Biology subjects

Pandey, R.

Publications and source records attributed to Pandey, R..

63 records · Page 4Linked to original sources

bioRxiv2019

High-resolution transcriptomic profiling of the heart during chronic stress reveals cellular drivers of cardiac fibrosis and hypertrophy

BackgroundCardiac fibrosis is a key antecedent to many types of cardiac dysfunction including heart failure. Physiological factors leading to cardiac fibrosis have been recognized for decades. However, the specific cellular and molecular mediators that drive cardiac fibrosis, and the relative impact of disparate cell populations on cardiac fibrosis, remain unclear. MethodsWe developed a novel cardiac single-cell transcriptomics strategy to characterize the cardiac cellulome--the network of cells that forms the heart. This method was utilized to profile the cardiac cellular ecosystem in response to two weeks of continuous administration of Angiotensin II, a pro-fibrotic stimulus which drives pathological cardiac remodeling. ResultsThis analysis uncovered multiple cell populations contributing to pathological remodeling of the extracellular matrix of the heart. Two phenotypically distinct fibroblast populations emerged after induction of tissue stress to promote fibrosis in the absence of smooth muscle actin-expressing myofibroblasts, a key pro-fibrotic cell population. Further, the cellular responses to Angiotensin II and the relative abundance of fibrogenic cells were sexually dimorphic. ConclusionsThese results offer a valuable resource for exploring the cardiac cellular landscape in health and after chronic cardiovascular stress. These data provide insights into the cellular and molecular mechanisms that promote pathological remodeling of the mammalian heart, highlighting early transcriptional changes which precede chronic cardiac fibrosis.

cell biology↗

bioRxiv2019

Real-time dynamics of Plasmodium NDC80 as a marker for the kinetochore during atypical mitosis and meiosis

Eukaryotic cell proliferation requires chromosome replication and precise segregation to ensure daughter cells have identical genomic copies. The genus Plasmodium, the causative agent of malaria, displays remarkable aspects of nuclear division throughout its lifecycle to meet some peculiar and unique challenges of DNA replication and chromosome segregation. The parasite undergoes atypical endomitosis and endoreduplication with an intact nuclear membrane and intranuclear mitotic spindle. To understand these diverse modes of Plasmodium cell division, we have studied the behaviour and composition of the outer kinetochore NDC80 complex, a key part of the mitotic apparatus that attaches the centromere of chromosomes to microtubules of the mitotic spindle. Using NDC80-GFP live-cell imaging in Plasmodium berghei we observe dynamic spatiotemporal changes during proliferation, including highly unusual kinetochore arrangements during sexual stages. We identify a very divergent candidate for the SPC24 subunit of the NDC80 complex, previously thought to be missing in Plasmodium, which completes a canonical, albeit unusual, NDC80 complex structure. Altogether, our studies reveal the kinetochore as an ideal tool to investigate the non-canonical modes of chromosome segregation and cell division in Plasmodium. Summary StatementThe dynamic localization of kinetochore marker NDC80 protein complex during proliferative stages of the malaria parasite life cycle reveals unique modes of chromosome segregation.

cell biology↗

bioRxiv2019

Genetic variation for root architectural traits in response to phosphorus deficiency in mungbean at the seedling stage

Roots enable the plant to survive in natural environment by providing anchorage and acquisition of water and nutrients. In this study, 153 mungbean genotypes were studied to compare root architectural traits under normal and low phosphorus conditions. Significant variations, medium to high heritability, near normal distribution and significant correlations were observed for studied root traits. Total root length (TRL) was positively correlated with total surface area (TSA), total root volume (TRV), total root tips (TRT) and root forks. The first two principal components explained the 79.19 % and 78.84% of the total variation under normal and low phosphorus conditions. TRL, TSA and TRV were major contributors of variation and can be utilized for screening of phosphorus uptake efficiency at seedling stage. Released Indian mungbean varieties were found to be superior for root traits than other genotypic groups. Based on comprehensive phosphorus efficiency measurement, IPM-288, TM 96-25, TM 96-2, M 1477, PUSA 1342 were found to be best five highly efficient genotypes whereas M 1131, PS-16, Pusa Vishal, M 831, IC 325828 were highly inefficient genotypes. These identified highly efficient lines are valuable genetic resources for phosphorus uptake efficiency that could be used in mungbean breeding programme.

