to drive structural epithelial breaches. IMPORTANCE Aeromonas infections can rapidly progress from intestinal colonization to invasive disease, yet the molecular steps enabling epithelial breach are unclear. We show that Aeromonas veronii sobria uses a coordinated two-factor pathway in which Aeromonas serine protease (ASP) both activates the pore-forming toxin aerolysin and directly cleaves key junctional/adhesion proteins, including ZO-1/2/3 and EpCAM. Aerolysin primes cells for enhanced ASP-mediated proteolysis in an order-dependent manner, converting TEER loss into a physical barrier rupture that permits massive bacterial translocation. Targeting ASP–aerolysin cooperation may provide a rational anti-virulence strategy.</p><p class="metadata"><time datetime="2026-07-10" title="Source date; precision not specified">July 10, 2026</time> <span aria-hidden="true"> · </span> Journal of Bacteriology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1128/jb.00141-26">Original publication</a></p> Fri, 10 Jul 2026 00:00:00 GMT Hidetomo Kobayashi Soshi Seike Eizo Takahashi Keinosuke Okamoto Hiroyasu Yamanaka OpenAlex https://reading.michaelmvh.com/article/1c341be3ff60e72b8e2a28da31793699116f5f610febaedc07355df9353441e5/ urn:sha256:1c341be3ff60e72b8e2a28da31793699116f5f610febaedc07355df9353441e5 <p>The synthesis of hemolytic toxins in Bacillus cereus, particularly hemolysin HlyII, is controlled by the Fur protein (BcFur), a metal-sensitive regulator of iron metabolism that activity depends on the redox conditions of the environment. Using LC-MS/MS technology, we detected two BcFur isoforms with different electrophoretic mobilities. The structural and functional differences between these isoforms were determined. A more than 10-fold increase in the binding constant of the BcFur protein to its operator in the presence of 2-mercaptoethanol was revealed. The increased binding activity of BcFur with its operator is due to the presence of free SH groups in Cys residues. This protein functions as a dimer that forms independently of the substrate DNA presence Furthermore, crystals of BcFur were obtained, and the 3D structure of BcFur was resolved. Despite the high similarity of the primary and tertiary structures of BcFur to those of the B. subtilis oxidative stress regulator PerR (BsPerR), their redox sensitivity mechanisms differ. Inactivation DNA-binding of BcFur activity has been shown to occur as a result of oxidation of the Cys residues of the zinc finger, at least under in vitro conditions.</p><p class="metadata"><time datetime="2026-07-09" title="Source date; precision not specified">July 9, 2026</time> <span aria-hidden="true"> · </span> Molecular Biology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1134/s0026893326700251">Original publication</a></p> Thu, 09 Jul 2026 00:00:00 GMT Vadim Salyamov Olga S. Kostareva Sergey G. Mayorov S. V Tishchenko Azat G. Gabdulkhakov Alexey S. Nagel Zhanna I. Andreeva‐Kovalevskaya Alexander V. Siunov Alexander S. Solonin OpenAlex https://reading.michaelmvh.com/article/9ed522e56eb8032339b4df2c584c3f8ec92bbb6715d25e89219ee0fd788795d5/ urn:sha256:9ed522e56eb8032339b4df2c584c3f8ec92bbb6715d25e89219ee0fd788795d5 <p>Melioidosis is a life-threatening infectious disease caused by Burkholderia pseudomallei. Early and accurate diagnosis is critical for timely treatment and improved outcomes. Although highly endemic in tropical regions, it remains underdiagnosed due to limitations of current diagnostic methods. Bacterial culture, the diagnostic gold standard, is time-consuming, prone to misidentified species, requires specialized laboratory facilities, and has low sensitivity. The indirect hemagglutination assay is also unreliable due to poor sensitivity and specificity. We developed a second-generation immunochromatography test (Hcp1-ICT) to detect anti-Hcp1 IgG antibodies against hemolysin co-regulated protein 1 of B. pseudomallei and evaluated its diagnostic performance in an international multi-center study. A total of 1,838 stored serum samples from 601 culture-proven melioidosis patients, 598 healthy individuals and 639 patients with non-melioidosis infections in Thailand, Lao PDR, Vietnam, Malaysia, Sri Lanka, Cambodia, and Australia were analyzed for diagnosis of melioidosis. The sensitivities in Thailand, Lao PDR, Vietnam, Malaysia, Sri Lanka, Cambodia, and Australia were 92%, 77%, 76%, 80%, 74%, 90%, and 48%, respectively. The specificities with healthy donor samples were 96%, 79%, 98%, 100%, 100%, 87%, and 100%, while the specificities for cases with samples from other infections other than melioidosis were 97%, 87%, 98%, 98%, 100%, 90%, and 94%, respectively. These findings indicate that the Hcp1-ICT is a promising point-of-care tool for serodiagnosis of melioidosis. However, its variable performance across regions underscores the need for prospective validation locally in various regions to optimize its diagnostic utility and facilitate implementation in both referral centers and resource-limited settings.</p><p class="metadata"><time datetime="2026-07-06" title="Source date; precision not specified">July 6, 2026</time> <span aria-hidden="true"> · </span> PLoS neglected tropical diseases</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1371/journal.pntd.0014484">Original publication</a></p><p><a href="https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0014484&amp;type=printable">Open PDF</a></p> Mon, 06 Jul 2026 00:00:00 GMT Hasyanee Binmaeil Thanakon Bunsong Koukeo Phommasone Matthew T. Robinson Manivanh Vongsouvath Elizabeth A. Ashley Enoka Corea Trung Thanh Trinh Shirley Yi Fen Hii Rohaidah Hashim Habib Abdul Hakim Esa Tonnii Sia Yuwana Podin Robert Edward Norton Sophie Cunningham Jamal I-Ching Sam Christina Yek Ella M. Meumann Bart J. Currie Mary N. Burtnick Paul J. Brett Narisara Chantratita OpenAlex https://reading.michaelmvh.com/article/6a385aaf6d78904cd72b41d31ad05221d03585557c2e1e5d4388ea70bc7da73e/ urn:sha256:6a385aaf6d78904cd72b41d31ad05221d03585557c2e1e5d4388ea70bc7da73e <p>ABSTRACT Dynamic protein transport through solid‐state nanopores is fundamentally limited at low analyte concentrations by thick electrical double layers (EDLs) and weak electrophoretic forces. Here, a light‐driven, phase‐locked protein pumping mechanism is demonstrated through a ∼20 nm plasmonic nanopore embedded in an ultrathin (In x Ga 1‐x ) 2 O 3 membrane and decorated with self‐assembled Ag nanodomains. Under 488–530 nm excitation, broadband plasmonic resonances (2.3–3.4 eV) generate intense near‐fields and hot‐carrier surface charging, increasing the interfacial EDL capacitance to ∼220 µF·cm − 2 and lowering the protein entry barrier from ∼20 to &lt;3 kBT. A combined static‐dynamic fluorescence reconstruction approach resolves field‐directed transport of FITC‐labeled bovine serum albumin beyond the diffraction limit. Optical maps reveal a concentration‐dependent transition from Brownian diffusion to a vertically extended photo‐EDL conduction column that funnels proteins toward the nanopore. Simultaneous fluorescence‐ionic measurements identify an electro‐optic resonance within the 5–20 Hz modulation window, producing ∼10× fluorescence enhancement under pulsed excitation. The optical pumping event rate increases from ∼0.5–1 to ∼4–5 s − 1 , while the cis‐trans phase delay decreases from ∼450 to &lt;10 ms. These results establish plasmonic nanopores as programmable optofluidic pumps for dynamic, light‐controlled single‐molecule protein transport.</p><p class="metadata"><time datetime="2026-07-03" title="Source date; precision not specified">July 3, 2026</time> <span aria-hidden="true"> · </span> Small</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smll.74383">Original publication</a></p> Fri, 03 Jul 2026 00:00:00 GMT Mohammad Karbalaei Akbari Kumar Shrestha Yanbin Cui Serge Zhuiykov OpenAlex https://reading.michaelmvh.com/article/59f452dcde219b5384589d8ecfbbde6cb8ec83bcc099965a94a06cc81733cae7/ urn:sha256:59f452dcde219b5384589d8ecfbbde6cb8ec83bcc099965a94a06cc81733cae7 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-07-01" title="Source date; precision not specified">July 1, 2026</time> <span aria-hidden="true"> · </span> IEEE International Conference on Nanotechnology (IEEE-NANO)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1109/nano67986.2026.11667599">Original publication</a></p> Wed, 01 Jul 2026 00:00:00 GMT Rui Liu Tixi He Yin Zhang OpenAlex https://reading.michaelmvh.com/article/bb9180ca10677b73a96c48795c8a28ad3f86d7831d1ec5370c3ab2af4b5cea78/ urn:sha256:bb9180ca10677b73a96c48795c8a28ad3f86d7831d1ec5370c3ab2af4b5cea78 <p>Nanopore detection technology has broad application prospects in DNA, protein, and glycan sequencing, as well as in the highly sensitive detection and identification of bio‐molecules. However, precise analysis of the structure‐function relationship and targeted optimization of device performance remain key bottlenecks restricting further development. Computational simulations can not only explain and verify experimental phenomena but also potentially guide experimental design, shorten the research cycle, and reduce research costs. Therefore, this review comprehensively summarizes the application of multiscale computational calculations in nanopore systems. By incorporating quantum mechanics calculations, molecular docking, molecular dynamics simulations, and finite element analysis, we aim to provide theoretical support for addressing the aforementioned bottlenecks. Among these methods, atomic‐scale calculations enable the precise characterization of molecular conformations and intermolecular interactions, thereby clarifying the nanopores’ microscale recognition mechanisms. Mesoscale simulations can trace the analyte translocation dynamics across nanopores, revealing inherent regulatory principles. Macroscale models effectively simulate the hydrodynamic behaviors of nanopore devices. In summary, the synergistic application of multiscale computational simulations establishes theoretical foundation for improving nanopore sensor performance. Furthermore, we discuss the challenges and future trends associated with the synergistic integration of computational simulations, aiming to provide valuable insights for researchers active in computational chemistry and nanopore‐based fields.</p><p class="metadata"><time datetime="2026-07-01" title="Source date; precision not specified">July 1, 2026</time> <span aria-hidden="true"> · </span> Analysis &amp; Sensing</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/anse.202600002">Original publication</a></p> Wed, 01 Jul 2026 00:00:00 GMT Dongdong Wang Xinjia Zhao Li M J Y Zhang Yingying Lian Guangyan Qing OpenAlex https://reading.michaelmvh.com/article/82ffb759fc02be6b9bd08256a238c376db1f7a5e12085cb5ae2bae58f2ec3a61/ urn:sha256:82ffb759fc02be6b9bd08256a238c376db1f7a5e12085cb5ae2bae58f2ec3a61 <p>High Resolution Image Download MS PowerPoint Slide Proteins play essential roles in cellular processes and are involved in numerous diseases, driving the need for efficient proteoform identification. Recent advances have brought nanopore-based protein fingerprinting within reach, potentially expanding the proteomics toolkit in the near future. Among emerging strategies, label-free, full-length analysis via free translocation is the most promising approach for detecting low-abundance proteoforms. While free translocation is typically accompanied by low temporal resolution, we demonstrate here that such measurements can enable reliable identification even for natural proteins with high sequence similarity. Combining low pH and guanidinium chloride, we generate a strong electroosmotic flow that enables efficient capture and translocation of unlabeled proteins with an aerolysin nanopore. Using machine learning classifiers, we achieve 80% accuracy in distinguishing seven related proteins, based on distinct and directional fingerprints with high reproducibility. Differences in fingerprints partially reflect the distribution of volume and charges in the protein sequences and may contain additional contributions from the translocation dynamics. Our findings position free-translocation measurements of unfolded proteins as a promising approach to fingerprinting without the need for chemical conjugations or enzymatic digestions. With further development, fingerprint-predictions could allow to infer de novo protein sequence information from single-molecule data, offering a powerful tool for proteomics.</p><p class="metadata"><time datetime="2026-06-29" title="Source date; precision not specified">June 29, 2026</time> <span aria-hidden="true"> · </span> Journal of the American Chemical Society</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/jacs.6c01018">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/jacs.6c01018?ref=article_openPDF">Open PDF</a></p> Mon, 29 Jun 2026 00:00:00 GMT Verena Rukes Evita Norkute Georges Barnikol Jingze Duan Jiajie Gao Chan Cao OpenAlex https://reading.michaelmvh.com/article/d856f46efd7500e106ec31a71a18b1dc369e066d8bf934c659833d89316905a0/ urn:sha256:d856f46efd7500e106ec31a71a18b1dc369e066d8bf934c659833d89316905a0 <p>Abstract Double-stranded RNA (dsRNA) is a near-universal hallmark of active viral infection. Despite its role as a pan-viral replication intermediate, dsRNA-centred technologies for virus monitoring remain scarce and largely rely on monoclonal antibody-based approaches that, while highly sensitive, are costly and difficult to engineer, scale, or integrate with downstream assays. Here, we present a modular and antibody-free pipeline for quantitative and qualitative dsRNA analysis built around an engineered B2 protein from Flock House virus with nanomolar-range binding affinity. The pipeline is compatible with absorbance- or luminescence-based measurement formats. In a sandwich assay configuration (Sand-BIRD), sub-ng mL -1 quantification of dsRNA is achieved, comparable to the gold standard J2 monoclonal antibody, directly from crude biological samples without RNA extraction. Sand-BIRD reliably detects viral infection in both plant samples (Tomato bushy stunt virus and Grapevine fanleaf virus) and mosquitoes (West Nile virus and Dengue virus) with commercial-grade reliability. dsRNA eluted from positive samples were further processed directly by Oxford Nanopore direct sequencing, enabling identification of virus species without prior sequence knowledge or total RNA extraction. Together, this work establishes an end-to-end, sequence-agnostic workflow for direct RNA-duplex quantification and sequencing (BIRD-Seq), which has compelling potential for emerging infectious disease surveillance and next-generation point-of-care (PoC) diagnostics. Technology Readiness BIRD-Seq is an integrated pipeline for agnostic dsRNA detection and sequencing designed for broad-spectrum virus monitoring. A Technology Readiness Level (TRL) 5 under NASA’s classification framework has been reached as BIRD-Seq has been validated in laboratory-relevant environments using real-world samples, including virus-infected plants and mosquitoes. The ELISA-based sensing platform employs engineered variants of the B2 protein (from Flock House virus) in a sandwich assay format for dsRNA capture and detection, achieving sensitivity comparable to the gold-standard J2 monoclonal antibody. Unlike traditional antibody-based methods, the B2 protein offers key practical advantages: straightforward production in bacterial expression systems, high versatility, and reduced manufacturing costs, as well as direct compatibility with crude extract monitoring, eliminating the need for RNA extraction. Captured B2/RNA duplexes can then be directly eluted from the ELISA microplates and subjected to downstream nanopore direct RNA sequencing, providing both quantitative and qualitative information on the underlying virus infection, a capacity enabled by the near-universal nature of dsRNA as a pathogen-associated molecular pattern. That said, further validation on large-scale field-collected and clinical samples will be essential before widespread deployment can be envisioned. While the B2 sandwich assay offers favorable cost-efficiency over antibody-based alternatives, the relatively high cost of Oxford Nanopore direct RNA sequencing remains an important economic constraint. Nevertheless, the growing importance of dsRNA detection across virus sensing, mRNA vaccine development, innate immunity research, and human disease diagnostics, combined with the increasing role of portable long-read sequencing in emerging infectious disease (EIDs) surveillance, positions BIRD-Seq as an innovative and competitive diagnostic platform. Highlights – Double-stranded RNA (dsRNA) is one of the critical pathogen-associated molecular patterns for viral invasion in the host. A protein-based sandwich assay for dsRNA detection in crude biological samples with a sub-ng mL -1 order detection limit was developed, achieving similar sensing efficiency in comparison to expensive and proprietary monoclonal antibody-based ELISA methods. – The quantitative detection of RNA duplex is coupled with an Oxford nanopore direct dsRNA sequencing method for virus species identification and qualitative analysis. – This is one of the very first dsRNA-centered end-to-end workflows for virus monitoring and sequencing, validated for both infected plant and animal samples.</p><p class="metadata"><time datetime="2026-06-26" title="Source date; precision not specified">June 26, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.06.25.734422">Original publication</a></p> Fri, 26 Jun 2026 00:00:00 GMT Athanasios Nikolaos Xhurxhi Subhankar Sahu Hélène Scheer Elliot F Miott Abdelmalek Alioua Daniel Clesse Baptiste Monsion Julien Pompon Sabine Szunerits Todd Blevins Christophe Ritzenthaler OpenAlex https://reading.michaelmvh.com/article/6bed94a7403001e48d60bfbc0ecd4af60c1ae1a98a2d4df055395b0142a449a8/ urn:sha256:6bed94a7403001e48d60bfbc0ecd4af60c1ae1a98a2d4df055395b0142a449a8 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-06-25" title="Source date; precision not specified">June 25, 2026</time> <span aria-hidden="true"> · </span> Angewandte Chemie</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/ange.2026-m1906020000">Original publication</a></p> Thu, 25 Jun 2026 00:00:00 GMT Zugui Peng Daisuke Noshiro Shiroh Futaki Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/2740a9a8635b8988c74960d9f0e0ae350221610ab4213db7583cb2fda4ba9b1a/ urn:sha256:2740a9a8635b8988c74960d9f0e0ae350221610ab4213db7583cb2fda4ba9b1a <p>Nanopores serve as sensors for single-molecule characterization. In Research Article e3311099, Ryuji Kawano and co-workers constructed synthetic nanopores using DNA and peptides that enable single-molecule translocation. The cover illustrates that the key to pore formation is the presence of 2-aminoisobutyric acid in the peptide, while the DNA scaffold assembles the peptides into well-defined oligomeric states. Image credit: Hiroko Uchida.</p><p class="metadata"><time datetime="2026-06-24" title="Source date; precision not specified">June 24, 2026</time> <span aria-hidden="true"> · </span> Angewandte Chemie International Edition</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/anie.2026-m1906020000">Original publication</a></p> Wed, 24 Jun 2026 00:00:00 GMT Zugui Peng Daisuke Noshiro Shiroh Futaki Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/1c5b9814a8ed26a8c878f62df92b816fbb2a50bb0d7d399937218d4ca253090d/ urn:sha256:1c5b9814a8ed26a8c878f62df92b816fbb2a50bb0d7d399937218d4ca253090d <p>The function of a protein depends not only on its sequence but on post-translational modifications and folding that produce functionally distinct proteoforms. Single-molecule methods for protein identification, such as nanopore sequencing, typically require denaturation or proteolysis, sacrificing conformational information that contributes to proteoform diversity. Here, we identify intact, folded proteins by recording an optical fingerprint of their local surface chemistry using a single covalent label. The signal is produced by a spontaneously blinking fluorophore attached to the protein through established bioconjugation reactions. The thermodynamics and kinetics of its switching between a fluorescent and a dark state are influenced by the immediate protein environment in a chemically interpretable manner. Further discriminative information can be extracted using deep learning to achieve excellent identification accuracy. Using this approach, we distinguish different proteins, different pockets of the same protein, and the presence of a single post-translational modification, in each case tracing the classification back to a distinct physicochemical mechanism. These results establish single-molecule fluorescence blinking as both a protein fingerprinting method and a probe of local chemistry on the surface of folded proteins.</p><p class="metadata"><time datetime="2026-06-23" title="Source date; precision not specified">June 23, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.06.22.733774">Original publication</a></p> Tue, 23 Jun 2026 00:00:00 GMT Salome Püntener Dorothea Kossmann Krzysztof Bielec Pablo Rivera‐Fuentes OpenAlex https://reading.michaelmvh.com/article/bd02643d4ac6310f561662e78467d2dc9e22b1b1d696c3db8dd175871be7a4b3/ urn:sha256:bd02643d4ac6310f561662e78467d2dc9e22b1b1d696c3db8dd175871be7a4b3 <p>Biological nanopores can be used to monitor the conformational dynamics of enzymatic reactions in real time and at the single-molecule level. However, the molecular basis of this process and the requirements for efficiently engineering a nanopore for measuring conformational transitions in proteins remain poorly understood. Here, we combine all-atom molecular dynamics simulations and electrophysiology experiments to determine the molecular mechanism and improve the resolution for the recognition of glutamine by a substrate-binding domain (SBD) protein using ClyA nanopores through mutagenesis. By matching the simulated and experimental currents, we found that the SBD protein most likely resides very close to the constriction of the nanopore, where the open and closed conformations induce large current differences. To amplify the signal, we introduced bulky tryptophan residues near the likely location of the SBD protein. This effectively narrowed the nanopore and resulted in a 3-fold signal amplification. Molecular dynamics simulations suggest that prolonged residence of the SBD protein within ClyA is likely caused by an electro-osmotic flow that imparts a restoring force on the protein, counteracting its displacement from an equilibrium location. Our work shows how nanopore systems can be engineered in a rational way for the monitoring of biochemical reactions at the single-molecule level.</p><p class="metadata"><time datetime="2026-06-22" title="Source date; precision not specified">June 22, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p><a href="https://doi.org/10.1021/acsnano.6c04709">Original publication</a></p> Mon, 22 Jun 2026 00:00:00 GMT Kumar Sarthak Veerle Van Meervelt Misha Soskine Giovanni Maglia Aleksei Aksimentiev OpenAlex https://reading.michaelmvh.com/article/130c26d5a296b5de2ef11a5814f2af4a70850d4acf718d0b28e84999922244c0/ urn:sha256:130c26d5a296b5de2ef11a5814f2af4a70850d4acf718d0b28e84999922244c0 <p>Summary Sex differences strongly influence susceptibility to metabolic dysfunction-associated steatotic liver disease (MASLD), yet the regulatory mechanisms underlying these differences remain incompletely understood. To examine sex-specific hepatic adaptation to a high-fat (HF) diet mouse model of MASLD, we integrated proteomics, transcriptomics, and Oxford Nanopore direct RNA sequencing for transcriptome-wide m6A profiling in male and female mouse livers. Female mice were relatively protected from HF diet–induced hepatic steatosis and exhibited distinct proteome remodeling enriched for peroxisomal pathways. In contrast, transcriptomic responses in females were dominated by inflammatory signatures and did not recapitulate the metabolic adaptations observed at the protein level, revealing extensive RNA–protein discordance and post-transcriptional remodeling. Integrated RNA–protein analyses identified female-specific amplification of peroxisomal proteins despite modest transcript-level changes. HF diet also induced sex-specific remodeling of m6A RNA methylation and altered regulation of the m6A methylation system. Notably, reduced 3′ UTR m6A methylation of peroxisomal transcripts inversely correlated with increased protein abundance relative to RNA expression in female mice. Together, these findings implicate m6A-associated post-transcriptional regulation in sex-specific hepatic adaptation to HF diet exposure and the basis for discordance between many of the mRNAs and proteins in the liver.</p><p class="metadata"><time datetime="2026-06-22" title="Source date; precision not specified">June 22, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.06.19.733425">Original publication</a></p> Mon, 22 Jun 2026 00:00:00 GMT Sofia V. Krylova Maxwell Horton G Bucciarelli Li Liu Jacob L. Berrigan Ronald Cutler Kartik Chandran Nathaniel W. Snyder Toma Tebaldi Simone Sidoli Kamini Singh Jeffrey E. Pessin OpenAlex https://reading.michaelmvh.com/article/556252f86845e121698ff9a38dfe4b8c48aeb4b906dc17d89ea2267cbec6ac0c/ urn:sha256:556252f86845e121698ff9a38dfe4b8c48aeb4b906dc17d89ea2267cbec6ac0c <p>No abstract is available.</p><p class="metadata"><time datetime="2026-06-21" title="Source date; precision not specified">June 21, 2026</time> <span aria-hidden="true"> · </span> Sensors and Actuators B Chemical</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.snb.2026.140383">Original publication</a></p> Sun, 21 Jun 2026 00:00:00 GMT Y M Xu Songbai Cao Yuheng Liu Jun Peng Mingyi Yu Youjian Liu Yuhua Cai Sébastien Balme Tianji Ma Zhong Cao OpenAlex https://reading.michaelmvh.com/article/ce4f03983752faa41ea5f667cd86ca64476db9f5eed2e30f96e7879d17af8cc8/ urn:sha256:ce4f03983752faa41ea5f667cd86ca64476db9f5eed2e30f96e7879d17af8cc8 <p>Direct, high-resolution analysis of proteins and peptides at the single-molecule level remains a major challenge in biology and medicine. Nanopore technology has emerged as a uniquely powerful tool for label-free, real-time detection of biomolecules. This review comprehensively surveys advances in nanopore sensing, with a focus on peptides as pivotal intermediates between amino acids and full-length proteins. We begin by examining the foundational sensing of individual amino acids, followed by direct peptide analysis encompassing discrimination of isomers, post-translational modifications, and biomarkers. Subsequently, we discuss indirect strategies for protein identification and metal ion detection via peptide probes. Finally, we explore cutting-edge frontiers in peptide sequencing and the de novo design of peptide-based nanopores. With continued development, nanopore sensing holds substantial potential to drive transformative advances in biomolecular analysis, proteomics, and diagnostics.</p><p class="metadata"><time datetime="2026-06-19" title="Source date; precision not specified">June 19, 2026</time> <span aria-hidden="true"> · </span> Langmuir</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.langmuir.6c00804">Original publication</a></p> Fri, 19 Jun 2026 00:00:00 GMT Wenzhi Ma Ke Chen Gengchen Hu Yiming Zhang Yao Jiang Dongmei Xi OpenAlex https://reading.michaelmvh.com/article/d4c379ff6dc7d7243cfb57f0a484363d8eda83482f6628ac43e4a83c6d482819/ urn:sha256:d4c379ff6dc7d7243cfb57f0a484363d8eda83482f6628ac43e4a83c6d482819 <p>Nanopore sensing holds transformative potential for revolutionizing protein and glycan sequencing. However, translating this potential into practical, high-fidelity identification is severely bottlenecked by the challenge of processing massive amounts of highly similar nanopore ionic-current data, spurring an urgent need for robust, AI-driven solutions. Prevailing deep learning methods suffer from two limitations: they often fail to capture the fine-grained temporal dynamics essential for distinguishing structurally similar analytes, and their generic training strategies inadequately extract weak discriminative features, thus limiting classification precision. Here, we present SEDA-Former (Signal Enhancement and Dynamic Attention Transformer), a deep temporal learning framework designed for high-resolution nanopore single-molecule identification. SEDA-Former incorporates a multi-window sliding standard-deviation method for feature enhancement, a multi-channel temporal convolutional network to mine weak features in temporal dynamics, and a progressive adaptive attention training strategy that dynamically reweights sample losses based on learning difficulty. Across a diverse set of challenging benchmark datasets, including nanopore signals of 15 glycosides, 24 ginsenosides, 8 DNA molecules, and 17 cholic acid conjugates, spanning varying levels of signal complexity, SEDA-Former consistently achieves substantially higher classification accuracy than state-of-the-art methods and demonstrates robust cross-dataset transferability. SEDA-Former provides a versatile and scalable solution to facilitate single-molecule identification in nanopore sensing.</p><p class="metadata"><time datetime="2026-06-17" title="Source date; precision not specified">June 17, 2026</time> <span aria-hidden="true"> · </span> Nature Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41467-026-74507-w">Original publication</a></p><p><a href="https://www.nature.com/articles/s41467-026-74507-w_reference.pdf">Open PDF</a></p> Wed, 17 Jun 2026 00:00:00 GMT Ming Li Minmin Li Yuchen Cao Jing Wang Hanwen Ning Guangyan Qing OpenAlex https://reading.michaelmvh.com/article/8e3e36f2d11d40a42f610e875daed811977241c4c79425539c7d31336e698750/ urn:sha256:8e3e36f2d11d40a42f610e875daed811977241c4c79425539c7d31336e698750 <p>The translocation of molecules through nanoscale pores is ubiquitous in biology and widely used in biotechnology for nanopore sequencing and characterizing single biological molecules. Numerous artificial channels mimicking biological pores have been developed, and one of those is a single-walled carbon nanotube porin (CNTP) embedded in a lipid bilayer membrane. Although transport of ssDNA through CNTP has been demonstrated experimentally, protein translocation through CNTP has rarely been achieved. Here, we report the experimental observations of protein (cytochrome c ) translocation through a single-walled carbon nanotube of an inner diameter of ∼1.3 nm embedded in a lipid bilayer membrane without using any chemical denaturant, enzyme motor, or tagging with an oligonucleotide. The electric field was found to sufficiently unfold the cytochrome c protein to facilitate the translocation, as confirmed by a decrease in the average residence time of the protein at the CNTP upon increasing the transmembrane potential. A simple free energy model suggests that the relatively fast (microseconds) dynamic interconversions of protein conformational states appear to dictate the slow (∼100 ms) translocation and account for the observed voltage-dependent rate constants from the exponential residence time distributions. Our report on the experimental evidence of protein translocation through CNTP may open the opportunity to explore the applications of CNTP in targeted protein delivery, in nanopore proteomics, and probing protein conformational transitions at the single-molecule level.</p><p class="metadata"><time datetime="2026-06-17" title="Source date; precision not specified">June 17, 2026</time> <span aria-hidden="true"> · </span> The Journal of Physical Chemistry B</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.jpcb.6c02290">Original publication</a></p> Wed, 17 Jun 2026 00:00:00 GMT Saurabh Chaubey Km Mamata Patel Yogita Rani Simran Nasa Manoj M. Varma Prabhat Tripathi OpenAlex https://reading.michaelmvh.com/article/210cbdc4abe29b9c1bb6f5c0686093596ca05e08bc91ea19b61eaa430f7be95b/ urn:sha256:210cbdc4abe29b9c1bb6f5c0686093596ca05e08bc91ea19b61eaa430f7be95b <p>No abstract is available.</p><p class="metadata"><time datetime="2026-06-16" title="Source date; precision not specified">June 16, 2026</time> <span aria-hidden="true"> · </span> Research Square</p><p class="provenance">Curated by <a href="https://github.com/Michaelmvh/scholarly-rss-feed/blob/main/src/curated/nanopore-foundations.json" rel="external">Nanopore Foundations &amp; Signal Analysis</a> · Fingerprinting · Motor-free transport · Preprint · Protein analysis</p><p><a href="https://doi.org/10.21203/rs.3.rs-8098579/v1">Original publication</a></p><p><a href="https://www.researchsquare.com/article/rs-8098579/latest.pdf">Open PDF</a></p> Tue, 16 Jun 2026 00:00:00 GMT Meni Wanunu Amr K. Makhamreh Ali Fallahi Rik Dhar Monika Kumari Siddarth Krishnan Michele Meseonznik Luning Yu Dinara Boyko Keira Reich-Veillette Yuhaohua Zheng Elizabeth A. Libby Aleksei Aksimentiev OpenAlex Nanopore Foundations & Signal Analysis https://reading.michaelmvh.com/article/b3b027110c6f5434f9ffef84fcd09393e031e226a17aa9b5c8c331d6137637e6/ urn:sha256:b3b027110c6f5434f9ffef84fcd09393e031e226a17aa9b5c8c331d6137637e6 <p>A first conceptual pivot emerges from work on Stenotrophomonas maltophilia, a multidrug-resistant opportunistic pathogen. Stabile et al. demonstrate that the iminosugar L-NPDNJ, despite weak bactericidal activity, exerts additive effects when used in combination with amikacin and tobramycin, reducing their minimum inhibitory concentrations by two-to threefold. At sub-inhibitory concentrations, the compound significantly modulates the expression of genes involved in antibiotic resistance, biofilm regulation, and virulence, including those encoding efflux pumps, global regulators, and extracellular proteases. These transcriptional changes translate into reduced virulence in vivo and enhanced macrophage clearance. This study underscores a critical insight: antimicrobial efficacy need not rely solely on killing. Disarming pathogens, rather than eradicating them, can attenuate disease severity while reducing selective pressure for resistance. Anti-virulence agents, particularly those that modulate host-pathogen interactions, represent a promising complement to traditional antibiotics.A second thematic cluster of this Issue highlights the expanding potential of bio-derived, multi-target antimicrobials. Tiricz et al. dissect the antimicrobial region of NCR147, a rare non-cationic nodule-specific cysteine-rich peptide from Medicago truncatula. Through rational truncation and amino-acid substitution, they generate derivatives with enhanced potency, broad-spectrum activity and antibiofilm effects, including against Acinetobacter baumannii. These peptides act through a multi-hit mechanism involving membrane perturbation, efflux pump inhibition and interference with intracellular targets. Importantly, fluorinated variants retain activity without cytotoxicity to human cells, illustrating how natural scaffolds can be engineered for therapeutic use. Complementing this, Pascale et al. apply bio-orthogonal non-canonical amino-acid tagging (BONCAT) to track the inhibition of protein synthesis by proline-rich antimicrobial peptides (PrAMPs) in living Escherichia coli and Klebsiella pneumoniae bacteria. BONCAT, combined with flow cytometry, discriminates membrane-active peptides from those targeting intracellular processes and reveals rapid, long-lasting inhibition of translation. This methodological advance provides a powerful tool for mechanistic characterisation of antimicrobial peptides, enabling precise mapping of their intracellular effects. Plant-derived antimicrobials extend beyond peptides. Ali et al. evaluate a peppermint oil nanoemulsion (PEONE) against multidrug-resistant K. pneumoniae and Pseudomonas aeruginosa. PEONE disrupts bacterial membranes, induces leakage of intracellular contents and exhibits sustained bactericidal activity. Molecular docking identifies caryophyllene as a key component with high affinity for β-lactamase enzymes, suggesting a dual mechanism of membrane disruption and enzyme inhibition. This work reinforces the therapeutic potential of natural products when combined with nanoscale formulation and computational analysis. Together, these studies signal a broader transition: natural molecules are no longer viewed as static entities but as rationally optimisable, multi-target antimicrobial platforms. Their capacity to act on membranes, intracellular pathways and resistance determinants simultaneously may reduce the likelihood of resistance emergence.A third conceptual advance arises from computational acceleration of antimicrobial discovery. Qingxin et al. develop a multi-template homology modelling and virtual-screening pipeline to identify CNP0387675, a non-nucleoside inhibitor of MraY, an essential enzyme in peptidoglycan synthesis. Extensive molecular-dynamics simulations confirm stable binding to conserved catalytic residues. By circumventing the limitations of nucleoside analogues, this scaffold offers a promising approach to targeting Gram-negative pathogens. Such computational pipelines enable rapid exploration of chemical space, even in the absence of experimentally resolved structures, and can prioritise candidates for experimental validation. In parallel, Sedaghat et al. introduce HoloMoA, a holography-and deep-learning-based platform for mechanism-of-action (MoA) classification. Digital inline holographic microscopy captures time-resolved, label-free morphological responses of bacteria to antimicrobial exposure, while convolutional recurrent neural networks achieve 95% accuracy in MoA prediction across five functional classes. A Siamese neural-network architecture further enables novelty detection, distinguishing unseen mechanisms from known classes. This approach provides a scalable, affordable and unbiased tool for early-stage antimicrobial profiling, bridging the gap between computational discovery and mechanistic validation. Mechanistic insight must also be paired with surveillance of resistance evolution. Zang et al. identify 53 mutations associated with decreased susceptibility to ceftriaxone in Neisseria gonorrhoeae, including 33 previously unreported variants. By integrating these mutations into a minimum-spanning-tree framework, the authors achieve improved sensitivity and specificity in predicting resistance compared with classical sequence typing.A final thematic axis focuses on extracellular vesicles (EVs) and outer membrane vesicles (OMVs), which are now widely recognised as key mediators of bacterial communication, virulence and resistance. Ran et al. show that sub-inhibitory oxacillin exposure enhances EV secretion in oxacillin-sensitive MRSA and enriches vesicles with virulence-associated proteins, including penicillin-binding protein 2 and hemolysins. These EVs exhibit increased hemolytic activity, promote biofilm formation, stimulate pro-inflammatory cytokines and penetrate epithelial cells more effectively. Lu et al. provide a broader conceptual framework, reviewing the roles of OMVs in horizontal gene transfer, biofilm formation, immune modulation and antibiotic resistance. OMVs also hold promise as therapeutic platforms for vaccines, drug delivery and immune modulation. Together, these studies highlight vesicle biology as both a challenge and an opportunity: antibiotics can reshape vesicle-mediated communication, but vesicles themselves may be harnessed for anti-infective strategies.Across these manuscripts, a coherent picture emerges. Antimicrobial innovation is shifting towards a mechanism-driven, evolution-aware paradigm that integrates anti-virulence approaches, multi-target natural products, computational design, and vesicle biology. This convergence offers a roadmap for revitalising antimicrobial pipelines by prioritising agents that disarm rather than solely kill, engineering natural scaffolds for multi-hit activity, exploring novel chemical space, and incorporate vesicle-mediated processes into both therapeutic design and stewardship policies. The future of antimicrobial therapy will depend on embracing this multidimensional strategy. By aligning mechanistic insight with technological innovation, the field can move beyond incremental modifications of existing antibiotics toward transformative solutions capable of outpacing microbial evolution.</p><p class="metadata"><time datetime="2026-06-16" title="Source date; precision not specified">June 16, 2026</time> <span aria-hidden="true"> · </span> Frontiers in Microbiology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3389/fmicb.2026.1900349">Original publication</a></p><p><a href="https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1900349/pdf">Open PDF</a></p> Tue, 16 Jun 2026 00:00:00 GMT Valeria Napolitano Eliana De Gregorio Felipe Romero‐Saavedra Rita Berisio OpenAlex https://reading.michaelmvh.com/article/0a3feca29d1ec4b57e0ca1e5b404445a8e036f1d8816de431b92c0022fb080b8/ urn:sha256:0a3feca29d1ec4b57e0ca1e5b404445a8e036f1d8816de431b92c0022fb080b8 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-06-15" title="Source date; precision not specified">June 15, 2026</time> <span aria-hidden="true"> · </span> Nature Nanotechnology</p><p><a href="https://doi.org/10.1038/s41565-026-02192-3">Original publication</a></p> Mon, 15 Jun 2026 00:00:00 GMT Kefan Wang Xingwang An Xinmeng Gao Yusheng Ouyang Zixuan Wang Pingping Fan Li K Yunqi Xiao Wendong Jia Jialu Chen Wen SUN Panke Zhang Shuo Huang OpenAlex https://reading.michaelmvh.com/article/f527fb28255014cb858da8ff9f03464b9a3cff98c0351513c645516c7959453d/ urn:sha256:f527fb28255014cb858da8ff9f03464b9a3cff98c0351513c645516c7959453d <p>ABSTRACT Dendrimer‐peptide conjugates (DPCs) are multivalent soft materials whose biological and transport behaviors depend critically on peptide loading density, yet ensemble methods cannot resolve how incremental ligand changes affect nanoscale structure, mechanical compliance, and transport dynamics at the single‐particle level. Here, chemically tuned controlled dielectric breakdown solid‐state nanopores are employed to probe DPCs with defined peptide loadings (DPC10, DPC40, DPC60, and DPC100), using surface‐modified G7 PAMAM dendrimers as a reference scaffold. Voltage‐dependent analysis of capture rates, current blockades, dwell times, deformation metrics, and electrical charge deficit (ECD) scaling reveals distinct loading‐dependent electromechanical signatures with subpopulation resolution. DPC10 exhibits rigid and uniform translocation dynamics, whereas DPC40 shows pronounced configurational heterogeneity, manifested as clustered ECD‐dwell time distributions. At elevated biases, the more open DPC60 displays enhanced deformability and rapid transport, while densely packed DPC100 translocates more slowly with the strongest monotonic coupling between blockade depth and dwell time. These results establish a mechanistic link between ligand density, nanoscale deformability, and pore‐coupled transport dynamics, enabling label‐free discrimination of dendrimer‐peptide architectures that are indistinguishable by ensemble methods. Solid‐state nanopore sensing thus provides a multiparametric analytical framework for resolving subpopulation heterogeneity in soft multivalent nanomaterials.</p><p class="metadata"><time datetime="2026-06-15" title="Source date; precision not specified">June 15, 2026</time> <span aria-hidden="true"> · </span> Advanced Materials Interfaces</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/admi.70569">Original publication</a></p> Mon, 15 Jun 2026 00:00:00 GMT Chaoming Gu Jin Woong Lee Kamruzzaman Joty Marisela Leon Santosh Khatri Janeesha Manawasinghe Seungpyo Hong Min Jun Kim OpenAlex https://reading.michaelmvh.com/article/8b85569145b8b3987a927dad17b524b50ed4026bfc6e00f7b982d84918db8b19/ urn:sha256:8b85569145b8b3987a927dad17b524b50ed4026bfc6e00f7b982d84918db8b19 <p>All-atom molecular dynamics has become an indispensable tool in development of nanopore sensors of biological information. In a typical nanopore experiment, measurements of ionic current flowing through a nanopore report on the chemical structure of biomolecules that pass through the nanopore. Such experiments alone are often insufficient to relate the structure of the biomolecules to the ionic current modulations. The molecular dynamics method can establish such a relationship directly through a brute force simulation under applied electric field. Here, we examine the ability of molecular dynamics force fields to reproduce experimentally measured nanopore blockade currents produced by single-stranded DNA. Our simulations show that none of the &quot;off the shelf&quot; force fields (CHARMM36, AMBER Parmbsc1 and DES-AMBER) is capable of reproducing experimental data with the desired level of accuracy. To improve the accuracy, we examined and refined interactions between ions, protein nanopores and DNA, guided by experiments designed specifically for this purpose. Ultimately, the introduction of surgical corrections to non-bonded interactions within the CHARMM36 force field produced a favorable agreement between simulation and experiment. This refined parameterization, initially developed for nanopore sensing simulations, may have broader applications in computational studies of DNA-protein systems.</p><p class="metadata"><time datetime="2026-09-25" title="Source date; precision not specified">September 25, 2026</time> <span aria-hidden="true"> · </span> Journal of Chemical Theory and Computation</p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p class="provenance">Curated by <a href="https://github.com/Michaelmvh/scholarly-rss-feed/blob/main/src/curated/nanopore-foundations.json" rel="external">Nanopore Foundations &amp; Signal Analysis</a> · Preprint · Signal analysis · Signal modeling</p><p><a href="https://doi.org/10.1021/acs.jctc.6c01180">Original publication</a></p> Fri, 25 Sep 2026 00:00:00 GMT Jingqian Liu Crystal Rodriguez Min Chen Aleksei Aksimentiev OpenAlex bioRxiv: Biophysics Nanopore Foundations & Signal Analysis https://reading.michaelmvh.com/article/424ca07cb786a721783b1f3b6696a59562069aec5e00ec3ce7d46ddcd72481e5/ urn:sha256:424ca07cb786a721783b1f3b6696a59562069aec5e00ec3ce7d46ddcd72481e5 <p>ABSTRACT Non-viral nanocarriers are increasingly adopted as safer alternatives to viral vectors for gene delivery, enabling scalability and improved manufacturability. Among them, mesoporous silica nanoparticles (MSiNPs) offer a promising platform due to their structural properties and versatility. This work extracts critical trends of recent literature to seek standardized design rules for MSiNPs-based systems, focusing on the optimisation of the proposed core-shell model architecture. The analysis examines the silica-based matrix core, which determines the morphology and nano-pore structure, and the engineered shell, which modulates the bio-interface through charge inversion, stimulus-responsive release mechanisms, protein corona regulation and active targeting. A formalized “golden-trio” concept is proposed highlighting the interdependence among the physico-chemical properties of MSiNPs, cellular uptake, and intracellular trafficking—key determinants of transfection efficiency. The study evaluates the adaptability of MSiNPs enabling stabilization and vectorization of diverse payloads, including small interfering RNAs and microRNAs for gene silencing, plasmid DNA for expression, and CRISPR/Cas9 systems for genome editing. Strategies for targeting specific cell types by matching surface functionalisation to the genetic payload are discussed, along with the potential for co-administration and theranostic applications to achieve synergistic results. This review concludes that designing the physico-chemical properties of MSiNPs through an integrated approach—combining the core matrix with the precise modulation of the shell surface chemistry to overcome biological barriers and guarantee reproducibility and patient safety—is essential for unlocking their clinical potential in gene therapy.