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Singh, A.

Publications and source records attributed to Singh, A..

At least 541 records · Page 30Linked to original sources

Hydrogen sulfide blocks HIV rebound by maintaining mitochondrial bioenergetics and redox homeostasis

A fundamental challenge in HIV eradication is to understand how the virus establishes latency, maintains stable cellular reservoirs, and promotes rebound upon interruption of antiretroviral treatment (ART). Here, we discovered an unexpected role of the ubiquitous gasotransmitter hydrogen sulfide (H2S) in HIV latency and reactivation. We show that reactivation of HIV-1 is associated with down-regulation of the key H2S producing enzyme cystathionine-{gamma}-lyase (CTH) and reduction in endogenous H2S. Genetic silencing of CTH disrupts redox homeostasis, impairs mitochondrial function, and remodels the transcriptome of latent cells to trigger HIV reactivation. Chemical complementation of CTH activity using a slow-releasing H2S donor, GYY4137, suppressed HIV reactivation and diminished virus replication. Mechanistically, GYY4137 blocked HIV reactivation by inducing the Keap1-Nrf2 pathway, inhibiting NF-{kappa}B, and recruiting the epigenetic silencer, YY1, to the HIV promoter. In latently infected CD4+ T cells from ART-suppressed human subjects, GYY4137 in combination with ART prevented viral rebound and improved mitochondrial bioenergetics. Moreover, prolonged exposure to GYY4137 exhibited no adverse influence on proviral content or CD4+ T cell subsets, indicating that diminished viral rebound is due to a loss of transcription rather than a selective loss of infected cells. In summary, this work provides mechanistic insight into H2S-mediated suppression of viral rebound and suggests the inclusion of an H2S donor in the current ART regimen to achieve a functional HIV-1 cure.

microbiology↗

Transfer RNA-derived non-coding RNAs (tncRNAs): Uncovering hidden regulators of transcriptional regulatory circuits in plants

The lateral emergence of distinct classes of non-coding RNAs has led to better insights into the eukaryotic regulatory networks. Among them, the existence of transfer RNA (tRNA)-derived non-coding RNAs (tncRNAs) demands their exploration in the plant kingdom. Here, we have designed a methodology to uncover the bigger picture of tncRNAome in plants. Using this, we have identified diverse tncRNAs of length 14-50 nt in ~2500 small RNA sequencing (sRNA-seq) samples of six major angiosperms, and further studied their various features including length, codon-usage, cleavage pattern, and modified tRNA nucleosides. Codon-dependent generation of tncRNAs indicates that the process is highly specific rather than being mere random tRNA degradation. Analysis for nucleotide composition of tncRNA cleavage positions indicates that they are generated through precise endoribonucleolytic machinery. Certain tRNA nucleoside modifications on tncRNAs were found to be conserved across the plants, and hence may influence tRNA cleavage, as well as tncRNA functions. Pathway enrichment analysis revealed that common tncRNA targets were majorly involved in the metabolic and developmental processes of plants. Also, many tRFs were found to be associated with transposable elements. Distinct tissue-specific tncRNA clusters indicate their role in plant development under normal physiological conditions. Furthermore, the identification of a significant number of differentially expressed tncRNAs under several abiotic and biotic stresses highlights their probable role as gene expression modulators during various stress conditions. Thus, this study will be beneficial to investigate the emerging role of tncRNAs as prospective biomarkers in plant development and stress. HighlightsO_LIComputational pipeline for accurate identification of genuine transfer RNA-derived non-coding RNAs (tncRNAs) using small RNA sequencing (sRNA-seq) datasets. C_LIO_LISix major tncRNA classes of length ranging from 14 to 50 nt were identified in ~2,500 sRNA-seq datasets in six different angiosperms. C_LIO_LItRNA nucleoside modifications may affect tncRNA cleavage in plants. C_LIO_LIConserved tncRNAs target transcripts are involved in plant growth, development, and metabolism. C_LIO_LItncRNAs are expressed in a tissue-dependent, and stress-specific manner in plants. C_LI

bioinformatics↗

Temporal resolution of melanogenesis determine fatty acid metabolism as key skin pigment regulator

