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Khabre desk
Recent reporting, analysis and explainers from the Biology desk.
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Researchers brought two archaeal strains from a lineage closely related to the ancestor of eukaryotic cells into culture. Their simple internal organization, elaborate surfaces, microbial partnerships and protein-dependent lifestyle offer clues about how complex cells arose.
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A bioRxiv preprint introduces LangAAI, a model that uses antibody and antigen sequences to model antibody hypervariable regions without requiring 3D structures. The authors report that changing the antigen input to a non-binding decoy particularly affects sequence recovery in the CDR3 loop.
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A bioRxiv preprint reports XXY and XXYY females at frequencies as high as 88% in some strains of four Drosophila species. The researchers link the pattern to a bias in the chromosome types carried by eggs.
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A bioRxiv preprint reports that DFCP1 assembles into a helical coat that concentrates the membrane lipid PI3P and helps organise sites where cells repair damaged lysosomes.
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In a preprint, researchers report that antibiotic selection on human airway tissue favoured Pseudomonas aeruginosa clones that preserved the tissue and survived treatment better. The finding suggests that standard susceptibility measurements can miss infection traits shaped by the host environment.
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A bioRxiv preprint reports that microbiome-colonized rice and two defined bacterial communities had less rice blast disease in a gnotobiotic experimental system. The results suggest that microbes can shape rice immune responses as well as act against the fungus.
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A bioRxiv preprint describes a single-amplicon sequencing workflow that recovered high-quality rhinovirus genomes from clinical specimens and enterovirus coding sequences from isolates. The authors report lower reagent costs and shorter processing time than hybridization capture sequencing.
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A bioRxiv preprint describes Carbon-A, a 1.2-billion-parameter model for predicting protein-coding genes across eukaryotes. Its authors used the model to create a database covering 48,167 genome assemblies and report strong performance across 42 benchmarks.
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OpenAI says it worked with PerturbAI and Scripps Research to use thousands of GPT-Rosalind agents to analyse a whole-brain mouse CRISPR atlas in 32 minutes. The agents linked gene-disruption effects with scientific literature to produce leads for follow-up research.
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A Nature correspondence links research into how single-celled algae sense light to the discovery of channelrhodopsins and the development of optogenetics. Its authors say this line of work underpins this year’s Nobel Prize in Physiology or Medicine.
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A bioRxiv preprint introduces Chaperone, a framework for coordinating protein-design tools. Its authors report reduced token use and GPU costs across nine design tasks, alongside results from several protein-design campaigns.
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A 30-month study of wild mosquitoes in western Kenya found that Microsporidia MB infection was associated with lower odds of Plasmodium falciparum infection. The association was stronger in mosquitoes with high-intensity symbiont infections.
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A bioRxiv preprint reports that Cell Painting PLUS uses additional organelle-resolved imaging to improve morphological profiling of compounds. In tests of 284 compounds in U2OS cells, it performed better than conventional Cell Painting for identifying compounds that interfere with lysosome function.
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A bioRxiv preprint reports that simulated mixtures of E. coli strains made sequence-type and serotype prediction less reliable than detection of individual resistance and virulence genes. Increasing the dominant strain’s abundance improved strain-level predictions, while longer reads alone did not resolve the challenge.
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A bioRxiv preprint reports that canary breeds selected for song differ from other breeds in neural development, song-related brain regions and auditory sensitivity. Genome-wide findings point to many genes contributing to song divergence, including an ADGRV1 variant associated with singing and hearing traits.
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A bioRxiv preprint reports that a butterfly population’s female-heavy sex ratio returned to near parity in 2024–2025 as the frequency of feminizing Wolbachia fell. The population had reached 93.1% females in 2022.
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A bioRxiv preprint reports cryo-EM structures showing aphidicolin blocking human DNA polymerases δ and ε at the site where they add DNA building blocks. Reconstituted assays and the structures suggest that differences in how the enzymes grip the DNA template help explain why Pol δ is more sensitive.
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A bioRxiv preprint reports that wheat resistance to four soil-borne pathogens is shaped by many genetic factors, with some genomic regions shared across diseases. The authors say the patterns also depend on pathogen, environment and local genetic context.
