Biology subjects

Pandit, A.

Publications and source records attributed to Pandit, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Primary cilia promote resistance to EGFR tyrosine kinase inhibitor, osimertinib, in non-small cell lung cancer

Patients with advanced non-small cell lung cancer (NSCLC) and mutations in epidermal growth factor receptor (EGFR) benefit from EGFR tyrosine kinase inhibitors (TKIs). Osimertinib, a third-generation EGFR TKI, is standard first-line therapy for EGFR-mutated NSCLC, but most patients develop resistance to it. Here, we demonstrate that increased formation of primary cilia, microtubule-based sensory organelles, is associated with osimertinib-refractory NSCLC progression. EGFR-mutated, osimertinib-resistant human NSCLC cells had increased cilia formation and acetylation of -tubulin and reduced histone deacetylase 6 (HDAC6) activity compared to their osimertinib-sensitive counterparts. HDAC6 inhibition increases cilia formation in osimertinib-sensitive NSCLC cells, and overexpression of exogenous HDAC6 sensitized osimertinib-resistant NSCLC cells to osimertinibs anti-proliferative effects. Because intraflagellar transport (IFT) proteins are essential for primary cilium formation and function, we knocked down IFT88 in osimertinib-resistant NSCLC cells, which reversed osimertinib resistance in orthotopic and subcutaneous mouse models of lung cancer. Mechanistically, increased sodium influx during osimertinib-induced inhibition of EGFR signalling promotes cilia formation through sustained HDAC6 inactivity and greater -tubulin acetylation. Inhibition of sodium influx with dibutyryl-cAMP decreased cilium formation, increased sensitivity to osimertinib, and reduced tumor progression in mice bearing osimertinib-resistant lung tumors. Collectively, our findings suggest that enhanced primary cilium formation mediates EGFR TKI resistance and that targeted inhibition of ciliogenesis may prevent or overcome osimertinib resistance.

cancer biology↗

bioRxiv2026

Modified RNA Extraction Methods to Eliminate Agarose Impurities in Precision-Cut Lung Slices

Precision-cut lung slices (PCLS) have emerged as a powerful tool for studying the biology of viable human lung tissue. However, the presence of agarose impurities compromises RNA yield and integrity during the extraction process. We tested whether using an alternative Plant kit RNA extraction method to wash agarose impurities or pre-dissolving agarose from PCLS implementing a dissolving buffer for routine RNA isolation in gel-electrophoresis would improve RNA quantity, quality, and integrity. Our results show that RNA quantity and integrity are highly compromised when using a conventional method of RNA extraction. The plant kit and dissolution of agarose increased the RNA quantity to 0.42{+/-}0.11 and 0.65{+/-}0.17 {micro}g/PCLS (measured by the Qubit) and integrity number to 6.60{+/-}0.59 and 9.13{+/-}0.39 (measured by the Bioanalyzer), respectively. The presence of impurities in conventional and Plant kit extractions misled to an overestimation of the RNA quantity and quality using the NanoDrop. The Plant kit and agarose dissolution showed a significant transcript integrity increase in GUSB (p<0.0001) and COL1A1 (p<0.05) expression, validating these methods over conventional extraction. We encourage laboratories applying PCLS experimentation to implement alternative methods to remove agarose impurities during RNA extraction, as well as to rely on sensitive quantitative techniques, such as the Qubit and Bioanalyzer, for RNA quantification and integrity measurements.

cell biology↗

bioRxiv2026

Developmentally inspired bioprinting of nascent multicellular human heart tissue through in situ differentiation and morphogenesis of iPSCs