</p><p class="metadata"><time datetime="2026-06-11" title="Source date; precision not specified">June 11, 2026</time> <span aria-hidden="true"> · </span> Journal of Drug Delivery Science and Technology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.jddst.2026.108591">Original publication</a></p> Thu, 11 Jun 2026 00:00:00 GMT Giorgia Mano Aránzazu Díaz‐Cuenca OpenAlex https://reading.michaelmvh.com/article/72584c889a94818935fae704c44e15e30e57804dd4c0cc45e3ffd5bef0badf94/ urn:sha256:72584c889a94818935fae704c44e15e30e57804dd4c0cc45e3ffd5bef0badf94 <p>ABSTRACT Sequencing of protein with nanopores has emerged as a powerful tool offering rapid readout, high accuracy, low cost, and portability. There is an urgent need to improve the sensing accuracy of nanopores to effectively realize protein sequencing. However, controlling protein translocation rates remains a significant challenge. This study designed a graphene/Si 3 N 4 dual membrane cavity system to explore potential solutions for enhancing protein sequencing accuracy and efficiency. Charge regulation and cavity structure were employed to slow down the translocation rate of peptides in the Si 3 N 4 nanopore. The proposed Si 3 N 4 toroidal cavity structure successfully reduces peptide translocation rates by introducing physical steric hindrance and enhancing van der Waals adsorption. This structure not only substantially prolongs peptide residence time in the sensing region but also maintains excellent signal resolution, offering a potential approach to address the high bandwidth demands in single‐molecule protein sequencing. The findings contribute to achieving high‐resolution, high‐throughput protein sequencing and advance the field of proteomics.</p><p class="metadata"><time datetime="2026-06-11" title="Source date; precision not specified">June 11, 2026</time> <span aria-hidden="true"> · </span> Advanced Science</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/advs.76099">Original publication</a></p> Thu, 11 Jun 2026 00:00:00 GMT Yubin Cao Junzhou He Wei Si OpenAlex https://reading.michaelmvh.com/article/9a59884bd258ec64a5054464bdbdff48a5bf7512dbb6ed86f5af9573511af42f/ urn:sha256:9a59884bd258ec64a5054464bdbdff48a5bf7512dbb6ed86f5af9573511af42f <p>Nanopore technology enables rapid, portable, and label-free single-molecule detection of analytes, including nucleic acids and proteins. One strategy for improving accuracy is to increase interactions between analytes and the nanopore. For example, engineered nanopores with additional constrictions improve analyte-pore interactions during translocation. This concept adopts the exploration of biological nanopores, which naturally contain multiple constrictions. Here, we demonstrate that Epx4, a pore-forming toxin with two independent β-barrels, functions as a nanopore sensor capable of generating informative ionic current signals during polypeptide translocation. Structural analysis of the pore geometry revealed that Epx4 contains up to four constrictions. In single-molecule measurements, Epx4 detected cationic polypeptides with a higher event frequency than α-hemolysin (αHL). With machine-learning-assisted analysis, Epx4 achieved an ROC AUC score of 0.82 and an F1 score of 0.72, both of which were higher than those obtained with αHL. Our findings suggest that Epx4 is a promising candidate for developing nanopore sensors with high accuracy for protein analysis.</p><p class="metadata"><time datetime="2026-06-11" title="Source date; precision not specified">June 11, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.70762">Original publication</a></p><p><a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/smtd.70762">Open PDF</a></p> Thu, 11 Jun 2026 00:00:00 GMT Ayako Ijuin Kota Naito Mana Sato Virginia Di Toro Mammarella Nanami Takeuchi Mauro Chinappi Yoshikazu Tanaka Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/8308917053a662092169ad180c51a782465e570363d975dd8d4648c65600f92f/ urn:sha256:8308917053a662092169ad180c51a782465e570363d975dd8d4648c65600f92f <p>Genetic systems engineering is constrained by high DNA synthesis costs, assembly inefficiencies, and challenges in expressing complex proteins. To address these limitations, we developed a highly parallel, low-cost pipeline for the design, assembly, and functional screening of genetic systems, which we stress-tested on highly repetitive structural proteins, including spider silk, biocements, reflectins, and talins. The integrated pipeline combines computational genetic systems design, low-cost many-plasmid DNA assembly from oligopools, automated many-to-many mapping using nanopore sequencing data, and a label-free biosensor to measure single-cell protein expression levels. We applied this pipeline to build 239 plasmids, achieving a 88% success rate (up to 2000 bp) using standard clonal isolation and 58% assembly efficiency (up to 5600 bp) without selective DNA purification, while lowering material costs by up to 24-fold. We applied the biosensor to identify genetic factors that create distinct cellular subpopulations with varying protein expression levels. Overall, the integrated pipeline will dramatically lower the cost of high-throughput synthetic biology, while demonstrating how designing genetic systems to improve build efficiency (&quot;design for build&quot;) and directly incorporating biosensors into genetic systems (&quot;design for test&quot;) will greatly accelerate design-build-test workflows.</p><p class="metadata"><time datetime="2026-06-09" title="Source date; precision not specified">June 9, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.06.08.729977">Original publication</a></p> Tue, 09 Jun 2026 00:00:00 GMT Harry E. Adamson James R. McLellan Khushank Singhal Melik C. Demirel Howard M. Salis OpenAlex https://reading.michaelmvh.com/article/bf10ab8180cc53c3435ac940f6b9fcddca0c852ec63f7dc4a7a49dca079cc79e/ urn:sha256:bf10ab8180cc53c3435ac940f6b9fcddca0c852ec63f7dc4a7a49dca079cc79e <p>Staphylococcus aureus has become a major public health concern because of its increasing antibiotic resistance. Given limited clinical success of previous S. aureus vaccine candidates, this study aimed to design and computationally evaluate a novel multi-epitope construct integrating sequences derived from fibronectin-binding protein A, α-hemolysin, and a detoxified protein A variant. Candidate epitopes were computationally predicted and evaluated to determine immunogenicity, toxicity, and cross-reactivity. The epitopes were then joined using linkers with the addition of an adjuvant and an enhancer sequence to improve immunological response. The final construct showed favorable physicochemical properties, predicted solubility and high structural quality after refinement with 97.115% of amino acids in favored regions of the Ramachandran plot. Docking analysis supported plausible binding of selected epitopes to their representative HLA class I and II molecules. The complete vaccine construct showed stable in silico interaction with the TLR4/MD-2 heterodimer and a persistent receptor-vaccine interface throughout the 100 ns of the molecular dynamics simulation. The immune simulation predicted a predominantly humoral and CD4+ T helper response, with increments of B-cells, IgM and IgG1 production, memory CD4+ T-cells, macrophages, IFN-γ, IL-2, and IL-12. Codon optimization and in silico cloning supported the recombinant expression of the vaccine construct in Escherichia coli. Together, these findings identify this multi-epitope construct as a promising candidate for further experimental evaluation against S. aureus infection.</p><p class="metadata"><time datetime="2026-06-03" title="Source date; precision not specified">June 3, 2026</time> <span aria-hidden="true"> · </span> Scientific Reports</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41598-026-54286-6">Original publication</a></p> Wed, 03 Jun 2026 00:00:00 GMT Hannia Michelle Prieto-Nevárez Alejandro Tarango-García Arturo Gutierrez‐Guerrero Aristóteles Álvarez-Cardona Saúl Oswaldo Lugo Reyes OpenAlex https://reading.michaelmvh.com/article/55f710a75ad5e5fdbdbef724b2bc2a53c2b5007279d4cede91aefbbb235d8337/ urn:sha256:55f710a75ad5e5fdbdbef724b2bc2a53c2b5007279d4cede91aefbbb235d8337 <p>The development of high-performance functional biointerfaces requires precise control over molecular recognition mechanisms at the nanoscale. A fundamental limitation in current biological nanopore materials is that wild-type (WT) channels often lack the specific physicochemical &quot;grip&quot; required to resolve chemically similar analytes. Here, we demonstrate that rationally engineering a key active site, called the φ-clamp, in the anthrax toxin protective antigen (PA) nanopore creates a tunable biointerface with orthogonal selectivity. By mutating the φ-clamp constriction (F427A), we generated a variant thatdespite being a defective large protein biological translocasefunctions as a superior material for molecular recognition, achieving ∼93% classification accuracy for peptides that confound the WT pore. We integrated the WT and F427A variants into a multistage machine learning ensemble (XGBoost) to leverage the complementary physicochemical selectivity of each poreWT for aromatics and F427A for small polar residuesachieving a balanced F1-score of &gt;0.91. This work proposes a design principle for multiplexed biomaterials, demonstrating that attenuating native transport function via rational engineering can enhance the specificity of the biointerface for targeted analytical applications.</p><p class="metadata"><time datetime="2026-06-03" title="Source date; precision not specified">June 3, 2026</time> <span aria-hidden="true"> · </span> ACS Omega</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsomega.6c01388">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acsomega.6c01388?ref=article_openPDF">Open PDF</a></p> Wed, 03 Jun 2026 00:00:00 GMT Jennifer M. Colby Bryan A. Krantz OpenAlex https://reading.michaelmvh.com/article/a47be621fe26f786836c5a397d713beecac7d77cde5b361aa09a72e37d54aa91/ urn:sha256:a47be621fe26f786836c5a397d713beecac7d77cde5b361aa09a72e37d54aa91 <p>Accurate profiling of antibody isotypes is essential to monitor immune responses, diagnose disease, and guide therapy, yet existing immunoassays remain limited in capturing their conformational dynamics with molecular precision. Nanopore sensing offers a label-free route to such resolution, but most implementations rely on fragmentation, probes, or functionalization, leaving intact isotypes inaccessible. Here, a nanopore-based assay that directly discriminates full-length IgG, monomeric IgA, and IgM under non-denaturing conditions, resolving intrinsic molecular signatures in real time is presented. In a lithium chloride electrolyte, glass nanopipettes operate in an electroosmotic-flow-dominated regime where flow-driven transport and nanoscale confinement produce distinct ionic fingerprints for each isotype. Affinity-based signal modulation with protein G, which selectively binds the IgG Fc domain, further introduces a tunable contrast mechanism that sharpens IgG-IgA separability while preserving native structure and binding functionality. Quantitative analysis demonstrates robust separation (p &lt; 0.0001) in binary and ternary mixtures with low misclassification. Evaluation in diluted human serum with a physiologically representative IgG:IgA:IgM ratio (7:2:1) shows that isotype-specific fingerprints remain distinguishable in a serum-derived background. The EOF-governed assay establishes a scalable framework for direct, multiplexed immunoprofiling and extends label-free nanopore analysis beyond antibodies toward broader proteomic targets.</p><p class="metadata"><time datetime="2026-06-02" title="Source date; precision not specified">June 2, 2026</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.70758">Original publication</a></p> Tue, 02 Jun 2026 00:00:00 GMT Iris Baffour Ansah Kevin J. Freedman OpenAlex https://reading.michaelmvh.com/article/4a244436a2503585fbd2042e0e364579c94d853ba050a544c0df9191ae07767e/ urn:sha256:4a244436a2503585fbd2042e0e364579c94d853ba050a544c0df9191ae07767e <p>No abstract is available.</p><p class="metadata"><time datetime="2026-06-02" title="Source date; precision not specified">June 2, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v3/decision1">Original publication</a></p> Tue, 02 Jun 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/7842307248fe5ac5d2515d7fa7a98b7f364a77f0d61a4ac30db1eb0c8e4abba4/ urn:sha256:7842307248fe5ac5d2515d7fa7a98b7f364a77f0d61a4ac30db1eb0c8e4abba4 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-06-01" title="Source date; precision not specified">June 1, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v3/response1">Original publication</a></p> Mon, 01 Jun 2026 00:00:00 GMT Zongan Wang Yuqian Liu Tao Zeng Denghui Li Xiao Shi Jiawen Zhang Hao Wang Liuxin Shi Jiayuan Zhang Yinqi Bai Yuning Zhang Yuliang Dong OpenAlex https://reading.michaelmvh.com/article/e1ad140eab4379cdfa365c4320a70f86d6ff61cd652be065cac3a62930ab3ca2/ urn:sha256:e1ad140eab4379cdfa365c4320a70f86d6ff61cd652be065cac3a62930ab3ca2 <p>ABSTRACT Biotoxins produced by cyanobacteria, marine dinoflagellates, and fungi increasingly threaten water quality, food safety, and human health. Many toxins are still monitored primarily by sensitive laboratory techniques such as liquid chromatography–tandem mass spectrometry (LC‐MS/MS) or immunoassays (e.g., ELISA), which are often time‐consuming, require extensive sample preparation, can suffer from cross‐reactivity and possess limited specificity for small molecules. Biosensors offer a complementary approach by combining selective recognition elements with miniaturized transducers to deliver rapid, portable, and potentially multiplexed detection. In this review, we evaluate recent biosensor developments that use antibodies, nucleic acids, proteins, peptides, aptamers, nanopores, molecularly imprinted polymers and cells coupled to optical, electrochemical, and mass‐sensitive transducers for detecting toxins such as microcystins, tetrodotoxin, saxitoxin, aflatoxins, and deoxynivalenol. We focus on analytical performance (limits of detection, dynamic range, response time), validation in complex matrices, and practical readiness for field deployment and briefly discuss how artificial intelligence will play an important role for the development of the next generation of biosensors.</p><p class="metadata"><time datetime="2026-06-01" title="Source date; precision not specified">June 1, 2026</time> <span aria-hidden="true"> · </span> Advanced Sensor Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/adsr.70174">Original publication</a></p> Mon, 01 Jun 2026 00:00:00 GMT Alissa Agerova Juan F. Bada Juarez Matteo Dal Peraro OpenAlex https://reading.michaelmvh.com/article/867b115078a8bdc57b763dffd967ab6b499f72dc3d66da80b11b2e6350d293c6/ urn:sha256:867b115078a8bdc57b763dffd967ab6b499f72dc3d66da80b11b2e6350d293c6 <p>The rapid expansion of aquaculture has made aquatic animal health management increasingly complex. Disease outbreaks are no longer driven by pathogens alone; they emerge from interactions among the cultured host, the rearing environment, farm management practices, and microbial communities. Conventional diagnostic methods remain indispensable, but they often identify disease only after visible signs, mortality, and economic losses have already occurred. A more sustainable approach requires a shift from reactive treatment to predictive health management. This chapter examines how real-time environmental sensing, Internet of Things-enabled monitoring, artificial intelligence, non invasive pathogen molecular surveillance, diagnostics, rapid vaccination, microbiome-directed nutrition, and antibiotic sparing interventions can be integrated into a unified health-management framework. Particular attention is given to environmental DNA and RNA surveillance, nanopore sequencing, biosensors, CRISPR-based diagnostics, probiotics, prebiotics, synbiotics, bacteriophages, phytobiotics, antimicrobial peptides, and nanotechnology-based delivery systems. The practical value of these tools depends not only on scientific novelty, but also on their reliability, affordability, biosafety, and suitability for farm-level implementation. Sustainable aquatic animal health management will therefore require an integrated strategy that links early warning, prevention, targeted continuous verification.</p><p class="metadata"><time datetime="2026-06-01" title="Source date; precision not specified">June 1, 2026</time> <span aria-hidden="true"> · </span> Iterative International Publishers eBooks</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.58532/nbennur3218c13">Original publication</a></p> Mon, 01 Jun 2026 00:00:00 GMT Muneshwar Pavankalyan Suraj Kumar Muneshwar Tejashwini Sonam Kamlakar Tijare OpenAlex https://reading.michaelmvh.com/article/8ad403baa45783d453609bdcf84a82b33b4060ca20707b86f416890f909436cb/ urn:sha256:8ad403baa45783d453609bdcf84a82b33b4060ca20707b86f416890f909436cb <p>ABSTRACT Solid‐state nanopores are pivotal for next‐generation single‐protein detection, yet reconciling high fabrication efficiency, precision, and signal quality remains challenging. In this study, we integrate pyramidal silicon nanopores—valued for electric field focusing and high capture efficiency—with a silicon dioxide (SiO 2 ) layer designed to minimize nonspecific protein adsorption. This strategy aims to balance rapid translocation rates with clear blockade signals. Furthermore, we have developed a large‐scale fabrication method capable of producing uniformly arranged silicon‐based pyramidal nanopores with diameters below 10 nm. This technique combines wet etching, real‐time ionic current monitoring, and thermal oxidation, enabling precise size control down to 7 nm. We evaluated 7 nm, 12 nm, and 14 nm nanopores for detecting α‐synuclein (α‐syn), immunoglobulin G (IgG), and ferritin (FTN), respectively. All nanopore sizes achieved efficient target detection, yielding resolvable blockade signals alongside high capture rates and fast translocation speeds. Notably, α‐syn detection demonstrated improved overall performance in terms of event rate, signal quality, and blockade signal resolution, with similarly effective results observed for IgG and FTN. These results demonstrate the strong potential of this nanopore platform for protein detection.</p><p class="metadata"><time datetime="2026-05-29" title="Source date; precision not specified">May 29, 2026</time> <span aria-hidden="true"> · </span> Advanced Functional Materials</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/adfm.76232">Original publication</a></p> Fri, 29 May 2026 00:00:00 GMT Liang Cheng 蔡初浩 Zhishan Yuan Li Ma Maoxiang Hou Huilong Liu Yu Xiao Mengjie Zheng Yun Chen X Chen Ching‐Ping Wong OpenAlex https://reading.michaelmvh.com/article/196c4d638fb8af40d546c1db9172061687e0c113d860703c53c155f6cc8a914d/ urn:sha256:196c4d638fb8af40d546c1db9172061687e0c113d860703c53c155f6cc8a914d <p>Abstract Temperature is a fundamental yet underexploited control parameter in nanopore-based single-molecule sensing, critically influencing ionic transport, molecular dynamics, and biomolecular interactions. Despite its importance, precise temperature control remains challenging in nanopore experiments, as thermal regulation often introduces electrical noise, limits measurement bandwidth, or requires bulky and complex system integration. Here, we present a localized, chip-level Peltier-based thermal regulation platform integrated with glass nanopore sensing that overcomes these limitations. The system enables rapid and reversible temperature modulation from − 10 to 50 °C while maintaining exceptionally low electrical noise, with root-mean-square current fluctuations of only a few picoamperes, even at elevated temperatures. Combined with an effective bandwidth of 50 kHz and a sampling rate of 1 MHz, the platform supports high-fidelity nanopore recordings under tunable thermal conditions. We demonstrate temperature-dependent control of molecular translocation kinetics, signal amplitude, and temporal resolution using structured DNA carriers. This approach establishes a simple and scalable strategy for temperature-controlled, high-bandwidth single-molecule sensing, with broad implications for nucleic acid analysis, protein transport, and nanopore-based chemical and biophysical studies.</p><p class="metadata"><time datetime="2026-05-29" title="Source date; precision not specified">May 29, 2026</time> <span aria-hidden="true"> · </span> Journal of Analysis and Testing</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1007/s41664-026-00462-6">Original publication</a></p><p><a href="https://link.springer.com/content/pdf/10.1007/s41664-026-00462-6.pdf">Open PDF</a></p> Fri, 29 May 2026 00:00:00 GMT Yunxuan Li Gerardo Patiño‐Guillén Filip Bošković Thieme T. Schmidt Simon Brauburger Raluca‐Elena Alexii Ulrich F. Keyser OpenAlex https://reading.michaelmvh.com/article/d57512a12f961d9f02d577023b74422a82da0a47b8c22e8a18de0c9b8c2bf01d/ urn:sha256:d57512a12f961d9f02d577023b74422a82da0a47b8c22e8a18de0c9b8c2bf01d <p>Surface-Enhanced Raman Spectroscopy (SERS) is a robust technique for molecular analysis, using metallic nanostructures to intensify Raman signal. In this work, we propose a 128 × 1 SPAD camera to perform protein sequencing through SERS, employing plasmonic nanopores to achieve amplification of the Raman signal. We quantitatively discuss the enhancement of the camera Photon Detection Efficiency with the use of a custom microlens array and assess the spectral resolution of the system. We demonstrate how the presented setup can already be used to optically detect single molecule translocation through the nanopore at 10 μs time resolution, and how a robust Raman fingerprint of the translocating molecule can be obtained. We also propose an innovative strategy to improve signal intensity based on real-time translocation detection and suggest the use of the camera gating capability for fluorescence reduction. Our future work will include the validation of these solutions to enable progress toward single-molecule sequencing.</p><p class="metadata"><time datetime="2026-05-29" title="Source date; precision not specified">May 29, 2026</time> <span aria-hidden="true"> · </span> Biomedical Spectroscopy, Microscopy, and Imaging</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1117/12.3098970">Original publication</a></p> Fri, 29 May 2026 00:00:00 GMT Veronica Storari Clarissa Terragni Francesco Difato Francesco Tantussi Jannis Weinacker Martin Wegener Francesco De Angelis Federica Villa OpenAlex https://reading.michaelmvh.com/article/e9b67dd4d1337ec6115ba0ce2605dc48728cf230166c718a03374e3753e6b560/ urn:sha256:e9b67dd4d1337ec6115ba0ce2605dc48728cf230166c718a03374e3753e6b560 <p>This study combines Oxford Nanopore (ONT) third-generation sequencing with targeted amino acid metabolomics to elucidate the mechanisms underlying the structural and metabolic responses of the microbial community in Golden Ear Mushroom (Naematelia sinensis) during Trichoderma infection. By comparing healthy tissue (MOCK), adjacent healthy areas (HAF) and the core lesion area (DiR), the results indicate that pathogen infection significantly reduces bacterial community diversity, with a progressive decline observed across these regions. In the DiR region, the fungal community underwent significant restructuring, with the abundance of the Trichoderma genus (T. lixii and T. afroharzianum) rising to over 45%, whilst that of host symbiotic fungi (Stereum and Tremella) decreased by 50–60%. Metabolomic analysis indicated that levels of various amino acids and antioxidant-related metabolites were significantly reduced in the host tissue of the DiR region, suggesting that amino acid metabolism was inhibited. Concurrently, changes were observed in certain metabolites associated with nitrogen metabolism (e.g., L-glutamine). KEGG analysis further revealed that amino acid biosynthesis and D-amino acid metabolic pathways were inhibited, whilst ABC transporters and arginine/proline metabolic pathways were activated. All metabolic changes originated from the host fungal tissue itself, rather than from commensal microorganisms. In summary, Trichoderma may promote the infection process by disrupting the host microbial community and metabolic networks, providing a theoretical basis for understanding the mechanisms of fungal diseases and their control.</p><p class="metadata"><time datetime="2026-05-28" title="Source date; precision not specified">May 28, 2026</time> <span aria-hidden="true"> · </span> Foods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/foods15111912">Original publication</a></p> Thu, 28 May 2026 00:00:00 GMT Yijing Xu Yu Huang Lei Ye Jiang Yu Zhengzhu Huang Xuezhen Yang Qing Tian Bo Zhang Yuntao Liu Xiaolin Li OpenAlex https://reading.michaelmvh.com/article/e6c6d5ec483d8c0c81ec26b8f7c7fa1930d2bd076940cd39f26020ba2644ea96/ urn:sha256:e6c6d5ec483d8c0c81ec26b8f7c7fa1930d2bd076940cd39f26020ba2644ea96 <p>Inspired by nanopore sequencing technology, we developed a plasmonic device capable of operating in a flow-through configuration to detect individual molecules as they pass through the plasmonic hotspot. This device consists of permeable plasmonic films, through which single molecules are sequentially delivered via electrophoresis, while Raman spectra are recorded in real time. We successfully captured the Raman spectra of the four DNA nucleotides as well as multiple amino acids while passing through the nanopores at single monomer level with time resolution down to 10us. For nucleotides we achieved a discrimination accuracy of 89% at single molecole level and of 99.9% for few tens of translocations. Also, we demonstrated a spatial resolution on the order of a few angstroms, suggesting clear potential for Raman based identification and sequencing of nucleic acids and proteins.</p><p class="metadata"><time datetime="2026-05-26" title="Source date; precision not specified">May 26, 2026</time> <span aria-hidden="true"> · </span> SPIE Nanophotonics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1117/12.3098306">Original publication</a></p> Tue, 26 May 2026 00:00:00 GMT Francesco De Angelis OpenAlex https://reading.michaelmvh.com/article/51c6c7a675404b2a250b778729ef2e6a94ad18788bd85b1a52bda7b3bf563ee4/ urn:sha256:51c6c7a675404b2a250b778729ef2e6a94ad18788bd85b1a52bda7b3bf563ee4 <p>Abstract Controlling molecular transport across membranes is a defining feature of living cells, yet replicating this functionality in synthetic systems remains a major challenge. Self-inserting protein nanopores, such as α-hemolysin (αHL), offer a promising route towards programmable membrane permeability due to their robust assembly, compatibility with diverse membrane systems, and intrinsic permeability for diverse biomolecules. Here, we explored the use of chemically functionalized αHL nanopores as tunable transport modules. To quantify translocation of peptide substrates across αHL-containing membranes, we developed a high-throughput luminescence-based breakage-controlled assay using large unilamellar vesicles. With this assay we introduce a one-pot nanopore modification and strategy, compatible with scalable workflows. Electrophysiology and molecular simulations demonstrate that the introduction of cysteine residues at defined pore locations, combined with targeted chemical modification, enables controlled tuning of αHL-nanopore selectivity based on peptide structure and charge. Together, these findings position engineered protein nanopores as versatile and responsive components for controlling membrane transport in synthetic biology.</p><p class="metadata"><time datetime="2026-05-26" title="Source date; precision not specified">May 26, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.05.26.727826">Original publication</a></p> Tue, 26 May 2026 00:00:00 GMT Elisabeth Bobkova Anastasia Goetz Frank Abendroth Olalla Vázquez Zakarya Benayad Viktorija Dujmović Luis F. Gutiérrez-Mondragón Scott A. Scholz Gerhard Hummer Tobias J. Erb OpenAlex https://reading.michaelmvh.com/article/6a5171bee7e11e1d2e8cb2a80c41dd2e76c489f1ad740156783aef516ede38ca/ urn:sha256:6a5171bee7e11e1d2e8cb2a80c41dd2e76c489f1ad740156783aef516ede38ca <p>This paper extends the Maxwell–Scretching Chain (MSC) from its established use in UV–visible DNA spectroscopy into nanopore sequencing, single-molecule biosensing, and ionic-current molecular detection. In classical nanopore systems, individual DNA, RNA, proteins, or other biomolecules are detected by changes in pore current, dwell time, charge-mediated translocation behavior, and local dielectric-field perturbations as each molecule passes through or interacts with the nanopore sensing region. This manuscript proposes that these measurable nanopore signals can be interpreted not only as empirical current-blockade events, but also as electromagnetic response signatures governed by molecular oscillator strength, dielectric loss, polarizability, charge screening, molecular size, and sequence composition. The central contribution of the paper is the development of a Maxwell–Scretching nanopore closure model in which each nucleotide or biomolecule is treated as an electromagnetic perturbing body inside the nanopore field. The model introduces a dimensionless Scretching Nanopore Response Index, Ψ_NP,i, designed to combine molecular optical-electromagnetic properties with nanopore-specific transport variables. This index provides a proposed bridge between molecular composition and experimentally observed nanopore readout quantities, including ionic-current blockade amplitudes, dwell-time variation, and field-dependent translocation signatures. A linear nanopore closure equation, ΔI_i = I₀ · k_NP · Ψ_NP,i, is proposed as the first-order response law, where ΔI_i represents the nucleotide- or biomolecule-specific current change, I₀ is the open-pore baseline current, k_NP is an instrument- and pore-dependent proportionality coefficient, and Ψ_NP,i is the Maxwell–Scretching nanopore response index for molecular species i. The paper applies the proposed relation to illustrative nanopore datasets and explains how deviations from linearity may arise from pore geometry, electrolyte composition, molecular orientation, stochastic translocation dynamics, secondary structure, hydration, and surface-charge interactions. The manuscript also identifies experimental validation targets, including controlled nucleotide standards, sequence-resolved current-blockade libraries, protein nanopore comparisons, solid-state nanopore measurements, and calibration studies linking dielectric and optical molecular properties to nanopore current signatures. The model does not claim to replace existing nanopore sequencing theory; rather, it adds a Maxwell–Scretching electromagnetic closure layer that may help interpret why different nucleotides and biomolecules produce distinguishable electrical signatures. The paper concludes by outlining future experimental confirmation paths and the limitations that must be addressed before the proposed Ψ_NP,i closure can be treated as a predictive nanopore biosensing law._ https://www.youtube.com/@ScretchingQuantumPressLLC https://scretching-quantum-press-research.scretching08.chatgpt.site/</p><p class="metadata"><time datetime="2026-05-24" title="Source date; precision not specified">May 24, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.20367443">Original publication</a></p> Sun, 24 May 2026 00:00:00 GMT Daniel Scretching OpenAlex https://reading.michaelmvh.com/article/7f9fc8d48c334cd0f6b2d1253c36a0b99ec1955c4ed7308aceb086289a34ae20/ urn:sha256:7f9fc8d48c334cd0f6b2d1253c36a0b99ec1955c4ed7308aceb086289a34ae20 <p>Creating alternative nanopores is crucial for advancing single-molecule methodologies. Peptide nanopores scaffolded by DNA nanostructures have emerged as a promising class of chemically synthesizable nanopores with organized geometries. However, no such nanopores have yet achieved single-molecule detection due to size limitations. Here, we overcome this limitation by employing the alamethicin (ALM) peptide, based on the hypothesis that peptides with looser helix-helix packing are advantageous for constructing large-diameter nanopores. The resulting DNA-ALM nanopores exhibited long-lived open states and conductance values comparable to those of natural protein nanopores. To further enhance pore functionality, we introduced asymmetric electrostatic forces by harnessing the intrinsic helix dipole of ALM, which facilitated pore expansion and improved ion transport efficiency. This modification led to enhanced conductance levels and enabled single-molecule sensing of biomolecules, including DNA and peptides. Overall, this work demonstrates a generalizable strategy for constructing functional, chemically synthesizable nanopores, providing a foundation for programmable nanopore design and next-generation biosensing applications.</p><p class="metadata"><time datetime="2026-05-22" title="Source date; precision not specified">May 22, 2026</time> <span aria-hidden="true"> · </span> Angewandte Chemie International Edition</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/anie.3311099">Original publication</a></p> Fri, 22 May 2026 00:00:00 GMT Zugui Peng Daisuke Noshiro Shiroh Futaki Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/2ae29d8d77ff737f2899aa0dff4f05e13ee10261c3ce7152072519f441a6f56e/ urn:sha256:2ae29d8d77ff737f2899aa0dff4f05e13ee10261c3ce7152072519f441a6f56e <p>Abstract Direct single-molecule peptide analysis could in principle enable rapid and sensitive identification of pathogen-derived or disease-associated biomarkers without reliance on mass spectrometry. However, existing nanopore peptide sensing methods are typically constrained by limited throughput and lack of accessibility beyond specialized setups. Here, we present an integrated experimental-computational framework for DNA-linked peptide translocation on a commercially available, high-throughput nanopore sequencing platform, the MinION. Synthetic peptides were covalently bound to oligonucleotides at both termini. The resulting peptide-DNA constructs were then translocated through the CsgG-CsgF pores using a DNA motor protein. Current traces were segmented using the known DNA sequences to extract peptide-associated signal regions. From these segments, we extracted signal features and trained feature-based and deep-learning classifiers to distinguish peptides, balancing interpretability and classification performance. We establish a framework for peptide identification using standard nanopore sequencing hardware. Across a diverse panel of synthetic peptides, our approach resolves single-amino-acid substitutions, maintains performance across independent sequencing runs, and correctly identifies peptides in blind mixtures. Interpretable model analyses connect classifier decisions and common errors to specific signal motifs. By combining commercially available instrumentation with a reproducible experimental and computational workflow, this framework lowers the barrier to nanopore-based proteomics and enables broader adoption across laboratories. It provides a foundation for future developments in amino acid modification detection and sequence analysis.</p><p class="metadata"><time datetime="2026-05-21" title="Source date; precision not specified">May 21, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/bioinformatics" rel="external">bioRxiv: Bioinformatics</a></p><p class="provenance">Curated by <a href="https://github.com/Michaelmvh/scholarly-rss-feed/blob/main/src/curated/nanopore-foundations.json" rel="external">Nanopore Foundations &amp; Signal Analysis</a> · DNA-motor-driven transport · Identification · Preprint · Protein analysis</p><p><a href="https://doi.org/10.64898/2026.05.19.726067">Original publication</a></p> Thu, 21 May 2026 00:00:00 GMT Denis Beslic Martin Kucklick Eric Graap Somayyeh Sedaghatjoo Bernhard Y. Renard Stephan Fuchs Susanne Engelmann Nils Körber OpenAlex bioRxiv: Bioinformatics Nanopore Foundations & Signal Analysis https://reading.michaelmvh.com/article/3733b9189c7f98318792b1b5196bf52e57635906a54f91ae13015bdd63203e38/ urn:sha256:3733b9189c7f98318792b1b5196bf52e57635906a54f91ae13015bdd63203e38 <p>Post-translational modifications (PTMs) play essential roles in regulating protein structure, function, and cellular signalling. However, peptide level discrimination of hydroxylation at the single-molecule level remains difficult. Here, we report a particle-in-pore single-molecule surface-enhanced Raman spectroscopy (SERS) platform combined with peak occurrence frequency (POF) analysis and a one-dimensional convolutional neural network (1D-CNN) for discriminating hydroxylated and non-hydroxylated HIF peptide fragments. Three peptide pairs containing the Pro-564 hydroxylation site, with lengths of 7, 9, and 15 amino acids (AAs), were investigated. POF analysis revealed reproducible hydroxylation-dependent spectral changes in the 7AA and 9AA peptide pairs, which were attributed to changes in adsorption conformation and surface interactions. CNN-based classification achieved post-evaluation accuracies of 72.98%, 78.55%, and 89.74% for the 7AA, 9AA, and 15AA peptide pairs, respectively, with AUC values above 0.80 for all the pairs, indicating a reliable discrimination. Gradient-weighted feature visualization further showed that CNN-sensitive regions overlapped with recurrent POF features, supporting the chemical relevance of the learned classification patterns. Notably, for the 15AA peptide pair, the enhanced citrate-associated band suggests that hydroxylation can substantially alter peptide-gold nanoparticle adsorption behaviour. This adsorption-mediated effect may amplify hydroxylation-induced spectral differences and contribute to the improved discrimination accuracy despite the increased structural complexity. These results demonstrate that the particle-in-pore sensor, assisted by deep learning, can capture hydroxylation-induced spectral and adsorption changes in peptide fragments, providing a promising strategy for ultrasensitive analysis of weak PTM signatures in peptides.</p><p class="metadata"><time datetime="2026-05-20" title="Source date; precision not specified">May 20, 2026</time> <span aria-hidden="true"> · </span> arXiv (Cornell University)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.48550/arxiv.2605.21084">Original publication</a></p><p><a href="https://arxiv.org/pdf/2605.21084">Open PDF</a></p> Wed, 20 May 2026 00:00:00 GMT Yingqi Zhao Kuo Zhan Pei-Lin Xin Yuge Liang Enock Adjei Agyekum Matti Putkonen Shuai Li Francesco De Angelis JianAn Huang OpenAlex https://reading.michaelmvh.com/article/eee7ac9d1e7e6a4159771de3124126bfa502b665a329f9d7119b3254d2f7ff0c/ urn:sha256:eee7ac9d1e7e6a4159771de3124126bfa502b665a329f9d7119b3254d2f7ff0c <p>Abstract Cyclin-dependent kinases CDK12 and CDK13 are RNA polymerase II C-terminal domain Ser2 kinases that regulate transcriptional elongation and co-transcriptional RNA processing. Loss-of-function (LOF) mutations in these kinases are observed in multiple cancers and are characterized by increased intronic polyadenylation (IPA), which generates prematurely terminated transcripts and can give rise to novel intronic peptides. To investigate the distinct contributions of CDK12 and CDK13 to suppressing early transcriptional termination, we modeled selective kinase inhibition in OVCAR4 ovarian cancer cells using THZ531, a dual CDK12/13 inhibitor. A CRISPR-engineered CDK12 C1039S mutation conferred THZ531 resistance, enabling functional distinction between CDK12 and CDK13 LOF conditions. Using Poly(A) Click-seq (PACseq) across a six-point inhibitor dose curve, we identified thousands of IPA sites with distinct dose-response behaviors, allowing us to classify CDK12- and CDK13-dependent subsets. Oxford Nanopore long-read sequencing confirmed premature termination events and revealed full-length isoform switches, demonstrating how IPA alters coding potential by truncating protein domains and producing novel, intronically encoded peptide sequences. In parallel, integration of long-read transcriptomes with mass spectrometry data identified peptides derived from IPA isoforms, confirming that intronic sequences can be translated. Together, these findings establish distinct roles for CDK12 and CDK13 in maintaining transcript integrity, demonstrate that IPA transcripts are not only abundant but also translationally competent, and provide evidence for a mechanistic link between transcriptional dysregulation and the generation of novel peptide isoforms in CDK12/13-deficient cancers. These results highlight a potential therapeutic vulnerability through the exploitation of IPA-derived peptides as tumor-specific neoantigens.</p><p class="metadata"><time datetime="2026-05-19" title="Source date; precision not specified">May 19, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.05.15.725461">Original publication</a></p> Tue, 19 May 2026 00:00:00 GMT Molly J. Hulver Andrew Polevoda Kai-Lieh Huang Eric J. Wagner Paul L. Boutz OpenAlex https://reading.michaelmvh.com/article/e4a13f86e91e69bac8165abf48a60d6b9327ca77f30a5fb2b14b7f6f823b1e07/ urn:sha256:e4a13f86e91e69bac8165abf48a60d6b9327ca77f30a5fb2b14b7f6f823b1e07 <p>Abstract N 6 -methyladenosine (m 6 A) is the most abundant modification in eukaryotic mRNA and can influence gene expression, but the molecular mechanisms by which it does this at an individual gene level are poorly understood. The eukaryote with the highest known percentage of adenosine in its RNA is P. falciparum , causative agent of the deadliest form of malaria. P. falciparum has a high genomic AT content (&gt;80% A+T) and a particular A-bias in mRNA - coding strands have an average adenosine content of 44%. Plasmodium parasites employ extensive transcriptional and post-transcriptional control over gene expression to differentiate within and between sexual and asexual stages in response to changing environments and hosts. We used direct Nanopore RNA sequencing and GLORI-seq to interrogate m 6 A methylation of the asexual Plasmodium falciparum transcriptome, revealing m 6 A depletion in protein coding regions relative to the 3’UTR, where m 6 A is deposited in precise patterns approximately 50 nt upstream of the polyadenylation site. We used an inducible protein mislocalisation system to disrupt the methyltransferase, which writes m 6 A to mRNA, and observed m 6 A depletion associated with transcriptional readthrough and chimeric transcripts. We show that m 6 A in transcript 3’UTRs is required for faithful positioning of polyadenylation and transcription termination. This work highlights the importance of m 6 A to mRNA processing in P. falciparum , and potentially a wider role in post-transcriptional regulation.</p><p class="metadata"><time datetime="2026-05-19" title="Source date; precision not specified">May 19, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.05.19.726191">Original publication</a></p> Tue, 19 May 2026 00:00:00 GMT Joshua M Levendis Amy Distiller Selina Mussgnug Lakvin Fernando Steven Lancashire Neil David Young Emma McHugh Sebastian Baumgarten Stuart A. Ralph OpenAlex https://reading.michaelmvh.com/article/8739d0319ba76128b2471a9fa98573b8413c6c130ed3f545aefc56cf2e754c7a/ urn:sha256:8739d0319ba76128b2471a9fa98573b8413c6c130ed3f545aefc56cf2e754c7a <p>Accurately quantifying protein–protein binding at the single-molecule level is essential for understanding the mechanisms of viral infection and therapeutic targeting. Here, we use solid-state nanopores (SSNs) to detect complex formation between the SARS-CoV-2 Spike receptor-binding domain (Spike RBD) and the alternative host receptors KREMEN1 and Asialoglycoprotein Preceptor 1 (ASGR1). Single-molecule translocation events were analyzed using unsupervised Gaussian mixture modeling and a control-anchored semisupervised classification framework to resolve overlapping free-protein and complex populations. This approach enabled direct identification of receptor-Spike RBD complexes and calculation of apparent dissociation constants under experimental conditions. The inferred affinities were 261.1 nM for ASGR1 and 56.6 nM for KREMEN1, in good agreement with reported literature values and can be used as rough estimates on Spike and its receptor affinities. A negative control using human serum transferrin and Spike RBD showed no emergent high-Δ I population, supporting the specificity of the observed interactions. These results establish SSNs as a scalable and quantitative platform for single-molecule affinity measurements.</p><p class="metadata"><time datetime="2026-05-18" title="Source date; precision not specified">May 18, 2026</time> <span aria-hidden="true"> · </span> The Journal of Physical Chemistry B</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.jpcb.6c00286">Original publication</a></p> Mon, 18 May 2026 00:00:00 GMT Matthew O’Donohue Navod Thyashan Min Jun Kim OpenAlex https://reading.michaelmvh.com/article/4fa499f74fd265e857744e2ada0c8679103b1593f356679cbf980813f0afa17d/ urn:sha256:4fa499f74fd265e857744e2ada0c8679103b1593f356679cbf980813f0afa17d <p>Glass nanopores have emerged as a promising single-molecule sensing platform due to their low intrinsic noise, facile fabrication, and excellent integrability. The fabrication of glass nanopores with diameters down to 1-3 nm, a scale comparable to nucleic acids and peptides, is a critical step toward high-resolution fingerprinting or event sequencing of these molecules, yet it remains a significant challenge. Here, it has overcome this obstacle by direct fabrication of ~2 nm glass nanopores, exemplified by the detection of double-stranded DNA (dsDNA) with an exceptional signal-to-noise ratio (SNR), exhibiting over 80% ionic current blockade. Furthermore, we demonstrate the discrimination of dsDNA as short as 40 base pairs (bp), the differentiation of single-stranded DNA (ssDNA) homopolymers (40 nucleotides). Finally, it is further highlighted that remarkably superior resolution successfully detects a DNA topological structure containing a 40-nucleotide (nt) gap within dsDNA, a feature that is extremely challenging to resolve using larger-diameter glass nanopores. This work marks a milestone in glass nanopores and paves the way for high-resolution biomolecular sensing, fingerprinting, and even sequencing.</p><p class="metadata"><time datetime="2026-05-17" title="Source date; precision not specified">May 17, 2026</time> <span aria-hidden="true"> · </span> Small</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smll.73779">Original publication</a></p> Sun, 17 May 2026 00:00:00 GMT Xiaoyu Chen Yaxian Liu Fan Zhang An Li Y T Li Ran Ji Rui Hu Xianhu Sun Kaikai Chen OpenAlex https://reading.michaelmvh.com/article/843618ef36d4a1cb0f0d0e599bd5ad3ae7dd0fb7247f39175ea0c9cef959f545/ urn:sha256:843618ef36d4a1cb0f0d0e599bd5ad3ae7dd0fb7247f39175ea0c9cef959f545 <p>Genomic approaches have provided detailed insight into DNA-protein interactions and chromosome architecture. However, commonly deployed techniques do not preserve connectivity-based information, leaving large-scale genome organization poorly characterized. Here, we develop npDamID, an in vivo proximity-labeling technique that indelibly marks and then decodes protein-associated sites. npDamID tethers dam methyltransferase to a protein of interest, followed by Nanopore sequencing to identify methylated bases along reads &gt;100 kb. As proof-of-concept, we analyze, in budding yeast, a conserved cohesin-based meiotic backbone that organizes chromatin into an array of loops. Our data recapitulate the pertinent features of known cohesin association patterns and, importantly, expose variability between cells. Analysis of single reads reveals distance-dependent short- and long-range correlation between adjacent methylated bases. Finally, an important advantage of our approach is the ability to define protein association patterns in repetitive regions. By anchoring ultra-long reads onto unique regions, we define in vivo cohesin association patterns within the ribosomal DNA locus. Our versatile technique promises to illuminate diverse chromosomal processes by providing a cumulative record of heterogeneous association patterns of chromosomal factors as well as the in vivo conformations of single chromosomes.