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A bioRxiv preprint maps about 400,000 effects of μ-opioid receptor variants across 15 opioids. The researchers report that ligands with different signalling efficacy rely on different regions of the receptor.
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A bioRxiv preprint reports that correcting ambient RNA before detecting doublets can leave more doublet-containing droplets in single-cell RNA-sequencing data. The authors recommend detecting doublets first, except when using CellBender.
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A bioRxiv preprint reanalysed 115 whole-body RNA-sequencing libraries from female Anopheles gambiae kept at 27, 30 or 32°C. A gene-expression clock estimated warmer mosquitoes as older, but its age offset stopped widening after day five.
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A bioRxiv preprint reports that two introns from the PRK gene increased reporter expression in Chlamydomonas reinhardtii by up to 35-fold compared with intronless versions. The researchers also used one of the introns to produce detectable patchoulol under conditions where a reference intron was insufficient.
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A bioRxiv preprint reports SPEAR, a method combining laser microdissection and mass spectrometry to measure RNA modifications in small regions of preserved tissue. In human diffuse glioma samples, the authors found lower levels of several methylated RNA modifications in higher-grade foci than in low-grade regions.
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A bioRxiv preprint reports cryo-EM structures of the flagellar motor in Borrelia burgdorferi, revealing stators that remain attached to the motor while disengaged from its rotor. The authors propose that this arrangement lets the bacterium regulate torque by switching individual stators in and out of engagement.
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A bioRxiv preprint describes a two-part fertilization apparatus in male Cryptosporidium parasites. In infected mice, conditional inactivation of the membrane-fusion protein HAP2 blocked fertilization and oocyst production, and the authors report that it rapidly cleared infection.
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A bioRxiv preprint reports that centromeres in isolated human metaphase chromosomes have a distinct force response, including softening at some force levels. The researchers also found that topoisomerase IIα is recruited to centromeric regions under significant tension.
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A bioRxiv preprint reports Epulopiscium-related 16S sequences across human and animal gut samples. In human samples, the authors found age- and disease-associated differences in their abundance.
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A bioRxiv preprint maps the maturation of human choroid-plexus organoids and reports that their response to valproic acid depends on developmental stage. Early changes recovered after the drug was withdrawn, while some late-stage transporter impairments persisted.
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A bioRxiv preprint benchmarking differential scanning fluorimetry across 26 laboratories found good repeatability within instruments but moderate differences between them. The fluorescence readout and analysis workflow also affected apparent protein melting temperatures.
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A bioRxiv preprint describes three triple-negative breast cancer subtypes defined by differences in tumour cells and their surrounding tissue. The authors link the groups to distinct immune, fibrotic and metabolic patterns.
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A bioRxiv preprint comparing human H1N1 strains collected from 1977 to 2024 reports a recurring preference for α2,6-sialylated glycans. The study also found changes in binding avidity and a binding-null egg-adapted mutant.
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A bioRxiv preprint combines data from eight healthy Indian cohorts into a reference atlas and proposes a four-part Indian Gut Health Index. The authors report geographic patterns in the data, while noting that cohort and geography effects are strongly intertwined.
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A Nature study describes DRT10, a bacterial antiviral system that uses a noncoding RNA to guide repeat-DNA synthesis. Its RNA-templated mechanism has parallels with eukaryotic telomerase.
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A bioRxiv preprint maps labeled nutrients across adult female fruit flies, finding distinct patterns of metabolism in different body regions. In flies with gut tumors, alanine’s contribution to malate increased, and reducing gut alanine uptake lowered tumor burden.
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A taxonomic study in Phytotaxa recognises five species in the giant waterlily genus Victoria, including V. colombiana in Colombia’s upper Orinoco and V. mattogrossensis in the Pantanal. The researchers compared plant morphology and mapped populations against South American river drainage patterns.
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An Anthropic-authored bioRxiv preprint reports that Claude Code agents surveyed 1.9 billion protein clusters and identified a family of phage reverse transcriptases associated with tandem DNA repeats. The researchers also report that the repeat arrays are highly expressed during Staphylococcus phage infection.
