Biology subjects

Kumar, S.

Publications and source records attributed to Kumar, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

High cRel-expressing germinal center B cells favor precursor plasma cell generation

Germinal centers (GCs) are the site of antibody affinity maturation by the process of somatic hypermutation (SHM) and produce long-lived plasma cells (PCs). GC B cells circulate between two distinct zones: the light zone (LZ) and the dark zone (DZ). It has been demonstrated that the transcription factor NF{kappa}B cRel is required for B cell proliferation and GC B cell maintenance. cRel-deleted GC B cells show reduced SHM and affinity maturation. In contrast, transgenic overexpression of cRel does not affect SHM and results in little or no increase in affinity maturation. Therefore, the function of cRel in regulating SHM and GC B cell-derived PC generation remains unknown. To understand the function of cRel in GC B cell selection, we have used cRel fluorescence reporter mice, which provide insight into cRel function in GC B cells at the level of natural expression variation. We found that about 6-9% of LZ cells increased cRel expression compared to DZ cells, and high cRel-expressing LZ cells showed increased SHM and increased expression of IRF4 and cyclin D2, though cMyc expression remained similar. Combining single-cell RNA-Seq and flow cytometry, we revealed that high cRel-expressing LZ cells are enriched for precursor PCs (pre-PCs), not precursor memory B cells (pre-MBCs). Our findings provide insight into the physiologic function of cRel in regulating GC B cell output.

immunology↗

bioRxiv2026

PSEN1 mutant marmoset fibroblasts mimic multi-omic signatures of Alzheimer's disease

INTRODUCTIONThe slow, age-related development of Alzheimers disease (AD) and inaccessibility of early-stage brain tissue necessitates model studies to understand its origins and progression. Non-human primate models can provide a platform for linking molecular changes to translatable phenotypes. Here, we assess fibroblast lines derived from marmosets with engineered variants in the PSEN1 gene. METHODSFibroblast cultures were obtained from 10 animals and assayed using a NanoString AD gene expression panel and label-free proteomics. We compared mutant expression changes to human AD signatures in human iPSC-derived neurons and postmortem brains to assess disease relevance. RESULTSGene products involved in amyloid-beta interaction and regulation were differentially expressed, providing evidence for the functional relevance of the engineered fibroblasts. Both gene and protein expression changes in the undifferentiated fibroblasts correlated with human iPSCs from AD donors reprogrammed into neuronal lineages, as well as postmortem brains derived from case-control cohorts. Altered expression profiles were noted based on marmoset donor sex and mutation status, highlighting underlying sex-specific biology relevant to Alzheimers disease. DISCUSSIONThese findings demonstrate that disease-relevant pathways and processes are altered in fibroblasts from mutant marmosets, emphasize the complementarity of transcriptomic and proteomic profiling in AD, and provide a roadmap for more advanced molecular studies of AD in aging marmosets and marmoset-derived cell models.

genomics↗

bioRxiv2026

α-Synuclein Facilitates Spontaneous Dopamine Release in a Calcium- and Phosphorylation-Dependent Manner

-Synuclein (aSyn) is central to Parkinsons disease pathogenesis, yet its native physiological role at the presynapse remain poorly defined. Here, super-resolution imaging in dopaminergic neurons reveals that endogenous aSyn localises within nanometres of L-type voltage-gated calcium channels (LTCC), with closer proximity under both spontaneous neuronal activity and stimulated conditions compared to when extracellular calcium is chelated. Blocking Ca2+/calmodulin-dependent kinase II (CaMKII) reduces aSyn clustering at LTCC under spontaneous activity, suggesting that calcium entry and downstream calcium-dependent kinase activity contribute to aSyn localisation. Moreover, quantitative single-molecule analyses indicate that calcium increases the abundance of both total and serine129 phosphorylated (pS129) aSyn in synaptosomes under spontaneous conditions, and NMR analysis reveals that both calcium and S129 phosphorylation increase the binding affinity of aSyn to synaptic vesicles. Functional assays further demonstrate that LTCC blockade elevates intracellular DA levels exclusively in the presence of aSyn under spontaneous but not stimulated conditions. Finally, biochemical fractionation and multi-colour single-molecule imaging reveal that aSyn preferentially associates with small vesicles that are not obligately coupled to full-fusion associated recycling pools. These results suggest that aSyn acts as a calcium- and phosphorylation-regulated modulator of spontaneous DA release through pathways that are largely independent of full-fusion recycling mechanisms, and that pS129 aSyn is not solely a pathological marker but may also reflects physiological regulation. Together, these insights provide a framework for understanding how therapeutic strategies targeting aSyn may impact its normal synaptic functions.

