Biology subjects

Das, S.

Publications and source records attributed to Das, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Population structure amplifies mutation load

The interplay of mutation and natural selection is key to evolution: Mutations introduce genetic variation, whereas selection favours higher-fitness individuals. The balance between the two is quantified by the mutation load--the reduction in mean population fitness due to deleterious mutations. In large well-mixed populations, selection dominates, and the mutation load is proportional to the mutation probability per reproduction event. However, the role of spatial structure in shaping mutation-selection dynamics is poorly understood. Here, we use evolutionary graph theory to show that heterogeneous spatial structures generically amplify the effect of mutation relative to selection. In contrast to well-mixed populations, the mutation load in heterogeneous structures can remain substantial even when the mutation rate is very small, signaling a breakdown of selection. For example, in star-shaped populations the mutation rate is effectively amplified by a factor proportional to the population size. When mutation is coupled to reproduction, this leads to the proliferation of less-fit types over fitter ones, a scenario of "survival of the weakest". The reduction of natural selection may help explain, for example, tumour heterogeneity in spatially structured tissues. It also suggests that heterogeneous social networks can promote the persistence of unpopular opinions, thereby fostering diversity. By showing how spatial structure modulates the effect of selection, our work points to potentially new ways of steering evolution toward desired outcomes.

evolutionary biology↗

bioRxiv2025

Single-molecule imaging reveals activity-dependent regulation of Camk2a mRNAs at dendritic spines

AbstractPostsynaptic calcium/calmodulin-dependent protein kinase type II (CaMKII) integrates fleeting Ca2+ transients into long-term synaptic potentiation (LTP). A persistent presence of CaMKII at dendritic spines during the maintenance of LTP facilitates the prolongation of synaptic transmission. Yet, it remains unclear how the perpetuation of CaMKII, despite protein turnover, is achieved at dendritic spines. By visualizing endogenous Camk2a mRNAs at single molecule resolution using a newly developed mouse model, we identified a rapid activity-dependent localization of mRNAs to stimulated spines near the postsynaptic density (PSD) of hippocampal neurons. This spine localization was conferred by cis-acting regulatory elements termed cytoplasmic polyadenylation elements (CPEs) in Camk2a mRNA. Spine-localized Camk2a underwent on-site translation, which persisted for extended periods. These findings uncovered a novel local regulation of Camk2a mRNA, which serves to supply dendritic spines with a steady pool of highly concentrated CaMKII for maintaining long-lasting synaptic plasticity.

neuroscience↗

bioRxiv2025

Copy number of the blaNDM-1 gene (New Delhi metallo-β-lactamase-1) and meropenem susceptibility in Enterobacterales: Consideration for treatment with meropenem?

Some Enterobacterales carrying blaNDM were still susceptible to meropenem, exhibiting meropenem minimum inhibitory concentration (MIC) values below the clinical breakpoint. As this phenomenon is a rare observation, this study investigated the underlying regulatory mechanisms contributing to the low MIC values and evaluated the efficacy of meropenem as a therapeutic preference for such isolates. Six clinical blaNDM-positive Enterobacterales exhibited meropenem MICs between 0.5-2.0 mg/L. Successful transmission of blaNDM into recipient E. coli J53 indicated its presence on plasmids. Conventional Sanger and whole-genome sequencing revealed that no truncation or deletion was observed within blaNDM or its core promoter region up to 120 bp upstream. Quantitative real-time PCR of blaNDM showed significantly lower expression levels of blaNDM, i.e., 0.2-0.5 in study isolates, compared to a clinical blaNDM-possessing isolate (expression=1) exhibiting a high meropenem MIC value (64 mg/L). Droplet digital PCR (ddPCR) further demonstrated that these isolates carried a lower copy number of the blaNDM gene, compared to the blaNDM-possessing isolate with high meropenem MIC (64 mg/L). Furthermore, the in vitro time-kill assay exhibited bactericidal efficacy of meropenem >3 log10 decrease in cfu/mL over the 24 hours from the starting inoculum. Administration of meropenem in in vivo neutropenic mice produced a 4-log cfu reduction compared to untreated controls at the start of dosing. Our data suggest that a reduction in blaNDM gene dosage, reflecting lower expression of blaNDM, correlates with lower meropenem MIC values. Meropenem is effective against these isolates when the meropenem MICs for the isolates are 0.5-2.0 mg/L. ImportanceThe production of NDM by Enterobacterales poses one of the most urgent global public health threats due to its plasmid-mediated spread, leading to treatment failure by exhibiting high MICs against a broad-spectrum of antibiotics. However, in rare instances, blaNDM-1-positive clinical Enterobacterales with unexpectedly low meropenem MICs (0.5-2.0 mg/L) raise a further question of reconsidering meropenem as a potential therapeutic option in these specific cases. This study identified that low MICs were associated with reduced expression and lower copy number of the plasmid-mediated blaNDM gene, despite intact promoter regions. Both in vitro and in vivo assays validated the bactericidal activity of meropenem against these isolates. The study raised an argument about the potential limitations of relying solely on genotypic detection of resistance genes for therapeutic decision-making, which emphasises the need for further investigation. As a safe medication, repurposing meropenem for neonatal treatment may eliminate the need for other toxic drugs.

