Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 613 records · Page 34Linked to original sources

bioRxiv2020

A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum (Hausmann) (Hemiptera: Aphididae)

Woolly apple aphid (WAA, Eriosoma lanigerum Hausmann) (Hemiptera: Aphididae), is a major pest of apple trees (Malus domestica, order Rosales) and is critical to the economics of the apple industry in most parts of the world. Here, we generated a chromosome-level genome assembly of WAA - representing the first genome sequence from the aphid subfamily Eriosomatinae - using a combination of 10X Genomics linked-reads and in vivo Hi-C data. The final genome assembly is 327 Mb, with 91% of the assembled sequences anchored into six chromosomes. The contig and scaffold N50 values are 158 kb and 71 Mb, respectively, and we predicted a total of 28,186 protein-coding genes. The assembly is highly complete, including 97% of conserved arthropod single-copy orthologues based on BUSCO analysis. Phylogenomic analysis of WAA and nine previously published aphid genomes, spanning four aphid tribes and three subfamilies, reveals that the tribe Eriosomatini (represented by WAA) is recovered as a sister group to Aphidini + Macrosiphini (subfamily Aphidinae). We identified syntenic blocks of genes between our WAA assembly and the genomes of other aphid species and find that two WAA chromosomes (El5 and El6) map to the conserved Macrosiphini and Aphidini X chromosome. Our high-quality WAA genome assembly and annotation provides a valuable resource for research in a broad range of areas such as comparative and population genomics, insect-plant interactions and pest resistance management.

genomics↗

bioRxiv2020

The antidepressant sertraline provides a novel host directed therapy module for augmenting TB therapy

A prolonged therapy, primarily responsible for development of drug resistance by Mycobacterium tuberculosis (Mtb), obligates any new TB regimen to not only reduce treatment duration but also escape pathogen resistance mechanisms. With the aim of harnessing the host response in providing support to existing regimens, we used sertraline (SRT) to stunt the pro-pathogenic type I IFN response of macrophages to infection. While SRT alone could only arrest bacterial growth, it effectively escalated the bactericidal activities of Isoniazid (H) and Rifampicin (R) in macrophages. This strengthening of antibiotic potencies by SRT was more evident in conditions of ineffective control by these frontline TB drug, against tolerant strains or dormant Mtb. SRT, could significantly combine with standard TB drugs to enhance early pathogen clearance from tissues of mice infected with either drug sensitive/ tolerant strains of Mtb. Further, we demonstrate an enhanced protection in acute TB infection of the highly susceptible C3HeB/FeJ mice with the combination therapy signifying the use of SRT as a potent adjunct to standard TB therapeutic regimens against bacterial populations of diverse physiology. This study advocates a novel host directed adjunct therapy regimen for TB with a clinically approved anti-depressant to achieve quicker and greater control of infection.

immunology↗

bioRxiv2020

T cells Mediate Progression of Load-Induced Osteoarthritis

Osteoarthritis (OA) is a degenerative disease that manifests as joint damage and synovial inflammation. To date, most studies have focused on the decrease in cartilage stiffness, chondrocyte viability, and changes in matrix-degrading enzymes. With the exception of a few inflammatory cytokines and macrophages, the immune response in OA is poorly characterized, and the crosstalk of joint damage with T and B cells in local lymph nodes is unknown. Here, using an in vivo mouse model of mechanical loading of mouse tibia, we demonstrate that CD8+ T cells and subsets of CD4+ T cells, and not B cells, increase in the local lymph nodes and contribute to the progression of load-induced OA pathology. We demonstrate that T cell response is sex- and age-dependent. Mechanical loading of T cell knock-out mice that lack {beta} T cell receptor carrying cells resulted in attenuation of both cartilage degradation and osteophyte formation in loaded joints, with a concomitant increase in {gamma}{delta}+ T cells. Restricting the migration of T cells in lymphoid tissues through the systemic treatment using Sphingosine-1-phosphate (S1P) inhibitor, decreased localization of T cells in synovium, and attenuated cartilage degradation. Our results lay the foundation of the role T cells play in the joint damage of load-induced OA and allude to the use of S1P inhibitors and T cell immunotherapies for slowing the progression of OA pathology.