neuroscience↗

bioRxiv2026

Learning to select computations in recurrent neural circuits

Two hallmarks of biological computation are its flexibility and efficiency. These features are often attributed to cognitive control processes that balance external utility against computational cost. However, how the brain could implement such adaptive control remains unknown. Here, we provide one possible answer by combining the computational theory of rational meta-reasoning with a meta-learning algorithm recently proposed as a model of prefrontal cortex. This yields a recurrent neural network model that learns to select computations. In simple choice tasks, the model approximates the algorithms and representations of optimal symbolic models and reproduces neural dynamics observed in macaque orbitofrontal cortex. In multi-step planning tasks, the model replicates key behavioral signatures of human planning strategies and captures human neural dynamics associated with step-by-step mental simulation. Our framework unifies meta-reasoning and meta-learning by showing that learning to reason can be understood as learning to learn from information generated by ones own cognitive operations, providing a mechanistic account of how adaptive control of thought can be implemented in neural systems.

neuroscience↗

bioRxiv2026

Quantitative evaluation of LED based optical autofocus module

We report an improved version of the open-source optical autofocus module ("openAF") for light microscopy using a light emitting diode (LED), together with a method to independently quantify the performance of optical autofocus systems using 2D autocorrelation analysis of astigmatic imaging of fluorescent nanobeads. We apply the latter for both the LED-based and the previous super luminescent diode (SLD) based implementations of the openAF optical autofocus approach used in conjunction with a 100x 1.4 NA oil-immersion objective lens. The new approach accounts for power variations in the autofocus light source and we demonstrate that the convenient LED-based system can provide axial stability with a standard deviation <10 nm over at least 45 minutes when switched on from cold, during which the LED power varies as it reaches thermal equilibrium.

bioengineering↗

bioRxiv2026

Cycle-by-cycle respiration waveforms are coupled with the shape of neural oscillations

Beyond sustaining life, breathing is a vital physiological rhythm that shapes cognition, perception, emotional regulation, and mental health. Breathing has a direct effect on neuronal excitability and is coupled to neural oscillations across a variety of brain regions. Notably, both respiration and neural oscillations are asymmetric and not perfectly rhythmic: for example, every breath has a different shape and duration, and is interspersed with variable pauses. Here, we examined the coupling between breathing and the brain by quantifying the nonsinusoidal features of each breath and comparing it to the shape of each corresponding neural oscillation cycle. By leveraging invasive human brain recordings from 16 participants, we found respiration-neural waveform coupling on a breath-by-breath, cycle-by-cycle basis across limbic and cortical forebrain regions. For decades, the dominant perspective on cognition and mental health have focused on the brain, but recent work is highlighting the importance of brain-body interactions. Our results show that the coupling between breathing and neural activity is much richer than previously appreciated, and our approach opens new avenues for studying these peripheral-to-central nervous system interactions in a more robust, temporally precise manner.

neuroscience↗

bioRxiv2026

ARACRA: Automated RNA-seq Analysis for Chemical Risk Assessment

Transcriptomic analysis is considered a powerful approach for biomarker discovery, however still exploring large scale omics dataset to extract meaningful biological insights remains a challenge for biologists. To address this gap, we present ARACRA a fully automated RNA-seq analysis pipeline including entire transcriptomics workflow from raw FASTQ files to the transcriptomics Point of Departure (tPoD) with human-in-the-loop review process. Overall, the analysis is performed in two phases: Phase 1 carries out the acquisition of raw reads, pre-alignment quality control, alignment to reference genome and quantification of gene expression. Whereas, Phase 2 performs statistical analysis including Differential Gene Expression analysis and Dose-Response modelling. Two phases are separated by an extensive quality control step which allows the user to visually inspect the quality of data processed and helps in filtering noise and outlier samples. ARACRA facilitates end-to-end analysis of RNA-Seq data through an interactive web-based application developed on nextflow and streamlit for minimizing computational complexities while ensuring correct downstream processing. Availability and implementationARACRA is freely available online at the GitHub with MIT License and stream lit-based web application: ARACRA. Researchers can use the demo data or even upload their own data to do the analysis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/716912v1_fig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@15170a9org.highwire.dtl.DTLVardef@1bb9822org.highwire.dtl.DTLVardef@1010f3aorg.highwire.dtl.DTLVardef@8ee6e6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1:C_FLOATNO Overall Architecture of ARACRA C_FIG

