Biology subjects

Sharma, S.

Publications and source records attributed to Sharma, S..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Inhibition of PfCLK3 a master regulator of malaria parasite RNA-splicing provides the basis for a radical cure for malaria

Emerging resistance to front-line anti-malarials means there is a race to discover new drugs with novel mechanisms of action that remain effective across multiple stages of the parasite life cycle. Previously we reported the malaria protein kinase, PfCLK3, as a target offering a cure, prophylaxis and transmission blocking. The homology between PfCLK3 and human kinases suggested that the mechanism of parasiticidal activity of PfCLK3 inhibitors is disruption of RNA processing. Here, we use whole genome RNA-sequencing to reveal that selective PfCLK3 inhibition extensively affects RNA-splicing with 2039 splice-junctions across 1125 genes mis-spliced in treated wild type parasites compared to controls. The function of mis-spliced transcripts showed that the affected genes were involved in numerous essential parasite processes associated with multiple life cycle stages and revealed transcripts and introns particularly susceptible to inhibition. Our study supports the role of PfCLK3 as an important regulator of spliceosome activity and establishes the distinct mechanism of parasiticidal activity of PfCLK3 inhibitors from current front-line treatments.

molecular biology↗

bioRxiv2025

Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

Chronic exposure to the common aeroallergen house dust mite (HDM) induces lung inflammation and DNA damage, but its impact on lung cancer development remains largely unexplored. Using whole-genome sequencing, RNA-seq, and DNA methylation profiling, we assessed HDM effects in lung epithelial cell lines and a mouse orthotopic lung cancer model. HDM accelerated tumor growth without altering mutational burden. Transcriptomic and epigenetic analyses revealed tissue-specific effects: in normal lung, HDM enhanced pro-inflammatory and immune activation programs, whereas in tumors it suppressed T cell responses, antigen presentation, and chemokine signaling. Immune deconvolution showed a shift toward myeloid enrichment and lymphoid suppression, with reduced cytotoxic T and NK signatures. Notably, HDM-driven tumor promotion was abolished in Il17a-/- but not Il1b-/-mice, identifying IL-17A as a critical mediator. These findings demonstrate that chronic aeroallergen exposure reshapes the lung microenvironment to promote immune suppression and accelerate lung cancer progression. HighlightsChronic house dust mite (HDM) exposure accelerates lung tumor growth through non-mutagenic, immune-mediated mechanisms. HDM activates pro-inflammatory and immune programs in normal lung tissue but suppresses antitumor T cell responses in tumors. Multi-omics profiling reveals epigenetic silencing of immune genes and a myeloid-enriched, lymphoid-deficient tumor microenvironment. HDM-driven tumor promotion depends on IL-17A but not IL-1{beta}, establishing IL-17A as a central driver of lung tumor promotion.

cancer biology↗

bioRxiv2025

Peripheral Complement C4 Protein in Schizophrenia: Association with Gene Copy Number and Immune Cell Subtypes

The lack of disease-modifying treatments for schizophrenia necessitates the exploration of novel aspects of its pathophysiology, including innate immune mechanisms in the periphery. C4 protein activation, associated with the complement cascade of innate immunity, associates with symptoms and predicts outcomes. However, C4 protein activation does not coincide with expected changes to other proteins in the complement cascade, suggesting another source of C4 protein activation. Using a combination of fresh whole blood from ten anonymous donors and a large set of publicly available microarray data, we show, for the first time, that C4 protein is found and expressed primarily in neutrophils and monocytes. Then, we compared the correlation between C4 protein in neutrophils, classical monocytes, plasma and the number of C4A gene copies. We determined the number of C4A genes using digital droplet PCR, C4 protein in neutrophils (15 patients/21 controls) and plasma (30 patients/38 controls) using western blotting, and classical monocytes (30 patients/38 controls) using flow cytometry. We found a moderate positive correlation between the number of C4A gene copies and the amount of C4 protein only in neutrophils and only in the schizophrenia group (Spearmans rho, r = 0.64, p = 0.01, Cohens d [~]1.67). Our results indicate a convergence of innate immunity mechanisms associated with schizophrenia. This novel mechanism of innate immunity in schizophrenia deserves further study to determine whether it could be a useful drug target.

