Biology subjects

Kumar, V.

Publications and source records attributed to Kumar, V..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Morphomolecular Longitudinal Endoscopy of Carcinogenesis

Current diagnostic approaches for head and neck cancer rely primarily on white-light endoscopy and tissue biopsy, providing only static, episodic assessments that fail to capture dynamic changes in tumour biology over time. This absence of continuous, detailed molecular and microscopic structural information makes early identification of dysplasia or cancer difficult and can delay critical treatment. Here, we introduce a unified, label-free endoscopic platform that combines Raman spectroscopy (RS) and optical coherence tomography (OCT) within a miniaturised, forward-viewing fibre-optic probe. This integration enables simultaneous video-rate OCT imaging and subsecond RS acquisition linking morphological and molecular tissue trajectories in vivo. We developed an explainable AI-based fusion framework that learns joint temporal representations of biochemical and structural features to classify tissue states while highlighting the most influential predictors. In a longitudinal 4NQO-induced murine model of carcinogenesis, the system tracked epithelial transformation in real-time from hyperplasia through dysplasia to neoplasia. By capturing temporally resolved morphomolecular trajectories in vivo, this platform establishes a new paradigm for early cancer detection and real-time surveillance, supporting timely and individualised clinical decision-making.

bioengineering↗

bioRxiv2025

Stress-dependent growth of breast cancer models emerges from a cellular volume checkpoint

Mechanoresponsive cell proliferation is a feature of growing tumours, despite the suppression of many other regulatory checkpoints in cancer, but the underlying cell-scale mechanisms driving this behaviour have not yet been established. In this study we propose a biophysical model for cell growth as governed by actively controlled osmolarity, which we integrate with a discrete particle framework to simulate growth and remodelling of breast cancer spheroids. Confinement and biomechanical feedback from the extracellular environment are analysed through a neuralnetwork-accelerated finite element solver. Combining the framework with experiments, our model reveals that stress-dependent spheroid growth can arise from a sizing checkpoint for mitosis. Under sufficient extracellular loading, cell growth is restricted by high hydrostatic forces in competition with osmotic pressure from biomolecule synthesis, which prevents cells from surpassing a critical volume. Our model provides new insight into mechanosensitive growth arrest in breast cancer, potentially serving as a computational tool for analysing growth in a wider range of normal and malignant biological tissues.

cancer biology↗

bioRxiv2025

Pulsed-electron illumination does not reduce beam damage for imaging biological macromolecules

Radiation damage remains a fundamental limitation in cryo-electron microscopy (cryo-EM), constraining the total electron dose that can be used and thus limiting high-resolution imaging of biological specimens. Recent studies have proposed that temporally structured or pulsed electron beams could reduce radiation damage by allowing time for energy dissipation between individual electron interactions. To evaluate this hypothesis, we conducted a systematic investigation using a radiofrequency (RF) driven 300 kV Titan Krios microscope equipped with cold field emission gun (c-FEG) to generate highly regular pulsed electron beams for specimens under cryogenic conditions. We compared radiation damage in three representative samples: paraffin 2D crystals, bacteriorhodopsin (purple membrane) 2D crystals, and plunge-frozen tobacco mosaic virus (TMV) in vitreous ice, under both pulsed and conventional (= random) illumination, while keeping all other imaging conditions constant. Radiation damage was quantified by tracking the decay of computed diffraction intensities to determine the critical dose (Ne). We observed no statistically significant difference in critical dose between pulsed and random illumination across all 3 samples. Our findings provide a critical reference point for future development and evaluation of temporally modulated electron sources in cryo-EM instrumentation.