genetics↗

bioRxiv2019

A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease

BackgroundLate-onset Alzheimers disease (LOAD) is the most common form of dementia worldwide. To date, animal models of Alzheimers have focused on rare familial mutations, due to a lack of frank neuropathology from models based on common disease genes. Recent multi-cohort studies of postmortem human brain transcriptomes have identified a set of 30 gene co-expression modules associated with LOAD, providing a molecular catalog of relevant endophenotypes.\n\nResultsThis resource enables precise gene-based alignment between new animal models and human molecular signatures of disease. Here, we describe a new resource to efficiently screen mouse models for LOAD relevance. A new NanoString nCounter(R) Mouse AD panel was designed to correlate key human disease processes and pathways with mRNA from mouse brains. Analysis of three mouse models based on LOAD genetics, carrying APOE4 and TREM2*R47H alleles, demonstrated overlaps with distinct human AD modules that, in turn, are functionally enriched in key disease-associated pathways. Comprehensive comparison with full transcriptome data from same-sample RNA-Seq shows strong correlation between gene expression changes independent of experimental platform.\n\nConclusionsTaken together, we show that the nCounter Mouse AD panel offers a rapid, cost-effective and highly reproducible approach to assess disease relevance of potential LOAD mouse models.

neuroscience↗

bioRxiv2019

Plasmodium condensin core subunits (SMC2/SMC4) mediate atypical mitosis and are essential for parasite proliferation and transmission

Condensin is a multi-subunit protein complex regulating chromosome condensation and segregation during cell division. In Plasmodium spp., the causative agent of malaria, cell division is atypical and the role of condensin is unclear. Here we examine the role of SMC2 and SMC4, the core subunits of condensin, during endomitosis in schizogony and endoreduplication in male gametogenesis. During early schizogony SMC2/SMC4 localize to a distinct focus, identified as the centromeres by NDC80 fluorescence and ChIP-seq analyses, but do not form condensin I or II complexes. In mature schizonts and during male gametogenesis, there is a diffuse SMC2/SMC4 distribution on chromosomes and in the nucleus, and both condensin I and II complexes form at these stages. Knockdown of smc2 and smc4 gene expression revealed essential roles in parasite proliferation and transmission. The condensin core subunits (SMC2/SMC4) form different complexes and may have distinct functions at various stages of the parasite life cycle.

cell biology↗

bioRxiv2019

ApicoTFdb: The comprehensive web repository of apicomplexan transcription factors and regulators.

Despite significant progress in apicomplexans genome sequencing and genomics, the current list of experimentally validated TFs in these genomes is incomplete and mainly consists of AP2 family of proteins, with only a limited number of non-AP2 family TFs and TAFs. We have performed systematic bioinformatics aided prediction of TFs and TAFs in apicomplexan genomes, and developed ApicoTFdb database which consists of experimentally validated as well as computationally predicted TFs and TAFs in 14 apicomplexan species. The predicted TFs are manually curated to complement the existing annotations. The current version of the database includes 1310 TFs, out of which 833 are novel and computationally predicted TFs, representing 22 distinct families across 14 apicomplexan species. The predictions include TFs of TUB, NAC, BSD, CCAAT, HTH, Cupin/Jumonji, winged-helix, and FHA family proteins, not reported earlier in the genomes. Apart from TFs, ApicoTFdb also classifies TAFs into three main subclasses-TRs, CRRs and RNARs, representing 3047 TAFs in 14 apicomplexan species are analyzed in this study. The database is equipped with a set of useful tools for comparative analysis of a user-defined list of the proteins. ApicoTFdb will be useful to the researchers interested in less-studied gene regulatory mechanisms mediating the complex life cycle of the apicomplexan parasites. The database will aid the discovery of novel drug targets to much needed combat the growing drug resistance in the parasites.

bioinformatics↗

bioRxiv2018

Metformin Intervention Prevents Cardiac Dysfunction in a Murine Model of Adult Congenital Heart Disease