immunology↗

bioRxiv2025

A Mammalian Genomic Signature Shaped by Single Nucleotide Variants Controlling Transcriptome Integrity and Diversity

BackgroundMany functional features of mammalian genomic sequences remain poorly defined, especially how sequence motifs and genetic variants within non-coding regions (NCRs) regulate transcriptome integrity and diversity. We have shown that G-tracts unusually positioned between the polypyrimidine tract and 3' AG repress usage of the AG and are enriched at cryptic splice sites in cancer cells but their broader role across the extensive NCRs of mammalian genomes is unknown. ResultsHere, we identify a widely evolved genomic signature, G-tract-AG motifs consisting of guanine tracts closely upstream of AG dinucleotides, which is significantly associated with single-nucleotide variants (SNVs) identified in genome-wide association studies, particularly within NCRs. Approximately 9,000 such G-tracts within human genes are disrupted by variants of the cis-splicing quantitative trait loci in the Genotype-Tissue Expression project. Functionally, G-tracts repress splicing at the adjacent 3' AG, primarily by stalling the second transesterification step. Disruption of G-tracts by SNVs relieves this repression, enabling splicing and generating novel transcript isoforms. These G-tract-disrupting SNVs are in cis across the majority of protein-coding genes and are among thousands of rare variants causing genetic diseases. ConclusionsG-tract-AG signatures are widespread bipartite motifs with dual functions: G-tracts repress AG usage to safeguard transcriptome integrity, while SNV-induced disruption releases AGs for splicing to promote transcriptome diversity. Our findings provide mechanistic insights into the regulation of transcriptome integrity and diversity by a mammalian genomic signature, particularly for NCR SNVs associated with diverse traits and a new framework for their functional annotation.

genetics↗

bioRxiv2025

Robust software development practices improve citations of RNA-seq tools

RNA sequencing (RNA-seq) has emerged as an exemplary technology in biology and clinical applications, offering a crucial complement to other transcriptomic profiling protocols due to its high sensitivity, precision, and accuracy in characterizing transcriptomes. However, the rapid proliferation of RNA-seq tools necessitates the adoption of robust software development practices. Such development underscores the critical need to examine how RNA-seq tools are developed, maintained, and distributed; and whether the data they generate is reproducible as all of these factors are essential for ensuring software reliability, transparency, and trust in scientific findings. We conducted a comprehensive assessment of 434 RNA-seq tools developed between 2008 and 2024, categorizing them based on the type of analysis they perform. Our evaluation encompassed their software development and distribution methodologies, as well as the attributes contributing to their widespread adoption and dependability within the biomedical community, which were quantified by factors such as package manager availability, containerization, multithreading support, documentation quality, and inclusion of example datasets. Our findings establish the first documented positive association between rigorous software development practices and their adoption of published RNA-seq tools as measured by citations (Mann-Whitney U test, p-value = 4.9 x 10-26). By identifying key characteristics of widely adopted software, our findings guide developing robust and user-friendly RNA-seq tools, thereby reinforcing the call for rigorous community-wide standards.

bioinformatics↗

bioRxiv2025

T-cell signaling relies on partial CD45-exclusion at sub-micron sized cellular contacts

How cell contact initiates T-cell activation is uncertain. The local exclusion of the receptor-type protein tyrosine phosphatase CD45 at cell contacts is believed to trigger immune receptor signaling but this is yet to be observed for T cells interacting with authentic cellular targets. Here, quantitative imaging of T cells interacting with tumor cells presenting either native or clinically relevant bi-specific TCR ligands, revealed that they form multiple sub-micron sized close contacts with their targets. The contacts were stabilised by the adhesion protein CD2, but efficient ligand detection required both CD2 and integrin ligation. CD45 was excluded from close contacts at the time of ZAP70 recruitment and signaling, but only partially (30- 40%). A single-cell, mass cytometric analysis showed that this change in kinase/phosphatase activity provoked strong T-cell activation and potent cytotoxicity via very small changes in signaling fluxes. Spatial stochastic simulations suggested that the proximal T-cell signaling network is optimised for efficient antigen discrimination in the setting of partial CD45 exclusion. Our work re-frames early T-cell activation as a process initiated by relatively subtle changes in kinase/phosphatase activity acting on small numbers of signaling effectors at minute cellular contacts.

