Biology subjects

Pal, A.

Publications and source records attributed to Pal, A..

At least 91 records · Page 5Linked to original sources

bioRxiv2022

The "LINC" in between Δ40p53-miRNA axis in the regulation of cellular processes

Previous research has shown that {Delta}40p53, the translational isoform of p53, can inhibit cell growth independently of p53 by regulating microRNAs. Here, we explored the role of {Delta}40p53 in regulating the long non-coding RNA-microRNA-cellular process axis, specifically focusing on LINC00176. Interestingly, LINC00176 levels were predominantly affected by the overexpression/stress-mediated induction and knockdown of {Delta}40p53 rather than p53 levels. Additional assays revealed that {Delta}40p53 transactivates LINC00176 transcriptionally and could also regulate its stability. RNA immunoprecipitation experiments revealed that LINC00176 sequesters several putative microRNA targets, which could further titrate several mRNA targets involved in different cellular processes. To understand the downstream effects of this regulation, we ectopically overexpressed and knocked down LINC00176 in HCT116 p53-/- (harboring only {Delta}40p53) cells, which affected their proliferation, cell viability, and expression of epithelial markers. Our results provide essential insights into the pivotal role of {Delta}40p53 in regulating the novel LINC00176 RNA-microRNA-mRNA axis independent of FL-p53 and in maintaining cellular homeostasis.

cancer biology↗

bioRxiv2022

A systems biology approach to disentangle the direct and indirect effects of global transcription factors on gene expression in Escherichia coli

Delineating the pleiotropic effects of global transcriptional factors (TFs) is critical in understanding the system-wide regulatory response in a particular environment. Currently, with the availability of genome-wide TF binding and gene expression data for Escherichia coli, several gene targets can be assigned to the global TFs albeit inconsistently. Here, using a systematic integrated approach with emphasis on metabolism, we characterize and quantify the direct effects as well as the growth-rate mediated indirect effects of global TFs using deletion mutants of FNR, ArcA, and IHF regulators under glucose fermentative condition. Apart from the previous known metabolite-TF interactions, we predicted with high confidence several novel interactions arising from the allosteric effects of the intracellular metabolites. Our combined experimental and compendium level computational analyses revealed the co-expressed genes regulated by these TFs as well as the coordination of the direct and indirect target gene expressions in the context of the economy of intracellular metabolites. Besides, we extended our analysis to combinatorial deletions of these TFs to determine their cross-talk effects as well as conserved patterns of regulatory interactions. Overall, this study leverages the fundamentals of TF-driven regulation which could serve as a better template for deciphering mechanisms underlying complex phenotypes.

systems biology↗

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↗

bioRxiv2022

Guardian crypt-base-goblet-cells protect the human colonic stem cell niche by triggering cholinergic calcium signal-dependent MUC2 secretion and luminal flushing

Mucus secreting goblet cells play a vital role in the maintenance of tissue homeostasis. Here we report the discovery of an enigmatic mechanism for the generation of calcium signals that couple cholinergic input to secretion of hydrated mucus in the human colonic stem cell niche. Mechanistic insights for this study were derived from native human colonic crypts and crypt-like organoids expressing MUC2-mNEON. Importantly, we demonstrate that the human colonic stem cell niche is also a cholinergic niche, and that activation of muscarinic receptors initiates calcium signals at the apical pole of intestinal stem cells and neighbouring crypt-base-goblet-cells. The calcium signal trigger zone is defined by a microdomain of juxtaposed calcium stores expressing TPC1 and InsP3R3 calcium channels. Co-activation of TPC1 and InsP3R3 is required for generation of cholinergic calcium signals and downstream secretion of hydrated mucus, which culminates in the flushing of the colonic stem cell niche.

cell biology↗

bioRxiv2021

Coupled protein quality control during nonsense mediated mRNA decay

Translation of mRNAs containing premature termination codons (PTCs) can result in truncated protein products with deleterious effects. Nonsense-mediated decay (NMD) is a surveillance path-way responsible for detecting and degrading PTC containing transcripts. While the molecular mechanisms governing mRNA degradation have been extensively studied, the fate of the nascent protein product remains largely uncharacterized. Here, we use a fluorescent reporter system in mammalian cells to reveal a selective degradation pathway specifically targeting the protein product of an NMD mRNA. We show that this process is post-translational, and dependent on an intact ubiquitin proteasome system. To systematically uncover factors involved in NMD-linked protein quality control, we conducted genome-wide flow cytometry-based screens. Our screens recovered known NMD factors, and suggested a lack of dependence on the canonical ribosome-quality control (RQC) pathway. Finally, one of the strongest hits in our screens was the E3 ubiquitin ligase CNOT4, a member of the CCR4-NOT complex, which is involved in initiating mRNA degradation. We show that CNOT4 is involved in NMD coupled protein degradation, and its role depends on a functional RING ubiquitin ligase domain. Our results demonstrate the existence of a targeted pathway for nascent protein degradation from PTC containing mRNAs, and provide a framework for identifying and characterizing factors involved in this process.