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A bioRxiv preprint describes ModDNA, a sequence-design and cloning toolkit for building custom DNA molecules up to 100 kilobases. The researchers used the constructs in single-molecule visualisation assays, including an assay of DNA loop extrusion by human condensin I.
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Biohub, US federal agencies and industry partners announced a combined $1.8 billion commitment to develop open, AI-ready biological data and measurement technologies. The initiative aims to support predictive models of cell behaviour; the announcement describes planned work, not a completed virtual cell.
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A bioRxiv preprint describes REZCUE, a method for imaging archived tissue in three dimensions while preserving DNA, RNA and proteins for later molecular analysis. The authors report its use across commercial antibodies and in a multi-omic analysis of one archived breast cancer specimen.
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A two-year field study of 60 Zea accessions found that some had 20–40% of their nitrogen derived from the atmosphere. Aerial-root traits changed more consistently across the domestication continuum than this measure of biological nitrogen fixation.
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A bioRxiv preprint reports that LptZ connects surface lipoprotein transport with outer membrane vesicle formation in Bacteroides. Experiments in an lptZ mutant also point to an expanded role for the bacterial Lpt transport machinery.
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A bioRxiv preprint reports that the host protein HNRNPM binds stem-loop 5 in the SARS-CoV-2 5′-UTR and promotes protein synthesis from the viral RNA. Mutations in the structure’s lower stem reduced both HNRNPM binding and protein synthesis.
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A bioRxiv preprint describes four rounds of computational screening that identified natural hydroxymethylfurfural oxidases with improved activity on a key FDCA-production reaction. Some candidates approached an engineered benchmark under the tested conditions.
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A bioRxiv preprint introduces AuditPPI, a framework for examining the signals behind protein-interaction predictions. Its authors report that benchmark performance can reflect cellular context and other cues, with limited evidence that the predictive signals specifically capture interaction interfaces.
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A bioRxiv preprint reports that Plasmodium male-gamete axonemes retain key surface motility modules but have a reduced set of proteins inside their microtubule doublets. It also describes proteins involved in doublet organization and the progressive assembly of outer dynein arms.
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A bioRxiv preprint describes a transformer model trained on 8.8 million measured SARS-CoV-2 RBD–ACE2 interactions. It predicts receptor-binding compatibility across animal species and pairs predictions with uncertainty estimates to help prioritise surveillance.
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Nature has retracted a 2014 study that reported miRNAs and the NMD pathway regulate ribosomal frameshifting in CCR5 mRNA. The journal says a cryptic splice site created artefactual reporter variants, and follow-up assays found no detectable frameshifting with a revised reporter.
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A bioRxiv preprint reports that increased nuclear acetyl-CoA in lab-grown neurons from people with sporadic Alzheimer’s disease was linked to altered RNA-protein acetylation and splicing. Inhibiting the enzyme ACLY reversed these changes in the cell model.
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A bioRxiv preprint reports that rice peptide OsRALF7 can trigger infection-structure formation in the rice blast fungus. Experiments in rice plants also suggest the peptide helps guide where those structures form.
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A bioRxiv preprint uses dengue virus genome data and phylodynamic analysis to reconstruct global lineage spread. It finds an asymmetric pattern, with Asia continuing to seed transmission elsewhere and spread to the Americas increasing.
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A genome-scale analysis combining bat DNA with fossil anatomy identifies Europe as the probable origin of bats, and therefore powered flight, in the late Palaeocene. The study also revises relationships among bat families and places laryngeal echolocation before the diversification of living bats.
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A bioRxiv preprint reports that mice developed opioid-induced hyperalgesia even when spinal microglia were absent. The findings also separate changes in microglial appearance from a necessary role in the measured opioid effects.
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A bioRxiv preprint describes ProxiNet, a framework that learns cellular proximity from spatial transcriptomics and applies those relationships to dissociated single-cell RNA sequencing. The authors report spatial validation and use the approach to identify inferred neighborhoods in an Alzheimer dataset.