bioinformatics↗

bioRxiv2026

Receptor-guided AAV Tropism Engineering via MATCH

Precise control over viral tropism remains a major challenge in the development of gene delivery technologies. We present MATCH (Modulation of AAV Tropism through Conjugation to Homing proteins), a modular biochemical method that enables programmable, receptor-guided retargeting of adeno-associated viruses (AAVs) through site-specific covalent protein conjugation. By incorporating a SpyTag peptide motif into selected AAV capsid loops, MATCH allows one-step, stoichiometrically defined attachment of recombinant SpyCatcher-linked targeting proteins to the viral surface. Using mosaic AAV-DJ and AAV9 capsids with controlled SpyTag incorporation, we achieve efficient assembly and tunable ligand display. MATCH-AAVs conjugated to an anti-CD3 single-chain antibody efficiently activate and transduce resting human T cells within mixed PBMC populations in vitro, achieving transduction levels of up to [~]58% of total PBMCs. Conjugation to transferrin receptor (TfR1)-binding proteins yielded enhanced brain transduction in vivo, with murine TfR1-targeted MATCH-AAV9 exhibiting up to an 84-fold increase in brain expression relative to wild-type AAV9. Human TfR1-targeted vectors similarly enabled robust, receptor-dependent transduction both in vitro and in humanized mouse models. Both TfR-targeted vectors enabled widespread transduction of the parenchyma, consistent with TfR1-mediated crossing of the blood-brain barrier. Finally, we establish a streamlined one-pot "Mix-and-MATCH" production strategy in which capsid and targeting ligands are co-expressed during vector generation, yielding functional, targeted AAVs at titers comparable to conventional production. This simple and generalizable synthetic-biology approach provides a versatile toolkit for rational AAV tropism engineering, offering a scalable route to custom vector design for research and therapeutic applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/715691v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1935815org.highwire.dtl.DTLVardef@7c05faorg.highwire.dtl.DTLVardef@6c8857org.highwire.dtl.DTLVardef@16b2097_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2026

Myeloid Gi signaling acts as a weight-independent immunometabolic switch controlling systemic insulin sensitivity

Metabolic dysfunction does not necessarily correlate with adiposity. Metabolically healthy obese individuals and insulin-resistant lean individuals represent a fundamental paradox that implicates immune cell intrinsic mechanisms in the pathogenesis of type 2 diabetes. Here, we identify myeloid Gi signaling as a previously unrecognized determinant of whole-body glucose homeostasis. Single-cell transcriptomic analysis of adipose tissue macrophages from obese mice and humans reveals marked alteration in Gnai isoform, suggesting that myeloid Gi signaling is functionally engaged during metabolic disease. Using complementary myeloid-specific rodent models of Gi inhibition (pertussis toxin) and chemogenetic Gi activation (DREADD), we demonstrate that inhibition of Gi signaling improves glucose tolerance and enhances insulin sensitivity under both regular chow and high-fat diet conditions, independent of body weight and energy expenditure. Whereas acute Gi activation in lean mice modestly enhances glucose disposal, the same intervention during diet-induced obesity markedly impairs systemic glucose homeostasis, revealing context-dependent pathway function. Mechanistically, Gi inhibition amplifies macrophage cAMP-CREB signaling to drive IL-6 production, engaging STAT3- and AMPK-dependent pathways in adipose tissue and skeletal muscle to support insulin action. Conversely, Gi activation engages a previously uncharacterized G{beta}{gamma}-mTOR/AKT-JNK cascade, driving IL-1{beta} secretion that directly impairs insulin signaling in adipocytes and myotubes. Pharmacological IL-6 receptor blockade abolishes the metabolic benefits of Gi inhibition, whereas IL-1 receptor antagonism fully rescues Gi activation-induced metabolic dysfunction, establishing these cytokines as obligate downstream effectors. This signaling architecture is conserved in human macrophages, and ATAC-seq profiling reveals chromatin remodeling at cAMP-CREB and IL-6 regulatory pathway loci, consistent with the observed transcriptional reprogramming. Together, these findings establish myeloid Gi signaling as a weight-independent immunometabolic switch that couples opposing cytokine programs to systemic insulin sensitivity and identify this pathway as a therapeutic target in obesity-associated metabolic disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/713834v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@15e4576org.highwire.dtl.DTLVardef@224cd5org.highwire.dtl.DTLVardef@1e24888org.highwire.dtl.DTLVardef@1080bf3_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