molecular biology↗

bioRxiv2021

Macrophage cell lines and murine infection by Salmonella Typhi L-form bacteria

Antibiotic resistance of pathogenic bacteria has emerged as a major threat to public health worldwide. While stable resistance due to the acquisition of genomic mutations or plasmids carrying antibiotic-resistance genes is well-established, much less is known about the temporary and reversible resistance induced by antibiotic treatment, such as the one due to treatment with bacterial cell-wall inhibiting antibiotics like ampicillin. Typically, ampicillin concentration in the blood and other tissues gradually increases over time after initiation of the treatment. As a result, the bacterial population is exposed to a concentration gradient of ampicillin. This is different from in vitro drug testing where the organism is exposed to fixed drug concentrations from the beginning till the end. To mimic the mode of antibiotic exposure of microorganisms in the tissues, we cultured the wild type, ampicillin-sensitive Salmonella Typhi Ty2 strain (S. Typhi Ty2) in the presence of increasing concentrations of ampicillin over a period of 14 days. This resulted in the development of a strain that exhibited several features of the so-called L-form of bacteria, such as the absence of cell wall, altered shape and slower growth rate compared with the parental strain. Studies on the pathogenesis of S. Typhi L-form showed efficient infection of the murine and human macrophage cell lines. More importantly, S. Typhi L-form was also able to establish infection in a mouse model to the extent comparable to its parental strain. These results suggested that L-form generation following initiation of antibiotic treatment could lead to drug escape of S. Typhi and direct spread to new cells (macrophages), which sustain the infection. Oral infection by the L-form bacteria underscores the potential of rapid disease transmission through faeco-oral route, highlighting the need for new approaches to decrease the reservoir of infection.

microbiology↗

bioRxiv2021

Selective Control of Synaptically-Connected Circuit Elements by All-Optical Synapses

Understanding percepts, engrams and actions requires methods for selectively modulating synaptic communication between specific subsets of interconnected cells. Here, we develop an approach to control synaptically connected elements using bioluminescent light: Luciferase-generated light, originating from a presynaptic axon terminal, modulates an opsin in its postsynaptic target. Vesicular-localized luciferase is released into the synaptic cleft in response to presynaptic activity, creating a real-time Optical Synapse. Light production is under experimenter-control by introduction of the small molecule luciferin. Signal transmission across this optical synapse is temporally defined by the presence of both the luciferin and presynaptic activity. We validate synaptic Interluminescence by multi-electrode recording in cultured neurons and in mice in vivo. Interluminescence represents a powerful approach to achieve synapse-specific and activity-dependent circuit control during behavior in vivo.

neuroscience↗

bioRxiv2021

Stably Accelerating Stiff Quantitative Systems Pharmacology Models: Continuous-Time Echo State Networks as Implicit Machine Learning

Quantitative systems pharmacology (QsP) may need to change in order to accommodate machine learning (ML), but ML may need to change to work for QsP. Here we investigate the use of neural network surrogates of stiff QsP models. This technique reduces and accelerates QsP models by training ML approximations on simulations. We describe how common neural network methodologies, such as residual neural networks, recurrent neural networks, and physics/biologically-informed neural networks, are fundamentally related to explicit solvers of ordinary differential equations (ODEs). Similar to how explicit ODE solvers are unstable on stiff QsP models, we demonstrate how these ML architectures see similar training instabilities. To address this issue, we showcase methods from scientific machine learning (SciML) which combine techniques from mechanistic modeling with traditional deep learning. We describe the continuous-time echo state network (CTESN) as the implicit analogue of ML architectures and showcase its ability to accurately train and predict on these stiff models where other methods fail. We demonstrate the CTESNs ability to surrogatize a production QsP model, a >1,000 ODE chemical reaction system from the SBML Biomodels repository, and a reaction-diffusion partial differential equation. We showcase the ability to accelerate QsP simulations by up to 56x against the optimized DifferentialEquations.jl solvers while achieving <5% relative error in all of the examples. This shows how incorporating the numerical properties of QsP methods into ML can improve the intersection, and thus presents a potential method for accelerating repeated calculations such as global sensitivity analysis and virtual populations.