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Exposomics combines measurements of environmental and lifestyle exposures with genetic information. A 2026 analysis found that groups of exposure markers explained more variation in disease-related traits than markers assessed individually, while researchers work to connect those patterns to individual risk.
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A bioRxiv preprint describes MIMOSA, a framework that guides antibody-generating models using the structure of a known binder interface. The authors report experimentally validated binders against three targets, with hit rates of 20–26%.
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A bioRxiv preprint reports that BXD34 mice resisted diet-induced obesity and insulin resistance despite eating more, alongside widespread urinary nutrient loss. The strain was also profoundly susceptible to acute kidney injury.
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A Nature editorial argues that brain-organoid research needs international oversight as human lab-grown brain tissue is integrated into animal brains. It points to independent, multidisciplinary ethics advisers as one way to guide research.
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A bioRxiv preprint reports that tumour-cell states, mutations, tumour architecture and immune signals were associated with differences in ctDNA release in ten patients with non-metastatic HR+/HER2− breast cancer. The findings offer a biological framework for understanding why tumour DNA detected in tissue may differ from what appears in blood.
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Researchers report a single-nucleus atlas spanning 21 adult human tissues and four donors, combining gene-expression and chromatin-accessibility data. It maps candidate regulatory elements and gene links, and uses sequence-to-function models to predict effects of fine-mapped variants.
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A bioRxiv preprint uses single-cell transcriptomics to reconstruct an unusual anaerobic mitochondrion in the rhizarian flagellate PCE SSF. The proposed metabolism includes hydrogen production and a reduced, branched pathway for processing carbon.
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A bioRxiv preprint reports that mitochondrial DNA mutations arising during mice’s first two months were sufficient to drive age-related pathologies. The authors also found that tissue-specific selection and mitochondrial fusion influenced the mutations’ later fate.
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A bioRxiv preprint describes DS3dRNA, a method that scores interactions among groups of RNA structural elements to design sequences for target structures. The authors report improved benchmark performance and experimental activity in designed Mango II and twister RNAs.
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A bioRxiv preprint reports that rare and common STARD9 variants are associated with different lipid disorders and opposite changes in lysosome positioning. The authors connect those differences to cholesterol handling in cells and, in knockout mice, to intestinal cholesterol absorption.
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A bioRxiv preprint uses a polymer-physics model to explain how ecDNA copy number may shape regulatory contacts in cancer-cell condensates. In the model, contacts in oncogene-associated regions grow stronger and become less variable as copy number increases.
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A bioRxiv preprint reports H5N1 and H5N5 infections in six red foxes in Norway between 2022 and 2024. The investigation found systemic infection and detected a mammalian-adaptation marker in two H5N1 viruses.
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Anthropic says Claude agents identified a previously uncharacterised system in bacteriophages, built around a reverse transcriptase and an array of DNA repeats. Early lab experiments found that the array is expressed as distinct short RNAs; the system’s function is still under investigation.
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Anthropic says Claude agents identified a previously uncharacterized enzyme system in bacteriophages, built around a known reverse transcriptase and an array of DNA repeats. Early laboratory experiments found that the array is expressed as distinct short RNAs, but the system’s function is still being investigated.
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A study of human and great-ape cartilage found roughly threefold lower glycosaminoglycan levels in humans and traced this difference to widespread changes in skeletal gene regulation. The authors suggest the shift may have influenced human skeletal traits and vulnerability to degenerative disease.
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A global analysis of 58,319 outbreak events across 32 diseases found shared landscape associations for several vector-borne infections, but less consistent patterns for directly transmitted zoonoses. The study also found that outbreak reporting was strongly associated with access to healthcare.
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A bioRxiv preprint presents a physics-based framework that combines protein, nucleic-acid and metabolite models to simulate biomolecular condensates. Its authors report predictions for more than 60 disordered proteins and simulations of RNA- and protein–nucleic-acid condensates.
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A bioRxiv preprint reports genome-pattern evidence for an ancient whole-genome duplication shared by bryozoans. Few duplicate genes remain, but retained copies are enriched for cilia-related genes.