Traditional heart tissue bioprinting typically relies on using human induced pluripotent stem cell (iPSC)-derived cardiomyocytes that are pre-differentiated in 2D culture. This approach differs fundamentally from embryonic heart development, where mesodermal progenitors differentiate into cardiomyocytes within 3D, matrix-rich, and shape-morphing microenvironments. Here, we introduce a novel developmentally inspired approach that enables in situ mesodermal and cardiac differentiation of iPSCs within bioprinted, shape-morphing pluripotent tissues. Using embedded bioprinting, Matrigel bioinks with high-density iPSC suspensions were deposited into granular support hydrogels to generate pluripotent tissue constructs with defined architectures. These constructs exhibited shape-morphing behaviour, tunable by modulating the support bath viscoelasticity. Support bath mechanics also regulated iPSC fate, with softer formulations reducing spontaneous differentiation. Building on this, mesodermal induction and cardiogenesis were directly driven within the morphing constructs via temporal WNT pathway modulation, resulting in multicellular cardiac tissues in which cardiomyocytes, fibroblasts, and endothelial cells co-emerge from a common progenitor pool. Importantly, these nascent tissues underwent structural maturation, with immunofluorescence and gene expression profiling revealing cardiac progenitors alongside maturing cardiomyocytes. Together, these findings highlight the potential for a new paradigm in biofabrication focused on printing pluripotent organ rudiments that recapitulate key aspects of embryonic development and support progressive tissue maturation.

bioengineering↗

bioRxiv2025

Multiomics Integration Reveals a Metabolic Myopathy in Cardiometabolic HFpEF

BackgroundSkeletal muscle dysfunction is a major peripheral determinant of exercise intolerance and physical disability in heart failure with preserved ejection fraction (HFpEF). Metabolic and mitochondrial dysfunction are considered to be key components of skeletal muscle dysfunction, but comprehensive profiling of metabolic pathways has not been conducted. Elucidation of dysregulated metabolic pathways is essential to determine viable targets for the treatment of exercise intolerance in HFpEF. MethodsMale ZSF1 Obese rats (HFpEF) and Wistar Kyoto (WKY) lean normotensive controls were studied at 26 weeks of age. Gastrocnemius was subjected to bulk RNA-seq, proteomics, metabolomics, and lipidomics analysis. The R package limma was used to determine differential expression in all omics layers (absolute fold-change>1.5, FDR0.05, unless otherwise indicated). Additional targeted plasma and skeletal muscle (soleus and EDL) metabolomics and lipidomics were performed on HFpEF and control rats. ResultsPathway level analysis for RNA seq and proteomics revealed significant downregulation of oxidative phosphorylation (NES -2.1, p<0.005), electron transport chain (NES -2.0, p<0.005), and TCA cycle (-1.8, p<0.05). The most upregulated pathways were PPAR signaling (NES 2.2, p<0.0001), tryptophan metabolism (NES 1.8, P<0.005), and amino acid oxidation (NES 1.8, p<0.005) pathways. Metabolomics revealed an accumulation of TCA cycle intermediate, isocitrate, and phosphate reduction. Branched-chain amino acids were significantly increased, whereas amino acids related to tryptophan metabolism were reduced and shifted towards increased serotonin accumulation. Phospholipid species were differentially regulated with increased palmitoylated phosphatidylcholines but reduced arachidonoyl-PC species. Phosphatidylethanolamines (PE) species (16:0/16:1-18:0/18:2) were increased. ConclusionOur multiomics analysis of skeletal muscle in HFpEF revealed severe mitochondrial dysfunction that was characterized by reduced complex I and II activity. Mitochondrial and peroxisomal lipid overload results in a shift in membrane phospholipid accumulation and composition. Reduced BCAA oxidation and dysregulation of tryptophan metabolism are key features of amino acid metabolism that reduce anaplerosis and promote the accumulation of toxic metabolites. Comparative analysis of other skeletal muscle disorders suggests that an acquired metabolic myopathy exists in cardiometabolic HFpEF.

physiology↗

bioRxiv2025

Clonal overlap and convergent clustering of T-cell receptor signatures in Crohn's disease in monozygotic twins