immunology↗

bioRxiv2025

Lepr Haploinsufficiency Accelerates Alzheimer-like Neurodegeneration via CDK5 Hyperactivation

Leptin signaling has neuroprotective effects and is increasingly linked to Alzheimers disease (AD). Beyond metabolism, leptin modulates {beta}-amyloid metabolism, tau phosphorylation, and synaptic plasticity. While homozygous Lepr mutations are well studied, the impact of heterozygous mutations on neurodegeneration is unclear. To assess partial Lepr loss, one-year-old db/+ mice were evaluated for metabolic, behavioral, and neuropathological changes. Tests included glucose tolerance, memory assays, A{beta}42 and tau levels, CDK5 activity, and transcriptomics. Human LEPR variants were curated and classified using ACMG guidelines. Aged db/+ mice showed metabolic dysfunction, cognitive deficits, and AD-like pathology. Compared to controls, db/+ mice had increased body weight, insulin resistance, memory impairments, elevated A{beta}42, tau hyperphosphorylation, CDK5 hyperactivation, and astrocyte activation. Transcriptomics revealed altered synaptic and mitochondrial pathways. Thirty-three pathogenic or likely pathogenic human LEPR variants were identified. Lepr haploinsufficiency contributes to age-related cognitive decline and AD-like pathology, suggesting it as a genetic risk factor and therapeutic target.

neuroscience↗

bioRxiv2025

Nuclear Fetuin-A Drives Adipocyte Senescence via HIF-1 α During Obesity

Fetuin-A (FetA), a liver derived glycoprotein, has emerged from genome-wide association studies and epidemiological surveillance as a serum biomarker linked to obesity-driven type 2 diabetes mellitus (T2D), primarily due to its contribution to adipose tissue dysfunction. Here, we uncovered an eccentric role of nuclear FetA in visceral white adipocytes of obese T2D conditions. Hypoxia-inducible factor-1 (HIF-1) facilitates the nuclear translocation of FetA via direct interaction, a process that promotes the emergence of a senescence-associated secretory phenotype (SASP). While nuclear co-localization of FetA and HIF-1 strongly promotes adipocyte senescence, silencing FetA alone is sufficient to prevent senescence, even in conditions of HIF-1 overexpression or lipid-rich hypoxic stress. Although nuclear FetA does not directly bind to DNA, it enhances HIF-1 transcriptional activity, potentiating the activation of senescence markers such as {beta}-galactosidase and p53. Selective knockdown of FetA in obese mice notably reduced adipocyte senescence in visceral white adipose tissue (vWAT) and improved fasting glycemic control. Collectively, our findings reveal a previously unrecognized nuclear function for FetA in orchestrating adipocyte senescence in obesity, establishing nuclear FetA as a potential therapeutic target for obesity related metabolic diseases.

cell biology↗

bioRxiv2025

Filomicelle-Embedded Composite Hydrogels for Localized Gelation within the Anterior Chamber of the Eye

Nanocarriers hold transformative potential for treating anterior segment eye diseases, yet corneal epithelium impermeability necessitates intraocular injection. Given the discomfort and infection risk, an injectable hydrogel-based depot offers a promising strategy for sustained nanocarrier delivery in intraocular therapy. However, because the aqueous humor is a large, fluid-filled environment, achieving spatially confined gelation remains a key challenge as injected materials rapidly diffuse. Herein, we present a composite hydrogel (C-gel) that enables localized in situ gelation and sustained nanocarrier release within the anterior chamber. This is achieved using poly(ethylene glycol)-b-poly(propylene sulfide) (PEG-b-PPS) filomicelles (FMs), whose filamentous structure confines crosslinking reactions spatially, promoting efficient gel formation. As a result, 90% of the injected polymer is retained within the crosslinked hydrogel matrix. Embedded FMs then undergo oxidation-induced cylinder-to-sphere transitions, facilitating gradual release of micellar nanocarriers. The rheological properties, gelation timing, and microstructure of the C-gel are adjustable, allowing precise control of nanocarrier release dynamics. In vivo evaluation in mice confirmed excellent biocompatibility without inducing intraocular pressure elevation, ocular toxicity, or immune cell infiltration. Sustained release of nanocarriers was observed for over a month under conditions mimicking that of the anterior chamber of the eye, underscoring the potential of C-gels for long-term drug delivery in anterior segment eye diseases therapy.

