Biology subjects

Srivastava, P.

Publications and source records attributed to Srivastava, P..

29 records · Page 2Linked to original sources

bioRxiv2021

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy Body diseases

Parkinsons disease (PD), Parkinsons disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of disease-modifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular "window" of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.

neuroscience↗

bioRxiv2021

Targeting the artemisinin resistant malaria by repositioning of the anti-Hepatitis C Virus drug Alisporivir

The rapid emergence of P. falciparum-resistant strains raises an urgent need to find new antimalarial drug candidates. This study reports the rational repositioning of the anti-Hepatitis C Virus drug, Alisporivir, a non-immunosuppressive analog of cyclosporin A (CsA) against multiple, drug-resistant strains of P. falciparum. Alisporivir being non-hemolytic has been proven to be a better drug than CsA. Indeed, our study also demonstrated the same. Alisporivir inhibited chloroquine-sensitive parasite growth with an IC50 of 196.6nM. Alisporivir also inhibited the growth of chloroquine-resistant parasites with an IC50 of 422.1nM. Alisporivir exhibited, anti-malarial activity in in vivo. Further, we exploited the Cyclophilins targeting potential of Alisporivir against artemisinin-resistant malaria parasite owing to the fact that PfCyP-19B is one of the genes that is overexpressed in artemisinin-resistant parasite revealed by a population transcriptomic study. Our semiquantitative real-time transcript and immunofluorescence analysis confirmed the overexpression of PfCyP-19B in Artemisinin-resistant P. falciparum (PfKelch13R539T). Artemisinin resistance is attributed to slow clearance of ring stage parasites. Ring survival assay (RSA) is designed to access the potency of compounds on these dormant slow clearing parasites leading to drug resistance. Thus, the potency of Alisporivir against PfKelch13R539T was evaluated by RSA. A 2.5-fold decrease in parasite survival was detected with Alisporivir. Further, combination of Alisporivir with DHA found to potentiate the efficacy of DHA by 4.55-fold. These results support the hypothesis that targeting of resistance mechanism is a potential approach to deal with resistant parasite. Overall, this study demonstrates the rational reposition of Alisporivir against resistant malaria resistance.

microbiology↗

bioRxiv2020

Racial and ethnic imbalance in neuroscience reference lists and intersections with gender

Discrimination against racial and ethnic minority groups exists in the academy, and the associated biases impact hiring and promotion, publication rates, grant funding, and awards. Precisely how racial and ethnic bias impacts the manner in which the scientific community engages with the ideas of academics in minority groups has yet to be fully elucidated. Citations are a marker of such community engagement, as well as a currency used to attain career milestones. Here we assess the extent and drivers of racial and ethnic imbalance in the reference lists of papers published in five top neuroscience journals over the last 25 years. We find that reference lists tend to include more papers with a White person as first and last author than would be expected if race and ethnicity were unrelated to referencing. We show that this imbalance is driven largely by the citation practices of White authors, and is increasing over time even as the field diversifies. To further explain our findings, we examine co-authorship networks and find that while the network has become markedly more integrated in general, the current degree of segregation by race/ethnicity is greater now than it has been in the past. Citing further from oneself on the network is associated with greater balance, but White authors preferential citation of White authors remains even at high levels of network exploration. We also quantify the effects of intersecting identities, determining the relative costs of gender and race/ethnicity, and their combination in women of color. Our findings represent a call to scientists and journal editors of all disciplines to consider the ethics of citation practices, and actions to be taken in support of an equitable future.

neuroscience↗

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

lncRNA Mediated Hijacking of T-cell Hypoxia Response Pathway by Mycobacterium Tuberculosis Predicts Latent to Active Progression in Humans

Cytosolic functions of Long non-coding RNAs including mRNA translation masking and sponging are major regulators of biological pathways. Formation of T cell-bounded hypoxic granuloma is a host immune defence for containing infected Mtb-macrophages. Our study exploits the mechanistic pathway of Mtb-induced HIF1A silencing by the antisense lncRNA-HIF1A-AS2 in T cells. Computational analysis of in-vitro T-cell stimulation assays in progressors (n=119) versus non-progressor (n=221) tuberculosis patients revealed the role of lncRNA mediated disruption of hypoxia adaptation pathways in progressors. We found 291 upregulated and 227 downregulated DE lncRNAs that were correlated at mRNA level with HIF1A and HILPDA which are major players in hypoxia response. We also report novel lncRNA-AC010655 (AC010655.4 and AC010655.2) in cis with HILPDA, both of which contain binding sites for the BARX2 transcription factor, thus indicating a mechanistic role. Detailed comparison of infection with antigenic stimulation showed a non-random enrichment of lncRNAs in the cytoplasmic fraction of the cell in TB progressors. The lack of this pattern in non-progressors replicates indicates the hijacking of the lncRNA dynamics by Mtb. The in-vitro manifestation of this response in the absence of granuloma indicates pre-programmed host-pathogen interaction between T-cells and Mtb regulated through lncRNAs, thus tipping this balance towards progression or containment of Mtb. Finally, we trained multiple machine learning classifiers for reliable prediction of latent to the active progression of patients, yielding a model to guide aggressive treatment.