IntroductionThe dysregulated immune-response in Crohns disease might result from disturbances in the T-cell receptor (TCR) repertoire. To investigate this hypothesis, we compared the peripheral TCR repertoire within T-cell subsets in twin pairs, concordant and discordant for Crohns disease. MethodsWe performed TCR and TCR{beta} sequencing on peripheral flow-sorted CD4+ memory gut- homing (integrin4{beta}7+), non-gut-homing (integrin4{beta}7-), and regulatory T-cells (Tregs) from Dutch monozygotic Crohns disease concordant twins (N=8), monozygotic Crohns disease discordant twins (N=8), and healthy controls (N=4). TCR diversity and clonality, overlap between individuals, convergence and enrichment, and clustering of the TCR repertoire was studied and compared to previously reported Crohns disease-related TCRs. ResultsOverall diversity and clonality was comparable between Crohns disease patients, healthy cotwins and healthy controls. Comparing T-cell subsets, a decreased diversity and increased clonality was observed for Tregs. Concordant Crohns disease twins had an increased overlap in TCRs for Tregs and CD4+ memory gut-homing T-cells. Using TCR convergence, enrichment and subsequent clustering analyses, we identified eight clusters of TCRs potentially related with Crohns disease. The identified Crohns disease-related TCR signatures have not previously been described in relation to Crohns disease, and have thus far mostly unknown antigen specificity. ConclusionsIncreased overlap in the TCR repertoires of monozygotic twin pairs concordant for Crohns disease suggest that (antigen-driven) skewing of the TCR repertoire could play a role in the pathophysiology of Crohns disease. The identified TCR-based Crohns disease signatures are prime targets for further study into the pathogenesis of Crohns disease.

immunology↗

bioRxiv2025

Cerebral Organoids with Integrated Endothelial Networks Emulate the Neurovascular Unit and Mitigate Core Necrosis

Cerebral organoids (COs) are multicellular, self-organized, in vitro, 3D brain-like tissues used for developmental biology, disease modelling and drug screening. However, their lack of vascularity renders them less physiologically accurate. Vascularization of COs remains challenging due to the different requirements between COs and vascular cells, limited vascular network penetration within the organoid, and the absence of luminal perfusion. Here, we devised an encapsulation approach in which human brain microvascular endothelial cells (HBMVECs) were delivered to developing COs from progressively degrading extracellular matrix (ECM)-based hydrogel droplets. By tuning this hydrogel concentration and media composition, we observed enhanced vascular-like network formation that expanded within the organoid tissue. Using pathway inhibitors, we showed that a subset of the endothelial cells (ECs) originated from the CO itself, promoting network integration. Endothelial networks displayed blood-brain barrier (BBB) features, including astrocytic end-footlike interactions, pericyte wrapping, and collagen-laminin basal lamina. Vascularized COs exhibited greater media internalization and up to three-fold lower apoptosis than non-vascularized COs. This comprehensive 3D neurovascular model is a promising platform for cerebrovascular research and drug testing applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/650161v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@175edb7org.highwire.dtl.DTLVardef@1499b91org.highwire.dtl.DTLVardef@184567borg.highwire.dtl.DTLVardef@149c8e4_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG HighlightsO_LIAddition and angiogenic stimulation of human brain microvascular endothelial cells (HBMVECs) co-cultured with cerebral organoids (COs) generate multicellular vascular-like networks C_LIO_LIVascularization induces changes in organoid morphology but not on tissue stiffness C_LIO_LIEndothelial networks morphological features are correlated with the concentration of the supporting matrix C_LIO_LIA number of the endothelial cells (ECs) in the networks originate from the organoid itself C_LIO_LIEndothelial networks integrate within the organoid tissue interacting with astrocytes and pericyte-like cells, and are surrounded by basement membrane-like depositions C_LIO_LIVascularized COs exhibit higher media diffusion, and a reduced necrotic core compared to non-vascularized COs C_LI

bioengineering↗

bioRxiv2025

Unprecedented Cytotoxicity of Transition Metal Metallacarboranes on Triple Negative Breast Cancer Cells and a Vertebrate Cancer Model

Metallacarboranes have long been the subject of attention in the context of medicinal chemistry because of their promising characteristics and unconventional interactions with biological entities. The metal centre has been shown to have a significant influence on the internalisation and cytotoxicity of compounds in human cell lines. Additionally, specific nanomolar concentrations of metallacarboranes have demonstrated toxic effects on MDA-MB-231 cells under in vitro and in vivo conditions. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/635527v1_ufig1.gif" ALT="Figure 1"> View larger version (67K): org.highwire.dtl.DTLVardef@116eb95org.highwire.dtl.DTLVardef@1c4a181org.highwire.dtl.DTLVardef@474c3forg.highwire.dtl.DTLVardef@dec88c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Two distinct durable human class-switched memory B cell populations are induced by vaccination and infection