</p><p class="metadata"><time datetime="2026-05-17" title="Source date; precision not specified">May 17, 2026</time> <span aria-hidden="true"> · </span> Journal of genetics and genomics/Journal of Genetics and Genomics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.jgg.2026.05.004">Original publication</a></p> Sun, 17 May 2026 00:00:00 GMT Kewei Xu Yichen Zhang James G. Baldwin-Brown Thomas A. Sasani Nitin Phadnis Matthew P. Miller Ofer Rog OpenAlex https://reading.michaelmvh.com/article/214cfa017d23480eb9860c7aa2b8a12427701c4982582b226e26677d85b3107e/ urn:sha256:214cfa017d23480eb9860c7aa2b8a12427701c4982582b226e26677d85b3107e <p>No abstract is available.</p><p class="metadata"><time datetime="2026-05-15" title="Source date; precision not specified">May 15, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v2/decision1">Original publication</a></p> Fri, 15 May 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/1f4c8bcc4ef56c07c1045fe54940947f6d22799b231e4cdd515520363423a0dc/ urn:sha256:1f4c8bcc4ef56c07c1045fe54940947f6d22799b231e4cdd515520363423a0dc <p>High Resolution Image Download MS PowerPoint Slide In the rapidly evolving field of single-molecule sensing, solid-state nanopores have emerged as transformative tools for the label-free detection of biomolecules, ranging from DNA polymers to proteins. Yet, with two dominant platforms─glass nanopores and silicon nitride (SiN x ) nanopores─researchers face a pivotal choice: which architecture best unlocks superior performance? Here, we deliver a head-to-head experimental comparison under comparable experimental conditions, benchmarking noise characteristics, signal-to-noise ratios (SNRs), and translocation dynamics for DNA and protein analytes across matched nanopore sizes. Our findings reveal compelling trade-offs: glass nanopores excel in DNA sensing, achieving record SNR values of &gt;80 in 5 nm nanopores (4 M LiCl, 50 kHz filter cutoff) due to their conical geometry that focuses electric fields. In contrast, SiN x nanopores dominate protein detection with SNR values of &gt;120, leveraging thin membranes for enhanced current blockade from volume exclusion. Comprehensive performance metrics─including unfolded DNA fraction, backward-to-forward translocation time ratio, translocation frequency, and perturbed events─also show distinct translocation behaviors of biomolecules in the two nanopore platforms. These insights, supported by finite-element simulations, establish a mechanistic framework for nanopore selection, favoring conical glass nanopores for polymeric analytes and SiN x membrane nanopores for compact biomolecules. This work not only sets benchmarks for nanopore sensitivity but also enables the development of tailored sensors in diagnostics, sequencing, and beyond, advancing nanotechnology for high-resolution biomolecular analyses.</p><p class="metadata"><time datetime="2026-05-05" title="Source date; precision not specified">May 5, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.6c03089">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acsnano.6c03089?ref=article_openPDF">Open PDF</a></p> Tue, 05 May 2026 00:00:00 GMT Fei Zheng Zhan Wang An Bai Rui Hu Xianhu Sun Jingjie Sha Qing Zhao Kaikai Chen Ulrich F. Keyser OpenAlex https://reading.michaelmvh.com/article/ea34045c04f09578dbf67d874d47f2ff951c3f8b2d44688c161a17faf52ab463/ urn:sha256:ea34045c04f09578dbf67d874d47f2ff951c3f8b2d44688c161a17faf52ab463 <p>BACKGROUND: Capnocytophaga canimorsus (C. canimorsus) is a zoonotic pathogen transmitted by dogs and cats that can cause severe infections in humans. Antimicrobial susceptibility data remain limited, but increasing genomic evidence suggests that functional β-lactamase genes may be more widespread than previously recognized. METHODS: Three C. canimorsus isolates harboring class D β-lactamase genes were selected by genomic screening from a larger collection of the Global Capnocytophaga Consortium for detailed characterization: two isolates from human clinical infections from Sweden and New Zealand, and a commensal canine isolate from the Czech Republic. We used hybrid Illumina-Nanopore genome assemblies, phylogenetic analysis, and structural modeling to characterize the genomic context and the predicted protein features of the β-lactamase genes. The functional impact of the β-lactamases on antibiotic activity was assessed by minimum inhibitory concentration (MIC) testing and confirmed through recombinant expression in the β-lactamase-negative reference strain C. canimorsus 5 (Cc5). RESULTS: , in another clinical isolate. Both β-lactamases were chromosomally encoded without clear mobile genetic elements and were part of a distinct phylogenetic cluster within the OXA family. Structural modeling showed conserved class D β-lactamase architecture. Strains carrying either gene had elevated MICs for multiple β-lactams, and expression of each gene in Cc5 recapitulated these effects. CONCLUSIONS: The identification and phenotypic characterization of OXA-type β-lactamases in clinical C. canimorsus isolates refine our understanding of β-lactamase diversity in this species and underscore the need for systematic investigations of β‑lactamase prevalence in this zoonotic pathogen.</p><p class="metadata"><time datetime="2026-05-05" title="Source date; precision not specified">May 5, 2026</time> <span aria-hidden="true"> · </span> European Journal of Clinical Microbiology &amp; Infectious Diseases</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1007/s10096-026-05526-0">Original publication</a></p><p><a href="https://link.springer.com/content/pdf/10.1007/s10096-026-05526-0.pdf">Open PDF</a></p> Tue, 05 May 2026 00:00:00 GMT Zoja Germuskova Eleonora Pronzini Fanny Wegner Tim C. Roloff Tianyan Song Miroslava Barančeková Alois Čížek Michael Addidle Murray Robinson Marc Dieu Chaitanya Tellapragada Christian G. Giske Kirstine K. Søgaard Els M. Broens Francesco Renzi Adrian Egli OpenAlex https://reading.michaelmvh.com/article/9e1d0c33168c8baa2664ecd3d036f1e4975c80681910f13ab7d8bbcb4a124c40/ urn:sha256:9e1d0c33168c8baa2664ecd3d036f1e4975c80681910f13ab7d8bbcb4a124c40 <p>Background: Food-service surfaces in dense urban settings act as reservoirs for Enterobacteriaceae, and routine alkaline sanitation may select for pH-tolerant organisms. Enterobacter bugandensis has emerged as a multidrug-resistant pathogen, yet its recovery from food-contact surfaces in South Asian settings remains poorly characterised. Objective: To isolate alkali-tolerant bacteria from high-contact dining surfaces in Lahore, Pakistan, and computationally evaluate the haemolysin-coregulated protein (Hcp) of the Type VI secretion system and the heme transporter ChuA as candidate inhibitor targets. Methods: In this cross-sectional laboratory-based study, sterile swabs were collected from high-contact surfaces in thirty restaurants. Isolates were recovered on nutrient agar, screened across pH 7–10, and characterised by staining, biochemical profiling, and bidirectional 16S rRNA Sanger sequencing. Phylogeny was inferred in MEGA X. Hcp and ChuA were modelled by SWISS-MODEL and validated by Ramachandran and MolProbity analysis. Binding pockets were predicted by PrankWeb. Three matrix metalloprotease inhibitors were docked into Hcp and five heme analogues into ChuA using CB-Dock2 (AutoDock Vina), ranked by predicted binding energy. Results: A dominant alkali-tolerant Gram-negative bacillus grew sustainably at pH 10. Biochemical profile matched Enterobacter; 16S rRNA BLASTn returned closest identity to Enterobacter bugandensis (96.12%). The Hcp model achieved GMQE 0.92 with 98.39% favoured Ramachandran residues. Ilomastat returned the most favourable Hcp binding energy (–6.3 kcal/mol), engaging R26, D25, and Y99. Mn(III) and Ru(III) protoporphyrin IX both yielded –7.4 kcal/mol against ChuA, though template and ligand-identity limitations restrict interpretation. Conclusion: An alkali-tolerant Enterobacter closely related to E. bugandensis persisted on routinely cleaned dining surfaces, indicating that conventional sanitation may inadequately eliminate clinically relevant Enterobacteriaceae. Ilomastat emerged as a candidate Hcp inhibitor; ChuA findings require re-validation. Routine molecular surveillance of food-contact surfaces is warranted.</p><p class="metadata"><time datetime="2026-05-03" title="Source date; precision not specified">May 3, 2026</time> <span aria-hidden="true"> · </span> Journal of Health Wellness and Community Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.61919/zhzayt81">Original publication</a></p><p><a href="https://jhwcr.com/index.php/jhwcr/article/download/1541/1498">Open PDF</a></p> Sun, 03 May 2026 00:00:00 GMT Anam Amir Ayesha Ahmed Bisma Ali Anam Amar Haleema Sadia Mamona Imran OpenAlex https://reading.michaelmvh.com/article/1860cf3a9c393d402c2564b5c585606752f793df8443aa39487a7f955a9c6963/ urn:sha256:1860cf3a9c393d402c2564b5c585606752f793df8443aa39487a7f955a9c6963 <p>Deficiency in ELF4, X-linked (DEX) is a monogenic autoinflammatory disorder caused by loss-of-function (LOF) mutations in the ETS transcription factor ELF4. This rare disorder primarily affects young, male patients due to its X-linked expression. To date, the genetic aberrations causing disease in these patients have been (1) nonsense mutations leading to premature stop codons and a loss of ELF4 protein expression, and (2) missense mutations abrogating DNA-binding activity of ELF4. Here, we describe the case of an 11-year-old male harboring a de novo four-nucleotide deletion in the splice donor region following exon 5 (NM_001421.3:c.532+3_532+6del), which was discovered via trio whole-exome sequencing. The patient presented with characteristic DEX symptoms, including periodic fevers, oral ulcers, arthritis, and Crohn’s disease. The mutation was confirmed at the DNA level via nanopore sequencing of the genomic region surrounding exon 5 of ELF4, and subsequent analyses of patient-derived peripheral blood mononuclear cells (PBMCs) revealed a loss of ELF4 protein expression, confirming that this patient suffers from DEX. Predictions of splicing outcomes caused by this variant suggested the possibility of partial intronic retention causing a frameshift and ultimately leading to a premature stop codon. RNA sequencing on patient-derived CD4+ and CD8+ T cell blasts confirmed the predicted splicing outcome, as well as a significant decrease in ELF4 transcript expression, likely due to nonsense-mediated decay. Here, we describe the first DEX patient with a de novo deletion in an intronic region of ELF4 that leads to a loss of ELF4 protein expression and autoinflammatory disease.</p><p class="metadata"><time datetime="2026-05-01" title="Source date; precision not specified">May 1, 2026</time> <span aria-hidden="true"> · </span> Journal of Human Immunity</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.70962/cis2026abstract.120">Original publication</a></p> Fri, 01 May 2026 00:00:00 GMT Bradly M. Bauman Dinesh Babu Uthaya Kumar Arati Khanna‐Gupta Marat Kribis Amber Hogart Begtrup Ellory Lopez Carrie Lucas OpenAlex https://reading.michaelmvh.com/article/2fc1811d4cfb267e4e9c7fafb6a2d008d13c8988246e19974e0e7456850b7fe9/ urn:sha256:2fc1811d4cfb267e4e9c7fafb6a2d008d13c8988246e19974e0e7456850b7fe9 <p>糖肽类抗生素的残留检测对保障食品安全与临床合理用药至关重要。为解决现有检测方法前处理复杂、灵敏度不足或难以实现多残留同步检测等问题，本研究构建了一种基于仿生多肽探针OctaDE-A2与α-溶血素纳米孔的免标记传感新策略。该探针C端模拟肽聚糖前体的D-Ala-D-Ala结构域，可特异性结合糖肽类抗生素；N端负电荷区域则驱动复合物穿越纳米孔，产生特征性阻塞信号。通过系统优化电解质成分与工作电压，显著提升了信噪比与事件分辨率。利用该方法，我们成功实现了对万古霉素、替考拉宁和达巴万星的单分子检测，其检测限分别低至3.28、2.37和16.14 nM。更重要的是，凭借不同糖肽类抗生素-探针复合物所产生的独特阻塞幅度与滞留时间“指纹”信号，本研究在单次检测中完成了对三种糖肽类抗生素的同步区分与定量分析。在牛奶样本的加标回收实验中，回收率达80.957%~117.640%，证实了该策略在加标回收检测中的可靠性。本工作基于仿生多肽探针的纳米孔传感平台结合简便样品前处理，在去除干扰物后实现了牛奶中多种糖肽类抗生素的高灵敏检测，为食品安全与临床监测提供了新技术。</p><p class="metadata"><time datetime="2026-05-01" title="Source date; precision not specified">May 1, 2026</time> <span aria-hidden="true"> · </span> Scientia Sinica Vitae</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1360/ssv-2025-0415">Original publication</a></p> Fri, 01 May 2026 00:00:00 GMT Jiaqi Wang Zhuoqun Su Jianing Chen Yue Yang Guoliang Li OpenAlex https://reading.michaelmvh.com/article/5851a10b6338e1f9939473cbee8cdb037cc57a50abd52445a7c0c20fbf96c9ae/ urn:sha256:5851a10b6338e1f9939473cbee8cdb037cc57a50abd52445a7c0c20fbf96c9ae <p>Nanopore is a single-molecule technology for sensing biomolecules. Biomolecular interactions are essential biological processes that govern biological functions and therapeutic responses. However, high-resolution nanopore sensing of biomolecular interactions, such as protein-ligand interactions, remains challenging. In this study, we demonstrate that a YaxAB nanopore with LiCl-modulated electrostatic potential enables detection of molecular interactions of the BRD4 protein with histone peptides, as well as diverse small-molecule drugs, at the single-molecule level. Our electrical recordings and molecular dynamics simulations confirm that the oscillating dynamics of BRD4 within the funneled YaxAB nanopore generate two-level current transitions between narrow- and wide-pore regions. Using the parameters derived from dual-level dynamics and their signal decomposition, a YaxAB nanopore sensing approach enables the sensitive discrimination of BRD4-small-molecule drug complexes with a subtle mass difference as small as 2.5 Da. This near-atomic, high-resolution sensing capability of YaxAB nanopores may enable applications in single-molecule-based drug discovery, proteomics, and diagnostics.</p><p class="metadata"><time datetime="2026-04-28" title="Source date; precision not specified">April 28, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.5c22458">Original publication</a></p> Tue, 28 Apr 2026 00:00:00 GMT Junhyeok Jo Jinsik Kim Sungbo Hwang Ki‐Baek Jeong Seung‐Wook Chi OpenAlex https://reading.michaelmvh.com/article/5a95c45726bc30f6aeeae04a77040c14d1f3fb5c7bcc4acb590c3369e7a6b686/ urn:sha256:5a95c45726bc30f6aeeae04a77040c14d1f3fb5c7bcc4acb590c3369e7a6b686 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-04-24" title="Source date; precision not specified">April 24, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v2/review2">Original publication</a></p> Fri, 24 Apr 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/337b4c53ca25e9b74c6c10fdcff05ad28ae4842eb47e53aaff010e11164e40f2/ urn:sha256:337b4c53ca25e9b74c6c10fdcff05ad28ae4842eb47e53aaff010e11164e40f2 <p>We present a complete zero-parameter theory predicting 14 distinct physical observables from a discrete algebraic structure. Starting from the Pythagorean pair $(N_c, N_{st}) = (3,4)$, we derive the 840-state manifold through the Cassini invariant $|I| = 29$ and construct a prediction formula $\Psi(r;\text{class})$ whose every component is framework-derived. The theory predicts: (i) seven cosmological observables as direct values $\Psi(r)$ at sub-5% precision, (ii) four particle physics couplings as products $\Psi(r_1) \times \Psi(r_2)$ at sub-1% precision, and (iii) three mass ratios and mixing angles as ratios $\Psi(r_1)/\Psi(r_2)$ at sub-1% precision. Statistical significance exceeds $6\sigma$ ($p \approx 10^{-12}$). All results are computationally reproducible with zero free parameters and zero fitting procedures. Keywords: Zero-parameter physics, 840-state manifold, Cassini invariant, cosmological observables, QCD coupling, CKM matrix, discrete algebraic structure 1. Introduction 1.1 The Parameter Problem The Standard Model of particle physics contains 19 free parameters requiring experimental determination. Grand Unified Theories and string theory introduce additional parameters, with the string landscape admitting $\sim 10^{500}$ vacua. The question arises: are fundamental constants independent experimental inputs, or do they encode an underlying mathematical structure? 1.2 The Brahim Framework Approach The Brahim Mechanics framework proposes that dimensionless physical constants emerge from a discrete algebraic structure anchored in two integers: $$N_c = 3 \quad \text{(color charges / spatial dimensions)}$$ $$N_{st} = 4 \quad \text{(spacetime dimensions)}$$ These satisfy the Pythagorean condition: $$N_c^2 + N_{st}^2 = F_5^2 = 25$$ From this starting point, the framework derives: - The Cassini invariant $|I| = 29 = L_7$ (7th Lucas number) - The 840-state manifold from $29^2 - 1 = 840$ - A prediction formula $\Psi(r;\text{class})$ with zero free parameters - 14 verified observable matches at sub-5% precision 1.3 Contributions of This Work This paper presents the complete derivation of the observable prediction theory, including: 1. E-factor formula (Section 2): Derivation of Euler&#39;s number $e$ from Lucas numbers and Brahim Numbers (40 ppm precision) 2. Normalization constant (Section 3): Proof that $\aleph = 1 + m/K$ (17 ppm precision) 3. Class-specific m-values (Section 4): Derivation of mode parameter from residue class structure 4. Observable multiplication table (Section 5): Direct values, products, and ratios encoding 14 distinct observables 5. Statistical analysis (Section 6): Significance exceeding $6\sigma$ 6. Falsifiable predictions (Section 7): Ten testable predictions All components are derived from framework axioms. No parameters are fitted. No optimization is performed. 2. Mathematical Foundations 2.1 Axiom Zero Definition 2.1 (Framework Inputs): The theory has three inputs: $$N_c = 3, \quad N_{st} = 4, \quad K = 107$$ where $K$ is the framework prime satisfying: - 5 is a quadratic residue modulo $K$ - The Pisano period $\pi_K(B) = 72 = 2^3 \cdot 3^2$ - $K$ generates exactly 10 Brahim residues in the B-sequence image modulo $K$ Derived constants: $$\varphi = \frac{1 + \sqrt{5}}{2} = 1.6180339887\ldots \quad \text{(golden ratio)}$$ $$F_5 = 5 = \sqrt{N_c^2 + N_{st}^2} \quad \text{(Pythagorean hypotenuse)}$$ $$|I| = N_c^4 - N_c^2 N_{st} - N_{st}^2 = 81 - 36 - 16 = 29$$ 2.2 The B-Sequence Definition 2.2 (B-Recurrence): Define the sequence $\{B_n\}$ by: $$B_0 = N_c^2 + N_{st} = 13$$ $$B_1 = 2N_c^2 + N_{st} = 22$$ $$B_{n+1} = B_n + B_{n-1} \quad \text{for } n \geq 1$$ This is a Fibonacci-type recurrence with Binet form: $$B_n = A\varphi^n + B\psi^n$$ where $\psi = (1-\sqrt{5})/2$ and coefficients determined by initial conditions. Theorem 2.3 (Cassini Identity): For all $n \geq 1$: $$B_{n+1} B_{n-1} - B_n^2 = (-1)^{n+1} |I|$$ where $|I| = 29$ is the invariant. Proof: Direct computation using Binet form and properties of the quadratic form $I(x,p) = x^2 - N_c xp + p^2$. The transformation $T:(x,p) \mapsto (2x-p, x-p)$ preserves $|I|$ up to sign alternation. 2.3 The 840-State Manifold Theorem 2.4 (Manifold Structure): The invariant $|I| = 29$ is the unique Lucas prime $p &lt; 600$ satisfying: $$p^2 - 1 = 840 = 2^3 \cdot 3 \cdot 5 \cdot 7$$ This four-channel Chinese Remainder Theorem decomposition: $$\mathbb{Z}/840\mathbb{Z} \cong \mathbb{Z}/8\mathbb{Z} \times \mathbb{Z}/3\mathbb{Z} \times \mathbb{Z}/5\mathbb{Z} \times \mathbb{Z}/7\mathbb{Z}$$ encodes the manifold state count. Proof: The Lucas numbers $L_n$ satisfy $L_7 = 29$. Computing $29^2 - 1 = 841 - 1 = 840$ and factoring gives the stated decomposition. Exhaustive search over Lucas primes $p &lt; 600$ confirms uniqueness. Connection to framework capacity: $$N_{st}^{\text{manifold}} = \sum_{d=1}^{12} L(d) = 1 + 3 + 4 + 7 + 11 + 18 + 29 + 47 + 76 + 123 + 199 + 322 = 840$$ where $L(d)$ denotes the $d$-th Lucas number (framework indexing: $L_0 = 1, L_1 = 3, L_2 = 4, \ldots$). 2.4 The Dimension Function Definition 2.6 (φ-adic Logarithm): The dimension function $D: \mathbb{R}_+ \to \mathbb{R}$ is: $$D(x) = -\frac{\ln x}{\ln \varphi} = \log_\varphi(1/x)$$ Theorem 2.7 (Chiral Fold Identity): For all $x &gt; 0$: $$D(x) + D(1/x) = 0$$ Proof: Direct calculation: $$D(x) + D(1/x) = -\frac{\ln x}{\ln \varphi} - \frac{\ln(1/x)}{\ln \varphi} = -\frac{\ln x - \ln x}{\ln \varphi} = 0$$ This $\mathbb{Z}_2$ symmetry at $D = 0$ connects to the Riemann Hypothesis critical line through: $$\frac{107}{214} = \frac{1}{2} = \text{Re}(s)\big|_{\text{critical line}}$$ 3. The E-Factor Derivation 3.1 Framework Formula for Euler&#39;s Number Theorem 3.1 (E-Factor): Euler&#39;s number $e$ is given by the framework formula: $$e = \frac{L(4) \cdot L(5) \cdot (B_2 + 1)}{L(7) \cdot B_2}$$ where: - $L(4) = 7$, $L(5) = 11$ (Lucas numbers) - $L(7) = 29 = |I|$ (Cassini invariant) - $B_2 = 42$ (second Brahim Number from the 10-element sequence) Explicit evaluation: $$e = \frac{7 \times 11 \times 43}{29 \times 42} = \frac{77 \times 43}{29 \times 42} = \frac{3311}{1218} = 2.7183908046\ldots$$ Comparison with exact value: $$e_{\text{exact}} = 2.7182818285\ldots$$ $$\text{e} = \frac{|e_{\text{framework}} - e_{\text{exact}}|}{e_{\text{exact}}} \times 10^6 = 40.1 \text{ ppm}$$ 3.2 Structural Components The formula decomposes into two framework-meaningful parts: Product term: $L(4) \cdot L(5) = 77$ This number appears in three fundamental identities: 1. Fine structure: $\alpha^{-1} = 214 - 77 = 137$ 2. 30-Edge identity: $\alpha^{-1} - C = 137 - 107 = 30$ (dodecahedron edges) 3. E-factor: $e \approx 77/29$ with correction Correction factor: $(B_2 + 1)/B_2 = 43/42 = 1.0238095238\ldots$ This quantum correction shifts the classical ratio $77/29 = 2.6552$ to the observed value: $$\frac{77}{29} \times \frac{43}{42} = 2.7183908\ldots \approx e$$ 3.3 Physical Interpretation The e-factor connects three structural components: - $L(4) \cdot L(5) = 77$: Fine structure product - $L(7) = 29$: Cassini invariant (manifold characteristic) - $B_2 = 42$: Biological partition constant ($840 = 20 \times 42$ amino acids) This unifies electromagnetic coupling, number theory, and biological structure through a single formula. 4. The Normalization Constant 4.1 Derivation of ℵ Theorem 4.1 (Normalization): The normalization constant $\aleph$ appearing in the observable formula is NOT a separate parameter but equals: $$\aleph = 1 + \frac{m}{K}$$ where $m$ is the mode parameter (Section 5) and $K = 107$ is the framework prime. Verification: For the verified class $(even, QR)$ with $m = 14$: $$\aleph_{\text{framework}} = 1 + \frac{14}{107} = 1.130841121\ldots$$ $$\aleph_{\text{empirical}} = 1.13065 \quad \text{(from fitting)}$$ $$\text{Error} = \frac{|\aleph_{\text{framework}} - \aleph_{\text{empirical}}|}{\aleph_{\text{empirical}}} \times 10^6 = 17.0 \text{ ppm}$$ 4.2 Implications The normalization is the lattice density renormalization factor that appears when extending $K$ modes to $K+m$ modes. It is not an external constant but an intrinsic part of the prediction formula. For all four residue classes: $$(even, QR): \quad \aleph = 1 + \frac{14}{107} = 1.130841$$ $$(even, NQR): \quad \aleph = 1 + \frac{28}{107} = 1.261682$$ $$(odd, QR): \quad \aleph = 1 + \frac{10}{107} = 1.093458$$ $$(odd, NQR): \quad \aleph = 1 + \frac{28}{107} = 1.261682$$ 5. Class-Specific Mode Parameters 5.1 The Four-Way Classification The 10 Brahim residues modulo $K = 107$ are partitioned by two binary properties: Parity: $r \bmod 2 \in \{0, 1\}$ (even vs. odd) Quadratic residue status: Whether $r$ is a QR modulo 53 This yields four classes with populations: $$(even, QR): \quad \{10, 42, 60\} \quad (n=3)$$ $$(even, NQR): \quad \{32, 80\} \quad (n=2)$$ $$(odd, QR): \quad \{47, 97\} \quad (n=2)$$ $$(odd, NQR): \quad \{27, 65, 75\} \quad (n=3)$$ 5.2 Mode Parameter Assignment Theorem 5.1 (Class-Specific m Values): Each residue class has a unique mode parameter $m$: $$(even, QR): \quad m = 14 = 2(N_c + N_{st})$$ $$(even, NQR): \quad m = 28 = 4(N_c + N_{st})$$ $$(odd, QR): \quad m = 10 = |B|$$ $$(odd, NQR): \quad m = 28 = 4(N_c + N_{st})$$ Derivation: For $(even, QR)$: The multiplicative order of $\varphi \equiv 6 \pmod{29}$ is: $$\text{ord}_{29}(\varphi) = 14 = 2(N_c + N_{st})$$ This determines the base mode for QR classes with even parity. For $(odd, QR)$: The mode equals the Brahim count: $$m = |B| = 10$$ For $NQR$ classes: The mode uses the full multiplicative group order: $$m = \ph</p><p class="metadata"><time datetime="2026-04-23" title="Source date; precision not specified">April 23, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.19707921">Original publication</a></p> Thu, 23 Apr 2026 00:00:00 GMT Elias Oulad Brahim OpenAlex https://reading.michaelmvh.com/article/63effd9dbe2f57a2f12f245361b911f87aa9983365f60bcc644e9837d45c5839/ urn:sha256:63effd9dbe2f57a2f12f245361b911f87aa9983365f60bcc644e9837d45c5839 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-04-22" title="Source date; precision not specified">April 22, 2026</time> <span aria-hidden="true"> · </span> Trends in Biochemical Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.tibs.2026.04.005">Original publication</a></p> Wed, 22 Apr 2026 00:00:00 GMT Ji Wang Junyi Chen Xun Xu OpenAlex https://reading.michaelmvh.com/article/6a39bd2cc2e7f5e5b6b6a2ef1380c75abaad3a6cf1a28ddb9d86a26254c052cb/ urn:sha256:6a39bd2cc2e7f5e5b6b6a2ef1380c75abaad3a6cf1a28ddb9d86a26254c052cb <p>Tau aggregation and hyperphosphorylation are key pathological hallmarks and early diagnostic biomarkers of Alzheimer’s disease (AD). However, the simultaneous profiling and quantitative analysis of Tau and its phosphorylated isoforms remain technically challenging. Here, by introducing an acidic aspartate residue at the G6 site of FraC G13F, we engineered a high-resolution FraC G6DG13F nanopore with enhanced temporal resolution for protonated polypeptide detection. Integrated with machine-learning algorithms, our nanopore-based workflow enabled the real-time identification of 12 tryptic peptides from native Tau (2N4R) protein with over 91.1% accuracy. Furthermore, positional phosphorylation isomers at either S400 or S402 of Tau (2N4R) were precisely resolved and quantified in mixed digestion samples, achieving classification accuracy exceeding 93% and sensitivity comparable to that of microgram-level mass spectrometry. This study demonstrates a promising advancement of global analysis of phosphorylated Tau in nanopore-based methods, highlighting its potential for high-resolution characterization and accurate quantification of proteins with PTMs.</p><p class="metadata"><time datetime="2026-04-20" title="Source date; precision not specified">April 20, 2026</time> <span aria-hidden="true"> · </span> Nano Letters</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.nanolett.6c00368">Original publication</a></p> Mon, 20 Apr 2026 00:00:00 GMT Yu Xin Defu Liu Ma Yk Zhijing Zhang Peng Chen Mengze Wu Yue Li Shanchuan Chen Shixin Yan Guiqin Song Lu Chen Qiantao Wang Jia Geng Ke Sun OpenAlex https://reading.michaelmvh.com/article/16916b4765d6735145298df31da83c59c81a0e293b3eb10d1471d0ee5da4cf24/ urn:sha256:16916b4765d6735145298df31da83c59c81a0e293b3eb10d1471d0ee5da4cf24 <p>The production of recombinant proteins is a fundamental process in biotechnology and drug development, yet it is frequently hindered by challenges such as low expression levels, protein aggregation, and improper post-translational modifications. This comprehensive troubleshooting guide provides a structured approach to diagnosing and resolving these issues across the entire protein expression pipeline. It begins by comparing the workhorse E. coli system with mammalian cell platforms, highlighting the trade-offs between rapid, high-yield production and the need for complex, human-like post-translational modifications. Detailed troubleshooting tables address specific problems like toxic protein expression, inclusion body formation, and plasmid instability, offering practical solutions such as adjusting induction temperatures, utilizing specialized host strains, and employing solubility-enhancing fusion tags. Beyond traditional optimization, the guide explores the integration of advanced computational tools and artificial intelligence. It highlights how deep learning frameworks like RiboDecode revolutionize codon optimization by utilizing ribosome profiling data to predict translation efficiency and mRNA stability, surpassing traditional rule-based methods. The article also addresses the implementation of high-throughput screening pipelines, emphasizing the importance of rigorous quality control using dynamic light scattering and intact mass analysis to prevent downstream assay failures. Finally, the guide provides extensive troubleshooting workflows for crucial protein validation techniques. It contrasts the high-throughput quantification capabilities of ELISA with the detailed characterization provided by Western blotting, offering solutions for common issues like high background signal, weak detection, and unexpected band sizes. Furthermore, it introduces mass spectrometry-based proteomics and emerging technologies like nanopore peptide profiling, detailing sample preparation protocols and strategies to overcome challenges related to sample complexity and protein degradation. By synthesizing foundational protocols with cutting-edge technologies, this guide serves as an essential resource for scientists seeking to optimize protein production and ensure robust analytical validation. Source: https://www.matscisci.com/posts/protein-expression-troubleshooting-guide-from-low-yields-to-validation</p><p class="metadata"><time datetime="2026-04-20" title="Source date; precision not specified">April 20, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.19658945">Original publication</a></p> Mon, 20 Apr 2026 00:00:00 GMT Materials Science OpenAlex https://reading.michaelmvh.com/article/888a6fc6d407021abcb5d6635d7c22bb0661ab6a46d928a5388faf08b9e92082/ urn:sha256:888a6fc6d407021abcb5d6635d7c22bb0661ab6a46d928a5388faf08b9e92082 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-04-18" title="Source date; precision not specified">April 18, 2026</time> <span aria-hidden="true"> · </span> Biosensors and Bioelectronics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bios.2026.118714">Original publication</a></p> Sat, 18 Apr 2026 00:00:00 GMT Junzhou He Yubin Cao Meiting Zeng Wei Si OpenAlex https://reading.michaelmvh.com/article/9094e8ae4bc3682931c9d34717fecf7d69a3684df5a6bd0b86be0a3b8783d392/ urn:sha256:9094e8ae4bc3682931c9d34717fecf7d69a3684df5a6bd0b86be0a3b8783d392 <p>Abstract Recent advances in two-dimensional material nanopores have promoted significant progress in biosensing technology with single-molecule precision. The potential of detecting single amino acids using graphene and MoS 2 nanopores is investigated here, using density functional theory combined with dielectric response calculations and quantum transport simulations. The electronic transport and the optical response of the nanopores are calculated, and their modifications in the presence of the selected amino acids are assessed. While the current-voltage characteristics of the nanopores show very modest modifications, the optical absorption spectra reveal quite evident modulations when an amino acid is present in the nanopore. The dielectric response of the MoS 2 nanopores exhibits a broader spectrum of photon energy compared to the graphene ones. Specifically, the calculated optical sensitivity in distinguishing among amino acids in MoS 2 nanopores reaches up to 90% compared to roughly 60% in graphene nanopores. For the latter, the calculated sensitivity in the transport mode, that is using the electronic current as a detection observable, is approximately 10 times lower. In the end, all observations are discussed in view of a potential broadband optical detection for protein detection platforms and biosensors.</p><p class="metadata"><time datetime="2026-04-17" title="Source date; precision not specified">April 17, 2026</time> <span aria-hidden="true"> · </span> npj 2D Materials and Applications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41699-026-00694-1">Original publication</a></p><p><a href="https://www.nature.com/articles/s41699-026-00694-1.pdf">Open PDF</a></p> Fri, 17 Apr 2026 00:00:00 GMT Longlong Li Maria Fyta OpenAlex https://reading.michaelmvh.com/article/7ff080521d0b0afb425f5a4bfd20d2497d536537726f50ae01cb7e138ded0e87/ urn:sha256:7ff080521d0b0afb425f5a4bfd20d2497d536537726f50ae01cb7e138ded0e87 <p>Background: Nasal colonization by Staphylococcus aureus is common in humans and represents a major reservoir for subsequent infection. However, not all colonizing strains cause disease, suggesting that differences in virulence gene expression may contribute to the transition from asymptomatic carriage to symptomatic infection. Aim: The present study investigated the transcriptional profile of two key virulence genes, spa (protein A) and hla (alpha-hemolysin), in nasal swab isolates from healthy carriers and symptomatic patients using quantitative reverse transcription PCR (RT-qPCR). Patients and Methods: A total of 100 nasal swab samples were collected from two groups: 50 healthy carriers and 50 symptomatic individuals presenting with nasal or respiratory infection. Bacterial RNA was extracted from confirmed S. aureus isolates and converted to cDNA. Quantitative RT-PCR was performed to measure transcription levels of spa and hla, with gyrB serving as the internal reference gene. Gene expression levels were calculated using the ΔΔCt method. Statistical comparisons between groups were performed using independent two-tailed Student’s t-tests. Effect sizes and statistical power were also evaluated. Results: Both virulence genes demonstrated significantly lower Ct values in symptomatic patients. The mean Ct value of spa was 28.5 ± 1.4 in healthy carriers compared with 25.9 ± 1.2 in symptomatic patients (P &lt; 0.0001). Similarly, hla showed Ct values of 30.1 ± 1.7 in healthy carriers and 26.8 ± 1.3 in symptomatic individuals (P &lt; 0.0001). Normalized expression analysis revealed substantial differences between groups. The mean ΔCt value for spa was 7.4 ± 1.1 in healthy carriers and 4.6 ± 1.0 in symptomatic patients, producing a ΔΔCt value of −2.8 and corresponding to a 6.96-fold increase in expression. For the hla gene, the mean ΔCt values were 9.0 ± 1.3 in healthy carriers and 5.5 ± 1.2 in symptomatic patients, generating a ΔΔCt of −3.5 and an 11.31-fold increase in expression among symptomatic individuals. Statistical analysis confirmed highly significant differences between groups, with t-values of 13.2 for spa and 14.8 for hla (both P &lt; 0.0001). Effect size analysis indicated very large differences in expression, with Cohen’s d values of 2.6 for spa and 2.9 for hla. Conclusions: The findings demonstrate that nasal isolates from symptomatic individuals exhibit markedly increased transcription of key virulence determinants compared with isolates from healthy carriers. The observed 6.96-fold increase in spa expression and 11.31-fold increase in hla expression suggest that activation of virulence gene transcription plays an important role in the transition from asymptomatic colonization to clinical infection. Quantitative profiling of virulence gene expression using RT-qPCR may therefore represent a valuable molecular approach for identifying potentially pathogenic nasal strains and improving early detection of infection-associated bacterial phenotypes.</p><p class="metadata"><time datetime="2026-04-14" title="Source date; precision not specified">April 14, 2026</time> <span aria-hidden="true"> · </span> World of Medicine : Journal of Biomedical Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://wom.semanticjournals.org/index.php/biomed/article/view/667">Original publication</a></p> Tue, 14 Apr 2026 00:00:00 GMT Hind Tahseen Ibrahim OpenAlex https://reading.michaelmvh.com/article/2eed5c3c5e5679ed697b0b90c0a9e77fb7b719633a83f5d08f9bef23511dc76a/ urn:sha256:2eed5c3c5e5679ed697b0b90c0a9e77fb7b719633a83f5d08f9bef23511dc76a <p>Parkinson&#39;s disease (PD) is closely associated with the misfolding of α-synuclein (αSyn) proteins, which remains obscure due to the long-standing challenge to elucidate monomeric αSyn structure. Here, we present a novel single-molecule technique to efficiently analyze αSyn monomer with Mycobacterium smegmatis porin A (MspA) nanopores. The nanopore signals elicited by αSyn consist of three distinct, reproducible current levels. Notably, through systematic measurement of αSyn fragments, reference peptide with α-helical structure and molecular dynamics simulation study, we demonstrate that these current levels correspond to α-helical and random-coil structures within the protein. The α-helical structures are successfully assigned to the specific αSyn subdomains. A biophysical parameter figure matrix derived from the αSyn signals is further generated and readily applied to profile the structural heterogeneity of monomeric αSyn variants. These results establish that MspA nanopores can directly sense the formation of α-helical structure in individual αSyn monomer, which advances our capability to investigate this highly flexible pathological protein and may contribute to elucidating its misfolding mechanism.</p><p class="metadata"><time datetime="2026-04-13" title="Source date; precision not specified">April 13, 2026</time> <span aria-hidden="true"> · </span> Angewandte Chemie International Edition</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/anie.202523298">Original publication</a></p> Mon, 13 Apr 2026 00:00:00 GMT Xiaoya Zhang Xinpei Wang Yue Zhang Dan Liu Xing Wei Yuxi Shao Zimeng Li Gang Huang OpenAlex https://reading.michaelmvh.com/article/797c211079e126f4ea9d846cff3fe6ab3a72eec5b2cfcf25ddac7ec99ff93b78/ urn:sha256:797c211079e126f4ea9d846cff3fe6ab3a72eec5b2cfcf25ddac7ec99ff93b78 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-04-12" title="Source date; precision not specified">April 12, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v2/review1">Original publication</a></p> Sun, 12 Apr 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/adfac812a59e2a6701cd9913fc3a5d0b33ceaa28daa16f3724d349a00ad1132a/ urn:sha256:adfac812a59e2a6701cd9913fc3a5d0b33ceaa28daa16f3724d349a00ad1132a <p>Solid-state nanopores are widely used for single-molecule sensing, yet transport direction is typically treated as a nuisance variable rather than an informative signal dimension. In this work, we investigate directional protein translocation in multilayer solid-state nanopores composed of$\operatorname{SiN}_{x}$, graphene, and a terminal two-dimensional material using a signal-centric analysis framework. Ionic current recordings obtained under forward and reverse bias conditions reveal polarity-dependent restructuring of the translocation signal space that cannot be captured by mean transport metrics alone. Unsupervised Gaussian mixture analysis identifies latent event subpopulations whose occupancies depend on transport direction, while feature-level evaluation using effect-size analysis shows that directionality is strongly voltage and feature-selective. In contrast, symmetric$\text{SiN}_{\mathrm{x}}$nanopores exhibit direction-independent behavior across all features. These results demonstrate that transport polarity can be treated as an additional sensing dimension in solid-state nanopore systems, enabling improved interpretation and operating-point selection without active gating or chemical functionalization.</p><p class="metadata"><time datetime="2026-04-10" title="Source date; precision not specified">April 10, 2026</time> <span aria-hidden="true"> · </span> IEEE Dallas Circuits and Systems Conference (DCAS)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1109/dcas69364.2026.11544297">Original publication</a></p> Fri, 10 Apr 2026 00:00:00 GMT Kamruzzaman Joty Chaoming Gu Sangyoup Lee Min Jun Kim OpenAlex https://reading.michaelmvh.com/article/c4363e2370eb33535d935e5f80c2e301fb2743e16ff1889c9c66f269a6e0a7a1/ urn:sha256:c4363e2370eb33535d935e5f80c2e301fb2743e16ff1889c9c66f269a6e0a7a1 <p>This comprehensive technical review examines the evolution and application of amino acid sequence representation methods, a foundational element of computational biology that translates biological sequences into machine-readable numerical formats. The article categorizes these methods into three distinct developmental stages. The first stage encompasses computational-based methods, which utilize manually engineered features derived from statistical patterns, physicochemical properties, and evolutionary conservation, including k-mer counting, Composition-Transition-Distribution, and Position-Specific Scoring Matrices. The second stage introduces word embedding-based approaches, such as Word2Vec and ProtVec, which adapt natural language processing techniques to capture local contextual relationships between amino acids. The third and most advanced stage involves large language models and transformer architectures, such as ESM3, AlphaFold3, and ProtTrans. These context-aware models leverage self-attention mechanisms and massive pre-training datasets to capture complex, long-range dependencies and sequence-structure-function relationships without relying on explicit feature engineering. Beyond categorization, the article delves into specialized methodologies, including nanopore-based amino acid detection, alignment-free sequence comparison, and graphical representations that integrate 3D structural data. It critically evaluates the performance trade-offs between static, rule-based encodings and dynamic, end-to-end learned representations across various predictive tasks, such as protein-protein interaction, binding affinity prediction, and therapeutic protein design. A significant portion of the review addresses practical implementation challenges, highlighting strategies for dimensionality reduction, transfer learning, and mitigating data sparsity in novel sequence analysis. The text emphasizes the necessity of rigorous validation frameworks and standardized benchmarking to ensure the biological relevance and computational reliability of these models. Ultimately, the guide provides researchers and drug development professionals with a structured decision framework for selecting optimal encoding strategies, balancing computational efficiency, predictive accuracy, and biological interpretability to advance therapeutic discovery and protein engineering. Source: https://www.proteineng.com/posts/amino-acid-sequence-representation-methods-from-foundational-encoding-to-advanced-ai-applications</p><p class="metadata"><time datetime="2026-04-09" title="Source date; precision not specified">April 9, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.19477709">Original publication</a></p> Thu, 09 Apr 2026 00:00:00 GMT protein engineering OpenAlex https://reading.michaelmvh.com/article/01780aa70cc0b458eaac5114b64456f3867d82b1a64394a90e77015a8bbc8da9/ urn:sha256:01780aa70cc0b458eaac5114b64456f3867d82b1a64394a90e77015a8bbc8da9 <p>Abstract Rapid and highly selective sensing of ultra-low concentration protein biomarkers remains a critical challenge important for early disease diagnosis and monitoring. Here, we use conical SiO 2 nanopore-based biosensing for the rapid detection of heart-type fatty acid binding protein (H-FABP). Antibodies were covalently immobilized on the nanopore surface through siloxane chemistry. The functionalized asymmetric nanopores generate a characteristic rectifying current–voltage response, which shows a distinct shift upon binding to the target protein due to partial neutralization of the negatively charged pore surface. The sensor exhibits excellent sensitivity in the attomolar to nanomolar concentration range with a detection limit (LOD) of ∼0.4 aM. Furthermore, the platform exhibits high selectivity, distinguishing H-FABP from non-target proteins (HSA and Hb) at concentrations six orders of magnitude higher. We also demonstrate that nanopores can be regenerated using sodium hypochloride and O 2 plasma treatment, enabling repeated functionalization and reuse.</p><p class="metadata"><time datetime="2026-04-09" title="Source date; precision not specified">April 9, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.04.07.717075">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/04/09/2026.04.07.717075.full.pdf">Open PDF</a></p> Thu, 09 Apr 2026 00:00:00 GMT Nahid Afrin Shankar Dutt María Eugenia Toimil‐Molares P. Kluth OpenAlex https://reading.michaelmvh.com/article/d8dcb88a40122c6a3173d283e863bd62875ce1a60869067be755dc348f648952/ urn:sha256:d8dcb88a40122c6a3173d283e863bd62875ce1a60869067be755dc348f648952 <p>Lactylation has recently emerged as a novel post-translational modification with critical implications for gene regulation and host–parasite interactions, as demonstrated for species of Plasmodium and Trypanosoma. Here, we applied an integrative approach combining in-silico and experimental analyses to detect protein lactylation in parasitic cnidarians in the class Myxozoa. In-silico analyses were conducted using data from seven myxozoan species, six obtained from public databases and one generated in this study. Experimental validation was based on Oxford Nanopore Technologies (ONT) genome sequencing and Western blotting of Myxobolus macroplasmodialis samples, a myxozoan parasite of the South American bryconid fish Salminus brasiliensis. This integrative approach enabled us to validate the in-silico analysis, to identify conserved lactylation sites in key stress-response proteins (including HSP70 and several metabolic enzymes), and to map electrochemical signatures of lactylation sites across the nanopore sequencing ONT dataset for M. macroplasmodialis. Comparative analyses across species demonstrated the predicted conserved regulatory roles and myxozoan species-specific variation in processes controlled by lactylation. Functional enrichment analyses further implicated lactylation in critical pathways, such as glycolysis, oxidative phosphorylation, and immune signaling, thus supporting its integration into core regulatory networks that underlie the functional biology of parasitism.</p><p class="metadata"><time datetime="2026-04-07" title="Source date; precision not specified">April 7, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.19460039">Original publication</a></p> Tue, 07 Apr 2026 00:00:00 GMT Amr G. A. Ibrahim Juliana Naldoni Antonio Maia Juliano Rodrigues Sangalli Caroline Munhoz Meira Rayline Thaimenne Alves Figueredo Beth Okamura Paul Long Edson A. Adriano OpenAlex https://reading.michaelmvh.com/article/bc170ef0324ae6aa55e31418b82a0d80146b65f1617e067ed3f0b51491075f9d/ urn:sha256:bc170ef0324ae6aa55e31418b82a0d80146b65f1617e067ed3f0b51491075f9d <p>Reliable identification of proteins and their post-translationally modified variants remains a formidable analytical challenge due to charge heterogeneity, sequence similarity, and comparable molecular weights. In this study, we demonstrate distinctive nanopore current fingerprints for clear identification of neurodegenerative disease-associated Tau protein and its phosphorylated variants using an asymmetric-electrolyte sensing system composed of different salts. The asymmetric configuration facilitates simultaneous detection of positively, neutrally, and negatively charged peptide fragments, resulting in 3.2-16-fold higher capture frequencies and 2.1-5.3-fold longer event durations, thereby yielding information-rich fingerprints that enhance protein recognition. Protein profiling was achieved within 1 min through integration with a droplet nanopore platform, which reduces sample consumption to the nanogram level while increasing throughput to &gt;1800 events per minute. This work advances the nanopore fingerprinting approach for rapid, high-throughput, and low-sample protein biomarker detection, offering strong potential for clinical proteomics and early disease diagnosis.</p><p class="metadata"><time datetime="2026-04-06" title="Source date; precision not specified">April 6, 2026</time> <span aria-hidden="true"> · </span> JACS Au</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/jacsau.6c00115">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/jacsau.6c00115?ref=article_openPDF">Open PDF</a></p> Mon, 06 Apr 2026 00:00:00 GMT Kai‐Li Xin Linlin Zhang Min Li Shao-Chuang Liu Han-Qing She Yi‐Lun Ying Yi-Tao Long Zheng‐Li Hu OpenAlex https://reading.michaelmvh.com/article/0bbd00821cc930b17e2296062d32cbe398533588f623311bceeb60101927cfab/ urn:sha256:0bbd00821cc930b17e2296062d32cbe398533588f623311bceeb60101927cfab <p>Public repository for the pooled yeast-two-hybrid method for high-throughput measurement of protein interaction perturbations, by missense variants, using Oxford Nanopore sequencing.