bioengineering↗

bioRxiv2025

Plant defense metabolite detoxification by a pathogenic fungus opens necrotic tissue to diverse bacteria in Arabidopsis thaliana

Foliar necrotic fungal pathogens pose a constant threat to plant health. Their virulence can be affected by both the host immune system, as well as diverse host-associated bacteria. Generally, how these factors interact is not well studied, but may provide insights toward sustainable plant protection. Sclerotinia sclerotiorum (Ssc) is a devastating, broad host range necrotrophic pathogen with limited control options. Here, we find that necrotic Ssc lesions strongly enrich diverse bacterial taxa. Arabidopsis thaliana, like other Brassica plants including crops, produce and store large amounts of aliphatic glucosinolates (aGLS). Upon Ssc invasion and tissue damage, myrosinase enzymes transform aGLS into toxic metabolites, including aliphatic isothiocyanates (aITCs). Adapted Ssc strains can detoxify aITCs by hydrolyzing them with the enzyme SaxA, which is important for its virulence. Here, we find that this detoxification is critical for bacterial enrichment in necrotic lesions, since a SaxA-deficient strain does not alter the bacteriome. Additionally, our results suggest that both aliphatic and other GLSs likely contribute specific effects to this phenomenon. Thus, we demonstrate a mechanism in which the interaction of host and pathogen factors together shape a pathogen-associated bacteriome, providing directions to better understand interactions of host bacteria with foliar necrotic pathogens.

microbiology↗

bioRxiv2025

A prognostic signature for lung adenocarcinoma in people who have never smoked

Knowledge of tumor cell dynamics can inform prognosis and treatment yet is largely lacking for lung adenocarcinoma in people who have never smoked (NS-LUAD). With RNA-seq data from 684 NS-LUAD and validation in an independent dataset, we identified three subtypes with distinct phenotypic traits and cell compositions. Additional genomic and histological data further characterized the subtypes. Steady, marked by low proliferation, high alveolar cell fraction, moderate-to-well differentiation, and fewer driver genes alterations, is linked to prolonged survival and low immune evasion. Proliferative shows high proliferation markers, TP53 mutations, and gene fusions. Chaotic, with high epithelial-to-mesenchymal transition markers, has the worst prognosis even within stage I tumors. Lacking known molecular or histological characteristics, this aggressive subtype is solely identified by transcriptomic data. A 60-gene signature recapitulates the overall classification and strongly predicts survival even within subgroups based on tumor stage or known genomic features, emphasizing its potential for improving NS-LUAD prognostication in clinical settings. SignificanceThe transcriptome of 684 lung adenocarcinomas in people who have never smoked (NS-LUAD) identifies three subtypes with different cellular dynamics, and genomic and morphologic features. A 60-gene signature accurately stratifies subjects for mortality risk, even in stage I, offering a clinically applicable tool for treatment decision making in NS-LUAD patients.