microbiology↗

bioRxiv2025

L2 loop engineering enhances the enzymatic activity and synergism property of the AA16 family Lytic polysaccharide monooxygenase enzyme from Aspergillus fumigatus.

Lytic polysaccharide monooxygenase (LPMO) is an enzyme that has enormous potential for industrial applications. It has a synergistic effect with the cellulase enzyme complex. The LPMO enzymes typically adopt a compact {beta}-sandwich fold that consists of a 7 to 9 {beta}-strand with a flat active site containing copper in its active site. There are a few loops in LPMO, among them the L2 loop is reported to take a key role in shaping the active site and substrate binding. Now, in this work, we want to investigate the role of the L2 loop in enzymatic activity and synergistic effect. In achieving our goal, we have replaced the L2 loop of our concerning AfLPMO16 with other L2 loops from different LPMOs: HiLPMO9B (PDB: 5NNS), McLPMO9 (PDB: 7NTL) and CsLPMO9 (PDB: 7EXK). Interestingly, L2 loop replacement from CsLPMO9 (PDB: 7EXK) showed enhanced activity and synergism compared to others. The secondary structural analysis by circular dichroism also suggested that it changed the structure significantly. Moreover, this is the first report of complete L2 loop engineering in LPMO.

biochemistry↗

bioRxiv2025

B Cell Tolerance and BCR Signaling Dysregulation in NF155-Mediated Autoimmune Nodopathies

ObjectiveAutoimmune nodopathies (AINs) are a group of rare, acquired autoimmune neuropathies with distinct clinical features and the presence of circulating autoantibodies - often of the immunoglobulin G4 (IgG4) subclass - targeting proteins at the node of Ranvier. Defects in B cell tolerance checkpoints have been implicated in several autoimmune diseases. Prior work identified defective B cell tolerance--reflected by a high frequency of self-reactive naive B cells--in patients with MuSK-positive myasthenia gravis (MG), mediated by IgG4 autoantibodies. Here, we investigated whether tolerance defects exist in neurofascin-155-mediated AIN (NF155-AIN), similar to MuSK+ MG. Additionally, we analyzed B and T cell transcriptomics and interactions at the single-cell level to explore the underlying pathomechanism. MethodsUsing a well-established assay, we assessed B cell tolerance fidelity by generating recombinant antibodies from new emigrant (NE) and mature naive (MN) B cell populations-- directly downstream of key tolerance checkpoints--from three NF155-AIN patients, and testing these antibodies for polyreactivity and autoreactivity, thereby determining the frequency of polyreactive and autoreactive B cells. The transcriptome of peripheral blood mononuclear cells (PBMC) was studied, with a special focus on naive B cells and CD4+ T cells at the single-cell level, along with characterization of cell-cell interactions. ResultsNF155-AIN patients have an elevated frequency of polyreactive B cells in the NE (37.4% compared to 9.7% in healthy controls (HCs), p = 0.03) and MN (31.5% compared to 10.5% in HCs, p = 0.03) compartments with increased B cell clones expressing autoreactive antibodies, consistent with a breach in early tolerance checkpoints. We observed abnormal B cell receptor (BCR) signaling characterized by low CD79B, CSK, BLNK, and BTK expression, which may contribute to a breach in B cell tolerance. We also observed evidence of impaired follicular helper T cells (Tfh) and regulatory T cells (Treg), which may limit the normal development and suppression of autoreactive B cells. Moreover, comparative gene expression analysis of B cells and CD4+ T cells from three patients with chronic inflammatory demyelinating polyneuropathy (CIDP) --a related autoimmune neuropathy-- confirmed that these differences are largely specific to NF155-AIN, supporting a distinct pathophysiology in this subset. ConclusionThese findings demonstrated a breach in early B cell tolerance checkpoints, defective BCR signaling, and disrupted T cell-B cell interactions in NF155-AIN, all of which may contribute to the development of pathogenic autoreactivity. These immunologic abnormalities appear distinct from those seen in CIDP, supporting NF155-AIN as a unique immunopathologic entity.