Therapeutic methods to modulate skin pigmentation has important implications for skin cancer prevention and for treating meta-inflammatory-triggered cutaneous conditions. Modulators of cAMP signalling of melanocyte have met with minimal clinical efficacy. Towards defining new potential targets, we followed temporal dynamics orchestrating melanocyte differentiation by using a cell-autonomous pigmentation model. Our study elucidates three dominant phases of synchronized metabolic and transcriptional reprogramming. The induction phase is concomitant with a paradoxical decrease in MITF levels, reduced proliferation, and increased anabolic metabolism mediated by AKT phosphorylation. The melanogenic phase shows rapid uptake of glucose and fatty acid, transiently forming lipid droplets through SREBF1-mediated regulation of fatty acid metabolism. This heightened bioenergetic activity impairs mitochondria and the recovery phase is marked by a shift to aerobic glycolysis and activation of the NRF2 detoxication pathway. Finally, we show that inhibitors of lipid metabolism indeed resolve hyper-pigmentary conditions in a guinea pig UV-tanning model. Our studies reveal metabolic control mechanisms of melanocytes that could govern the balance between differentiation and proliferation in a variety of cutaneous diseases.

cell biology↗

Integrative physiological, biochemical and transcriptomic analysis of hexaploid wheat roots and shoots provides new insights into the molecular regulatory network during Fe & Zn starvation

In plants, iron (Fe) & zinc (Zn) uptake and transportation from the rhizosphere to the grain is a critical process regulated by complex transcriptional regulatory networks. However, understanding the combined effect of Fe & Zn starvation on their uptake and transportation and the molecular regulatory networks that control them lack in wheat. Here, we performed a comprehensive physiological, biochemical and transcriptome analysis in two bread wheat genotypes, i.e. Narmada 195 and PBW 502, differing in inherent Fe & Zn content to understand the mechanism of Fe & Zn homeostasis. Compared to PBW 502, Narmada 195 exhibited increased tolerance to Fe & Zn withdrawal by an increased level of antioxidant enzymes and DPPH radical scavenging activity along with less malondialdehyde (MDA), H2O2 level, increased PS accumulation and lower reduction of root and shoot Fe & Zn content and length, leaf chlorosis, and leaf area. By integrating physiological and biochemical data along with co-expression & functional genome annotation and gene expression analysis, we identified 25 core genes associated with four key pathways, i.e. Met cycle (10), PS biosynthesis (4), antioxidant (3) and transport system (8) that were significantly modulated by Fe & Zn withdrawal in both the genotypes. Genes of these four pathways were more considerably up-regulated in Narmada 195, allowing better tolerance to Fe & Zn withdrawal and efficient uptake and transportation of Fe & Zn. Chromosomal distribution and sub-genome wise mapping of these genes showed a contribution from all the chromosomes except group 5 chromosomes with the highest number of genes mapped to chromosome 4 (24%) and sub-genome D (40%). Besides, we also identified 26 miRNAs targeting 14 core genes across the four pathways. Together, our work provides a crucial angle for an in-depth understanding of regulatory cross-talk among physiological, biochemical and transcriptional reprogramming underlying Fe & Zn withdrawal in wheat. Core genes identified can serve as valuable resources for further functional research for genetic improvement of Fe & Zn content in wheat grain. HighlightOur work provides a crucial angle for a comprehensive understanding of the regulatory mechanism underlying Fe & Zn withdrawal associated with physiological, biochemical and transcriptional reprogramming in wheat.

molecular biology↗

Disentangling the roles of inter and intraspecific variation on leaf trait distributions across the eastern United States

Functional traits are influenced by phylogenetic constraints and environmental conditions, but previous large-scale studies modeled traits either as species weighted averages or directly from the environment, precluding analyses of the relative contributions of inter- and intraspecific variation across regions. We developed a joint model integrating phylogenetic and environmental information to understand and predict the distribution of eight leaf traits across the eastern USA. This model explained 68% of trait variation, outperforming both species-only and environment-only models, with variance attributable to species alone (23%), the environment alone (13%), and their combined effects (25%). The importance of the two drivers varied by trait. Predictions for the eastern USA produced accurate estimates of intraspecific variation and deviated from both species-only and environment-only models. Predictions revealed that intraspecific variation holds information across scales, affects relationships in the leaf economic spectrum and is key for interpreting trait distributions and ecosystem processes within and across ecoregions.