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A bioRxiv preprint reports that bumble bees adjusted opt-out choices to task difficulty and transferred the strategy to new tactile and working-memory tasks without retraining. The findings suggest that uncertainty-guided decision-making can occur in a brain with about one million neurons.
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A bioRxiv preprint reports that lysosomal acid lipase helps release cholesterol during phagosome maturation. Inhibiting the enzyme changed membrane organisation and had different effects on the survival of two bacterial pathogens.
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Researchers developed an engineered budding-yeast system to test resistance-conferring mutations in genes from several pathogenic fungi. They also used random mutagenesis to identify new candidate mutations.
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Modern gene editing, high-resolution imaging and omics tools have expanded cell biology beyond the two classic forms of cell death. Researchers are also finding that some cells can delay death or recover after a death programme begins.
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A bioRxiv preprint reports that trimethoprim reduced phage production and toxin production in laboratory experiments with a clinical Shiga toxin-producing E. coli isolate. The effect persisted alongside DNA-damaging antibiotics that normally increase phage activity.
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A bioRxiv preprint presents stEDGE, a computational framework that uses local tissue boundaries to reconstruct nested spatial domains and transition interfaces. The authors report results across 15 tissue sections and an application to cell-resolved profiling of fibrotic human lung.
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Mouse lineage-tracing experiments and human stem-cell differentiation studies indicate that the developing brain arises from two parallel neural ectoderm progenitors. The finding concerns embryonic cell lineages, not two physically separate adult organs.
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A bioRxiv preprint reports that dermal bone thickens through invading osteoblasts that deposit new mineralised matrix inside older bone. The finding challenges the conventional view that growth relies mainly on bone-forming cells adding matrix at the surface.
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A bioRxiv preprint reports that DNA recovered from museum hair samples attributed to Thomas Jefferson supports his direct paternity of children descended from Sally Hemings. The study compares inherited DNA shared with known and putative descendants and remains a preprint.
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A bioRxiv preprint reports that maintaining 10% oxygen throughout human iPSC-cardiomyocyte differentiation favoured atrial rather than ventricular specification. The laboratory finding could help produce atrial cells but raises process-design concerns for manufacturing ventricular cells.
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A bioRxiv preprint links a focal 2026 meningococcal outbreak in Kent, UK, to genetic changes that may have been acquired from carriage-associated Neisseria. The researchers propose that such highly invasive variants can emerge briefly and then disappear because they are poorly suited to sustained transmission.
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A bioRxiv preprint presents Z-Hunt-DP, a dynamic-programming reformulation of a thermodynamic Z-DNA prediction method. The authors report that it preserved the original minimum-energy result while producing a 3.30 × 10^5 speedup at 20 dinucleotide positions.
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A Nature essay examines zoologist Paul Kammerer’s controversial experiments on inherited traits, the specimen-tampering accusation that damaged his reputation and why his scientific questions still resonate with modern biology.
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A bioRxiv preprint reports a previously uncharacterised porcine adenovirus in a New Zealand high-health pig herd affected by neonatal deaths and reproductive problems. Genome sequencing placed the virus in the Mastadenovirus genus but on a distinct lineage from characterised porcine adenoviruses.
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A bioRxiv preprint tracking seven Burkholderia multivorans strains from chronic infections in eight cystic fibrosis patients found that the emergence of a dominant bacterial lineage was associated with faster lung-function decline. The study also identified repeated evolutionary changes affecting bacterial functions linked to persistence in the airways.
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A new AI system trained on ageing-biology data combines specialist language models, 17 benchmark tasks and research tools operated through AI agents. In testing, the specialist models outperformed larger commercial models on many, but not all, ageing-related tasks.
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A bioRxiv preprint reports that synthetic, taxonomically complex bacterial communities rapidly evolved after adapting to novel plant hosts. The changes improved colonisation fitness while preserving the stability of the root microbiota.
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A bioRxiv preprint reports that the bacterial protein RfaH helps Escherichia coli RNA polymerase continue through prolonged pauses during long-range transcription. In experiments using reconstituted transcription and in vivo depletion, RfaH supported longer transcription runs than NusG and was required for successful conjugation.