neuroscience↗

bioRxiv2025

Assessing the Potential of Switchgrass (Panicum virgatum L.) for Storing Carbon Belowground: Insights from a Multi-Site US Study

Agricultural intensification depletes belowground carbon (C) stocks, partly due to the exclusion of deep-rooted perennial species from landscapes where they were once dominant. Reintroducing deep-rooted perennials to cultivated land may help to mitigate SOC loss and restore ecosystem function. We quantified the effect of replacing shallow-rooted annual crops with a deep-rooted perennial grass, switchgrass (Panicum virgatum L.), by comparing 10 to 30 year-old switchgrass stands with paired annual row crop fields across the central and eastern USA. We hypothesized that switchgrass would store more root C and SOC than neighboring shallow-rooted annual crops, and that these effects would extend deeper than 30 cm. We also evaluated whether switchgrass stimulates decomposition of SOC at depth using radiocarbon (14C) to quantify replacement of slow cycling isotopically depleted SOC. Finally, we explored whether the effect of switchgrass on SOC is moderated by soil chemical and physical properties. While the effect of switchgrass on SOC in the surface 100 cm was positive at most sites, the average effect was highly uncertain and statistically indistinguishable from zero (mean difference in SOC = 0.6 kg C m-2 [95% CI -0.8 to +1.9 kg C m-2]). By contrast, we found that root biomass C was consistently more deeply distributed and more abundant under switchgrass, yielding an estimated additional 0.6 kg C m-2 in the surface 100 cm of soil under switchgrass [95% CI +0.5 to +0.7 kg C m-2]. 14C measurements suggested that root C inputs were adding to existing SOC without stimulating decomposition. The effect of switchgrass on belowground C was not strongly related to any of the environmental factors that we evaluated. Our observations show that root biomass C can contribute substantially to belowground C stocks when deep-rooted perennial grasses replace shallow-rooted annual crops.

ecology↗

bioRxiv2025

Potassium channels mediate the inhibitory effect of exosomes on anti-tumor immunity in head and neck cancer

Head and neck squamous cell carcinomas (HNSCC) are aggressive cancers with a relatively low response rate to immunotherapy. Anti-tumor immune responses rely on cytotoxic T and NK cells infiltrating the tumor microenvironment to eliminate cancer cells. However, tumors activate multiple mechanisms to evade these responses. Tumor-derived small extracellular vesicles, also known as exosomes, reshape the tumor microenvironment by impairing cytotoxic T and NK cell function, promoting immune escape and metastasis. Transcriptomic analysis of healthy donor peripheral blood mononuclear cells (PBMCs) exposed to exosomes from HPV-negative HNSCC patient primary cancer cells revealed reduced cytotoxic cells and suppressed immune responses including cytotoxicity, chemokine production, and NK and T cell functions. Bead-based multiplex immunoassay showed that HNSCC-derived exosomes inhibited the release of effector cytokines (IL-2, TNF-, IFN-{gamma}) and cytotoxic molecules from activated CD8 T cells. While ion channels regulate Ca{superscript 2}-dependent cytotoxicity and cytokine production and release, their role in exosome-mediated immune suppression is unexplored. We found that tumor-derived exosomes selectively inhibit KCa3.1 channel activity in CD8 T cells by downregulating calmodulin, ultimately impairing Ca{superscript 2} signaling and IFN-{gamma} release. This study identifies a novel mechanism of exosome-mediated immunosuppression, positioning KCa3.1 as a promising therapeutic target to enhance immune surveillance and immunotherapy response in HNSCC.