pharmacology and toxicology↗

bioRxiv2021

Network rewiring promotes cooperation in an aspirational learning model

We analyze a cooperative decision-making model that is based on individual aspiration levels using the framework of a public goods game in static and dynamic networks. Sensitivity to differences in payoff and dynamic aspiration levels modulate individual satisfaction and affects subsequent behavior. The collective outcome of such strategy changes depends on the efficiency with which aspiration levels are updated. Below a threshold learning efficiency, cooperators dominate despite short-term fluctuations in strategy fractions. Categorizing players based on their satisfaction level and the resulting strategy reveal periodic cycling between the different categories. We explain the distinct dynamics in the two phases in terms of differences in the dominant cyclic transitions between different categories of cooperators and defectors. Allowing even a small fraction of nodes to restructure their connections can promote cooperation across almost the entire range of values of learning efficiency. Our work reinforces the usefulness of an internal criterion for strategy updates, together with network restructuring, in ensuring the dominance of altruistic strategies over long time-scales. Maintaining a public resource requires sustained cooperation through contributions by community members who benefit from it. Yet, a selfish individual who refuses to contribute can enjoy the benefits without paying the cost of sustaining the public good. If however, too many members of the community act selfishly, the public resource collapses to the detriment of all. The public goods game highlights such a social dilemma and provides a framework for exploring different mechanisms of strategic decision-making that allow cooperation and consequently the public good to be sustained. Among many mechanisms, the reorganization of social ties has been shown to be effective in promoting cooperation in PGG. However, the efficacy of most mechanisms in sustaining cooperation rely on individuals updating their strategy on the basis of information about the contributions of other members of the community. Often such information is either not forthcoming or cannot be effectively utilized. An alternative low-information model of behavioral updating relies on a comparison between the actual benefit received and the benefit aspired for. Individuals tend to retain their strategy if they are satisfied with the benefit received and change their strategy if they are unsatisfied. We show that such a simple reinforcement learning model along with modest restructuring of social ties over time can allow cooperation to be sustained. Our work shows that a low-information strategy-update model can be very effective in ensuring dominance of cooperators in social dilemmas.

animal behavior and cognition↗

bioRxiv2021

Ovine CD14- an immune response gene has a role against gastrointesinal nematode Haemonchus contortus -a novel report

CD14 (also known as monocyte differentiation antigen) is an important immune response gene known to be primarily responsible for innate immunity against bacterial pathogen and as pattern recognition receptor (PRR) binds with LPS (endotoxin), lipoproteins, lipotechoic acid of bacteria.So far very limited work has been conducted in parasitic immunology. In the current study, we reported the role of CD14 in parasitic immunology in livestock species (sheep) for the first time. Ovine CD14 is characterized as a horse-shoe shaped as a bent solenoid with a hydrophobic amino-terminal pocket for CD14 along with domains. High mutation frequency was observed, out of total 41 mutations identified, 23 mutations were observed to be thermodynamically unstable and 11 mutations were deleterious in nature, causing major functional alteration of important domains of CD14, an indicative for variations in individual susceptibility for sheeps against Haemonchus contortus infestations. In silico studies with molecular docking reveals a role of immune response against Haemonchus contortus in sheep, which is later confirmed with experimental evidence through differential mRNA expression analysis for sheep, which revealed better expression of CD14 in Haemonchus contortus infected sheep compared to that of healthy sheep. We confirmed the above findings with supportive evidences with haematological and biochemical analyses. Phylogenetic analysis was conducted to assess the evolutionary relationship with respect to human and observed that sheep may well be used as model organism due better genetic closeness compared to that of mouse.

genomics↗

bioRxiv2020

Deciphering colchicine like actions of clerodin in terms of microtubule destabilization based mitotic abnormalities, G2/M-phase arrest, and plant polyploidy

