Biology subjects

Pal, S.

Publications and source records attributed to Pal, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes

Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself. Here we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study (Li et al., 2022). With over 44,000 nuclei and 6,000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells. We justify assignment of key germline and somatic cell types using combinations of known markers, in situ hybridization, and analysis of extant protein traps. Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation. To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle. The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function in vivo.

developmental biology↗

bioRxiv2022

Neural activity and theta rhythmicity in the anterior hypothalamic nucleus are involved in regulating social investigation

Social interactions are highly complex, involving both approach and avoidance actions towards specific individuals, dependent on the social context. Currently, the brain regions subserving these behaviors are not fully known. The anterior hypothalamic nucleus (AHN) is a relatively unstudied and poorly defined brain area, known as part of the medial hypothalamic defensive system. Recent studies that examined the role of the AHN in various contexts have yielded contradicting results regarding its contribution to approach, avoidance, and escape behaviors. Yet, none of these studies has directly examined its role in social interactions. Here we explored the role of AHN neurons in regulating approach and avoidance actions towards distinct stimuli during various types of social interactions, using electrophysiological recording of neural activity in the AHN of behaving mice, c-Fos staining, and direct optogenetic stimulation. We found that theta rhythmicity in the AHN was enhanced during affiliative interactions, but decreased during aversive ones. Moreover, spiking activity of AHN neurons was found to be elevated more persistently during investigation of social stimuli, as compared to objects. Notably, AHN neuronal firing was found to be modulated by theta rhythmicity during social interactions. Finally, we found that during social interaction, direct optogenetic stimulation of AHN neurons augmented approach behavior towards stimuli associated with the optogenetic activation. Overall, our results suggest a context-dependent role for AHN neuronal activity in regulating approach behavior during social interactions, and for theta rhythmicity in mediating the valence of the social context.

neuroscience↗

bioRxiv2022

Genomics for reproduction in Anas platyrynchos-a novel report

Anas platyrynchos (ducks) are reared mostly for egg, which are very nutritious, that fetch better prices, however duck meat possess rich nutrient content. They possess the unique characteristics of disease resistance to the common avian diseases, even asymptomatic to avian influenza, with a scopeto evolve as one of the best poultry species The major limitation encountered is the lowered average egg production as well as higher age at first egg (an indicator for sexual maturity) for the indigenous ducks compared to that of exotic ones. In this current study, we attempt to explore the genes responsible for duck reproduction in terms of sexual maturity,egg production and fertility of the ducks. We had compared the genomic constitution for the Bengal duck with highest egg production with that of non-layer (infertile or sexually immature) ducks. We characterized the genes in indigenous ducks from ovarian tissues, identified important domains for characterized genes for the first time, and studied differential mRNA expression profiling for these genes with respect to layer and non-layer groups. Upregulation was observed for ESR2, DIAPH2, KMT2E, ASCF2 genes for Bengal duck in highest egg producing duck in comparison to non-layer duck, whereas downregulation was observed for KSR1, A2M, BMPR1B, ACVR1. In the next step, we explored the association with the genes which were actually responsible for egg production. Thus, duck may be utilized as a model for studying the molecular aspect of reproduction. Genes upregulated may be utilized for knock in of gene, whereas down regulated genes may be knocked out or knocked down through gene editing technologies for the improvement of reproductive performance of the duck in future. Molecular biomarkers may be developed with these genes for early selection of better reproducing ducks at day of hatch or even earlier.

genomics↗

bioRxiv2022

Cell-autonomous immune dysfunction driven by disrupted autophagy in C9orf72-ALS iPSC-derived microglia contributes to neurodegeneration