ecology↗

High frequency rTMS modulates functional connectivity nodes and boundaries differently in the human brain

Repetitive transcranial magnetic stimulation (rTMS) has gained considerable importance in the treatment of neuropsychiatric disorders, including major depression. However, it is not yet understood how rTMS alters brains functional connectivity. Here we report changes in functional connectivity captured by resting state functional magnetic resonance imaging (rsfMRI) within the first hour after 10Hz rTMS. We apply subject-specific parcellation schemes to detect changes (1) in network nodes, where the strongest functional connectivity of regions is observed, and (2) in network boundaries, where functional transitions between regions occur. We use support vector machines (SVM), a widely used machine learning algorithm that is robust and effective for the classification and characterization of time intervals of changes in node and boundary maps. Our results reveal that changes in connectivity at the boundaries are slower and more complex than in those observed in the nodes, but of similar magnitude according to accuracy confidence intervals. These results were strongest in the posterior cingulate cortex and precuneus. As network boundaries are indeed under-investigated in comparison to nodes in connectomics research, our results highlight their contribution to functional adjustments to rTMS.

neuroscience↗

Loss of Tsc1 in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts

Tuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated that Tsc1 loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses of Tsc1-deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using Translating Ribosome Affinity Purification (TRAP). Finally, we found that the FMRP target, SHANK2, was reduced in PC synapses, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.

neuroscience↗

GMSECT: Genome-Wide Massive Sequence Exhaustive Com-parison Tool for structural and copy number variations

GMSECT is a parallel robust Application Interface that efficiently handles the large genomic sequences for rapid and efficient processing. It is a message passing interface based parallel computing Tool that can be operated on a cluster for Massive Sequences Exhaustive Comparison, to identify matches such as the structural variants. The GMSECT algorithm can be implemented using other parallel application programming interfaces as well such as Posix-Threads or can even be implemented in a serial submission fashion. There is complete flexibility to the choice of comparison tool that can be deployed and with the optional parameters as of the choice of comparison tools to suit the speed, sensitivity and specificity of pair wise alignment. The algorithm is simple and robust, and can be applied to compare multiple genomes, chromosomes or large sequences, of different individuals for personalized genome comparison and works good for homologous as well as distant species. The tool can even be applied to smaller genomes like the microbial genome such as the Escherichia coli or algae such as Chlamydomonas reihardtti or yeast Saccharomyces cerevisiae to quickly conduct comparisons, and thus finds its application to the pharmaceuticals and microbial product based firms for research and development. The application Interface can efficiently and rapidly compare massive sequences to detect for the presence of numerous types of DNA variation existing in the genome ranging from single nucleotide polymorphism (SNPs) to larger structural alterations, such as copy-number variants (CNVs) and inversions. The new algorithm has been tested for comparing the chromosome 21 of Celeras R27c compilation with all the 48 chromosomes of Celeras R27c compilation and with all the 48 chromosomes of the human Build 35 reference sequence, which took just 2 Hours and 10 minutes using the pair wise blast algorithm choice and with 110 processors each with 2.2 GHz capacity and 2 GB memory. GMSECT facilitates rapid scanning and interpretation in personalized sequencing project. The application interface with the above resources and alignment choice is estimated to do exhaustive comparison of the human genome with itself in just 2.35 days. An exhaustive comparison of an individuals genome with a reference genome would comprise of a two self genome comparison and a non-self genome comparison which is estimated to take about 9.4 days with the above resources. With the advent of personalized genome sequencing project, it would be desirable to compare 100s of individuals genome with a reference genome. This would involve a non-self genome and a self genome comparison for each genome, and would take around 7 days for each individuals genome using GMSECT and the above mentioned resources.

