Biology subjects

Bhat, A.

Publications and source records attributed to Bhat, A..

35 records · Page 2Linked to original sources

bioRxiv2023

Use of multimodal sensory cues in predator avoidance by wild-caught zebrafish shoals

Shoaling in fishes is regulated by factors like predation, vegetation cover, water flow and food availability. Shoals detect and respond to changes in these ecological factors using a multimodal sensory system. Here, we examine the immediate response of wild-caught zebrafish (Danio rerio) shoals to cues from its natural predator, the snakehead (Channa sp.). Zebrafish shoals were recorded upon exposure to (1) olfactory predator cues, (2) visual predator cues, (3) both cues together, and (4) no cue. We tracked individuals and analysed shoal responses across these treatments. We found that compared to control treatments, shoals receiving either visual or olfactory cues had significantly greater: (i) cohesion, (ii) polarization and (iii) velocity. Interestingly, when the shoals received both cues simultaneously, the cohesion, polarization and velocity decreased and a significantly greater number of individual freezing events occurred. Therefore, zebrafish relied on both visual and olfactory cues to escape predation. However, when shoals were presented with both cues together, while freezing frequency increased, other responses were comparable to control treatments where no predator cue was provided. While this study indicates that multimodal cues elicit a different anti-predator response than the cues singly, more experiments are required to identify the underlying cause of this behaviour.

animal behavior and cognition↗

bioRxiv2022

What drives mixed-species shoaling among wild zebrafish? Role of predators, food access, abundance of conspecifics, and kin familiarity

Mixed-species groups commonly occur across a wide range of faunal communities and are known to provide several benefits to members. While zebrafish have often been observed to form mixed-species shoals with coexisting species, the factors determining their occurrence is not yet understood. Using laboratory-based experiments, we decipher the main ecological drivers of mixed-species shoaling in these tropical fish communities. Shoals comprising zebrafish (Danio rerio), flying barbs (Esomus danricus) and whitespots (Aplocheilus panchax) were collected from a stagnant canal at Haringhata (West Bengal, India). Experiments to assess foraging efficiency were conducted where single or mixed-species shoals (comprising 5 individuals) were given low or high amounts of food. Shoal choice experiments were also conducted to assess the preferences of test subjects (zebrafish individuals) for forming associations based on shoal composition and familiarity. Results from experiments on feeding efficiency revealed that foraging time varied substantially among the shoal types (i.e., single or mixed-species), and was dependent on the quantity of food available, but not linked to the body size of species composing the shoal. The choice experiments to examine preference for associations revealed that under predator risk, zebrafish associate more with mixed shoals, and showed comparable associations to shoals differing in the abundance of conspecifics. Furthermore, we found that zebrafish preferred to associate with familiar conspecific over unfamiliar mixed and unfamiliar conspecific shoals. Therefore, equitable food consumption in mixed shoals, greater association to mixed shoals in presence of predator and familiarity were found to be important drivers for choosing mixed-species shoaling by zebrafish.

animal behavior and cognition↗

bioRxiv2021

Attenuated transcriptional response to pro-inflammatory cytokines in schizophrenia hiPSC-derived neural progenitor cells