molecular biology↗

bioRxiv2025

A 3D in vitro model of the human hepatobiliary junction

Cholestasis, or disruption in bile flow, is a common yet poorly understood feature of many liver diseases and injuries. Despite this, many engineered human tissue models of liver disease fail to recapitulate physiological bile flow. Here, we present a 3D multicellular spheroid-based model of the human hepatobiliary junction, the interface between hepatocytes and cholangiocytes often disrupted in liver disease that is required for directing bile excreted by hepatocytes into the biliary ductal system. Building on advances in organoid and spheroid engineering, we co-aggregate human hepatocytes and intrahepatic cholangiocytes into adult hepatobiliary organoids (aHBOs) that structurally connect and functionally transport bile. aHBOs directionally transport bile from hepatocyte bile canaliculi to cholangiocyte-lined ductules, which we visualize through a high-throughput imaging assay. Hepatobiliary junction formation and bile flow dynamics are quantified over time using fluorescent bile acid analogs and AI-assisted image analysis. When subjected to hypoxia-reoxygenation, aHBOs recapitulate features of biliary dysfunction that mimics the cholestasis and ischemia-reperfusion injury that complicates liver transplant. Our findings suggest that 1) a reversible reduction in hepatocyte canalicular function under hypoxia, followed by 2) selective cholangiocyte death upon reoxygenation, are processes that potentially contribute to biliary dysfunction upon ischemic injury. This human-derived, scalable platform provides a phenotypically-relevant in vitro model for dissecting biliary pathophysiology and lays the groundwork for a therapeutic discovery platform for post-transplant ischemic cholangiopathy and other cholestatic liver diseases.

bioengineering↗

bioRxiv2025

Scar-associated endothelial-stellate cellular crosstalk drives fibrosis resolution in MASH

Fibrosis, or scarring, can affect many organs including liver, lung, heart, kidney, intestines etc. and is responsible for [~]40% of mortality in the industrialized world. Compared to other organs, fibrosis in the liver typically resolves when the source of injury is extinguished. Elucidating the molecular mechanisms that underlie spontaneous fibrosis resolution in the liver may lead to novel antifibrotic strategies for all organs. In this study we established a robust mouse model of fibrosis regression in MASH (Metabolic dysfunction-Associated Steatohepatitis), a highly prevalent chronic liver diseases worldwide, and performed single cell and in situ molecular profiling of the liver to define novel drivers of fibrosis regression. As fibrosis regressed, we detected a reduction of inflammatory cells and an expansion of endothelial cells. Prediction of cell-cell communication using the Calligraphy pipeline identified a Wnt9b-Sfrp2 crosstalk that emerges as fibrosis resolved in our model. To establish the Wnt9b-Sfrp2 crosstalk as a driver of fibrosis resolution we treated mice with recombinant Sfrp2, which slowed spontaneous fibrosis regression compared to vehicle treated mice. From our single cell datasets we identified a subset of endothelial cells, termed "Endo4", as the source of Wnt9b. Immunostaining of the Endo4 marker VWF using tissue clearing and 3D imaging revealed VWF+ vasculature enveloped by activated hepatic stellate cells (HSCs) that penetrated deep into the fibrotic septa, establishing Endo4 as de facto scar-associated endothelial cells and providing a structural basis of their cellular crosstalk with HSCs. Finally, using a recently developed in situ protease activity screen, prominent serine protease activity co-localized with both scar-associated Endo4 cells and HSCs. In summary, we uncovered an WNT-dependent endo-stellate crosstalk within the fibrotic niche as a novel regulatory node underlying murine MASH fibrosis regression, and a promising therapeutic target.

molecular biology↗

bioRxiv2025

Comparative regulomics provides novel insight into the evolution of wood formation across dicot and conifer trees

Understanding the regulatory program underlying wood formation is key to improving biomass production and carbon sequestration in trees. However, how wood formation evolved and how these programs have been rewired across lineages remains unclear. Here, we present the first high-spatial-resolution evo-devo resource spanning the wood transcriptomes of six tree species - three dicots and three conifers - capturing 250 million years of evolutionary divergence. Using orthology-aware co-expression network analysis, we identified genes with conserved and lineage-specific expression patterns. By integrating chromatin accessibility data and transcription factor motif analysis, we further inferred regulatory networks for xylem differentiation and secondary cell wall formation. We demonstrate how this dataset can be used to answer long standing questions in wood biology related to differences in acetylation of cell wall polymers and master regulators of xylem specification across dicot and conifer tree species. The data offer a foundational resource for the tree biology and evo-devo communities, and are publicly available at PlantGenIE.org.

genomics↗

bioRxiv2025

Neurobiological and Chemical Characterization of the Cyanobacterial Metabolite Veraguamide E

