Biology subjects

Mishra, A.

Publications and source records attributed to Mishra, A..

15 recordsLinked to original sources

bioRxiv2018

Two-component systems regulate swarming in Pseudomonas aeruginosa PA14

Swarming in Pseudomonas aeruginosa is a quorum-dependant motility over semi-solid surfaces. On soft agar, P. aeruginosa exhibits a dendritic swarm pattern, with multiple levels of branching. Swarm patterns vary considerably depending upon the experimental design. In the present study, we show that the swarm pattern is plastic and media dependent. We define several quantifiable, macroscale features of the swarm to study the plasticity observed across media. Further, through a targeted screen of 113 genes encoding two-component system (TCS) components, we show that 44 TCS genes regulate PA14 swarming in a contextual fashion. However, only four TCS genes are essential for swarming. Many swarming-defective TCS mutants are highly efficient in biofilm formation indicating an antagonistic relationship between swarming and biofilm states in P. aeruginosa.

microbiology↗

bioRxiv2018

Genetic Determinants of Cortical Structure (Thickness, Surface Area and Volumes) among Disease Free Adults in the CHARGE Consortium

Cortical thickness, surface area and volumes (MRI cortical measures) vary with age and cognitive function, and in neurological and psychiatric diseases. We examined heritability, genetic correlations and genome-wide associations of cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprised 22,822 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the United Kingdom Biobank. Significant associations were replicated in the Enhancing Neuroimaging Genetics through Meta-analysis (ENIGMA) consortium, and their biological implications explored using bioinformatic annotation and pathway analyses. We identified genetic heterogeneity between cortical measures and brain regions, and 161 genome-wide significant associations pointing to wnt/{beta}-catenin, TGF-{beta} and sonic hedgehog pathways. There was enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging.

genetics↗

bioRxiv2018

Amyloid β oligomers constrict human capillaries in Alzheimer’s disease via signalling to pericytes

Vascular compromise occurs early in Alzheimers disease (AD) and other dementias1-3. Amyloid {beta} (A{beta}) reduces cerebral blood flow4-6 and, as most of the cerebral vasculature resistance is in capillaries7, A{beta} might mainly act on contractile pericytes on capillary walls8-10. Employing human tissue to establish disease-relevance, and rodent experiments to define mechanism, we now show that A{beta} constricts brain capillaries at pericyte locations in human subjects with cognitive decline. Applying soluble A{beta}1-42 oligomers to live human cortical tissue constricted capillaries. Using rat cortical slices, this was shown to reflect A{beta} evoking capillary pericyte contraction, with an EC50 of 4.7 nM, via the generation of reactive oxygen species and activation of endothelin ET-A receptors. In freshly-fixed diagnostic biopsies from human patients investigated for cognitive decline, mean capillary diameters were less in subjects showing A{beta} deposition than in subjects without A{beta} deposition. For patients with A{beta} deposition, the capillary diameter was 31% less at pericyte somata than away from somata, predicting a halving of blood flow. Constriction of capillaries by A{beta} will contribute to the energy lack1-3 occurring in AD, which promotes further A{beta} generation11,12. This mechanism reconciles the amyloid hypothesis13-15 with the earliest events in AD being vascular1.

neuroscience↗

bioRxiv2018

Towards a universal structural and energetic model for prokaryotic promoters

With almost no consensus promoter sequence in prokaryotes, recruitment of RNA polymerase (RNAP) to precise transcriptional start sites (TSSs) has remained an unsolved puzzle. Uncovering the underlying mechanism is critical for understanding the principle of gene regulation. We attempted to search the hidden code in ~16500 promoters, of twelve prokaryotes representing two kingdoms, in their structure and energetics. Twenty eight fundamental parameters of DNA structure including backbone angles, base pair axis, inter base pair and intra base pair parameters were used and information was extracted from X-ray crystallography (XRC) data. Three parameters (solvation energy, hydrogen bond energy and stacking energy) were selected for creating energetics profiles using in-house programs. DNA was found to be inherently designed to undergo a change in every parameter undertaken, from some distance upstream of TSSs to adopt a signature state at these locations in all prokaryotes. These signature states might be the universal hidden codes recognised by RNAP. This observation was reiterated when randomly selected promoter sequences (with little sequence conservation) were subjected to structure generation; all developed into very similar three dimensional structures, quite distinct from those of conventional B-DNA and coding sequences. Fine structural details at important motifs (viz. -11, -35, -75 positions relative to TSS) of promoters reveal novel and pointed insights for RNAP interaction at these locations; it could be correlated that how some particular structural changes at -11 region may allow insertion of RNAP amino acids in inter-base pair space as well as facilitate the flipping out of bases from DNA duplex.

