Biology subjects

Mishra, D.

Publications and source records attributed to Mishra, D..

26 records · Page 2Linked to original sources

bioRxiv2023

The distinctive mechanical and structural signatures of residual force enhancement in myofibers

In muscle, titin proteins connect myofilaments together and are thought to be critical for contraction, especially during residual force enhancement (RFE) when force is elevated after an active stretch. We investigated titins function during contraction using small-angle X-ray diffraction to track structural changes before and after 50% titin cleavage and in the RFE-deficient, mdm titin mutant. We report that the RFE state is structurally distinct from pure isometric contractions, with increased thick filament strain and decreased lattice spacing, most likely caused by elevated titin-based forces. Furthermore, no RFE structural state was detected in mdm muscle. We posit that decreased lattice spacing, increased thick filament stiffness, and increased non-crossbridge forces are the major contributors to RFE. We conclude that titin directly contributes to RFE. One-Sentence SummaryTitin contributes to active force production and residual force enhancement in skeletal muscles.

physiology↗

bioRxiv2022

Identification of prognostic biomarkers for suppressing tumorigenesis and metastasis of Hepatocellular carcinoma through transcriptome analysis

Cancer is one of the deadliest diseases developed through tumorigenesis and could be fatal if reached at metastatic phase. The novality of present investigation is to explore the prognostic biomarkers in hepatocellular carcinoma (HCC) that could develop glioblastoma multiforme (GBM) due to metastasis. The analysis was done using RNA-Seq datasets for both HCC (PRJNA494560 and PRJNA347513) and GBM (PRJNA494560 and PRJNA414787) from Gene Expression Omnibus (GEO). This study identified 13 hub genes found to be overexpressed in both GBM and HCC. Promoter methylation study showed these genes to be hypomethylated. Validation through genetic alteration and missense mutations resulted in chromosomal instability leading to improper chromosome segregation causing aneuploidy. A 13-gene predictive model was obtained and validated using KM plot. These hub genes could be prognostic biomarkers and potential therapeutic targets, inhibition of which could suppress tumorigenesis and metastasis.

bioinformatics↗

bioRxiv2022

Demystifying the role of prognostic biomarkers in breast cancer through integrated transcriptome and pathway enrichment analyses

Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of death in women. There has been discovered an increasing number of molecular targets for BC prognosis and therapy. However, it is still urgent to identify new biomarkers. Therefore, we evaluated biomarkers that may contribute to the diagnosis and treatment of BC. We searched TCGA datasets and identified differentially expressed genes (DEGs) by comparing tumor (100 samples) and non-tumor (100 samples) tissues using the Deseq2 package. Pathway and functional enrichment analysis of the DEGs were done using DAVID (The Database for Annotation, Visualization, and Integrated Discovery) database. The protein-protein interaction (PPI) network was identified using the STRING database and visualized through Cytoscape software. Hub gene analysis of the PPI network was done using Cytohubba plugins. The associations between the identified genes and overall survival (OS) were analyzed using Kaplan-Meier plot. Finally, we have identified hub genes at the transcriptome level. A total of 824 DEGs were identified, which were mostly enriched in cell proliferation, signal transduction, and cell division. The PPI network comprised 822 nodes and 12145 edges. Elevated expression of the 5 hub genes AURKA, BUB1B, CCNA2, CCNB2, and PBK are related to poor OS in breast cancer patients. A promoter methylation study showed these genes to be hypomethylated. Validation through genetic alteration and missense mutations resulted in chromosomal instability leading to improper chromosome segregation causing aneuploidy. The enriched functions and pathways included the cell cycle, oocyte meiosis, and the p53 signaling pathway. The identified five hub genes in breast cancer have the potential to become useful targets for the diagnosis and treatment of breast cancer.

bioinformatics↗

bioRxiv2022

In Silico insight to identify Potential Inhibitors of BUB1B from Mushroom bioactive compounds to Prevent Breast cancer metastasis

BUB1B (BUB1 Mitotic Checkpoint Serine/Threonine Kinase B) gene belongs to the spindle assembly checkpoint protein family, proven to be associated with many kinds of cancers. Protein kinases are crucial in metaphase to anaphase cellular transition. It is a primary element of spindle assembly checkpoint (SAC). This SAC is responsible for guarding the proper chromosomal segregation while any chromosomal instability hinders its normal functioning. The chromosomal instability may lead to cancer progression. And it occurs mainly due to overexpression of BUB1B in many cancer types especially in breast cancer metastasis. This could be controlled by designing proper inhibitor of this gene. For this purpose, there are proved existence of various mushroom compounds possessing some important medicinal properties with proven anti- cancerous effects. Proper screening and identification of molecules having these anti-cancerous effects and showing affinity against BUB1B with inhibition properties could be obtained from these compounds. So this study has incorporated 70 bioactive compounds (handpicked through literature mining) of distinct mushrooms that were considered and explored for identifying a suitable drug candidate. Their ADME/T properties were obtained to predict the drug-likeness of these 70 mushroom compounds based on Lipinskis rule of 5 (RO5). The screening of these bioactive compounds and subsequent molecular docking against BUB1B provided compounds with the best conformation-based binding affinity. The best 2 complexes, i.e., BUB1B- Lepiotaprocerin D and BUB1B-Peptidoglycan, were subjected to the molecular dynamics simulation. Both the complexes were observed for their affinity, stability, and flexibility in protein-ligand complex systems. The MD simulation study revealed that Lepiotaprocerin D has an energetically favorable binding affinity with BUB1B. Results showed that the formation of a hydrogen bond between ASN123, SER157 residue and Lepiotaprocerin D has strengthened the affinity of Lepiotaprocerin D with BUB1B. Hence, this study identified Lepiotaprocerin D as a potential and novel inhibitor for BUB1B that could be a plausible drug candidate for checking and controlling the spread of breast cancer metastasis.