</p><p class="metadata"><time datetime="2026-04-06" title="Source date; precision not specified">April 6, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.19444012">Original publication</a></p> Mon, 06 Apr 2026 00:00:00 GMT Luke Lambourne OpenAlex https://reading.michaelmvh.com/article/8e28fdb0c993af815a29768e9df76cadacaa090fd81060bd1f532a45de11c1ab/ urn:sha256:8e28fdb0c993af815a29768e9df76cadacaa090fd81060bd1f532a45de11c1ab <p>The RNA methyltransferase METTL3, catalyzing N6-methyladenosine (m6A) modification, is implicated in oncogenesis. METTL3 inhibitors have shown potent anti-tumor efficacy across diverse preclinical models and are being tested in early-phase clinical trials. However, how cells fundamentally and dynamically respond to disruption of the m6A RNA methylation machinery and what drives resistance to the catalytic inhibition of METTL3 remains unknown. Using genome-wide CRISPR sensitization and resistance screens in sensitive and resistant cancer models, we identify the nuclear m6A-reader YTHDC1 as a critical determinant of METTL3 inhibition response. Genetic depletion of YTHDC1 markedly sensitizes cells to METTL3 inhibitor (METTL3i) treatment in vitro and in vivo across solid and hematologic cancers, and its overexpression drives primary resistance. A YTHDC1-condensate imaging screen identified YTHDC1 interactor PABPN1, a PAXT complex component and a resistance hit from our CRISPR screen, as a negative regulator of YTHDC1 condensate dynamics. PABPN1 overexpression restores METTL3i sensitivity in resistant models, whereas its loss induces resistance, highlighting that the state of YTHDC1 nuclear condensates functionally mediate METTL3i response. Mechanistically, catalytic blockade of METTL3 remodels YTHDC1 condensates, increasing their intensity, size, and number while reducing their biophysical dynamics in sensitive cancer models and patient samples. In contrast, healthy human blood cells retain dynamic condensates, and resistant cancers display static condensates. Integrating direct RNA nanopore m6A mapping, bulk-RNAseq and quantitative proteomics in YTHDC1-overexpression model, we find that residual m6A modification persist on transcripts, and YTHDC1 drives restoration of MYC/BCL-2 programs upon METTL3 inhibition. Furthermore, YTHDC1 enhances binding to MYC and BCL-2 mRNAs under METTL3i treatment, preserving their translation despite global m6A loss. Accordingly, MYC overexpression phenocopies YTHDC1-mediated resistance to METTL3i, confirming its functional relevance. Therapeutically, co-targeting with a newly developed YTHDC1 inhibitor or the clinically approved BCL-2 inhibitor venetoclax synergistically enhances METTL3i efficacy in vitro and in vivo in clinically relevant models including AML patient-derived xenografts. Together, these findings uncover adaptive reorganization of the m6A machinery across hematologic and solid cancers. The YTHDC1 pathway and its condensate state act as predictive biomarkers and enhancers of therapeutic efficacy in METTL3-targeted cancers. Combinatorial targeting of METTL3 and YTHDC1/BCL-2 as a strategy to overcome therapeutic resistance. Citation Format: Xuejing Yang, Maria Eleftheriou, Eliza Yankova, Siân Evans, Theodore M. Nelson, Isaac Wakiro, Emily Batchelor, Kathryn Chang, Joao M. Dias, Aspen Pierson, Genevieve Girard, Rhoshini Raghuraman, Demetrios Aspris, Vidur Tandon, Grace Han, Lydia P. Tsamouri, Hanzhi Luo, James Russell, Maria T. Bejar, Maria P. Alcolea, Ajay Edakkara, Muxin Gu, Rupert Öllinger, Malgorzata Gozdecka, Brian J. Huntly, Roland Rad, Lina Vasiliauskaitė, Yaara Ofir-Rosenfeld, George S. Vassiliou, Yuanming Cheng, Mansi Arora, Richard C. Centore, Christopher E. Mason, Oliver Rausch, Shilpi Arora, Konstantinos Tzelepis, Michael G. Kharas. Condensate dynamics drive adaptive METTL3 inhibitor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3983.</p><p class="metadata"><time datetime="2026-04-03" title="Source date; precision not specified">April 3, 2026</time> <span aria-hidden="true"> · </span> Cancer Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1158/1538-7445.am2026-3983">Original publication</a></p> Fri, 03 Apr 2026 00:00:00 GMT Xuejing Yang Maria Eleftheriou Eliza Yankova Siân Evans Theodore M. Nelson Isaac Wakiro Emily Batchelor Kathryn Chang João M.L. Dias Aspen Pierson Genevieve Girard Rhoshini Raghuraman Demetrios Aspris Vidur Tandon Grace Y. Q. Han Lydia P. Tsamouri Hanzhi Luo James D Russell Maria Teresa Béjar Maria Pilar Alcolea Ajay Edakkara Muxin Gu Rupert Öllinger Malgorzata Gozdecka Brian J.P. Huntly Roland Rad Lina Vasiliauskaitė Yaara Ofir-Rosenfeld George S. Vassiliou Yuanming Cheng Mansi Arora Richard C. Centore Christopher E. Mason Oliver Rausch Shilpi Arora Konstantinos Tzelepis Michael G. Kharas OpenAlex https://reading.michaelmvh.com/article/faca8a4f43240a498dd6a3c174d44668934294fe801bf8340602a20f8ab7a228/ urn:sha256:faca8a4f43240a498dd6a3c174d44668934294fe801bf8340602a20f8ab7a228 <p>Abstract When preclinical research fails to replicate human biology, scientific progress stalls, clinical trials falter, and patients continue to suffer. While many factors contribute to these failures, lack of attention to pre-analytic variability is a seminal issue. We recently reported that even short-term exposure to ambient air is sufficient to trigger signaling changes in tumor and non-malignant biospecimens. Those changes in turn alter their biology and responsiveness to targeted therapies. Thus, characterization of tumors collected and processed under physioxia (3% O2) instead of current practice of collection and processing under ambient air (21% O2) will help to identify clinically relevant biomarkers that are affected by O2 tensions. This approach may help to reduce clinical trial failure rates and increase clinical translation of preclinical studies. Towards this goal, we collected human specimens (biopsies, ascites and pleural effusions from 94 donors) under physioxia, then divided the same specimen into two groups; one group maintained under physioxia, the other group exposed to ambient air. Both were for 45-60 minutes before fixing/processing. Samples were subjected to various biomarker analysis using IHC/IF, Western blotting to measure proteins, and nanopore sequencing for DNA methylation. We found the levels of pAKT, a clinically used biomarker of targeted therapy, were constantly higher in clinical samples under physioxia compared to ambient air. Similar effects of O2 tension on pERK and MDM4 levels occurred in cells isolated from ascites or pleural effusion in a time-dependent manner. A significant decrease in pEGFR and p53 levels were observed in cells under physioxia. Moreover, O2 tension-dependent differences extended to key epigenetic regulators including TET2. TET2 levels were lower under physioxia compared to ambient air. Consistently, nanopore sequencing revealed distinct differences in DNA methylation patterns under physioxia and ambient air. The observed differences in signaling pathways extended to cultured cells from ascites fluids and pleural effusions. However, there is a specificity in the effects of O2 tensions on biomarkers as we did not observe significant differences in pPDGFRβ, ATE1 and many other biomarkers under two O2 conditions. These results imply that the O2 tension affects specific biomarkers and epigenome. Collectively, O2 tension could result in dynamic and extensive changes in cell membrane, cytoplasmic and nuclear biomarkers. Observable changes of biomarkers could occur within an hour following exposure to ambient O2, and some changes could last for prolonged period. Thus, our current study lays out a new physiologically relevant biomarker validation/discovery platform, which may accelerate evaluation of physiologically relevant signaling networks, new drug discovery, and enhance clinical translation of preclinical observations. Citation Format: Ruizhong Wang, Adedeji Adebayo, Stephanie Adama, Steven M. Westphal, Hala Fatima, Carla S. Fisher, Hongyu Gao, Yunlong Liu, Ryla G. House, GEORGE SANDUSKY, Sean D. McCabe, Zhongping He, Jamunabai M. Prakash, Amber Roberts, Matt E. Thomas, Mohammad Al-Haddad, Sujani Yadlapati, Pam Rockey, William Berry, Mary B. James, Rana German, Emily M. Nelson, April M. Giron, Troy Moeller, Noah Xique, Kathy D. Miller, Harikrishna Nakshatri. The impact of oxygen exposure on clinical biomarkers - an underrecognized source of pre-analytic variability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7293.</p><p class="metadata"><time datetime="2026-04-03" title="Source date; precision not specified">April 3, 2026</time> <span aria-hidden="true"> · </span> Cancer Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1158/1538-7445.am2026-7293">Original publication</a></p> Fri, 03 Apr 2026 00:00:00 GMT Ruizhong Wang Adedeji Kolawole Adebayo Stephanie Adama Steven M. Westphal Hala Fatima Carla Suzanne Fisher Hongyu Gao Yunlong Liu Ryla G. House George Earl Sandusky Sean McCabe Zhongping He Jamunabai Prakash Amber Roberts Matt E. Thomas Mohammad Al‐Haddad Sujani Yadlapati Pam Rockey William Berry Mary B. James Rana German Emily M. Nelson April M. Giron Troy Moeller Noah Xique Kathy D. Miller Harikrishna Nakshatri OpenAlex https://reading.michaelmvh.com/article/24867f41419ceb19c73b983003374a3caed525e56d373c6280715d53503a8941/ urn:sha256:24867f41419ceb19c73b983003374a3caed525e56d373c6280715d53503a8941 <p>High-throughput solid-state nanopore experiments generate continuous MHz-rate data streams in which only a small fraction of data contains informative molecular information. This creates storage and processing bottlenecks that limit experimental scalability. We introduce Data Sieving, a GPU-accelerated acquisition framework that integrates real-time event detection directly into the measurement pipeline and selectively stores and allows real-time analysis of snapshots around molecular translocations. The system employs a lightweight rolling-average and min-max trigger to identify event candidates in parallel across channels. This architecture reduces stored data volume by up to 98% while preserving complete molecular signatures across a wide temporal range, from microsecond-scale protein dynamics to second-scale nucleic acid nanoparticle events. Continuous baseline monitoring enables autonomous closed-loop actuation; in high-concentration DNA experiments, automatic declogging restored pore conductance, reducing the time spent in a non-productive clogged state to near-zero and without interrupting parallel measurements. Validated across DNA, protein, and nucleic acid nanoparticle measurements, Data Sieving links data storage directly to molecular information content rather than experiment duration, enabling scalable, real-time operation of parallel nanopore sensors. The approach provides a hardware-agnostic foundation for long-duration, high-bandwidth single-molecule experiments and other event-driven sensing platforms. By using algorithms intrinsically compatible with low-latency digital architectures, this framework provides a clear path toward high-bandwidth, highly multiplexed recording across hundreds of individual nanopore channels in both solid-state and biological pores.</p><p class="metadata"><time datetime="2026-04-02" title="Source date; precision not specified">April 2, 2026</time> <span aria-hidden="true"> · </span> PubMed</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.48550/arxiv.2604.02166">Original publication</a></p> Thu, 02 Apr 2026 00:00:00 GMT Matteo Cartiglia Natan Biesmans Wannes Peeters Wouter Botermans Koen Ongena Liam Vandekerckhove Wouter Renckens Eric Beamish Elizabeth Skelly Kirill A. Afonin Pol Van Dorpe Sanjin Marion OpenAlex https://reading.michaelmvh.com/article/5041a001159b2edf919f81edd26fcbbfb97c7dec49f88769e37bea1993c8fe5e/ urn:sha256:5041a001159b2edf919f81edd26fcbbfb97c7dec49f88769e37bea1993c8fe5e <p>Tiller number is a crucial agronomic trait that directly influences the grain yield per unit area of rice. Alternative polyadenylation (APA), an essential post-transcriptional regulatory mechanism, plays a significant role in rice growth and development by generating transcripts with varying 3ʹ untranslated region (3ʹUTR) lengths. However, the specific role of APA in rice tillering remains poorly understood. We employed nanopore DNA sequencing and tandem mass tag proteomics to analyze tiller axillary buds at different developmental stages in rice. Our findings revealed that genes at the early stages of tillering (effective tillering) tend to utilize longer transcripts, whereas those at the later stages (ineffective tillering) favor shorter transcripts. APA-related genes in both the effective and ineffective tillering stages are enriched in known rice tillering-associated pathways, such as the terpenoid backbone biosynthesis pathway and the carotenoid biosynthesis pathway. Additionally, APA-related genes at the ineffective tillering stage are further enriched in pathways such as leaf and organ senescence. The results demonstrated that APA-mediated gene length variation regulates rice tillering in a spatiotemporally specific pattern, and APA further impacts the protein abundance of genes involved in tillering. Genes that utilize the distal AAUAAA signal and produce longer transcripts exhibit stronger expression than those using the proximal signal, while genes using the proximal AAUAAA signal and generating shorter transcripts show stronger expression than those using the distal signal. This study clarifies the regulatory patterns of APA in rice tillering, laying a molecular foundation for potential breeding of rice with ideal plant architecture.</p><p class="metadata"><time datetime="2026-03-31" title="Source date; precision not specified">March 31, 2026</time> <span aria-hidden="true"> · </span> Rice Science</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.rsci.2026.03.002">Original publication</a></p> Tue, 31 Mar 2026 00:00:00 GMT Xinyi LI Junying Huang Dahu Zhou Yicong Cai Xiaorong Chen Lifang HU Linjuan Ouyang Junru Fu Qingshun Quinn Li Haohua He Haihui Fu OpenAlex https://reading.michaelmvh.com/article/a3c3da259ef8df81f8a0c6b337403fcbfdb130ffc1906896dbf4dab647feed4d/ urn:sha256:a3c3da259ef8df81f8a0c6b337403fcbfdb130ffc1906896dbf4dab647feed4d <p>Achieving zero-dalton resolution─the discrimination of biomolecules with identical mass─remains a fundamental challenge in molecular analysis. Nanopore sensing can resolve short peptide isomers, but whether discrimination persists when peptide length approaches the nanopore saturation limit is unclear. Here, we demonstrate robust nanopore-based discrimination of two 13-residue α-synuclein isomers using wild-type aerolysin at lengths approaching full nanopore sensing region occupancy. Isomer separation requires full peptide accommodation within the nanopore and arises from intrinsic structural differences amplified by ion-specific effects under nanoscale confinement. Complementary ion mobility–mass spectrometry and molecular simulations corroborate these intrinsic conformational distinctions under native conditions. The presence of salts strongly modulates peptide conformation; specifically, KCl and NaCl favor extended states, whereas LiCl and CaCl 2 promote compact, folded conformations that amplify intrinsic structural differences, enabling near-perfect isomer separation (up to 100%). Remarkably, we demonstrate that isomer discrimination is insensitive to the order of pore entry, the specific conformations adopted (stretched, coiled, or globular), or whether peptides fully translocate or remain trapped. This robustness suggests that exploiting folded or partially folded peptide states─maximizing residue occupancy within the nanopore─may provide a path to extending zero-dalton discrimination to longer isomeric peptides. More broadly, this work outlines a strategy for advancing single-molecule proteomics and next-generation molecular fingerprinting, including applications to structurally complex biomolecules.</p><p class="metadata"><time datetime="2026-03-25" title="Source date; precision not specified">March 25, 2026</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c08253">Original publication</a></p> Wed, 25 Mar 2026 00:00:00 GMT Mazdak Afshar Bakshloo Leïla Bechtella Jianjun Tao Alina Asandei Camille Dejoux Manuela Pastoriza‐Gallego Jérôme Mathé Nathalie Basdevant Régis Daniel Abdelghani Oukhaled OpenAlex https://reading.michaelmvh.com/article/1bf34447b8352debcc76714ccef048354d0edd433f140de7e85d6375d0c2f265/ urn:sha256:1bf34447b8352debcc76714ccef048354d0edd433f140de7e85d6375d0c2f265 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-03-25" title="Source date; precision not specified">March 25, 2026</time> <span aria-hidden="true"> · </span> Research Repository (Delft University of Technology)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.4233/uuid:08711975-9182-433f-99b4-ec13cb172acb">Original publication</a></p> Wed, 25 Mar 2026 00:00:00 GMT Justas Ritmejeris OpenAlex https://reading.michaelmvh.com/article/069715f3d0b95bc0e3f5aaccff8857ee3e89eecf33fabf7a0430b9e57852d089/ urn:sha256:069715f3d0b95bc0e3f5aaccff8857ee3e89eecf33fabf7a0430b9e57852d089 <p>Nanopore sequencing raw data with data processing scripts and processed data presented in chapter 6 of PhD thesis by Justas Ritmejeris. Data was acquired using Oxford Nanopore Technologies MinION sequencing platform and preprocessed and separated into single-channel timetraces that were further used for filtering out bad events and selecting only the events that matched necessary criteria of DNA sequencing squiggles.</p><p class="metadata"><time datetime="2026-03-25" title="Source date; precision not specified">March 25, 2026</time> <span aria-hidden="true"> · </span> 4TU.ResearchData</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.4121/ebcd8292-b1e4-4f54-b42e-f067ba6a19d2">Original publication</a></p> Wed, 25 Mar 2026 00:00:00 GMT Justas Ritmejeris OpenAlex https://reading.michaelmvh.com/article/f1930d5d199d8f67832436f4937530509362ffcb28473743c83df5f456e9eb10/ urn:sha256:f1930d5d199d8f67832436f4937530509362ffcb28473743c83df5f456e9eb10 <p>Digital immunoassays enable highly sensitive detection of biomolecules, offering absolute quantification rather than relying on bulk signal intensity. We adapt a digital immunoassay scheme for a nanopore sensor, a versatile platform for single-molecule counting. Current nanopore sensors have demonstrated great progress when counting nucleic acids but struggle with proteins due to variability in translocation behavior and limited recognition strategies. While recent advancements have highlighted the promise of nanopore platforms for protein studies, precise quantification remains a challenge. Here, building on previous work, we present a nanopore-based digital immunoassay that employs gold nanoparticle-mediated molecular amplification with a single-molecule readout. This approach translates protein recognition into quantifiable DNA, enabling a precise digital assay. This assay employs a DNA NanoLock probe combined with a paramagnetic bead-based immunocapture, where the target proteins trigger a structural transformation of the NanoLock, converting their presence into a binary DNA-based signal. By incorporating AuNPs carrying hundreds of DNA proxy reporters, we effectively amplify the detectable signal by 2 orders of magnitude, significantly improving sensitivity. We validate the performance of this system by detecting the glial fibrillary acidic protein, a biomarker for traumatic brain injury and neurodegenerative diseases, in plasma samples and demonstrate high femtomolar-level sensitivity (∼40 pg/mL). Using the NanoLock probe, we further mitigate previous challenges, with reduced assay times (hours) and extended dynamic range (3-log). The self-calibrating nature of this digital approach offers robust, reproducible measurements across different nanopores, eliminating interdevice variability.</p><p class="metadata"><time datetime="2026-03-24" title="Source date; precision not specified">March 24, 2026</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.5c16690">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acsnano.5c16690?ref=article_openPDF">Open PDF</a></p> Tue, 24 Mar 2026 00:00:00 GMT Liqun He Breeana Elliott Philipp Mensing Kyle Briggs Michel Godin Jonathan D. Flax James L. McGrath Vincent Tabard‐Cossa OpenAlex https://reading.michaelmvh.com/article/5023e4ecd548adca04786f988caaa30e63631872c8481ea644d961fc7c02d71e/ urn:sha256:5023e4ecd548adca04786f988caaa30e63631872c8481ea644d961fc7c02d71e <p>Directional control of biomolecular transport in solid-state nanopores is crucial for replicating the rectification and gating behaviors of biological channels. Here, we report material-dependent directionality in multilayer nanopores formed in SiN x + graphene + hBN and SiN x + graphene + MoS 2 heterostructures using chemically tuned controlled dielectric breakdown. Transport-defined asymmetry emerges across the nanopore population, giving rise to polarity-dependent differences in capture rate and translocation kinetics over more than half a million holo-human serum transferrin (hSTf) protein events. Single-molecule analysis combined with electrostatic simulations indicates that terminal-layer composition and layer order modulate the local electric field distribution, leading to orientation-dependent transport kinetics. These results highlight that heterointerface engineering in multilayer nanopores can encode transport polarity at the single-molecule level, providing a materials-based strategy to regulate protein translocation dynamics and enhance signal separability for nanopore-based protein sensing.</p><p class="metadata"><time datetime="2026-03-23" title="Source date; precision not specified">March 23, 2026</time> <span aria-hidden="true"> · </span> ACS Applied Nano Materials</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsanm.6c01041">Original publication</a></p><p><a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC13166148/pdf/nihms-2167489.pdf">Open PDF</a></p> Mon, 23 Mar 2026 00:00:00 GMT Kamruzzaman Joty Chaoming Gu Sangyoup Lee Min Jun Kim OpenAlex https://reading.michaelmvh.com/article/f4cd28c4187fff70ad8c887c386dc9af3efd64a7d8b8779b5b4a04df100516a8/ urn:sha256:f4cd28c4187fff70ad8c887c386dc9af3efd64a7d8b8779b5b4a04df100516a8 <p>Peptides are key biomolecules in biology and medicine, yet their reliable detection and discrimination in complex mixtures remain highly challenging, particularly under clinical requirements of robustness and accuracy. Surface-enhanced Raman spectroscopy (SERS) offers molecular specificity but is hindered by spectral overlap, variability, and fluctuations that limit its applicability in practical settings. In this work, we investigate the performance of SERS flow-through strategy using plasmonic nanopores to record Raman spectra from single molecules as they translocate one by one through sub-2 nm hotspots. As a stringent test, we investigated the discrimination of vasopressin and oxytocin, two peptides differing by only two amino acids. Using electrophoretic delivery and ultrafast SERS detection with a single-photon avalanche diode camera, we captured spectra on microsecond time scales. Machine-learning analysis achieved 70.5% classification accuracy at the single-peptide level, rising to 99% discrimination when averaging 40 events. These results establish flow-through nanopore SERS as a promising route toward single-molecule peptide identification in biomedical settings.</p><p class="metadata"><time datetime="2026-03-20" title="Source date; precision not specified">March 20, 2026</time> <span aria-hidden="true"> · </span> ACS Photonics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsphotonics.5c02676">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acsphotonics.5c02676?ref=article_openPDF">Open PDF</a></p> Fri, 20 Mar 2026 00:00:00 GMT Kirill M. Khabarov Ilaria Micol Baldi María Blanco-Formoso Foroogh Khozeymeh Veronica Storari Federica Villa Francesco Difato Francesco Tantussi Francesco De Angelis OpenAlex https://reading.michaelmvh.com/article/d2cc8ee885134bfb3cd41f42c23088820ae443f0b46fd49246fcf2eb774bd130/ urn:sha256:d2cc8ee885134bfb3cd41f42c23088820ae443f0b46fd49246fcf2eb774bd130 <p>The translocation of large proteins through nanopores smaller than their native dimensions opens opportunities to probe endogenous biological processes, assess protein stability, and enable nanopore-based linearization for protein sequencing. Here, we demonstrate that electroosmotic flow (EOF) drives the passage of megadalton proteins through geometric constrained nanopores. Using glass nanopipettes with tip diameters up to 2.5-fold smaller than the proteins, we show that EOF actively captures, aligns, and deforms macromolecules─including immunoglobulin M (IgM) and α 2 -macroglobulin (α 2 M)─facilitating translocation through extreme confinement. Electrostatic potential analysis and quantitative modeling reveal that dipole enhancement and subsequent protein unfolding reduce the energetic barrier to pore entry and enable structural accommodation during transport. By fine-tuning voltage and ionic strength, a critical EOF-electrophoretic balance governing translocation kinetics is identified. Furthermore, voltage reversals change the EOF direction to achieve &gt;70% recapture efficiency, allowing reversible protein transport and ensemble-level interrogation of conformational dynamics. These findings establish an electrohydrodynamic framework for controlled macromolecular passage and expand nanopore sensing capabilities for precision proteomics and structural biology.</p><p class="metadata"><time datetime="2026-03-18" title="Source date; precision not specified">March 18, 2026</time> <span aria-hidden="true"> · </span> Journal of the American Chemical Society</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/jacs.5c22239">Original publication</a></p> Wed, 18 Mar 2026 00:00:00 GMT Iris Baffour Ansah Sushmita Joardar Kevin J. Freedman OpenAlex https://reading.michaelmvh.com/article/816dae07d8f884b69892f32ee015319eab8d32766f585645cf40eca83ac8ebb6/ urn:sha256:816dae07d8f884b69892f32ee015319eab8d32766f585645cf40eca83ac8ebb6 <p>Accurate identification of amino acids within peptides and proteins is essential for understanding physiological and pathological mechanisms. While nanopore-based ionic current measurements have enabled single-molecule discrimination of the 20 proteinogenic amino acids, this approach offers limited insight into the chemical structure of analytes. Here, we present a novel strategy for fabricating silver plasmonic nanopores via liquid-liquid interface-confined chemical reduction within quartz nanopipettes. The resulting tapered porous Ag nanostructures are precisely positioned at the pipet tip and exhibit strong surface-enhanced Raman scattering (SERS) activity. Characteristic SERS spectra are obtained from single molecules of tryptophan and aspartic acid as they translocate through the plasmonic nanopore, allowing for statistical spectral analysis. This Ag plasmonic nanopore architecture provides a platform for integrating dynamic SERS detection into single-molecule analysis, thereby bridging the gap between single-molecule sensing and structural identification.</p><p class="metadata"><time datetime="2026-03-18" title="Source date; precision not specified">March 18, 2026</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.6c00437">Original publication</a></p> Wed, 18 Mar 2026 00:00:00 GMT Zheng Wang Yanru Ding Cai Gao Wang Li Yue Yin Xing‐Hua Xia Xiao-Lei Xing Lina Ji Kang Wang OpenAlex https://reading.michaelmvh.com/article/c27b061dfe9ab5914e16b256b2847052fdf1f2eecada331042a5568a791d5b9a/ urn:sha256:c27b061dfe9ab5914e16b256b2847052fdf1f2eecada331042a5568a791d5b9a <p>Abstract Efficient integration of proteins into amphiphilic polymer membranes offers new opportunities in synthetic biology and nanotechnology. Long-term protein reconstitution into artificial membranes remains challenging due to a lack of stabilising protein-membrane interactions found in native lipid bilayers. Here, we redesigned the transmembrane region of a CytK-4D β-barrel nanopore for stable insertion into 3.5–6.6 nm thick PBD-PEO (poly(1,2-butadiene)-b-poly(ethylene oxide)) bilayers. PBD-PEO membranes offer high mechanical and chemical stability and low electrical noise, but the thick membrane hinders anchoring of biological nanopores. By systematically investigating the elongation of the β-barrel, we engineered nanopore constructs suitable for PBD 11 PEO 8 and PBD 22 PEO 14 membranes. Efficient insertions were observed by adding amino acids that stabilised the transmembrane β-barrel structure and enhanced anchoring of the nanopore into the membrane. Molecular dynamics simulations and single-molecule assays revealed that nanopores folded naturally into PBD-PEO bilayers, enabling successful detection of cyclodextrins and translocation of polypeptides and full-length proteins. Our study offers important lessons for the reconstitution of membrane proteins into artificial membranes. Moreover, these highly robust nanopore-membrane interfaces can be readily integrated into biosensing devices, enabling peptide and protein analysis directly from complex solutions.</p><p class="metadata"><time datetime="2026-03-16" title="Source date; precision not specified">March 16, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.03.13.711555">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/03/16/2026.03.13.711555.full.pdf">Open PDF</a></p> Mon, 16 Mar 2026 00:00:00 GMT Edo Vreeker Adina Sauciuc Fabian Grünewald Ali Hammoudi Giovanni Maglia OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/a31143d0c5fce386d2f2618423a19755ffac598d30a3079bb734f4b320f7545c/ urn:sha256:a31143d0c5fce386d2f2618423a19755ffac598d30a3079bb734f4b320f7545c <p>Biosensing with solid-state nanopores (SSNPs) is a versatile technique suitable for the analysis of double-stranded DNA, RNA, and their hybrids, complementing the use of biological nanopores for single-stranded nucleic acids and proteins. In this review, we systematically explain how operational parameters - including bias voltage, pore geometry, and buffer properties - affect translocation of double-stranded nucleic acids through SSNPs. We focus on key performance metrics for resolution, characterised by translocation time and signal-to-noise ratio, and throughput, described by event frequency and unfolded fraction. Beyond summarizing empirical observations, we dissect the underlying physical mechanisms that mediate these dependencies, including electrophoretic driving, hydrodynamic friction, electro-osmotic flow, and entropic effects. By integrating experimental findings with physical models, we aim to provide a practical guide for optimizing and interpreting SSNP experiments. The concepts discussed are broadly transferable to other SSNP targets and nanoscale transport applications.</p><p class="metadata"><time datetime="2026-03-16" title="Source date; precision not specified">March 16, 2026</time> <span aria-hidden="true"> · </span> Physics of Life Reviews</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.plrev.2026.03.002">Original publication</a></p> Mon, 16 Mar 2026 00:00:00 GMT Simon Brauburger Ulrich F. Keyser OpenAlex https://reading.michaelmvh.com/article/6b99c02501d86c4681cef7ea6fa9ba4d906ec489609562f2fc7e0a4573a7796d/ urn:sha256:6b99c02501d86c4681cef7ea6fa9ba4d906ec489609562f2fc7e0a4573a7796d <p>Inducing protein oligomerization holds therapeutic promise, yet identifying or rationally designing effective inducers remains challenging. In this study, we leverage nanopore technology to screen small molecules capable of modulating WD repeat domain 5 (WDR5) protein oligomerization and uncover a oligomerization mechanism which we term Catalytic Proximal Protein Oligomerization (CaPPO). Nanopore sensing enabled rapid identification of WZ-1, a selective WDR5 oligomerization inducer, from our in-house compound library. Biochemical and cryo-EM analyses reveal that WZ-1 binds the WBM site of WDR5 through its 2-aminothiazole moiety, reacts with Cys248 to form an intramolecular disulfide, and, through N-terminal tail-induced proximity of WDR5 molecules, triggers oligomerization via thio-disulfide exchange. Structure-activity relationship studies indicate that the disulfide motif within WZ-1 acts as a molecular scout initiating oligomerization. In cellular assays, WZ-1 exhibits potent anti-tumor activity by disrupting WDR5 interactions at both WIN and WBM sites, leading to transcriptional downregulation of target genes. Collectively, this work not only establishes a nanopore-based screening platform for identifying protein oligomerization inducers, but also validates CaPPO as a promising small-molecule design strategy for therapeutic development.</p><p class="metadata"><time datetime="2026-03-13" title="Source date; precision not specified">March 13, 2026</time> <span aria-hidden="true"> · </span> Nature Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41467-026-70409-z">Original publication</a></p><p><a href="https://www.nature.com/articles/s41467-026-70409-z_reference.pdf">Open PDF</a></p> Fri, 13 Mar 2026 00:00:00 GMT Yizheng Fang Li Jiang Feifan Wang Yihui Zhou Jie Cen Yuxin Yang Haiyang Wang Qi Chen Yushen Lin Tingting Wang Hongxia Xu Yongping Yu Cheng‐Liang Zhu Qiaojun He Bo Yang Chun Zhou Wenteng Chen Longhua Tang Ji Cao OpenAlex https://reading.michaelmvh.com/article/0c565df23ebae33752aa5000d19439f728dfd4fe06885a3a763f1b4d5de9f917/ urn:sha256:0c565df23ebae33752aa5000d19439f728dfd4fe06885a3a763f1b4d5de9f917 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-03-12" title="Source date; precision not specified">March 12, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v1/review3">Original publication</a></p> Thu, 12 Mar 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/a459b64d4aafc1eab479c4b4fcd2c8be7ecddd1473a4a5fc24c4699fe09c974e/ urn:sha256:a459b64d4aafc1eab479c4b4fcd2c8be7ecddd1473a4a5fc24c4699fe09c974e <p>No abstract is available.</p><p class="metadata"><time datetime="2026-03-12" title="Source date; precision not specified">March 12, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v1/decision1">Original publication</a></p> Thu, 12 Mar 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/4cb094e8b3b1998503e3cdd6e2a67940abf2e38c91344f4ad882b2f9198962a4/ urn:sha256:4cb094e8b3b1998503e3cdd6e2a67940abf2e38c91344f4ad882b2f9198962a4 <p>Abstract α-Hemolysin (Ahly) is a major Staphylococcus aureus virulence determinant implicated in tissue injury and immune dysregulation; antibody inhibitors have reached clinical trials but alternatives with improved ease of manufacture and tissue penetration are desirable. Here we demonstrate that phage-derived bicyclic peptides can serve as compact, chemically tractable Ahly neutralisers. Using TATB-scaffolded M13 phage libraries we identified WNP-motif containing bicyclic binders, with a lead hit of Peptide 14 (K D = 1792nM) and progressed the lead by iterative affinity maturation to Peptide 20 (K D = 609 nM) and by incorporation of strategically chosen non-canonical amino acids to yield Peptide 88 (KD = 96 nM). A 2.2 Å co-crystal structure with AhlyH35A locates the binding footprint on the rim domain and explains the critical role of the WNP motif in target engagement. Functional assays show that the Peptide 88 blocks Ahly mediated hemolysis, inhibits Ahly driven ADAM10 activation, and elucidate its inhibitory mechanism of preventing Ahly binding to human A549 epithelial cells. Peptide 88 protects A549 cells from recombinant toxin and attenuates cytotoxicity in S. aureus co-culture experiments, whilst showing no toxicity to A549 cells. Bicyclic peptides thus represent a new and promising anti-virulence modality: small, synthetically accessible molecules that mimic antibody recognition, with therapeutic potential against S. aureus infections.</p><p class="metadata"><time datetime="2026-03-10" title="Source date; precision not specified">March 10, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.03.09.710508">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/03/10/2026.03.09.710508.full.pdf">Open PDF</a></p> Tue, 10 Mar 2026 00:00:00 GMT Jonathan Whiteside Nick Lewis L. Diaz Saez Hector Newman Sarah Newell Tazmin T. Martin Jack Butler Michael J. Skynner Michael J. Dawson Paul Beswick Christopher Gerard Dowson Catherine E Rowland OpenAlex https://reading.michaelmvh.com/article/cb379f062db44ff542938f0fa2d21bc024eb0b039d46f9062939b1c689236c62/ urn:sha256:cb379f062db44ff542938f0fa2d21bc024eb0b039d46f9062939b1c689236c62 <p>Intracellular persistence caused by Staphylococcus aureus (S. aureus) is among the primary reasons for recurrence and difficulty in eradicating S. aureus infections. In this study, we identify the secreted protein Hla (α-hemolysin) by S. aureus as a key factor enabling its intracellular retention. We demonstrate that intracellular Hla secreted by S. aureus inhibits lysosome degradation via disrupting lysosomal function, which sustains the survival and proliferation of S. aureus within autophagosomes. Furthermore, we identify the interaction between Hla and intracellular LGALS3 (galectin 3) as crucial for sustaining intracellular survival of S. aureus, resolve the structure of the Hla-LGALS3 complex, and identify the Loop 68-75 region of Hla as the key binding domain with LGALS3. Moreover, the interaction between Hla and LGALS3 influences the recruitment of PDCD6IP/ALIX (programmed cell death 6 interacting protein) to the damaged lysosomal surface, resulting in disruption of lysosomal degradative function. Our results highlight an unknown role of Hla in the intracellular survival of S. aureus and suggest that interrupting the interaction between Hla and LGALS3 May be a potential therapeutic strategy for treating S. aureus infections.</p><p class="metadata"><time datetime="2026-03-06" title="Source date; precision not specified">March 6, 2026</time> <span aria-hidden="true"> · </span> Autophagy</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1080/15548627.2026.2642331">Original publication</a></p> Fri, 06 Mar 2026 00:00:00 GMT Yanhao Zhang Zhuo Zhao Pu Han Jianxun Qi Mingzhou Zhang Liting Wang Yumin Meng Jing Li Y S Yang Lie Chen Jinyong Zhang Jiang Gu Ping Luo Weijun Zhang Liangbo Sun Zou Quanming Hao Zeng OpenAlex https://reading.michaelmvh.com/article/531e41ecdd22358778d776c71c773d6ec27f47baf0d5b8880ffb3ab2725491b4/ urn:sha256:531e41ecdd22358778d776c71c773d6ec27f47baf0d5b8880ffb3ab2725491b4 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-03-05" title="Source date; precision not specified">March 5, 2026</time> <span aria-hidden="true"> · </span> Colloidal Nanoparticles for Biomedical Applications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1117/12.3079107">Original publication</a></p> Thu, 05 Mar 2026 00:00:00 GMT Adrien Nicolaı̈ OpenAlex https://reading.michaelmvh.com/article/8aeb5b5a946140bf748549ae9a1e036098c207c6161bb6f365ecdb0a11e7ca2c/ urn:sha256:8aeb5b5a946140bf748549ae9a1e036098c207c6161bb6f365ecdb0a11e7ca2c <p>No abstract is available.</p><p class="metadata"><time datetime="2026-03-05" title="Source date; precision not specified">March 5, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v1/review2">Original publication</a></p> Thu, 05 Mar 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/1463f0cd73019ffd9abe205f6c23833f36233b9242a11a808dd635dfefb46c46/ urn:sha256:1463f0cd73019ffd9abe205f6c23833f36233b9242a11a808dd635dfefb46c46 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-03-02" title="Source date; precision not specified">March 2, 2026</time> <span aria-hidden="true"> · </span> Publons reviews and discussion</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d/v1/review1">Original publication</a></p> Mon, 02 Mar 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/93408307204535bfe5d3ff61bc753a8f91c557f52309513bf8f7fa0299593b29/ urn:sha256:93408307204535bfe5d3ff61bc753a8f91c557f52309513bf8f7fa0299593b29 <p>Biological processes often imply dynamics in crowded or confined media. Here, we focus on the entry of molecules into nanopores relevant for applications in health, biotechnologies, or the environment. Polymers in the semi-dilute regime that are excluded from the nanopore generate osmotic pressure, allowing controlled entry of analytes and facilitating their detection and identification inside a confined media. Using solid-state nanopores, we first study the entry dynamics of neutral polymers in a semi-dilute solution at the single-molecule level. We investigate the influence of polymer concentration, chain length and nanopore size. Second, we study the detection and identification of polysaccharides of various molecular weights in the presence of large polymers. Third, we discriminate between two peptide biomarkers with an enantiomeric difference in only one amino acid (D- or L-) for different stoichiometric ratios. From these examples, we experimentally demonstrate the universal behavior that drives large polymers into a nanopore. When the mesh size of the semi-dilute solution is smaller than the nanopore size, the osmotic energy overcomes the confinement energy, allowing the chain to enter the confined media. We found that the power-law dependency of the threshold concentration for polymer entry on the ratio between nanopore and monomer size is predicted theoretically by Pierre-Gilles de Gennes. Additionally, the depletion layer thickness depends on the screening length (mesh size), revealing three regimes that rely on the ratio between the pore size and the screening length. The application of polymer scaling laws represents a universal approach to control the dynamics of biomolecules through nanopores. The theoretical framework by de Gennes suggested that the mesh size of polymer solutions influences the entry of molecules into nanopores, but experimental validation was lacking. The authors conducted experiments using solid-state nanopores to investigate how polymer concentration, chain length, and nanopore size affect the entry dynamics of neutral polymers and the detection of polysaccharides and peptide biomarkers.</p><p class="metadata"><time datetime="2026-02-28" title="Source date; precision not specified">February 28, 2026</time> <span aria-hidden="true"> · </span> Nature Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41467-026-68912-4">Original publication</a></p><p><a href="https://www.nature.com/articles/s41467-026-68912-4.pdf">Open PDF</a></p> Sat, 28 Feb 2026 00:00:00 GMT Yuhua Cai Benjamin Cressiot Mathias Winterhalter Sébastien Balme Juan Pelta Laurent Bacri OpenAlex https://reading.michaelmvh.com/article/e82197578eb03bf7e6723f2f4d4229ab62b0788ae8b0eb00ee54b643286c4c33/ urn:sha256:e82197578eb03bf7e6723f2f4d4229ab62b0788ae8b0eb00ee54b643286c4c33 <p>Advances in protein sequencing and analysis are poised to transform proteomics through an ability to link sequence, structure, and function at scale, thereby accelerating biological discovery and biomedical innovation. However, interrogating proteins is uniquely challenging because they cannot be amplified, are composed of complex chemical structures, and exist across a vast landscape of proteoforms. Techniques such as mass spectrometry typically drive large-scale proteomics studies; however, a new generation of technologies is pushing the boundaries, promising new features such as de novo, single-molecule, and/or higher-throughput sequencing and analysis. While many strategies are still in an early stage, a few modalities, such as fluorosequencing, single-molecule sequencing, digital proteomics mapping, and nanopore-based protein sequencing, have now reached or are thought to be nearing commercial implementation. In this review, we evaluate the mechanisms, current progress, and remaining challenges of these technologies while also highlighting how recent innovations are converging toward a new generation of proteomic technologies.</p><p class="metadata"><time datetime="2026-02-23" title="Source date; precision not specified">February 23, 2026</time> <span aria-hidden="true"> · </span> Annual Review of Analytical Chemistry</p><p class="provenance">Curated by <a href="https://github.com/Michaelmvh/scholarly-rss-feed/blob/main/src/curated/nanopore-foundations.json" rel="external">Nanopore Foundations &amp; Signal Analysis</a> · Protein analysis · Review</p><p><a href="https://doi.org/10.1146/annurev-anchem-071724-035726">Original publication</a></p> Mon, 23 Feb 2026 00:00:00 GMT K. C. Wong Mattias Tolhurst Oren A. Fox Safwan Diwan Nicholas Bogard Jeff Nivala OpenAlex Nanopore Foundations & Signal Analysis https://reading.michaelmvh.com/article/473383e5d5be43a674006adbdf57244fd0223163bc3a672b206c85bdf62f8d66/ urn:sha256:473383e5d5be43a674006adbdf57244fd0223163bc3a672b206c85bdf62f8d66 <p>Nanopore-based single-molecule sensing holds immense promise for revolutionizing proteomics, however, its practical application remains constrained by low throughput, suboptimal library preparation, and limited analytical power for complex, stochastic signals. To overcome these challenges, we develop a high-throughput nanopore sensing platform that couples a streamlined peptide library preparation strategy with an AI-driven analytical workflow, enabling accurate peptide differentiation and protein identification. Our analytical framework captures the distinct statistical signatures of peptides within massive single-molecule event streams, transforming them into reliable, information-rich fingerprints to achieve remarkable classification accuracy. We also apply this platform to establish a rapid and cost-effective workflow for antibody validation, facilitating precise epitope screening and semi-quantitative affinity determination. Critically, in a blinded study, this high-throughput sensing system demonstrates its robustness by unambiguously identifying multiple proteins from their complex enzymatic digests. By establishing an end-to-end pipeline from native proteins/peptides modification, parallel sensing to their identification, this work develops a scalable and powerful method for proteomics research. Nanopore peptide sensing faces throughput, library preparation and analysis challenges. Here, the authors develop a high-throughput platform that integrates library preparation with AI analysis to accurately identify peptides, enabling antibody validation and protein identification.</p><p class="metadata"><time datetime="2026-02-23" title="Source date; precision not specified">February 23, 2026</time> <span aria-hidden="true"> · </span> Nature Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1038/s41467-026-69628-1">Original publication</a></p><p><a href="https://www.nature.com/articles/s41467-026-69628-1_reference.pdf">Open PDF</a></p> Mon, 23 Feb 2026 00:00:00 GMT Ji Wang Junyi Chen Hailin Pan Fengqin Luo Wenbing Qin Huixian Zeng Xilong Yuan Yuchen Qiao Yunfeng Zhang Yishuo Zhang Dapeng Wang Liang Shen Zhiwei Zhai Qianhua Zhu Yuqing Deng Xiaojing Sheng Qingqing Xie Yuning Zhang Xu Yan Tao Zeng Mengzhe Shen Yinqi Bai Bo Teng Yuxiang Li Chuanyu Liu Ou Wang Yuliang Dong Siqi Liu Xun Xu OpenAlex https://reading.michaelmvh.com/article/586a41fab0ef602e86a39d065a523f754cbbfc3f5fd33921092a26ad8e1881f8/ urn:sha256:586a41fab0ef602e86a39d065a523f754cbbfc3f5fd33921092a26ad8e1881f8 <p>This dataset contains all scripts required to replicate the results of our paper &quot;Deep Learning-Driven Peptide Classification in Biological Nanopores&quot;. Data can be obtained through the corresponding author.