immunology↗

bioRxiv2025

Dual role of Human antigen R in Dengue virus infection: suppression of replication and promotion of cap-independent translation

Host RNA-binding proteins (RBPs) play a pivotal role in regulating dengue virus (DENV) translation and replication through interactions with untranslated regions (UTRs) of viral RNA. We investigated host proteins associated with detergent-resistant membranes (DRMs) of the DENV replication complex and identified Human antigen R (HuR) as a key RBP enriched in the DRM. HuR was found to negatively regulate DENV replication by binding the DENV-3'UTR and impeding the association of polypyrimidine tract-binding protein (PTB), a known RNA stabilizer. Additionally, infection-induced modulation of HuR stabilized host mRNAs involved in innate immunity. Interestingly, in vivo validation in AG129 mice model highlights an inverse correlation between HuR expression and viral load and implicates HuR in cytokine dysregulation. Notably, HuR promoted cap-independent translation of viral RNA during later stages of infection, when cap-dependent translation is suppressed. These findings reveal a dual role for HuR: restricting viral RNA replication while enhancing translation, highlighting its critical, phase-specific function in the DENV life cycle. Author summaryUnderstanding how Dengue virus interacts with human cells is key to finding better treatments. Our study looked at a human protein called HuR, which normally control the stability and the use of RNA inside our cells. We discovered that HuR has two important but opposite roles during dengue infection. Early on, it slows down the viruss ability to make copies of its genetic material, helping to reduce infection. But later, when the virus struggles to use the normal method of making proteins, HuR steps in to help the virus make its proteins in a different way. This double-edged role of HuR shows how the virus cleverly uses host cell machinery at different stages of infection. Overall, this study uncovers the novel role of a specific RNA-binding protein of the host in orchestrating dengue virus infection and pathogenesis, highlighting its potential as a target for antiviral therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/666571v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@1a5a0fdorg.highwire.dtl.DTLVardef@ec7734org.highwire.dtl.DTLVardef@860cf0org.highwire.dtl.DTLVardef@bb65f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

An ancient evolutionary origin for IL-1 cytokines as mediators of immunity

Inflammation is a hallmark of immune responses. Its mechanistic underpinnings in mammals are well-defined: pro-inflammatory cytokines of the interleukin 1 (IL-1) superfamily establish and support microenvironments that promote immune cell activities. Despite a growing number of reports on inflammatory processes and components of the IL-1 signaling axis in several invertebrate lineages, orthologs of these central cytokines have not been detected outside of the jawed vertebrates. Here, protein structure prediction algorithms were applied to identify genes encoding a family of IL-1 proteins with homologs throughout Eumetazoa (termed "IL-1anc" to reflect their ancestral evolutionary origin). Using Petromyzon marinus (sea lamprey) and Strongylocentrotus purpuratus (purple sea urchin) as model systems, we demonstrate that IL-1anc proteins share important features with mammalian IL-1/IL-1{beta} including expression patterns, protein localization, and processing. Together, our data indicate that the IL-1 superfamily and associated circuitry represent a foundational module of animal immunity that far predates the jawed vertebrates.

immunology↗

bioRxiv2025

Exposure to third generation cephalosporin induces L-form transition in Shigella sonnei, potentially acting as a bacterial reservoir for persistent infection