Ver Es structure was validated by {superscript 1}H NMR, HRMS, and molecular networking analyses. Computational docking and NMR titration confirmed direct, saturable, and tight binding of Ver E to the human Sigma-2 receptor/transmembrane protein 97 ({sigma}2R/TMEM97). Functional calcium imaging in primary mouse sensory neurons revealed that Ver E increases intracellular Ca{superscript 2} levels without modulating store-operated calcium entry (SOCE). Multi-well microelectrode array experiments using human induced pluripotent stem cell (hiPSC) derived nociceptors showed that Ver E significantly reduced neuronal activity at physiological temperatures, but not under heat-stress conditions. Ver E exhibited no cytotoxicity at concentrations up to 30 {micro}M in HEK293 cells, and immunocytochemistry confirmed that it does not alter phosphorylated eIF2 (p-eIF2) expression, indicating a mechanism distinct from integrated stress response modulators. Collectively, these findings position Ver E as a non-toxic compound capable of selectively modulating neuronal excitability, thereby advancing the development of novel therapeutics for pain management. SignificanceNatural products have long been recognized as a rich source of therapeutics, accounting for over 60% of currently approved small-molecule drugs and underscoring their pivotal role in drug discovery. Marine cyanobacteria produce structurally diverse secondary metabolites with a wide array of biological activities. Among these are the veraguamides, a family of depsipeptides that have shown promise as future therapeutics in our recent studies. This work presents a detailed biological and chemical characterization of veraguamide E (Ver E), isolated from a Panamanian marine cyanobacterial collection. The {sigma}2R/TMEM97 system has been identified as a promising target to address unmet need for non-opioid therapeutics which can modulate neuronal excitability in the context of chronic pain. Discovery and identification of novel compounds which modulate this system can help us better understand its function as well as allow us to develop future therapeutics targeting this pathway. HighlightsO_LIVeraguamide E specifically binds {sigma}2R/TMEM97 receptor with high affinity. C_LIO_LIComputational docking and NMR confirm a distinct binding mechanism. C_LIO_LIVer E modulates calcium signaling in mouse DRG neurons and human iPSC-derived nociceptors. C_LIO_LIVer E demonstrates no detectable cytotoxicity in human cell lines. C_LI

neuroscience↗

bioRxiv2025

Cytokine-induced memory-like responses in endothelial cells link chronic inflammation to vascular disease risk

Chronic inflammation plays a central role in the progression of both infectious and vascular diseases, yet its impact on endothelial cells (ECs), which form the interface between blood and tissue, remains poorly understood. Given their constant exposure to inflammatory cytokines such as TNF- and IFN-{gamma}, we set out to investigate how cytokine induced inflammation shapes EC function at the molecular level. Using primary human umbilical vein endothelial cells (HUVECs), we modeled repeated cytokine exposure to simulate a chronically inflamed microenvironment. Transcriptomic and epigenetic profiling revealed that ECs respond to this chronic stimulation with durable transcriptional and chromatin changes. These responses included phenotypes resembling immune cell priming, training, and tolerance, which are commonly associated with innate immune memory, a phenomenon whereby innate immune cells mount altered response following previous stimulation. Although we did not observe classical trained immunity pathways, several genes known to mediate immune training, including TLR2, IL1B, and HDAC9, exhibited persistent activation following TNF- re-exposure. IFN-{gamma} stimulation uniquely induced sustained expression and chromatin accessibility at MHC class II loci, suggesting cytokine-specific modes of reprogramming. Functionally, re-stimulated ECs exhibited enhanced monocyte adhesion in a 3D vessel-on-chip model, highlighting the relevance of these molecular changes to vascular inflammation. Moreover, the regulatory regions altered by cytokine exposure were enriched for disease-associated SNPs, particularly those linked to COVID-19, sepsis, and cardiovascular disorders. In summary, these findings reveal that repeated exposure to cytokines as seen in chronic inflammation can induce memory-like responses in ECs and suggest that endothelial reprogramming may contribute to vascular dysfunction.

molecular biology↗

bioRxiv2025

An iPSC-based iMSC Model for Osteogenesis Imperfecta: A Platform for Disease Modeling and Drug Screening