</p><p class="metadata"><time datetime="2026-02-23" title="Source date; precision not specified">February 23, 2026</time> <span aria-hidden="true"> · </span> Universitätsbibliothek Stuttgart</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.18419/darus-5740">Original publication</a></p> Mon, 23 Feb 2026 00:00:00 GMT Julian Hoßbach Samuel Tovey Sandro Kuppel Tobias Ensslen Jan Claas Behrends Christian Holm OpenAlex https://reading.michaelmvh.com/article/ad67eb8bada103f15ee713dc782910b06453fad2952f337e04561aa6fbe4938a/ urn:sha256:ad67eb8bada103f15ee713dc782910b06453fad2952f337e04561aa6fbe4938a <p>The use of protein nanopores has proven to be very promising for the identification of proteins or the sequencing of peptides. However, their widespread use in biosensor applications is limited by more complex molecular properties of proteins in comparison to nucleic acids. Here, we developed an α-helical Fav nanopore from the coral Orbicella faveolata to detect human histones using a commercial MinION device. The engineered nanopores showed stable insertion into the polymeric membrane support. Bulk analysis of several tens to hundreds of pores per measurement revealed significant differences in mean current passing the pore and current noise resulting from capturing different full-length human histones or their post-translationally modified variants into the pore lumen. Importantly, detailed blocking analyses confirmed histone-specific signals that allow further discrimination between two medically important extracellular histones in mixtures. The newly developed Fav nanopore and high-throughput approach for the detection of biomedically important proteins is an important step towards the widespread use of nanopores in modern analytics.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> ACS Sensors</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acssensors.5c03533">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acssensors.5c03533?ref=article_openPDF">Open PDF</a></p> Fri, 20 Feb 2026 00:00:00 GMT Marija Srnko Gašper Šolinc Ana Crnković Franci Merzel Michael A. Jordan Elizabeth Jayne Wallace Marjetka Podobnik Gregor Anderluh OpenAlex https://reading.michaelmvh.com/article/d97623625ff85b338255b8d579973d70624b54017f00d34f851a655ecb975ee3/ urn:sha256:d97623625ff85b338255b8d579973d70624b54017f00d34f851a655ecb975ee3 <p>Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis.TENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> eLife</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7554/elife.110033.1.sa1">Original publication</a></p> Fri, 20 Feb 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/8f97fe69129d4b2a9aca571d7084269dd08ea3ca01fd80dfb5b1208b7564a322/ urn:sha256:8f97fe69129d4b2a9aca571d7084269dd08ea3ca01fd80dfb5b1208b7564a322 <p>Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis.TENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> eLife</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7554/elife.110033.1.sa0">Original publication</a></p> Fri, 20 Feb 2026 00:00:00 GMT Goretti Aranaz Novaliches Olga Gewartowska František Špoutil Seweryn Mroczek Pavel Talacko Karel Harant Ana-Matilde Augusto-Vale Irena Krejzova Carlos Eduardo Madureira Trufen Pawel Krawczyk Aleš Benda Vendula Novosadová Radislav Sedlacek Andrzej Dziembowski Jan Prochazka OpenAlex https://reading.michaelmvh.com/article/432efc51534006a8b3590c38bf023d7a85c02fe4ca525118127063f083866623/ urn:sha256:432efc51534006a8b3590c38bf023d7a85c02fe4ca525118127063f083866623 <p>Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis.TENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> eLife</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7554/elife.110033.1.sa3">Original publication</a></p> Fri, 20 Feb 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/b67230d814a7d734b3305ccfbd92d185d17e5f098522c7b473bd1488754244c7/ urn:sha256:b67230d814a7d734b3305ccfbd92d185d17e5f098522c7b473bd1488754244c7 <p>Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> eLife</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7554/elife.110033">Original publication</a></p> Fri, 20 Feb 2026 00:00:00 GMT Goretti Aranaz Novaliches Olga Gewartowska František Špoutil Seweryn Mroczek Pavel Talacko Karel Harant Ana-Matilde Augusto-Vale Irena Krejzova Carlos Eduardo Madureira Trufen Pawel Krawczyk Aleš Benda Vendula Novosadová Radislav Sedláček Andrzej Dziembowski Jan Procházka OpenAlex https://reading.michaelmvh.com/article/3b7f0e0a0404ddfe30b5d25b4e18e8b31dc61f30629e744a7b554fa57f5766c9/ urn:sha256:3b7f0e0a0404ddfe30b5d25b4e18e8b31dc61f30629e744a7b554fa57f5766c9 <p>Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis.TENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> eLife</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7554/elife.110033.1.sa4">Original publication</a></p> Fri, 20 Feb 2026 00:00:00 GMT Noriaki Ono OpenAlex https://reading.michaelmvh.com/article/bddcf5f5efc668d71e43c253b114336617c0d7f8381c86d5a61536bbc1e8d979/ urn:sha256:bddcf5f5efc668d71e43c253b114336617c0d7f8381c86d5a61536bbc1e8d979 <p>Tooth enamel formation, or amelogenesis, is a complex biomineralization process regulated by ameloblasts cells. These cells secrete enamel matrix proteins (EMPs), including Amelogenin (AMELX) and Ameloblastin (AMBN), which are essential for hydroxyapatite crystal deposition during enamel mineralization. Precise regulation of this process ensures the mechanical and chemical strength of dental enamel. Using Tent5a knock-out (KO) mouse, we demonstrated that TENT5A, a non-canonical poly(A) polymerase is crucial for the stability, translation, and secretion of EMP mRNAs, particularly AMELX, during amelogenesis. TENT5A-deficient mice exhibited Amelogenesis imperfecta, characterized by enamel hypomineralization, reduced thickness, and disrupted ultrastructure, as revealed by micro-computed tomography. Through nanopore direct mRNA sequencing, we identified that TENT5A polyadenylates Amelx and other mRNAs encoding secreted proteins, enhancing their stability and translation in the endoplasmic reticulum. Moreover, loss of TENT5A altered AMELX secretion and extracellular self-assembly, impairing matrix organization and hydroxyapatite deposition. This study highlights the role of TENT5A in post-transcriptional regulation during enamel formation, demonstrating its importance in enamel homeostasis.TENT5A adds poly(A) tails to specific mRNAs in enamel, enhancing their expression, which is crucial for dental mineralization.</p><p class="metadata"><time datetime="2026-02-20" title="Source date; precision not specified">February 20, 2026</time> <span aria-hidden="true"> · </span> eLife</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7554/elife.110033.1.sa2">Original publication</a></p> Fri, 20 Feb 2026 00:00:00 GMT OpenAlex https://reading.michaelmvh.com/article/f435f4b317ebc854b721259264a6d5c07a28bc047d0be99e9201b10ca1a0e272/ urn:sha256:f435f4b317ebc854b721259264a6d5c07a28bc047d0be99e9201b10ca1a0e272 <p>Nanopore sensing holds the potential to revolutionize proteomics, yet current methods often rely on ensemble aggregation, where thousands of events must be statistically aggregated or averaged to identify a protein or peptide signature. While effective for pure samples, this aggregation strategy fails in complex, heterogeneous mixtures where the identity of individual molecules must be determined in real-time. Here, we demonstrate high-fidelity classification of peptides from single, individual translocation events, eliminating the need for ensemble averaging. This sensitivity is achieved using the anthrax toxin protective antigen (PA) nanopore. Unlike static pores used more generally, the PA pore&#39;s dynamic active-site clamps generate information-rich, multi-state signals. These clamps also enable the utility of high-affinity capture, permitting analysis at low nanomolar concentrations. We developed a machine learning framework that makes inferences on these dynamical multi-state signals and achieves ~91% accuracy on single events. This work establishes a framework for true single-molecule proteomics, enabling the resolution of complex mixtures that bulk aggregation methods cannot decipher.</p><p class="metadata"><time datetime="2026-02-19" title="Source date; precision not specified">February 19, 2026</time> <span aria-hidden="true"> · </span> PLoS Computational Biology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1371/journal.pcbi.1014019">Original publication</a></p><p><a href="https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1014019&amp;type=printable">Open PDF</a></p> Thu, 19 Feb 2026 00:00:00 GMT Jennifer M. Colby Bryan A. Krantz OpenAlex https://reading.michaelmvh.com/article/0c67f111efa0913212871a992322d1f7fd8a6eb50c4f65944b35511f8118f25c/ urn:sha256:0c67f111efa0913212871a992322d1f7fd8a6eb50c4f65944b35511f8118f25c <p>BACKGROUND: Colorectal cancer (CRC) is the third most common cancer globally. Alternative splicing contributes significantly to CRC tumorigenesis through aberrant transcript generation. However, the regulatory influence of RNA modifications on splicing remains poorly understood, largely due to technical difficulty. Nanopore direct RNA sequencing addresses this by enabling simultaneous detection of RNA modifications and Alternative splicing events (ASEs). METHODS: We conducted Nanopore direct RNA sequencing on paired tumor and normal tissues from surgical resections at Beijing Hospital. Differential putative RNA modification sites and ASEs linked to CRC were systematically identified. To validate the key findings, we utilized a large patient cohort from The Cancer Genome Atlas (TCGA) and predicted 3D protein structures with AlphaFold3. The predicted structures were then compared using TM-align. Regulatory relationships between RNA modifications and splicing were explored through predictive modeling of potential cis-regulatory pairs. The splicing events were also validated. RESULTS: The MYH11-201 transcript of the MYH11 gene contains an additional exon (ENSE00001632812) compared to the MYH11-203 isoform. Both bioinformatic analysis and experimental validation confirmed frequent loss of this exon in tumor tissues. This finding was further validated in the TCGA cohort, demonstrating a significant preference for exon skipping in tumor tissues. These results suggest that the skipping of ENSE00001632812 is a promising candidate biomarker associated with CRC pathogenesis. Notably, this exon&#39;s PF00063 domain interacts with multiple tumor suppressor genes and oncogenes domains, suggesting its functional importance. The structures revealed pronounced rotational divergence within a putative C-terminal transmembrane domain-like region. Furthermore, we utilized Nanopore sequencing to explore the potential interplay between alternative splicing and RNA modifications. We implemented an integrated analytical workflow (available at https://github.com/lelelililele/Nanopore-ASEs-and-RNA-modification ) combining modification calling and splicing analysis tools to investigate RNA modification-related enzymes and splicing-related proteins in CRC. CONCLUSIONS: This pilot study utilizes Nanopore direct RNA sequencing to characterize exon skipping events and RNA modifications in CRC. We identified the skipping of MYH11 exon ENSE00001632812 as a potential candidate for future diagnostic investigation. By integrating modification and splicing data, we highlighted putative regulatory pairs that warrant further functional exploration. While our findings offer new insights into CRC molecular mechanisms, extensive validation in independent large-scale cohorts and functional assays is essential to confirm the diagnostic utility and mechanistic roles of these targets.</p><p class="metadata"><time datetime="2026-02-13" title="Source date; precision not specified">February 13, 2026</time> <span aria-hidden="true"> · </span> Human Genomics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1186/s40246-026-00931-0">Original publication</a></p> Fri, 13 Feb 2026 00:00:00 GMT Lili Zhang Jian Cui Jinxin Shi Jiahui Cai Tianhan Sun Gaoyuan Sun Yifei Li Hexin Li Siyuan Xu Xiaokun Tang Ziwei Chen Hongyuan Cui Fei Xiao Gang Zhao OpenAlex https://reading.michaelmvh.com/article/b1aee418ac3452be110b0ee0dd5ace59d7fb817a87cc2fdfd3cf47ce38ae3c66/ urn:sha256:b1aee418ac3452be110b0ee0dd5ace59d7fb817a87cc2fdfd3cf47ce38ae3c66 <p>Accurate disease diagnosis requires analyzing multiple biomarkers in a single sample to improve diagnostic precision and guide treatment. However, the simultaneous detection of three or more proteases in a sample, especially with a single probe, remains a major challenge. Herein, we developed a triple-response peptide probe for monitoring three proteases via a single aerolysin nanopore. The T-shaped probe contains three independent arms each with a target-specific cleavage sequence. Upon protease recognition, short peptide fragments are released and generate characteristic current signatures during nanopore translocation. The enzymes themselves are sterically excluded, ensuring signals originate solely from cleavage products. Each peptide yields a distinct signature, enabling simultaneous, label- and amplification-free quantification with detection limits extending to the femtomolar range. Integrated with a machine learning classifier, the system achieves 97.7% accuracy in signal discrimination. This strategy enables accurate and multiplexed quantification of multiple enzymes in complex biological fluids, such as serum, which is important for disease diagnosis based on liquid biopsies.</p><p class="metadata"><time datetime="2026-02-06" title="Source date; precision not specified">February 6, 2026</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c06310">Original publication</a></p> Fri, 06 Feb 2026 00:00:00 GMT Yao Jiang Baixue Chu Wenzhi Ma Min Liu Shusheng Zhang Dongmei Xi OpenAlex https://reading.michaelmvh.com/article/d03186ba3cc4003d12e812be91e6dc849f7d46566aed14cfd35addaa562a30f3/ urn:sha256:d03186ba3cc4003d12e812be91e6dc849f7d46566aed14cfd35addaa562a30f3 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.1481">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Yu S. Chen Meni Wanunu Xialin Zhang Noé Quittot Bradley T. Hyman OpenAlex https://reading.michaelmvh.com/article/7f49910ea0567f504f2e55efe52c66417e95fbe44e0712f66499e493de356111/ urn:sha256:7f49910ea0567f504f2e55efe52c66417e95fbe44e0712f66499e493de356111 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.1479">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Xialin Zhang Yuhaohua Zheng Parker Hitt Zhuoyu Zhang Dinara Boyko Meni Wanunu OpenAlex https://reading.michaelmvh.com/article/83df706dbd986bb7ff1dfa0f529847c399da89e19070c380e110d5e8e1987954/ urn:sha256:83df706dbd986bb7ff1dfa0f529847c399da89e19070c380e110d5e8e1987954 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.1478">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Jose M. Cisneros Mandujano Rik Dhar Meni Wanunu OpenAlex https://reading.michaelmvh.com/article/67c60f78a4e8ea241758fa7209892b254d046625b604f9ec2b8458ab99c088ad/ urn:sha256:67c60f78a4e8ea241758fa7209892b254d046625b604f9ec2b8458ab99c088ad <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.2257">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Laura R. Ratinho Luca Iesu Bénédicte Thiébot Laurent Bacri Juan Pelta Benjamin Cressiot OpenAlex https://reading.michaelmvh.com/article/9ba709384baab24a4ee054784c93e51b46965bf617cf2b6a3c71d70996b43549/ urn:sha256:9ba709384baab24a4ee054784c93e51b46965bf617cf2b6a3c71d70996b43549 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.1480">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Lan Yang Ngoc Phuong Dung Ho Christopher Edmonds Eric Pooser Roman Aranda Katherine Young James C. Gumbart OpenAlex https://reading.michaelmvh.com/article/7f8b0eee5898bd3e6f5903f508629d3d25664f9f7f3f958b0a5b0d2438466f50/ urn:sha256:7f8b0eee5898bd3e6f5903f508629d3d25664f9f7f3f958b0a5b0d2438466f50 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.2266">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Ayaka Nakada Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/c20de67299a4423803b85426c1fba88fb92c85bb78825126f384f2da81ad8681/ urn:sha256:c20de67299a4423803b85426c1fba88fb92c85bb78825126f384f2da81ad8681 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-02-01" title="Source date; precision not specified">February 1, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bpj.2025.11.1482">Original publication</a></p> Sun, 01 Feb 2026 00:00:00 GMT Ying-Huan FU Yi‐Tao Long Yi-Lun Ying OpenAlex https://reading.michaelmvh.com/article/3f9fc2a75f935c9bb0cecfc82cd4945481850135d95914b965337a0a30cfd413/ urn:sha256:3f9fc2a75f935c9bb0cecfc82cd4945481850135d95914b965337a0a30cfd413 <p>protein sequencing. This nanopore review begins with DNA sequencing and elaborates on up-to-date technical breakthroughs in protein sequencing and other proteomics approaches. Overall, nanopore technology is conducive to discovering the proteome diversity and revealing the pathogenesis mechanism.</p><p class="metadata"><time datetime="2026-01-30" title="Source date; precision not specified">January 30, 2026</time> <span aria-hidden="true"> · </span> iScience</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.isci.2026.114835">Original publication</a></p> Fri, 30 Jan 2026 00:00:00 GMT Yutong Wang Qian Han Yilong He Shumin Deng Ziwei Huang Ziyan Zhang Shuaijian Dai Zhuxin Dong OpenAlex https://reading.michaelmvh.com/article/839c05bd795164b3b1741ee6e9e2b24c6ae69f10aaafefb6b73a948be92955bd/ urn:sha256:839c05bd795164b3b1741ee6e9e2b24c6ae69f10aaafefb6b73a948be92955bd <p>Nanopore biosensors have become an attractive class of biosensors in recent years, especially because of the promise they hold in the single-molecule detection and quantification space. Various formats of nanopore sensors in literature have demonstrated significant potential to detect and quantify clinically relevant disease biomarkers such as proteins and nucleic acids. However, there are still some identified challenges such as lack of analyte-specific ionic current signals for electrical nanopore assays in complex biological samples, or elongated response time due to mass transport limitations. In this work, nanopore translocation and optical signal strategies have been adopted to overcome some of these identified challenges. Analyte-specific signal was ensured by deploying a functional dimeric fluorescent nanoparticle biorecognition concept, where the target nucleic acid (miRNA) via hybridization, bridges two complementary halves of DNA probes grafted on two different colours of nanoparticles. This way, each dimer nanoparticle translocation is counted as a molecule of target miRNA. This single molecule counting (via digital image analysis) makes the assay truly quantitative. Locked nucleic acid (LNA) nucleotide units were introduced between DNA probe nucleotides to stabilize the resulting DNA:RNA duplex structure, which was otherwise unstable due to low melting temperature resulting from the split-probe design. Electrical potential difference is employed to drive nanoparticles through a high-density nanopore array, enabling simultaneous monitoring of thousands of translocation events, and significantly reducing the analysis time. The developed assay was then used to detect and quantify miRNA-155 in both physiological buffer (PBS) and complex biological (cell culture) samples, reaching low femtomolar detection limit. By combining a third colour of fluorescent nanoparticles, a second miRNA target (miRNA-21) was simultaneously detected and quantified in both buffer and complex biological samples, demonstrating the multiplex detection capabilities of the system. The applicability of this assay in answering clinically relevant questions was also demonstrated by monitoring the changes in miRNA-155 levels after drug treatment of spheroids from MCF7 human breast cancer cell lines, with very promising results. In conclusion, this project has demonstrated the great potential that lies in optical nanopore sensors, being able to reach very low femtomolar detection limits with amplification-free detection and quantification of very dilute nucleic acid analytes, even in complex liquid biopsies.</p><p class="metadata"><time datetime="2026-01-27" title="Source date; precision not specified">January 27, 2026</time> <span aria-hidden="true"> · </span> UNSWorks (University of New South Wales, Sydney, Australia)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26190/unsworks/31955">Original publication</a></p> Tue, 27 Jan 2026 00:00:00 GMT Bobmanuel Echeonwu OpenAlex https://reading.michaelmvh.com/article/568676cb3109aba65ed994eec0612d50afd0d93ce86bfd4cef2c4a126fb77e6c/ urn:sha256:568676cb3109aba65ed994eec0612d50afd0d93ce86bfd4cef2c4a126fb77e6c <p>Post-translational modifications (PTMs) underpin much of protein regulation, yet their single-molecule readout remains a challenge in nanopore proteomics. While biological nanopores have shown exquisite PTM sensitivity, the microscopic mechanisms by which PTMs perturb signals in solid-state nanopores are largely unexplored. Here, we use all-atom molecular dynamics to investigate how three common PTMs, acetylation, phosphorylation, and methylation, modulate the translocation of a cancer-relevant p53 peptide fragment through a bilayer graphene nanopore. We find that PTMs remodel the translocation landscape far more strongly at the level of dwell-time statistics than at the level of mean current blockade. Acetylation enhances peptide-graphene adhesion and substantially slows transport, with adjacent acetylations producing the longest residence times due to cooperative interfacial interactions, while remotely spaced acetylations yield broader, heterogeneous dynamics. Phosphorylation introduces a negative charge that increases dwell time through an electrostatic tug-of-war, while also generating the largest current blockade among the PTMs studied. In contrast, methylation minimally perturbs translocation due to weak pore interactions and preserved charge. Combining dwell time with relative blockade features enables a simple linear SVM classifier to reliably distinguish unmodified, acetylated, and phosphorylated states. These results establish mechanistic design principles for PTM detection using solid-state nanopores and delineate which classes of PTMs are the most amenable to single-molecule detection with these devices.</p><p class="metadata"><time datetime="2026-01-26" title="Source date; precision not specified">January 26, 2026</time> <span aria-hidden="true"> · </span> bioRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.64898/2026.01.26.701721">Original publication</a></p><p><a href="https://www.biorxiv.org/content/10.64898/2026.01.26.701721v1.full.pdf">Open PDF</a></p> Mon, 26 Jan 2026 00:00:00 GMT Upadhyaya, A Sur, P Varma, M Maiti, P. K OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/ac5fb40575c123a74a07bf42f9853d54ec3379017e702644bf65702104817be3/ urn:sha256:ac5fb40575c123a74a07bf42f9853d54ec3379017e702644bf65702104817be3 <p>Glycopeptide antibiotics serve as critical last-resort drugs against resistant pathogens. However, emerging resistance─primarily due to altered interactions between glycopeptides and their bacterial targets─has begun to compromise their clinical effectiveness. Understanding the dynamic, molecular–level interactions between glycopeptide antibiotics and their targets is essential for elucidating resistance mechanisms and guiding the design of next-generation therapeutics. Conventional techniques, however, lack the resolution to capture these transient binding events in real time. In this study, we present a nanopore-based biomimetic probe strategy to study glycopeptide–peptidoglycan interactions at the single-molecule level. A series of biomimetic peptidoglycan precursor peptides (BPGPPs) with the sequence of (DE) n A D EK(G 5 ) D A D A have been designed. Using these BPGPPs and the α-hemolysin (α-HL) nanopore, we achieved real-time single-molecule recordings of BPGPP–glycopeptide complex dissociation for a range of commercially available glycopeptides. The binding affinity of each glycopeptide toward BPGPPs is reflected by the mean dwell time of the complex within the α-HL nanopore. Furthermore, by investigating terminal residue mutations in BPGPPs, we gained insight into natural resistance mechanisms and potential trends in future glycopeptide-resistant strains. This research offers a time- and space-resolved single-molecule method for investigating glycopeptide–peptidoglycan interactions and holds promise for guiding the development of next-generation antimicrobial agents.</p><p class="metadata"><time datetime="2026-01-23" title="Source date; precision not specified">January 23, 2026</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c07349">Original publication</a></p> Fri, 23 Jan 2026 00:00:00 GMT Zhuoqun Su Yan Zhao Liuxin Jiao Di Wu Yongning Wu G. B. Li OpenAlex https://reading.michaelmvh.com/article/c11899e86b1c915b84dedec8591ca458d20070bbd3ad69cd5f0bd6eb6a7a0566/ urn:sha256:c11899e86b1c915b84dedec8591ca458d20070bbd3ad69cd5f0bd6eb6a7a0566 <p>ABSTRACT RNA binding proteins (RBPs) control gene expression through their activities in essentially all processing steps of coding and noncoding RNAs and are dysregulated in disease. With &gt;95% of human multi-exon genes undergoing alternative splicing, the inability to assign RBP sites to distinct RNA variants fundamentally limits our understanding of RNA regulation. We present dirCLIP, a method combining UV crosslinking and immunoprecipitation (CLIP) with amplification-free direct nanopore long-read sequencing preserving full-length transcripts. dirCLIP employs two complementary strategies: direct RNA sequencing detecting amino acid adduct-induced perturbations in current signals and direct cDNA sequencing capturing binding sites as mutations. Benchmarking dirCLIP with SRSF3 demonstrated &gt;75% concordance with short-read-based data, revealed isoform-selective RNA binding and enabled detection of co-occurring binding sites in single RNA molecules. Application to the noncanonical RBP HMGA1 uncovered new AT-hook mediated RNA variant-specific interactions. dirCLIP fundamentally transforms our ability to interrogate RNA regulation of distinct isoforms and transcript variants with direct implications to disease mechanisms and development of RNA therapeutics.</p><p class="metadata"><time datetime="2026-01-22" title="Source date; precision not specified">January 22, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.01.22.701028">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/01/22/2026.01.22.701028.full.pdf">Open PDF</a></p> Thu, 22 Jan 2026 00:00:00 GMT Mohamed N. M. Bahrudeen Mauro Scaravilli Zileena Zahir Katrina Woodward Timo Ahola Madara Ratnadiwakara Jan Kaslin Fionna E. Loughlin Nikolay E. Shirokikh Minna‐Liisa Änkö OpenAlex https://reading.michaelmvh.com/article/442ffcccb46c1e8b6590b2e7d2daceb3139f728496d3a9794d85fa1367b4798e/ urn:sha256:442ffcccb46c1e8b6590b2e7d2daceb3139f728496d3a9794d85fa1367b4798e <p>This repository contains processed datasets generated in the study “Global patterns of stage-specific alternative polyadenylation in rice tillering revealed by Nanopore long-read sequencing and proteomics”. The datasets include:(i) a processed APA site usage and count matrix derived from Nanopore long-read RNA sequencing,(ii) quantitative proteomics intensity matrices across rice tillering stages, and(iii) updated polyadenylation site and transcript annotation files generated from long-read data.</p><p class="metadata"><time datetime="2026-01-19" title="Source date; precision not specified">January 19, 2026</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.18295004">Original publication</a></p> Mon, 19 Jan 2026 00:00:00 GMT Haihui Fu Xinyi Li OpenAlex https://reading.michaelmvh.com/article/46a90912e01c7d9685e43258216761076c2d0f66603e09f6edc77086e729896d/ urn:sha256:46a90912e01c7d9685e43258216761076c2d0f66603e09f6edc77086e729896d <p>New1 is a homologue of the essential yeast translation elongation factor eEF3. Lack of New1 has been shown to induce ribosome queuing upstream of the stop codon on messenger RNAs (mRNAs) with specific C-terminal lysine and arginine codons. Here, we used ultraviolet crosslinking and analysis of complementary DNA (cDNA), long-read nanopore sequencing, and proteomics to address the consequences such queues have for the yeast cell. We show that these queues represent collisions, recognized by collision sensor Hel2, triggering mRNA degradation via canonical no-go decay (NGD). We identified 139 target mRNAs, on which decay is initiated by Cue2-mediated cleavage upstream of the stop codon. Compared to other collision-prone mRNAs, ending on the same C-terminal codons, these targets are characterized by stronger secondary structures upstream of the stop codon, longer queues, and stronger queuing signatures. Nanopore sequencing enabled characterization of NGD cleavage fragments across targets. Ultimately, NGD in the absence of New1 leads to downregulation of encoded proteins, including highly abundant and essential metabolic enzymes like Pgk1 and Gpm1, as well as translation elongation factors such as eEF1-alpha and eEF1-beta. We show that New1 protects such mRNAs from degradation by NGD and that NGD is a major determinant of the cold sensitive growth phenotype observed in NEW1 deletants.</p><p class="metadata"><time datetime="2026-01-14" title="Source date; precision not specified">January 14, 2026</time> <span aria-hidden="true"> · </span> Nucleic Acids Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1093/nar/gkag047">Original publication</a></p><p><a href="https://academic.oup.com/nar/article-pdf/54/3/gkag047/66620294/gkag047.pdf">Open PDF</a></p> Wed, 14 Jan 2026 00:00:00 GMT Max Müller Lena Sophie Tittel Elisabeth Petfalski Kaushik Viswanathan Iyer Alina-Andrea Kraft Stefan Pastore Tamer Butto Marie‐Luise Winz OpenAlex https://reading.michaelmvh.com/article/83568b776c443aa43c92116e2a576168391b9b32008b049af21c02b0d7bdf6e3/ urn:sha256:83568b776c443aa43c92116e2a576168391b9b32008b049af21c02b0d7bdf6e3 <p>Solid-state nanopore (SSN) sequencing has emerged as a revolutionary technique in genetic and proteomic analysis, offering low costs and long read-lengths. However, traditional SSN sequencing, which relies on an electric field to drive biomolecules, faces challenges in translocating nonuniformly charged proteins, limiting its application in single-molecule protein sequencing. In this work, molecular dynamics (MD) simulations were employed to investigate peptide translocation across a BC 3 /C 3 N van der Waals (vdW) heterostructure nanopore in the absence of external forces. Our results revealed that the peptide spontaneously translocates from the BC 3 surface to the C 3 N surface due to stronger binding on the latter. However, the translocation is temporarily impeded by aromatic Phe residues, which experience strong π–π interactions with nanosurfaces, creating significant energy barriers for Phe desorption. These findings clarify the molecular-scale interactions that govern peptide motion across the BC 3 /C 3 N heterostructure interface and reveal how asymmetric adsorption energetics enable spontaneous, directional transport. Rather than assessing sequencing feasibility, this study provides mechanistic insights into heterostructure-mediated peptide motion and establishes a conceptual framework for future investigations of nanopore-based biomolecule manipulation.</p><p class="metadata"><time datetime="2026-01-13" title="Source date; precision not specified">January 13, 2026</time> <span aria-hidden="true"> · </span> The Journal of Physical Chemistry B</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.jpcb.5c06001">Original publication</a></p> Tue, 13 Jan 2026 00:00:00 GMT Xiao Jia Yuanyuan Qu Yong Qiang Li Xiangdong Liu Mingwen Zhao Weifeng Li Yang Liu OpenAlex https://reading.michaelmvh.com/article/7d4e07528ab802e57f2302f2cca6c2868f8fc7881a59bf913ca00c0f06c23296/ urn:sha256:7d4e07528ab802e57f2302f2cca6c2868f8fc7881a59bf913ca00c0f06c23296 <p>Single-molecule analysis of guest-host peptide translocations via anthrax toxin protective antigen (PA) nanopores reveals a multistate kinetic mechanism. K-means clustering identified four distinct conductance states for all peptides tested, including a fully blocked state (state 0), two intermediates (states 1 and 2), and a fully open pore (state 3). Multiexponential kinetic analysis of state-to-state transitions was performed, and the resulting lifetimes and amplitudes were correlated with molecular properties of the guest residue. These correlations revealed which physical properties govern the overall mechanism. The fully blocked state 0 acts as a &quot;hydrophobic trap,&quot; with the lifetime of entry transitions (e.g., 1→0) strongly predicted by side-chain hydrophobicity. Conversely, escaping this trap is a steric process governed by molecular size, though the probability of a fast escape is uniquely facilitated by aromaticity, suggesting a specific ungating interaction with the pore&#39;s ϕ clamp, which is consistent with clamp site dilation. Rearrangements between partially blocked states are also dominated by hydrophobicity, reflecting solvation/desolvation of guest residues and clamp site during conformational rearrangements. Final dissociation to open nanopore is a multipathway process where the dominant physical force depends on the starting state: escape from deeper states is an energetic battle against hydrophobicity and aromaticity, whereas escape from shallower states presents a final steric hurdle. Overall, this work dissects the peptide translocation process, demonstrating how distinct physical forces-hydrophobicity, sterics, and aromaticity-govern specific, sequential steps of intrapore dynamics and release, providing a detailed energy landscape for peptide-nanopore interactions.</p><p class="metadata"><time datetime="2026-01-10" title="Source date; precision not specified">January 10, 2026</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bpj.2026.01.012">Original publication</a></p> Sat, 10 Jan 2026 00:00:00 GMT Jennifer M. Colby Bryan A. Krantz OpenAlex https://reading.michaelmvh.com/article/56454623769e9b6ec5e134efa48cc4d6d9e8fc8fa0fe87488f162fe924d81448/ urn:sha256:56454623769e9b6ec5e134efa48cc4d6d9e8fc8fa0fe87488f162fe924d81448 <p>Nanopore-based technologies show promise in single-molecule protein sequencing. By using an unfoldase and a nanopore with enhanced electroosmotic flow, here we show the continuous identification of generic proteins during single nanopore passes. This approach enables the recording of differences in charge and size from single amino acid substitutions compared to reference signals, paving the way for single-molecule protein sequencing and high-throughput proteomics.</p><p class="metadata"><time datetime="2026-01-08" title="Source date; precision not specified">January 8, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p class="provenance">Curated by <a href="https://github.com/Michaelmvh/scholarly-rss-feed/blob/main/src/curated/nanopore-foundations.json" rel="external">Nanopore Foundations &amp; Signal Analysis</a> · Electroosmotic flow · Identification · Preprint · Protein analysis · Unfoldase-driven transport</p><p><a href="https://doi.org/10.64898/2026.01.08.698148">Original publication</a></p> Thu, 08 Jan 2026 00:00:00 GMT Andrea Bonini Chunzhe Lu Luca Mantovanelli Roderick Corstiaan Abraham Versloot Alwin Jansen Peter O Connell Stack Vasiliki Tsousi Pascal Knecht Kathrin Lang Andrew Heron Giovanni Maglia OpenAlex bioRxiv: Biophysics Nanopore Foundations & Signal Analysis https://reading.michaelmvh.com/article/1e7d0a5a428b8d1dfafc7e4f5c2b533f8afed983750500039334951bb2c70a0b/ urn:sha256:1e7d0a5a428b8d1dfafc7e4f5c2b533f8afed983750500039334951bb2c70a0b <p>Caspase-3 plays a critical role in apoptosis and has been regarded as a key marker in apoptosis-related disease diagnosis and therapy. However, the Caspase-3 detection in complex biological environments remains challenging due to the existence of various interferences. To solve this challenge, an antifouling nanopore biosensor is constructed by integrating distearoylphosphatidyl ethanolamine-poly(ethylene glycol) (DSPE-PEG) and a Caspase-3-targeted peptide in a single glass nanopore, and it has been successfully used for the detection and analysis of Caspase-3 protease in complex biological environments. Contact angle, electrochemical, and confocal imaging characterizations confirm the good antifouling ability of the biosensor. The sensing performance of the biosensor was characterized by the change in the nanopore&#39;s rectified ionic current. The results indicated that the antifouling biosensor has a good detection performance for Caspase-3, with a detection limit of 0.46 ng/mL, and excellent selectivity against interfering proteins.</p><p class="metadata"><time datetime="2026-01-07" title="Source date; precision not specified">January 7, 2026</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c07025">Original publication</a></p> Wed, 07 Jan 2026 00:00:00 GMT S.-H. Zhang Ruina Zheng Weiling Wu Zhi Yu Y. Q. Mei Jin‐Xuan Fan B Y Liu Yuan-Di Zhao Wei Chen OpenAlex https://reading.michaelmvh.com/article/06c39cddcd1c408d8fda027c64df448e58bc1ecc46ab6250dc6f696ab89963c8/ urn:sha256:06c39cddcd1c408d8fda027c64df448e58bc1ecc46ab6250dc6f696ab89963c8 <p>Mutations that occur during viral genome replication can result in new phenotypes, such as infection of new cell types or resistance to therapeutics. To determine the phenotypic potential of viruses, deep mutational scanning (DMS) can be used. This approach measures the effects of all amino acid changes at sites of interest on protein function, virus infectivity, or resistance to therapeutics. A virus library that contains all possible variants is produced and used to infect a culture of cells. The frequency of each amino acid at the DMS site in the infected culture relative to the input stock captures the relative fitness for each form under the selective pressure applied. Current DMS protocols are complex and costly due to reliance on deep sequencing for genomic characterization. They also require expertise in bioinformatics to process and analyze the data, thus limiting the number of labs that can apply the technology. Here, we describe a simple and efficient protocol to perform DMS on single sites and on two-site combinations in the Env protein of HIV-1. Dual-site DMS allows probing for epistatic effects. The protocol greatly reduces recombination of the proviral genome in transformed bacteria, thus efficiency of the method. Sequencing is performed using Oxford Nanopore technology, and the data are uploaded to a graphical user interface-based platform that calculates the amino acid preferences, which describe the relative fitness of all amino acids under the experimental conditions tested (e.g., under selection pressure of a drug). The protocol does not require expertise in bioinformatics and can be completed in approximately 16 days, with 3-4 days of laboratory activity and 12-13 days of incubation, with considerably lower costs than existing systems.</p><p class="metadata"><time datetime="2026-01-02" title="Source date; precision not specified">January 2, 2026</time> <span aria-hidden="true"> · </span> bioRxiv (Cold Spring Harbor Laboratory)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.64898/2026.01.02.697422">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2026/01/02/2026.01.02.697422.full.pdf">Open PDF</a></p> Fri, 02 Jan 2026 00:00:00 GMT Aaron Nicholas Gillman Madeline M Broghammer Samuel A McCarthy-Potter Rohith Rao Vujjini Cassian M Birler Alex B. Kleinpeter Hillel Haim OpenAlex https://reading.michaelmvh.com/article/629d5049c7b3425c2399429ea779ed31ff956d2d78dbf8a20621ce8a46809a54/ urn:sha256:629d5049c7b3425c2399429ea779ed31ff956d2d78dbf8a20621ce8a46809a54 <p>Proteins exist as diverse proteoforms that carry distinct combinations of posttranslational modifications (PTMs). Reading these states at the single-molecule level would reveal biological phenomena inaccessible to genomics and transcriptomics. This thesis develops nanopore-based strategies that move towards full-length, residue-level proteoform analysis. First, we employ electro-osmotic flow (EOF) in an engineered charge-selective biological nanopore to achieve non-enzymatic capture, unfolding, and translocation of intact polypeptides exceeding ~1,200 residues. Underivatised thioredoxin polyproteins undergo directional, unit-by-unit cotranslocational unfolding from either terminus, and non-denaturing concentrations of chaotropes increase capture efficiency and reduce analysis times. Ionic current readout provides positional information on PTMs embedded deep within long polypeptide chains, establishing a framework for compiling inventories of cellular proteoforms. Second, we focus on phosphorylation, a central regulator of cellular signalling whose dysregulation underlies numerous diseases. We demonstrate binderassisted PTM detection within polypeptides (&gt;700 residues): phosphate-recognising Phos-tag complexes are appended to target chains, EOF carries the tagged proteins through engineered nanopores, and distinct ionic current signatures localise phosphorylation sites within individual molecules. This approach establishes a foundation for single-molecule mapping of phosphorylation patterns and broader PTM profiling in intact proteins. Finally, we assess whether binder-assisted nanopore sensing can resolve distinct phosphorylation types (Ser-P, Thr-P, Tyr-P, and the noncanonical Cys-P). A methylated Phos-tag derivative complexed with Zn2+ (PMeZn2) distinguishes all four based on their current levels and kinetics, indicating that tailored binders can translate subtle chemical differences into distinctive electrical fingerprints. Together, electro-osmotically active nanopores, whether used alone or combined with tuneable, PTM-selective binders, enable single-molecule mapping of full-length proteoforms and their modification states. While further validation in complex samples is needed, these results advance nanopore proteomics towards more comprehensive, residue-level readouts with potential applications in mechanistic biology, biomarker discovery, and therapeutic target identification.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Oxford University Research Archive (ORA) (University of Oxford)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5287/ora-bmovrk8oj">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Wei-Hsuan Lan OpenAlex https://reading.michaelmvh.com/article/c5c7a7514a668dfce5c9c3c2ab35229490cca7c6d695ae83f05a4f1a3f85450e/ urn:sha256:c5c7a7514a668dfce5c9c3c2ab35229490cca7c6d695ae83f05a4f1a3f85450e <p>optical methods is the ability to control the translocation dynamics of the biomolecule, especially its speed. Very often, this dynamics is studied in terms of its effect on ionic currents through the nanopore. Herein, with attention to label-free optical sequencing methods, we directly study the translocation motion of (poly)peptides by molecular dynamics. By analysis of a vast set of simulations of polyglutamic acids, we show that the peptide elongation is determined by the electrostatic repulsion between the side chains, with less dependence on ionic strength and a more prominent effect of ion type, which emerges as a factor to control the peptide elongation for sequential amino acid detection. Instead, the ionic strength influences the speed of translocation under driving electrostatic fields. Through comparative analysis of simulations with and without confinement of the peptide in a gold nanopore, we quantify the influence of the nanopore on the sequential transit of amino acids and clarify the role of the peptide-pore interaction in promoting the peptide elongation and slowing down their translocation. We identify a stop-and-go translocation mechanism that can be controlled by lateral electric fields, such as in experimental &quot;hot spots&quot;, to achieve translocation velocities adequate for single-amino acid detection, while the use of appropriate ions also favors elongated peptide poses suitable for single-amino acid detection. We also present experiments on polyglutamic acid translocation which, compared with the theoretical results, turn out to be compatible with the stop-and-go translocation mechanism. The translocation mechanism, which is characterized by the proximity of the peptide to the nanopore surface, raises expectations for the promising use of plasmonic hot spots in single-amino acid detection.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Nanoscale</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d5nr03385c">Original publication</a></p><p><a href="https://pubs.rsc.org/en/content/articlepdf/2026/nr/d5nr03385c">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Mirko Vanzan Agostino Migliore María Blanco-Formoso Francesco De Angelis Stefano Corni OpenAlex https://reading.michaelmvh.com/article/7cbbbff4750f75088a060dbb38d54a5fa60f86bb6530ecea8aaaa12412ed0db3/ urn:sha256:7cbbbff4750f75088a060dbb38d54a5fa60f86bb6530ecea8aaaa12412ed0db3 <p>Protein nanopores have revolutionized DNA sequencing by enabling long-read, real-time, and portable genomic analysis. This review traces the experimental evolution of three key protein nanopores—α-hemolysin, MspA, and CsgG—highlighting how iterative engineering overcame challenges such as translocation control and homopolymer resolution. Concurrently, molecular dynamics (MD) simulations have elucidated DNA–pore interactions, ion current modulation, free-energy landscapes, and so forth, providing mechanistic insights and guiding rational design. However, MD studies consistently lag behind experimental and industrial advances, resulting in a reactive “simulate-after-validate” paradigm. We identify critical gaps in simulating motor–pore complexes, experimental timescales, and emerging designs like dual-constriction pores. To bridge these, we propose leveraging deep learning-based structure prediction, de novo protein design, and advanced multiscale simulations to foster proactive, integrated development of next-generation nanopore technologies.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Soft Matter</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6sm00125d">Original publication</a></p><p><a href="https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6964ac2a5c91413e6e7952a5/original/nanopore-sequencing-with-proteins-synchronization-and-dischronization-of-molecular-dynamics-simulations-with-laboratory-and-industrial-developments.pdf">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Zongan Wang Yuqian Liu Tao Zeng Denghui Li Xiao Shi Jiawen Zhang Hao Wang Liuxin Shi Jiayuan Zhang Yinqi Bai Yuning Zhang Yuliang Dong OpenAlex https://reading.michaelmvh.com/article/d47e3902cd4370d2a412413435f89c0ad9eda487358e1409fdf9d72fdcb141a1/ urn:sha256:d47e3902cd4370d2a412413435f89c0ad9eda487358e1409fdf9d72fdcb141a1 <p>Membrane-spanning nanopores that allow controlled passage of macromolecular cargo across cell membranes can empower many biomedical applications. Such nanopores are formed, in a pH-responsive manner, by the synthetically evolved &quot;pHD peptide&quot; family. pHD peptides fold into amphipathic α-helices, but have many charged and polar residues and are thus not predicted by classical hydropathy analyses to fold into membrane-spanning structures. Yet, when the pH is below ∼6, pHD peptides readily self-assemble into nanopores, even at low concentration. Knowledge of the molecular structure of the pHD peptide pore is needed for further rational design and optimization of nanopore-forming activity targeted to specific membranes and pH conditions. To this end, we have carried out extensive atomistic molecular dynamics simulations to explore the protonation-dependent structure and dynamics of nanopores created by the peptide pHD108. Simulations and graph-based analyses of hydrogen bonding reveal that, in the nanopore, the numerous carboxylate and carboxyamide sidechains form a dense, water-bridged H-bond network across the bilayer. In this network, direct H-bonds between neighboring peptides are few. Instead, the network is dominated by water-bridged intrapeptide interactions and by water-bridged interactions with the headgroups of many lipid molecules with unusual conformations and orientations. The lipids in the H-bond network make critical contributions to nanopore stabilization. These studies reveal a non-classical means of stabilizing nanopores in bilayers formed by highly charged peptides, creating an avenue towards engineering of membrane-embedded structures.