Shigellosis remains a major global health burden, and the increasing prevalence of multidrug-resistant (MDR) Shigella strains is complicating effective antibiotic therapy. Bacteria may survive antibiotics by transitioning into cell wall-deficient L-forms, which are intrinsically resistant to {beta}-lactams and can revert to a virulent state, potentially causing relapsing infections. Here we characterized a clinical MDR isolate Shigella sonnei HK8, a.k.a. PD552A, whose genome contains key resistance (gyrA, PBP3) and virulence (icsA) genes. Exposure to ceftriaxone induced a transition into a viable L-form state that was hyper-adhesive to macrophages in vitro. However, this survival adaptation was linked to a profound loss of pathogenicity. Using murine and guinea pig models, the L-form variant was shown to be profoundly attenuated, failing to cause the keratoconjunctivitis, diarrheal disease, or significant histopathology characteristic of the wild-type strain. These findings reveal a critical virulence-survival trade-off, positioning the L-form as a "stealth" phenotype that enables bacterial persistence at the expense of acute virulence. This offers a potential mechanism for asymptomatic carriage and recurrent infections, highlighting a previously underappreciated mechanism by which antibiotic treatment may resolve acute symptoms while permitting the persistence of a cryptic bacterial reservoir capable of driving recurrent infection. ImportanceOur research provides critical insight into the challenge of antibiotic treatment failure in shigellosis. By integrating experimental validation of reversible L-form transitions with mathematical modelling, we uncover a crucial virulence-survival trade-off. We show that MDR S. sonnei survives ceftriaxone by adopting a "stealth" phenotype, quantified by a high Stealth Index - maintaining bacterial burden while evading host inflammatory detection. These findings imply that standard antibiotics may resolve acute symptoms while inadvertently selecting for a cryptic, persistent reservoir poised for relapse. This work challenges the conventional view of therapeutic success and highlights an urgent need to develop novel diagnostic and therapeutic strategies capable of identifying and eliminating these resilient, "stealth" L-form persisters to achieve true bacterial clearance and prevent chronic infections.

microbiology↗

bioRxiv2025

Lifestyle transition from rural to urban setting changes the gut bacterial profile in an ethnic community of northeast India

The human gut microbiome undergoes transformation due to various exogenous and endogenous influences. Lifestyle has been one of the major contributors of gut microbiome composition. Our study investigated the effect of migration on the gut microbiome of the Mishing ethnic community in India associated with urban migration from their pastural lifestyle. Gut bacterial diversity was profiled using 16S rRNA amplicon sequencing. We observed notable alterations in microbial diversity and composition, including changes in the core microbiome. While Bifidobacterium, Lactococcus and Streptococcus significantly increased (p < 0.01) among the migrant population there was depletion in bacteria such as Succinivibrio and Prevotella. This change in core microbiome was further reflected on the functional profile of the bacterial community harbored by the urban and rural dwellers. While the rural population was enriched in fatty acid biosynthesis pathways, amino acid and Vitamin B2 biosynthesis pathways were more prominent in the microbiome of the urban dwellers. We further observed increase in diversity and richness of the microbiome following migration. Co-analysis with ASVs from food samples consumed by the Mishing rural population revealed that 51 ASVs among the rural dwellers were from a widely consumed beverage, Apong which were completely absent among the migrants. Our analyses highlight the dietary preferences, particularly abstinence from specific foods and beverages, may modulate the alterations in gut microbial profiles. While the cross-sectional design and amplicon sequencing limited our ability to assess temporal and functional changes, our findings highlight a measurable impact of lifestyle and dietary transitions on the gut microbiome.

microbiology↗

bioRxiv2025

Dietary fatty acids as determinants of cuticular wax profiles in Tribolium castaneum

Cuticular waxes are complex mixtures of hydrocarbons and other lipophilic compounds that form an outer protective layer over the insect cuticle playing a role in ecological interactions as well as physiological processes. While CHC profiles are largely genetically determined, several studies have linked diet to cuticular hydrocarbons and limited research indicates a potential influence of dietary fatty acids. Considering this, the current work investigates the effect of nine cereal flours, i.e., wheat, rice, maize, barley, oat, ragi, sorghum, soybean and gram, each with a distinct fatty acid composition, on the cuticular wax profile of Tribolium castaneum (Coleoptera: Tenebrionidae), a globally significant stored grain insect. Fatty acid compositions of the nine flours and the cuticular waxes from the beetle populations reared on each diet were characterized using gas chromatography mass spectrometry (GC-MS). In all the beetle populations, the most abundant compound was 1-pentadecene, followed by cis-9-tetradecen-1-ol and 1-heptadecene, irrespective of the diet. While no qualitative differences in cuticular wax composition were found, significant quantitative variation in cuticular wax profile was observed across dietary groups. Similarity percentage (SIMPER) analysis revealed a cumulative Bray- Curtis dissimilarity of 47.72 among the flour samples based on their fatty acid profiles, and a dissimilarity of 18.51 among T. castaneum populations reared on these flours based on their cuticular wax composition. Non-metric multidimensional scaling (NMDS) further indicated substantial variation in the cuticular wax profiles of beetle populations raised on different dietary sources. Pearsons correlation analysis between the concentrations of individual cuticular wax components and the fatty acid content of the respective diets demonstrated strong correlations between specific cuticular compounds and dietary fatty acids. Notably, levels of 1-pentadecene in the beetle cuticle were strongly associated with the concentrations of hexadecanoic and octadecanoic acids in the flours. These results support the hypothesis that, alongside endogenous conserved biosynthetic pathways, dietary fatty acid composition contributes to the modulation of insect cuticular chemistry. This dietary influence may have important implications for understanding insect ecological plasticity and diet-mediated changes in surface chemistry.