bioinformatics↗

Brain Dynamics of Spatial Reference Frame Proclivity in Active Navigation

Recent research into navigation strategy of different spatial reference frame proclivities (RFPs) has revealed that the parietal cortex plays an important role in processing allocentric information to provide a translation function between egocentric and allocentric spatial reference frames. However, most studies merely focused on a passive experimental environment, which is not truly representative of our daily spatial learning/navigation tasks. This study investigated the factor associated with brain dynamics that causes people to switch their preferred spatial strategy in different environments in virtual reality (VR) based active navigation task to bridge the gap. High-resolution electroencephalography (EEG) signals were recorded to monitor spectral perturbations on transitions between egocentric and allocentric frames during a path integration task. Our brain dynamics results showed navigation involved areas including the parietal cortex with modulation in the alpha band, the occipital cortex with beta and low gamma band perturbations, and the frontal cortex with theta perturbation. Differences were found between two different turning-angle paths in the alpha band in parietal cluster event-related spectral perturbations (ERSPs). In small turning-angle paths, allocentric participants showed stronger alpha desynchronization than egocentric participants; in large turning-angle paths, participants for two reference frames had a smaller difference in the alpha frequency band. Behavior results of homing errors also corresponded to brain dynamic results, indicating that a larger angle path caused the allocentric to have a higher tendency to become egocentric navigators in the active navigation environment.

neuroscience↗

Delineating the complex mechanistic interplay between autophagy and monocyte to macrophage differentiation: a functional perspective

Autophagy is an extremely essential cellular process aimed to clear redundant and damaged materials. In this study, we demonstrated that mTOR dependent classical autophagy is ubiquitously triggered in differentiating monocytes. Moreover, autophagy plays a decisive role in sustaining the process of monocyte to macrophage differentiation. We have delved deeper into understanding the underlying mechanistic complexities that trigger autophagy during differentiation. We have also shown that autophagy directs monocyte differentiation via protein degradation. Further, we delineated the complex cross-talk between autophagy and cell-cycle arrest in differentiating monocytes. This study also inspects the contribution of adhesion on various steps of autophagy and its ultimate impact on monocyte differentiation. Our study reveals new mechanistic insights into the process of autophagy associated with monocyte differentiation and would undoubtedly help to understand the intricacies of the process better for the effective design of therapeutics as autophagy and autophagy-related processes have enormous importance in human patho-physiology. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cell biology↗

Novel newt regeneration genes regulate Wingless signaling to restore patterning in Drosophila eye

A fundamental process of regeneration, which varies among animals, recruits conserved signaling pathways to restore missing parts. Only a few animals like newts can repeatedly regenerate lost body parts throughout their lifespan that can be attributed to strategic regulation of conserved signaling pathways by newts regeneration tool-kit genes. Here we report use of genetically tractable Drosophila eye model to demonstrate the regeneration potential of a group of unique protein(s) from newt (Notophthalmus viridescens), which when ectopically expressed can significantly rescue missing photoreceptor cells in a Drosophila eye mutant. These newt proteins with signal peptides motifs exhibit non-cell-autonomous rescue properties and their regeneration potential even extends into later stages of fly development. Ectopic expression of these newt genes can rescue eye mutant phenotype by promoting cell proliferation and blocking cell death. These novel newt genes downregulate evolutionarily conserved Wingless (Wg)/Wnt signaling pathway to promote rescue. Modulation of Wg/Wnt signaling levels by using antagonists or agonists of Wg/Wnt signaling pathway in eye mutant background where newt gene(s) is ectopically expressed suggests that Wg signaling acts downstream of newt genes. Our data highlights the regeneration potential of novel newt proteins that regulate conserved pathways to trigger a robust regeneration response in Drosophila model with weak regeneration capability.

developmental biology↗

Condensation of the Drosophila Nerve Cord is Oscillatory and depends on Coordinated Mechanical Interactions