genomics↗

bioRxiv2025

Dilated cardiomyopathy remodels cardiac neuronal subtypes in a murine model

The autonomic nervous system is comprised of two parallel chains sympathetic and parasympathetic nervous system that innervates myocardium heterogeneously. However, excessive sympathetic signalling is a hallmark of cardiac dysfunction including myocardial infarction and cardiomyopathies. In current research article, first, we carried out echocardiography on DCM-Tg9 mice to characterize cardiac output parameters and performed scRNAseq analysis in a dilated cardiomyopathy mouse model of heart-failure over wildtype control mice. We analysed differential gene expressions and performed pathway enrichment analysis. The important findings of our research indicate the increment within a specific neuronal subpopulation (NA1b) out of three adrenergic cardiac innervating neuronal subpopulation. We also observed significant increase in M-current potassium ion channel (Kcnq2 ion channel) and genes involved in pathways from oxidative phosphorylation and neurodegeneration pathways. These observations have clearly interpreted that significantly elevated expression of M-current ion channels might be involved with hyperactivated sympathetic signalling in heart-failure mice. HighlightsO_LIWe identified three adrenergic neuronal subtypes that innervate myocardium and one of these neuronal subtypes, NA1b, predominantly presents during the heart-failure. C_LIO_LIOur results indicated presence of m-current ion channels (Kcnq2) significantly elevated during heart failure in a murine dilated cardiomyopathy model. C_LIO_LIThe pathway enrichment analyses showed increased expression of genes that are involved in neurodegenerative and oxidative pathways. C_LI

neuroscience↗

bioRxiv2025

Metabolic regulation of copper homeostasis governs the Sec61-dependent protein translocation process in Saccharomyces cerevisiae

Concentration of cellular labile pool of copper must be strictly regulated because disruption in copper homeostasis results in diseases. In Saccharomyces cerevisiae, elevated levels of labile copper impair cell viability by inhibiting Sec61-mediated protein translocation into the endoplasmic reticulum. We investigated how metabolic pathways, specifically mitochondrial respiration and autophagy, contribute to copper homeostasis and the translocation of secretory proteins. We show that copper selectively inhibits protein translocation in yeast cells grown in minimal medium but not in rich medium, highlighting a critical role of nutrients in modulating copper toxicity. Supplementation of specific amino acids suppresses the copper-induced defects in protein translocation and cell death, identifying amino acids suppressors of the copper toxicity. Using a panel of gene deletion mutants affecting mitochondrial functions, autophagy, peroxisomes, and lipid droplets, we demonstrate that metabolic pathways regulate sub-cellular distribution of copper and translocation of secretory proteins. Further, disruption of redox and pH homeostasis, and pharmacological inhibition of respiration, reveals that correct subcellular trafficking of copper is essential to prevent inhibitory effects on protein translocation process. Together, our findings provide mechanistic insights into how metabolic status influences cellular copper homeostasis and the secretory pathway of proteins, with broader implications for understanding diseases of copper metabolism.

cell biology↗

bioRxiv2025

Design of Orthogonal Far-Red, Orange and Green Fluorophore-binding Proteins for Multiplex Imaging

Fluorescent proteins and small molecule dyes have complementary strengths for biological imaging: the former are genetically manipulatable enabling tagging of specific proteins and detection of protein interactions, while the latter have greater photostability and brightness but are difficult to target. To combine these strengths, we used de novo protein design to generate binders to three bright, stable, cell-permeable dyes spanning the visible spectrum: JF657 (far red), JF596 (orange-red) and JF494 (green). For each dye, we obtain nanomolar binders with weak or no binding to the other two dyes; the accuracy of the design approach is confirmed by a crystal structure of one binder which is very close to the design model. Fusion of the JF567, JF596 and JF494 binders to three different targets followed by staining with the three dyes simultaneously enables multiplex imaging. We further expand functionality by incorporating an active site carrying out nucleophilic aromatic substitution to form a covalent linkage with the dye, and developing split versions which reconstitute fluorescence at subcellular locations where both halves are present, enabling both protein-protein interaction detection and chemically induced dimerization with fluorescence reporting. Our designs combine the advantages of fluorescent proteins and small molecule dyes and should be broadly useful for cellular imaging.

biochemistry↗

bioRxiv2025

AXL tyrosine kinase inhibition rescues immune checkpoint blockade-resistant melanoma in a tumor microenvironment-dependent fashion