genomics↗

bioRxiv2018

Spatial Awareness of a Bacterial Swarm

Bacteria are perhaps the simplest living systems capable of complex behaviour involving sensing and coherent, collective behaviour an example of which is the phenomena of swarming on agar surfaces. Two fundamental questions in bacterial swarming is how the information gathered by individual members of the swarm is shared across the swarm leading to coordinated swarm behaviour and what specific advantages does membership of the swarm provide its members in learning about their environment. In this article, we show a remarkable example of the collective advantage of a bacterial swarm which enables it to sense inert obstacles along its path. Agent based computational model of swarming revealed that independent individual behaviour in response to a two-component signalling mechanism could produce such behaviour. This is striking because independent individual behaviour without any explicit communication between agents was found to be sufficient for the swarm to effectively compute the gradient of signalling molecule concentration across the swarm and respond to it.

biophysics↗

bioRxiv2018

Single-nucleotide and Copy-number variance related to severity of Hypospadias

The genetic association of Hypospadias-risk studies has been conducted in Caucasians, Chinese-Han populations and few in Indian populations. Although no comprehensive approach has been followed to assess genetic involvement in the severity of the disorder. The study evaluated to establish the correlation between genotyped SNPs/CNVs and Hypospadias-severity by an association in a total 30 SNPs in genes related to sex hormone-biosynthesis and metabolism; embryonic-development and Phospholipase-D-signalling pathways on 138 surgery-confirmed hypospadias-cases from North-India (84 Penile and 28 cases of Penoscrotal-Hypospadias compared against 31 cases of Glanular+Coronal), and analyzed and identified copy number variants (CNVs) in four Familial samples (18 members) and three paired-sporadic cases (6 samples) using array-based comparative-genomic-hybridization and validated in 32 Hypospadias samples by TaqMan assay. Based on Odds Ratio at 95% CI, Z Statistic and Significance Levels, STS gene-rs17268974 was associated with Penile-Hypospadias and 9-SNPs (seven-SNPs (rs5934740; rs5934842; rs5934913; rs6639811; rs3923341; rs17268974; rs5934937) of STS gene; rs7562326-SRD5A2 and rs1877031-STARD3 were associated with Penoscrotal-Hypospadias. On aggregate analysis with p <0.001, we identified homozygous-loss of Ch7:q34 (PRSS3P2, PRSS2). On validation in previously CNV-characterized and new (32-hypospadias-cases), we identified PRSS3P2-loss in most of the grade 3 and 4 hypospadias. Hence, Grade 1 and 2 (coronal and granular) show no-PRSS3P2-loss and no-association with SNPs in STS; SRD5A2; STARD3-gene but Grade 3 and 4 (Penile and Penoscrotal) show PRSS3P2-loss accompanied with the association of SNPs in STS; SRD5A2; STARD3. Hence, homozygous-loss of PRSS3P2 accompanied with the association of STS; SRD5A2; STARD3 may link to the severity of the disease.

genomics↗

bioRxiv2018

An atlas of silencer elements for the human and mouse genomes

The study of gene regulation is dominated by a focus on the control of gene activation or controlling an increase in the level of expression. Just as critical is the process of gene repression or silencing. Chromatin signatures have allowed for the global mapping of enhancer cis-regulatory elements, however, the identification of silencer elements by computational or experimental approaches in a genome-wide manner are lacking. We present a simple but powerful computational approach to identify putative silencers genome-wide. We used a series of consortia data to predict silencers in over 100 human and mouse cell or tissue types. We performed several analyses to determine if these elements exhibited characteristics expected of a silencers. Motif enrichment analyses on putative silencers determined that motifs belonging to known transcriptional repressors are enriched, as well as overlapping known transcription repressor binding sites. Leveraging promoter capture HiC data from several human and mouse cell types, we found that over 50% of putative silencer elements are interacting with gene promoters having very low to no expression. Next, to validate our silencer predictions, we quantified silencer activity using massively parallel reporter assays (MPRAs) on 7500 selected elements in K562 cells. We trained a support vector machine model classifier on MPRA data and used it to refine potential silencers in other cell types. We also show that similar to enhancer elements, silencer elements are enriched in disease-associated variants. Our results suggest a general strategy for genome-wide identification and characterization of silencer elements.

genomics↗

bioRxiv2017

Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives with Adult Patients with Celiac Disease and Controls