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A Purdue University team reports a loop-mediated isothermal amplification assay for detecting Balamuthia mandrillaris. In laboratory testing, the assay detected multiple isolates with higher sensitivity than conventional PCR and produced a visible colour-based result.
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A bioRxiv preprint reports that the protein PBF/PTTG1IP helps coordinate cell adhesion, front–rear polarity and directional movement. The findings come from mouse fibroblasts and human thyroid cancer cells, making them preclinical mechanistic evidence.
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Researchers at King's College London report TomoFLIM, a compressed multiphoton fluorescence lifetime imaging method. In a preprint benchmark, it reproduced a 60-second raster-scanned dataset in 3.75 seconds.
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A bioRxiv preprint reports metabolic changes and multiorgan pathology in ageing mice exposed to 450 nm LED light for 40 weeks.
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A bioRxiv preprint reports that repeated measurements of circulating alanine aminotransferase, combined with time since acetaminophen exposure, estimated liver necrosis in mice. The method could let researchers follow liver injury in the same animals instead of using separate groups at every timepoint.
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A bioRxiv preprint presents a continuous three-dimensional structural map of a whole adult human heart at 8.01-micron isotropic voxel size. The dataset brings myocardial structure, electrical conduction tissue, blood vessels, lymphatic collectors and autonomic nerves into one spatial framework.
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A bioRxiv preprint reports that blocking the P2Y6 receptor reduced CCL2 but increased CXCL1 release from mouse macrophages stimulated through TLR3. The findings identify extracellular-nucleotide signaling as a selective regulator of inflammatory chemokine responses in this cell model.
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A Nature study tested nearly all single amino-acid mutations in RSV’s fusion protein and measured their effects on two antibodies used to prevent severe disease in infants. Resistance-associated sequence patterns were rare in current surveillance data, while the results provide a framework for tracking viral escape.
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A Nature study in Arabidopsis maps how salicylic acid activates plant defence genes through NPR1 and relieves NPR3/NPR4-mediated repression. It identifies MED15A and chromatin changes that connect hormone perception to transcription.
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A bioRxiv preprint using data from 1,494 donors finds that many single-cell gene-expression studies may lack sufficient statistical power to detect small effects. Cell counts, gene-expression levels and sequencing depth strongly influenced which findings were detected and reproduced.
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A bioRxiv preprint reports valerolactam production in engineered Corynebacterium glutamicum, reaching 3.6 g/L after pathway design and fed-batch process optimization.
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A bioRxiv preprint identifies phosphatidylinositol (PI) as the preferred direct substrate of the enzyme PLCXD2. In a PLCXD2-deficient retinal model, the loss was associated with altered lipid products, synaptic abnormalities, retinal-layer thinning and weaker electrical responses from photoreceptors.
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A bioRxiv preprint maps how cryogenic focused ion beam milling affects structural preservation at different depths. The apparent damage profile varied with the ion species, molecular reporter and lamella thickness.
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A bioRxiv preprint identifies the soil bacterium genus Trinickia as a candidate for supporting soybean drought resilience. Its abundance was strongly associated with greater root biomass during drought, while drought and rewetting produced different responses in the rhizosphere and bulk soil.
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A bioRxiv preprint describes a physics-based framework that combines machine learning, molecular mechanics and microkinetic modelling to predict enzyme reaction rates and selectivity. In tests on an oxidative amidase, the authors report near-experimental accuracy across substrates, mutations and enzyme homologues.
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A bioRxiv preprint reports the first three-dimensional structure of a class II GalT enzyme from Bifidobacterium longum at 2.25 Å resolution. The study links its unusual architecture to a preference for N-acetylated sugars involved in human milk oligosaccharide metabolism.
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A bioRxiv preprint reports reproducible shifts in seawater microbial community composition after controlled near-space exposure, while overall diversity remained relatively stable.
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A bioRxiv preprint identifies a previously undescribed association between the Saccharimonadia bacterium Candidatus Lutisaccharimonas and the phosphorus-accumulating Candidatus Phosphoribacter in wastewater treatment plants. The findings suggest that this microbial interaction could be relevant to biological phosphorus removal.