Maternal immune activation (MIA) during prenatal development is an environmental risk factor for psychiatric disorders including schizophrenia (SZ). This link is particularly well established in the case of schizophrenia. Converging lines of evidence from human and animal model studies have suggested that elevated cytokine levels in the maternal and fetal compartments are an important indication of the mechanisms driving this association. However, there is variability in susceptibility to the psychiatric risk conferred by MIA, likely influenced by genetic factors. How MIA interacts with a genetic profile susceptible to SZ is challenging to test in animal models. To address this gap, we examined whether differential gene expression responses occur in forebrain-lineage neural progenitor cells (NPCs) derived from human induced pluripotent stem cells (hiPSC) generated from three individuals with a diagnosis of schizophrenia and three healthy controls. Following acute (24 hour) treatment with either interferon-gamma (IFN{gamma}; 25 ng/l) or interleukin (IL)-1{beta} (10 ng/l), we identified, by RNA sequencing, 3380 differentially expressed genes (DEGs) in the IFN{gamma}-treated control lines (compared to untreated controls), and 1980 DEGs in IFN{gamma}-treated SZ lines (compared to untreated SZ lines). Of these, 359 genes responded differently to IFN{gamma} treatment in SZ relative to control lines, which were enriched for genes differentially expressed in adult SZ cases and in pathways related to the regulation of antigen processing, neuronal post-synaptic density, and the presynapse. There were no differentially expressed genes in the IL-1{beta}-treatment conditions after Benjamini-Hochberg correction. Gene set enrichment analysis however showed that IL-1{beta} impacts immune function and neuronal differentiation. Collectively, our data suggest that a) SZ NPCs show an attenuated transcriptional response to IFN{gamma} treatment compared to control NPCs; b) IL-1{beta} may be less relevant to NPC cultures than IFN{gamma} and c) the genes differentially regulated in schizophrenia lines are primarily mitochondrial, loss-of-function, pre- and post-synaptic genes. Our findings particularly highlight early synaptic development as a key target for future research into the mechanisms of association between maternal immune activation and schizophrenia risk. Highlights* There is a significant transcriptional response to IFN{gamma} treatment in human induced cortical neural progenitor cells (NPCs) * Differential expression implicates mitochondrial complex genes in this IFN{gamma}-dependent response, which are underexpressed in response to treatment in schizophrenia (SZ) NPCs. * SZ NPCs do not upregulate pre- and post-synaptic genes in response to IFN{gamma} as much as control NPCs * IL-1{beta} may be less relevant to NPC cultures than IFN{gamma} due to low IL1 receptor expression in NPCs.

neuroscience↗

bioRxiv2021

In vitro neurons learn and exhibit sentience when embodied in a simulated game-world

Integrating neurons into digital systems to leverage their innate intelligence may enable performance infeasible with silicon alone, along with providing insight into the cellular origin of intelligence. We developed DishBrain, a system which exhibits natural intelligence by harnessing the inherent adaptive computation of neurons in a structured environment. In vitro neural networks from human or rodent origins, are integrated with in silico computing via high-density multielectrode array. Through electrophysiological stimulation and recording, cultures were embedded in a simulated game-world, mimicking the arcade game Pong. Applying a previously untestable theory of active inference via the Free Energy Principle, we found that learning was apparent within five minutes of real-time gameplay, not observed in control conditions. Further experiments demonstrate the importance of closed-loop structured feedback in eliciting learning over time. Cultures display the ability to self-organise in a goal-directed manner in response to sparse sensory information about the consequences of their actions.

synthetic biology↗

bioRxiv2021

Inhibition of PDE4 by Roflumilast ameliorates sleep deprivation-induced cognitive dysfunction in C57BL/6J mice

Sleep deprivation (SD) interferes with long-term memory and cognitive functions by over-activation of phosphodiesterase (PDEs) enzymes. PDE4, a non-redundant regulator of the cyclic nucleotides (cAMP), is densely expressed in the hippocampus and is involved in learning and memory processes. In the present study, we investigated the effects of Roflumilast (ROF), a PDE4B inhibitor, on sleep deprivation induced cognitive dysfunction in a mouse model. Memory assessment was performed using a novel object recognition task and the hippocampal cAMP level was estimated by the ELISA method. The alterations in the expressions of PDE4B, amyloid-beta (A{beta}), CREB, BDNF, and synaptic proteins (Synapsin I, SAP 97, PSD 95) were assessed to gain insights into the possible mechanisms of action of ROF using the Western blot technique. Results show that ROF reversed SD induced cognitive decline in mice. ROF down-regulated PDE4B and A{beta} expressions in the brain. Additionally, ROF improved the cAMP level and the protein expressions of synapsin I, SAP 97, and PSD 95 in the hippocampal region of SD mice. Taken together, these results suggest that ROF can suppress the deleterious effects of SD-induced cognitive dysfunction via the PDE4B-mediated cAMP/CREB/BDNF signaling cascade.

