Biology subjects

Sarkar, R.

Publications and source records attributed to Sarkar, R..

21 records · Page 2Linked to original sources

bioRxiv2020

The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020.

BackgroundThis is a comprehensive analysis of 46 Indian SARS-CoV-2 genome sequences available from the NCBI and GISAID repository during early 2020. Evolutionary dynamics, gene-specific phylogeny and emergence of the novel co-evolving mutations in nine structural and non-structural genes among circulating SARS-CoV-2 strains in ten states of India have been assessed. Materials and methods46 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from the GISAID (39/46) or from NCBI (7/46) database. Phylogenetic study and analyses of mutation were based on the nine structural and non-structural genes of SARS-CoV-2 strains. Secondary structure of RdRP/NSP12 protein was predicted with respect to the novel A97V mutation. ResultsPhylogenetic analyses revealed the evolution of "genome-type clusters" and adaptive selection of "L" type SARS-CoV-2 strains with genetic closeness to the bat SARS-like coronaviruses than pangolin or MERS-CoVs. With regards to the novel co-evolving mutations, 2 groups are seen to circulate in India at present: the "major group" (52.2%) and the "minor group" (30.4%), harboring four and five co-existing mutations, respectively. The "major group" mutations fall in the A2a clade. All the minor group mutations, except 11083G>T (L37F, NSP6) were unique to the Indian isolates. ConclusionThe study highlights rapidly evolving SARS-CoV-2 virus and co-circulation of multiple clades and sub-clades, driving this pandemic worldwide. This comprehensive study is a potential resource for monitoring the novel mutations in the viral genome, changes in viral pathogenesis, for designing vaccines and other therapeutics.

genomics↗

bioRxiv2019

Cooperation only for high rewards - a solvable task-based study on free-ranging dogs

The benefits of group living mostly surpass the disadvantages like sharing of resources and competition over food, space and mates, driving the evolution of social organization. Group living can be facilitated by social tolerance and cooperation among the group members. Social canids (e.g. wolves) display cooperative breeding, hunting, and prosocial activities in different contexts. Unlike cooperative pack-living wolves (Canis lupus lupus), their descendants, domesticated dogs (Canis lupus familiaris), show varying levels of associations from solitary to stable social groups. Free-ranging dogs are group-living but prefer to forage solitarily, hence providing an excellent opportunity for investigating social tolerance and coordinated task performance among the members in various situations. We tested 113 adult-only groups of free-ranging dogs in three different tasks to investigate group responses and performance in problem-solving situations in the presence of an unfamiliar human. Task 1 (unfamiliar, single food reward) and 2 (familiar, single food reward) examined group responses and cooperation from the perspective of familiarity, while Task 3 (familiar, multiple food rewards) enabled us to test whether increased food rewards promote social tolerance and food sharing among the group members. Regardless of significantly higher performance in Task 2 compared to Task 1, cooperation and food sharing were significantly lower in both. Task 3 revealed a strong positive correlation between food sharing and social tolerance, but not between success and social tolerance, suggesting a tendency for cooperation. We conclude that context-dependent cooperation and tolerance among group members facilitate group-living in free-ranging dogs.\n\nSignificance statementGroup living is a common phenomenon in the animal world where the members of a group show social tolerance and co-operative behaviours towards each other. This need for cooperative intents increases manifolds while groups face different problem-solving situations in their day to day lives. Here, we tested a large number of free-ranging dog groups to understand general cooperative intents such as social tolerance and food sharing in different problem-solving conditions. We found shreds of evidence of context-dependent cooperation and social tolerance among group members with minimal display of aggression. It is not adaptive for the dogs to fight or display aggression over resources. Alternatively, use of subtle cues such as display of dominance and subordination seem to be more plausible mechanisms for the development of efficient scavenging strategies and maintaining hierarchy.

animal behavior and cognition↗

bioRxiv2017

Reprogramming, oscillations and transdifferentiation in epigenetic landscapes

Waddingtons epigenetic landscape provides a phenomenological understanding of the cell differentiation pathways from the pluripotent to mature lineage-committed cell lines. In light of recent successes in the reverse programming process there has been significant interest in quantifying the underlying landscape picture through the mathematics of gene regulatory networks. We investigate the role of time delays arising from multistep chemical reactions and epigenetic rearrangement on the cell differentiation landscape for a realistic two-gene regulatory network, consisting of selfpromoting and mutually inhibiting genes. Our work provides the first theoretical basis of the transdifferentiation process in the presence of delays, where one differentiated cell type can transition to another directly without passing through the undifferentiated state. Additionally, the interplay of time-delayed feedback and a time dependent chemical drive leads to long-lived oscillatory states in appropriate parameter regimes. This work emphasizes the important role played by time-delayed feedback loops in gene regulatory circuits and provides a framework for the characterization of epigenetic landscapes.

systems biology↗