immunology↗

bioRxiv2020

The role of incoherent feedforward circuits in regulating precision of event timing

Triggering of cellular events often relies on the level of a key gene product crossing a critical threshold. Achieving precision in event timing in spite of noisy gene expression facilitates high-fidelity functioning of diverse processes from biomolecular clocks, apoptosis and cellular differentiation. Here we investigate the role of an incoherent feedforward circuit in regulating the time taken by a bacterial virus (bacteriophage lambda) to lyse an infected Escherichia coli cell. Lysis timing is the result of expression and accumulation of a single lambda protein (holin) in the E. coli cell membrane up to a critical threshold level, which triggers the formation of membrane lesions. This easily visualized process provides a simple model system for characterizing event-timing stochasticity in single cells. Intriguingly, lambdas lytic pathway synthesizes two functionally opposite proteins: holin and antiholin from the same mRNA in a 2:1 ratio. Antiholin sequesters holin and inhibits the formation of lethal membrane lesions, thus creating an incoherent feedforward circuit. We develop and analyze a stochastic model for this feedforward circuit that considers correlated bursty expression of holin/antiholin, and their concentrations are diluted from cellular growth. Interestingly, our analysis shows the noise in timing is minimized when both proteins are expressed at an optimal ratio, hence revealing an important regulatory role for antiholin. These results are in agreement with single cell data, where removal of antiholin results in enhanced stochasticity in lysis timing.

systems biology↗

bioRxiv2020

Cell size statistics in cell lineages and population snapshots with different growth regimes and division strategies.

Growing populations of bacteria control their growth and division reaching narrow distributions of cell-sizes. In this paper we explored how different combinations of growth regimes and division mechanisms lead to different cell-size statistics in these populations. Deterministic and stochastic modeling were used to describe the size distribution of a population of cells that is observed from two different perspectives: as single cell lineages, i.e. random paths in the lineage tree, or as snapshots, at given times, of a population in which all descendants of a single ancestor cell are observed. Our time-dependent approaches allowed us to obtain both the transient dynamics and the steady state values for the main statistical moments of the cell-size distribution. Also, we established mathematical relationships among the statistics in the two considered perspectives, thus improving our knowledge of how cells control their growth and proliferation.

systems biology↗

bioRxiv2020

GroEL/ES Buffers Entropic Traps In Folding Pathway During Evolution Of A Model Substrate

The folding landscape of proteins can change during evolution with the accumulation of mutations that may introduce entropic or enthalpic barriers in the protein folding pathway, making it a possible substrate of molecular chaperones in vivo. Can the nature of such physical barriers of folding dictate the feasibility of chaperone-assistance? To address this, we have simulated the evolutionary step to chaperone-dependence keeping GroEL/ES as the target chaperone and GFP as a model protein in an unbiased screen. We find that the mutation conferring GroEL/ES dependence in vivo and in vitro encode an entropic trap in the folding pathway rescued by the chaperonin. Additionally, GroEL/ES can edit the formation of non-native contacts similar to DnaK/J/E machinery. However, this capability is not utilized by the substrates in vivo. As a consequence, GroEL/ES caters to buffer mutations that predominantly cause entropic traps, despite possessing the capacity to edit both enthalpic and entropic traps in the folding pathway of the substrate protein.

molecular biology↗

bioRxiv2020

An optimal lysis time maximizes bacteriophage fitness in quasi-continuous culture

Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progeny are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly rate is maximized. Noting that previous tests of lysis time optimality rely on batch culture, we implemented a quasi-continuous culture system to observe productivity of a panel of isogenic phage {lambda} mutants differing in lysis time. We report that {lambda} phage productivity in our experiments is maximized around an optimal lysis time of 63 min, which is the lysis time of the {lambda} "wildtype" strain. We discuss this finding in light of recent results that lysis time variation is also minimized in the {lambda} "wildtype" strain.