IntroductionOsteogenesis Imperfecta (OI) is a rare genetic disorder of connective tissue, primarily caused by mutations in the COL1A1 or COL1A2 genes. Research is hampered by the limitations of primary patient-derived cells, which are obtained through invasive methods and have finite proliferative capacity and high variability. While induced pluripotent stem cell (iPSC) models exist, direct differentiation to osteoblasts is often inefficient and may not fully replicate disease characteristics. Our study aimed to develop and characterize a robust iPSC-derived mesenchymal stem cell (iMSC) model of OI using a simple two-step differentiation protocol to serve as a platform for disease modeling and drug screening. MethodsBone marrow MSCs (BMMSCs) were isolated from two OI patients with heterozygous missense mutations, in COL1A1 (c.2299G >A) and COL1A2 (c.982G>A). The patient BMMSCs were reprogrammed into iPSCs using an integration-free Sendai virus. The resulting OI-iPSCs were characterized for pluripotency via immunofluorescence and RT-PCR, trilineage differentiation potential, and karyotype analysis. A two-step protocol was used to differentiate the OI-iPSCs into OI-iMSCs via mesodermal lineage. The OI-iMSCs were then characterized for morphology, immunophenotype by flow cytometry, and trilineage differentiation capacity. Functional osteogenic differentiation was assessed by Alizarin Red S staining and RT-PCR analysis of key osteogenic genes. Sanger sequencing confirmed the retention of patient-specific mutations in the OI-iMSCs. ResultsPatient-derived BMMSCs were successfully differentiated into adipocytes and chondrocytes but showed impaired osteogenic potential. The reprogramming process successfully generated stable OI-iPSC lines that expressed key pluripotency markers, demonstrated trilineage potential, and maintained a normal karyotype. Critically, while direct osteogenic differentiation of these iPSCs failed to recapitulate the primary cell phenotype, the two-step differentiation protocol successfully produced a homogeneous population of iMSCs. These OI-iMSCs displayed characteristics of MSC surface markers (CD73+, CD90+, CD105+) and recapitulated the disease phenotype seen in the original patient BMMSCs. Specifically, COL1A1-iMSCs exhibited cellular rolling and detachment, while COL1A2-iMSCs showed poor mineralization during osteogenic differentiation. Both OI-iMSC lines showed significantly decreased calcium deposition and downregulation of key osteogenic genes (RUNX2, ALP, COL1) compared to controls. ConclusionOur study successfully established an iMSC-based cellular model of OI that recapitulates patient-specific disease phenotypes, including impaired osteogenic differentiation. The two-stage differentiation of iPSCs to iMSCs proved more reliable than direct osteogenic differentiation for modeling the disease. iMSC model circumvents the limitations of primary cells by providing a scalable and homogeneous source of patient-specific cells. Our platform offers a valuable and robust tool for investigating OI pathophysiology and for high-throughput screening of potential therapeutic molecules, advancing efforts toward personalized therapies

genetics↗

bioRxiv2025

A systemic clock brake: Period1 stabilizes the circadian network under environmental stress

Precise alignment between internal circadian clocks and environmental light cycles is essential for physiological homeostasis and survival. However, the molecular mechanisms that preserve this synchrony across central and peripheral tissues remain poorly defined. Here, we uncover an unexpected role for the core clock gene Period1 (Per1) as a systemic modulator of circadian stability, regulating light-induced re-entrainment across the brain and body. In Per1-deficient mice, we show that loss of Per1 accelerates clock realignment, influencing transcriptomic, metabolic, hormonal, and behavioral indicators of circadian realignment across multiple organ systems, including the suprachiasmatic nucleus (SCN) and peripheral tissues such as the liver, adipose tissue, and adrenal glands. Notably, this accelerated adaptation confers protection against jetlag-induced sleep disturbances, weight gain, and metabolic imbalance, underscoring a systemic role for Per1 in maintaining circadian network stability. Mechanistically, unbiased spatial transcriptomics identified reduced expression of the arginine vasopressin (AVP), a key neuropeptide mediating SCN intercellular coupling, as the driver of circadian network instability. Weakened SCN synchrony permits enhanced flexibility of peripheral oscillator responses, expediting whole-body adaptation to shifted light-dark schedules. These findings position Per1 as a critical regulator of circadian robustness, a buffer against light over-responsiveness, identifying a potential molecular target for mitigating circadian misalignment in contexts such as jetlag, shift work, and metabolic disease. TeaserWhat if beating jetlag was as simple as switching off a gene? Researchers show that disabling Per1, a core circadian regulator, accelerates body clock realignment and protects against sleep and metabolic disruption--highlighting new therapeutic possibilities for jetlag and shift work.

neuroscience↗

bioRxiv2025

Developmental coordination of mitochondrial dynamics and membrane remodeling drives organelle morphogenesis

