Biology subjects

Sharma, R.

Publications and source records attributed to Sharma, R..

At least 199 records · Page 11Linked to original sources

bioRxiv2021

Long term consumption of green tea EGCG enhances healthspan and lifespan in mice bymitigating multiple aspects of cellular senescence in mitotic and post-mitotic tissues, gutdysbiosis and immunosenescence

Cellular senescence is emerging as the causal nexus of aging, and its potential modulators present an effective strategy to counter age-related morbidity. The current study profiled the extent of cellular senescence in different organs of mice at four different time-points of lifespan, and explored the influence of epigallocatechin gallate (EGCG) consumption in impacting multiple aspects of aging biology. We report that adipose and intestinal tissues are highly vulnerable to cellular senescence as evident by age-associated increase in DNA damage response, activation of cell cycle inhibitors (p53/p21) and induction of SASP (p38MAPK/NF-{kappa}B/Cox-2). Further, a distinct modulation of nutrient signaling pathway mediators (AMPK/Akt/SIRT3 and 5), and a decrease in autophagy effectors was also observed in aging animals. Systemic inflamm-aging markers (TNF-/IL-l{beta}) and splenic CD4/CD8 ratio increased with age, while NK cell population decreased. Metagenomic analyses revealed age-related decrease in the diversity of microbial species while an increase in the abundance of various pathogenic bacterial genera was also observed. Long term EGCG consumption enhanced lifespan of animals by attenuating markers of DNA damage, cell cycle inhibitors and SASP in adipose, intestine and liver tissue. Mechanistically, EGCG inhibited the activation of AMPK and Akt and enhanced mitochondrial SIRT3 and SIRT5 expression, as well as autophagic response in adipose and intestinal tissues. Systemic presence of inflamm-aging markers decreased while expression of T cell immune response regulator CD69 increased in EGCG fed animals. EGCG also improved age-related decrease in the diversity of microbial species and suppressed the growth of pathogenic microbes. In short, our results provide compelling evidence that post-mitotic adipose tissue is a major site of cellular senescence and SASP activation, and that chronic EGCG consumption can influence several aspects of aging and senescence resulting in improved organismal healthspan and lifespan.

molecular biology↗

bioRxiv2020

Meta-Analysis of Allergy Genome-Wide Association Studies

Allergies are complex conditions involving both environmental and genetic factors. The genetic basis underlying allergic disease is investigated through genetic association studies. Genome-wide association studies (GWAS) leverage sequenced data to identify genetic mutations, such as single-nucleotide polymorphisms (SNPs), associated with phenotypes of interest. Machine learning can be used to analyze large datasets and generate predictive models. In this study, several classification models were created to predict the significance level of SNPs associated with allergies. Summary statistics were obtained from the GWAS Catalog and combined from several studies. Biological features such as chromosomal location, base pair location, effect allele, and odds ratio were used to train the models. The models ranged from simple linear regressions to multi-layer neural networks. The final models reached accuracies of 80% and reflect the features that have the largest impact on a SNPs association level.

bioinformatics↗

bioRxiv2020

Trends of genetic changes uncovered by Env- and Eigen-GWAS in wheat and barley

The process of crop breeding over the last century has delivered new varieties with increased genetic gains, resulting in higher crop performance and yield. However in many cases, the underlying alleles and genomic regions that have underpinned this success remain unknown. This is due, in part, to the difficulty in generating sufficient phenotypic data on large numbers of historical varieties to allow such analyses to be undertaken. Here we demonstrate the ability to circumvent such bottlenecks by identifying genomic regions selected over 100 years of crop breeding using the age of a variety as a surrogate for yield. Using environmental genome-wide association scans (EnvGWAS) on variety age in two of the worlds most important crops, wheat and barley, we found strong signals of selection across the genomes of our target crops. EnvGWAS identified 16 genomic regions in barley and 10 in wheat with contrasting patterns between spring and winter types of the two crops. To further examine changes in genome structure in wheat and barley over the past century, we used the same genotypic data to derive eigenvectors for deployment in EigenGWAS. This resulted in the detection of seven major chromosomal introgressions that contributed to adaptation in wheat. The deployment of both EigenGWAS and EnvGWAS based on variety age avoids costly phenotyping and will facilitate the identification of genomic tracts that have been under selection during plant breeding in underutilized historical cultivar collections. Our results not only demonstrate the potential of using historical cultivar collections coupled with genomic data to identify chromosomal regions that have been under selection but to also guide future plant breeding strategies to maximise the rate of genetic gain and adaptation in crop improvement programs. Significance Statement100 years of plant breeding have greatly improved crop adaptation, resilience, and productivity. Generating the trait data required for these studies is prohibitively expensive and can be impossible on large historical traits. This study reports using variety age and eigenvectors of the genomic relationship matrix as surrogate traits in GWAS to locate the genomic regions that have undergone selection during varietal development in wheat and barley. In several cases these were confirmed as associated with yield and other selected traits. The success and the simplicity of the approach means it can easily be extended to other crops with a recent recorded history of plant breeding and available genomic resources.