bioinformatics↗

bioRxiv2020

Septins disruption controls tumor growth and enhances efficacy of Herceptin

Septin expressions are altered in cancer cells and exhibit poor prognoses in malignancies. As the first approach to develop a septin filament targeting agent, we optimized the structure of Forchlorfenuron (FCF), a known plant cytokinin to generate UR214-9, which contrary to FCF, causes septin-2/9 filamental structural catastrophe in cancer cells without altering cellular septin protein levels. In-silico docking using septin-2/septin-2 dimer complex showed that UR214-9 displaced the guanine carbonyl oxygen from the GDP binding domain and showed increased binding energy than FCF(-8.59vs-7.21). UR214-9 reduced cancer cell growth, downregulated HER2/STAT-3 axis and controlled growth of HER2+ pancreatic, breast and ovarian cancer xenografts in NSG mice and enhanced response of Herceptin against HER2+breast cancer xenograft. Transcriptome analysis of UR214-9 exposed cells demonstrated significant perturbation of <20 genes compared to afatinib which impacted >1200 genes in JIMT-1 breast cancer cells indicating target specificity and non-transcriptional functions of UR214-9. In summary, disrupting septins via UR214-9 is a new approach to control the growth of HER2+ malignancies.

cancer biology↗

bioRxiv2019

Analysis and subsequent molecular docking of selected phytochemicals with SLC6A3 and SLC6A4 as potential therapeutic agents for Obsessive-Compulsive Disorder (OCD)

Obsessive-Compulsive Disorder (OCD) is one of the most problematic disorders of the brain. It lies in the category of moodomics disorders and can be identified by the presence of recurring intrusive thoughts (\"compulsions\") and urges to do certain things repeatedly (\"obsessions\"), with a definite lack of control on these tendencies and their intensity affecting the patients daily life. It is known to be associated with not only anxiety disorder but also depression, with its cause being unknown, although possessing genetic components. Several separate methods are being attempted to develop an effective therapy for OCD but this field of research requires more focus. In the present course of research, there is an attempt to signify the molecular analysis approach by testing potential drugs computationally with previously identified targets, i. e. dopamine active transporter (DAT or SLC6A3) and sodium-dependent serotonin transporter (SERT or 5-HTT or SLC6A4) - two proteins which have been observed playing a major role in the manifestation of OCD symptoms. Their 3D structure prediction has already been done in the previous course of study. In continuation to the previous study, there is an attempt to screen out the potentially useful phytochemicals against this moodomics disorder. Several potentially useful phytochemicals are known to associate with SLC6A3 and SLC6A4, which have been identified through the text mining of various publications. First of all, these phytochemicals are analysed through the use of Molinspiration software followed by selection of the ones suitable as drug candidates using Lipinskis Rule of five and finally, best docking configurations identified using AutoDock 4 in order to obtain potential therapeutics for OCD patients. Nuciferine, Epicatechin (EC), Retinal, Aphidicolin and Salvinorin A are showing good docking scores but among all these phytochemicals, Nuciferin, an extract of Indian Lotus plant, appears to be the one most suitable compound on the basis of binding energy calculations. Hence, we can say this could be a good revealing therapeutic agent for this disorder.

bioinformatics↗

bioRxiv2019

Chronic corticosterone administration induces negative valence and impairs positive valence behaviors in mice

Behavioral approaches utilizing rodents to study mood disorders have focused primarily on negative valence behaviors associated with potential threat (anxiety). However, for disorders such as depression, positive valence behaviors that assess reward processing may be more translationally-valid and predictive of antidepressant treatment outcome. Chronic corticosterone (CORT) administration is a well-validated pharmacological stressor that increases negative valence behaviors (David et al., 2009; Gourley et al., 2008a,b; Gourley et al., 2012; Olausson et al., 2013). However, whether chronic stress paradigms such as CORT administration also lead to deficits in positive valence behaviors remains unclear. We treated male C57BL/6J mice with chronic CORT and assessed both negative and positive valence behaviors. We found that CORT induced negative valence behaviors associated with anxiety in the open field and NSF. Interestingly, CORT also impaired instrumental acquisition, reduced sensitivity to a devalued outcome, reduced breakpoint in progressive ratio, and impaired performance in probabilistic reversal learning. Taken together, these results demonstrate that chronic CORT administration at the same dosage both induces negative valence behaviors associated with anxiety and impairs positive valence behaviors associated with reward processing. These data suggest that CORT administration is a useful experimental system for preclinical approaches to studying stress-induced mood disorders.\n\nSignificance StatementChronic exposure to stress can precipitate mood disorders such as anxiety and depression. However, most studies focus on the effects of chronic stress on increasing negative affect behaviors. Elucidating how chronic stress impacts translationally-valid positive valence behaviors is less studied. Here, we show that chronic pharmacological stress induces negative affect behaviors associates with anxiety and impairs reward-related, positive valence behaviors in mice.