bioinformatics↗

bioRxiv2021

RNA silencing by CRISPR in plants does not require Cas13

RNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation and expanded function including anti-viral immunity. Here, we report the use of CRISPR-Cas13 in plants to reduce both viral and endogenous RNA. Unexpectedly, we discovered that crRNA designed to guide Cas13 could, in the absence of the Cas13 protein, cause substantial reduction in RNA levels as well. We demonstrate Cas13-independent guide-induced gene silencing (GIGS) in three plant species, including stable transgenic Arabidopsis. We determined that GIGS utilizes endogenous RNAi machinery despite the fact that crRNA are unlike canonical triggers of RNAi such as miRNA, hairpins or long double-stranded RNA. These results suggest that GIGS offers a novel and flexible approach to RNA reduction with potential benefits over existing technologies for crop improvement. Our results demonstrate that GIGS is active across a range of plant species, evidence similar to recent findings in an insect system, which suggests that GIGS is potentially active across many eukaryotes.

plant biology↗

bioRxiv2021

Effects of high dosage methamphetamine on glutamatergic neurotransmission in the nucleus accumbens and prefrontal cortex.

RationaleMethamphetamine (METH) induces changes in the glutamatergic system and elicits cellular alterations in the cortico-accumbens circuit. ObjectiveWhile there is a body of literature on the effects of METH on dopaminergic transmission, there is a gap in knowledge regarding the effects of a high dose of METH on synaptic glutamatergic neurotransmission, specifically in brain regions involved in goal directed behavior (nucleus accumbens core; NAc core) and executive functions (prefrontal cortex;PFC). MethodsIn order to fill that gap we assessed synaptic glutamatergic transmission using a well established METH administration regime (4 x 4 mg/kg ip at 2 hr intervals) followed by 7 days of abstinence. Rats were then sacrificed and whole cell and field recordings were performed in the NAc core and medial PFC. ResultsMETH treatment elicited a significant decrease in paired pulse ratio in NAc core and a significant increase in AMPA/NMDA ratio driven by increases in AMPA currents. On the other hand, there were no significant changes in measures of synaptic glutamate in the PFC. ConclusionThese results suggest that a high dose of METH treatment followed by a period of abstinence elicits significant increases in indices of glutamatergic transmission in the NAc core with no detectable changes in mPFC, denoting that neurons and glutamate terminals in this limbic region have a higher susceptibility to a neurotoxic METH regime.

neuroscience↗

bioRxiv2020

Differential expression of proteins in human prostate cancer tissues probed by MALDI imaging mass spectrometry

Histopathology, the gold-standard method for diagnosis of human prostate cancer, is based on the analysis of changes in cellular morphology and tissue architecture in chemically stained tissue sections. Even at the very early stages of cancer with minimal phenotypic changes in cellular morphologies, there might be detectable changes in the expression profiles of proteins. Over the last decade, imaging mass spectrometry has been used to explore the spatial distribution and expression profiles of several molecules with their twodimensional heterogeneity retained across the tissue section. In the present study, using MALDI mass spectrometry based tissue imaging, we report the differential expression of three proteins, vinculin, ribonuclease T2 and 60 kDa heat shock protein across human prostate tissue sections in regions pathologically demarcated as frankly malignant. In an independent analysis, quantitative proteomics revealed that in cancerous prostate tissues, ribonuclease T2 and 60 kDa heat shock protein were significantly overexpressed by 22.26- and 6 folds respectively compared to benign condition. Our results show the utility of this approach to probe differential protein expression in architecturally intact cancer tissues. In addition, we propose that ribonuclease T2 and 60 kDa heat shock protein might be developed as diagnostic biomarkers for prostate cancer in future.

biophysics↗

bioRxiv2020

Investigating the genomic landscape in novel coronavirus (2019-nCoV) genomes to identify non-synonymous mutations for use in diagnosis and drug design

Novel coronavirus has wrecked medical and health care facilities claiming ~5% death tolls globally. All efforts to contain the pathogenesis either using inhibitory drugs or vaccines largely remained futile due to a lack of better understanding of the genomic feature of this virus. In the present study, we compared the 2019-nCoV with other coronaviruses, which indicated that bat-SARS like coronavirus could be a probable ancestor of the novel coronavirus. The protein sequence similarity of pangolin-hCoV and bat-hCoV with human coronavirus was higher as compared to their nucleotide similarity denoting the occurrence of more synonymous mutations in the genome. Phylogenetic and alignment analysis of 591 novel coronaviruses of different clades from Group I to Group V revealed several mutations and concomitant amino acid changes. Detailed investigation on nucleotide substitution unfolded 100 substitutions in the coding region of which 43 were synonymous and 57 were of non-synonymous type. The non-synonymous substitutions resulting into 57 amino acid changes were found to be distributed over different hCoV proteins with maximum on spike protein. An important diamino acid change RG to KR was observed in ORF9 protein. Additionally, several interesting features of the novel coronavirus genome have been highlighted in respect to various other human infecting viruses which may explain extreme pathogenicity, infectivity and simultaneously the reason behind failure of the antiviral therapies. SummaryThis study presents a comprehensive phylogenetic analysis of SARS-CoV2 isolates to understand discrete mutations that are occurring between patient samples. This analysis will provide an explanation for varying treatment efficacies of different inhibitory drugs and a future direction towards a combinatorial treatment therapies based on the kind of mutation in the viral genome.

genetics↗