genetics↗

bioRxiv2020

Modeling CRISPR gene drives for suppression of invasive rodents

Invasive rodent populations pose a threat to biodiversity across the globe. When confronted with these new invaders, native species that evolved independently are often defenseless. CRISPR gene drive systems could provide a solution to this problem by spreading transgenes among invaders that induce population collapse. Such systems might be deployed even where traditional control methods are impractical or prohibitively expensive. Here, we develop a high-fidelity model of an island population of invasive rodents that includes three types of suppression gene drive systems. The individual-based model is spatially explicit and allows for overlapping generations and a fluctuating population size. Our model includes variables for drive fitness, efficiency, resistance allele formation rate, as well as a variety of ecological parameters. The computational burden of evaluating a model with such a high number of parameters presents a substantial barrier to a comprehensive understanding of its outcome space. We therefore accompany our population model with a meta-model that utilizes supervised machine learning to approximate the outcome space of the underlying model with a high degree of accuracy. This enables us to conduct an exhaustive inquiry of the population model, including variance-based sensitivity analyses using tens of millions of evaluations. Our results suggest that sufficiently capable gene drive systems have the potential to eliminate island populations of rodents under a wide range of demographic assumptions, but only if resistance can be kept to a minimal level. This study highlights the power of supervised machine learning for identifying the key parameters and processes that determine the population dynamics of a complex evolutionary system.

ecology↗

bioRxiv2020

The new kid on the block: A dominant-negative mutation of phototropin1 enhances carotenoid content in tomato fruits

Phototropins, the UVA-blue light photoreceptors, endow plants to detect the direction of light and optimize photosynthesis by regulating chloroplasts positioning and stomatal gas exchange. Little is known about their functions in other developmental responses. A tomato Non-phototropic seedling1 (Nps1) mutant, bearing an Arg495His substitution in the vicinity of LOV2 domain in phototropin1, dominant-negatively blocks phot1 and phot2 responses. The fruits of Nps1 mutant were enriched in carotenoids, particularly lycopene, than its parent, Ailsa Craig. Contrarily, CRISPR/CAS9-edited loss of function phototropin1 mutants displayed subdued carotenoids than the parent. The enrichment of carotenoids in Nps1 fruits is genetically linked with the mutation and exerted in a dominant-negative fashion. Nps1 also altered volatile profiles with high levels of lycopene-derived 6-methyl 5-hepten2-one. The transcript levels of several MEP and carotenogenesis pathways genes were upregulated in Nps1. Nps1 fruits showed altered hormonal profiles with subdued ethylene emission and reduced respiration. Proteome profiles showed a causal link between higher carotenogenesis and increased levels of protein protection machinery, which may stabilize proteins contributing to MEP and carotenogenesis pathways. Given the enhancement of carotenoid content by Nps1 in a dominant-negative fashion, it offers a potential tool for high lycopene-bearing hybrid tomatoes. One-sentence summaryA dominant-negative phototropin1 mutation enhances carotenoid levels, alters metabolite homeostasis, and protein quality control machinery in tomato fruits.

plant biology↗

bioRxiv2020

Extrinsic noise acts to lower protein production at higher translation initiation rates

Any cellular process at the microscopic level is governed by both extrinsic and intrinsic noise. In this article, we incorporate extrinsic noise in a model of mRNA translation and carry out stochastic simulations of the same. We then evaluate various statistics related to the residence time of the ribosome on the mRNA and subsequent protein production. We also study the effect of slow codons. From our simulations, we show that noise in the translation initiation rate rather than the translation termination rate acts to significantly broaden the distribution of mRNA residence times near the membrane. Further, the presence of slow codons acts to increase the mean residence times. However, this increase also depends on the number and position of the slow codons on the lattice. We also show that the the slow codons act to mask any effect from the extrinsic noise themselves. Our results have implications towards a better understanding of the role the individual components play during the translation process.