physiology↗

bioRxiv2026

Diet-conditioned microbiota enhances fecal microbiota transplantation efficacy in alcoholic liver disease through caproic acid-PPARα signaling

Background and AimFecal microbiota transplantation (FMT) in Alcohol-related liver disease (ALD) has shown therapeutic potential, with variable efficacy and unclear mechanism. Because dietary protein influences gut microbiota composition, we hypothesized that donor dietary preconditioning could enhance FMT efficacy. We therefore examined in a murine ALD model if high-protein donor diet improves FMT outcome. MethodsALD was induced in C57BL/6N mice using a Lieber-DeCarli ethanol diet combined with thioacetamide administration for 12 weeks. FMT was performed using stool from diet-modulated donors, and recovery was assessed on day7 post-FMT. Multi-omics analysis using 16s rRNA and mass spectroscopy was performed for Gut microbiota composition, plasma- and stool-metabolome, and hepatic proteomes. Multi-omics outcomes were validated in ALD animal and Huh7 hepatocytes. ResultsBoth protein-based FMTs improved ALD recovery; Veg-FMT demonstrated superior efficacy, significantly reducing hepatic injury (AST 1.2-fold, p=0.002; bilirubin 1.2-fold, p=0.03; steatosis 1.7-fold,p=0.01) and restoring gut barrier integrity (occludin 1.5-fold,p=0.04; mucin 2 2.2-fold, p=002; and plasma endotoxin 1.7-fold, p=0.02). A significant 2-fold increase was observed in Lachnospiraceae NK4A136, Coriobacteriaceae UCG-002, and short-chain fatty acids, particularly caproic acid. Functional validation confirmed that caproic acid promoted hepatic fatty acid {beta}-oxidation through PPAR-dependent mechanisms, reducing triglyceride accumulation and lipogenesis in both cellular and animal models. ConclusionDonor preconditioning with a plant-protein enriched diet enhances FMT efficacy in ALD by gut microbiota modulation with increased metabolites like caproic acid. These findings highlight a microbiota-metabolite-host axis through which diet-modulated FMT improves hepatic lipid metabolism and injury, and identifies a pathway via which FMT imparts its effect. SignificanceThis study identifies a mechanistic basis for improving fecal microbiota transplantation (FMT) efficacy in alcohol-related liver disease (ALD) by demonstrating that dietary preconditioning of donor microbiota improves therapeutic outcomes. We show that plant protein-modulated donor microbiota supplements abstinence-associated recovery through increased production of the microbial metabolite caproic acid, which promotes hepatic fatty acid {beta}-oxidation via PPAR signaling. These findings highlight donor dietary conditioning and microbiota-derived metabolites, rather than microbial composition alone, as important determinants of FMT efficacy. The results suggest that microbial metabolites such as caproic acid may represent potential therapeutic targets or biomarkers to enhance and standardize microbiota-based interventions in ALD. Although the current work is based on a murine model, the identified microbiota-metabolite-host metabolic axis provides a framework for future translational studies aimed at optimizing FMT strategies in liver disease.