Memory lymphocytes are durable cells that persist in the absence of antigen, but few human B cell subsets have been characterized in terms of durability. The relative durability of eight non-overlapping human B cell sub-populations covering 100% of all human class-switched B cells was interrogated. Only two long-lived B cell populations persisted in the relative absence of antigen. In addition to canonical germinal center-derived switched-memory B cells with an IgD-CD27+ CXCR5+ phenotype, a second, non-canonical, but distinct memory population of IgD-CD27- CXCR5+ DN1 B cells was also durable, exhibited a unique TP63-linked transcriptional and anti-apoptotic signature, had low levels of somatic hypermutation, but was more clonally expanded than canonical switched-memory B cells. DN1 B cells likely evolved to preserve immunological breadth and may represent the human counterparts of rodent extrafollicular memory B cells that, unlike canonical memory B cells, can enter germinal centers and facilitate B cell and antibody evolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/624972v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@169c77forg.highwire.dtl.DTLVardef@1a872f5org.highwire.dtl.DTLVardef@1360cforg.highwire.dtl.DTLVardef@38d7ed_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

EFFICIENT RIBOSOMAL RNA DEPLETION FROM DROSOPHILA TOTAL RNA FOR NEXT-GENERATION SEQUENCING APPLICATIONS

We developed a cost-effective enzyme-based rRNA-depletion method tailored for Drosophila melanogaster, addressing the limitations of existing commercial kits and the lack of peer-reviewed alternatives. Our method employs single-stranded DNA probes complementary to Drosophila rRNA, forming DNA-RNA hybrids. These hybrids are then degraded using the RNase H enzyme, effectively removing rRNA and enriching all non-ribosomal RNAs, including mRNA, lncRNA and small RNA. When compared to a commercial rRNA removal kit, our approach demonstrated superior rRNA removal efficiency and mapping percentage, confirming its effectiveness. Additionally, our method successfully enriched the non-coding transcriptome, making it a valuable tool for studying ncRNA in Drosophila. The probe sequences and rRNA-depletion protocol are made freely available, offering a reliable alternative for rRNA-depletion experiments.

molecular biology↗

bioRxiv2024

Dopamine D2 receptor agonists abrogate neuroendocrine tumour angiogenesis to inhibit chemotherapy-refractory small cell lung cancer progression

Small cell lung cancer (SCLC) is difficult to treat due to its aggressiveness, early metastasis, and rapid development of resistance to chemotherapeutic agents. Here, we show that treatment with a dopamine D2 receptor (D2R) agonist reduces tumour angiogenesis in multiple in vivo xenograft models of human SCLC, thereby reducing SCLC progression. An FDA-approved D2R agonist, cabergoline, also sensitized chemoresistant SCLC tumours to cisplatin and etoposide in patient-derived xenograft models of acquired chemoresistance in mice. Ex vivo, D2R agonist treatment decreased tumour angiogenesis through increased apoptosis of tumour-associated endothelial cells, creating a less favourable tumour microenvironment that limited cancer cell proliferation. In paired SCLC patient-derived specimens, D2R was expressed by tumour-associated endothelial cells obtained before treatment, but D2R was downregulated in SCLC tumours that had acquired chemoresistance. D2R agonist treatment of chemotherapy-resistant specimens restored expression of D2R. Activation of dopamine signalling is thus a new strategy for inhibiting angiogenesis in SCLC and potentially for combatting chemotherapy-refractory SCLC progression.