pharmacology and toxicology↗

bioRxiv2021

FMO rewires metabolism to promote longevity throughtryptophan and one carbon metabolism

Flavin containing monooxygenases (FMOs) are promiscuous enzymes known for metabolizing a wide range of exogenous compounds. In C. elegans, fmo-2 expression increases lifespan and healthspan downstream of multiple longevity-promoting pathways through an unknown mechanism. Here, we report that, contrary to its classification as a xenobiotic enzyme, fmo-2 expression leads to rewiring of endogenous metabolism principally through changes in one carbon metabolism (OCM). Using computer modeling, we identify decreased methylation as the major OCM flux modified by FMO-2 that is sufficient to recapitulate its longevity benefits. We further find that tryptophan is decreased in multiple mammalian FMO overexpression models and is a validated substrate for FMO enzymes. Our resulting model connects a single enzyme to two previously unconnected key metabolic pathways and provides a framework for the metabolic interconnectivity of longevity-promoting pathways such as dietary restriction. FMOs are well-conserved enzymes that are also induced by lifespan-extending interventions in mice, supporting a conserved and critical role in promoting health and longevity through metabolic remodeling.

molecular biology↗

bioRxiv2020

Inhibition of phosphodiesterase - 10A by Papaverine protects human cortical neurons from quinolinic acid-induced oxidative stress and synaptic proteins alterations

Phosphodi esterase-10A (PDE10A) hydrolyse the secondary messengers cGMP and cAMP which play critical role in neurodevelopment and brain functions. PDE10A is linked to progression of neurodegenerative diseases like Alzheimers, Parkinsons, Huntingtons diseases etc and a critical role in cognitive functions. The present study was undertaken to determine the possible neuroprotective effects and the associated mechanism of papaverine (PAP) against quinolinic acid (QUIN) induced excitotoxicity using human primary cortical neurons. Cytotoxicity potential of PAP was analysed using MTS assay. Reactive oxygen species (ROS) and mitochondrial membrane potential were measured by DCF-DA and JC10 staining, respectively. Caspase 3/7 and cAMP levels using ELISA kits. Effect of PAP on the CREB, BNDF and synaptic proteins such as SAP-97, synaptophysin, synapsin-I, PSD-95 expression was analysed by Western blotting technique. Pre-treatment with PAP increased intracellular cAMP and nicotinamide adenine dinucleotide (NAD+) levels, restored mitochondrial membrane potential ({Delta}{Psi}m), and decreased ROS and caspase3/7 content in QUIN exposed neurons. PAP up-regulated CREB and BDNF, and synaptic proteins expression. In summary, these data indicate that PDE10A involves in QUIN mediated neurotoxicity and its inhibition can elicit neuroprotection by reducing the oxidative stress and protecting synaptic proteins via upregulation of cAMP signalling cascade.

neuroscience↗

bioRxiv2020

Control and mechanisms of pulsatile flows in epithelial monolayers

Collective motions of epithelial cells in vivo are essential for morphogenesis in developmental biology. Tissues elongate, contract, flow, and oscillate, thus sculpting embryos. These tissue level dynamics are known, but the physical mechanisms at the cellular level are unclear, with various behaviors depending on the tissues and species. Moreover, investigations on in vitro tissue behavior usually focus on only one type of cell dynamics and use diverse theoretical approaches, making systematic comparisons between studies challenging. Here, we show that a single epithelial monolayer of Madin Darby Canine Kidney (MDCK) cells can exhibit two types of local tissue kinematics, pulsations and long range coherent flows. We analyzed these distinct motions by using quantitative live imaging. We also report that these motions can be controlled with internal and external cues such as specific inhibitors, and friction modulation of the substrate by microcontact printing method. We further demonstrate with a unified vertex model that both behaviors depend on the competition between velocity alignment and random diffusion of cell polarization. When alignment and diffusion are comparable, a pulsatile flow emerges, whereas the tissue undergoes long-range flows when velocity alignment dominates. We propose that environmental friction, acto-myosin distributions, and cell polarization kinetics are important in regulating the dynamics of tissue morphogenesis.

biophysics↗

bioRxiv2020

Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression.