During development, organs must form with precise shapes and sizes. Organ morphology is not always obtained through growth; a classic counterexample is condensation of the nervous system during Drosophila embryogenesis. The mechanics underlying such condensation remain poorly understood. Here, we combine in toto live-imaging, biophysical and genetic perturbations, and atomic force microscopy to characterize the condensation of the Drosophila ventral nerve cord (VNC) during embryonic development at both subcellular and tissue scales. This analysis reveals that condensation is not a unidirectional continuous process, but instead occurs through oscillatory contractions alternating from anterior and posterior ends. The VNC mechanical properties spatially and temporally vary during its condensation, and forces along its longitudinal axis are spatially heterogeneous, with larger ones exerted between neuromeres. We demonstrate that the process of VNC condensation is dependent on the coordinated mechanical activities of neurons and glia. Finally, we show that these outcomes are consistent with a viscoelastic model of condensation, which incorporates time delays due to the different time scales on which the mechanical processes act, and effective frictional interactions. In summary, we have defined the complex and progressive mechanics driving VNC condensation, providing insights into how a highly viscous tissue can autonomously change shape and size.

developmental biology↗

A Programmable Toolkit to Dynamically Signal Cells using Peptide Strand Displacement

The native extracellular matrix communicates and interacts with cells by dynamically displaying signals to control their behavior. Mimicking this dynamic environment in vitro is essential in order to unravel how cell-matrix interactions guide cell fate. Here, we present a synthetic platform for the temporal display of cell adhesive signals using coiled-coil peptides. By designing an integrin-engaging coiled-coil pair to have a toehold (unpaired domain), we were able to use a peptide strand displacement reaction to remove the cell cue from the surface. This allowed us to test how the on-demand display of RGDS ligands at variable duration and periodicity of ligand exposure influence cell spreading degree and kinetics. Transient display of V{beta}3 selective ligands instructed fibroblast cells to reversibly spread and contract in response to changes in ligand exposure over multiple cycles, exhibiting a universal kinetic response. Also, cells that were triggered to spread and contract repeatedly exhibited greater enrichment of integrins in focal adhesions versus cells cultured on persistent RGDS-displaying surfaces. This dynamic platform will allow us to uncover the molecular code by which cells sense and respond to changes in their environment and will provide insights into ways to program cellular behavior.

bioengineering↗

Meta-analysis of orthogonal OMICs data from COVID-19 patients unveils prognostic markers and antiviral factors.

While our battle with the COVID-19 pandemic continues, a multitude of Omics data has been generated from patient samples in various studies, which remains to be translated. We conducted a meta-analysis of published transcriptome and proteome profiles of nasal swab and bronchioalveolar lavage fluid (BALF) samples of COVID-19 patients, to shortlist high confidence upregulated host factors. Subsequently, mRNA overexpression of selected genes was validated in nasal swab/BALF samples from a cohort of COVID-19 positive/negative, symptomatic/asymptomatic individuals. Analysis of these data revealed S100 family genes (S100A6, S100A8, S100A9, and S100P) as prognostic markers of COVID-19 disease. Furthermore, Thioredoxin gene (TXN) was identified as a significant upregulated host factor in our overlap analysis. An FDA-approved drug Auranofin, which inhibits Thioredoxin reduction, was found to mitigate SARS-CoV-2 replication in vitro and in vivo in the hamster challenge model. Overall, this study translates COVID-19 host response Big Data into potential clinical interventions.

microbiology↗

Sterile Inflammation Alters Neutrophil Kinetics in Mice

Neutrophils play a crucial role in establishing inflammation in response to an infection or injury, but their production rates, as well as blood and tissue residence times, remain poorly characterized under these conditions. Herein, using a biomaterial implant model to establish inflammation followed by in vivo tracking of newly formed neutrophils, we determine neutrophil kinetics under inflammatory conditions. To obtain quantifiable information from our experimental observations, we develop an ordinary differential equation-based mathematical model to extract kinetic parameters. Our data show that in the presence of inflammation resulting in emergency granulopoiesis-like conditions, neutrophil maturation time in the bone marrow and half-life in the blood reduces by about 40%, compared to non-inflammatory conditions. Additionally, neutrophil residence time at the inflammatory site increases by two-fold. Together, these data improve our understanding of neutrophil kinetics under inflammatory conditions, which could pave the way for therapies that focus on modulating in vivo neutrophil dynamics.

immunology↗

Sexual dimorphism in gene expression: coincidence and population genomics of two forms of differential expression in Drosophila melanogaster