Congenital heart disease (CHD) is the most frequent birth defect worldwide and the number of adult patients with CHD, now referred to as ACHD, is increasing. However the mechanisms whereby ACHD predisposes patients to heart dysfunction are still unclear. ACHD is strongly associated with metabolic syndrome, but how ACHD interacts with poor modern lifestyle choices and other comorbidities, such as hypertension, obesity and diabetes, is mostly unknown. Using a genetic mouse model of ACHD we showed that ACHD mice placed under metabolic stress (high fat diet) displayed decreased heart function. Comprehensive physiological, biochemical and molecular analysis showed that ACHD hearts exhibited early changes in energy metabolism that preceded cardiac dysfunction. Restoration of metabolic balance by metformin prevented the development of heart dysfunction in ACHD mice. This study reveals that early metabolic impairment reinforces heart dysfunction in ACHD predisposed individuals and diet or pharmacological interventions can be used to modulate heart function and attenuate heart failure and may be an important avenue for intervention in ACHD.

genetics↗

bioRxiv2017

Insights into regeneration from the genome, transcriptome and metagenome analysis of Eisenia fetida

Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaete Capitella telata, and the freshwater leech Helobdella robusta have been sequenced and studied. The terrestrial annelids, in spite of their ecological relevance and unique biochemical repertoire, are represented by a single rough genome draft of Eisenia fetida (North American isolate), which suggested that extensive duplications have led to a large number of HOX genes in this annelid. Herein, we report the draft genome sequence of Eisenia fetida (Indian isolate), a terrestrial redworm widely used for vermicomposting assembled using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm, showed that many miRNA gene families have also undergone extensive duplications. Genes for several important proteins such as sialidases and neurotrophins were identified by RNA sequencing of tissue samples. We also used de novo assembled RNA-Seq data to identify genes that are differentially expressed during regeneration, both in the newly regenerating cells and in the adjacent tissue. Sox4, a master regulator of TGF-beta induced epithelial-mesenchymal transition was induced in the newly regenerated tissue. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. The metagenome of the worm, characterized using 16S rRNA sequencing, revealed the identity of several bacterial species that reside in the nephridia of the worm. Comparison of the bodywall and cocoon metagenomes showed exclusion of hereditary symbionts in the regenerated tissue. In summary, we present extensive genome, transcriptome and metagenome data to establish the transcriptome and metagenome dynamics during regeneration.

genomics↗

bioRxiv2017

Differential Strengths Of Molecular Determinants Guide Environment Specific Mutational Fates

Under the influence of selection pressures imposed by natural environments, organisms maintain competitive fitness through underlying molecular evolution of individual genes across the genome. For molecular evolution, how multiple interdependent molecular constraints play a role in determination of fitness under different environmental conditions is largely unknown. Here, using Deep Mutational Scanning (DMS), we quantitated empirical fitness of [~]2000 single site mutants of Gentamicin-resistant gene (GmR). This enabled a systematic investigation of effects of different physical and chemical environments on the fitness landscape of the gene. Molecular constraints of the fitness landscapes seem to bear differential strengths in an environment dependent manner. Among them, conformity of the identified directionalities of the environmental selection pressures with known effects of the environments on protein folding proves that along with substrate binding, protein stability is the common strong constraint of the fitness landscape. Our study thus provides mechanistic insights into the molecular constraints that allow accessibility of mutational fates in environment dependent manner.\n\nAuthor SummaryEnvironmental conditions play a central role in both organismal adaptations and underlying molecular evolution. Understanding of environmental effects on evolution of genotype is still lacking a depth of mechanistic insights needed to assist much needed ability to forecast mutational fates. Here, we address this issue by culminating high throughput mutational scanning using deep sequencing. This approach allowed comprehensive mechanistic investigation of environmental effects on molecular evolution. We monitored effects of various physical and chemical environments onto single site mutants of model antibiotic resistant gene. Alongside, to get mechanistic understanding, we identified multiple molecular constraints which contribute to various degrees in determining the resulting survivabilities of mutants. Across all tested environments, we find that along with substrate binding, protein stability stands out as the common strong constraints. Remarkable direct dependence of the environmental fitness effects on the type of environmental alteration of protein folding further proves that protein stability is the major constraint of the gene. So, our findings reveal that under the influence of environmental conditions, mutational fates are channeled by various degrees of strengths of underlying molecular constraints.

evolutionary biology↗