Background & Aims Aspirin has potent anti-platelet activities and possibly helps regression of fibrosis. We investigated antifibrotic mechanisms of aspirin in the murine CCl4 model and in patients with hepatic fibrosis.Methods Multiomics analysis identified networks and molecular targets regulated by aspirin which were validated in murine model and in patients with liver fibrosis.Results Biochemical/histopathological changes and hepatic fibrosis were greater in CCl4-treated mice compared to CCl4-aspirin (CCl4+ASA) or control mice (p<0.05). In CCl4+ASA mice, integrated proteome-metabolome analysis showed an increase in autophagy, drug metabolism, glutathione and energy metabolism (p<0.05) and decrease in inflammatory pathways, arachidonic acid and butanoate metabolism (p<0.05). Global cross-correlation analysis linked fibrosis markers with protein-metabolite pathways (r2>0.5, p<0.05). Liver proteome enrichment for immune clusters using blood transcription module correlated with histidine and tryptophan metabolism (r2>0.5, p<0.05). Aspirin decreased Ryanodine-receptor-2 (RYR2;oxidative-stress), Arginase-1 (ARG-1;urea cycle), Arachidonate-5-lipoxygenase (ALOX5;leukotriene metabolism), and Kynurenine-3-monooxygenase (KMO;tryptophan metabolism; p<0.05) which correlated with reduction in α-SMA, PDGFR-β and degree of hepatic fibrosis (r2>0.75; p<0.05) in animal and human studies, and, in-vitro analysis. Aspirin modulated intracellular-calcium and oxidative-stress levels by reducing RYR2 expression in activated LX-2 cells. It modulated the liver microbiome and its functions which also correlated with ARG1, ALOX5, RYR2 expression (r2>0.5, p<0.05). Metaproteome analysis showed significant microbiome similarity at phylum level in murine liver tissues and fecal samples. Aspirin increased the abundance of Firmicutes (Ruminococcaceae, Lachnospiraceae, and Clostridiaceae) and their functionality, as assessed by glycerol-3-phosphate dehydrogenase (NAD(P)(+) and dTMP-kinase activity (p<0.05).Conclusions Aspirin demonstrates broad beneficial effects following oxidative injury, inflammation, and hepatic fibrosis. Aspirin induces distinctive hepatic proteome/metabolome and intrahepatic microbiome changes which are indicative of fibrosis regression and could be further explored as therapeutic targets.Competing Interest StatementThe authors have declared no competing interest.View Full Text

molecular biology↗

bioRxiv2020

Gravin-associated kinase signaling networks coordinate γ-tubulin organization at mitotic spindle poles

Mitogenic signals that regulate cell division often proceed through multi-enzyme assemblies within defined intracellular compartments. The anchoring protein Gravin restricts the action of mitotic kinases and cell-cycle effectors to defined mitotic structures. In this report we discover that genetic deletion of Gravin disrupts proper accumulation and asymmetric distribution of {gamma}-tubulin during mitosis. We utilize a new precision pharmacology tool, Local Kinase Inhibition (LoKI), to inhibit the Gravin binding partner polo-like kinase 1 (Plk1) at spindle poles. Using a combination of gene-editing approaches, quantitative imaging, and biochemical assays we provide evidence that disruption of local Plk1 signaling underlies the {gamma}-tubulin distribution defects observed with Gravin loss. Our study uncovers a new role for Gravin in coordinating {gamma}-tubulin recruitment during mitosis and illuminates the mechanism by which signaling enzymes regulate this process at a distinct subcellular location.

cell biology↗

bioRxiv2020

Evolutionarily related small viral fusogens hijack distinct but modular actin nucleation pathways to drive cell-cell fusion