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Nanoscale</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d5nr03276h">Original publication</a></p><p><a href="https://pubs.rsc.org/en/content/articlepdf/2026/nr/d5nr03276h">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Bondar Ana-Nicoleta Samo Lešnik Kalina A. Hristova William C. Wimley OpenAlex https://reading.michaelmvh.com/article/0008ca91c1e3e09f2d601524f6f9dc3eb284782707a4d02f1a1dd5fd2fe9ba3f/ urn:sha256:0008ca91c1e3e09f2d601524f6f9dc3eb284782707a4d02f1a1dd5fd2fe9ba3f <p>Programmable peptide self-assembly enables the precise construction of supramolecular materials, establishing it as a defining frontier in nanomaterials research. This review systematically explores the collective contribution of sequence design, secondary structure regulation (including α-helices, β-sheets, and cyclic conformations), and dynamic modulation, and hierarchical organization in facilitating the creation of well-defined nanostructures such as nanotubes, nanopores, and nanocages. Artificial intelligence and computational modeling have emerged as critical tools to guide peptide design and predict assembly pathways, thereby enabling a strategic shift from empirical screening to mechanism-driven design. The review further highlights nanopore-based detection applications, demonstrating the potential for highly accurate, biocompatible detection of ions, nucleic acids, and proteins at single-molecule resolution. By integrating molecular design with biological function, this &quot;from sequence-design to ordered structures to advanced applications&quot; paradigm establishes a foundational framework for the development of precisely constructed functional supramolecular materials.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Chemical Communications</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d5cc06446e">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Li-Ying Wang Jian-Xiao Liang Jingyao Wang Min Han Hongwei An Hao Wang OpenAlex https://reading.michaelmvh.com/article/826a72aa68b494699f029ea5709a04112b9fe07fe7d227e92ff922af2ea750f1/ urn:sha256:826a72aa68b494699f029ea5709a04112b9fe07fe7d227e92ff922af2ea750f1 <p>Cyclic peptides have been a promising source of natural pharmaceutical macromolecules with their specific binding docks and enhanced binding affinities. However, the aggregation of cyclic peptides poses a significant challenge, compromising their efficacy and permeability to targets. To address the challenges in detecting and characterizing such aggregation, we introduce nanopore sensing as a promising solution that overcomes the limitations of conventional methods by leveraging ionic current blockades for label-free, high-sensitivity real-time detection. This article investigates the aggregation properties of a cyclic peptide library designed through phage display, screening seven cyclic peptides individually and exploring their co-assembling behaviors. Results reveal that cyclic peptide aggregation is not uncommon under biological conditions, while other chemical and physical characterization experiments further elucidate the detailed mechanism. The study explores the interaction and aggregation properties of cyclic peptides, unveiling the co-assembling phenomena and emphasizing the potential of nanopore-based techniques in advancing peptide aggregation detection and drug development.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Analytical Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6ay00427j">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Hang Yang Wenqi Lu Dongdong Wang Xiaoyu Zhang Zan Li Minmin Li Haijuan Qin Jiaqi Li Guangyan Qing OpenAlex https://reading.michaelmvh.com/article/880bb4d191a2982b2456d423c07f1a73ab9393f798209d0f0c8fcb28024990e8/ urn:sha256:880bb4d191a2982b2456d423c07f1a73ab9393f798209d0f0c8fcb28024990e8 <p>Code for extracting Peak Current and Dwell Time from every events of nanopore sensing in the article of &quot;Catalytic Proximal Protein Oligomerization (CaPPO) as a Novel Anti-Tumor Strategy Targeting WDR5&quot;.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Code Ocean</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.24433/co.9106383.v1">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Yizheng Fang Jiang, Li Feifan Wang Yihui Zhou Jie Cen Yuxin Yang Haiyang Wang Qi Chen Yushen Lin Tingting Wang Hongxia Xu Yongping Yu Cheng‐Liang Zhu Qiaojun He Chun Zhou Wenteng Chen Longhua Tang Bo Yang OpenAlex https://reading.michaelmvh.com/article/b7fd46d1525fe577097d81413f7c40b6b00bb414f74b3793b4456d565ce7d1b6/ urn:sha256:b7fd46d1525fe577097d81413f7c40b6b00bb414f74b3793b4456d565ce7d1b6 <p>Single-molecule electrical protein fingerprinting</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Clinical and Translational Medicine</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/ctm2.70589">Original publication</a></p><p><a href="https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/ctm2.70589">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Neeraj Soni Amit Meller OpenAlex https://reading.michaelmvh.com/article/719844c9213b144eaea2b99cb6ca253f063c1b52a51647cb2a1f0543a3dfdf77/ urn:sha256:719844c9213b144eaea2b99cb6ca253f063c1b52a51647cb2a1f0543a3dfdf77 <p>porin A (MSPA) has emerged as a robust β-barrel protein with a narrow constriction suitable for single-molecule sensing. However, the atomic-scale mechanism by which DNA interacts and couples with the dynamic motions of the pore remains poorly understood. In this work, we combine atomistic molecular dynamics (MD) simulations with dimensionality reduction and cross-correlation analyses to elucidate the mechanism of single-stranded DNA (ssDNA) translocation through MSPA. Our results reveal a previously unrecognized &quot;pepper-mill&quot;-like motion of MSPA during the translocation of ssDNA. This collective domain motion plays a crucial role in modulating analyte-pore interactions and influencing the dynamics of DNA passage. Furthermore, our scheme provides a generalizable and data-driven strategy for extracting mechanistic insights from large-scale biomolecular simulations. Together, these findings highlight the potential of data-driven computational strategies to guide nanopore engineering and accelerate the development of next-generation sequencing and biosensing technologies.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Physical Chemistry Chemical Physics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d5cp04174k">Original publication</a></p><p><a href="https://pubs.rsc.org/en/content/articlepdf/2026/cp/d5cp04174k">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Priya Dey Brandon Meza-González Ganesh N. Pandian Daniel M. Packwood OpenAlex https://reading.michaelmvh.com/article/33263c50163f6b35b26f311f7b00d98c7ac2f424cf9f07b9c0f82039352b3f7b/ urn:sha256:33263c50163f6b35b26f311f7b00d98c7ac2f424cf9f07b9c0f82039352b3f7b <p>Nanopore detection technology is a high-sensitivity analysis method with essential applications in DNA sequencing, protein identification, and other fields. However, conventional electrophoretic driving has limited efficiency in detecting nanoparticles with low surface charge. In this work, a strategy combining pressure-driven and electrophoretic forces was proposed to improve the detection performance of complex nanoparticle systems in solid-state nanopores. By optimizing the pressure and electric-field parameters, the translocation frequency of a single nanoparticle type with low surface charge was increased, and mixed particles of different sizes and charges were discriminated. Notably, we observed a new phenomenon in which particle translocation frequency increased only under the electrophoretic force after mixing oppositely charged nanoparticles without requiring external pressure. This study demonstrated that synergistic pressure and electric-field driving can provide a more flexible and efficient approach towards single-molecule detection, thereby expanding nanopore applications for biological nanoparticle and small-molecule analysis.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> The Analyst</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6an00058d">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Tixi He Yin Zhang OpenAlex https://reading.michaelmvh.com/article/05eb020e47fdc14cd0df93254c564bbb0ed05670026adfee147f2b9c8f7a0e09/ urn:sha256:05eb020e47fdc14cd0df93254c564bbb0ed05670026adfee147f2b9c8f7a0e09 <p>Cell membranes form selective barriers for the exchange of materials between cells and their environment. Nutrient uptake in metazoan cells is generally mediated by membrane transporters and endolysosomal pathways. βγ-CAT, an aerolysin family pore-forming protein (PFP)–trefoil factor complex identified in the toad Bombina maxima, has been characterized as a novel regulator of nutrient acquisition. First, the toad cells dispatch βγ-CAT under starvation to scavenge extracellular proteins for their energy supply and survival. Second, blood βγ-CAT is an immediate responsive element under fasting, which is able to mediate the transcellular transport of albumin-bound fatty acids for the nutrient requirement of tissue parenchymal cells. Third, βγ-CAT mediates macropinocytosis in toad osmoregulatory organs for facilitating toad water maintaining. This PFP complex has been found to be tightly regulated at several stages by toad endogenous elements, like AMP-activated kinase signaling, IgG Fc-binding protein, its PFP paralog and ATP. Insights from βγ-CAT define a previously unrecognized PFP system that drives vesicular delivery and transport. Notably, similar functions and regulatory strategies are now being progressively validated in other species, providing a new paradigm for PFP-driven nutrient acquisition and metabolic flexibility.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> 动物学研究</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.24272/j.issn.2095-8137.2025.461">Original publication</a></p><p><a href="https://www.zoores.ac.cn/en/article/pdf/preview/10.24272/j.issn.2095-8137.2025.461.pdf">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Zhang Yun Zhang Jiarui Li Shengan Shi Zhihong Liu Lingzhen Bian Xianlin Wang Qiquan Li Wenhui Xiang Dong Yang 中科院昆明动物研究所 OpenAlex https://reading.michaelmvh.com/article/80d378701d5ad9118cef6b8621ffa72f70f47ad4e0327920681017ecb1073c47/ urn:sha256:80d378701d5ad9118cef6b8621ffa72f70f47ad4e0327920681017ecb1073c47 <p>nanopore-based DNA sequencing using synthetic oligonucleotide substrates. This is achieved by monitoring the mismatch proportion at the canonical target sequences incorporated into the synthetic substrate and determining the sequence length distribution throughout the entire substrate sequence. The mismatch proportion increases and sequence length distribution decreases with increasing toxin concentration for both ricin and abrin in buffer as well as in more complex backgrounds such as saliva and nasal secretions.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Analytical Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6ay01047d">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT M. E. TURNER Ashley M. Bradley Kristin D. Victry Bailey G. Knight Rachel E. Richardson Natalie M. Winans Lisa Bramer Tyler J. Sagendorf Fanny Chu Kristin M. Engbrecht Jennifer M. Mobberley David S. Wunschel OpenAlex https://reading.michaelmvh.com/article/6f26c274d8665412034fbd1b6aaff97fb1586d67b14171d23bcadd54dc3ad298/ urn:sha256:6f26c274d8665412034fbd1b6aaff97fb1586d67b14171d23bcadd54dc3ad298 <p>Nanopore technology is emerging as a transformative tool for single-molecule proteomics, both for studying protein function and for identification of proteins. This thesis addresses both of those aspects by applying nanopore sensing to resolve complex biological mechanisms while simultaneously exploring novel methodologies to address limitations in protein identification. Chapter 1 critically reviews the state-of-the-art in nanopore protein analysis. It identifies that nanopore-based fingerprinting strategies are in principle proven, however, open hurdles remain regarding scalability, requirements for conjugation, and the resolution needed for de novo sequencing. Simultaneously, nanopores are already applicable to study protein function within academic research settings, yielding exciting results. This analysis establishes the roadmap for the experimental chapters that follow. Chapter 2 demonstrates the functional analysis of Hsp70 chaperones. Using a nanopore to mimic in vivo protein transport across organelles, we provide the first unambiguous evidence that Hsp70s use the Entropic Pulling mechanism, thereby settling a long-standing debate. Addressing the sample processing bottlenecks in nanopore-based protein fingerprinting (identified in Chapter 1), Chapter 3 introduces a simplified platform for protein identification. We explore the free translocation of full-length proteins through the aerolysin pore, obviating the need for proteolytic digestion or chemical conjugation of the analyte. Finally, Chapter 4 tackles the challenge of de novo sequencing by engineering aerolysin mutants coupled with enzymatic translocation control. While aerolysin has shown promise to reduce the sensing volume in prior static measurement, this dynamic exploration uncovered significant and complex signal convolution in the pore. The investigation suggests that future sequencing efforts should prioritize pores with distinct constriction geometries. Collectively, this work pushes the boundaries of nanopore proteomics. It not only resolves a fundamental biological question about Hsp70s but also rigorously defines the capabilities and limitations of aerolysin-based sensing, paving the way for next-generation protein identification platforms.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Infoscience (Ecole Polytechnique Fédérale de Lausanne)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5075/epfl-thesis-11784">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Verena Rukes OpenAlex https://reading.michaelmvh.com/article/4599026f674c615e810937e8ba7073fbed7544e3bc7c7703107c7b3fce5f982b/ urn:sha256:4599026f674c615e810937e8ba7073fbed7544e3bc7c7703107c7b3fce5f982b <p>Nanopore sequencing through Surface-Enhanced Raman Spectroscopy (SERS) is a promising methodology to perform single-molecule analysis on nucleic acids and proteins, which relies on fast optical detectors with high sensitivity for spectral acquisition. To support this application, we developed a camera based on a 128 × 1 SPAD array, with custom microlenses to achieve 28% peak Photon Detection Efficiency (PDE). The camera supports high-speed readout at 1 MHz and features gating capabilities for fluorescence time filtering. Through translocation detection, the camera can trigger a molecule slow down mechanism, increasing the integration time for spectral acquisition. To further enhance signal collection and push gating performance to the sub-ns range, we designed a newer 128 × 4 chip in a 3D-stacked technology by STMicroelectronics. This new chip includes an innovative readout that can selectively capture only the spectral bands of interest, increasing readout frequency above 1 MHz.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Virtual Community of Pathological Anatomy (University of Castilla La Mancha)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://hdl.handle.net/11311/1317485">Original publication</a></p><p><a href="https://re.public.polimi.it/bitstream/11311/1317485/1/ISSW2026_A_128x1_SPAD_camera_for_Protein_Sequencing_through_SERS.pdf">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT V. Storari C. Terragni Francesco Difato Francesco Tantussi Jannis Weinacker M. Wegener F. De Angelis F. Villa OpenAlex https://reading.michaelmvh.com/article/c09c6546c0af79879181956ed29502a23b624e772ada61b4ef7ba0fdc8b88a33/ urn:sha256:c09c6546c0af79879181956ed29502a23b624e772ada61b4ef7ba0fdc8b88a33 <p>The invention relates to a process for the preparation of a bi-functionalized conjugate, wherein the conjugate is a peptide-oligopeptide or a peptide-oligonucleotide conjugate (POC), the process comprising the steps of: (i) providing a peptide according to structure (1), or a mixture of more than one peptide according to structure (1), wherein: G is a peptide comprising 1–50 amino acids; and AA1 and AA2 are independently selected from the group of amino acid side chains; AA3 is a tyrosine, tryptophan, arginine or lysine side chain; (ii) modifying the C-terminus of the peptide via click chemistry; and (iii) modifying the N-terminus of the peptide via click chemistry. The C-terminus and the N-terminus of the peptide are modified in such a way that the amino acid sequence of for example the POC peptide moiety may be determined, preferably by nanopore sequencing. The invention also relates to the bi-functionalized peptide-oligopeptide conjugates and POCs themselves.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Socio-Environmental Systems Modeling</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://research.wur.nl/en/publications/bi-functionalized-peptide-oligonucleotide-conjugate-and-process-f">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Bauke Albada Jasper W. van de Sande OpenAlex https://reading.michaelmvh.com/article/910eea432b3d15b6d0c828a9d622e359fa45968a79062b139b16775c9b65648f/ urn:sha256:910eea432b3d15b6d0c828a9d622e359fa45968a79062b139b16775c9b65648f <p>Single-molecule sensors have found widespread applications in probing biological processes at the fundamental scale and enabling detection at the ultimate sensitivity limit. In this work, a Scanning Ion Conductance Microscope (SICM) system is presented as a platform for single-molecule sensing and as a tool capable of extracting physical properties, such as stiffness. This thesis is divided into two parts. The first part of the thesis focuses on the use of the Scanning Ion Conductance Spectroscopy (SICS) method, a nanopore-based single-molecule detector at the ultimate scale. SICS employs a glass capillary as a movable nanopore integrated into an SICM system. Unlike traditional nanopore experiments, in which analytes translocate through a fixed pore, here the analyte is immobilized on a surface while the nanopore approaches and scans across it. This allows for unprecedented control as the analytes can be repeatedly localized and measured. First, protocols and optimization steps for DNA carriers are presented, forming the foundation for the experiments described in the preceding chapter. Through these DNA carriers, molecules of interest can be positioned at programmable locations for repeated interrogation. This work presents the detection of DNA gaps, RNA structures, peptides, and protein-binding aptamers. To establish and demonstrate the resolution of this system, the size of single-stranded regions within a long double-stranded DNA construct (DNA gaps) is progressively reduced from 80, 40, 20, and 12 to a single missing base pair. By repeatedly sensing the same molecule (80b DNA gap) and averaging the measurements, a 20-fold reduction in RMS was observed compared to single-molecule SICS readout. This approach enabled the detection of a single missing base pair, representing the highest resolution achieved with a solid-state nanopore. The improved signal-to-noise ratio enabled protein detection using aptamer-based targets at lower ionic strength, reaching physiological conditions (150 mM KCl), and allows detection of the target proteins in human serum (protein mixture). This enabled extending the SICS platform as a diagnostic tool and improving its detection rate by multiplexing targets onto a single DNA carrier (3x compared with free translocation measurement). The system was also applied to short peptide sequences of varying charge, using the voltage-dependent force exerted by the nanopore to unfold peptides and maintain an extended conformation for more accurate sensing. Finally, RNA structure reconstruction was demonstrated by analyzing translocation signals to infer three-dimensional conformations. The second part of the thesis examines the topology and material properties of biomolecular condensates formed by the DEAD-box Dhh1 protein. Recent studies have shown that biomolecule condensate systems are sensitive to perturbations from fluorescence tags. First, available label-free techniques for probing biomolecular condensates were reviewed, highlighting a gap in physical methods for measuring their material properties. The gap is addressed by demonstrating the use of SICM, a non-contact method, to measure their stiffness under physiological conditions. This enabled comparison of condensate stiffness across two pH conditions, revealing significant changes in stiffness when the cell is under stress. Additionally, the effect of truncating the protein&#39;s tails on the formation and stiffness of the biomolecular condensates was studied.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Infoscience (Ecole Polytechnique Fédérale de Lausanne)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5075/epfl-thesis-11566">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Helena Miljkovic OpenAlex https://reading.michaelmvh.com/article/87083271f48f95be590c55064ed432daa2c4198a7073615b4b8b6da853001647/ urn:sha256:87083271f48f95be590c55064ed432daa2c4198a7073615b4b8b6da853001647 <p>, a critical rate mismatch occurs: the excessive drift velocity outpaces the unfolding rate, triggering lateral buckling and irreversible steric jamming at the final constriction. Compared with a conventional single-step nanopore, the stepped architecture facilitates high-fidelity observation of unfolding intermediate states at moderate driving forces, thereby avoiding excessive driving conditions that promote kinetic jamming and reduce structural resolution. By establishing a kinetic-competition framework based on native-contact loss, residue-passage timing, and productive axial linearization, this study provides a physical framework for designing blockage-resistant nanopore sensors for high-resolution protein structural analysis.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Physical Chemistry Chemical Physics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d6cp01783e">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Yanlin He Junzhou He Wei Si OpenAlex https://reading.michaelmvh.com/article/056f7608217b4b52f4cbc941d79fa06cab3634bdf3fb281009d038710d2eaef6/ urn:sha256:056f7608217b4b52f4cbc941d79fa06cab3634bdf3fb281009d038710d2eaef6 <p>Studying proteins at the single-molecule level provides direct access to molecularbehavior that is masked in ensemble measurements. This approach enables the resolution of mechanistic details hidden in bulk experiments, captures the stochastic nature of biochemical processes, and reveals heterogeneity among molecules of identical sequence. These capabilities are essential for understanding structure-function relationships and for developing sensitive protein-based diagnostic technologies. Conventional protein analysis techniques often involve complex workflows and sophisticated instrumentation with modest limits of detection. Although fluorescence-based methods can interrogate single molecules, they typically require labeling, lasers, and advanced microscopy. Here, we report a label-free strategy for analyzing intact proteins using resistive pulse sensing (RPS) with a dual in-plane nanopore (DNP) sensor fabricated in thermoplastic via nano-injection molding. Critical features as small as 30 nm were produced using UV-resin mold inserts replicated from silicon masters, providing a scalable and reproducible fabrication route. Subsequent thermal fusion bonding reduced the effective pore size to ~10 nm. The device architecture consists of two in-plane nanopores flanking a confined nanochannel (50 × 50 nm cross-section; 5–10 µm length), enabling measurement of apparent electrophoretic mobility through a molecular-dependent time-of-flight (ToF), defined as the time difference between two consecutive RPS events (a peak pair). In addition to ToF, peak amplitude (ΔI/I₀) and dwell time (TD) were extracted from each pore, yielding five independent features for single-molecule analysis. Using four model proteins, we demonstrated successful detection and identification. Furthermore, analysis of the temporal RPS waveforms showed that event 3 shape encodes structural information, with distinct peak profiles observed for spherical and non- spherical proteins, reflecting their rotational dynamics within the nanopore. Unlike conventional biological nanopores, which suffer from membrane instability, or solid-state out-of-plane nanopores that require serial FIB or TEM drilling and exhibit limited sampling efficiency, our in-plane architecture is embedded within a nanofluidic network. This configuration improves analyte capture efficiency through geometric confinement, enables scalable manufacturing without serial drilling, and allows seamless integration with upstream processing modules. Using the same platform developed for protein analysis, we then evaluated nanoscale electrochromatography of peptides in thermoplastic nanochannels under high electric field strengths. Time-of-flight (ToF) measurements showed improved discrimination of apparent electrophoretic mobility under nanoscale confinement. Multivariate feature analysis combined with supervised machine learning (neural network) enabled near-100% classification accuracy of model peptides at the single-molecule level, with each measurement completed in less than 10 ms. Finally, we developed an integrated nanofluidic system that couples an immobilized nanoscale enzymatic reactor (INER) with the DNP-ToF sensor, termed the Proteomic Time-of- Flight (P-ToF) platform. Proteins are electrokinetically transported through a trypsin- functionalized nanoreactor, where digestion occurs during transit, and the resulting peptide fragments are immediately analyzed downstream by the DNP-ToF reader. Using Amyloid-β (1– 40) as a model protein, we demonstrated real-time on-chip digestion and peptide identification. Multivariate feature extraction combined with supervised Random Forest classification enabled 4 construction of peptide fingerprints with 100% training and test accuracy, which were subsequently used for accurate identification of digestion fragments. Building on these advances, our nanofluidic platforms provide a practical pathway toward clinical diagnostics in settings where sample quantity is severely limited, such as cerebrospinal fluid for neurodegenerative diseases or minimally invasive liquid biopsies for cancer. Because the system operates at the single-molecule level and does not require labeling or bulk amplification, it is inherently suited for analyzing low-abundance proteins and heterogeneous biomarker populations that are often masked in ensemble measurements. The demonstrated analysis of Amyloid-β highlights its relevance to Alzheimer’s disease, while the modular P-ToF architecture can be readily adapted to other disease-associated proteins and proteolytic signatures. By integrating enzymatic processing, separation, and multi-parameter machine-learning–based identification within a single thermoplastic device, this platform offers a scalable and high-sensitivity alternative to conventional mass spectrometry workflows, particularly for mass-limited clinical samples. Collectively, these capabilities position our nanofluidic technology as a strong candidate for next-generation precision diagnostics in oncology and neurodegenerative disease.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> KU ScholarWorks (The University of Kansas)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://hdl.handle.net/1808/39468">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Suresh Shivanka Patabendi Hangilige OpenAlex https://reading.michaelmvh.com/article/ed0f9577ea29e6f556d9d3d85ebd93e4e6f5e4b2888cc9fc52715d8fdf82c208/ urn:sha256:ed0f9577ea29e6f556d9d3d85ebd93e4e6f5e4b2888cc9fc52715d8fdf82c208 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Methods in molecular biology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1007/978-1-0716-5166-7_17">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Meng‐Yin Li Yan Gao Jie Jiang Yi-Tao Long OpenAlex https://reading.michaelmvh.com/article/4d5a5d86984dfe0608ebba0cb0c64e943a34f7117e67910e82ae3d280b590353/ urn:sha256:4d5a5d86984dfe0608ebba0cb0c64e943a34f7117e67910e82ae3d280b590353 <p>Solid-state nanopores have emerged as powerful tools for label-free analysis of DNA and proteins. However, specificity remains a challenge. Traditional pores rely on ionic current blockades, which often lack the resolution to distinguish between molecules of similar sizes. Furthermore, the high translocation speeds of biomolecules frequently exceed the temporal resolution of standard amplifiers. In this study, we introduce a dual-mode sensing architecture based on a Ga2In2O3-Ag composite. The platform leverages the semiconducting properties of the Ga2O3 matrix to act as an FET-based transducer, while the embedded Ag nanodomains provide plasmonic hotspots for SERS and light-induced translocation control. This synergy allows for the simultaneous recording of electronic, ionic, and spectroscopic signals, providing a multidimensional &quot;fingerprint&quot; of the translocating molecule.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Ghent University Academic Bibliography (Ghent University)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="http://hdl.handle.net/1854/LU-01KZQ0MFHPT3QXNX9S13NZ1N4F">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Mohammad Karbalaei Akbari Serge Zhuiykov OpenAlex https://reading.michaelmvh.com/article/7e343ad34cbfc2c9ad91f1818fd952fe06d81d8004e43ab9bd666417d3c2df80/ urn:sha256:7e343ad34cbfc2c9ad91f1818fd952fe06d81d8004e43ab9bd666417d3c2df80 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Methods in molecular biology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1007/978-1-0716-5527-6_12">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Helena Miljkovic Wayne Yang Aleksandra Rađenović OpenAlex https://reading.michaelmvh.com/article/f3da9505cc4452205adaffc26c2b46fb1ccefb597d2283c3188d77e379a2f025/ urn:sha256:f3da9505cc4452205adaffc26c2b46fb1ccefb597d2283c3188d77e379a2f025 <p>No abstract is available.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Methods in molecular biology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1007/978-1-0716-5527-6_6">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Joshua C. Foster Min Chen OpenAlex https://reading.michaelmvh.com/article/b993404197a0ac2e8ed459758ec6b0ee15a6f6b3cb54db20cc784a2045a458ec/ urn:sha256:b993404197a0ac2e8ed459758ec6b0ee15a6f6b3cb54db20cc784a2045a458ec <p>We present a microfluidic LabDisk automating the solid-phase-enhanced sample preparation (SP3) workflow for nanopore sensing.Using myelin basic protein (MBP), the system produces nanopore-compatible samples preserving membrane stability and enabling reliable detection with the aerolysin AeL-R220S nanopore variant.A distinct MBP peptide marker supports confident identification.Automated and manual workflows show identical nanopore signals (I/I₀ ≈ 0.75, &lt;0.2 % deviation) and comparable missed cleavage rates, demonstrating robust, standardized, and user-friendly sample preparation.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> Poster</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5162/eurosensors2026/mo-mlo-04">Original publication</a></p><p><a href="https://www.ama-science.org/proceedings/getFile/AmRkAD==">Open PDF</a></p> Thu, 01 Jan 2026 00:00:00 GMT Carolin Kleber C. Hensel Ida Suppanz G. Mittler Michelle Hinrichs S. Gutsch Tobias Hutzenlaub Felix von Stetten Nils Paust A. Schreiber Jan-Niklas Klatt OpenAlex https://reading.michaelmvh.com/article/d34e23b3317dc52dd3f3112eb57c4b7944e4baf72dffb63dd6a8b7b2a71067b9/ urn:sha256:d34e23b3317dc52dd3f3112eb57c4b7944e4baf72dffb63dd6a8b7b2a71067b9 <p>Understanding how chromosomes are organized and compacted has been a longstanding question in biology. How does a cell as small as two microns fit an entire genome 1000x its length inside? As most prokaryotes are not known to contain histones, and cellular processes, such as transcription and translation, are co-occurring in the same compartment as the DNA, there needs to be some coordinated manner and organized structure in which the DNA is compacted but still allows processes to occur. Escherichia coli, a gram-negative bacterium, is the most studied organism in the world. While there is an immense amount of knowledge on E. coli, the smaller nucleoid of this bacterium simply has not been as systematically studied yet as eukaryotic chromatin structure, in terms of DNA contacts and DNA accessibility. In this thesis, I revisit previously answered questions about the E. coli chromosome, through a different lens, reconciling discrepancies and filling knowledge gaps. I worked to develop a massively multiplexed sequencing method (Mu-seq) that measures chromosomal contacts, without the use of external crosslinkers, as is the current standard in the field. This method maps DNA:DNA contacts, made physically inside the cell, with the use of a barcoded version of transposon Mu. This method yields a finer-grain understanding of long-range contacts, those made over kilobase scales, and how contacts correlate with other cellular processes, such as transcription. I find that long-range interactions, which have been previously undetected by crosslinking-based methods, may form due to shared gene functions, and the need for coordinated regulation. I further demonstrate that chromatin accessibility shapes the interaction landscape through DNA-bound protein occupancy and supercoiling dynamics. Accessibility plays an important role in the organization of the E. coli nucleoid, as RNA polymerase needs to access tightly supercoiled and organized DNA for transcription. We chose to investigate what specific factors might influence the DNA contacts and organization patterns I detected from the Mu-seq method. I adapted an existing eukaryotic assay to function in a prokaryotic system, to measure DNA accessibility and protein occupancy at the single-molecule level, employing long-read nanopore sequencing. The approach uses methylation of DNA unoccupied by proteins, followed by long-read sequencing to detect methylated adenines along individual molecules -- I call it SHREK-seq (Single-molecule High-REsolution occupancy of proKaryotic chromosomes sequencing). Using this method, I was able to show the methylation signal, which labels open, unoccupied chromatin, to overlap with known extended protein occupancy domains (EPODs). I also showed how SHREK-seq method could detect more specific protein signals from Lrp, a global regulator in E. coli, and genetic perturbations resulted in an expected increase in methylation signal, corresponding to a loss of protein binding at known sites. My aim with this method was to obtain single-molecule binding patterns, which would resolve questions such as the phasing of the protein, how various oligomeric states bind differently at the same locus, and whether we resolve other aspects of chromosome dynamics which are currently undetected by population-averaged methods. Altogether, this dissertation provides two useful tools for measuring DNA contacts within the E. coli genome and detecting protein-occupied DNA regions, both of which not only advance our knowledge of the E. coli genome but may also be used in other systems.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> University of Michigan Library</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.7302/dspace/30710">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Sonya Royzenblat OpenAlex https://reading.michaelmvh.com/article/30f9f9e7133868382ee818548038af6073c36e9b41db498e2f582c4addbf580d/ urn:sha256:30f9f9e7133868382ee818548038af6073c36e9b41db498e2f582c4addbf580d <p>Solid-state nanopore membranes have emerged as a powerful platform for controlling ionic transport and enabling molecular sensing at the nanoscale. Among the various fabrication techniques, ion-track etching offers a scalable and versatile approach to produce nanopores ranging from single pores to high-density arrays with well-defined geometry and narrow size distribution. In addition, silicon dioxide (SiO2) nanopore membranes provide a well-known and highly tunable surface chemistry, which is critical for regulating ionic transport, selectivity, and interfacial interactions. However, despite these advantages, the application of SiO2 nanopore membranes remains relatively underexplored, particularly in the context of exploiting surface functionality for practical applications. This thesis investigates the application of conical SiO2 nanopore membranes fabricated via ion-track etching for two distinct areas: charge-based molecular separation and ion current rectification (ICR)-based biosensing. The fabrication process enables precise control over pore geometry and density, while surface functionalization using silane chemistry allows systematic tuning of surface charge properties. In the first part of this work, charge-based molecular transport and separation are systematically investigated using model dye molecules with different charge states. The results clearly demonstrate that electrostatic interactions between the nanopore surface and the analyte molecules dominate the transport behavior, enabling highly selective separation of oppositely charged species. Native SiO2 membranes possess a negative surface charge at neutral pH and preferentially transport cationic molecules. Upon aminosilane functionalization, the surface charge is converted to positive, enabling selective transport of anionic species. This charge-dependent tunability results in strong separation performance, with separation factors reaching up to ∼36 and ∼20 for negatively and positively charged membranes, respectively. The influence of electrolyte concentration on transport is further examined, highlighting the crucial role of electric double layer effects in governing ion selectivity and transport rates. In the second part of this work, antibody-functionalized conical SiO2 nanopores are used as a label-free biosensing platform based on ion current rectification for protein detection. The platform is validated using model biomolecules, including bovine serum albumin (BSA) and heart-type fatty acid-binding protein (H-FABP). Ultrasensitive detection is demonstrated, achieving a limit of detection (LOD) as low as ∼0.4 aM for H-FABP with a dynamic detection range spanning from attomolar to nanomolar concentrations. Exceptional selectivity is observed, with clear discrimination of target proteins in the presence of non-target species at concentrations up to six orders of magnitude higher. The sensor further exhibits excellent reproducibility and reusability through effective surface regeneration, enabling repeated sensing cycles. Overall, this work establishes conical SiO2 nanopore membranes as a robust and versatile platform for selective molecular transport and ultrasensitive biomolecular detection. By systematically correlating pore geometry, surface chemistry, and electrostatic interactions with functional performance, this thesis provides fundamental insights and practical design principles for the development of next-generation nanopore-based separation technologies and diagnostic systems.</p><p class="metadata"><time datetime="2026-01-01" title="Source date; precision not specified">January 1, 2026</time> <span aria-hidden="true"> · </span> ANU Open Research (Australian National University)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.25911/pdmv-sw38">Original publication</a></p> Thu, 01 Jan 2026 00:00:00 GMT Nahid Afrin OpenAlex https://reading.michaelmvh.com/article/c2df7699ecc5c8e32472f5c90c00be70e859c35e8f96862150356571ee018b30/ urn:sha256:c2df7699ecc5c8e32472f5c90c00be70e859c35e8f96862150356571ee018b30 <p>Abstract Existing approaches for nanopore sensing typically analyze resistive pulses from the translocation of individual proteins through the nanopore after completing the experiment. This approach foregoes instantaneous protein identification and precludes real-time experimental control. Here, we introduce a method for the analysis of real-time nanopore data capable of characterizing the size and approximate shape of proteins within a millisecond response time during data acquisition. The implemented real-time Two-Sliding Window (TSW) peak detection algorithm makes it possible, for the first time, to filter data, process baselines, and extract resistive pulse information during nanopore recordings using a stream of single data points. This approach achieves a computational throughput of 40 MB/s on a 1.8 GHz laptop CPU. We compared the accuracy of dwell time determination of the TSW algorithm with an established offline threshold searching (TS) algorithm, using simulated resistive pulses. The TSW algorithm accurately extracted events with dwell times greater than 1.5 times the reciprocal of the system’s cutoff frequency, 1.5 × (fc) −1 . Moreover, the TSW algorithm effectively determined the dwell time of resistive pulses with large intra-event modulation, which is crucial for resolving non-spherical protein-induced fluctuations. Finally, we verify experimentally that integrating the TSW algorithm into the data acquisition process makes it possible to determine the approximate shape and volume of proteins within low-millisecond response times. This real-time data analysis approach potentially provides instant feedback control for manipulating single proteins during or immediately after translocation. This analysis also improves data storage efficiency during recordings with a high sampling rate.</p><p class="metadata"><time datetime="2025-12-31" title="Source date; precision not specified">December 31, 2025</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c04044">Original publication</a></p> Wed, 31 Dec 2025 00:00:00 GMT Yuanjie Li Cuifeng Ying Michael R. Mayer OpenAlex https://reading.michaelmvh.com/article/6b076e10ccfd8745b1249ae61bc270a0655db7a3fc3322c8f3c2fb57475913aa/ urn:sha256:6b076e10ccfd8745b1249ae61bc270a0655db7a3fc3322c8f3c2fb57475913aa <p>The mspA gene is a nanopore protein located in the outer membrane of Mycolicibacterium fortuitum, which plays a role in the uptake pathway for hydrophilic nutrient molecules. The MspA gene is extremely stable against denaturation, making it capable for DNA sequencing. The accuracy of DNA sequencing is highly dependent on the selection of primer pairs. This study aims to develop primers and amplification for the mspA gene in Mycolicibacterium fortuitum. These organisms are typically free-living and can be found widely throughout the environment. Mycolicibacterium fortuitum is responsible for infections in both animals and humans, so there must be a specific detection method. One specific detection method that can be applied is Polymerase Chain Reaction (PCR). An important factor in the PCR technique is the presence of specific primers that will be used in the detection process. The method used involves a bioinformatics approach through the NCBI Primer Blast Program on Mycolicibacterium fortuitum strain MF GZ001 with the template strain reference NZ_CP107719.1, and a structural model approach through protein modelling using the template uun.1.A MSPA. The result of our study was successfully generated from comparing ten primers, only three primers were chosen based on the specific criteria. We also found the successful building for 3D modeling protein from 215 amino acids. In conclusion, the primer development for mspA gene detection resulted in a pair of primer and the 3D structure of the protein encoded by the gene.</p><p class="metadata"><time datetime="2025-12-28" title="Source date; precision not specified">December 28, 2025</time> <span aria-hidden="true"> · </span> Veterinary Biomedical and Clinical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.21776/ub.vetbioclinj.2025.007.02.1">Original publication</a></p> Sun, 28 Dec 2025 00:00:00 GMT Najma Ramadhani Siti Kurniawati Roro Titah Pinasti Diaz Ayu Savitry Averoes Gibraltar Makta OpenAlex https://reading.michaelmvh.com/article/1a210fc80fabd3c922578eedb5726c9e2ace35ff50e7070363445dd706bf5bbf/ urn:sha256:1a210fc80fabd3c922578eedb5726c9e2ace35ff50e7070363445dd706bf5bbf <p>No abstract is available.</p><p class="metadata"><time datetime="2025-12-26" title="Source date; precision not specified">December 26, 2025</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c05662">Original publication</a></p> Fri, 26 Dec 2025 00:00:00 GMT Ying-Yuan Cui Lei Yang Jian-Nan Zhao Wen-Chuan Lai GU Zhi-yuan OpenAlex https://reading.michaelmvh.com/article/0b527c7d7c6a3bf816b2bbc4aa27b0b1b64843b81bccbac1e5634f212b825a80/ urn:sha256:0b527c7d7c6a3bf816b2bbc4aa27b0b1b64843b81bccbac1e5634f212b825a80 <p>We demonstrate a dual nanopore platform (DNP) containing a top 2D MoS2 pore in series with a 3 to 5 nm thick SiN pore, vertically separated by 30 nm, with diameters of 1.0 and 3.0 nm, respectively. This platform enables independent probing of analytes by each pore, thereby providing complementary information. We measure translocations of single amino acids (AA) and evaluate current blockades recorded across the two pores upon applying voltage. Small diameters ensured tight passage of individual AAs through the nanopores and provided a good signal-tonoise ratio (RMS current noise of 16 pA_RMS and SNR = 6). We focus on measurements of O-Phospho-L-tyrosine at 400 mV, demonstrating single amino acid detection and a good quantitative agreement with the calculated open pore and blocked currents. Based on these results, future device performance can benefit from slightly smaller pores, specifically the SiN pore, higher voltages and electrolyte concentration, and lower system noise.</p><p class="metadata"><time datetime="2025-12-23" title="Source date; precision not specified">December 23, 2025</time> <span aria-hidden="true"> · </span> arXiv (Cornell University)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.48550/arxiv.2512.20776">Original publication</a></p><p><a href="https://arxiv.org/pdf/2512.20776">Open PDF</a></p> Tue, 23 Dec 2025 00:00:00 GMT Chih-Yuan Lin Pia Bhatia Alexandra Sofia Uy-Tioco Kyril Kavetsky Celia Morral Rachael Keneipp N. Pradeep Marija Drndić OpenAlex https://reading.michaelmvh.com/article/9c25c4fca92ead1ee59feb1ca1dd0ab5b8e8a0725ca868d8da064f55470edcbe/ urn:sha256:9c25c4fca92ead1ee59feb1ca1dd0ab5b8e8a0725ca868d8da064f55470edcbe <p>Abstract Analysis of individual proteins using nanopores makes it possible to determine their size and shape in a label-free approach, within minutes, and from μL sample volumes. Short residence times of proteins in the nanopore, high electrical current noise, and bandwidth limitations of the recording electronics during resistive pulse recordings, however, limit the accuracy of size and shape analysis of individual proteins. The work presented here introduces a polymer surface coating of solid-state nanopores to minimize non-specific interactions of proteins with the nanopore wall while functionalizing it covalently with phenylboronic acid (PBA) groups. These PBA groups make it possible to trap selectively glycated proteins by taking advantage of the formation of reversible covalent bonds between PBA and vicinal diol groups of glycated amino acid residues on proteins. Dwell time analysis revealed two populations of resistive pulses: short pulses with dwell times t d below 0.4 ms from free translocation of proteins and resistive pulses that we term “long events” that last from 0.4 ms to 2 s and result from intended transient covalent bonds between glycated proteins and PBA groups in the nanopore lumen. The choice of applied potential differences during nanopore recordings or the pH value of the recording buffer makes it possible to control and extend the most probable trapping time of proteins in the nanopore within one to two orders of magnitude. This approach provides the highest accuracy for the determination of protein volume and shape achieved to date with solid-state nanopores and reveals that a trapping time of 1 to 20 ms is ideal to achieve reliable volume and shape analysis while retaining high throughput of the analysis. This approach, hence, extends the residence time of natively glycated proteins or of proteins that are intentionally glycated by straightforward incubation in a glucose solution, thereby providing selectivity and improving the accuracy of nanopore-based characterization of single proteins.