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A bioRxiv preprint analysing 16,645 bench-grafted grapevines found that scion genetics explained a limited share of success variation. The study identified one modest, reproducible signal on chromosome 7, while most variation was linked to events affecting entire grafting bundles.
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A chromosome-level reference genome and resequencing data from 80 Saimaa ringed seals show extremely limited Y-chromosomal diversity compared with other ringed seals. The bioRxiv preprint estimates that the population retains about 1% of the broader Y-chromosomal diversity and 5% of mitochondrial diversity.
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A bioRxiv preprint presents the first genome-wide maps of four major histone modifications in the reef-building coral Pocillopora damicornis. The maps associate distinct chromatin states with gene expression, receptor-related genes, developmental functions and transposable element-like regions.
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Researchers are culturing Asgard archaea, rare microbes whose genomes link them to the ancestors of eukaryotic cells. Microscopy is revealing cell protrusions, movement and possible partnerships that may illuminate how complex life began.
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The European Union has changed how gene-edited crops are regulated, dividing them into NGT-1 and NGT-2 categories. The framework could ease adoption of CRISPR-based crop improvements, but limits on the number and size of edits may restrict more complex traits.
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A University of Gothenburg preprint models glycan motifs as a containment hierarchy rather than independent features. Across 45 glycomics datasets, the authors report more estimated true positives and identify motif redistributions that conventional marginal analysis misses.
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Researchers at Shandong University and BGI Research describe DiffGSP, a computational framework that models mRNA diffusion to reconstruct spatial gene-expression patterns. The work is a bioRxiv preprint evaluated across diverse spatial-transcriptomics datasets.
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A bioRxiv preprint comparing environmental DNA sampling with camera trapping found that water samples detected established coypu populations more reliably with less field effort in southern France. The researchers propose using eDNA for rapid screening and camera traps for information about animal activity and habitat use.
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A Nature study identifies RNF213 as an enzyme that marks abnormal glycogen, or polyglucosan, for autophagy in brain cells. Experiments in engineered cells and mice link the pathway to protection against polyglucosan accumulation.
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A bioRxiv preprint reports that interleukin-27 induces a cytotoxic CD4+ T-cell program distinct from conventional Th1 cells. The findings combine proteomic analysis with evidence from acute murine cytomegalovirus infection.
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A Nature study analysed a large-scale proteogenomic dataset from 29 healthy human tissues and identified 13,910 protein variants, including non-genetic amino-acid substitutions. The findings suggest that errors and variation during protein production may expand the set of protein forms with potential biological functions.
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A bioRxiv preprint reports that blood DNA methylation patterns vary across development, chronic disease and aging in humans and other mammals. The researchers also describe epigenetic clocks designed to predict expected mortality across species and tissues.
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A bioRxiv preprint reports that binding of the substrate eIF2α relieves an autoinhibitory loop in the mammalian GCN2 kinase. The finding revises the proposed roles of ribosomes and deacylated tRNAs in the integrated stress response.
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A bioRxiv preprint identifies how the Pmk1, Mst12 and Bip1 network coordinates the infection process of the rice blast fungus. The network controls appressorium function, effector deployment and invasive growth.
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A bioRxiv preprint reports that the protein language model ESM-2 retains meaningful biological information in intrinsically disordered protein regions, despite assigning them less attention. The authors also derive structural features of these proteins from the model’s internal signals.
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A KU Leuven-led bioRxiv preprint describes a modular click-chemistry method for attaching fluorophores and DNA to CRISPR-Cas9 ribonucleoproteins without tying the engineering process to how the complex is assembled. In vitro experiments reported by the authors found that modifying an already formed complex provided two-fold greater accessibility of attached DNA.
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A bioRxiv preprint analyses 435 thalidomide-affected limbs and proposes that the unusual order of bone reductions follows the sequential exit of developing bones from a sensitive window.
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Apple researchers describe SimpleDesign, a Transformer-based model that jointly generates protein sequences and three-dimensional structures using a single-stage training approach. The system was trained on more than 2 million sequence–structure pairs, but the supplied evidence reports no experimental validation of its designs.