Recent studies on celiac disease (CeD) have shown the role of gut microbiota alterations in CeD pathogenesis. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific taxa between pre-diseases and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to faecal samples indicating larger disruption of microbiota at disease site. Increased abundance of specific Helicobacter ASVs were observed in duodenum of CeD when compared to FDR (p < 0.01). In case of fecal samples CeD microbiome and Actinomyces. In addition, predicted functional metagenome showed reduced ability of gluten that ecosystem level diversity measures (except in the duodenum) were not significantly different is characterized by reduced abundance of beneficial taxa such as Akkermansia, Ruminococcus degradation by CeD faecal microbiota in comparison to FDRs and controls.

microbiology↗

bioRxiv2017

Genome-Wide Mining, Characterization and Development of miRNA-SSRs in Arabidopsis thaliana

Simple Sequence Repeats (SSRs), also known as microsatellites are short tandem repeats of DNA sequences that are 1-6 bp long. In plants, SSRs serve as a source of important class of molecular markers because of their hypervariabile and co-dominant nature, making them useful both for the genetic studies and marker-assisted breeding. The SSRs are widespread throughout the genome of an organism, so that a large number of SSR datasets are available, most of them from either protein-coding regions or untranslated regions. It is only recently, that their occurrence within microRNAs (miRNA) genes has received attention. As is widely known, miRNA themselves are a class of non-coding RNAs (ncRNAs) with varying length of 19-22 nucleotides (nts), which play an important role in regulating gene expression in plants under different biotic and abiotic stresses. In this communication, we describe the results of a study, where miRNA-SSRs in full length pre-miRNA sequences of Arabidopsis thaliana were mined. The sequences were retrieved by annotations available at EnsemblPlants using BatchPrimer3 server with miRNA-SSR flanking primers found to be well distributed. Our analysis shows that miRNA-SSRs are relatively rare in protein-coding regions but abundant in non-coding region. All the observed 147 di-, tri-, tetra-, penta- and hexanucleotide SSRs were located in non-coding regions of all the 5 chromosomes of A. thaliana. While we confirm that miRNA-SSRs were commonly spread across the full length pre-miRNAs, we envisage that such studies would allow us to identify newly discovered markers for breeding studies.

bioinformatics↗

bioRxiv2017

Evolution of dispersal syndrome and its corresponding metabolomic changes

Dispersal is one of the strategies for organisms to deal with climate change and habitat degradation. Therefore, investigating the effects of dispersal evolution on natural populations is of considerable interest to ecologists and conservation biologists. Although it is known that dispersal itself can evolve due to selection, the behavioral, life-history and metabolic consequences of dispersal evolution are not well understood. Here we explore these issues by subjecting four outbred laboratory populations of Drosophila melanogaster to selection for increased dispersal. The dispersal-selected populations had similar values of body size, fecundity and longevity as the non-selected lines (controls), but evolved significantly greater locomotor activity, exploratory tendency, and aggression. Untargeted metabolomic fingerprinting through NMR spectroscopy suggested that the selected flies evolved elevated cellular respiration characterized by greater amounts of glucose, AMP and NAD. Concurrent evolution of higher level of Octopamine and other neurotransmitters indicate a possible mechanism for the behavioural changes in the selected lines. We discuss the generalizability of our findings in the context of observations from natural populations. To the best of our knowledge, this is the first report of the evolution of metabolome due to selection for dispersal and its connection to dispersal syndrome evolution.

evolutionary biology↗

bioRxiv2017

SWELL1 is a glucose sensor required for β-cell excitability and insulin secretion

Insulin secretion from the pancreatic {beta}-cell initiated by activation of voltage-gated Ca2+ channels (VGCC) to trigger Ca2+-mediated insulin vesicle fusion with the {beta}-cell plasma membrane. The firing of VGCC depends on the {beta}-cell membrane potential, which is in turn mediated by the balance of depolarizing (excitatory) and hyperpolarizing (inhibitory) ionic currents1-3. While much attention has focused on inhibitory potassium currents4-10 there is little knowledge about the excitatory currents required to depolarize the {beta}-cell, including the molecular identity of these excitatory currents3. Here we show that SWELL1 (LRRC8a) mediates a swell-activated, depolarizing chloride current (ICl,SWELL) in {beta}-cells. Hypotonic and glucose-stimulated {beta}-cell swelling activates SWELL1-mediated ICl,SWELL and this is required for both glucose-stimulated and hypotonic swell-mediated activation of VGCC-dependent intracellular calcium signaling in {beta}-cells. SWELL1 KO MIN6 cells and {beta}-cell targeted SWELL1 KO murine islets exhibit significantly impaired glucose-stimulated insulin secretion, with preserved insulin content in vitro. Tamoxifen-inducible {beta}-cell targeted SWELL1 KO mice have normal fasting insulin levels but display markedly impaired glucose-stimulated insulin secretion. Our results reveal a physiological role for SWELL1 as a glucose sensor - linking glucose-mediated {beta}-cell swelling to SWELL1-dependent activation of VGCC-triggered calcium signaling, and highlights SWELL1-mediated \"swell-secretion\" coupling as required for glucose-stimulated insulin secretion.