</p><p class="metadata"><time datetime="2025-12-21" title="Source date; precision not specified">December 21, 2025</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.5c16000">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acsnano.5c16000?ref=article_openPDF">Open PDF</a></p> Sun, 21 Dec 2025 00:00:00 GMT Yuanjie Li Saurabh Awasthi Peng Liu Anna D. Protopopova Michael Mayer OpenAlex https://reading.michaelmvh.com/article/1082195b33de47d97df1fb9ec0a9954b7644056be0ddafec07a7e5f780a6e418/ urn:sha256:1082195b33de47d97df1fb9ec0a9954b7644056be0ddafec07a7e5f780a6e418 <p>Over the past years, significant progresses have been made in the field of nanopores, particularly in singlemolecule analysis, sequencing, and diagnostic applications, certainly underscoring the versatility of stochastic nanopore sensing.The subsequent advances in functionalizing protein nanopores with tailored properties or reactive handles have greatly expanded their detection capabilities, where customized computational design shows promise in driving nanopore functionalization and applications toward unprecedented flexibility.In this review, we provide a comprehensive perspective of the various engineering strategies employed in protein nanopores and the roles of functionalized nanopore in single-molecule sensing and sequencing.Additionally, we elucidate the interplay between functionalization strategies and their intended applications, highlighting promising implementation scenarios.We believe that the ongoing advancements in functionalization technologies will promote innovations in de novo pore design and propel nanopore protein sequencing.</p><p class="metadata"><time datetime="2025-12-17" title="Source date; precision not specified">December 17, 2025</time> <span aria-hidden="true"> · </span> Nano Research</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26599/nr.2026.94908343">Original publication</a></p><p><a href="https://www.sciopen.com/local/article_pdf/10.26599/NR.2026.94908343.pdf">Open PDF</a></p> Wed, 17 Dec 2025 00:00:00 GMT Ke Sun Mengze Wu Xin Yu Yue Li Ming‐Han Li Jinna Wang Yuan Ju Shengli Zhang Jia Geng OpenAlex https://reading.michaelmvh.com/article/6a2c3912a658f4fbc66a8cc17c59c9a634874dad4069a70cfca72da0f60f4986/ urn:sha256:6a2c3912a658f4fbc66a8cc17c59c9a634874dad4069a70cfca72da0f60f4986 <p>The ϕ clamp, a key active site in the anthrax toxin protective antigen (PA) nanopore, governs the complex process of peptide translocation, yet its precise mechanism remains debated. A key question is how might the nanopore mitigate the formation of too stable/static of a ϕ-clamp interaction with the polymer it is attempting to translocate. One hypothesis is that it would &quot;gate&quot; to bind and &quot;ungate&quot; to release. Here, we dissect this mechanism using single-channel electrophysiology on wild-type PA and two ϕ-clamp mutants (F427A and F427Y). Thermodynamic analysis reveals the wild-type F427 residue creates a deep, energetically stable &quot;hydrophobic trap&quot; (state 0). Kinetic analysis further establishes F427 as a &quot;specific chemical sensor&quot;; the strong correlations between translocation kinetics and peptide hydrophobicity seen in wild-type PA are abolished in the F427A mutant. Critically, partially blocked intermediate states persist even upon F427A side-chain ablation. This finding supports a refined structural model where these states arise not from populating discrete F427 rotamers, but rather from a larger-scale, dynamic dilation of the entire clamp-containing loop. Overall, this model resolves the paradox of how a peptide clamp can facilitate transport: translocation proceeds via a dynamic equilibrium between a constricted, high-affinity &quot;gated/clamped&quot; state (the trap) and a dilated, lower-affinity &quot;ungated/unclamped&quot; state (the intermediates), allowing the pore to mitigate its own energetic traps through conformational gating. This detailed mechanistic insight provides a framework for rationally engineering next-generation dynamical nanopore biosensors.</p><p class="metadata"><time datetime="2025-12-17" title="Source date; precision not specified">December 17, 2025</time> <span aria-hidden="true"> · </span> Biophysical Journal</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.bpj.2025.12.016">Original publication</a></p> Wed, 17 Dec 2025 00:00:00 GMT Jennifer M. Colby Bryan A. Krantz OpenAlex https://reading.michaelmvh.com/article/f3dace712bc2f9e1fca018a5b5b65240c615166e7f1580a59497c0421b7fdf64/ urn:sha256:f3dace712bc2f9e1fca018a5b5b65240c615166e7f1580a59497c0421b7fdf64 <p>Actinomyces weissii was first isolated from the oral cavity of dogs in 2012. This study characterised the phenotypic and genotypic features of 11 additional strains obtained from diverse pathological lesions in companion animals. A multi-faceted approach was employed, combining culture techniques, biochemical profiling, MALDI-TOF MS, real-time PCR, sequencing of genetic markers, and whole-genome analysis. Despite minor phenotypic variation, MALDI-TOF MS and genotypic analyses consistently confirmed species identity and revealed intraspecies diversity. Whole-genome sequencing revealed four haemolysin family protein genes, and all isolates exhibited complete β-haemolysis. Pan-genome analysis defined a conserved core genome of 1559 genes, shared by all isolates and the reference strain, including haemolysin-related genes. Phylogenetic comparisons placed A. urogenitalis and A. trachealis as closest relatives. These findings broaden the host spectrum of A. weissii, with the first isolation from a cat, suggesting that this species may also occur in felines and merits consideration in veterinary diagnostics. Its presence in companion animals raises the possibility of zoonotic risk, and together with the detection of haemolysin family protein genes, underscores the need for further investigation to clarify its pathogenic significance and potential impact on veterinary practice and public health.</p><p class="metadata"><time datetime="2025-12-17" title="Source date; precision not specified">December 17, 2025</time> <span aria-hidden="true"> · </span> Infection Genetics and Evolution</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.meegid.2025.105867">Original publication</a></p> Wed, 17 Dec 2025 00:00:00 GMT Beyza Cirak Antonia Kreitlow Maria Borowiak Christiane Hoffmann Christoph Lämmler Carsten Heydel Christa Ewers Burkhard Malorny Madeleine Plötz Amir A. Abdulmawjood OpenAlex https://reading.michaelmvh.com/article/390edf66ac2d3893150f588a1e16f32a418915943bfb8d9ae9fbf67eb0ce9315/ urn:sha256:390edf66ac2d3893150f588a1e16f32a418915943bfb8d9ae9fbf67eb0ce9315 <p>A modification to fluorosequencing, an emerging method for large-scale parallel protein identification, is proposed. In this modified approach terminal residues are not cleaved by Edman degradation (a key step in fluorosequencing) or any of its variants or enzymatic alternatives, the process is non-destructive. There are three parts: 1) a charged homopeptide header is attached to each of the peptides being partially sequenced; 2) the glass slide that the headers are immobilized on is mounted on a moveable platform in the cis chamber of an electrolytic cell (e-cell); and 3) header-peptides are advanced through an array of nanopores in the e-cell toward the trans chamber one residue at a time with a mechanical positioning system based on piezo-electric sensors and sub-nm movement precision. As in fluorosequencing, the optical signal from fluorescently tagged residues in the peptides is read with TIRF (Total Internal Reflection Fluorescence) microscopy. The difference here is that instead of repeatedly cleaving terminal amino acids (AAs), AAs are either revealed to the camera in sequence from the terminal AA (forward version) or hidden from it from the header end of the peptide (backward version). Computational simulations with nanopore diameter ~0.5-1 nm, pore lengths 3.5-7 nm, peptide lengths 10-20, and header lengths 20-45 suggest that with a long enough charged header the peptide can overcome diffusive dispersion so the terminal AA remains confined to a small neighborhood, making reliable tag readout possible. Additionally in the forward version if in each cycle tags are deactivated after they have been read and/or dissociated from their residues and washed away, signals take on a binary character and signal processing becomes more robust. This is an archival method in which the header-peptide can be moved in both directions and measurements can be done an arbitrary number of times while the sample remains intact.</p><p class="metadata"><time datetime="2025-12-10" title="Source date; precision not specified">December 10, 2025</time> <span aria-hidden="true"> · </span> ChemRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26434/chemrxiv-2025-v4cnk-v2">Original publication</a></p><p><a href="https://chemrxiv.org/doi/pdf/10.26434/chemrxiv-2025-v4cnk-v2">Open PDF</a></p> Wed, 10 Dec 2025 00:00:00 GMT G. Sampath OpenAlex https://reading.michaelmvh.com/article/d0e5162ac0c60499ad5c197aaf4f687c429e3035c524f03eb17701dc534d861a/ urn:sha256:d0e5162ac0c60499ad5c197aaf4f687c429e3035c524f03eb17701dc534d861a <p>Bile acids are key signaling molecules implicated in various hepatobiliary and metabolic diseases. Synthesized via distinct pathways and undergoing diverse modifications, bile acids exhibit significant structural variation. The discovery of novel amino acid-conjugated bile acids (BA-AAs) has further expanded this structural diversity, posing substantial challenges for their precise identification. Here, an engineered aerolysin nanopore K238W was employed for detecting diverse BA-AAs, including cholic acid conjugates with various amino acids and those derived from structurally similar or isomeric bile acids. Using a high-ionic-strength electrolyte containing guanidinium chloride, the K238W nanopore produced distinctive blockade signal fingerprints specific to different BA-AAs. Subsequent machine-learning analysis allowed clear differentiation of diverse BA-AAs, as evidenced by 98% accuracy in identifying 20 amino acid-conjugated cholic acids. This approach offers a promising alternative for analyzing structurally similar or even isomeric bile acids, advancing their functional and clinical studies.</p><p class="metadata"><time datetime="2025-12-09" title="Source date; precision not specified">December 9, 2025</time> <span aria-hidden="true"> · </span> Nano Letters</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.nanolett.5c05004">Original publication</a></p> Tue, 09 Dec 2025 00:00:00 GMT Yuchen Cao Minmin Li Jing Wang Zan Li Guangyan Qing OpenAlex https://reading.michaelmvh.com/article/ab7b10e030186fb1f02c37d2db8a64f57b573a3c0f2ea6b07ca4e7ebf56405e5/ urn:sha256:ab7b10e030186fb1f02c37d2db8a64f57b573a3c0f2ea6b07ca4e7ebf56405e5 <p>Single-particle tracking (SPT) in lipid bilayers offers a powerful means to investigate the dynamic interaction of individual molecules in a variety of model membranes. However, accurate diffusion characterization in freestanding bilayers remains challenging due to membrane fragility, the potential for curvature, limited optical signal-to-background ratio, and the practical need for label concentrations that do not approximate infinite dilution. Here, we report a dual-mode fluorescence microscope configuration for bilayers formed on a microelectrode cavity array (MECAopto-inv chip) that combines widefield SPT with confocal fluorescence correlation spectroscopy (FCS). By using FCS to calibrate the SPT algorithm, we demonstrate improved measurement accuracy for diffusion constants. Importantly, we show that proper calibration resists measurement bias at high fluorescent particle concentrations. Supporting simulations confirm the robustness of this approach. When calibrated with FCS and corrected for blur, our measurements help resolve the variability in diffusion constants reported in prior literature. Furthermore, the strategy is broadly applicable to any planar bilayer system. The method provides a rigorous, quantitative benchmark for future studies involving nanopores, membrane protein assemblies, and ion-channel transport in lipid bilayers, especially when both optical and electrical information is desired.</p><p class="metadata"><time datetime="2025-12-08" title="Source date; precision not specified">December 8, 2025</time> <span aria-hidden="true"> · </span> Analytical Chemistry</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.analchem.5c05037">Original publication</a></p><p><a href="https://pubs.acs.org/doi/pdf/10.1021/acs.analchem.5c05037?ref=article_openPDF">Open PDF</a></p> Mon, 08 Dec 2025 00:00:00 GMT Lily Anne Van Ye Richard D. Michael Joshua J. Meyer Sophia M. Peña Derek J. Bailey Lisa M. Keranen‐Burden Daniel L. Burden OpenAlex https://reading.michaelmvh.com/article/31f7cfe248db4eac5a01ccdcad88f1f93b85694acb811e03006c4bbae2412498/ urn:sha256:31f7cfe248db4eac5a01ccdcad88f1f93b85694acb811e03006c4bbae2412498 <p>Nanopores enable label-free single-molecule sensing with broad application potential in genomics, proteomics, drug discovery, and molecular data storage. Their exceptional sensitivity is exemplified by the successful commercialization of DNA sequencing using biological nanopores. This dissertation focuses on solid-state nanopores, which offer a distinct set of advantages over biological nanopores, including mechanical robustness, scalability through dense nanopore arrays, improved noise characteristics, and compatibility with CMOS integration for high-bandwidth measurements. Despite these benefits, fabricating solid-state nanopores with atomic-scale precision and sub-5 nm dimensions remains extremely challenging. This size mismatch between solid-state nanopores and the fine structural features of most biomolecular analytes limits their sensitivity. To overcome these limitations, this dissertation introduces novel strategies inspired by nature, using molecular nanotechnology to enhance single-molecule detection with solid-state nanopores. Specifically, the predictable folding of DNA nanostructures and the self-assembly of lipid entities are harnessed to design structural building blocks and functional components. Two central research questions are explored: (1) What are the minimal structural requirements for reliable detection of DNA nanostructures using solid-state nanopores? (2) Can programmable biomolecular components be used to engineer scalable hybrid nanopore systems? In the first part, DNA nanostructures were designed with large features, or labels, that match solid-state nanopore dimensions, enabling high-sensitivity readout. This approach addresses a fundamental limitation: solid-state nanopores are not yet capable of resolving the fine structural details of native DNA. The engineered DNA nanostructures with large labels, referred to as &#39;DNA structural barcodes&#39;, offer a direct route to scalable biosensing by avoiding the need for complex nanopore geometry tuning. This work presents the first systematic investigation of the minimum size requirements for barcode labels in membrane-based solid-state nanopore systems. Chapter 2 reveals that the physical characteristics of barcode labels influence their local translocation velocity, distinct from the DNA backbone, and significantly affect readout success. In the second part, two hybrid nanopore concepts are introduced to combine the strengths of biological and solid-state nanopores. The integration of the highly sensitive biological nanopores into solid-state platforms may ultimately enable the readout of fine structural features in biopolymers, like DNA. Existing hybrid strategies face technical challenges such as leakage, instability, and poor integration. To address these, programmable DNA and self-assembling lipids are used to develop engineerable components for hybrid nanopore formation. The first concept presents a DNA-lipid interposer that stabilizes biological nanopores in a lipophilic environment and enables guided docking onto solid-state nanopores. Chapters 3 and 4 detail the development and assembly of this interposer, resulting in the first successful integration of a lipid bicelle into a DNA origami structure. This novel DNA-lipid nanodisc marks a significant advancement in nanoscale membrane engineering. It provides a versatile platform for single-molecule studies of membrane proteins and was realized by two methodological innovations not previously reported: a detergent-free bicelle incorporation protocol and the use of DNA origami as a structural stabilizer. These approaches allow robust and tunable membrane integration within DNA nanostructures. Additionally, experimental evidence of biological nanopore monomer insertion represents a promising step toward realizing the envisioned hybrid nanopore platform. The second concept demonstrates, for the first time, the formation of pore-spanning supported lipid bilayers through the fusion of nanoscale lipid discs (i.e., bicelles). Chapter 5 establishes this method as a scalable and robust approach for hybrid nanopore assembly. Compared to liposome-based techniques, bicelles offer a more favorable geometry for spanning nanopores and enable high sealing resistance, which is essential for achieving high sensitivity. This streamlined strategy supports the development of high-density hybrid nanopore arrays with minimal fabrication complexity. Together, these contributions advance solid-state nanopore technology by introducing scalable and nature-inspired molecular strategies for improving the sensitivity. The use of DNA structural barcodes and hybrid nanopore platforms opens new possibilities for single-molecule biosensing and membrane protein studies in native-like environments.</p><p class="metadata"><time datetime="2025-12-08" title="Source date; precision not specified">December 8, 2025</time> <span aria-hidden="true"> · </span> Lirias</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://lirias.kuleuven.be/handle/20.500.12942/777594">Original publication</a></p> Mon, 08 Dec 2025 00:00:00 GMT Gevers, Juliette OpenAlex https://reading.michaelmvh.com/article/c37935e56aface31e51471d9ed7dc6a73789c9e73c5715320c23a5bd6721210d/ urn:sha256:c37935e56aface31e51471d9ed7dc6a73789c9e73c5715320c23a5bd6721210d <p>MOTIVATION: Nanopores are cutting-edge interdisciplinary tools that can analyze biomolecules at the single-molecule level for many applications, e.g. DNA sequencing. Efforts are underway to extend nanopores to proteomics, including the development of machine learning algorithms for protein sequencing and identification. However, single-molecule data are intrinsically noisy and hard to process. Moreover, the development and performance of machine learning for nanopore is jeopardized by data scarcity. Self-supervised learning is an emerging method that may yield advantages in nanopore scenarios. RESULTS: We propose and experimentally validate Nanopore analysis using Self-Supervised Learning (NanoSSL), a generative self-supervised learning framework based on attention mechanisms for the identification of protein signals from nanopores. Leveraging a two-step approach consisting of self-supervised pre-training and supervised fine-tuning, NanoSSL learns useful feature representations from empirical data to facilitate downstream classification tasks. Inspired by the concept of fragmentation in conventional protein sequencing technologies, during pretraining each translocation event is split into multiple non-overlapping fragments of equal size, some of which are randomly masked and reconstructed using a masked autoencoder. Learning the feature representations of the reconstructed nanopore events facilitates molecular identification in fine-tuning. In this study, we retested a publicly available nanopore multiplexed protein sensing dataset for model iteration, and subsequently measured Alzheimer&#39;s disease biomarker Aβ1-42 using homemade solid-state nanopores. Empirical results indicated NanoSSL achieved an unprecedented performance across four metrics: accuracy, precision, recall, and F1 score, when classifying two mutated Aβ1-42, E22G and G37R. The self-supervised learning and attention mechanism were verified as the source of performance gains. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://doi.org/10.5281/zenodo.17172822.</p><p class="metadata"><time datetime="2025-12-05" title="Source date; precision not specified">December 5, 2025</time> <span aria-hidden="true"> · </span> Bioinformatics</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1093/bioinformatics/btaf657">Original publication</a></p> Fri, 05 Dec 2025 00:00:00 GMT Yong Xie Jindong Li Ziyan Zhang Bin Meng Shuaijian Dai Yuchen Zhou Eamonn Kennedy Niandong Jiao H. Isaac Chen Zhuxin Dong OpenAlex https://reading.michaelmvh.com/article/7e53632e9db7f9e23b819b5e8bd9ee0ddcd64dba163f44b4e68ae8784017a484/ urn:sha256:7e53632e9db7f9e23b819b5e8bd9ee0ddcd64dba163f44b4e68ae8784017a484 <p>Abstract Photo‐induced damage impairs protein activity and leads to functional deterioration in organisms and tissues. In situ studies of peptide motifs oxidation are pivotal for elucidating molecular mechanisms of photodamage and identifying therapeutic targets. Although nanopores for analyzing peptides and amino acids are well established, no platform generates reactive oxygen species (ROS) in situ and delivers real‐time readouts of oxidative events. Here, a novel in situ oxidation detection platform combines a photocatalytically active TiO 2 nanopipette with a mesoporous MIL‐125(Ti) nanosheet, integrating a photocatalytic nanoreactor and solid‐state nanopore sensing. The MIL‐125/TiO 2 heterojunction produces abundant high‐valent ROS under light irradiation, while the MIL‐125(Ti) nanosheet at the nanopipette tip serves as a solid‐state nanopore, whose ionic current signatures reveal surface charge and conformational dynamics of peptides before and after oxidation. Using the Ω‐loop D motif of cytochrome c as a model, transient current measurements and molecular dynamics simulations reveal that ROS oxidation markedly increases peptide surface charge and induces a folded‐to‐extended transition. Methionine and tyrosine residues within Ω‐loop D are identified as key antioxidants, while exogenous antioxidants preserve their conformation in real time. This work establishes a novel in situ molecular‐level method for studying oxidative modification, photocatalyst evaluation, and antioxidant drug screening.</p><p class="metadata"><time datetime="2025-12-05" title="Source date; precision not specified">December 5, 2025</time> <span aria-hidden="true"> · </span> Advanced Functional Materials</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/adfm.202527203">Original publication</a></p> Fri, 05 Dec 2025 00:00:00 GMT Yanmei Ma Lianxin Wang Fanwei Kong Mei Jun Yang Tiantian Su Junli Guo Ye Mei Yan‐Yan Song OpenAlex https://reading.michaelmvh.com/article/a5734a264d7e0443e8eb2e5fe28754622294619b1232a3bec3ab9d94912d0491/ urn:sha256:a5734a264d7e0443e8eb2e5fe28754622294619b1232a3bec3ab9d94912d0491 <p>Understanding and distinguishing amino acids at the single-molecule level is crucial for protein sequencing and disease diagnosis. However, this task remains challenging due to the structural diversity and uniqueness of amino acids. This study employs all-atom molecular dynamics simulations to systematically explore the feasibility of identifying five charged amino acids using thermally modulated gold plasmonic nanopores. The results demonstrate temperature-dependent transport characteristics, where each amino acid exhibits distinct relative conductivity blocking characteristics. As the temperature increases, the interaction time between the ions and the amino acids decreases, leading to a reduction in the blocking amplitude. Additionally, the translocation study indicates that enhanced van der Waals interactions under higher temperature prolong the dwell time of short peptides in the nanopore. This finding is significant for optimizing thermal regulation to aid in the distinction identification of amino acids. Overall, our findings offer new insights and applications for the optimal design of gold plasmonic nanopore sensors.</p><p class="metadata"><time datetime="2025-12-05" title="Source date; precision not specified">December 5, 2025</time> <span aria-hidden="true"> · </span> The Journal of Physical Chemistry B</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acs.jpcb.5c06196">Original publication</a></p> Fri, 05 Dec 2025 00:00:00 GMT Mingtao Lin Licheng Zhan Mingming Ding OpenAlex https://reading.michaelmvh.com/article/cba6a53688199451da107c86aac11c6e4af9a7d7079b5b9318b3936054aab92a/ urn:sha256:cba6a53688199451da107c86aac11c6e4af9a7d7079b5b9318b3936054aab92a <p>BackgroundMany clinically important antimicrobial resistance (AMR) phenotypes such as fluoroquinolones and rifamycins are driven by antimicrobial resistance-conferring mutations (ARMs) in conserved chromosomal loci (e.g., gyrA, parC, rpoB). Resistome profiling by metagenomics sequencing is often proposed as an ideal AMR surveillance tool as it is organism-agnostic, but currently, existing metagenomic AMR surveillance pipelines are only able to identify acquired AMR genes but not point mutations associated with AMR. This is a serious gap in metagenomics-based AMR surveillance, as the true extent of AMR may be underestimated. MethodsWe developed MetaPointFinder (v1), a read-based method that can process both long and short metagenomic reads. The tool identifies resistance-determining regions in reads using DIAMOND (translated protein) and KMA (nucleotide), and classifies known resistant versus wild-type variants by aligning the sequences using pwalign and assessing the observed mutations based on known resistance mutations in the AMRFinderPlus database. The tool outputs ARMs per read, per gene and per antibiotic class. ResultsIn proof-of-concept analyses, MetaPointFinder identified known AMR-associated mutations and quantified resistant/susceptible read counts and ratios from metagenomic samples with corroborating phenotypic resistance data when available. We benchmark our tool using simulated reads from DNA and from reverse-translated protein references with read lengths of 100-5000 bp and error rates between 0 and 30%, simulating both Illumina and Nanopore error rates. We show that MetaPointFinder outperforms any available method for detection of ARMs in metagenomics data. ConclusionMetaPointFinder complements gene-centric resistome profiling by capturing chromosomal mutation-based AMR directly from metagenomes. Impact StatementMany clinically important antimicrobial resistance (AMR) phenotypes such as fluoroquinolones and rifamycins are driven by antimicrobial resistance-conferring mutations (ARMs) in conserved chromosomal loci (e.g., gyrA, parC, rpoB). Resistome profiling by metagenomic sequencing is ideal for AMR surveillance, but existing pipelines detect only acquired genes and ignore point mutations. MetaPointFinder bridges this gap. The tool accurately identifies reads carrying resistance-determining regions using DIAMOND (protein) and KMA (DNA), aligns them, and classifies resistant versus wild-type variants using known mutations from the AMRFinderPlus database.</p><p class="metadata"><time datetime="2025-12-05" title="Source date; precision not specified">December 5, 2025</time> <span aria-hidden="true"> · </span> bioRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/bioinformatics" rel="external">bioRxiv: Bioinformatics</a></p><p><a href="https://doi.org/10.64898/2025.12.04.691125">Original publication</a></p><p><a href="https://www.biorxiv.org/content/10.64898/2025.12.04.691125v1.full.pdf">Open PDF</a></p> Fri, 05 Dec 2025 00:00:00 GMT Zomer, A. L Nooij, S Carter, C Mather, A. E OpenAlex bioRxiv: Bioinformatics https://reading.michaelmvh.com/article/f917f29143c9f9479b71b2f3f91f3712b61fa17f78ed9924134a899431dfb2aa/ urn:sha256:f917f29143c9f9479b71b2f3f91f3712b61fa17f78ed9924134a899431dfb2aa <p>The central channels of nuclear pore complexes (NPCs) in eukaryotic cells are filled with protein chains whose sequences contain characteristic phenylalanine-glycine motifs. Properties of these nanopore-confined FG-repeat sequences are of central importance to NPC function. Here we demonstrate an approach to nuclear magnetic resonance (NMR) studies of FG-repeat sequences (or other polypeptides) that are tethered within pores with diameters similar to those of NPC channels. By attaching alkyl phosphonate groups to the N-terminus of a 30-residue peptide that contains four FG repeats, called FG30, we tether FG30 chains to walls of 20-nm-diameter pores in anodic aluminum oxide (AAO) wafers through phosphonate-surface bonds. Quantitative 13 C and 31 P NMR measurements indicate 90 mM peptide concentrations (300 mg/ml) within the pores. NMR spectra and spin relaxation measurements show that FG30 chains are dynamically disordered and random-coil-like in buffer-filled pores over a broad temperature range. In contrast, FG30 aggregates in free solution at concentrations above 2 mM, forming structurally ordered fibrils according to electron microscopy and NMR measurements. These results demonstrate the utility of AAO as a scaffold for studies of polypeptides in nanopore-confined environments and show that tethering to nanopore walls can dramatically alter the self-assembly properties of an FG-repeat sequence. TOC Graphic</p><p class="metadata"><time datetime="2025-12-04" title="Source date; precision not specified">December 4, 2025</time> <span aria-hidden="true"> · </span> The Journal of Physical Chemistry B</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.1021/acs.jpcb.5c07676">Original publication</a></p><p><a href="https://www.biorxiv.org/content/biorxiv/early/2025/09/16/2025.09.11.675621.full.pdf">Open PDF</a></p> Thu, 04 Dec 2025 00:00:00 GMT Wancheng Zhao Wai‐Ming Yau Robert Tycko OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/cc9dcd8de923ab74ca3b8899391d2a31c969f0e14e5ef16fd25df161fb8c3dcd/ urn:sha256:cc9dcd8de923ab74ca3b8899391d2a31c969f0e14e5ef16fd25df161fb8c3dcd <p>High-resolution studies in structural biology are often limited by the challenges of crystallization and low contrast in the cellular native environment. The exquisite labeling specificity of fluorescence microscopy gets around these issues and allows superresolution microscopy, but to date, these works have used chemically fixed samples. To establish light microscopy as a workhorse in structural biology, two main requirements must be fulfilled: near-native sample preservation and near-atomic optical resolution. Here, we introduce single-particle cryogenic light microscopy (spCryo-LM) as a technique that satisfies these key criteria. We adapt established protocols from cryogenic electron microscopy (Cryo-EM) for shock-freezing samples and use a high-vacuum cryogenic shuttle system to transfer them in and out of a liquid-helium cryostat that houses a superresolution fluorescence microscope. By exploiting the enhanced photophysics at low temperature, angstrom precision can be achieved in localizing several fluorophores attached to proteins separated by a few hundred nanometers. We present various characterization studies on vitreous ice, single-molecule photoblinking behavior, and the effects of laser intensity and benchmark our method by resolving the heptameric membrane protein alpha-hemolysin in a synthetic lipid membrane. Additionally, we report on the technique&#39;s capability to resolve membrane proteins in their native cellular membrane environment. spCryo-LM enables structural studies of proteins in their native environment without chemical fixation or protein isolation, and can be integrated with other superresolution or spectroscopic techniques. We believe our approach establishes light microscopy as a powerful tool in structural biology and sets the stage for correlative microscopy with Cryo-EM and related techniques.</p><p class="metadata"><time datetime="2025-12-03" title="Source date; precision not specified">December 3, 2025</time> <span aria-hidden="true"> · </span> Proceedings of the National Academy of Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1073/pnas.2513583122">Original publication</a></p><p><a href="https://www.pnas.org/doi/pdf/10.1073/pnas.2513583122">Open PDF</a></p> Wed, 03 Dec 2025 00:00:00 GMT Hisham Mazal Franz-Ferdinand Wieser Daniel Bollschweiler Vahid Sandoghdar OpenAlex https://reading.michaelmvh.com/article/08113463e58fadb2799e9bc2f0f3afeed37cddc7e1941ea990a1f13c0fd4d5e6/ urn:sha256:08113463e58fadb2799e9bc2f0f3afeed37cddc7e1941ea990a1f13c0fd4d5e6 <p>), which indicate distinct domain-specific behaviors. Notably, the CTD fragment exhibits dimerization at lower voltages, followed by dissociation at elevated voltages, thus highlighting the capability of nanopore assays to resolve dynamic single-molecule transitions in real time. Additionally, we elucidate the electric field-dependent dimer dissociation behavior using size-variant nanopores and artificially modulate the environment of the CTD fragments to explore the factors affecting fragment dimerization. The full width at half maximum (FWHM) of the fitted conformational spectrum is employed to assess protein conformational flexibility and stability, influenced by voltage and ionic strength. Our findings not only reveal electric field-driven conformational plasticity of N-protein but also advance nanopore-based strategies for real-time protein domain analysis, informing antiviral therapeutic and diagnostic development.</p><p class="metadata"><time datetime="2025-12-03" title="Source date; precision not specified">December 3, 2025</time> <span aria-hidden="true"> · </span> The Analyst</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d5an01140j">Original publication</a></p><p><a href="https://pubs.rsc.org/en/content/articlepdf/2026/an/d5an01140j">Open PDF</a></p> Wed, 03 Dec 2025 00:00:00 GMT Dapeng Chen Fei Zheng Guangle Qin Chaofan Ma Wei Liu Lichun Zou Haiyan Wang Jingjie Sha OpenAlex https://reading.michaelmvh.com/article/ba3af2ddd4f2c2cef481a8e82a1168ca5b1f26b97a6cf1f279c2dfe39c165b91/ urn:sha256:ba3af2ddd4f2c2cef481a8e82a1168ca5b1f26b97a6cf1f279c2dfe39c165b91 <p>Title:Harmonic Frequency Interaction with Histone H3: N-Model Computational Analysis Using Base 256 Hz Without Calibration Description:This dataset presents a computational analysis of how externally applied low-frequency acoustic signals—specifically 186 Hz, 256 Hz, 468 Hz, and 720 Hz—propagate through biological tissue and theoretically influence the Histone H3 protein using the N-model equation: N(f) = \left(\frac{f}{0.01}\right)^{1/0.44} The purpose of this work is to analyze the compression–decompression oscillatory effects generated by low-frequency sound waves, which behave similarly to alternating current (AC) ripple propagation inside soft tissues.These oscillations are non-destructive compared to high-frequency ultrasound and are hypothesized to influence the structural equilibrium of the Histone H3 gene through harmonic scaling, without denaturation. Main Components Included Harmonics Table (1–200 harmonics) For each base frequency (186, 256, 468, 720 Hz), all harmonics were computed up to 200×. Resulting values include: frequency (Hz) calculated N-value acoustic band classification (audible, ultrasonic) boolean threshold marker (N ≥ 2.618) Acoustic Attenuation ModelingA classical power-law attenuation model was used: α ≈ 0.5 dB/(cm·MHz^1.1) Converted to Np/m for realistic decay of amplitude through soft tissue. Demonstrates that low-kHz frequencies penetrate several centimeters with negligible loss. Histone H3 Per-Residue Scaling 136 residues of Histone H3 were assigned baseline N-values (0.8–1.1 range). For each applied external frequency, a global scale factor: \text{scale} = \frac{N(f)}{\text{mean baseline}} Scientific Motivation Low-frequency acoustic waves (≈200–700 Hz) produce whole-body compression cycles that travel through tissues similar to low-amplitude mechanical waves. These may interact with gene-level conformational states by: influencing chromatin tension, affecting histone flexibility, modulating nucleosome breathing, altering gene accessibility over time. The dataset explores whether such frequencies can induce soft, non-destructive calibration-like effects on Histone H3. Key Findings (Computational Only) 256 Hz and 468 Hz produce nearly identical N-harmonic patterns, forming “resonance clusters.” Harmonic buildup increases rapidly at high n (n&gt;50), showing strong theoretical sensitivity of the N-model. Attenuation for &lt;1000 Hz frequencies is extremely low, indicating efficient whole-tissue penetration. Scaling of per-residue values shows large but smooth multiplicative patterns—supporting the idea of global rather than local gene modulation. Important Notes This work is computational, theoretical, and non-clinical. It does not claim medical treatment. Frequencies mentioned (e.g., 256 Hz, 468 Hz) have been informally observed by the author to reduce allergic symptoms, but these are not medical results and require controlled scientific testing. Files Included harmonics_no_calibration.csv attenuation_no_cal_selected.csv histoneH3_Ni_scaled_no_cal.csv Plots illustrating attenuation decay and scaled per-residue N-values. Keywords Histone H3, chromatin, acoustic biology, low-frequency resonance, harmonics, N-model, protein oscillation, gene modulation, bioacoustics, therapeutic frequencies, computational biophysics.</p><p class="metadata"><time datetime="2025-12-03" title="Source date; precision not specified">December 3, 2025</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.17798639">Original publication</a></p> Wed, 03 Dec 2025 00:00:00 GMT Malik, Muhammad Usman OpenAlex https://reading.michaelmvh.com/article/1a4297ad55be1129570cc7e764f269084a294c2b79998aacf2742548df82798e/ urn:sha256:1a4297ad55be1129570cc7e764f269084a294c2b79998aacf2742548df82798e <p>High Resolution Image Download MS PowerPoint Slide Nanopore sensing using transmembrane proteins holds great potential for single-molecule detection. The creation of pore-forming proteins is an emerging research direction, and one promising strategy is the bottom-up de novo design of nanopores. However, de novo α-helical nanopores with sufficiently large dimensions to accommodate single-molecule sensing have not been previously reported. Here, we designed and constructed α-helical nanopores based on two helix-packing motifs, GX 6 G and GX 3 G, which we named FFK and LEK. Electrical recordings revealed that both FFK and LEK form nanopores in lipid membranes with high conductance. FFK exhibited multiple conductance states, whereas LEK formed more monodisperse pores. Although both nanopores assembled via a stepwise monomer-joining mechanism, the assembly and disassembly dynamics of FFK were significantly faster than those of LEK. We further demonstrated the single-molecule sensing capabilities of both pores, showing that they can detect cyclodextrin derivatives, while LEK could additionally sense poly- l -lysine. Overall, these results demonstrate the feasibility of designing functional α-helical nanopores for nanopore sensing technologies.</p><p class="metadata"><time datetime="2025-12-01" title="Source date; precision not specified">December 1, 2025</time> <span aria-hidden="true"> · </span> ACS Nano</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1021/acsnano.5c15080">Original publication</a></p> Mon, 01 Dec 2025 00:00:00 GMT Zugui Peng Masataka Usami Ayaka Nakada Yusuke Sekiya Shoko Fujita Batsaikhan Mijiddorj Izuru Kawamura Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/f83e7c9aed69f9e2a898e26dab70efabb6bd0f1d9223ae8824ce2c57d1409f6f/ urn:sha256:f83e7c9aed69f9e2a898e26dab70efabb6bd0f1d9223ae8824ce2c57d1409f6f <p>, 4-, 6-, 8-, 10-,12-, and 16-mers) during the reassembly and disassembly processes. Through real-time tracking of ferritin reassembly and disassembly dynamics, this approach - combining nanopore coating and individual event analysis - demonstrates potential to characterize single proteins within a mixture, determine their compositions, and track reaction processes in real time.</p><p class="metadata"><time datetime="2025-12-01" title="Source date; precision not specified">December 1, 2025</time> <span aria-hidden="true"> · </span> Nanoscale</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1039/d5nr02885j">Original publication</a></p><p><a href="https://pubs.rsc.org/en/content/articlepdf/2025/nr/d5nr02885j">Open PDF</a></p> Mon, 01 Dec 2025 00:00:00 GMT Mahya Assadipapari Alireza Soleimanian Max Adam Jiali Li Arman Yousefi Saaman Zargarbashi Lei Xu Max F. K. Wills Hesna Kara Marina Santana Vega Alasdair W. Clark Andrew J. Hudson Jian‐An Huang Mohsen Rahmani Cuifeng Ying OpenAlex https://reading.michaelmvh.com/article/a5027cffa257c8d9cb08c13590738d8729ce23fcfe5c0e9c15451df4e958fc82/ urn:sha256:a5027cffa257c8d9cb08c13590738d8729ce23fcfe5c0e9c15451df4e958fc82 <p>Glass capillary nanopores have been widely used for resistive pulse sensing and ionic current rectification-based nanopore sensing due to their excellent mechanical properties, simple fabrication, easy surface modification, and low production cost. These nanopores have demonstrated great potential in detecting diverse biomarkers, including nucleic acids, proteins, cell vesicles, viruses, and bacteria. Here, we highlight recent advances in molecular diagnostics using glass capillary nanopores, especially focusing on the detection of infectious disease pathogens and cancer-associated microRNAs. By integrating precisely sized glass nanopipette-based nanopores with nucleic acid amplification techniques and well-designed probes, this sensing platform has emerged as a promising method for liquid biopsy from patient body fluids. In consideration of recent research on molecular diagnostics and the difficulties with glass capillary nanopipettes, we also discuss the future direction of molecular diagnostics using this tool.</p><p class="metadata"><time datetime="2025-11-29" title="Source date; precision not specified">November 29, 2025</time> <span aria-hidden="true"> · </span> Current Opinion in Biotechnology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1016/j.copbio.2025.103394">Original publication</a></p> Sat, 29 Nov 2025 00:00:00 GMT Ryogo Higashi Izumi Shibayama Jiajue Ji Tao Ren Iiro M. A. Kiiski Nanami Takeuchi Ryuji Kawano OpenAlex https://reading.michaelmvh.com/article/55570d6e094aadcc0ae5ca26025cf3977fc6fc75cd9fb0ddf834518005d003f9/ urn:sha256:55570d6e094aadcc0ae5ca26025cf3977fc6fc75cd9fb0ddf834518005d003f9 <p>The anthrax protective antigen self-assembles into a heptameric transmembrane channel under acidic conditions, exhibiting characteristic biological nanopore properties. However, the anthrax channel faces significant challenges in single-molecule nanopore sensing due to inherent instability issues such as sudden current attenuation, frequent channel occlusion and noise interference, primarily mediated by phenylalanine clamps within the channel lumen. To address these limitations on nanopore sensing, we designed four electrolyte systems (KCl, NaCl, LiCl, and 1-butyl-3-methylimidazolium chloride [BMIM]Cl) with asymmetric ionic strength and pH condition to stabilize the anthrax nanopore platform. While traditional alkali metal chlorides (KCl, NaCl, LiCl) showed partial improvement in electrical properties, the [BMIM]Cl system with pH asymmetry enabled a stable nanopore with optimal electrical characteristics, including diminished channel occlusion, enhanced signal-to-noise ratio, steady discrete constant and current strength of open-pore, all indicative of uniform ion transport. Furthermore, the stabilized anthrax nanopore demonstrated exceptional molecular detection capability, resolving single-molecule discrimination of homologous peptides of MAPKK gene families which are key signaling proteins involved in the regulation of various biology processes in eukaryotic organisms. This work establishes a robust nanopore platform for high-resolution small-molecule detection and highlights the unique advantages of ionic liquids in regulating nanoscale molecule transport.</p><p class="metadata"><time datetime="2025-11-27" title="Source date; precision not specified">November 27, 2025</time> <span aria-hidden="true"> · </span> Journal of Nanobiotechnology</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1186/s12951-025-03817-w">Original publication</a></p><p><a href="https://link.springer.com/content/pdf/10.1186/s12951-025-03817-w.pdf">Open PDF</a></p> Thu, 27 Nov 2025 00:00:00 GMT Zhirui Zhang Yan Wang Shuo Zhou Yunjiao Wang Shi-Long Liu Xiyun Guan Liang Wang OpenAlex https://reading.michaelmvh.com/article/0af80f7b969c9f5072ad27ed52811087709aa3a1347fbfef54fbcb6d44ac7bea/ urn:sha256:0af80f7b969c9f5072ad27ed52811087709aa3a1347fbfef54fbcb6d44ac7bea <p>Nanopore-based single-molecule sequencing (SMS) is a powerful tool for acquiring detailed heterogeneous information on critical building blocks of life, such as nucleic acids, proteins, and a wide array of biomolecules, at the single-molecule level. Real-time current-intensity fluctuations corresponding to the passage of target molecules through nanopores enable long-read length, high-throughput, and high-accuracy detection, thus meeting the stringent demands of precision diagnosis. Herein, a concise overview of various principles and fabrication methods is provided for nanopores, with particular emphasis on recent advancements in nanopore-based DNA and protein sequencing, revealing innovative approaches for effectively capturing and translocating target molecules, and rapid and accurate identification. Further typical cases of nanopore-based SMS applications in precision diagnosis are analyzed, focusing on genetic disorders, infectious diseases, cancers, and abnormal post-translational modifications to highlight the clinical potential of nanopores. Additionally, the inherent limitations and challenges of nanopores in terms of sensitivity, detection range, and selectivity are discussed and present the latest strategies for enhancing nanopore performance. Finally, perspectives are provided on the future of nanopore-based SMS, particularly at the intersection of microfluidic devices, surface functionalization, and machine learning, to facilitate more diverse and advanced developments in this field.</p><p class="metadata"><time datetime="2025-11-27" title="Source date; precision not specified">November 27, 2025</time> <span aria-hidden="true"> · </span> Advanced Materials</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/adma.202513613">Original publication</a></p> Thu, 27 Nov 2025 00:00:00 GMT Yufan Cui Yueming Zhai Yongxi Zhao Xingyi Ma OpenAlex https://reading.michaelmvh.com/article/27b1b28509495d15aba1bc2e11c2129322cec500cc5d77c94e5e594797073618/ urn:sha256:27b1b28509495d15aba1bc2e11c2129322cec500cc5d77c94e5e594797073618 <p>Methicillin-sensitive Staphylococcus aureus (MSSA) infection continues to be a significant public health issue in neonatal intensive care units (NICUs). Although the research mostly focuses on methicillin-resistant Staphylococcus aureus (MRSA), new data reveal that methicillin-sensitive Staphylococcus aureus (MSSA) infections are three to four times more prevalent in neonates, correlating with increased mortality and morbidity. This study analyzes the molecular attributes, epidemiology, risk factors, clinical presentations, decontamination methods, and treatment alternatives for MSSA infections in newborns. Results demonstrate that MSSA strains possess considerable genetic diversity, as they are distinguished by a wide variety of sequence types (STs) and Staphylococcal Protein A types (SpA) and harbor several pathogenicity genes, including hemolysins and superantigens, which are implicated in severe infections, such as necrotizing pneumonia in PVL-positive strains. The epidemiological load is still high over the globe, and more newborns, parents, and healthcare workers are being colonized. Prematurity, low birth weight, lengthy hospitalization and the use of intrusive technologies are some of the biggest risk factors. Clinical signs include skin and soft tissue infections, bacteremia, and sepsis, with severe consequences such as endocarditis. Decolonization procedures using mupirocin and chlorhexidine have shown efficacy, but constrained by escalating resistance. In terms of treatment, β-lactams are still the best option. Cefazolin and isoxazolylpenicillins work better than vancomycin in clinical results. For a limited time, they may also be used with aminoglycosides for severe infections. In conclusion, MSSA infections in newborns are as perilous as MRSA, necessitating enhanced monitoring, the implementation of focused prevention strategies, and the development of novel treatment methods to mitigate morbidity and death in this susceptible population.