virus

This study shows L-cysteine inhibits Vibrio parahaemolyticus growth by increasing ROS levels, disrupting membrane integrity, and reducing virulence.

The paper identifies and characterizes CisR, a small RNA that inhibits CTXφ phage production by repressing cep mRNA through Hfq-dependent base-pairing, linking phage activation to cell density and nutrient availability in V. cholerae.

The paper compares the evolutionary changes in the central complex and mushroom bodies across Heliconiini butterflies, finding conservation in the central complex and expansion in the mushroom bodies linked to foraging behavior.

This study investigates esca disease in grapevines, showing local transcriptomic changes and systemic DNA methylation alterations in symptomatic and asymptomatic leaves.

This study identifies the regulatory mechanisms of nitrogenase in Vibrio natriegens, showing that NtrBC is not essential but important for timely expression, while NifA autoactivation suffices for nitrogenase gene expression.

The paper introduces ProteomeLM-HPI, a language model adapted to predict cross-species host-pathogen interactions using proteome context and fine-tuning.

The paper identifies a Plasmopara viticola strain from Reunion Island that breaks down three grapevine resistance loci, Rpv1, Rpv3.1, and Rpv10, through genomic and pathogenicity analyses.

This study shows that supplemental irrigation during heat waves reduces anthocyanin loss in Cabernet Sauvignon grapes, with no additional benefit from excessive watering.

This study examines how Botrytis cinerea infection alters the microbiome of grape berries during noble rot, identifying microbial shifts and associations across infection stages and vintages.

The paper identifies a 667-nucleotide region in SARS-CoV-2 nsp15 that binds nucleoprotein and enhances defective genome accumulation, revealing a new packaging signal element.

LucaPhylo infers phylogenetic trees from unaligned protein sequences using hyperbolic geometry and protein language models, achieving accuracy comparable to alignment-based methods for divergent RNA viruses.

This study uses MD simulations to show that preorganized thumb-subdomain motions in SARS-CoV-2 polymerase drive functional transitions through structurally coupled regulatory regions.

The paper analyzes DrBHV diversity across Latin America and the Caribbean, showing widespread co-infection and geographic spread, suggesting vaccine vectors could be locally sourced.

The paper identifies JEV envelope protein mutations that may reduce vaccine effectiveness by analyzing sequence variation and structural stability.

The paper shows that the Q226H mutation in H5N1 hemagglutinin allows binding to human-type a2-6 sialic acid receptors, suggesting a path towards human adaptation.

This study identifies distinct roles of TRAP and TRP1 adhesins in Plasmodium sporozoite motility and invasion, showing differential signaling requirements for gliding and transmission.

The paper uses long-read sequencing to study HIV transmission and population dynamics in acute infection, finding high multilineage transmission rates and rapid viral evolution.

This study simulates antibody-spike protein binding for SARS-CoV-2 variants and finds a decline in binding strength with viral evolution, but some re-entrance of binding strength for most antibodies.

This study identifies a conserved SARS-CoV-2 5-UTR stem-loop region that activates OAS1, a key antiviral protein, through structural and functional analyses.

The paper investigates the emergence of the influenza A/H3N2 K subclade, finding limited antigenic change and age-dependent vaccine responses, suggesting non-antigenic selection pressures.

This paper predicts influenza virus host tropism and zoonotic spillover risk using protein sequence embeddings, achieving high precision and recall scores across multiple host classifications.

The paper uses cryo-electron tomography to study NiV fusion protein assemblies and shows nanobodies block inter-trimer interactions, inhibiting viral entry.

This study benchmarks how reference genome selection affects taxonomic profiling accuracy across bacterial and viral datasets, showing context-dependent impacts on accuracy and computational efficiency.

The paper estimates neutral mutation rates and fitness effects of mutations in influenza proteins using phylogenetic analysis of over 100,000 sequences, revealing context-dependent patterns across viruses.

This paper demonstrates that pangenome variation graphs improve SNP detection in lumpy skin disease virus by capturing more genetic diversity and identifying variants missed by linear reference mapping.

The paper analyzes SARS-CoV-2 spike evolution in Canada, finding that variant emergence, not vaccine deployment, drove episodic positive selection at the provincial level.

This study investigates how Vibrio parahaemolyticus quorum sensing regulates phage VP882 transmission by controlling receptor accessibility and enabling superinfection.

The paper introduces a Vector-Symbolic Architecture for encoding viral pangenomes and evaluates its effectiveness in species classification, finding that a flat species-level model outperforms genus-level and hierarchical approaches.

This paper describes an Illumina-based whole-genome sequencing method for measles virus, showing it can detect 10,000 genome copies with high accuracy.