microbiology↗

bioRxiv2026

A Complete Genome for the Common Marmoset

The common marmoset is a New World monkey (NWM) commonly used as a model organism to investigate questions in primate evolution and human disease, including Alzheimers and other neurodegenerative diseases, as well as neuropsychiatric disorders. Here we present the first telomere-to-telomere (T2T) reference genome for the common marmoset, adding over 88 Mb of sequence and resolving challenging genomic regions. An additional near-T2T assembly from a second unrelated individual yields a total of four high-quality haplotypes for analysis. The improved contiguity and accuracy of these assemblies enable unprecedented insights into complex and rapidly evolving genomic regions such as centromeres, sex chromosomes, ribosomal DNA (rDNA) structure, and the major histocompatibility complex (MHC). We fully resolved all marmoset centromeres, uncovering dimeric alpha satellites with chromosomal specificity and stratified inactive layers documenting ancestral centromere turnover. We assembled six acrocentric autosomes with gene-poor, satellite-rich short arms and provide evidence that most of them can harbor rDNA and all of them share large pseudo-homologous regions (PHRs). The Y chromosome, but not the X chromosome, carries active rDNA and PHRs, and the rDNA copy number is sexually dimorphic. Chromosomes that share PHRs also share closely related centromeric satellite DNA, supporting a model of ongoing recombinational exchange between heterologous chromosomes facilitated by rDNA. We discovered multiple novel, marmoset-specific MHC genes that are predicted to protect against pathogens encountered in its environment. Leveraging this complete reference, we further identified over 500 transcribed genes with transcript models or expansions specific to the marmoset lineage. Together with additional long-read marmoset assemblies, these genomes were used to construct a marmoset pangenome, providing a robust reference framework for short-read mapping across diverse individuals. This resource will improve the utility of the common marmoset as a biomedical model organism and fill key gaps in our understanding of primate evolution.

genomics↗

bioRxiv2026

Light Chain Dominant Quaternary Epitope Recognition and IgG3 Switching Drive Broad Dengue and Zika Virus Neutralization

Defining how antibodies achieve broad neutralization across antigenically related flaviviruses is essential for rational therapeutics and vaccine design. Here, we describe 3A06, a human monoclonal antibody that neutralizes dengue virus (DENV) serotypes 1-3 and zika virus (ZIKV). Notably, subclass switching to IgG3 exhibits expanded neutralizing activity against all four DENV serotypes. High-resolution cryo-electron microscopy (cryo-EM) analysis of 3A06 Fab bound to chimeric ZIKV virions shows that 3A06 engages a quaternary epitope spanning three E protomers. Functional analyses identify a major functional contribution from the light-chain, where somatic hypermutations are critical for neutralization potency, and reversion of improbable mutations substantially reduces neutralization and increases antibody dependent enhancement (ADE) at sub-neutralizing concentrations. Cryo-EM analyses of intact IgG3 in complex with chimeric DENV2 and DENV4 show that the conformational clexibility and extended IgG3 Fc-hinge enable bivalent engagement across E-protein rafts in multiple concigurations, overcoming geometrical constraints that limit binding in the IgG1 format. Together, these results define a distinct mode of epitope recognition relative to previously characterized E-dimer epitope (EDE)-specific broadly neutralizing antibodies (bnAbs), and demonstrate how IgG3 subclass architecture can expand virus neutralization breadth. These insights inform the rational engineering of antibodies and vaccines targeting quaternary epitopes on flaviviruses to overcome viral diversity.

immunology↗

bioRxiv2026

YdbL directly modulates YdbH-YnbE bridge formation to maintain Escherichia coli outer membrane homeostasis

Gram-negative bacteria pose a threat to global healthcare mainly because their outer membrane (OM) provides an intrinsic barrier to many antimicrobials. Key to this barrier function is the asymmetric structure of the OM, with phospholipids constituting the inner leaflet and lipopolysaccharides the outer leaflet. Although the mechanism of phospholipid transport between the inner membrane (IM) and OM remains poorly understood, recent studies implicate TamB, YhdP, and YdbH as functionally redundant proteins mediating this process in Escherichia coli. Accordingly, collective loss of these three paralogs is lethal and any one of them is sufficient for growth. YdbH is anchored to the IM and its periplasmic repeating {beta}-sheet groove domain interacts with the OM lipoprotein YnbE via {beta}-strand augmentation to form an intermembrane bridge. Additionally, YnbE multimerizes, and the periplasmic protein YdbL is proposed to modulate YnbE multimerization to facilitate its stacking on the C-terminus of YdbH. Here, we demonstrate that excess YdbL specifically inhibits the function of the YdbH-YnbE complex since overexpression of ydbL causes lethality in the {Delta}yhdP {Delta}tamB double mutant but the presence of both ydbH and ynbE in trans abrogates this lethality. We resolve high-resolution structural data for YdbL and ascertain its interaction site with the YnbE C-terminal -helix, with residues mediating this interface highly conserved and critical for YdbL function. Finally, we show that YdbL is protected from degradation by the protease DegP when complexed with YnbE. Overall, our data supports a model in which YdbL ensures proper YdbH-YnbE intermembrane bridge formation by directly interacting with YnbE.