evolutionary biology↗

bioRxiv2020

Omics BioAnalytics: Reproducible Research using R Shiny and Alexa

SummaryHigh-throughput technologies produce complex high-dimensional datasets which are analyzed using a variety of ever-evolving bioinformatics tools. Well-designed web frameworks enable more intuitive and efficient analysis such that less time is spent on coding and more time is spent on interpretation of results and addressing insightful biological questions aided by interactive visualizations. Here, we present Omics BioAnalytics, a full-service Web framework that enables comprehensive, multi-level characterization, analysis, and integration of omics datasets. Blending web-based (R Shiny) and voice-based (Amazons Alexa) analytics, Omics BioAnalytics can be used both by expert computational biologists and non-coding biological domain experts, alike. Our web framework can be utilized to explore complex datasets and identify biosignatures and discriminative biomarkers of health and disease processes, and generate testable hypotheses relating to underlying molecular mechanisms. AvailabilityOmics BioAnalytics is freely available at https://github.com/singha53/omicsBioAnalytics and the web app is deployed at https://amritsingh.shinyapps.io/omicsBioAnalytics/. The source code for the companion Alexa Skill can be found at https://github.com/singha53/omics-bioanalytics-alexa-skill.

bioinformatics↗

bioRxiv2020

HGF-induced activation of NEPHRIN and NEPH1 serves as a novel mechanism for recovery of podocytes from injury

When activated, slit diaphragm proteins NEPHRIN and NEPH1 enable signaling pathways leading to podocyte actin cytoskeleton reorganization, which is critical for podocyte recovery from injury. However, the mechanisms through which these proteins are activated remain unknown. This study presents a novel concept showing ligand-induced activation of NEPHRIN and NEPH1. We first identified phosphatase SHP-2, which directly dephosphorylated these proteins. We next identified HGF, a known SHP-2 modulator, as a rapid inducer of NEPHRIN and NEPH1 phosphorylation. Using baculovirus expressed recombinant purified proteins, SPR (surface plasma resonance), molecular modeling and peptide binding approaches, we show that HGF directly binds NEPHRIN and NEPH1 extracellular domains. Further, using cultured podocytes and Drosophila nephrocytes, we demonstrate that while HGF treatment repaired injured podocytes, the addition of inhibitory NEPH1 or NEPHRIN peptides blocked HGF-induced recovery. Overall, this study shows novel activation and deactivation mechanisms for NEPHRIN and NEPH1 that are required for their function.

cell biology↗

bioRxiv2020

Probabilistic Approach to Understand Errors in Sequencing and its based Applications

Next Generation Sequencing has been applied in many areas of biology, including quantification of gene expression, Genome-Wide Association Study (GWAS), gene finding, Motif discovery and much more. Due to the vast area of application and importance in key findings in the field, massive genomic data is being generated using high throughput sequencing. Therefore, sequencing quality also needs to be evaluated in light of different applications. In order to develop effective diagnostic and therapeutic approaches, we need to accurately characterize and identify sequencing errors and distinguish these errors from their true genetic variant in sequencing, i.e. misreads follow a binomial distribution and it further can be approximated to the Poisson process for longer sequences. However, the insertion and deletion rates are 1000 times lower than substitution error rates and, therefore, less significant. The model assumes that error arrival at a position is not dependent on an error at other positions. Furthermore, errors in sequences can cause an error in studies based on multiple sequences and they also follow Binomial - Poisson Distribution (for example - Alignment is a merging of two Binomial processes for short sequences and it further can be approximated to Poisson for long sequences (for example - genomic sequence). It provides a systematic way to evaluate the accuracy in sequencing-based applications. Many error suppressing algorithms or techniques are there, and our Binomial Poisson model can provide a further systematic understanding of error behavior in short sequences so that more techniques for error removal can be developed with much efficient suppression rates.

genomics↗

bioRxiv2020

Modulation of macrophage defense responses by Mycobacterial persistence protein MprA (Rv0981) in human THP-1 cells: effect of single amino acid variation on host-pathogen interactions