The most common genetic mutation found in familial and sporadic amyotrophic lateral sclerosis (ALS), as well as fronto-temporal dementia (FTD), is a repeat expansion in the C9orf72 gene. C9orf72 is highly expressed in human myeloid cells, and although neuroinflammation and microglial pathology are widely found in ALS/FTD, the underlying mechanisms are poorly understood. Here, using human induced pluripotent stem cell-derived microglia-like cells (hiPSC-MG) harbouring C9orf72 mutation (mC9-MG) together with gene-corrected isogenic controls (isoC9-MG) and C9ORF72 knock-out hiPSC-MG (C9KO-MG), we show that reduced C9ORF72 protein is associated with impaired phagocytosis and an exaggerated inflammatory response upon stimulation with lipopolysaccharide, driven by sustained activation of NLRP3 inflammasome and NF-{kappa}B signalling. Analysis of the hiPSC-MG C9ORF72 interactome revealed an association of C9ORF72 with key regulators of autophagy, a process involved in the homeostatic regulation of the innate immune response. We found impaired initiation of autophagy in C9KO-MG and mC9-MG. Furthermore, through motor neuron-microglial (MN-MG) co-culture studies, we identified that autophagy deficit in mC9-MG led to increased vulnerability of C9 MNs to excitotoxic stimulus. Pharmacological activation of autophagy ameliorated the sustained activation of NLRP3 inflammasome and NF-{kappa}B signalling, reversed the phagocytic deficit found in mC9-MG and also reduced MN death in MN-MG co-cultures. We validated these findings in blood-derived macrophages from people with C9orf72 mutation. Our results reveal an important role for C9ORF72 in regulating microglial immune homeostasis and identify dysregulation in human myeloid cells as a contributor to neurodegeneration in ALS/FTD. TeaserDisrupted autophagy led immune activation in microglia results in enhanced motor neuronal death in C9orf72-ALS.

neuroscience↗

bioRxiv2022

Claudin5 protects the peripheral endothelial barrier in an organ and vessel type-specific manner

The pathogenesis of numerous diseases is characterised by disruption of the junctions that form the endothelial cell (EC) barrier, the composition of which may differ greatly between organs. However, the expression level variability and precise contribution of different junctional proteins is poorly understood. Here, we focus on organs with continuous endothelium to identify structural and functional in vivo characteristics of the EC barrier. Assembly of multiple single-cell RNAseq datasets into a single integrated database revealed the variability in EC barrier patterning. Across tissues Claudin5 exhibited diminishing expression along the arteriovenous axis, which correlates with EC barrier integrity. Functional analysis identified tissue-specific differences in leakage patterning and response to agonist-induced leakage. We uncover that Claudin5 loss enhances agonist-induced leakage in an organotypic, vessel type-specific and size-selective manner in an inducible, EC-specific, knock-out mouse. Mechanistically, Claudin5 loss induces no change in junction ultrastructure but alters composition, with concomitant loss of zonula occludens-1 (ZO-1) expression and upregulation of VE-Cadherin. These findings uncover the organ-specific organisation of the EC barrier and distinct importance of Claudin5 in different vascular beds and will aid our ability to modify EC barrier stability in a targeted, organ-specific manner.

cell biology↗

bioRxiv2022

DNA-functionalized Gold Nanorods for Targeted Triple-modal Optical Imaging and Photothermal Therapy of Triple-negative Breast Cancer

Targeted imaging and therapy for triple-negative breast cancer (TNBC) in the perioperative period are believed to be imperative for better disease management and improved life expectancy. Still, they are not yet available in clinical settings, and only a few nanoparticle-based theranostic agents potentially offer these capabilities. Herein, we develop an innovative class of biocompatible triple-modality nanoprobes (TMNPs) that offer optical imaging using optoacoustic, fluorescence, and surface-enhanced Raman scattering (SERS), as well as photothermal therapy (PTT) with near-infrared (NIR) light. The TMNPs are fabricated by immobilizing positively charged NIR fluorophores on negatively charged DNA-coated gold nanorods (AuNR), then silica encapsulation. The DNA-based design allows the screening of commercially available positively charged NIR fluorophores for the optimum fluorescence and SERS signals. After the design optimization, we functionalize TMNPs with folate groups to target folate receptor1 (FOLR1)-overexpressing TNBC in vitro and in vivo. Our results reveal that TMNPs preferentially accumulate in the FOLR1 positive tumors in TNBC patient-derived xenograft mouse models and show excellent imaging capabilities with all three imaging modalities. Selective exposure of the tumor with NIR laser further shows efficient thermal tissue ablation without causing systemic toxicity. Collectively, TMNP holds great promise for real-time multiplexed imaging of cancer biomarkers and therapeutic capability.