Phenotypic sexual dimorphism can be mediated by sex differences in gene expression. We examine two forms of sexual dimorphism in gene expression in Drosophila melanogaster: (i) sex-biased gene expression (SBGE) in which the sexes differ in the amount a gene is expressed and (ii) sexual dimorphism in isoform usage, i.e., sex-specific splicing (SSS). In whole body (but not head) expression, we find a negative association between SBGE and SSS, possibly suggesting these are alternate routes to resolving sexual antagonistic selection. Next, we evaluate whether expression dimorphism contributes to the heterogeneity among genes in rmf, the intersexual genetic correlation in body expression that constrains the extent to which a genes expression can evolve independently between the sexes. We find lower rmf values for genes with than without SSS. We find higher rmf values for male- than female-biased genes (except genes with extreme male-bias), even though male-biased genes are known to have greater evolutionary divergence in expression. Finally, we examine population genetic patterns in relation to SBGE and SSS because genes with expression dimorphism have likely experienced a history of sex differences in selection. SSS is associated with reduced values of Tajimas D and elevated Direction of Selection (DoS) values, suggestive of higher rates of adaptive evolution. Though DoS is highly elevated for genes with extreme male bias, DoS otherwise tends to decline from female-biased to unbiased to male-biased genes. Collectively, the results indicate that SBGE and SSS are differentially distributed across the genome and are associated with different forms of selection.

evolutionary biology↗

AlnC: An extensive database of long non-coding RNAs in Angiosperms

Long non-coding RNAs (lncRNAs) play a major role in diverse biological processes that are contemplated to have diverse regulatory roles in plants. While lncRNAs have been described and annotated in major plant species, many of plant species lack annotated lncRNAs despite the availability of transcriptome data in public repositories. In this study, we have identified and annotated the lncRNAs in the transcriptomic data from the 1000 plant genome project (1KP), and developed a user-friendly, open-access database called AlnC. This can be used for the exploration of lncRNAs in 682 Angiosperm plants. The current version of AlnC offers 10,855,598 annotated lncRNA transcripts across 809 sample tissues of diverse flowering plants. To enhance the AlnC interface, we have provided the features for browsing, searching and downloading of lncRNA data, interactive graphics, and online BLAST service. In addition to these information, each lncRNA record is annotated with possible Short open reading frames (e.g. sORFs) to facilitate the study of peptides encoded within lncRNAs. With this user-friendly interface, we assume that AlnC will serve as a rich source of lncRNAs that will contribute to small-and large-scale studies in a wide range of flowering plants.

bioinformatics↗

Redefining tumor classification and clinical stratification through a colorectal cancer single-cell atlas

Colorectal cancer (CRC), a disease of high incidence and mortality, has had few treatment advances owing to a large degree of inter- and intratumoral heterogeneity. Attempts to classify subtypes of colorectal cancer to develop treatment strategies has been attempted by Consensus Molecular Subtypes (CMS) classification. However, the cellular etiology of CMS classification is incompletely understood and controversial. Here, we generated and analyzed a single-cell transcriptome atlas of 49,859 CRC cells from 16 patients, validated with an additional 31,383 cells from an independent CRC patient cohort. We describe subclonal transcriptomic heterogeneity of CRC tumor epithelial cells, as well as discrete stromal populations of cancer-associated fibroblasts (CAFs). Within CRC CAFs, we identify the transcriptional signature of specific subtypes (CAF-S1 and CAF-S4) in more than 1,500 CRC patients using bulk transcriptomic data that significantly stratifies overall survival in multiple independent cohorts. We also uncovered two CAF-S1 subpopulations, ecm-myCAF and TGF{beta}-myCAF, known to be associated with primary resistance to immunotherapies. We demonstrate that scRNA analysis of malignant, stromal, and immune cells exhibit a more complex picture than portrayed by bulk transcriptomic-based Consensus Molecular Subtypes (CMS) classification. By demonstrating an abundant degree of heterogeneity amongst these cell types, our work shows that CRC is best represented in a transcriptomic continuum crossing traditional classification systems boundaries. Overall, this CRC cell map provides a framework to re-evaluate CRC tumor biology with implications for clinical trial design and therapeutic development.

cancer biology↗