How complex organelles remodel their architecture during development remains a fundamental question in cell biology. Using the Drosophila nebenkern, a giant multilamellar mitochondrion that transforms into two elongated mitochondrial derivatives during spermiogenesis, we dissect the challenges underlying large organelle morphogenesis. We show that this transformation is achieved through coordinated control of fusogenicity, membrane geometry, and membrane redistribution. PINK1/Parkin-dependent downregulation of the mitofusin Marf reduces mitochondrial fusogenicity and stabilizes organelle separation following division. Concurrently, membrane tubulation establishes a geometric template for DRP1 recruitment, specifying a deterministic fission plane within a large mitochondrial sheet structure. Mitochondrial elongation is accompanied by the formation of mitochondria-derived inverted vesicles (MDiVs), previously undescribed double-membraned structures that may redistribute membrane through inward budding independently of canonical fission and fusion. More broadly, our work establishes a framework for understanding how membrane geometry, regulated fusogenicity, and vesicle-mediated remodeling cooperate to generate complex organelle architectures during development. Significance statementLarge organelles pose unique challenges for scaling and division because canonical membrane dynamics must be coordinated across extensive membrane architectures. Using a giant multilamellar mitochondrial structure as a model, we show that organelle morphogenesis is achieved through independent yet coordinately regulated mechanisms that spatially pattern division, stabilize partitioning, and redistribute membranes through intraorganellar vesicles with an inverted topology. These findings reveal principles of organelle morphogenesis that extend beyond conventional fission-fusion models.

developmental biology↗

bioRxiv2025

Galectin-3 C-epitope, ANP, PPIA, and albumin function as drug-responsive panel biomarkers and therapeutic targets in aging and pressure overload-induced cardiac hypertrophy

Biological aging (BA) and pressure overload-induced cardiac hypertrophy (PO-CH) are marked by myocardial thickening, fibrosis, and functional decline, culminating in an increased risk of heart failure. Effective clinical management requires biomarkers that not only track disease progression but also monitor therapeutic response. Using Amalaki Rasayana (AR), a cardioprotective nutraceutical-based medicine, in rat models of BA and PO-CH, we identified a panel of serum biomarkers whose treatment-induced decline was associated with disease regression. Among them, galectin-3 emerged in both full-length and oligomeric C-epitope cleaved forms, with the latter closely linked to pathological surface remodeling. Treatment with AR and its bioactive component gallic acid (GA) suppressed extracellular galectin-3 C-epitope oligomer accumulation by inhibiting full-length galectin-3 secretion through phosphorylation-dependent mechanisms and promotion of intracellular retention. Concurrently, serum levels of atrial natriuretic peptide (ANP), cyclophilin A (PPIA), and albumin (ALB) were consistently modulated by therapy. Validation in sera from elderly individuals and cardiac hypertrophy patients responding to conventional treatments supported the translational relevance of this biomarker panel. These findings establish a novel, mechanistically grounded biomarker set--galectin-3 C-epitope, ANP, PPIA, and ALB--for monitoring therapeutic response in cardiac hypertrophy, and position AR as a promising medicinal intervention against age- and pressure-induced cardiac pathology. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/657024v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@2498d8org.highwire.dtl.DTLVardef@aeb4fcorg.highwire.dtl.DTLVardef@1ec2f9eorg.highwire.dtl.DTLVardef@12a4392_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIGalectin-3 C-epitope, ANP, PPIA, and ALB are elevated in aging and pressure overload driven left ventricular hypertrophy. C_LIO_LIAmalaki rasayana (AR) and Gallic Acid (GA) reduce these markers in cardiac tissue and circulation. C_LIO_LIAR and GA inhibit galectin-3 secretion and oligomeric binding to cardiomyocyte surfaces. C_LIO_LIAR and GA regulation predominantly occurs via phosphorylation-dependent cytoplasmic retention of galectin-3. C_LIO_LIThese markers serve as potential therapeutic targets and diagnostic biomarkers. C_LI

pathology↗

bioRxiv2025

High throuput label free rapid screening to identify cell penetrating peptide

Fluorophore-peptide tagging is a widely used method for tracking peptide. However, this approach is slow and costly, which hinders the design and screening of native cell penetrating peptide. The extrinsic fluorophore ANS (1-anilino-8-naphthalene sulfonate) can monitor change in membranes hydrophobicity during the internalization of cationic peptide. This property makes ANS a potentially attractive low cost tool for high throughput rapid screening of native peptides with cellular penetration property.