cancer biology↗

bioRxiv2024

Single-cell Landscape of Immune Cells in Blood and Skin in Psoriasis

BackgroundPsoriasis is a systemic inflammatory disease for which there is currently no cure, in part due to an incomplete understanding of its pathophysiology. MethodsTo better understand the immune response in psoriasis, we performed single-cell RNA sequencing (scRNA-seq) on peripheral blood mononuclear cells (PBMCs) and on lesional and non-lesional skin samples from a cohort of 11 psoriasis patients and 8 healthy controls. Additionally, we conducted flow cytometry on PBMCs from a separate cohort of 13 psoriasis patients and 11 ankylosing spondylitis. FindingsOur study revealed altered immune signatures of specific myeloid and lymphocyte subsets in blood and skin, both in terms of cell numbers and gene expression. Specifically, we discovered elevated proportions of circulating CD14++ monocytes, increased expression of major histocompatibility complex (MHC) class II molecule by circulating CD16+ monocytes, as well as increased expression of genes related to skin homing and to pro-inflammatory responses in psoriasis by circulating plasmacytoid dendritic cells (pDCs). Circulating CD8+ T effector memory cells in psoriasis patients exhibited reduced abundance but increased skin-homing potential. In psoriatic lesions, we observed a hyperinflammatory myeloid-cell state and enrichment of IL17-producing cells with a tissue-resident memory T-cell signature. InterpretationThe changes in immune cell numbers and gene expression indicate a significant alteration in the immune landscape of psoriasis patients. This suggests that the immune system in psoriasis is reprogrammed, affecting both innate and adaptive branches. These findings provide new insights into the aberrant immune-cell signatures in the circulation and skin lesions in psoriasis, and thereby help to understand its pathophysiology. FundingThis study was financially supported by the National Natural Science Foundation of China (U23A6012), Science and Technology Planning Project of Guangzhou (2024A03J0055, 202206080005), Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine (ZYYCXTD-C-202204).

systems biology↗

bioRxiv2024

4D bioprinting shape-morphing tissues in granular support hydrogels: Sculpting structure and guiding maturation

During embryogenesis, organs undergo dynamic shape transformations that sculpt their final shape, composition, and function. Despite this, current organ bioprinting approaches typically employ bioinks that restrict cell-generated morphogenetic behaviours resulting in structurally static tissues. Here, we introduce a novel platform that enables the bioprinting of tissues that undergo programmable and predictable 4D shape-morphing driven by cell-generated forces. Our method utilises embedded bioprinting to deposit collagen-hyaluronic acid bioinks within yield-stress granular support hydrogels that can accommodate and regulate 4D shape-morphing through their viscoelastic properties. Importantly, we demonstrate precise control over 4D shape-morphing by modulating factors such as the initial print geometry, cell phenotype, bioink composition, and support hydrogel viscoelasticity. Further, we observed that shape-morphing actively sculpts cell and extracellular matrix alignment along the principal tissue axis through a stress-avoidance mechanism. To enable predictive design of 4D shape-morphing patterns, we developed a finite element model that accurately captures shape evolution at both the cellular and tissue levels. Finally, we show that programmed 4D shape-morphing enhances the structural and functional properties of iPSC-derived heart tissues. This ability to design, predict, and program 4D shape-morphing holds great potential for engineering organ rudiments that recapitulate morphogenetic processes to sculpt their final shape, composition, and function.

bioengineering↗

bioRxiv2024

Unbounding fish: Assessing vulnerability to overexploitation for transboundary fish populations