neuroscience↗

bioRxiv2018

Signalling pathways drive heterogeneity of ground state pluripotency

Pluripotent stem cells (PSCs) can self-renew indefinitely while maintaining the ability to generate all cell types of the body. This plasticity is proposed to require heterogeneity in gene expression, driving a metastable state which may allow flexible cell fate choices. Contrary to this, naive PSC grown in fully defined 2i environmental conditions, containing small molecule inhibitors of MEK and GSK3 kinases, show homogenous pluripotency and lineage marker expression. However, here we show that 2i induces greater genome-wide heterogeneity than traditional serum-containing growth environments at the population level across both male and female PSCs. This heterogeneity is dynamic and reversible over time, consistent with a dynamic metastable equilibrium of the pluripotent state. We further show that the 2i environment causes increased heterogeneity in the calcium signalling pathway at both the population and single-cell level. Mechanistically, we identify loss of robustness regulators in the form of negative feedback to the upstream EGF receptor. Our findings advance the current understanding of the plastic nature of the pluripotent state and highlight the role of signalling pathways in the control of transcriptional heterogeneity. Furthermore, our results have critical implications for the current use of kinase inhibitors in the clinic, where inducing heterogeneity may increase the risk of cancer metastasis and drug resistance.

molecular biology↗

bioRxiv2018

Separable recruitment of DNA Polymerase α for leading- and lagging-strand replication initiation

During eukaryotic DNA replication, DNA polymerase alpha/primase (Pol ) initiates synthesis on both the leading and lagging strands. It is unknown whether leading- and lagging-strand priming are mechanistically identical, and whether Pol associates processively or distributively with the replisome. Here, we titrate cellular levels of Pol in S. cerevisiae and analyze Okazaki fragments to study both replication initiation and ongoing lagging-strand synthesis in vivo. We observe that both Okazaki fragment initiation and the productive firing of replication origins are sensitive to Pol abundance, and that both processes are disrupted at similar Pol concentrations. When the replisome adaptor protein Ctf4 is absent or cannot interact with Pol , lagging-strand initiation is impaired at Pol concentrations that still support normal origin firing. Additionally, we observe that activation of the checkpoint becomes essential for viability upon severe depletion of Pol . Using strains in which the Pol -Ctf4 interaction is disrupted, we demonstrate that this checkpoint requirement is not solely caused by reduced lagging-strand priming. Our results suggest that Pol recruitment for replication initiation and ongoing lagging-strand priming are distinctly sensitive to the presence of Ctf4. We propose that the global changes we observe in Okazaki fragment length and origin firing efficiency are consistent with distributive association of Pol at the replication fork, at least when Pol is limiting. Author summaryHalf of each eukaryotic genome is replicated continuously as the leading strand, while the other half is synthesized discontinuously as Okazaki fragments on the lagging strand. The bulk of DNA replication is completed by DNA polymerases {varepsilon} and {delta} on the leading and lagging strand respectively, while synthesis on each strand is initiated by DNA polymerase -primase (Pol ). Using the model eukaryote S. cerevisiae, we modulate cellular levels of Pol and interrogate the impact of this perturbation on both replication initiation on DNA synthesis and cellular viability. We observe that Pol can associate dynamically at the replication fork for initiation on both strands. Although the initiation of both strands is widely thought to be mechanistically similar, we determine that Ctf4, a hub that connects proteins to the replication fork, stimulates lagging-strand priming to a greater extent than leading-strand initiation. We also find that decreased leading-strand initiation results in a checkpoint response that is necessary for viability when Pol is limiting. Because the DNA replication machinery is highly conserved from budding yeast to humans, this research provides insights into how DNA replication is accomplished throughout eukaryotes.

molecular biology↗

bioRxiv2018

Genomic copy-number loss is rescued by self-limiting production of DNA circles

Copy-number changes generate phenotypic variability in health and disease. Whether organisms protect against copy-number changes is largely unknown. Here, we show that Saccharomyces cerevisiae monitors the copy number of its ribosomal DNA (rDNA) and rapidly responds to copy-number loss with the clonal amplification of extrachromosomal rDNA circles (ERCs) from chromosomal repeats. ERC production is proportional to repeat loss and reaches a dynamic steady state that responds to the addition of exogenous rDNA copies. ERC levels are also modulated by RNAPI activity and diet, suggesting that rDNA copy number is calibrated against the cellular demand for rRNA. Lastly, we show that ERCs reinsert into the genome in a dosage-dependent manner, indicating that they provide a reservoir for ultimately increasing rDNA array length. Our results reveal a DNA-based mechanism for rapidly restoring copy number in response to catastrophic gene loss that shares fundamental features with unscheduled copy-number amplifications in cancer cells.

molecular biology↗