BackgroundImmune checkpoint blockade (ICB) achieves durable responses in approximately half of patients with advanced melanoma, but the mechanistic basis for resistance in the remaining patients remains incompletely defined. AXL tyrosine kinase has emerged as a candidate resistance mediator, yet clinical development of AXL inhibitors has yielded heterogeneous results in unselected patient populations, suggesting that cell-type and tumor microenvironment context may critically govern therapeutic response. MethodsWe characterized AXL expression across cell types in ICB-resistant melanoma using publicly available single-cell RNA sequencing datasets and The Cancer Genome Atlas (TCGA). In vivo efficacy was assessed in the YUMM1.7 PD-1-resistant syngeneic melanoma model using three pharmacologically distinct AXL inhibitors (warfarin, bemcentinib, and cabozantinib) as monotherapy and in combination with anti-PD-1 therapy. Tumor-associated macrophage (TAM) context-dependency was established using anti-CSF1R and anti-F4/80 depletion strategies. Functional PD-L1:PD-1 checkpoint interactions were quantified in tumor sections by immune Forster Resonance Energy Transfer (iFRET). TAM secretome reprogramming was characterized by 40-plex Luminex immunoassay in polarized RAW264.7 macrophages. ResultsAXL expression in ICB-resistant melanoma was predominantly localized to TAMs rather than tumor cells by single-cell analysis, with AXL+ TAMs distributed across both M1-like and M2-like phenotypic compartments. AXL inhibition significantly reduced tumor burden and synergized with anti-PD-1 therapy in vivo; however, efficacy was abolished by depletion of the monocyte-derived myeloid compartment (anti-CSF1R) and enhanced by depletion of tissue-resident TAMs (anti-F4/80), establishing TAM-context dependency. iFRET revealed a paradoxical gain of PD-L1:PD-1 interaction efficiency in anti-PD-1-treated resistant tumors, a functional resistance signature detectable by iFRET but not by PD-L1 expression that was reversed by AXL combination therapy. In vitro secretome profiling demonstrated that combination therapy reprograms macrophage secretome in a polarization-context-dependent manner, amplifying pro-inflammatory cytokines including IL-6 and GM-CSF in M2-like macrophages while selectively dampening T cell chemokine production. ConclusionsThese findings establish AXL as a TAM-resident immune target in ICB-resistant melanoma whose therapeutic relevance is governed by tumor-immune micronenvironment (TiME) macrophage composition rather than tumor cell AXL expression. TAM polarization contexture represents a candidate stratification axis for AXL inhibitor-based combination strategies, and iFRET-measured checkpoint interaction offers a functional complement to PD-L1 expression for monitoring resistance and response. Key MessagesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIAXL tyrosine kinase has been studied predominantly as a tumor-intrinsic mesenchymal marker and therapeutic target in melanoma, with prior clinical development of AXL inhibitors predicated on tumor cell AXL expression as the primary biomarker; the contribution of TAM-expressed AXL to ICB resistance and the dependence of therapeutic response on TiME composition have not been defined. C_LI What this study addsO_LIAXL expression in ICB-resistant melanoma is predominantly localized to tumor-associated macrophages distributed across both M1-like and M2-like phenotypic compartments, reframing AXL as a TAM immune target whose therapeutic relevance is governed by TiME macrophage composition rather than tumor cell AXL expression. C_LIO_LICombination AXL inhibition and anti-PD-1 reprograms the macrophage secretome in a polarization-context-dependent manner and reverses a paradoxical gain of functional PD-L1:PD-1 checkpoint interaction in resistant tumors -- a resistance signature detectable by spatial iFRET but not by PD-L1 expression. C_LI How this study might affect research, practice or policyO_LIThe context-dependent effects of AXL inhibition (immunostimulatory in M2-heavy TiMEs, potentially counterproductive in M1-heavy TiMEs) indicate that TAM polarization profiling should be incorporated into clinical trial design for AXL inhibitor-based combinations, and that unselected enrollment may obscure meaningful efficacy signals in the subset most likely to benefit. C_LIO_LIiFRET-based quantification of functional checkpoint interaction represents a candidate dynamic biomarker for ICB resistance monitoring that is orthogonal to PD-L1 immunohistochemistry and may identify resistant patients who retain immunosuppressive checkpoint interactions that can be disrupted by AXL targeting. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/667666v2_ufig1.gif" ALT="Figure 1"> View larger version (90K): org.highwire.dtl.DTLVardef@521de1org.highwire.dtl.DTLVardef@127a933org.highwire.dtl.DTLVardef@d56132org.highwire.dtl.DTLVardef@e03ef9_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Early-Life Poultry-Derived Lactobacilli Drive Microbial Succession and Gut Immune Modulation in Broiler Chickens