zoology↗

bioRxiv2025

Dichotomous transcriptome divergence at the cell-type level between the Drosophila male and female germlines

Gene expression evolution in reproductive organs plays a central role in species divergence, yet cell-type-resolved patterns in invertebrates remain poorly understood. We used single-nucleus RNA-sequencing to profile testis and ovary transcriptomes from the sibling species Drosophila melanogaster and D. simulans. Despite conserved cellular composition, we observed highly cell-type-specific expression and coexpression network divergence between species. In the testis, mitotic cells were conserved across species, mirroring patterns in mammals, while divergence peaked in late spermatocytes. In the ovary, divergence was less pronounced, peaking in early germline and late-stage follicle cells, and enriched on the X chromosome, consistent with a faster-X effect driven by positive selection. Genes expressed in these cell types exhibited narrower expression breadth, younger phylogenetic age, and elevated rates of protein evolution in both tissues. Our findings reveal contrasting evolutionary regimes in male and female germlines, shaped by adaptive and non-adaptive mechanisms, contingent on cell type and chromosomal context.

evolutionary biology↗

bioRxiv2025

Microbial Scl1 Activates TGFBR1 receptor kinase signalling to Drive Fibrosis-Inflammation Axis in Alcohol-Associated Liver Disease

Background and AimsAlcohol consumption alters gut microbiota, which can affect metabolism, immune regulation, and signalling pathways and lead to alcohol-associated liver disease (ALD). We investigated how alcohol-associated gut microbiota (AGMs) modulate liver kinome signalling to drive inflammation and fibrosis in ALD. MethodLiver kinome and metaproteome changes were studied in rats (n=6/group) colonized with stool of severe alcohol-related hepatitis (SAH) patients (SAH[->]healthy-rats) or healthy human donors (HD[->]ALD-rats). AGM-associated liver kinome changes were cross-correlated with bacterial genera. A bacterial protein; Streptococcal collagen-like protein 1 (Scl1) was identified with affinity for TGF{beta}R1. This was validated by molecular docking and immunoprecipitation-LCMS assay. Expression of Streptococcus pneumonia and pyogenes was done in stool of SAH patients (n=10). Also, Scl1 was quantified in patient stool (n=24) and liver tissue (n=19) samples. Validation was performed by assessing Scl1 level in plasma and Streptococcus level in stool samples before and after fecal microbiota transplantation (FMT) in SAH patients. ResultsStool metaproteomics showed significant increase in 10 bacterial genera (Streptococcus, Staphylococcus, and Clostridium) in SAH[->]Healthy-rats, mirroring changes seen in ALD-rats (FC>1.5, p<0.05). Clusters of Orthologous Groups analysis indicated increased post-translational modifications (PTMs) and decreased lipid metabolism in ALD-rats and SAH[->]Healthy-rats. Liver kinome profiling showed 85 upregulated kinases in SAH[->]Healthy-rats, with 34 overlapping with ALD-rats, associated with inflammation (Mapk14, Map3k10 and others), fibrosis (Tgfbr1, Igf1r, and others), lipid metabolism (Cdk14, Cdk18) and regeneration (Met, Bmpr1a and others). FMT from healthy human-donors to ALD-rats reversed the expression of Streptococcus (10-fold), Staphylococcus (3-fold), and Clostridium (5-fold), along with 18 kinases associated with inflammation (Btk, Camk4, Nuak1) and fibrosis (Tgfbr1, Col4a1, Fgfr2 and others). Strong association (r{superscript 2}>0.9, p<0.05) was seen between Streptococcus abundance and fibrosis and inflammation-related kinases. Level of Scl1 was significantly high in SAH and ALD-rat stool samples (FC>2, p<0.05). It showed strong affinity for TGF{beta}R1, as validated by molecular docking (>86%confidence) and immunoprecipitation assays (>100FC,p<0.05), indicating it as a potential ligand for TGF{beta}R1. Concordantly, expression of Scl1 was highest amongst all the known ligands for TGF{beta}R1 (p<0.05) suggesting Scl1 is a major contributor for TGF{beta}R1 activation and its downstream signalling in these patients. Following fecal microbiota transplantation, expression of Scl1 in plasma and Streptococcus levels in stool were significantly reduced by 2.1-folds and 1.9 folds respectively in SAH patients. Further, Scl1 levels SAH plasma is capable of predicting poor therapeutic response and 30-day mortality with high accuracy (AUC=0.92, cutoff >70 normalized abundance). ConclusionAlcohol induced gut dysbiosis alters the liver kinome, promoting inflammation, fibrosis, and lipid dysregulation. Streptococcal Scl1 is identified as a bacterial protein mimicking human collagen and capable of activating fibrotic signalling pathway through TGF{beta}R1in liver and is capable of predicting poor response in SAH. FMT from healthy donor restores microbial imbalance and harmful microbial-host interactions.