microbiology↗

bioRxiv2026

Diversity and Genomic Organization of Non-B DNA Motifs in Haplotype-Resolved Human Genome Assemblies

Long-read sequencing and telomere-to-telomere genome assemblies now enable the exploration of previously inaccessible repetitive and structurally complex regions of the human genome. Using 130 haplotype-resolved genome assemblies from 65 individuals across diverse populations, we systematically analyzed six major classes of non-B DNA motifs. By evaluating their biophysical stability, we distinguished structurally stable motifs from those forming unstable secondary structures and mapped their distribution across individuals and genomic contexts. Our work revealed significant variation at the population level in both motif abundance and predicted structural stability, uncovering previously unrecognized diversity in non-B DNA landscapes. Non-B DNA motifs exhibit notable, structure-specific enrichment in highly repetitive and evolutionarily dynamic regions that remain largely unresolved in short-read-based genomes, including centromeres, segmental duplications, structural variant breakpoints, and mobile element insertions. Our findings provide a refined view of the potential secondary-structure organization within repetitive regions of the human genome and highlight structural stability as a key factor shaping the distribution of non-B DNA motifs in regions linked to genome instability, evolution, and human variation.

genomics↗

bioRxiv2026

Adaptive Remodeling of the MPXV B21R Receptor-Binding Domain Enhances DC-SIGN Interaction and Identifies Conserved CTL Targets for T-Cell Vaccine Development

Global Mpox transmission is imposing public health concern as the number of cases is progressively increasing since its first major outbreak in 1996. Therefore, understanding its global epidemiological transformation and its underlying mechanism is crucial to decipher the immune evasion strategies exhibited by recent MPXV strains. In the present study, we analyzed the trend of global Mpox epidemiology and identified the current multinational outbreak which has initiated in 2017 from Africa. To explore the molecular basis of this transformation, we considered the B21R protein of MPXV as it may have played a role in viral adaptation and immune escape mechanism as one of the important MPXV structural proteins. Our data shows that Mpox has significantly transformed from 1996 to 2025, where MPXV strains from 2022, 2023, and 2024 are closely clustered whereas 2025 is closely related to 2017 MPXV strain. Structural modeling of B21R using AlphaFold uncovers a modular architecture comprising a putative receptor-binding N-terminal region (p-RBD), a central ectodomain, and a membrane-anchored C-terminal segment. Mapping solvent accessibility across the full-length B21R protein revealed that p-RBD exhibited highest solvent exposure compared to other B21R protein domains. As a potential cellular receptor for entry into the host targeted cell, we evaluated the interaction of p-RBD of B21R protein with CRD region of DC-SIGN, which showed the gradual increase in the binding affinity with acquired mutations. Moreover, we found alteration in the O-linked glycosylation sites at p-RBD regions of B21R protein which is crucial for the MPXV entry into the host cell. Importantly, we observed significant changes in linear B cell epitopes of p-RBD, impacting the humoral immunity, while CTL epitopes remained conserved. Hence, we showed the significance of B21R p-RBD as a T-cell based vaccine candidate for prevention of Mpox. This study provides novel insights into the recent global transmission of the Mpox and explored a plausible mechanism of humoral immune escape strategies through progressive mutations in the B21R protein and potential development of T-cell based vaccine candidate. Significance statementOur study represents the global transmission dynamics of Mpox and immune evasion strategy of recent MPXV strains. Epidemiological transformation analysis revealed that the current multinational outbreak of Mpox originated in Africa in 2017, highlighting the expanding global footprint of MPXV. Our analysis based on the B21R protein shows the evolutionary adaptation of the MPXV associated with progressive mutations responsible for increased affinity towards the DC-SIGN receptor and potential reason for increased infectivity. Importantly, alterations in O-linked glycosylation sites and linear B cell epitopes show potential antigenic drift in the recent Mpox outbreaks showing immune escape strategies. These findings provide insights into Mpox epidemiology and the molecular basis of MPXV adaptation, informing vaccine design, therapeutic strategies, and improved countermeasures against future outbreaks. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/708970v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@7d949forg.highwire.dtl.DTLVardef@a8918corg.highwire.dtl.DTLVardef@eba49forg.highwire.dtl.DTLVardef@84c331_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2026