Probiotic supplementation supports poultry gut health by modulating microbiome and promoting immune development, yet limited information is known about the effects of early, particularly embryonic, supplementation. In this study, we investigated the effects of administering a lactobacilli cocktail in ovo (embryonic day 18), post-hatch, or both on gut immunity and the succession of the cecal microbiota in broilers over five weeks. 16S rRNA gene-based sequencing of cecal contents revealed a steady increase in Shannon diversity during the first three weeks (PERMANOVA, p < 0.005), with community structure stabilizing by week 3 across all groups. In ovo lactobacilli administration improved early hatch rates and modulated microbial composition during early succession, including reductions in Klebsiella and Enterococcus, and enrichment of Lactobacillus, during the first two weeks (MaAsLin2, q < 0.25). These microbiome shifts were accompanied by a reduced expression of pro-inflammatory cytokines (IFN-{gamma}, IL-1{beta}, and IL-8) in cecal tonsils. These findings highlight the transient yet critical role of early-life probiotic interventions in shaping gut microbial colonization and immune response in broiler chickens. More importantly, a single in ovo lactobacilli dose yielded effects comparable to weekly oral or combined administration.

microbiology↗

bioRxiv2025

Morphometric Interpretation of Postganglionic Sympathetic Neurons that Innervate Myocardium

Background and AimsThe sympathetic nervous system modulates cardiac functions through neurotransmitters such as neuropeptide-Y and galanin released by postganglionic neurons. Hence, we hypothesize that dendritic and axonal morphological architecture of cardiac-innervating neurons might reflect the communicating input and output signals either within the postsynaptic neurons or to the adjacent myocardial cells. MethodsIn the current study, we carried-out morphometric analyses of cardiac-innervating neurons, measuring dendritic size, shape, and neuronal-polarity. We used retrograde tracers (adeno-associated virus conjugate to fluorophores) injected either from left-ventricular myocardial tissue or fore-limb skin tissue-beds. Stellate ganglia were harvested from the mice for imaging and morphometric analysis. ResultsOur findings revealed that cardiac-projecting neurons exhibit a multipolar structure and are significantly larger in cross-sectional area and volume compared to forelimb skinpad-innervating neurons. InterpretationThese morphological characteristics may offer valuable insights into the neural architecture underlying cardiac remodelling, although further investigation is needed. This study focuses solely on the structural, not functional, features of cardiac-innervating neurons to better understand their specialization within the autonomic nervous system.

neuroscience↗

bioRxiv2025

XAI-based Data Visualization in Multimodal Medical Data

Explainable Artificial Intelligence (XAI) is crucial in healthcare as it helps make intricate machine learning models understandable and clear, especially when working with diverse medical data, enhancing trust, improving diagnostic accuracy, and facilitating better patient outcomes. This paper thoroughly examines the most advanced XAI techniques used in multimodal medical datasets. These strategies include perturbation-based methods, concept-based explanations, and example-based explanations. The value of perturbation-based approaches such as LIME and SHAP in explaining model predictions in medical diagnostics is explored. The paper discusses using concept-based explanations to connect machine learning results with concepts humans can understand. This helps to improve the interpretability of models that handle different types of data, including electronic health records (EHRs), behavioural, omics, sensors, and imaging data. Example-based strategies, such as prototypes and counterfactual explanations, are emphasised for offering intuitive and accessible explanations for healthcare judgments. The paper also explores the difficulties encountered in this field, which include managing data with high dimensions, balancing the tradeoff between accuracy and interpretability, and dealing with limited data by generating synthetic data. Recommendations in future studies focus on improving the practicality and dependability of XAI in clinical settings.

bioengineering↗