microbiology↗

bioRxiv2025

Heightened subcortical reactivity to uncertain-threat is associated with future internalizing symptoms, conditional on stress exposure

BackgroundAnxiety, depression, and related internalizing illnesses are a leading burden on global public health, and often emerge during times of stress. Yet the underlying neurobiology has remained enigmatic, hindering treatment development. MethodsHere we used a combination of tools--including a well-established threat-anticipation fMRI paradigm and longitudinal assessments of internalizing symptoms and negative life events (NLEs)--to identify the neural systems associated with future internalizing illness in a risk-enriched sample of 224 emerging adults followed for 2.5 years. We performed parallel analyses in an overlapping sample of 209 participants who completed a popular threat-related faces paradigm. ResultsHere we show that heightened reactivity to uncertain-threat anticipation in the bed nucleus of the stria terminalis and the periaqueductal gray is associated with a worsening longitudinal course of broadband internalizing symptoms among individuals with low levels of NLE exposure. These associations were specific to uncertain threat and generally remained significant when controlling for concurrent measures of threat-elicited distress or psychophysiological arousal, highlighting the added value of the neuroimaging measures. Symptom trajectories were unrelated to amygdala and frontocortical reactivity to anticipated threat. Contrary to past research, amygdala reactivity to threat-related faces was unrelated to future symptoms. ConclusionsThese observations provide a novel neurobiological framework for conceptualizing transdiagnostic internalizing risk and lay the groundwork for mechanistic and therapeutics research. A racially diverse, risk-enriched sample and pre-registered, best-practices approach enhance confidence in the robustness and translational relevance of these results.

neuroscience↗

bioRxiv2025

Enhancing protective efficacy and immunogenicity of hemagglutinin-based influenza vaccine utilizing adjuvants developed by BECC

Seasonal influenza viruses continue to pose a significant threat, causing substantial morbidity and mortality in the US and worldwide despite the availability of vaccines and antivirals. These challenges may be addressed by improving vaccine immunogenicity through the inclusion of adjuvants that enhance immune responses against key antigens including influenza hemagglutinin (HA). BECC (Bacterial Enzymatic Combinatorial Chemistry) adjuvants are novel Toll-like Receptor 4 (TLR4) ligands created by modifying enzymes from lipid A synthesis pathways in Gram-negative bacteria. This study compares the ability of the biological and synthetic versions of these adjuvants to enhance the efficacy of recombinant HA (rHA) antigens in mouse influenza virus challenge. Mice immunized with rHA adjuvanted with BECCs stimulate the humoral and cell-mediated arms of the immune system without exhibiting cytotoxicity/pyrogenicity. A robust HA-specific immunoglobulin subtype, especially IgG2a, response was observed in mice adjuvanted with BECCs as compared to control adjuvants, MPL, and PHAD Further, animals adjuvanted with BECC470 cleared infection seven days post-infection, demonstrating their potential for further translational development. Vaccination adjuvanted with BECCs were also able to increase immune recognition of linear B and T cell epitopes when compared to control adjuvants, as well as induce durable immune response eighteen months post-vaccination. Together, these findings indicate that BECCs may serve as highly effective adjuvants in influenza vaccination. One Sentence Summary: Efficacy of engineered lipid A molecules as adjuvants for HA-based influenza vaccine

immunology↗

bioRxiv2025

Targetable BIRC5 dependency in therapy-resistant TP53 mutated acute myeloid leukemia