cell biology↗

bioRxiv2017

Pre-dispersal conditions and presence of opposite sex modulate density dependence and sex bias of dispersal

Density-dependent dispersal (DDD) has been demonstrated in many species and has several ecological and evolutionary consequences. Yet we know little about how robust DDD is to the various conditions experienced by individuals. In this study, we use three independent experiments on laboratory populations of Drosophila melanogaster to examine the effects of pre-dispersal adult density, sex of the dispersers and presence of mates on the robustness of DDD patterns. We show that DDD can be greatly affected by both pre-dispersal density and interaction between the sexes. Moreover, the direction of sex-biased dispersal can reverse completely due to an interaction between the pre-dispersal and dispersal densities. We also show that interaction between the sexes can lead to negative DDD at the population level, even if, by themselves, neither sex exhibits DDD. Finally, we discuss potential implications of our results for processes like evolutionary rescue from extinctions and genetic divergence of populations.

ecology↗

bioRxiv2017

A protein phosphatase network controls temporal and spatial dynamics of differentiation commitment in human epidermis

Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation. The transition between the two cell states, termed commitment, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension for up to 12h to induce differentiation. We find that cell detachment induces a network of protein phosphatases. The pro-commitment phosphatases - including DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA - promote differentiation by negatively regulating ERK MAPK and positively regulating AP1 transcription factors. Their activity is antagonised by concomitant upregulation of DUSP10. Boolean network modelling of phosphatase interactions identifies commitment as an inherently unstable biological switch between the stem and differentiated cell states. Furthermore, phosphatase expression is spatially regulated both in vivo and in vitro. We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.

developmental biology↗

bioRxiv2017

A protein phosphatase network controls the temporal and spatial dynamics of differentiation commitment in human epidermis

Epidermal homeostasis depends on a balance between stem cell renewal and terminal differentiation1,2. While progress has been made in characterising the stem and differentiated cell compartments3, the transition between the two cell states, termed commitment4, is poorly understood. Here we characterise commitment by integrating transcriptomic and proteomic data from disaggregated primary human keratinocytes held in suspension for up to 12h. We have previously shown that commitment begins at approximately 4h and differentiation is initiated by 8h5. We find that cell detachment induces a network of protein phosphatases. The pro-commitment phosphatases - including DUSP6, PPTC7, PTPN1, PTPN13 and PPP3CA - promote terminal differentiation by negatively regulating ERK MAPK and positively regulating key API transcription factors. Their activity is antagonised by concomitant upregulation of the anti-commitment phosphatase DUSP10. The phosphatases form a dynamic network of transient positive and negative interactions, with DUSP6 predominating at commitment. Boolean network modelling identifies a mandatory switch between two stable states (stem cell and differentiated cell) via an unstable (committed) state. In addition phosphatase expression is spatially regulated relative to the location of stem cells, both in vivo and in response to topographical cues in vitro. We conclude that an auto-regulatory phosphatase network maintains epidermal homeostasis by controlling the onset and duration of commitment.

cell biology↗

bioRxiv2017

Genetic polymorphism of Cytochrome-P450-2C9 (CYP2C9) in Indian populations

Cytochrome-P450-2C9 (CYP2C9) metabolizes wide range of drugs and highly express in human liver. Various mutations of CYP2C9 (R144C, I359L etc.), associated with drug-response, are highly diverse. We aimed to investigate the genetic diversity of CYP2C9 in Indian-subcontinent, using 1278 subjects from 36 populations. High frequency of CYP2C9*3 (0-0.179) was observed, comparative to other populations, including Europeans. Subjects having CYP2C9*3/*3 requires lower dose of warfarin, comparative to CYP2C9*1/*3 or CYP2C9*1/*1. Since, Indians are practicing marriage among their caste system, we predicted and observed high frequency (0-0.05) of CYP2C9*3/*3. Out of 21 populations, living outside of Indian subcontinent, only Toscani and Southern Han-Chinese have 0.009 and 0.01 CYP2C9*3/*3, respectively, lower than Indians. We found a non-synonymous mutation (L362V), observed only in Indian-subcontinent, and have 0-0.056 allelic, 0-0.037 L/V and 00.037 V/V genotype frequency. We observed unfavorable interatomic interactions between hydroxylation sites of warfarin and reactive oxyferryl heme in mutant, comparative to wild-type CYP2C9, in molecular dynamic simulations; and predict lower kinetic activity.

evolutionary biology↗