biochemistry↗

bioRxiv2025

difFUBAR: Scalable Bayesian comparison of adaptive evolution

While many phylogenetic methods exist to characterize evolutionary pressure at individual codon sites, relatively few allow direct comparison between different a priori selected sets of branches. Such comparisons may be useful for pinpointing precisely the codon sites that are under differing selective pressures due to differing environmental contexts, or differing genomic contexts via epistatic interactions. Indeed, this was only recently addressed by an approach, developed in the frequentist framework, that proposes a site-wise likelihood ratio hypothesis test. Previously, we have demonstrated that approximate grid-based Bayesian approaches to characterizing site-wise variation in selection parameters can outperform individual site-wise likelihood ratio tests. Such grid-based approaches can exhibit poor computational scaling when the number of site-wise parameters expands, but here we show that this is still tractable up to four parameters, and that a simple subtree-likelihood caching strategy can provide efficiency improvements in some cases. We propose difFUBAR, which allows the demarcation of two branch sets of interest and, optionally, a background set, and estimates joint site-specific posterior distributions over , {omega}1,{omega} 2, and{omega} BG using a Gibbs sampler. Evidence for hypotheses of interest can then be quantified directly from the posterior distribution, and we standardly report P ({omega}1 > {omega}2), P ({omega}2 > {omega}1), P ({omega}1 > 1), and P ({omega}2 > 1). We characterize the computational and statistical performance of this approach on previous simulations, comparing it to the site-wise likelihood ratio test approach, where it shows moderate statistical benefits, and substantial computational gains, typically being more than two orders of magnitude faster on the same datasets. We also demonstrate that it can scale to datasets of over ten thousand taxa, on a laptop in under ten minutes. difFUBAR is implemented in MolecularEvolution.jl - a Julia framework for phylogenetic model development - and can be run locally, or online via a Colab notebook.

bioinformatics↗

bioRxiv2025

Plasmodium Repetome: A mysterious space with a wealth of information

Eukaryotic proteomes harbour repetitive stretches of amino acids that may play critical roles in the biology of that organism. While several tandem repeats (TR) are known to contribute to protein structure and function, information about the vast majority of repeat regions remains obscure. In this article, we have analysed the repeat content of different Plasmodium species and found the leading human malaria-causing P. falciparum (Pf) and P. vivax to be exceptionally rich in TR regions (>40% TR containing proteins). Detailed analysis of Pf repetome showed this intracellular parasite to carry longer TRs, several of which were present in exported proteins important for parasite survival and immune evasion. The repeat regions of Pf were enriched in acidic amino acids and asparagine (Asn), where Asn was more abundant in short and intermediate TRs, suggesting an evolutionary bias influenced by replication slippage and positive selection. Gene ontology analysis of TR containing Pf proteins helped us to understand their cellular localization along with the molecular and biological processes they are involved in. The Pf variable surface antigen families with roles in important pathogenic processes like cytoadherence, immune evasion etc. had low repeat content present within seroreactive peptides. Three-dimensional structure predictions of TR regions revealed several repeats to adopt ordered super-secondary conformations that are known to facilitate intermolecular interactions. Overall, this is a comprehensive study attempting to gain insights on the importance of TRs in malaria parasite biology and suggests a novel route to understanding protein function through the characterization of repeat content.

bioinformatics↗

bioRxiv2025

SlHSFB3a developmentally regulates lateral root formation by modulating auxin signaling in tomato.

O_LIThe function of HSFs, known otherwise as master thermoregulators, in plant developmental remains largely uninvestigated. C_LIO_LIIn this study, we strategically analyze SlHSFB3a, a class B sub member of HSF transcription factor family, uniquely expresses in age-dependent tomato roots and improves root architecture by synchronizing auxin homeostasis. C_LIO_LIThis data demonstrates SlHSFB3a overexpressed transgenics display higher lateral root (LR) density and early LR emergence improving root architecture. Generation of CRISPR-Knockout mutants displayed contrasting phenotype, confirming SlHSFB3as vital role in root growth. In SlHSFB3a manipulated roots, concentration gradient auxin responses oscillated with increase in LR number. C_LIO_LIWe highlight the signal transduction of SlHSFB3a mediated auxin activation that enhances tomato LRs. SlHSFB3a directly inhibits auxin repressors, increases auxin flow via ARF7/LOB20 pathway and positively modulates LR growth. C_LI

plant biology↗

bioRxiv2025

Impact of Long-Term Integrated Nutrient Management Practices on Soil Bacterial Diversity: A 16S rRNA-Based Metagenomic Approach