bioengineering↗

bioRxiv2022

Role of mucin gene for growth in Anas platyrynchos - a novel report

Mucin gene is expressed at the mucous membrane of the inner layer of the internal organs. Intestinal mucin 2 (MUC2), a major gel-forming mucin, represents a primary barrier component of mucus layers. This is the first report of role of mucin gene in growth traits in animals. In the current study, we had randomly studied Bengal ducks (Anas platyrynchos) reared from day old to 10 weeks of age under organized farm and studied the growth parameters as well as body weight and average daily body weight gain. We had characterized mucin gene for Bengal duck and observed glycosylation and EGF1 (EGF like domain signature) as important domain for growth traits in duck. We observed better expression profile for mucin gene in high growing ducks in comparison to that of lower growing ducks with real time PCR. Hence mucin gene may be employed as a marker for growth traits.

genomics↗

bioRxiv2022

Role of RIGI, MDA5 and interferon alpha of duck in Duck Plague infection, a novel report

Duck Plague (DP) or Duck viral enteritis is an acute contagious and highly fatal disease in water fowl commonly caused by Anatidalphavirus-1 belonging from Herpesviridae family and contains double stranded DNA as genetic material. Pathogen associated molecular pattern (PAMP)s when identified by Pathogen Recognition Receptor (PRR)s acts as effective immunity system action against the pathogen. Melanoma Differentiation-Associated protein 5 (MDA5) and Retionic Acid Inducible Gene I (RIG1) are protein sensor commonly sense for viral double stranded RNA and helps for pro-inflammatory cytokine expression. Gut Associated Lymphoid Tissue (GALT)s have important role in immune response. The current study depicts the important role of three important immune response genes as RIGI, MDA5 and INFalpha in duck plague infestation for the first time. In silico studies followed by differential mRNA expression of RIG1, MDA5 and INFalpha was employed to detect effectiveness of gut associated immune responsiveness in liver, where kupfer cells are the major immune response cells. This was further confirmed through histological section of liver, kupfer cell and immunohistochemistry. This will be helpful to identify molecular mechanism of host innate immunity through duck plague virus infection in indigenous duck. This information may be helful for production of duck with the inherent resistance against duck plague virus infection through suitable biotechnological approaches as gene editing.Due to this inherent nature of better immunity in terms of resistance to other common avian diseases, duck will evolve as one of the major sustainable poultry species.The current study explores the scope to study host immunity against herpes virus in animal model.

genomics↗

bioRxiv2021

Interaction of hypoxia and nicotine acetylcholine receptor signaling network reveals a novel mechanism for lung adenocarcinoma progression in never-smokers

High incident of lung cancer among never smokers and their disease pathogenesis is an unexplained phenomenon. We have analyzed 1727 lung cancer patient data to understand the impact of smoking on overall survival of lung cancer patients and have observed a difference of only 47 days between smokers and never smokers in adenocarcinoma patients suggesting that the disease is equally fatal in never-smokers irrespective of gender. In this study, we have investigated the possible collaboration between the nAChR and hypoxia signaling pathway to elucidate a mechanism of disease progression in never-smokers. We report a previously unidentified increase in both acetylcholine and nAChR-7 levels in non small cell lung cancer cells in hypoxia. Similar increase in ubiquitously expressed nAChR-7 transcripts was also observed in other cancer lines. A direct binding of HIF-1 with the hypoxia response element (HRE) present at -48 position preceding the transcriptional start site in nAChR-7 promoter region was established. Significantly, the increased acetylcholine levels in hypoxia drove a feedback loop via modulation of PI3K/AKT pathway to stabilize HIF-1 in hypoxia. Further, Bungarotoxin, an antagonist of nAChR-7 significantly reversed hypoxia mediated metastasis and induction of HIF-1 in these cells. Our study gives a plausible explanation for the equally worse prognosis of lung adenocarcinoma in never-smokers wherein the nAChR signaling is enhanced in hypoxia by acetylcholine, in the absence of nicotine.

cancer biology↗

bioRxiv2021

A modular platform for on-demand vaccine self-assembly enabled by decoration of bacterial outer membrane vesicles with biotinylated antigens