SummeryGlobally coastal fisheries are managed according to political jurisdictions of nations and their provinces. This practice often results in multiple states/provinces managing a single genetically distinct fish population autonomously and without coordination. In multi-species, decentralized and data poor fisheries such management lead to poor assessment and eventually overharvest of fish. To assess overexploitation risk for such interjurisdictional populations, we propose a risk indicator IRIIS which incorporates 1) species-specific vulnerability 2) distribution of genetically-distinct populations with respect to jurisdictional boundaries and 3) differences in management practices across jurisdictions. As a case study we evaluated overexploitation risk for individual populations of nine commonly caught fish species spanning across multiple jurisdictions along Indias west coast. Our results indicate that interjurisdictional differences in management alters innate biological susceptibility. IRIIS is also sensitive to population-level differences and policy changes. Our analyses emphasize the need for population-level assessments and interjurisdictional cooperation to achieve sustainable fisheries. Science and society statementCoastal fisheries worldwide are managed through politically defined maritime jurisdictions, while fish populations are structured by biological processes such as dispersal, ocean currents, and natural barriers. This fundamental mismatch between biological population boundaries and jurisdictional management boundaries often results in the same population being exploited under multiple, uncoordinated governance regimes. In the context of the global overfishing crisis, such governance fragmentation can lead to inaccurate stock assessments and heightened risk of local population collapse. This challenge is particularly acute in developing and tropical countries, where fisheries are multispecies, data-limited, and increasingly decentralized to support community-based governance. While decentralization promotes social justice, it can inadvertently intensify the misalignment between biological and administrative boundaries, complicating sustainable management. In this manuscript, we introduce a robust framework -- the Integrative Risk Indicator for Interjurisdictional Stocks (IRIIS) -- which has a high applicability for multispecies, data-poor, and decentralized fisheries. Building on, and extending beyond, species-level Productivity Susceptibility Analysis (PSA), IRIIS integrates population genomics to delineate biologically meaningful population boundaries and combines these with fisheries policies and regulations across jurisdictions to quantify management-associated risks of overexploitation at the population level. We apply IRIIS to case studies of nine commercially important fish species harvested along the west coast of India. Our results demonstrate that the framework can (i) distinguish differential vulnerability among populations of the same species, (ii) explicitly capture management disparities across jurisdictions exploiting shared populations, and (iii) detect sensitivity to temporal changes in fisheries policies. By linking genomics, governance, and risk assessment, IRIIS provides a practical framework for identifying interjurisdictional management gaps and actionable entry points for policy coordination. This approach is particularly relevant for the Global South, where reconciling social equity objectives with ecological sustainability is both essential and challenging.

ecology↗

bioRxiv2024

Marcks and Marcks-like 1 proteins promote spinal cord development and regeneration in Xenopus

Marcks and Marcksl1 are abundant proteins that shuttle between the cytoplasm and membrane to modulate multiple cellular processes, including cytoskeletal dynamics, proliferation, and secretion. Here, we performed loss- and gain-of-function experiments in Xenopus laevis to reveal the novel roles of these proteins in spinal cord development and regeneration. We show that Marcks and Marcksl1 have partly redundant functions and are required for normal neurite outgrowth and proliferation of neuro-glial progenitors during embryonic spinal cord development and for its regeneration during tadpole stages. Rescue experiments in Marcks and Marcksl1 knockout animals further suggested that some of the functions of Marcks and Marcksl1 in the spinal cord are mediated by phospholipase D (PLD) signaling. Taken together, these findings identify Marcks and Marcksl1 as critical new players in spinal cord development and regeneration and suggest new pathways to be targeted for therapeutic stimulation of spinal cord regeneration in human patients.

developmental biology↗

bioRxiv2024

Trace DNA from kill sites identifies predating tigers

Predation ecology and evidence-based conflict management strategies require reliable and accurate identification of individual predators. Identifying predators is, however, complex, as they are secretive and individual identification is difficult. Trace DNA that predators leave behind at kill sites might provide an effective strategy to identify them but remains poorly evaluated at scale. We use non-invasive genetic samples from kill sites to assess their utility for predator identification. We systematically investigated 198 livestock kills in two critical source tiger populations in central India: Kanha and Bandhavgarh Tiger Reserves. We collected 342 salivary swabs from carcasses, 33 scat and 395 shed hair samples as potential sources of predator DNA, and individual tigers were identified using up to 123 SNP markers. All three sample sources identified predator species with high success (>95%). We identified individuals (with at least one sample per kill site, based on >40 SNPs) at 86% of all kill sites where tigers were detected. Shed hair samples were most effective for individual identification, followed by saliva and scat. Sample source and sampling season were the primary determinants of the number of SNPs typed per sample and the success of individual identification. Based on the site and type of sample collection, we classify species and individuals into three categories: true predator (high confidence as predator), circumstantial predator (medium confidence) and predator uncertain (low confidence). Individuals were classified as a true predator at 72 sites, circumstantial predator at 34 sites and predator uncertain at 49 sites. Our protocol allowed us to differentiate between predators and scavengers, even when multiple tigers were detected at the same kill site. Surprisingly, [~]40% of Bandhavgarhs tigers were identified at at least one kill site. We suggest that when paired with systematic kill site investigation and sample collection, these methods can be effectively used to understand predation ecology better and facilitate evidence-based conflict management.

genetics↗

bioRxiv2024

Unravelling the glycome in human intervertebral disc degeneration: Aberrant glycosylation modulates inflammation and metabolism.

