Biology subjects

Ray, M.

Publications and source records attributed to Ray, M..

23 records · Page 2Linked to original sources

bioRxiv2020

Elucidation of Genome Polymorphisms in Emerging SARS-CoV-2

The COVID-19 pandemic is having a devastating effect on the healthcare system and the economy of the world. The unavailability of a specific treatment regime and a candidate vaccine yet opens up scope for new approaches and discoveries of drugs for mitigation of the sufferings of humankind due to the disease. The present isolated whole-genome sequences of SARS-CoV-2 from 11 different nations subjected to evolutionary study and genome-wide association study through in silico approaches including multiple sequence alignment, phylogenetic study through MEGA7 and have been analyzed through DNAsp respectively. These investigations recognized the nucleotide varieties and single nucleotide mutations/polymorphisms on the genomic regions as well as protein-coding regions. The resulted mutations have diversified the genomic contents of SARS-CoV-2 according to the altered nucleotides found in 11 genome sequences. India and Nepal have found to have progressively more distinct species of SARS-CoV-2 with variations in Spike protein and Nucleocapsid protein-coding sites. These genomic variations might be the explanation behind the less case fatality rate of India and Nepal dependent on the populaces. The anticipated idea of this investigation upgrades the information about genomic medication and might be useful in the planning of antibodies against SARS-CoV-2.

bioinformatics↗

bioRxiv2020

Evaluation of Seed or Grain Storage Technologies from Indian Farming Societies Using A Hybrid and Multi-Attribute Approach

Soon after the introduction of green revolution, a parallel increment in percent food grain production and losses has been reported in India, which impedes the mission of achieving food security in India. In parts, among the major causes of these losses are the reluctance among farmers, especially of small holding, towards adoption of scientific storage methods/technologies and inability of the national agencies to meet the challenges imposed by the supply of surplus grains to them by the farmers. Although sets of traditional and improved grain storage technologies exist among Indian farming communities, a controversial account about their effectiveness and performance is available in the literature which negatively impacts the endeavour of bringing rapid developmental in the farming society. In a developing nation like India, a large section of farmers is often either unaware of the modern technologies or cannot logistically access them. They often rely on the traditional or semi-modern technologies without having a comprehensive account of the benefit and economic feasibility of the modern technologies. This impedes the vision of rapid development of the farmers and the process of infusing emerging technologies in the society. In order to develop an informative argument about the performance of the existing technologies, a nearly comprehensive study has been undertaken to compare the different traditional and improved grain storage structures used by Indian farmers. Both qualitative and quantitative parameters were compared individually and simultaneously to achieve their effect on performance individually and in unison. Another objective of the study was to test the applicability of hybrid and multi-attribute approach, based on Analytic Hierarchy Process (AHP) and the Technique for Order Preference by Similarity to Ideal Solution (TOPSIS) for the performance evaluation and ranking of the attributes and structures. Finally, based on analysis and ideas borrowed out of literature a set of theoretical and conceptual guidelines to assist improvement in these structures was brought in. The study will help understand the status of grain storage technologies in the developing, resource-poor society and also increase the adoption and access of farmers to better post-harvest seed storage technologies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2018

Over-expression of Hsp83 in grossly depleted hsrω lncRNA background causes synthetic lethality and l(2)gl phenocopy in Drosophila