Prior expectation shapes the emotional response to sounds: behavioural and neural correlates

Prior expectations are known to shape perception especially when a stimulus is ambiguous. Bayesian models of cognition posit perception is a precision-weighted combination of top-down and bottom-up information. We consider here affective responses to highly salient stimuli for which a dominant role of bottom-up processing has previously been emphasised. We study how predictions alter the perception of emotional stimuli in a paradigm in which neutral and aversive sounds were preceded by either predictive or non-predictive cues. Cues predicted the type of sound with 100% or 50% probability. Behavioural measures of trial-by-trial expectation and perceived aversiveness were collected before and after stimulus presentation, respectively. We show that prior expectations biased the perceived aversiveness of sounds towards predictions, but only when subjective expectations were considered (as opposed to the objective expectation based on conditional probability). Neural responses were recorded using EEG. During sound processing, we found P3 and LPP components were increased after non-predictive cues, but only for affective stimuli. Time-Frequency results uncovered a role of alpha-beta oscillations in the precision of predictions, as well as in the processing of unexpected stimuli. Our results indicate expectations directly alter the perception of affective stimuli and its processing, and emphasise the importance of behavioural measures to characterize this relationship.

neuroscience↗

bioRxiv2026

IL-35 produced by dendritic cells via TIM-3-STAT3 signaling contributes to the development of visceral leishmaniasis

Visceral leishmaniasis (VL), a life-threatening parasitic disease caused by Leishmania donovani (LD), progresses primarily due to profound immunosuppression. However, the molecular and cellular mechanisms underlying this immune dysfunction remain poorly defined. Here we show that early production of IL-35 by dendritic cells (DCs) is critical for immunosuppression and disease pathogenesis during LD infection. LD stimulated IL-35 expression in DCs through the TIM-3 receptor and the downstream transcription factor STAT3. IL-35 produced by DCs subsequently suppressed DC maturation and T cell proliferation, propagated immunosuppression by inducing IL-35 expression in T cells, and impaired type-1 anti-leishmanial immunity, thereby promoting disease progression. Genetic or pharmacologic inhibition of STAT3 markedly reduced IL-35 production by DCs, restored protective type-1 T cell responses, and promoted parasite clearance in vivo. Notably, treatment with WP1066, an FDA-designated orphan STAT3 inhibitor, significantly lowered parasite burden and disease severity in infected mice. Together, these findings uncover a previously unrecognized TIM-3-STAT3-IL-35 axis that drives immunosuppression and pathogenesis in VL and highlight STAT3 inhibition as a promising therapeutic strategy to restore host immunity and control infection.

immunology↗

bioRxiv2026

Mega-frequency mutagenesis: generation of non-random precise mutations with extremely high frequency upon adaptation of cancer cells to drugs and stress

Acquiring drug resistance is a major problem in cancer treatment. As cancers adapt to chemotherapy, chromatin landscape becomes altered in subpopulations of persister cells to acquire gene expression patterns that provide drug resistance. The increased level of stress-induced random mutagenesis in cancer has also been linked to acquisition of drug resistance. Here we show that during adaptation to conventional cytotoxic chemotherapies or targeted therapies, tens of thousands of mutations are generated, and the probability of acquisition of these mutations at specific positions can reach 50% and even higher. A large fraction of these mutations is highly recurrent and non-random. The patterns of the recurrent mutations are specific to the drug target and are unrelated to the chemical nature of the drug. Surprisingly, these mutations are progressively generated at the non-dividing pseudo-senescence stage following drug exposure, and at this stage, selection is not involved in their accumulation. Notably, these mutations are highly enriched within or near binding motifs of certain transcription factors, like KLF9, IRF1 and others. Therefore, a mechanism for precise generation of mutations at specific positions with extremely high rates appears to be triggered upon drug adaptation, and these precise mutations may affect activities of a set of transcription factors.

cancer biology↗