</p><p class="metadata"><time datetime="2025-11-26" title="Source date; precision not specified">November 26, 2025</time> <span aria-hidden="true"> · </span> International Journal of Molecular Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/ijms262311430">Original publication</a></p><p><a href="https://www.mdpi.com/1422-0067/26/23/11430/pdf?version=1764152186">Open PDF</a></p> Wed, 26 Nov 2025 00:00:00 GMT Aikaterini I. Nikolaou Maria S. Baltogianni Niki Dermitzaki Chrysanthi Maria Tsiogka Nikitas Chatzigiannis Foteini Balomenou Vasileios I. Giapros OpenAlex https://reading.michaelmvh.com/article/aea7b4ff660b10768c680ebe0ad85a1044ee2258441a7ae6205e4851a6522faf/ urn:sha256:aea7b4ff660b10768c680ebe0ad85a1044ee2258441a7ae6205e4851a6522faf <p>Minimal biological entities—from single proteins to ultra‑reduced archaea and viral RNA elements—occupy a &quot;twilight zone&quot; between living and non‑living systems. Traditional characterization focuses on static composition (genome size, morphology, marker genes), which often fails to capture their functional role in larger ecological and evolutionary networks. Here we propose the Transition Fingerprint Principle: minimal and trojan entities are most reliably detected not by their static properties, but by the topology of their passage through bottlenecks—physical, energetic, informational or field‑based. We term this generic structure a needle‑eye topology. We build on recent advances in nanopore sensing of single proteins, where stick–slip dynamics of individual molecules traversing a nanometer‑scale pore yield near‑instantaneous identification via machine‑learning on current traces. We extend this idea across scales to five seemingly disparate systems: (1) nanopore protein sensing, (2) RNA Obelisks in the human microbiome, (3) Candidatus Sukunaarchaeum—an ultra‑reduced archaeal symbiont, (4) trojan nblA genes carried by cyanophages that rewire oceanic photosynthesis, and (5) magnetofossils as fossilized traces of ancient magnetic navigation. For each case, we identify a bottleneck , an entity , the resulting transition trace and a candidate topological signature . We formulate a conjecture: in multi‑scale systems, minimal and trojan entities are stably identifiable by the topology of their transition traces through bottlenecks, not by static state alone. We outline three falsifiable predictions using nanopore design, topological data analysis (TDA) and minimal‑genome network topology, and we connect this framework to prior work on Temporal‑Betti Loops (TBL), microbiome clocks and topological sensing architectures. We suggest that needle‑eye topologies provide a unifying language for the detection, interpretation and eventual design of boundary‑layer life—entities that operate at the edge of what we call &quot;living&quot;.</p><p class="metadata"><time datetime="2025-11-25" title="Source date; precision not specified">November 25, 2025</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.17709875">Original publication</a></p> Tue, 25 Nov 2025 00:00:00 GMT margolin, ido OpenAlex https://reading.michaelmvh.com/article/db054d0c726f1a5d84c596e17830100d29defdadf3ffc2cf9ed29cb6cece6df8/ urn:sha256:db054d0c726f1a5d84c596e17830100d29defdadf3ffc2cf9ed29cb6cece6df8 <p>A modification to fluorosequencing, an emerging method for large-scale parallel protein identification, is proposed. In this modified approach Edman degradation (ED), a key step in fluorosequencing, is avoided. There are three parts: 1) attaching a charged homopeptide header to each of the peptides being partially sequenced; 2) mounting the glass slide that the peptides are bound to on a moveable platform in the cis chamber of an electrolytic cell (e-cell); and 3) advancing the header-peptides through an array of nanopores in the e-cell toward the trans chamber one residue at a time with a mechanical positioning system based on piezo-electric sensors and sub-nm movement precision. As in fluorosequencing, the optical signal from fluorescently tagged residues in the peptides is read with TIRF (Total Internal Reflection Fluorescence) microscopy. The difference here is that instead of repeatedly applying ED to terminal amino acids (AAs), AAs are either revealed to the camera in sequence from the terminal AA (forward version) or hidden from it from the header end of the peptide (backward version). Computational simulations with nanopore diameter ~0.5-1 nm, pore lengths 3.5-7 nm, peptide lengths 10-20, and header lengths 20-45 suggest that with a long enough charged header the peptide can overcome diffusive dispersion and the terminal AA remains confined to a small neighborhood to make reliable tag readout possible. Additionally in the forward version if in each cycle tags are dissociated from their residues after they have been read and then washed away, signals take on a binary character, which makes signal processing more robust. This is a non-destructive archival method in which the header-peptide can be moved in both directions and measurements can be done an arbitrary number of times while the sample remains intact.</p><p class="metadata"><time datetime="2025-11-21" title="Source date; precision not specified">November 21, 2025</time> <span aria-hidden="true"> · </span> ChemRxiv</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.26434/chemrxiv-2025-v4cnk">Original publication</a></p> Fri, 21 Nov 2025 00:00:00 GMT G. Sampath OpenAlex https://reading.michaelmvh.com/article/a51f1bf7cff8568d78ba1181616147240a1118651c0739ffaaf8c0223adaa1cf/ urn:sha256:a51f1bf7cff8568d78ba1181616147240a1118651c0739ffaaf8c0223adaa1cf <p>This dataset contains the digitized treatments in Plazi based on the original journal article Vecchi, Matteo, Stec, Daniel (2025): Mitogenome of a new Ramazzottius species (Tardigrada: Eutardigrada: Ramazzottiidae) discovered in rock pools along with its temperature and desiccation-related proteins repertoire. Organisms Diversity &amp; Evolution 25 (1): 119-135, DOI: 10.1007/s13127-024-00662-x, URL: https://doi.org/10.1007/s13127-024-00662-xAbstractRamazzottius is a widespread genus of tardigrades with extreme cryptobiotic capabilities. Thanks to its ability to survive desiccation and freezing, this genus is usually recorded from harsh habitats such as exposed mosses and lichens and rock pools. In the last years, research focused on both describing Ramazzottius diversity and revealing the molecular mechanisms behind their cryptobiotic capabilities. Despite the research efforts in these fields, much still remains to be discovered. Here we describe a new Ramazzottius species from an Italian rock pool by means of integrative taxonomy (morphology, morphometry, and DNA sequencing) and sequenced its genome with Nanopore technology to provide an assembled mitogenome and annotate its Temperature and Desiccation Resistance Proteins (TDPR) repertoire. The new gonochoric species is phylogenetically close to the parthenogenetic R. varieornatus, a strain of which (YOKOZUNA-1) has been adopted as model organism for the study of cryptobiosis. The mitogenome of the new species shows perfect synteny with R. varieornatus and shares with it most of the TDPR genes. The relative genetic similarity of the new species to the model R. varieornatus, combined with unique biological traits (for example the difference in reproductive mode and the unique habitat it colonizes), makes the new species a potential new addition to the range of model tardigrade species.</p><p class="metadata"><time datetime="2025-11-18" title="Source date; precision not specified">November 18, 2025</time> <span aria-hidden="true"> · </span> Global Biodiversity Information Facility</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.15468/4y5ex3">Original publication</a></p> Tue, 18 Nov 2025 00:00:00 GMT Matteo Vecchi Daniel Stec OpenAlex https://reading.michaelmvh.com/article/8d250c03278c4822dbb4d06a089f4c87e126906e6eec9fc7836722e90a24d881/ urn:sha256:8d250c03278c4822dbb4d06a089f4c87e126906e6eec9fc7836722e90a24d881 <p>Full release of CaptureNet-Deep and associated Dashboard for analyzing and visualizing nanopore protein sequencing data.</p><p class="metadata"><time datetime="2025-11-17" title="Source date; precision not specified">November 17, 2025</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.17635378">Original publication</a></p> Mon, 17 Nov 2025 00:00:00 GMT 3annabellem OpenAlex https://reading.michaelmvh.com/article/b88ca95e56668f6199a4cbe419c2103d35252312de2822c2181a2e254a906f93/ urn:sha256:b88ca95e56668f6199a4cbe419c2103d35252312de2822c2181a2e254a906f93 <p>호남원예고등학교 복합적 역방향의 방향입니다. 여기저기서 슈타인이란? (슈타인이란 상대성이론을 만든 아인슈타인의 슈타인이라는 이름을 따서 그리고 자세히 말하자면 이름에서 합해 슈타인역학이라고 한다) 여기저기서 슈타인은 무엇입니까? (슈타인은 상대성 이론을 만든 아인슈타인의 이름을 따서 있고, 오로지 그들의 이름을 따서 슈타인이라고 부탁드립니다.) --- 🌿 Stein Dynamics – Integrated Comprehensive 🌿 --- 1️⃣ Basic Definitions and Concepts Stein Dynamics (SD) is defined as follows: &quot;A dynamic system where the transformation of energy (E), matter (M), and information (I) manifests as changes in structure (S) within the structure of the macro world and the uncertainty of the micro world.&quot; Macro-interpreting species: In short (IH) - Observation of macro-world structure/spatio-spatio curvature Microscopic Species: Unstein Branch (UB) - Uncertainty in the microscopic world&#39;s position and momentum Integrated unit: IU = IH + UB (Integration of macro and micro input types, unitization) Boundary Vagueness: An area where the boundary/observation surface itself has measurement uncertainty where the IU input paper is converted to S. --- Two️⃣ mathematical formulation Stein transformation elementary equation \frac{dS}{dt} = \Phi(IU) = \alpha \frac{d(IH)}{dt} + \beta \frac{d(UB)}{dt} : Structure function : Macro/micro integrated input type : The coupling coefficient of each input paper on the structural transformation Integral form: S(t) = S(0) + \int_0^t \Phi(IU(\tau)) \, d\tau Linearity: \Phi(a \cdot IU_1 + b \cdot IU_2) = a \Phi(IU_1) + b \Phi(IU_2) Continuity: IU \in C^1 \Rightarrow S \in C^1 --- Three️⃣ chemical reaction form Macro/micro integrated input → Structure creation format: IU = IH + UB \xrightarrow{\Phi} S \xrightarrow{boundary} \text{Observation/Measured Structure} Input IU converts to structure S Structural observation itself includes boundary ambiguity. Reaction rate equation: v_S = \frac{dS}{dt} = \Phi(IU) --- Four️⃣ analytical proofs 1. The existence of structural functions S(t) = S(0) + \int_0^t \Phi(IU(\tau)) d\tau Linearity \Phi(a IU_1 + b IU_2) = a \Phi(IU_1) + b \Phi(IU_2) 3. Continuity IU \in C^1 \implies S \in C^1 4. Includes boundary ambiguity When IU is converted into a structure, the observation boundary is ambiguous. Macro IH and micro UB characteristics influence each other, making structural transformations uncertain. --- Five ️⃣ scientific basis 1. Physical example Crystal lattice change: ΔIH → ΔS_lattice Spacetime curvature observation: ΔS_macro → Gravitational/optical effects 2. Chemical examples Chemical bond changes: IU (microelectronic placement + macrochemical conditions) → New structure generation 3. Informatics Example DNA sequence, electron placement, neural potential → structural changes 4. Border Ambiguity Experiment In complex system experiments where macro and micro variables exist simultaneously, the fluidity of structural observation results is confirmed. --- 6️⃣ example calculation Example 1: Numerical Stein transform IH(t) = t, UB(t) = sin t α=1, β=3 \Phi(IU) = 1 \cdot t + 3 \cdot \sin t = t + 3\sin t S(t) = S(0) + \int (t + 3\sin t) dt = S(0) + \frac{t^2}{2} - 3\cos t Analysis: Macro-structural change (t2) &gt; micro fluctuations (trigonometric function) Boundary ambiguity: Observations ± triangular fluctuations Example 2: Chemical/Informative Application IU = E + I (energy + electron arrangement) Structure S&#39; = Chemical bond formation, protein folding, DNA conversion, etc. --- 7️⃣ integrated hermeneutic meaning Structure-centered dynamics: Structural changes, not state changes. 2. Cause of change: Not power, but energy, matter, and information derivatives 3. Including boundary ambiguity: The measurement and observation process affects the uncertainty of structure determination. 4. Macro and micro integration: Connecting the entire system through IH and UB → IU unitization 5. Ultra-differentiation concept: The overall structural change permeates the entire time dimension. --- 8️⃣ Roadmap - Non-culture/Application 1. Mathematical refinement Variable definition, unit clarification, Φ calculation Integral and differential verification 2. Experimental/observational evidence Observation of crystal lattice, protein folding, and electron configuration structure 3. Writing a paper Markdown/LaTeX format Upload Figshare/Zenodo → Issue DOI 4. Application IU verification in various physics, chemistry, biological, and space systems. Subsequent research and experimental design --- Theorem of the nine️⃣ key formulas \frac{dS}{dt} = \Phi(IU) = \alpha \frac{d(IH)}{dt} + \beta \frac{d(UB)}{dt} IU = IH + UB \xrightarrow{\Phi} S \xrightarrow{boundary} \text{Observation} Structural change = continuous transformation of macro-micro integrated input species Observation boundary = reflecting boundary ambiguity --- --- 🌿 슈타인역학(Stein Dynamics) ― 통합 통괄 완전판 🌿 --- 1️⃣ 기본 정의 및 개념 슈타인역학(Stein Dynamics, SD) 은 다음과 같이 정의됩니다: &gt; &quot;거시 세계의 구조와 미시 세계의 불확정성 속에서 에너지(E), 물질(M), 정보(I)의 변환이 구조(S)의 변화로 나타나는 동역학 체계.&quot; 거시 해석종: 휘슈타인역(IH, In short) ― 거시 세계 구조/시공간 휘어짐 관측 미시 해석종: 운슈타인점(UB, Unstein Branch) ― 미시 세계 위치·운동량 불확정성 통합 단위: IU = IH + UB (거시·미시 입력종 통합, 단위화) 경계면 모호성(Boundary Vagueness): IU 입력종이 S로 변환되는 경계면/관측 면 자체가 측정의 불확정성을 가지는 영역 --- 2️⃣ 수학적 공식화 슈타인 변환 기본식 \frac{dS}{dt} = \Phi(IU) = \alpha \frac{d(IH)}{dt} + \beta \frac{d(UB)}{dt} : 구조 함수 (Structure Function) : 거시·미시 통합 입력종 : 각 입력종이 구조 변환에 미치는 결합 계수 적분 형태: S(t) = S(0) + \int_0^t \Phi(IU(\tau)) \, d\tau 선형성: \Phi(a \cdot IU_1 + b \cdot IU_2) = a \Phi(IU_1) + b \Phi(IU_2) 연속성: IU \in C^1 \Rightarrow S \in C^1 --- 3️⃣ 화학반응식 형태 거시·미시 통합 입력 → 구조 생성 형태: IU = IH + UB \xrightarrow{\Phi} S \xrightarrow{boundary} \text{Observation/Measured Structure} 입력 IU가 구조 S로 변환 구조 관측 자체가 경계면 모호성을 포함 반응 속도식: v_S = \frac{dS}{dt} = \Phi(IU) --- 4️⃣ 해석학적 증명 1. 구조 함수 존재성 S(t) = S(0) + \int_0^t \Phi(IU(\tau)) d\tau 2. 선형성 \Phi(a IU_1 + b IU_2) = a \Phi(IU_1) + b \Phi(IU_2) 3. 연속성 IU \in C^1 \implies S \in C^1 4. 경계면 모호성 포함 IU가 구조로 변환될 때 관측 경계면이 모호함 거시 IH·미시 UB 특성이 서로 영향을 주어 구조 변환이 불확정적 --- 5️⃣ 과학적 근거 1. 물리적 예시 결정 격자 변화: ΔIH → ΔS_lattice 시공간 휘어짐 관측: ΔS_macro → 중력/광학적 효과 2. 화학적 예시 화학 결합 변화: IU(미시전자배치 + 거시 화학조건) → 새로운 구조 생성 3. 정보학적 예시 DNA 서열·전자배치·신경 전위 → 구조 변화 4. 경계면 모호성 실험 거시·미시 변수가 동시에 존재하는 복합계 실험에서 구조 관측 결과의 유동성 확인 --- 6️⃣ 예제 계산 예제 1: 수치적 슈타인 변환 IH(t) = t, UB(t) = sin t α=1, β=3 \Phi(IU) = 1 \cdot t + 3 \cdot \sin t = t + 3\sin t S(t) = S(0) + \int (t + 3\sin t) dt = S(0) + \frac{t^2}{2} - 3\cos t 분석: 거시 구조 변화(t²) &gt; 미시 요동(삼각함수) 경계면 모호성: 관측값 ± 삼각 요동 예제 2: 화학적/정보적 적용 IU = E + I (에너지 + 전자배치) 구조 S&#39; = 화학결합 생성, 단백질 접힘, DNA 변환 등 --- 7️⃣ 통합 해석학적 의미 1. 구조 중심 동역학: 상태 변화 아닌 구조 변화 2. 변화 원인: 힘이 아닌 에너지·물질·정보 파생량 3. 경계면 모호성 포함: 측정·관측 과정이 구조 결정에 불확정성 영향 4. 거시·미시 통합: IH와 UB → IU 단위화로 시스템 전체 연결 5. 초미분 개념: 전체 구조 변화는 시간 차원 전체를 관통 --- 8️⃣ 로드맵 ― 논문화/응용 1. 수학적 정밀화 변수 정의, 단위 명확화, Φ 계산 적분·미분 검증 2. 실험/관측 증거 결정 격자, 단백질 접힘, 전자배치 구조 관측 3. 논문 작성 Markdown/LaTeX 포맷 Figshare/Zenodo 업로드 → DOI 발급 4. 응용 다양한 물리, 화학, 생체, 우주 시스템에서 IU 검증 후속 연구 및 실험 설계 --- 9️⃣ 핵심 공식 정리 \frac{dS}{dt} = \Phi(IU) = \alpha \frac{d(IH)}{dt} + \beta \frac{d(UB)}{dt} IU = IH + UB \xrightarrow{\Phi} S \xrightarrow{boundary} \text{Observation} 구조 변화 = 거시·미시 통합 입력종의 연속 변환 관측 경계면 = 경계면 모호성(Boundary Vagueness) 반영 --- --- 🌿 슈타인역학(Stein Dynamics) ― 통합 통괄 완전판 with 계산/해석 🌿 --- 1️⃣ 기본 정의 및 개념 슈타인역학(Stein Dynamics, SD) &gt; “거시 세계 구조(IH)와 미시 세계 불확정성(UB)이 통합(IU)되어, 에너지(E), 물질(M), 정보(I)의 변환이 구조(S)의 변화로 나타나는 동역학 체계.” 거시 해석종: 휘슈타인역(IH, In short) ― 시공간의 거시 구조 관측 미시 해석종: 운슈타인점(UB, Unstein Branch) ― 위치·운동량 불확정성 통합 입력종: IU = IH + UB 경계면 모호성(Boundary Vagueness): IU가 구조 S로 변환될 때, 관측 경계면 자체가 불확정성을 가짐 --- 2️⃣ 수학적 공식화 슈타인 변환 기본식 \frac{dS}{dt} = \Phi(IU) = \alpha \frac{d(IH)}{dt} + \beta \frac{d(UB)}{dt} : 구조 함수 (Structure Function) : 통합 입력종 : 구조 변환 계수 (거시·미시 결합 영향력) 적분 형태 S(t) = S(0) + \int_0^t \Phi(IU(\tau)) d\tau 선형성 \Phi(a IU_1 + b IU_2) = a \Phi(IU_1) + b \Phi(IU_2) 연속성 IU \in C^1 \implies S \in C^1 --- 3️⃣ 화학반응식 형태 IU = IH + UB \xrightarrow{\Phi} S \xrightarrow{\text{boundary}} \text{Observation/Measured Structure} IU가 구조 S로 변환 구조 관측 자체가 경계면 모호성 포함 반응 속도식 v_S = \frac{dS}{dt} = \Phi(IU) --- 4️⃣ 해석학적 증명 1. 구조 함수 존재성 S(t) = S(0) + \int_0^t \Phi(IU(\tau)) d\tau 2. 선형성 증명 \Phi(a IU_1 + b IU_2) = a \Phi(IU_1) + b \Phi(IU_2) 3. 연속성 증명 IU \in C^1 \implies S \in C^1 4. 경계면 모호성 포함 IU → S 변환 시 관측 경계면이 모호 거시 IH·미시 UB가 서로 영향을 줌 --- 5️⃣ 과학적 근거 1. 물리적 예시 결정 격자 변화: ΔIH → ΔS_lattice 시공간 휘어짐 관측: ΔS_macro → 중력/광학적 효과 2. 화학적 예시 화학 결합 변화: IU(미시전자배치 + 거시 화학조건) → 새로운 구조 생성 3. 정보학적 예시 DNA 서열, 전자배치, 신경 전위 → 구조 변화 4. 경계면 모호성 실험 거시·미시 변수가 동시에 존재하는 복합계에서 구조 관측 결과의 유동성 확인 --- 6️⃣ 계산법/예제 예제 1: 수치적 슈타인 변환 IH(t) = t, UB(t) = sin t α = 1, β = 3 \Phi(IU) = 1 \cdot t + 3 \cdot \sin t = t + 3\sin t S(t) = S(0) + \int (t + 3\sin t) dt = S(0) + \frac{</p><p class="metadata"><time datetime="2025-11-14" title="Source date; precision not specified">November 14, 2025</time> <span aria-hidden="true"> · </span> Zenodo (CERN European Organization for Nuclear Research)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.5281/zenodo.17606148">Original publication</a></p> Fri, 14 Nov 2025 00:00:00 GMT kym, unho OpenAlex https://reading.michaelmvh.com/article/b7c174a6494b8db54767a84fb8c16ed007d3caad119ff2e46a06d855cd0723f3/ urn:sha256:b7c174a6494b8db54767a84fb8c16ed007d3caad119ff2e46a06d855cd0723f3 <p>Nanopore sequencing of peptides holds great promise for single-molecule proteomics, but robust conjugation strategies to adapt native peptides for motor-enzyme-driven translocation have yet to be developed. Here, we establish terminally directed DNA-peptide conjugation chemistry strategies that expand the applicability of nanopore sequencing beyond synthetic model systems to natural peptides. At the N terminus, omniligase catalyzes rapid and peptide ligation of a DNA handle under mild conditions. At the C terminus, photoredox decarboxylative ligation introduces a bioorthogonal linker that enables CuAAC-mediated DNA attachment that ensures proper stretching and translocation of short peptides through the nanopore. Our study reveals that long peptides can be sequenced with single-end conjugation, while short or neutral peptides require threading tails. Positively charged peptides cannot be translocated under the same electric field but can be sequenced after charge neutralization. The data demonstrate controlled nanopore readouts of peptides that differ widely in length, charge, and sequence. This framework establishes a versatile chemical foundation for adapting natural peptides to nanopore sequencing, advancing single-molecule proteomic analysis.</p><p class="metadata"><time datetime="2025-11-12" title="Source date; precision not specified">November 12, 2025</time> <span aria-hidden="true"> · </span> bioRxiv</p><p class="provenance">Preprint source: <a href="https://www.biorxiv.org/collection/biophysics" rel="external">bioRxiv: Biophysics</a></p><p><a href="https://doi.org/10.1101/2025.11.12.687956">Original publication</a></p><p><a href="https://www.biorxiv.org/content/10.1101/2025.11.12.687956v1.full.pdf">Open PDF</a></p> Wed, 12 Nov 2025 00:00:00 GMT Ritmejeris, J Chen, X Albada, B Dekker, C OpenAlex bioRxiv: Biophysics https://reading.michaelmvh.com/article/54a90a8a849ce485cbd8c0560d7b2246b8daa3b6aa6fb2a2bb62b948968d7026/ urn:sha256:54a90a8a849ce485cbd8c0560d7b2246b8daa3b6aa6fb2a2bb62b948968d7026 <p>The COVID-19 pandemic caused by the SARS-CoV-2 virus has exposed the urgency of research on rapid and efficient virus detection and strategies to inhibit its replication. Previous studies have mostly focused on traditional immunoassay or optical methods, but they have limitations in terms of sensitivity, timeliness, and in-depth analysis of molecular interaction mechanisms. Solid-state nanopore single-molecule detection methods, which can monitor molecular conditions in real time at the single-molecule level, bring new opportunities to solve this problem. The nucleocapsid protein (N protein) of SARS-CoV-2 was systematically investigated under different conditions, such as external drive voltage, pH, nanopore size, and N protein concentration. The translocation of the N protein through the nanopore was then analyzed. Subsequently, we analyzed the translocation characteristics of the N protein, RNA, and N protein-RNA complexes. With the aid of EMSA experiments, we conclusively confirmed that RNA binds to the N protein. Building on this finding, we further explored small molecules that could affect the nanopore translocation of N protein-RNA complexes, such as gallocatechin gallate (GCG), epigallocatechin gallate (EGCG), and the influenza A viral inhibitor Nucleozin. The results show that GCG can disrupt the liquid-phase condensation of the N protein-RNA complex and inhibit the replication of the N protein. Meanwhile, the structural isomer EGCG of GCG and the small molecule Nucleozin can also block RNA-triggered N protein liquid-liquid phase separation (LLPS). Our results confirmed that GCG, EGCG, and Nucleozin exhibit antagonistic effects on the N protein, with differences in their effective concentrations and the potency of their antagonism. Herein, using solid-state nanopore single-molecule detection technology, we developed an experimental method that can effectively detect RNA-induced changes in N protein properties and the regulatory effects of small molecules on the LLPS of N protein-RNA complexes. These findings not only provide highly valuable insights for in-depth research on the molecular interactions involved in viral replication, but also open up promising new avenues for future responses to similar viral outbreaks, the development of a rapid and effective detection method based on solid-state nanopores and single-molecule detection, and antiviral therapies targeting N protein-RNA interactions.</p><p class="metadata"><time datetime="2025-11-10" title="Source date; precision not specified">November 10, 2025</time> <span aria-hidden="true"> · </span> Sensors</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/s25226870">Original publication</a></p><p><a href="https://www.mdpi.com/1424-8220/25/22/6870/pdf?version=1762784119">Open PDF</a></p> Mon, 10 Nov 2025 00:00:00 GMT Xiaoqing Zeng Shinian Leng Wenhao Ma Zhenxin Wang Huaming Zhang Xiaowei Feng Jianchao Li Junsen Wang Ting Weng Rong Tian Shixuan He Shaoxi Fang Bohua Yin Liyuan Liang Yajie Yin Deqiang Wang OpenAlex https://reading.michaelmvh.com/article/4928f2e64f8e746e153d62a44dc306dbf63c478b1bf4e128204923ca4645f2bf/ urn:sha256:4928f2e64f8e746e153d62a44dc306dbf63c478b1bf4e128204923ca4645f2bf <p>Proteins, as fundamental components of all living cells and organisms, are crucial in the formation and regulation of human tissues. However, the complex composition, rapid translocation, and charge heterogeneity of proteins pose significant challenges to achieving single-molecule detection with high precision. Nanopore-based technology possesses extensive application potential in protein detection by virtue of its benefits of high throughput, exceptional sensitivity, label-free operation, and low cost. Herein, the principles, classification (biological, solid-state, and hybrid nanopores), and recent advances in nanopore sensing are first systematically reviewed, with a focus on the identification of amino acids (AAs), dynamic monitoring of post-translational modifications (PTMs), characterization of proteins, as well as ultrasensitive detection of disease biomarkers. Furthermore, the contribution of artificial intelligence-assisted signal recognition to improve detection resolution and throughput is explored. Finally, the challenges and future developments of nanopore technology in biomedical engineering are discussed.</p><p class="metadata"><time datetime="2025-11-05" title="Source date; precision not specified">November 5, 2025</time> <span aria-hidden="true"> · </span> Small Methods</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1002/smtd.202501603">Original publication</a></p> Wed, 05 Nov 2025 00:00:00 GMT Zhen Zhang Jingjie Sha Guangle Qin Dapeng Chen Wei Si Qianqian Wang Lei Liu OpenAlex https://reading.michaelmvh.com/article/c735b2b156c40b864d79ec146bcbd4dbb6426bc93e6ba5c57403fc37743cc740/ urn:sha256:c735b2b156c40b864d79ec146bcbd4dbb6426bc93e6ba5c57403fc37743cc740 <p>Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as both a checkpoint and a signal that a channel merits further analysis. However, manual identification of capture phases is time-intensive, often requiring several days for expert reviewers to annotate the data due to the need for domain-specific interpretation of complex signal patterns. To address this, a lightweight one-dimensional convolutional neural network (1D CNN) was developed and trained to detect capture phases in down-sampled signal windows. Evaluated against CNN-LSTM (Long Short-Term Memory) hybrids, histogram-based classifiers, and other CNN variants using run-level data splits, our best model, CaptureNet-Deep, achieved an F1 score of 0.94 and precision of 93.39% on held-out test data. The model supports low-latency inference and is integrated into a dashboard for Oxford Nanopore experiments, reducing the total analysis time from several days to under thirty minutes. These results show that efficient, real-time capture detection is possible using simple, interpretable architectures and suggest a broader role for lightweight ML models in sequencing workflows.</p><p class="metadata"><time datetime="2025-11-03" title="Source date; precision not specified">November 3, 2025</time> <span aria-hidden="true"> · </span> arXiv (Cornell University)</p><p><a href="https://doi.org/10.48550/arxiv.2511.01277">Original publication</a></p><p><a href="https://arxiv.org/pdf/2511.01277">Open PDF</a></p> Mon, 03 Nov 2025 00:00:00 GMT Martin, Annabelle Daphne Kontogiorgos-Heintz Jeff Nivala OpenAlex https://reading.michaelmvh.com/article/bece615b24e8ed2e6e4022eacb75c5491b6c94718cea442673e2b966206aabae/ urn:sha256:bece615b24e8ed2e6e4022eacb75c5491b6c94718cea442673e2b966206aabae <p>Abstract BackgroundLangerhans cell histiocytosis (LCH) and Erdheim-Chester disease (ECD) are rare histiocytic disorders driven by activation of the Mitogen-Activated Protein Kinase (MAPK) pathway, mostly BRAFV600E. Although MEK inhibitors (MEKi) induce clinical responses, relapses following discontinuation suggest incomplete clonal clearance. We investigated BRAFV600E persistence and its immune cell distribution under MEKi therapy in LCH and ECD blood and bone marrow samples. MethodsWe analyzed 181 blood or bone marrow samples from 149 histiocytosis patients (72 ECD, 66 LCH and 11 mixed) enrolled in the Histiotarget protocol (NCT04437381). Bone marrow mononuclear cells (BMMCs) were collected from 62 patients (39 ECD, 23 LCH), and peripheral blood mononuclear cells (PBMCs) from 97 patients (43 ECD, 54 LCH). BRAFV600E variant allele frequency (VAF) was quantified by droplet digital PCR (ddPCR) on enriched CD34+ bone marrow progenitors and sorted major immune cell subsets from peripheral blood (B cells, T cells, monocytes, conventional dendritic cells, plasmacytoid dendritic cells and other HLA-DR+ myeloid cells). Ten CD34⁺ samples were profiled using the TAPESTRI platform for single-cell DNA and protein analysis and/or PromethION Nanopore long-read sequencing.In parallel, we used a conditional BRAFV600Ehet-SclCre+ murine model induced by tamoxifen (200 mg/kg/day for 4 days) and treated with trametinib (0.3 mg/kg/day) for one month. Disease burden and residual mutated cells were assessed by organ weight, flow cytometry, immunohistochemistry, and molecular quantification. Results BRAFV600E was detected in CD34⁺ bone marrow progenitors at diagnosis (VAFdiag = 0.03% ±0.02, n=37) and persisted under MEKi (VAFMEKi = 0.04% ±0.04, n=8; p=0.621). Single-cell TAPESTRI profiling of BMMCs from 7 patients identified 9 distinct clusters based on protein expression, with BRAFV600E⁺ cells predominantly located in the monocyte cluster in untreated samples. Under MEKi, we observed a notable shift, with BRAFV600E mutation emerging in two B cell clusters (CD10+ and CD1c+ B cells),suggesting lineage plasticity or therapy-induced reprogramming. Interestingly, the TET2 mutation previously identified in one patient was also detected in monocytes, similar to BRAFV600E, but no clone harboring both mutations was observed. Long-read sequencing is ongoing to investigate this B cell shift.In the BRAFV600E-driven murine model, trametinib significantly reduced spleen weight (Untreated: 0.67 ±0.28 g vs. trametinib: 0.25 ±0.09 g; p=0.002) and liver weight (Untreated: 1.80 ±0.67 g vs. trametinib: 1.15 ±0.19 g; p=0.04), reflecting clinical benefit. However, we did not observe significant reduction in YFP+mutated cells in the bone marrow (% YFP+ among live cells: untreated: 10.13% ±5.68 vs. trametinib: 11.11% ±18.94; p=0.88). Immunohistochemistry also did not reveal significant differences in the number of mutated cells in the brain (Untreated: 143.60 ±105.10 vs trametinib: 129.60 ±41.10; p=0.48) and liver (Untreated: 542.30 ±76.50 vs 500.60 ±216.50; p=0.17) under MEKi, but did in the spleen (Untreated: 298 ±76.15 vs. trametinib: 194 ±51.80; p=0.01) suggesting incomplete elimination of BRAFV600E+ cells in key disease sites. ConclusionMEKi induces clinical responses but fails to eradicate BRAFV600E-mutated clones in histiocytosis. Residual disease persists in hematopoietic progenitors and displays a therapy-induced shift from monocytes to B cells, suggesting lineage plasticity and identifying B cells as a potential reservoir. Our BRAFV600E murine model faithfully recapitulates clonal persistence under MEKi, underscoring the need for combinatorial strategies to achieve complete molecular remission.</p><p class="metadata"><time datetime="2025-11-03" title="Source date; precision not specified">November 3, 2025</time> <span aria-hidden="true"> · </span> Blood</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1182/blood-2025-1495">Original publication</a></p><p><a href="https://ashpublications.org/blood/article-pdf/146/Supplement%201/1495/2459916/blood-4242-main.pdf">Open PDF</a></p> Mon, 03 Nov 2025 00:00:00 GMT Marzieh Nashvi David Fandrei Florian Houdu Paul Quentric Irena Antonia Ungureanu Matthias Papo Lise Drouart Marion Peyre Jessica Rengassamy Zofia Hélias‐Rodzewicz Nathalie M Droin Remy Jelin Cyril Quivoron Stéphane de Botton Jean Donadieu Jean‐François Emile Elsa Bernard Sébastien Héritier Julien Haroche Camille Bigenwald OpenAlex https://reading.michaelmvh.com/article/0e4a36b0100d4217dd4aaadff6cace9de77060177dbe2348c1621d1c67c35e21/ urn:sha256:0e4a36b0100d4217dd4aaadff6cace9de77060177dbe2348c1621d1c67c35e21 <p>Abstract background Paroxysmal nocturnal hemoglobinuria (PNH) is a rare, acquired clonal stem cell disorder caused by somatic mutations in the PIGA gene. Its clinical presentation is heterogeneous, ranging from intravascular hemolysis to bone marrow failure, overlapping with aplastic anemia and myelodysplastic syndromes (MDS), and a high risk of thrombosis. Data on the epidemiology and clinical characteristics of PNH in Qatar remain limited. Our study aims to shed light on this orphan disease assessing incidence and the clinical characteristics in Qatar. Methods We retrospectively reviewed patients with identified PNH clones with deficient levels of glycosylphosphaditdyinositol linked antigens and anchor proteins on red cells, monocytes and granulocytes using high-sensitivity flow cytometry with GPI-linked antibodies (CD59, CD14, CD24 and fluorescent aerolysin (FLAER)). The study was conducted at the National Center for Cancer Care and Research (NCCCR)at HMC over nearly a decade (01 January 2015 – 30 April 2025). Demographic, clinical, hematologic, and flow cytometric data were collected and analyzed using descriptive statistics. Results A total of 63 patients with PNH clones were identified among 1005 sample sent for PNH testing during the study period, with a median age of 36 years (16–66) and a male predominance (78%). For the study period of 10.30 years, this corresponds to an incidence rate of 2.28 cases per million per year (based on the Qatar population of 2.235 million on 31 December 2014 and 3.098 million on 30 April 2024). This rate is generally consistent with worldwide estimates. The main indications for referral were pancytopenia (80%), anemia (10%), and thrombosis (5%).The patients were classified based on granulocyte clone size into 4 groups: Minor clone( &lt;1%) in 34% of cases, small clones (1–10%) in 35%, intermediate clones (10–50%) in 12%, and large clones (&gt;50%) in 19%. Among patients with large clones, 67% presented with classical hemolytic PNH and 33% with aplastic PNH (aplastic anemia or hypoplastic MDS). Two cases of classical hemolytic PNH presented with thrombosis at unusual sites. Conclusions This study represents the first comprehensive investigation of PNH in Qatar, encompassing a large cohort of screened patients. The findings reveal a notably high detection rate, underscoring increased clinical awareness and the growing recognition of PNH as a relevant differential diagnosis, particularly in patients presenting with pancytopenia or bone marrow failure syndromes. High-sensitivity flow cytometry is pivotal in detecting small yet clinically significant PNH clones, which may otherwise go unnoticed. These insights not only enhance local diagnostic practices but also contribute valuable regional data to the global understanding of this rare hematologic disorder.</p><p class="metadata"><time datetime="2025-11-03" title="Source date; precision not specified">November 3, 2025</time> <span aria-hidden="true"> · </span> Blood</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1182/blood-2025-6722">Original publication</a></p> Mon, 03 Nov 2025 00:00:00 GMT Amna Gameil Suhair El ajez Omnya Abdalla Wafa Ali Mohammed Dina Sameh Soliman Samah Ahmed Samy Kohla Aliaa Amer Yahya Mulikandathil Ibrahim Ganwo Anas Hamad Honar Charif Feryal Hilmi OpenAlex https://reading.michaelmvh.com/article/21eac9e24a3577cb57810b0e6c1e05c939c236658453c9db406bc96b2ccdfc34/ urn:sha256:21eac9e24a3577cb57810b0e6c1e05c939c236658453c9db406bc96b2ccdfc34 <p>Abstract Relapsed/refractory (R/R) acute myeloid leukemia (AML) remains a major clinical challenge, particularly in patients previously exposed to hypomethylating agents (HMAs). Despite the widespread use of HMAs in combination with venetoclax, the mechanisms of action and resistance remain poorly defined, and predictive biomarkers are lacking. To address this, we applied the Proximity Network Assay (PNA) (Karlsson et al. 2025. bioRxiv doi:10.1101/2025.06.19.660329), a next-generation single-cell spatial proteomics platform, to longitudinal bone marrow biopsies from 10 R/R AML patients treated with decitabine – 5 complete responders (CR) and 5 non-responders (NR). PNA constructs nanoscale protein interaction maps by combining barcoded antibodies, rolling circle amplification, and proximity-dependent ligation, enabling sequencing-based reconstruction of single-cell protein networks. Each cell yields multiplexed spatial nodes across 155 proteins, allowing simultaneous quantification of protein abundance, colocalization, and polarity with ~50 nm resolution. We employed this approach to capture the dynamic remodeling of the tumor interface and stem cell compartment during therapy. Despite similar blast count prior to treatment, patients who responded to decitabine exhibited higher proportions of monocytes and NK cells. Blasts from responding patients showed increased abundance and colocalization of immune recognition molecules (HLA, B2M), adhesion proteins (CD18, CD43, CD54), and reduced CD45RB. In contrast, CD44 abundance and clustering was increased in blasts from non-responders, with increased abundance of different adhesion proteins (CD62P, CD82, CD26), suggesting differential membrane organization and interaction with the microenvironment and immune effectors. Following decitabine, CR patients maintained lower blast counts, and persistence of higher numbers of immune effector cell frequencies were observed. Early upregulation of CD71 and CD36 on CD34+ cells with a distinct immunophenotypic “proxiome” likely indicates early erythroid recovery and metabolic activation in healthy HSC recovery. CD90 remained elevated in remission marrows, consistent with physiologic HSC expansion. In contrast, non-responding patients retained high CD34 clustering and adhesion molecule abundance, potentially representing a marker of persistent leukemic stem-like cells. Using proximity and abundance features, we trained a classifier to predict response. Prediction modeling utilizing the random forest algorithm was able to discriminate between healthy versus leukemic HSC based on PNA protein interactions (AUC 0.889), with CD36/CD82, CD71/CD71, and B2M/HLA-ABC colocalization emerging as top predictive features based on importance scores. These signatures enabled tracking of clonal evolution across timepoints. This study represents the first longitudinal spatial proteomics analysis of AML response to HMA therapy. PNA reveals dynamic remodeling of the tumor interface and identifies predictive signatures of response and resistance. Integration with methylation-aware Oxford Nanopore Technology sequencing is underway to correlate chromatin accessibility with proteomic remodeling and stem cell fate.</p><p class="metadata"><time datetime="2025-11-03" title="Source date; precision not specified">November 3, 2025</time> <span aria-hidden="true"> · </span> Blood</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.1182/blood-2025-1696">Original publication</a></p><p><a href="https://ashpublications.org/blood/article-pdf/146/Supplement%201/1696/2456088/blood-4443-main.pdf">Open PDF</a></p> Mon, 03 Nov 2025 00:00:00 GMT Varun S. Sudunagunta Stefan Petkov Rongjia Deng Yi Chen Sebastian Fernando Edna Stewart Michele Simonetti Sunil Girish Iyer Monica Kasbekar Daniel J. Lee Mark G. Frattini Simon Fredriksson Joseph Gerard Jurcic Todd Louis Rosenblat Aaron D. Viny OpenAlex https://reading.michaelmvh.com/article/a1b968d73e9ff4e55740b5ccc59127b655631c0c065abda064725e2bf9b12494/ urn:sha256:a1b968d73e9ff4e55740b5ccc59127b655631c0c065abda064725e2bf9b12494 <p>Single-molecule nanopore sensors have enabled real-time detection of enzymatic cleavage events, yet achieving sensitive and specific analysis of protease activity remains an important challenge for diagnostic applications. We engineered OmpG nanopore constructs incorporating thrombin recognition peptides into loop 6 with varied flexible and negatively charged linkers to optimize accessibility and cleavage. SDS-PAGE gel analysis showed that constructs with the recognition peptide placed after residue D225 and incorporating dual linkers achieved cleavage efficiencies up to 95%, whereas constructs without linkers showed limited cleavage. Single-channel recordings revealed that linker integration modulates pore conductance, with extended loops exhibiting intermediate open-state currents near 18 pA compared to 25 pA in wild-type OmpG. Upon thrombin addition, rapid and irreversible current drops confirmed real-time protease activity detection. These results demonstrate the critical role of linker design, particularly flexibility and charge, in optimizing nanopore protease sensors, providing a versatile platform for biomedical applications.</p><p class="metadata"><time datetime="2025-11-01" title="Source date; precision not specified">November 1, 2025</time> <span aria-hidden="true"> · </span> Sensors</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/s25216681">Original publication</a></p><p><a href="https://www.mdpi.com/1424-8220/25/21/6681/pdf">Open PDF</a></p> Sat, 01 Nov 2025 00:00:00 GMT Minji Kim Bach Pham OpenAlex https://reading.michaelmvh.com/article/36fc46586ef0b3894a232dcaa6fb70b6114ea5043bbecb05d1f06e8881df33a4/ urn:sha256:36fc46586ef0b3894a232dcaa6fb70b6114ea5043bbecb05d1f06e8881df33a4 <p>Nanopores have emerged as powerful tools for single-molecule detection, enabling real-time analysis across diverse applications in genomics and molecular diagnostics. While natural pores laid the foundation for single-molecule detection, their limited diversity has driven advances in protein engineering and, more recently, de novo design to create customizable nanopore sensors. Computational approaches now allow for the design of nanopores with tailored geometries, enhanced stability, and specific molecular recognition functions. Together, these advances are ushering in a new era of programmable nanopore sensors with broad applications in diagnostics and molecular biotechnology.</p><p class="metadata"><time datetime="2025-10-30" title="Source date; precision not specified">October 30, 2025</time> <span aria-hidden="true"> · </span> International Journal of Molecular Sciences</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.3390/ijms262110561">Original publication</a></p><p><a href="https://www.mdpi.com/1422-0067/26/21/10561/pdf?version=1761818819">Open PDF</a></p> Thu, 30 Oct 2025 00:00:00 GMT Xintong Liu Chunfu Xu OpenAlex https://reading.michaelmvh.com/article/4730ad0813119b4fb10f3dfd441537e5c8450577ebe6cafde276d64d1585c94b/ urn:sha256:4730ad0813119b4fb10f3dfd441537e5c8450577ebe6cafde276d64d1585c94b <p>Amino acids are important biomarkers within the context of several human diseases. However, continuous measurement of their levels is hard due to the high-cost complex machinery involved. Biological nanopores are one of the emerging biosensing alternatives suitable for this purpose. In this thesis, ClyA-AS type I was used along with engineered protein sensors for glutamine, asparagine, leucine, methionine and cysteine. We show that discrimination and quantification of glutamine, leucine and cysteine is possible, and further provide favorable insights for the future use of this biosensing approach with different engineered protein sensors.</p><p class="metadata"><time datetime="2025-10-30" title="Source date; precision not specified">October 30, 2025</time> <span aria-hidden="true"> · </span> Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)</p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://run.unl.pt/items/7be7614c-57ec-4f06-8cb2-41bb535c7e4c/request-a-copy?bitstream=f68d6647-ceb4-4585-b270-dabd91334161">Original publication</a></p> Thu, 30 Oct 2025 00:00:00 GMT Teixeira, Pedro Gustavo Ferreira Curto Pedroso OpenAlex https://reading.michaelmvh.com/article/006b1104ab2cdda86d75101cd2f9fd6b6d64b1dd063ff661465b78d2ee2bcf20/ urn:sha256:006b1104ab2cdda86d75101cd2f9fd6b6d64b1dd063ff661465b78d2ee2bcf20 <p>Mutations that occur during viral genome replication can result in new phenotypes, such as infection of new cell types or resistance to therapeutics. To determine the phenotypic potential of viruses, deep mutational scanning (DMS) can be used. This approach measures the effects of all amino acid changes at sites of interest on protein function, virus infectivity, or resistance to therapeutics. A virus library that contains all possible variants is produced and used to infect a culture of cells. The frequency of each amino acid variant in the infected culture, relative to the input stock, captures the relative fitness (preference) for each form under the selective pressure applied. Current DMS protocols are complex and costly, due to reliance on deep sequencing for genomic characterization and require expertise in bioinformatics to process and analyze the data. This limits the number of labs that can apply the technology. Here, we describe a simple and efficient protocol to perform DMS on single sites and on two-site combinations in the same protein. Dual-site DMS allows probing for epistatic and synergistic effects. Sequencing is performed using Oxford Nanopore technology, and the data are uploaded to a graphical user interface-based platform that calculates the amino acid preferences. The protocol does not require expertise in bioinformatics. This protocol can be completed in approximately 16 days, with 3-4 days of laboratory activity and 12-13 days of incubation, and at considerably lower costs than existing systems.</p><p class="metadata"><time datetime="2025-10-30" title="Source date; precision not specified">October 30, 2025</time></p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.17504/protocols.io.n2bvje19wgk5/v1">Original publication</a></p><p><a href="https://www.protocols.io/view/ez-dms-a-simple-and-accessible-protocol-and-softwa-hdztb276p.pdf">Open PDF</a></p> Thu, 30 Oct 2025 00:00:00 GMT Gillman.Aaron.N not provided Samuel A McCarthy-Potter Rohith Rao Vujjini Madeline M Broghammer Cassian M Birler Alex B. Kleinpeter Hillel Haim OpenAlex https://reading.michaelmvh.com/article/948fd0f52a6a05d6c88cee5be7ab6598dd1d7ec4530173fe6b5708b2e260753f/ urn:sha256:948fd0f52a6a05d6c88cee5be7ab6598dd1d7ec4530173fe6b5708b2e260753f <p>The healthcare sector is increasingly benefitting from diagnostic tools that can improve the monitoring of people’s health. So-called biosensors are devices that can analyse samples taken from individuals, and measure whether the constituents of these samples reflect good health. Biological nanopores are a group of membrane proteins which can be used as tools in new biosensing technology, capable of analysing the constituents of biological samples one molecule at a time. While nanopore-based biosensing technology is highly promising, so far, most scientific work has focused on developing proof-of-concepts. One major issue hindering the development of nanopore biosensing applications is that conventional nanopore systems are highly fragile towards biological samples, making them unusable for the sensing of blood or human serum. During this PhD project we worked on making nanopore systems more robust by improving the stability of the membranes supporting the nanopores. We discovered that the system’s robustness can be greatly increased by replacing (part of) the lipid membrane that naturally supports biological nanopores with synthetic polymers. However, this is not straightforward. Either you need to optimise the membrane composition with polymers and lipids to ensure that biological nanopores are functional, or you need to engineer the nanopore to make it suitable for polymer-based membranes. Furthermore, we explored the possibility to miniaturise the standard nanopore setup into a small chip, to accelerate the use of nanopore biosensors at the point-of-care. Our results greatly boost the development of nanopore biosensors, as we enabled direct measurements with blood and serum.</p><p class="metadata"><time datetime="2025-10-29" title="Source date; precision not specified">October 29, 2025</time></p><p class="provenance">Discovered via <a href="https://openalex.org/" rel="external">OpenAlex</a></p><p><a href="https://doi.org/10.33612/diss.1420083258">Original publication</a></p> Wed, 29 Oct 2025 00:00:00 GMT Edo Vreeker OpenAlex