Fusion-associated small transmembrane (FAST) proteins are a diverse family of non-structural viral proteins that, once expressed on the plasma membrane of infected cells, drive fusion with neighboring cells, increasing viral spread and pathogenicity. Unlike viral fusogens with tall ectodomains that pull two membranes together through conformational changes, FAST proteins have short fusogenic ectodomains that cannot bridge the inter-membrane gap between neighboring cells. One orthoreovirus FAST protein, p14, has been shown to hijack the actin cytoskeleton to drive cell-cell fusion, but the actin adaptor-binding motif identified in p14 is not found in any other FAST protein. Here, we report that an evolutionarily divergent FAST protein, p22 from aquareovirus, also hijacks the actin cytoskeleton but does so through different adaptor proteins, Intersectin-1 and Cdc42, that trigger N-WASP-mediated branched actin assembly. We show that despite using different pathways, the cytoplasmic tails of p22 and p14 can be exchanging to create a potent chimeric fusogen, suggesting they are modular and play similar functional roles. When we replace p22s branched actin nucleator, N-WASP, with the parallel filament nucleator, formin, its ability to drive fusion is maintained, indicating that localized mechanical pressure on the plasma membrane coupled to a membrane-disruptive ectodomain is sufficient to drive cell-cell fusion. This work points to a common biophysical strategy used by FAST proteins to push rather than pull membranes together to drive fusion, one that may be harnessed by other short fusogens responsible for physiological cell-cell fusion.

cell biology↗

bioRxiv2020

Systematic characterization of somatic mutation-mediated microRNA regulatory network perturbations

Somatic mutations are a major source of cancer development. Many driver mutations have been identified in protein coding regions. However, the function of mutations located in microRNAs (miRNAs) and their target binding sites along the human genome remains largely unknown. Here, we built comprehensive cancer-specific miRNA regulatory networks across 30 cancer types to systematically analyze the effect of mutations on miRNA related pathways. 3,518,261 mutations from 9,819 samples were mapped to miRNA-gene interactions (mGI), and mutations in miRNAs versus in their target genes show a mutually exclusive pattern in almost all cancer types. Using a linear regression method, we further identified 89 driver mutations in 14 cancer types that can significantly perturb miRNA regulatory networks. We find that driver mutations play their roles by altering RNA binding energy and the expression of target genes. Finally, we demonstrate that mutated driver gene targets are significantly down-regulated in cancer and function as tumor suppressors during cancer progression, suggesting potential miRNA candidates with significant clinical implications. We provide this data resource (CanVar-mGI) through a user-friendly, open-access web portal. Together, our results will facilitate novel non-coding biomarker identification and therapeutic drug design.

bioinformatics↗

bioRxiv2020

Fright and Fight: Role of predation and competition on mate search tactics of wild male zebrafish

Mate search tactics and association preferences among organisms in natural habitats can be dynamic and are determined by inherent trait preferences as well as the cost-benefit trade-offs associated with each mating decision. Two of the prime factors regulating mating decisions are the presence of competing conspecifics and predatory threats, both of which have important fitness consequences for the individual. We studied the influence of these two factors separately in mate search tactics and association preferences among zebrafish males. Male zebrafish were presented with a choice of two patches, consisting of different number of females, of which one patch was also associated with a predatory threat. We found that males made a preferential choice for the patch with more number of females only when the numerical difference between choices are starkly different, irrespective of the predatory threat associated with the patch. This points towards the role of numerical cognition in assessing cost-benefit tradeoffs in male zebrafish. We also studied the association preference of males in a multi-choice setup, consisting of four separate mixed-sex groups of zebrafish varying in densities. Our results showed that while test males preferred to visit the male-biased patches more often, they spent more time near female-biased patches or patches with equal sex ratio patches indicating the role of complex interplay of social cues in determining the associative behavior of males to a patch. This study, thus, sheds further light on the interactive roles of social cues and cognitive abilities in mate association patterns in this species.

animal behavior and cognition↗

bioRxiv2020

What drives male association tendencies in wild zebrafish? Role of female and vegetation densities