We examined interactions between Hsp83 and hsr{omega} lncRNAs in hsr{omega}66 Hsp90GFP homozygotes, which almost completely lack hsr{omega} lncRNAs but over-express Hsp83. All +/+; hsr{omega}66 Hsp90GFP progeny died before third instar. Rare Sp/CyO; hsr{omega}66 Hsp90GFP reached third instar stage but phenocopied l(2)gl mutants, dying after prolonged larval life, becoming progressively bulbous and transparent with enlarged brain. Additionally, ventral ganglia were elongated. However, hsr{omega}66 Hsp90GFP/TM6B heterozygotes, carrying +/+ or Sp/CyO second chromosomes, developed normally. Total RNA sequencing (+/+, +/+; hsr{omega}66/hsr{omega}66, Sp/CyO; hsr{omega}66/hsr{omega}66, +/+; Hsp90GFP/Hsp90GFP, and Sp/CyO; hsr{omega}66 Hsp90GFP/hsr{omega}66 Hsp90GFP late third instar larvae) revealed similar effects on many genes in hsr{omega}66 and Hsp90GFP homozygotes. Besides additive effect on many of them, numerous additional genes were affected in Sp/CyO; hsr{omega}66 Hsp90GFP larvae, with l(2)gl and several genes regulating CNS being highly down-regulated in surviving Sp/CyO; hsr{omega}66 Hsp90GFP larvae, but not in hsr{omega}66 or Hsp90GFP single mutants. Hsp83 binds at these gene promoters. Several omega speckle associated hnRNPs too may bind with these genes and transcripts. Hsp83-hnRNP interactions are also known. Thus, elevated Hsp83 in altered hnRNP distribution and dynamics, following absence of hsr{omega} lncRNAs and omega speckles, background can severely perturb regulatory circuits with unexpected consequences, including down-regulation of tumor suppressor gene like l(2)gl.

developmental biology↗

bioRxiv2018

Pancreatic adenocarcinoma human organoids share structural and genetic features with primary tumors

Patient-derived pancreatic ductal adenocarcinoma (PDAC) organoid systems show great promise for understanding the biological underpinnings of disease and advancing therapeutic precision medicine. Despite the increased use of organoids, the fidelity of molecular features, genetic heterogeneity, and drug response to the tumor of origin remain important unanswered questions limiting their utility. To address this gap in knowledge, we created primary tumor- and PDX-derived organoids, and 2D cultures for in-depth genomic and histopathological comparisons to the primary tumor. Histopathological features and PDAC representative protein markers showed strong concordance. DNA and RNA sequencing of single organoids revealed patient-specific genomic and transcriptomic consistency. Single-cell RNAseq demonstrated that organoids are primarily a clonal population. In drug response assays, organoids displayed patient-specific sensitivities. Additionally, we examined the in vivo PDX response to FOLFIRINOX and Gemcitabine/Abraxane treatments, which was recapitulated in vitro by organoids. The patient-specific molecular and histopathological fidelity of organoids indicate that they can be used to understand the etiology of the patients tumor and the differential response to therapies and suggests utility for predicting drug responses.

cancer biology↗

bioRxiv2017

Altered hsrω lncRNA levels in activated Ras background further enhance Ras activity in Drosophila eye and induces more R7 photoreceptors

We exploited the high Ras activity induced differentiation of supernumerary R7 cells in Drosophila eyes to examine if hsr{omega} lncRNAs influence active Ras signaling. Surprisingly, either down- or up-regulation of hsr{omega} lncRNAs in sev-GAL4>RasV12 expressing eye discs resulted in complete pupal lethality and substantially greater increase in R7 photoreceptor number at the expense of cone cells. Enhanced nuclear p-MAPK and presence of sev-GAL4 driven RasV12 bound RafRBDFLAG in cells not expressing the sev-GAL4 driver indicated non-cell autonomous spread of Ras signaling when hsr{omega} levels were co-altered. RNA-sequencing revealed that down-and up-regulation of hsr{omega} transcripts in sev-GAL4>RasV12 expressing eye discs elevated transcripts of positive or negative modulators, respectively, of Ras signaling so that either condition enhances it. Altered hsr{omega} transcript levels in sev-GAL4>RasV12 expressing discs also affected sn/sno/sca RNAs and some other RNA processing transcript levels. Post-transcriptional changes due to the disrupted intra-cellular dynamicity of omega speckle associated hnRNPs and other RNA-binding proteins that follow down- or up-regulation of hsr{omega} lncRNAs appear to be responsible for the further elevated Ras signaling. Cell autonomous and non-autonomous enhancement of Ras signaling by lncRNAs like hsr{omega} has implications for cell signaling during high Ras activity commonly associated with some cancers.\n\nHighlightsOur findings highlight roles of hsr{omega} lncRNAs in conditionally modulating the important Ras signaling pathway and provide evidence for cell non-autonomous Ras signaling in Drosophila eye discs.

cell biology↗