Clerodin (C24H34O7), a clerodane diterpenoid, is a bitter principle of Clerodendrum viscosum. The present study aimed to decipher colchicine-like actions of clerodin in terms of microtubule destabilization based mitotic abnormalities, G2-M arrest, and plant polyploidy. Purified clerodin showed increased metaphase frequency in Human Peripheral Blood Lymphocytes (HPBLs), Human Embryonic Kidney cells (HEK-293), and Allium cepa root apical meristem cells. Both squashed slide of the onion root tip and flow cytometric analysis of radish protoplast revealed a significantly increased frequency of polyploid cells. Flow cytometric analysis showed an increase in frequencies of G2-M in MCF-7 cells from 6.10 to 16.25% after clerodin (200g/mL) treatment for 24 h. Confocal microscopy imaging of tubulin in clerodin-treated MCF-7 cells revealed microtubule destabilization. Molecular docking and LIGPLOT analysis indicate that clerodin interact in the colchicine binding site, including, single hydrogen bond with Asn 101 of -tubulin. In summary, our experimental data revealed that clerodin has metaphase arresting, microtubule destabilization, and polyploidy inducing ability similar to colchicine. Molecular docking analysis revealed for the first time that clerodin and colchicine interact at the common site of tubulin residue indicating a common mechanism of action. The results also indicate similar cytotoxic potentialities of both clerodin and colchicine even though they belong to different chemical groups. Thus, clerodin may be used in place of colchicine as a plant polyploidy inducing agent in plant breeding programs in Agriculture.

cell biology↗

bioRxiv2020

Paired motor cortex and spinal cord epidural stimulation strengthens sensorimotor connections and improves forelimb function after cervical spinal cord injury in rats.

Associative plasticity occurs when two stimuli converge on a common neural target. Previous efforts to promote associative plasticity have targeted cortex, with variable and moderate effects. In addition, the targeted circuits are inferred, rather than tested directly. In contrast, we sought to target the strong convergence between motor and sensory systems in the spinal cord. We developed spinal cord associative plasticity (SCAP), precisely timed pairing of motor cortex and dorsal spinal cord stimulations, to target this interaction. We tested the hypothesis that properly timed paired stimulation would strengthen the sensorimotor connections in the spinal cord and improve recovery after spinal cord injury (SCI). We tested physiological effects of paired stimulation, the pathways that mediate it, and its function in a preclinical trial. Subthreshold spinal cord stimulation strongly augmented motor cortex evoked muscle potentials at the time they were paired, but only when they arrived synchronously in the spinal cord. This paired stimulation effect depended on both cortical descending motor and spinal cord proprioceptive afferents; selective inactivation of either of these pathways fully abrogated the paired stimulation effect. SCAP, repetitive pairing of these pathways for 5 or 30 minutes in awake rats, increased spinal excitability for hours after pairing ended. To apply SCAP as therapy, we optimized the parameters to promote strong and long-lasting effects. This effect was just as strong in rats with cervical SCI as in uninjured rats, demonstrating that spared connections after moderate SCI were sufficient to support plasticity. In a blinded trial, rats received a moderate C4 contusive SCI. Ten days after injury, they were randomized to 30 minutes of SCAP each day for 10 days or sham stimulation. Rats with SCAP had significantly improved function on the primary outcome measure, a test of dexterity during manipulation of food, at 50 days after SCI. In addition, rats with SCAP had persistently stronger responses to cortical and spinal stimulation than sham stimulation rats, indicating a spinal locus of plasticity. SCAP rats had lasting improvements in H-reflex modulation. The groups had no difference in the rat grimace scale, a measure of pain. We conclude that SCAP strengthens sensorimotor connections within the spinal cord, resulting in improved reflex modulation and forelimb function after moderate SCI. Since both motor cortex and spinal cord stimulation are performed routinely in humans, this approach can be trialed in people with SCI or other disorders that damage sensorimotor connections and impair dexterity.

neuroscience↗

bioRxiv2020

Better expression profile of CD8 and CD4 gene in uterus of pregnant ewe in comparison to non-pregnant - a novel report

CD8 and CD4 T cells play a central role in the immune response to viruses and intracellular pathogens as well as functions for the maintenance of both the mother and fetus. The present study was conducted to explore the differential gene expression profile for CD8 and CD4 present in the uterus with reference to the gravid and non-gravid Garole sheep and confirmation through immuno histochemical studies. Better CD8 and CD4 gene expression was observed in the mid uterus of pregnant ewes compared to that of non-pregnant ewes, where CD8 expression was better to that of CD4. Gene expression profiling of CD8 and CD4 are reported here for the first time in sheep. CD8 and CD4 expression may be regarded as the useful factor for maintenance of pregnancy. The current observations demonstrate that during pregnancy in ewe the immune system may respond to changes in the maternal environment to maintain the size and function of the CD8 and CD4 T-cell compartment. CD8 and CD4 expression may be employed as marker for pregnancy detection in sheep, which remains always a challenge for sheep breeders.

immunology↗

bioRxiv2020

RIG-I has a role in immunity against Haemonchus contortus, a gastrointestinal parasite in Ovis aries- a novel report.