Mating strategies in species is context-dependent and driven by several ecological and demographic factors. In natural habitats, a multitude of ecological factors interact and these eventually determine mating preferences and mate choice decisions among species. While zebrafish (Danio rerio) is a widely studied biological model organism, our understanding of their mating preferences, strategies and their underlying ecological drivers are still limited. Here, we explore the role of ecological factors such as spatial variation (or patchiness) in mate density and associated vegetation cover in determining mate association tactics among males in a wild zebrafish population. We employed a multi-choice experimental design for a better representation of ecologically relevant scenarios. Our results revealed that when presented with patches with increasing female densities, males displayed only a marginal increase in preference for higher female density patches. However, when female density varied concomitantly with variation in vegetation cover, the males associated more with higher foliage density patches irrespective of the female density in that patch. Our findings throw light on the complex interaction between these two most basic ecological factors in determining mate search strategies and mate associations among these group-living fish species.

animal behavior and cognition↗

bioRxiv2019

Assemblies of F-actin and myosin-II minifilaments: steric hindrance and stratification at the membrane cortex

Recent in-vivo studies have revealed that several membrane proteins are driven to form nanoclusters by active contractile flows arising from F-actin and myosin at the cortex. The mechanism of clustering was shown to be arising from the dynamic patterning of transient contractile platforms (asters) generated by actin and myosin. Myosin-II, which assemble as minifilaments consisting of tens of myosin heads, are rather bulky structures and hence a concern could be that steric considerations might obstruct the emergence of nanoclustering. Here, using coarse-grained, agent-based simulations that respect the size of constituents, we find that in the presence of steric hindrance, the patterns exhibited by actomyosin in two dimensions, do not resemble the steady state patterns observed in our in-vitro reconstitution of actomyosin on a supported bilayer. We then perform simulations in a thin rectangular slab, allowing the separation of a layer of actin filaments from those of myosin-II minifilaments. This recapitulates the observed features of in-vitro patterning. Using super resolution microscopy, we find direct evidence for stratification in our in-vitro system. Our study suggests the possibility that molecular stratification may be an important organising feature of the cortical cytoskeleton in-vivo.

cell biology↗

bioRxiv2019

The roles of microtubules and membrane tension in axonal beading, retraction, and atrophy

Axonal beading--formation of a series of swellings along the axon--and retraction are commonly observed shape transformations that precede axonal atrophy in Alzheimers, Parkinson, and other neurodegenerative conditions. The mechanisms driving these morphological transformations are poorly understood. Here we report controlled experiments which can induce either beading or retraction and follow the time evolution of these responses. By making quantitative analysis of the shape modes under different conditions, measurement of membrane tension, and using theoretical considerations, we argue that membrane tension is the main driving force that pushes cytosol out of the axon when microtubules are degraded, causing axonal thinning. Under pharmacological perturbation, atrophy is always retrograde and this is set by a gradient in the microtubule stability. The nature of microtubule depolymerization dictates the type of shape transformation vis a vis beading or retraction. Elucidating the mechanisms of these shape transformations will facilitate development of strategies to prevent or arrest axonal atrophy due to neurodegenerative conditions.

biophysics↗

bioRxiv2019

Ncl1 mediated metabolic rewiring is critical during metabolic stress

Nutritional limitation has been vastly studied, however, there is limited knowledge of how cells maintain homeostasis in excess nutrients. In this study, using yeast as a model system, we show that some amino acids are toxic at higher concentrations. With cysteine as a physiologically relevant example, we delineated the pathways/processes that are altered and those that are involved in survival in presence of elevated levels of this amino acid. Using proteomics and metabolomics approach, we found that cysteine upregulates proteins involved in amino acid metabolism, alters amino acid levels, and inhibits protein translation, events that are rescued by leucine supplementation. Through a comprehensive genetic screen we show that leucine mediated effect depends on a tRNA methyltransferase (Ncl1), absence of which decouples cells transcription and translation, inhibits the conversation of leucine to ketoisocaproate and leads to TCA cycle block. We therefore, propose a role of Ncl1 in regulating metabolic homeostasis through translational control.

biochemistry↗