Engineered outer membrane vesicles (OMVs) derived from laboratory strains of bacteria are a promising technology for the creation of non-infectious, nanoparticle vaccines against diverse pathogens. As mimics of the bacterial cell surface, OMVs offer a molecularly-defined architecture for programming repetitive, high-density display of heterologous antigens in conformations that elicit strong B and T cell immune responses. However, antigen display on the surface of OMVs can be difficult to control and highly variable due to bottlenecks in protein expression and localization to the outer membrane of the host cell, especially for bulky and/or complex antigens. To address this shortcoming, we created a universal approach called AddVax (avidin-based dock- and-display for vaccine antigen cross (x)-linking) whereby virtually any antigen that is amenable to biotinylation can be linked to the exterior of OMVs whose surfaces are remodeled with multiple copies of a synthetic antigen receptor (SNARE) comprised of an outer membrane scaffold protein fused to a member of the avidin family. We show that SNARE-OMVs can be readily decorated with a molecularly diverse array of biotinylated subunit antigens, including globular and membrane proteins, glycans and glycoconjugates, haptens, lipids, and short peptides. When the resulting OMV formulations were injected in wild-type BALB/c mice, strong antigen-specific antibody responses were observed that depended on the physical coupling between the antigen and SNARE-OMV delivery vehicle. Overall, these results demonstrate AddVax as a modular platform for rapid self-assembly of antigen-studded OMVs with the potential to accelerate vaccine generation, respond rapidly to pathogen threats in humans and animals, and simplify vaccine stockpiling.

synthetic biology↗

bioRxiv2021

Fly Cell Atlas: a single-cell transcriptomic atlas of the adult fruit fly

The ability to obtain single cell transcriptomes for stable cell types and dynamic cell states is ushering in a new era for biology. We created the Tabula Drosophilae, a single cell atlas of the adult fruit fly which includes 580k cells from 15 individually dissected sexed tissues as well as the entire head and body. Over 100 researchers from the fly community contributed annotations to >250 distinct cell types across all tissues. We provide an in-depth analysis of cell type-related gene signatures and transcription factor markers, as well as sexual dimorphism, across the whole animal. Analysis of common cell types that are shared between tissues, such as blood and muscle cells, allowed the discovery of rare cell types and tissue-specific subtypes. This atlas provides a valuable resource for the entire Drosophila community and serves as a comprehensive reference to study genetic perturbations and disease models at single cell resolution.

genomics↗

bioRxiv2021

A Serpin27A-dependent Toll Signaling Underlies Host Genetics of Cancer Resistance in Drosophila

Cancer resistance varies amongst individuals, although its host genetic underpinnings remain largely elusive. Remissions of sarcomas were first reported following repeated injections of patients with mixtures of killed bacteria--Coleys toxins--a phenomenon, which was subsequently causally traced to induction of innate immunity. Here we reveal remission of Drosophila epithelial neoplasms by genetically triggered host innate immunity via Toll signaling. These neoplasms display capacities to receive and, in rare instances, induce Toll signaling. A tumor-induced and progressive Toll signaling, however, did not culminate in tumor suppression. By contrast, Drosophila hosts heterozygous for spn27A1 mutation, which constitutively produce activated Toll ligand, SpzAct, displayed comprehensive tumor remission via Toll-induced, NF-{kappa}B-mediated, tumor cell death. Our results reveal a novel node of host genetic cancer resistance via serpin-dependent Toll signaling.

cancer biology↗

bioRxiv2021

Pathology dynamics in healthy-toxic protein interaction and the multiscale analysis of neurodegenerative diseases

Neurodegenerative diseases are frequently associated with aggregation and propagation of toxic proteins. In particular, it is well known that along with amyloid-beta, the tau protein is also driving Alzheimers disease. Multiscale reaction-diffusion models can assist in our better understanding of the evolution of the disease. We have modified the heterodimer model in such a way that it can now capture some of critical characteristics of this evolution such as the conversion time from healthy to toxic proteins. We have analyzed the modified model theoretically and validated the theoretical findings with numerical simulations.

neuroscience↗

bioRxiv2020

An early cortical progenitor-specific mechanism regulates thalamocortical innervation

The cortical subplate is critical in regulating the entry of thalamocortical sensory afferents into the cortex. These afferents reach the subplate at embryonic day (E)15.5 in the mouse, but "wait" for several days, entering the cortical plate postnatally. We report that when transcription factor Lhx2 is lost in E11.5 cortical progenitors, which give rise to subplate neurons, thalamocortical afferents display premature, exuberant innervation of the E15.5 cortex. Embryonic mutant subplate neurons are correctly positioned below the cortical plate, but they display an altered transcriptome and immature electrophysiological properties during the waiting period. The sensory thalamus in these cortex-specific Lhx2 mutants displays atrophy, eventually leading to severe deficits in thalamocortical innervation. Strikingly, these phenotypes do not manifest if Lhx2 is lost in postmitotic subplate neurons. These results demonstrate a mechanism operating in subplate progenitors that has profound consequences on the growth of thalamocortical axons into the cortex.