systems biology↗

bioRxiv2020

FITs: Forest of imputation trees for recovering true signals in single-cell open chromatin profiles

The advent of single-cell open-chromatin profiling technology has facilitated the analysis of heterogeneity of activity of regulatory regions at single-cell resolution. However, stochasticity and availability of low amount of relevant DNA cause high drop-out rate and noise in single-cell open-chromatin profiles. We introduce here a robust method called as Forest of Imputation Trees (FITs) to recover original signals from highly sparse and noisy single-cell open-chromatin profiles. FITs makes a forest of imputation trees to avoid bias during the restoration of read-count matrices. It resolves the challenging issue of recovering open chromatin signals without blurring out information at genomic sites with cell-type-specific activity. FITs is generalized for wider applicability, especially for highly sparse read-count matrices. The superiority of FITs in recovering signals of minority cells also makes it highly useful for single-cell open-chromatin profile from in vivo samples. First made online as thesis work at https://repository.iiitd.edu.in/xmlui/handle/123456789/807

bioinformatics↗

bioRxiv2020

Optimal policy for attention-modulated decisionsexplains human fixation behavior

Traditional accumulation-to-bound decision-making models assume that all choice options are processed simultaneously with equal attention. In real life decisions, however, humans tend to alternate their visual fixation between individual items in order to efficiently gather relevant information [46, 23, 21, 12, 15]. These fixations also causally affect ones choices, biasing them toward the longer-fixated item [38, 2, 25]. We derive a normative decision-making model in which fixating a choice item boosts information about that item. In contrast to previous models [25, 39], we assume that attention enhances the reliability of information rather than its magnitude, consistent with neurophysiological findings [3, 13, 29, 45]. Furthermore, our model actively controls fixation changes to optimize information gathering. We show that the optimal model reproduces fixation patterns and fixation-related choice biases seen in human decision-makers, and provides a Bayesian computational rationale for the fixation bias. This insight led to additional behavioral predictions that we confirmed in human behavioral data. Finally, we explore the consequences of changing the relative allocation of cognitive resources to the attended versus the unattended item, and show that decision performance is benefited by a more balanced spread of cognitive resources.

neuroscience↗

bioRxiv2020

Dynamic multi-OMICs of glioblastoma reveal sensitivity to neddylation inhibition dependent on nuclear PTEN and DNA replication pathways

Withdrawal StatementThe authors have withdrawn their manuscript because the reported synergy of TOP2A inhibitors plus MLN4924 proved to be untrue (not reproducible). Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (mberens@tgen.org).

cancer biology↗

bioRxiv2020

On the origin of photoperiod non-responsiveness in barley

In barley, the transition from the vegetative to reproductive phase is complex and under the control of photoperiodic and temperature conditions. One major gene involved is PPD-H1, a PSEUDO-RESPONSE REGULATOR 7 (PRR7) that encodes a component of the circadian clock. Mutation at PPD-H1 resulted in the photoperiod non-responsive ppd-H1 alleles that are beneficial under high latitudinal environments as they allow vegetative growth during the long-day summer conditions whereby higher yields are harvested by farmers. Utilizing a diverse GWAS panel of world-wide origin and a genome-wide gene-based set of 50K SNP markers, a strong association of days to heading with the PPD-H1 gene was detected in multi-location field trials. Re-sequencing of the gene spanning putative causative SNPs, SNP22 (Turner et al. 2005) and SNP48 (Jones et al. 2008), detected recombination between the two, previously reported to be in complete LD. Phenotyping of the recombinants and phylogenetic relationships among haplotypes supported the original conclusion of Turner et al. (2005) that SNP22, present in the CCT domain, is the most likely causative SNP. To infer the origin of non-responsiveness, the PPD-H1 gene was re-sequenced in a geo-referenced collection of 2057 wild and domesticated barleys and compared with the allelic status of the 6000-year-old barley sample from the Yoram cave in the Masada cliff. A monophyletic and post-domestication origin in the Fertile Crescent was found in contrast to the pre-domestication origin proposed by Jones et al. (2008). We show that the photoperiod non-responsiveness originated from Desert type wild barley in the Southern Levant.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2020

Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples

The ongoing spread of pandemic coronavirus disease (COVID-19) is caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). In the lack of specific drugs or vaccines for SARS-CoV-2, demands rapid diagnosis and management are crucial for controlling the outbreak in the community. Here we report the development of the first rapid-colorimetric assay capable of detecting SARS-CoV-2 in the human nasopharyngeal RNA sample in less than 30 minutes. We utilized a nanomaterial-based optical sensing platform to detect RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2, where the formation of oligo probe-target hybrid led to salt-induced aggregation and changes in gold-colloid color from pink to blue in visible range. Accordingly, we found a change in colloid color from pink to blue in assay containing nasopharyngeal RNA sample from the subject with clinically diagnosed COVID-19. The colloid retained pink color when the test includes samples from COVID-19 negative subjects or human papillomavirus (HPV) infected women. The results were validated using nasopharangeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has detection limit as little as 0.5 ng of SARS-CoV-2 RNA. Overall, the developed assay rapidly detects SARS-CoV-2 RNA in clinical samples in a cost-effective manner and would be useful in pandemic management by facilitating mass screening.

microbiology↗

bioRxiv2020

Enhanced specificity of high sensitivity somatic variant profiling in cell-free DNA via paired normal sequencing: design, validation, and clinical experience of the MSK-ACCESS liquid biopsy assay

Circulating cell-free DNA (cfDNA) from blood plasma of cancer patients can be used to interrogate somatic tumor alterations non-invasively or when adequate tissue is unavailable. We have developed and clinically implemented MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), an NGS assay for detection of very low frequency somatic alterations in select exons and introns of 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 98% for a priori mutation profiling. To evaluate the performance and utility of MSK-ACCESS, we report results from the first 681 prospective blood samples (617 patients) that underwent clinical analysis to guide patient management. Somatic mutations, copy number, and/or structural variants were detected in 73% of the samples, and 56% of these circulating-tumor DNA (ctDNA) positive samples had clinically actionable alterations. The utilization of matched white blood cell sequencing allowed retention of somatic alterations while filtering out over 10,000 germline and clonal hematopoiesis variants, thereby greatly enhancing the specificity of the assay. Taken together, our experience illustrates the importance of analyzing a matched normal sample when interpreting cfDNA results and highlights the potential of cfDNA profiling to guide treatment selection, monitor treatment response, and identify mechanisms of treatment resistance.

genomics↗

bioRxiv2020

Phenotypic and molecular characterization of extended spectrum β-lactamase producing Escherichia coli and Klebsiella pneumoniae isolates from various samples of animal origin from Assam, India

Extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae has become a major threat globally. Here we have characterized ESBL producing E. coli and K. pneumoniae from various sources, studied antibiogram and resistance gene profiles. Out of 385 samples, 31 (8.05%) were positive for ESBL producing E. coli. Such isolates could be recovered from 10.05, 8.33, 15.63, 6.67 and 4.35 per cent of cattle milk, curd, chicken, pork and cattle faeces samples, respectively. A total of 59 (15.32%) samples were positive for ESBL producing K. pneumoniae, which were isolated from 14.35, 6.25, 21.43 and 34.78 per cent cattle milk, chicken, beef and cattle faeces, respectively. All the 90 isolates were confirmed as ESBL producers by CDT and ESBL-E strip tests. Antibiogram revealed that 74.19% and 69.49% of the ESBL producing E. coli and K. pneumoniae isolates, respectively showed resistance to ceftizoxime, 25.81% and 23.73% to both co-trimoxazole and tetracycline, 19.35% and 25.42% to ciprofloxacin, 9.68% and 16.95% to chloramphenicol, 3.23% and 5.08% to pipercillin-tazobactam, and 3.23% and 3.39% to gentamicin. Resistance gene profiling showed blaCTX-M gene as most predominant (100%). The blaTEM gene was found in 54.84% and 55.93%, blaSHV gene in 90.32% and 77.97%, Sul 1 gene in 90.32% and 86.44% of ESBL producing E. coli and K. pneumoniae isolates, respectively. The Int1 gene was detected in 70.97% and 62.71% isolates, while qnrB gene was found in 3.23% and 10.17% of E. coli and K. pneumoniae isolates, respectively.

molecular biology↗

bioRxiv2020

TRACE-Seq Reveals Clonal Reconstitution Dynamics of Gene Targeted Human Hematopoietic Stem Cells

Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may usher in a new class of medicines to treat genetic diseases of the blood and immune system. With state-of-the-art methodologies, it is now possible to correct disease-causing mutations at high frequencies in HSPCs by combining ribonucleoprotein (RNP) delivery of Cas9 and chemically modified sgRNAs with homologous DNA donors via recombinant adeno-associated viral vector serotype six (AAV6). However, because of the precise nucleotide-resolution nature of gene correction, these current approaches do not allow for clonal tracking of gene targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a novel methodology that utilizes barcoded AAV6 donor template libraries, carrying either in-frame silent mutations or semi-randomized nucleotide sequences outside the coding region, to track the in vivo lineage contribution of gene targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of [~]20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in immunodeficient mice. We anticipate that this methodology has the potential to be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

molecular biology↗

bioRxiv2020

Chromosome scale reference genome of Cluster bean (Cyamopsis tetragonoloba (L.) Taub.)