M. tuberculosis is one of the most successful human pathogens causing tuberculosis that leads to highest daily morbidity worldwide. The evasion of the host immune responses is an important strategy that M. tuberculosis adopts. MprA (Rv0981), the response regulator of two component system is known for DNA binding activity in the pathogen and its role in persistent infection in the host. MprA is recognized as a late stage antigen during infection. A variant form of the protein MprA with G70S polymorphism (MprA*) is observed in one of our local and in several global clinical isolates of M. tuberculosis. Here we report the nuclear localization of MprA and MprA* in differentiated macrophages. MprA and MprA* increase the expression of TGF-{beta} and IL-10, the immune suppressive cytokines in THP-1 derived macrophage cells. Concurrently the phago-lysosome fusion is significantly reduced as shown by infection with M.bovis BCG. We show that single nucleotide variation in clinical isolates lead to quantitative variations resulting in host immune suppression and support the survival and persistence of the pathogen.

microbiology↗

bioRxiv2020

How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography

SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.

genomics↗

bioRxiv2020

Stationary distributions and metastable behaviour for self-regulating proteins with general lifetime distributions

Regulatory molecules such as transcription factors are often present at relatively small copy numbers in living cells. The copy number of a particular molecule fluctuates in time due to the random occurrence of production and degradation reactions. Here we consider a stochastic model for a self-regulating transcription factor whose lifespan (or time till degradation) follows a general distribution modelled as per a multidimensional phase-type process. We show that at steady state the protein copy-number distribution is the same as in a one-dimensional model with exponentially distributed lifetimes. This invariance result holds only if molecules are produced one at a time: we provide explicit counterexamples in the bursty production regime. Additionally, we consider the case of a bistable genetic switch constituted by a positively autoregulating transcription factor. The switch alternately resides in states of up- and downregulation and generates bimodal protein distributions. In the context of our invariance result, we investigate how the choice of lifetime distribution affects the rates of metastable transitions between the two modes of the distribution. The phase-type model, being non-linear and multi-dimensional whilst possessing an explicit stationary distribution, provides a valuable test example for exploring dynamics in complex biological systems.

systems biology↗

bioRxiv2020

Social decision making is influenced by size of shoal but not personality or familiarity in Deccan Mahseer (Tor khudree)

Shoals formed by many piscine species are fission-fusion societies where decisions to leave or join a group can have consequences on the fitness of individuals. Some important factors that determine shoal choice are shoal size, familiarity and species composition. However, individuals and species often exhibit distinct shoaling preferences. Individual differences in shoaling preferences may also be related to personality traits such as boldness and sociability. In this study, we examined the link between shoaling decisions and personality traits in a hatchery reared population of an endangered megafish, the Deccan Mahseer (Tor khudree). We found that this fish exhibits a distinct preference for larger shoals at ratios of 1:2 or greater. However, they did not prefer to associate with an isolated familiar individual over unfamiliar ones or with a member of their own species over an invasive species. Moreover, shoaling preferences in individuals did not correlate with their boldness or sociability. These results suggest that hatchery reared mahseers which are reintroduced into natural habitats may shoal with invasive species, negatively affecting their viability. Modifying social behaviour of mahseers by amending rearing practices may be a useful strategy to improve outcomes of restocking interventions.

animal behavior and cognition↗

bioRxiv2020

Designing a multi-epitope peptide-based vaccine against SARS-CoV-2

COVID-19 pandemic has resulted so far 14,395,16 confirmed cases with 85,711 deaths from the 212 countries, or territories. Due to multifacet issues and challenges in implementation of the safety & preventive measures, inconsistent coordination between societies-governments and most importanly lack of specific vaccine to SARS-CoV-2, the spread of Wuhan originated virus is still uprising after taking a heavy toll on human life. In the present study, we mapped several immunogenic epitopes (B-cell, T-cell, and IFN-gamma) over the entire structural proteins of SARS-CoV-2 and by applying various computational and immunoinformatics approaches, we designed a multi-epitope peptide based vaccine that predicted high immunogenic response in the largest proportion of worlds human population. To ensure high expression of the recombinant vaccine in E. coli, codon optimization and in-silico cloning were also carried out. The designed vaccine with high molecular affinity to TLR3 and TLR4, was found capable to initiate effective innate and adaptive immune response. The immune simulation also suggested uprising high levels of both B-cell and T-cell mediated immunity which on subsequent exposure cleared antigen from the system. The proposed vaccine found promising by yielding desired results and hence, should be tested by practical experimentations for its functioning and efficacy to neutralize SARS-CoV-2.

