Understanding how environmental variation interacts with gene flow to shape population genomic patterns is a central goal in evolutionary biology. We investigated how geographic and environmental differences impact genomic variation in the clouded sulfur butterfly (Colias philodice eriphyle) by conducting whole-genome resequencing across replicated transects consisting of paired high- and low-elevation sites on both sides […]
PD-L2 Regulates Natural Antibody and IL-10 Secretion by B-1 cells
B-1 cells are innate-like lymphocytes that play a critical role in homeostasis by secreting natural antibodies, typically IgM, and immunosuppressive molecules such as IL-10. However, the regulation of these processes in B-1 cells remains poorly understood. Here, we demonstrate that PD-L2, a surface receptor expressed by all B-1 cells, regulates B-1 cell effector functions. We […]
Are frameworks independent from CDRs in antibodies? Exploring CDR-framework correlation networks of antibodies
The growing success of monoclonal antibodies (mAbs) in therapies highlights the importance of the humanization process in antibody design. This key step involves grafting selected complementarity-determining regions (CDRs) onto human frameworks (FWs) to reduce immunogenicity. However, the effect of this process on the antibody’s structure and dynamics is underexplored. This study uses molecular dynamics simulations […]
Rigorous Quantitative Analysis of Nonlinear Uncertain Biomolecular Systems using Validated Methods
The paper addresses the critical challenge of accurately characterising steady states in biomolecular systems, which are often complex, nonlinear, multistable and subject to significant uncertainties. Traditional numerical methods often fail to provide complete or guaranteed solutions under these conditions. To overcome these limitations, the research proposes and evaluates the application of interval analysis methodologies. We […]
Detection of Mid-parent Heterosis Genes in Large-Scale Unreplicated RNA-Seq Experiments
Mid-parent heterosis (MPH), characterized by hybrid trait values deviating from the mid-parent average, is a well-documented phenomenon whose genetic basis remains poorly understood. Identifying genes associated with MPH is crucial for uncovering the molecular mechanisms underlying heterosis. Recent large-scale RNA-sequencing (RNA-seq) experiments enable the evaluation of heterosis genes across numerous families; however, replication is often […]
Structural and biochemical studies of human PP2A(B55) holoenzyme and ENSA protein complex
The serine/threonine protein phosphatase 2A (B55) holoenzyme (PP2A(B55)), a key cell cycle regulator, is tightly regulated by ENSA, whose phosphorylation at Ser67 inhibits PP2A(B55). The structural basis for how pENSA orchestrates this inhibition to govern mitotic progression remains unclear. In this study, we disapproved the previous hypothesis of direct ENSA-PP2A A subunit interaction, and showed […]
evo3D: a generalised framework for structure-informed evolutionary analysis, implemented in R
Selection pressures often act at the level of protein structure, yet most evolutionary analyses remain confined to linear sequences. Early structure-informed approaches improved interpretation by mapping single-site metrics onto protein structures, and later methods introduced 3D sliding windows to capture spatial neighbourhoods missed by linear analyses. These frameworks, however, are restricted to predefined statistics and […]
How big is enough? Movement-informed zoning for African swine fever mitigation
1. African swine fever (ASF) poses a serious threat to domestic pigs and wild boar populations. Wild boar can disperse the virus, making effective containment crucial. One of the main control strategies involves establishing restricted zones around detected cases, i.e., areas with temporary restrictions on access and hunting; however, determining the appropriate size of these […]
Structural insights into xyloglucan recognition by an ABC transporter from a Gram-positive, thermophilic bacterium
Xyloglucan (an alpha-1,6-xylosyl-substituted beta-1,4-glucan) is a major hemicellulose of the primary cell wall of many plants and an important growth substrate for biomass-degrading bacteria in diverse ecological niches, including the gut microbiome and hot springs. In Gram-positive bacteria, xyloglucan is deconstructed into soluble oligosaccharides in the extracytoplasmic space before import by ATP-Binding Cassette (ABC) transporters, […]
Genomic Flexibility Through Extrachromosomal Amplifications: A Leishmania Survival Strategy
Leishmania parasites modulate gene copy number through extrachromosomal DNA (ecDNA) amplification, enabling adaptation to environmental stress. Under drug pressure, both linear and circular ecDNA amplifications (amplicons) carrying resistance genes emerge. However, how these ecDNA structures form, diversify, and coexist remains poorly understood. Here, using experimental evolution and Oxford Nanopore long-read sequencing, we show that a […]