Clusterbean (Cyamopsis tetragonoloba (L.) Taub.), also known as Guar is a widely cultivated dryland legume of Western India and parts of Africa. Apart from being a vegetable crop, it is also an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan which is widely used in cosmetics, pharmaceuticals, food processing, shale gas drilling etc. Here, for the first time we are reporting a chromosome-scale reference genome assembly of clusterbean, from a high galactomannan containing popular guar cultivar, RGC-936, by combining sequenced reads from Illumina, 10x Chromium and Oxford Nanopore technologies. The initial assembly of 1580 scaffolds with an N50 value of 7.12 Mbp was generated. Then, the final genome assembly was obtained by anchoring these scaffolds to a high density SNP map. Finally, a genome assembly of 550.31 Mbp was obtained in 7 pseudomolecules corresponding to 7 chromosomes with a very high N50 of 78.27 Mbp. We finally predicted 34,680 protein-coding genes in the guar genome. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted breeding of superior cultivars.

genomics↗

bioRxiv2020

Mutations in Tomato 1-Aminocyclopropane Carboxylic Acid Synthase2 Uncover Its Role in Development beside System II Responses

The role of ethylene in plant development is mostly inferred from its exogenous application. The usage of the mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato, 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterized two contrasting acs2 mutants; acs2-1 overproduces ethylene, has higher ACS activity, and increased protein levels, while acs2-2 is an ethylene under-producer, displays lower ACS activity, and protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles than the wild type. The acs2-1 showed early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely, acs2-2 had delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence of acs2-1/acs2-2 leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates intertwining of ethylene action with other phytohormones in regulating plant development.

plant biology↗

bioRxiv2020

No evidence for transient transformation via pollen magnetofection in several monocot species

The development of rapid and efficient transformation methods for many plant species remains an obstacle in both the basic and applied plant sciences. A novel method described by Zhao et al. (2017) used magnetic nanoparticles to deliver DNA into pollen grains of several dicot species, and one monocot (lily), to achieve transformation ("pollen magnetofection"). Using the published protocol, extensive trials by two independent research groups showed no indication of transient transformation success with pollen from two monocots, maize and sorghum. To further address the feasibility of magnetofection, lily pollen was used for side-by-side trials of magnetofection with a proven methodology for transient transformation, biolistics. Using a Green Fluorescent Protein reporter plasmid, transformation efficiency with the biolistic approach averaged 0.7% over three trials. However, the same plasmid produced no recognizable transformants via magnetofection, despite screening >3500 individual pollen grains. We conclude that pollen magnetofection is not effective for transient transformation of pollen for at least three species of monocots, and suggest that efforts to replicate the magnetofection protocol in dicot species would be useful to fully assess its potential. ARISING FROM Zhao et al. Nature Plants https://doi.org/10.1038/s41477-017-0063-z (2017)

plant biology↗

bioRxiv2020

A central amygdala-globus pallidus circuit conveys unconditioned stimulus information and controls fear learning

The central amygdala (CeA) is critically involved in a range of adaptive behaviors. In particular, the somatostatin-expressing (Sst+) neurons in the CeA are essential for classic fear conditioning. These neurons send long-range projections to several extra-amygdala targets, but the functions of these projections remain elusive. Here, we found in mice that a subset of Sst+ CeA neurons send projections to the globus pallidus external segment (GPe), and constitute essentially the entire GPe-projecting CeA population. Notably, chronic inhibition of GPe-projecting CeA neurons completely blocks auditory fear conditioning. These neurons are selectively excited by the unconditioned stimulus (US) during fear conditioning, and transient inactivation or activation of these neurons during US presentation impairs or promotes, respectively, fear learning. Our results suggest that a major function of Sst+ CeA neurons is to represent and convey US information through the CeA-GPe circuit, thereby instructing learning in fear conditioning.

neuroscience↗