neuroscience↗

bioRxiv2020

Coupled social-land dynamics and the future of sustainable consumption

Dietary patterns have long been a driver of global land use. Increasingly, they also respond to it, in part because of social forces that support adoption of sustainable diets. Here we develop a coupled social-land use dynamics model parameterised for 164 countries. We project global land use under 20 scenarios for future population, income, and agricultural yield. When future yields are low and/or population size is high, coupled social-land feedbacks can reduce the peak global land use by up to 2 billion hectares, if socio-economic barriers to adopting a sustainable diet are sufficiently low. In contrast, when population growth is low or yield is high, reductions in income elasticity can increase peak land use by 100 million hectares. The model also exhibits a regime of synergistic effects whereby simultaneous changes to multiple social and economic parameters are required to change land use projections. This research demonstrates the value of including coupled social-land feedbacks in land use projections.

evolutionary biology↗

bioRxiv2020

Transcription factor binding dynamics shape noise across biological processes

Noise in expression of individual genes gives rise to variations in activity of cellular pathways and generates heterogeneity in cellular phenotypes. Phenotypic heterogeneity has important implications for antibiotic persistence, mutation penetrance, cancer growth and therapy resistance. Specific molecular features such as presence of the TATA box sequence and promoter nucleosome occupancy have been associated with noise. However, the relative importance of these features in noise regulation has not yet been assessed. In addition, how well these features can predict noise also remains unclear. Here through an integrated statistical model of gene expression noise in yeast we found that the number of regulating transcription factors (TFs) was a key predictor of noise. With an increase in the number of regulatory TFs, we observed a rise in the number of TFs that bound cooperatively. In addition, increased number of TFs meant more overlaps in TF binding sites that caused competition between TFs for binding to the same region of the promoter. Through modeling of TF binding to promoter and applying stochastic simulations, we demonstrated that competition and cooperation among TFs could increase noise. Thus, our work uncovers a process of noise regulation that arises out of the dynamics of gene regulation and is not dependent on any specific transcription factor or specific promoter sequence.

systems biology↗

bioRxiv2020

Exploring phenotyping plasticity for improving deficit irrigation and growth performance in maize

Drought stress in maize often results in poor growth and reduced yield. Antioxidants play vital role in management of abiotic stresses. Drought or water deficit are detrimental to young seedlings establishment and transition from vegetative to reproductive growth in maize. Paclobutrazol (PBZ) has been widely used to confer abiotic stress tolerance in plants, however, its impact on root developmental attributes in maize and their relevance in drought management are least understood. Comprehensive experiments over a three year period (2017-2019) under early deficit (EDI) and terminal deficit (TDI) irrigation with or without paclobutrazol (PBZ) were conducted on five maize varieties (DDKL, DKC-9144, PG-2475, PG-2320 and Bio-9621). Plant shoot and root growth kinetics, phenological changes and physiological perturbations including antioxidant profile coupled with molecular regulation of root traits, showed DKC-9144 as best variety in terms of plant fitness and reproductive performance under deficit irrigation. Root developmental rates were key contributors towards improved plant biomass and cob yield under deficit irrigation tolerance. Structural equation modelling (SEM) demonstrated specific contribution of different root types (crown, brace and seminal roots) in maize towards improving water use efficiency, cob yield and plant height. From SEM, seminal root surface area and root length are proposed desired traits to improve water use efficiency and cob yield in DKC-9144 under deficit irrigation. Bi-variate analyses of twenty key traits of plant fitness and agronomic importance showed a strong correlation (r) between root traits and improved growth performance and yield stability indices.

plant biology↗

bioRxiv2020

Emergence of multiple variants of SARS-CoV-2 with signature structural changes

This study explores the divergence pattern of SARS-CoV-2 using whole genome sequences of the isolates from various COVID-19 affected countries. The phylogenomic analysis indicates the presence of at least four distinct groups of the SARS-CoV-2 genomes. The emergent groups have been found to be associated with signature structural changes in specific proteins. Also, this study reveals the differential levels of divergence patterns for the protein coding regions. Moreover, we have predicted the impact of structural changes on a couple of important viral proteins via structural modelling techniques. This study further advocates for more viral genetic studies with associated clinical outcomes and hosts response for better understanding of SARS-CoV-2 pathogenesis enabling better mitigation of this pandemic situation.

evolutionary biology↗