Intervertebral disc (IVD) degeneration is one of the major contributing causes of low back pain (LBP), a common health issue that imposes a significant socio-economic burden on society. Previous work has demonstrated a dysregulated glycome in animal models of IVD degeneration; however, the role of glycosylation in pathogenesis is unknown. The objective of this study was to characterise altered glycan expression in IVD degeneration and elucidate the functional role of this response. Glycans in human healthy (n=6) and degenerated IVD (n=6) were examined through UPLC-MS and MALDI-IMS. These findings were correlated with proteomic analysis by LC-MS and functional in vitro studies using RNA sequencing. IVD degeneration was associated with a hypersialylated N-glycome, predominantly -2,6 linked sialic acid. Confirming hypersialylation, we investigated sialylations functional role through mechanistic studies using a sialylation inhibitor (3Fax-peracetyl Neu5Ac). Sialylation inhibition in vitro modulated inflammatory and metabolic pathways, demonstrating a functional role for glycosylation in IVD degeneration. Brief summaryIVD degeneration is associated with altered glycosylation, a potential target for new therapies.

bioengineering↗

bioRxiv2023

On the road to losing connectivity: Fecal samples provide genome-wide insights into anthropogenic impacts on two large herbivore species in central India

Humans have impacted most of the planet, and the ensuing fragmentation results in small, isolated habitat patches posing a risk of genetic diversity loss, inbreeding and genetic load. Understanding how natural and anthropogenic landscape features affect gene flow among habitat patches is critical for maintaining connectivity. Genome-wide data is required to comprehend the impacts of recent fragmentation, which can be challenging when only non-invasive samples are available. Here, we build upon advancements in conservation genomics to address connectivity of two large herbivores, gaur (Bos gaurus) and sambar (Rusa unicolor) in central India. Given their habitat associations, we expected these species to respond similarly to habitat fragmentation. We used fecal-DNA and methylation-based host-DNA enrichment with modified ddRAD protocol to generate genome-wide single nucleotide polymorphism (SNP) data for 124 Gaur and 99 Sambar individuals. Our findings reveal that gaur populations in central India are fragmented, displaying high genetic differentiation, with drift significantly affecting small populations like Umred-Karhandala Wildlife Sanctuary. Although Sambar shows low genetic structure, another small population, Bor Tiger Reserve is genetically differentiated. Our results suggest that although landcover change and roads restrict animal movement, the extent of this impact varies across the two species. We show that different species, respond differently to landscape features, even with similar habitat associations. We highlight small and isolated populations requiring urgent conservation intervention. Such multi-species approaches enhance our understanding of cross-species connectivity patterns. We suggest shifting from single-species to multi-species holistic conservation approach in rapidly developing landscapes to better manage co-occurring endangered species.

genomics↗

bioRxiv2023

Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru

Genomic surveillance in response to coronavirus disease (COVID-19) pandemic is crucial for tracking spread, identify variants of concern (VoCs) and understand the evolution of its etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). India has experienced three waves of COVID-19 cases, which includes a deadly wave of COVID-19 that was driven by the Delta lineages (second/Delta wave) followed by another wave driven by the Omicron lineages (third/Omicron wave). These waves were particularly dramatic in the metropolitan cities due to high population density. We evaluated the prevalence, and mutational spectrum of SARS-CoV-2 variants/lineages in one such megapolis, Bengaluru city, across these three waves between October 2020 and June 2022. 15,134 SARS-CoV-2 samples were subjected to whole genome sequencing (WGS). Phylogenetic analysis revealed, SARS-CoV-2 variants in Bengaluru city belonged to 18 clades and 196 distinct lineages. As expected, the Delta lineages were the most dominant lineages during the second wave of COVID-19. The Omicron lineage BA.2 and its sublineages accounted for most of the COVID-19 cases in the third wave. Most number of amino acid changes were observed in spike protein. Among the 18 clades, majority of the mutations and least similarity at nucleotide sequence level with the reference genome were observed in Omicron clades.

genomics↗