RIG-I is associated to the DExD/H box RNA Helicases. It is a Pattern Recognition Receptor (PRR), playing a crucial role in the system and is a germ line encoded host sensor to perceive Pathogen Associated Molecular Patterns or PAMPs. So far reports were available for the role of RIG-I in antiviral immunity. This is the first report we have documented the role of RIG-I in parasitic immunity. Haemonchus contortus is a deadly parasite affecting sheep industry which has a tremendous economic importance and the parasite reported to be prevalent in the hot and humid agroclimatic region. We had characterized RIG-I gene in sheep (Ovis aries) and identified the important domains or binding site with Haemonchus contortus through in silico studies. Differential mRNA expression analysis revealed upregulation of RIG-I gene in abomassum of infected sheep compared to that of healthy sheep, further confirming the findings. Thus it is evident that in infected sheep, expression of RIG-I is triggered for binding to more pathogen (Haemonchus contortus). Genetic similar studies with human and other livestock species were conducted to reveal that sheep may be efficiently used a model organism for studying the role of RIG-I in antiparasitic immunity of human.

genomics↗

bioRxiv2020

Molecular characterization of RIGI, TLR7 and TLR3 as immune response gene of indigenous ducks in response to Avian influenza

Avian influenza is an alarming disease, which has every possibility to evolve as human to human pandemic situation due to frequent mutation and genetic reassortment or recombination of Avian influenza(AI) virus. The greatest concern is that till date no satisfactory medicine or vaccines are available, leading to massive culling of poultry birds causing huge economic loss, and ban on export of chicken products, which emphasise the need develop alternative strategy for control of AI. In the current study we attempt to explore the molecular mechanism of innate immune potential of ducks against common viral diseases including Avian influenza. In the present study, we have characterized immune response molecules as duck TLR3, TLR7, and RIGI and predicted to have potent antiviral activities against different identified strains of Avian influenza through in silico studies (molecular docking). Future exploitation involve immunomodulation with the recombinant protein, transgenic or gene-edited chicken resistant to bird flu.

genomics↗

bioRxiv2020

Wide variabilities identified among spike proteins of SARS Cov2 globally-dominant variant identified

SARS Cov2 is a newly emerged virus causing pandemic with fatality and co-morbidity. The greatest limitations emerged is the lack of effective treatment and vaccination due to frequent mutations and reassortment of the virus, leading to evolvement of different strains. We identified a wide variability in the whole genome sequences as well as spike protein variants (responsible for binding with ACE2 receptor) of SARS Cov2 identified globally. Structural variations of spike proteins identified from representative countries from all the continents, seven of them have revealed genetically similar, may be regarded as the dominant type. Novel non-synonymous mutations as S247R, R408I, G612D, A930V and deletion detected at amino acid position 144. RMSD values ranging from 4.45 to 2.25 for the dominant variant spike1 with other spike proteins. This study is informative for future vaccine research and drug development with the dominant type.

genomics↗

bioRxiv2020

Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Complex regulatory interactions between genetic and metabolic networks together confer robustness against external and internal perturbations in an organism such as Escherichia coli. In balanced exponential growth, this robustness is attributed to cost-effective metabolism by means of efficient resource allocation coordinated by the interplay of global transcriptional regulators with growth-rate dependent machinery. Here, we reappraise the role of global transcriptional regulators FNR, ArcA and IHF, integral to sustaining proteome-efficiency in anaerobic fermentative conditions, fundamental for optimal growth of E. coli. We reveal at the transcriptome and metabolome level, that absence of these global regulators ensued a disruption of nitrogen homeostasis, overexpression of otherwise unnecessary or hedging genes and impairment in core bottleneck steps and amino acid metabolism. Notably, our findings emphasize their importance in optimizing the metabolic proteome resources essential for rapid exponential growth. Consequentially, the perturbations in the metabolic proteome as a result of deletion of global regulators unbalances the ribosomal proteome share imposing a high translation program, though at the expense of lowered efficiency. We illustrate that disruption of this inherent trade-off between metabolic and ribosomal proteomic investment eventually culminate to lowered growth rates. Despite no changes in gene expression related to glucose import, our findings elucidate that the accumulations of intracellular metabolites directly modulated by growth rate, negatively impacts the glucose uptake. Our results employing the proteome allocation theory and quantitative experimental measurements, suffices to explain the physiological consequences of altered translational and metabolic efficiency in the cell, driven by the loss of these global regulators.

systems biology↗