TP53 mutations across multiple cancers, including acute myeloid leukemia (AML), are associated with poor outcomes irrespective of treatment modality. However, druggable vulnerabilities beyond canonical p53 targets remain largely unexplored. We identify BIRC5 (encodes survivin), an inhibitor of the apoptosis protein (IAP) family, as a novel vulnerability in TP53 mutant AML using an unbiased, comprehensive multiomics approach -- whole-genome CRISPR knockout screen, bulk and single-cell RNA-seq, proteomics, and high-throughput drug screen. Mechanistically, BIRC5 deletion in AML restored caspase-9 and -3/7 activity and downregulated other IAPs, implicating BIRC5 as the central post-mitochondrial regulator for blocking apoptosis. p53 stabilization suppressed BIRC5 selectively in TP53 wild-type AML, explaining BIRC5 upregulation in TP53 mutant lines and AML primary tumors (n > 700). Longitudinal single-cell RNAseq (n = 22 pairs) revealed expansion of BIRC5high stem and progenitor leukemia clones in TP53 mutant AML patients post-VenAza therapy. Survivin and IAP inhibitors emerged as top combination partners with VenAza in TP53 mutant AML cells and showed potent in vivo leukemic blast inhibition in cell line and patient-derived xenograft models along with primary tumors. Beyond AML, BIRC5 was upregulated broadly across 17 of 25 TP53 mutant cancers in the TCGA cohort, and combination with survivin inhibitors overcame chemotherapy resistance in TP53 deficient triple negative breast and colorectal cancers. These findings define BIRC5 as a critical, targetable dependency and unveil survivin/IAP inhibition as a promising therapeutic axis to overcome p53-related resistance across both hematologic and solid malignancies. Key PointsO_LIBIRC5 upregulation is a novel dependency in TP53 mutant AML that mediates therapy resistance by evasion of apoptosis. C_LIO_LICombination with Survivin/IAP inhibitors overcomes venetoclax/azacitidine resistance in TP53 mutant AML. C_LI

cancer biology↗

bioRxiv2025

Improving plant functional annotation from knowledge graphs using Graph Neural Networks

Annotating genes is essential to crop development, and understanding gene functions sheds light on developing crop improvement strategies, such as marker-assisted breeding, genetic modification, or pest resistance. Through an extensive experimental effort and computational annotation projection, tens of thousands of genes have been annotated across plant species, with most of the gene annotations focusing on a well-studied species, Arabidopsis thaliana, but this represents a small fraction of the hundreds of thousands of genes across these different plant species. Phenotypes and their traits result from multiple processes and events involving multiscale information encoded from different omics, such as genomes, proteomes, or transcriptomes. This stresses a need for an efficient computational approach to capture and integrate information from biological networks and transfer this knowledge from well-studied species to unknown species to annotate and discover functional relationships between annotations and genes. Despite recent progress, existing methods only consider one or a few omics levels to perform reasoning on functional annotation-to-gene relations. The main objective of this study is to generate and explore a large-scale plant biological knowledge graph, the DasDB, and to enrich gene functional annotation linked to genes in different species using graph neural networks (GNNs). Integrating various data sources from different omics has resulted in a comprehensive graph database, facilitating researchers in-depth understanding of complex biological networks at the highest level. In addition, applying GNNs on a large-scale knowledge graph database has shown promise in the ability of deep learning models to transfer this information from well-studied plant species to less-characterized plant species, outperforming the transfer of information done using only orthology relationships. This study benchmarks a new research direction in producing new functional annotation discovery in plant species with limited functional annotations. This pipeline was applied to a specific research problem: the mechanism involved in pea nodule nitrogen fixation. We identified known gene markers of this process through a systematic analysis of the DasDB, showing the relevance of our approach. Furthermore, new potential targets to better understand and improve this process were identified.

systems biology↗