biophysical modeling

Modeling circadian rhythm splitting under chronic light and the asymmetric transition kinetics between lighting conditions

The paper develops a biophysical model of the SCN to explain circadian rhythm splitting under chronic light and shows how E/I balance and chloride cotransporter dynamics drive this behavior.

Lysenin Induced Membrane Curvature on Erythrocytes and Nanoporous Mica Free Standing Membranes

This study shows lysenin pores induce membrane curvature into rigid dome-like structures, suggesting beta-PFTs alter host cell membranes beyond pore formation.

Charting the Structure and Functional Landscape of the SF3B1 Intrinsically Disordered Region

This study characterizes the conformational dynamics and phosphorylation-dependent changes in the SF3B1 N-terminal domain using a combination of biophysical and computational methods.

Next generation Human Neocortical Neurosolver model with biophysically realistic somatic, dendritic and synaptic dynamics

The paper updates the Human Neocortical Neurosolver model to include biophysically realistic dynamics in human neurons, enabling better interpretation of EEG/MEG signals.

Genome evolution and glycosyltransferase diversification shape asperosaponin biosynthesis in Dipsacus asperoides

The paper reconstructs the asperosaponin biosynthesis pathway in Dipsacus asperoides by integrating genomics, transcriptomics, and biochemical analyses, revealing gene family diversification and glycosylation order.

RNA Polymerase Backtracking Promotes Type III-A CRISPR DNA Targeting

The paper shows RNA polymerase backtracking promotes type III-A CRISPR DNA targeting by inhibiting GreA anti-backtracking factors, which suppress Cas10-Csm activity.

A topoietic model of collective morphogenesis and compartmentalization

The paper introduces topoiesis, a mechanism where diffusion and geometry drive collective morphogenesis and survival in Xenopus embryos under stress.

The Molecular Interplay of Tau and Motor Proteins on Microtubules

This study investigates how tau protein regulates motor proteins on microtubules using single-molecule imaging, cryo-EM, and MD simulations, revealing distinct mechanisms for inhibiting kinesin-1 and dynein.

Functional genomic characterization of anti-phage defense systems in vancomycin-resistant Enterococcus faecium

This study identifies anti-phage defense systems in VREfm genomes and finds limited associations between specific systems and phage resistance, with one candidate gene reducing susceptibility.

Myelin Governs Hippocampal Network Function through the Extracellular Space it Occupies, Not Only the Axons it Insulates

This study shows that myelin affects hippocampal network function by shaping extracellular space, not only by insulating axons, with demyelination altering diffusion, flow, and synaptic transmission.

Human senataxin uses distinct peripheral elements to unwind R-loops and act on RNA polymerase II

This study identifies distinct peripheral elements in senataxin that mediate R-loop unwinding and RNA polymerase II regulation through structural and biochemical analyses.

Seesaw configuration of the ODC-OAZ1-AZIN1 axis governs sensitivity to polyamine-targeting inhibitors of breast cancer cells

This study identifies a seesaw configuration of the ODC-OAZ1-AZIN1 axis that determines breast cancer cell sensitivity to polyamine-targeting inhibitors, offering a framework for personalized therapy.

Aβ42 facilitates the activation of Discoidin Domain Receptor 2 and Its nuclear enrichment in Alzheimer's Disease Model

This study shows Aβ42 activates DDR2 in Alzheimer's disease models by non-canonically bypassing collagen ligands and promotes its nuclear enrichment, with structural insights into the mechanism and potential therapeutic inhibition.

Collective multicellular patterns arising from cadherin-linked cytoskeletal domains

This study introduces a biophysical model that couples adhesion complex dynamics to intracellular mechanics, revealing multicellular patterns like polarization and stress chains.

Bacterial exo-α-sialidases subvert the complement system through desialylation

This study shows bacterial sialidases remove sialic acids from complement proteins, reducing complement activation and helping bacteria evade immune detection.

A Cryptic Binding Pocket Regulates the Metal-Dependent Activity of Cas9

This study identifies a cryptic divalent metal binding pocket that regulates Cas9's metal-dependent activity through conformational activation and catalytic efficiency.

Scanning and active sampling behaviours emerge from conserved insect neural circuits

This study shows that scanning behaviors in desert ants emerge from conserved neural circuits without a specialized module, using a biologically grounded model.

The Hunt for Cholesteryl Ester Hydrolases: Identification of Lipoprotein Lipase as a Cholesterylesterase

This study identifies lipoprotein lipase (LPL) as a neutral cholesteryl ester hydrolase in mammals through biochemical and pharmacological analyses.

Lipid gating of BK channels and mechanism of activation by negatively charged lipids

This study investigates how lipid interactions influence BK channel conductivity and activation, proposing a multi-modal mechanism involving lipid entry reduction and structural stabilization.

Evolutionary conservation and divergence of CXCL17 orthologs: functional evidence in reptiles and loss in the avian lineage

This study identifies functional CXCL17 orthologs in reptiles and shows their loss in birds, using bioinformatics and recombinant protein assays.

Transposon end recognition and pairing by I-F3 CRISPR-associated transposase

This study determines how the I-F3 CRISPR-associated transposase recognizes and pairs transposon ends for transposition using cryo-EM and biochemical analyses.

A novel virus lineage is abundant in metaviromes from Dehalococcoides-containing mixed cultures

The paper identifies a novel virus lineage, IME1, found in Dehalococcoides-containing cultures, characterized by features similar to filamentous bacterial viruses.

Patient-informed biomechanical modelling reveals mechanical mechanism of brain damage in idiopathic normal pressure hydrocephalus

This paper develops a biomechanical model of the brain to show that ventricular enlargement in iNPH causes mechanical strain in white matter, contributing to brain damage.

Mechanism of activation of an ancestral Tec kinase by PIP3

This study identifies how PIP3 activates an ancestral Tec kinase by displacing its PH domain from an inhibitory interaction with its kinase domain.

Low levels of metabolic auxotrophy among environmental Pseudomonas isolates

The paper combines experimental and bioinformatic methods to assess amino acid auxotrophy in 315 Pseudomonas isolates, finding most are prototrophic with few auxotrophs and multiple biosynthesis pathways.

Genomic and biochemical contexts determine the physiological role of a horizontally acquired gene

This paper shows that horizontally acquired mgtC genes can have different physiological roles depending on genomic and biochemical contexts in Salmonella enterica and other bacteria.

Stepwise Ligand Capture Primes PKR for Activation and RNA Discrimination

This study reveals how PKR's dsRBDs work together to enable selective RNA recognition and activation through a two-step ligand sampling mechanism.

Genomic Characterization of 30 Lytic Klebsiella pneumoniae Bacteriophages

This study characterizes 30 lytic Klebsiella pneumoniae bacteriophages, finding diverse genomic structures and no virulence or antibiotic resistance genes, with potential as antimicrobial agents against carbapenem-resistant K. pneumoniae.

Prophage {Phi}ESI promotes competitive dominance in the emergent Salmonella serovar Infantis lineage

This paper identifies {Phi}ESI, a prophage in Salmonella Infantis, as a competitive factor that helps the emergent lineage outcompete non-emergent strains by selectively lysing susceptible competitors.

Connectome-based biophysical modeling of a figure-ground discrimination circuit

The paper uses a Drosophila connectome and biophysical simulations to show that a reciprocal circuit between T4a motion detectors and vCH cells supports figure-ground discrimination through shunting inhibition.