bioinformatics↗

bioRxiv2020

Alternative MyD88 -Cyclin D1 signaling in breast cancer cells regulates TLR3 mediated cell proliferation

TLR3 mediated apoptotic changes in cancer cells are well documented and hence several synthetic ligands of TLR3 are being used for adjuvant therapy. But there are reports showing contradictory effect of TLR3 signaling which includes our previous report that had shown cell proliferation following surface localization of TLR 3. However, the underlying mechanism of cell surface localization of TLR3 and subsequent cell proliferation lacks clarity. This study addresses TLR3 ligand mediated signaling cascade that regulates a proliferative effect in breast cancer cells (MDA MB 231 and T47D) challenged with TLR3 ligand in the presence of MyD88 inhibitor. Evidences were obtained using immunoblotting, co-immunoprecipitation, confocal microscopy, Immunocytochemistry, ELISA, and flowcytometry. Results had revealed that TLR3 ligand treatment significantly enhanced breast cancer cell proliferation marked by an upregulated expression of cyclinD1 but the same were suppressed by addition of MyD88 inhibitor. Also, expression of IRAK1-TRAF6-TAK1 were altered in the given TLR3-signaling pathway. Inhibition of MyD88 disrupted the downstream adaptor complex and mediated signaling through TLR3-MyD88-NF-{kappa}B (p65)-IL6-Cyclin D1 pathway. TLR3 mediated alternative signaling of the TLR3-MyD88-IRAK1-TRAF6-TAK1-TAB1-NF-{kappa}B axis leads to upregulation of IL6 and cyclinD1. This response is hypothesized to be via the MyD88 gateway that culminates in proliferation of breast cancer cells. Overall, this study provides first comprehensive evidence on involvement of canonical signaling of TLR3 using MyD88 - Cyclin D1 mediated breast cancer cell proliferation. The findings elucidated herein will provide valuable insights into understand the TLR3 mediated adjuvant therapy in cancer.

cancer biology↗

bioRxiv2020

Transmembrane Stem Cell Factor Protein Therapeutics EnhanceRevascularization in Ischemia without Mast Cell Activation

Stem cell factor (SCF) is a cytokine that regulates hematopoiesis and other biological processes. While clinical treatments using SCF would be highly beneficial, these have been limited by toxicity related to mast cell activation. Transmembrane SCF (tmSCF) has differential activity from soluble SCF and has not been explored as a therapeutic agent. We created novel therapeutics using tmSCF embedded in proteoliposomes or lipid nanodiscs. Mouse models of anaphylaxis and ischemia revealed the tmSCF-based therapies did not activate mast cells and improved the revascularization in the ischemic hind limb. Proteoliposomal tmSCF preferentially acted on endothelial cells to induce angiogenesis while tmSCF nanodiscs had greater activity in inducing stem cell mobilization and recruitment to the site of injury. The type of lipid nanocarrier used altered the relative cellular uptake pathways and signaling in a cell type dependent manner. Overall, we found that tmSCF-based therapies can provide therapeutic benefits without off target effects.

bioengineering↗

bioRxiv2020

KnetMiner - Intelligent search and visualisation of connected data to explain complex traits and diseases

Generating new ideas and scientific hypotheses is often the result of extensive literature and database reviews, overlaid with scientists own novel data and a creative process of making connections that were not made before. We have developed a comprehensive approach to guide this technically challenging data integration task and to make knowledge discovery and hypotheses generation easier for plant and crop researchers. KnetMiner can digest large volumes of scientific literature and biological research to find and visualise links between the genetic and biological properties of complex traits and diseases. Here we report the main design principles behind KnetMiner and provide use cases for mining public datasets to identify unknown links between traits such grain colour and pre-harvest sprouting in Triticum aestivum, as well as, an evidence-based approach to identify candidate genes under an Arabidopsis thaliana petal size QTL. We have developed KnetMiner knowledge graphs and applications for a range of species including plants, crops and pathogens. KnetMiner is the first open-source gene discovery platform that can leverage genome-scale knowledge graphs, generate evidence-based biological networks and be deployed for any species with a sequenced genome. KnetMiner is available at http://knetminer.org.

bioinformatics↗