The growing worlds population, expected to surpass 9 billion by 2050, demands a 70-100% increase in farm productivity, posing significant challenges for sustainable agriculture. Conventional farming, reliant on chemical fertilizers and pesticides, negatively impacts environmental sustainability and food quality. Metagenomics, a culture-independent technique, has revolutionized the study of microbial communities by enabling comprehensive analysis of microbial diversity and function. This study evaluated the effects of combined nutrient management practices--including farmyard manure (FYM), wheat straw, green manure, and NPK fertilizers--on soil bacterial diversity using 16S rRNA-based metagenomic analysis. Key findings revealed the dominance of bacterial phyla such as Proteobacteria, Actinobacteria, and Firmicutes, which play critical roles in nutrient cycling, organic matter decomposition, and plant growth promotion. Distinct taxonomic distributions were observed across the samples, with Proteobacteria and Firmicutes dominating in control (T1), NPK (T2), and NPK_Green Manure (T5) treatments, while a shift in phyla composition was noted in NPK_FYM (T3) and NPK_WheatStraw (T4). Genus-level analysis revealed that Pseudomonas and Bacillus species were abundant in control (T1) and NPK (T2), while Sphingomonas species were dominant in NPK_FYM (T3). Further diversity analyses revealed significant variation across the samples, with T3 showing the highest richness and control (T1) showing the lowest richness. The rarefaction curve confirmed sufficient sampling for capturing microbial diversity, while beta diversity analysis, including Principal Coordinate Analysis (PCA) and Bray-Curtis clustering, indicated distinct microbial community structures across different treatments. The combined use of organic amendments with NPK fertilizer enhanced microbial diversity and population, indicating their potential to support resilient and productive soil ecosystems.

bioinformatics↗

bioRxiv2025

Metagenomic Profiling of Drinking Water Microbiomes: Insights into Microbial Diversity and Antimicrobial Resistance

Monitoring microbial components in drinking water is as essential as tracking its chemical composition. Although traditional culture-based methods provide valuable insight into microbial morphology and behaviour, their scope is restricted to culturable species. With the advent of high-throughput sequencing, we can now detect a wider range of microbes in any ecosystem, along with efficient insights into their functional potential and metabolic capabilities. In this study, metagenomic analyses were performed to fully understand the microbiome of drinking water supplied through public distribution systems in an Indian city. Our findings identified bacteria from the phyla Pseudomonadota, Planctomycetota, Bacteroidota, and Actinomycetota, consistent with previous studies of drinking water microbiomes of other countries. At the species level, Afipia carboxidovorans, Klebsiella pneumoniae, Pseudomonas aeruginosa, Sphingopyxis macrogoltabida, and Variovorax paradoxus were identified as members of the core microbiome. It was observed that the temperature of the water samples, even as little as a 5{o}C increase, influenced the composition and diversity of the microbial communities. No significant correlation was detected between the abundance of microbial species and the metal concentration in the sample. In addition, we traced the distribution of antibiotic resistance genes (ARGs), finding widespread resistance to aminoglycosides, tetracyclines, and macrolides in samples. In particular, ARGs such as adeF and ermR, which are known to be associated with multidrug resistance, were detected. Although this study did not directly assess the pathogenicity or mobility of these genes, their presence in potable water raises potential public health concerns due to the possibility of horizontal gene transfer (HGT) in environmental settings. Therefore, continuous monitoring of antibiotic resistance genes (ARGs) is imperative to accurately evaluate long-term risks and to guide evidence-based water quality management strategies. In summary, this study provides a comprehensive metagenomic overview of drinking water microbiota, ARGs, and water quality, offering a foundation for future surveillance and risk mitigation strategies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/636216v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@819c0org.highwire.dtl.DTLVardef@1d29372org.highwire.dtl.DTLVardef@1ce3cf9org.highwire.dtl.DTLVardef@1050997_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