Biology subjects

Talwar, C.

Publications and source records attributed to Talwar, C..

5 recordsLinked to original sources

bioRxiv2024

Integrated multi-platform approaches to gain insights into ecosystems fundamental ecology and habitat specific alterations

The increasing availability of metagenome-assembled genomes and environmental metagenomes provides unprecedented access to the metabolic potential and functional differences within the habitats. The hot spring microbiome with its diverse habitats and relatively well-characterized microbial inhabitants offers an opportunity to investigate core and habitat specific community structures at an ecosystem scale. Here, we employed tailored genome-resolved metagenomics and a novel approach that offers metagenomic overlaps to investigate the core and habitat-specific microbial diversity and multifunctionality of microbial residents of three habitats: microbial mat, sediment and water. We recovered 6% of the Ecosystem core community (ECC) in the habitats suggesting the widespread acquisition of Proteobacteria involving in the diverging trajectories of the hot spring and 72% of the Habitat specific community (HSC) in microbial mat, sediment and water habitats offers insights into specific adaptations due to extreme conditions. Strain-level resolution of metagenome-assembled genomes defined the habitat specific genotypes (HSGs) and comparative metagenomic analysis exposed ecosystem-core genotypes (ECGs). Further, the functional attributes of ECGs revealed a complete metabolic potential of nitrate reduction, ammonia assimilation and sulfate reduction. The highest cycling entropy scores (H) of N cycle suggested the enrichment of nitrogen fixing microbes commonly present in all three habitats. While specifically HSGs possessed the amino acid transport and metabolism functions in microbial mat (9.5%) and water (13%) and 19% of translation, ribosomal structure and biogenesis in sediment. Our findings provide insights into population structure and multifunctionality in the different habitats of hot spring and form specific hypotheses about habitat adaptation. The results illustrated the supremacy of using genome-resolved metagenomics and ecosystem core metagenomics postulating the differential ecological functions rather than that of explaining the presence of functions within ecosystem.

microbiology↗

bioRxiv2023

High-fat diets promote peritoneal inflammation and augment endometriosis-associated abdominal hyperalgesia

Immune dysfunction is one of the central components in the development and progression of endometriosis by establishing a chronic inflammatory environment. Western-style high-fat diets (HFD) have been linked to greater systemic inflammation to cause metabolic and chronic inflammatory diseases, and are also considered an environmental risk factor for gynecologic diseases. Here, we aimed to examine how HFD alter an inflammatory environment in endometriosis and discern their contribution to endometriotic-associated hyperalgesia. Our results showed that HFD-induced obesity enhanced abdominal mechanical allodynia that was induced by endometriotic lesions. Peritoneal inflammatory macrophages and cytokine levels increased by lesion induction were elevated by chronic exposure to HFD. Pain-related mediators in the dorsal root ganglia were further stimulated after lesion induction under the HFD condition. Although HFD did not affect inflammatory macrophages in the peritoneal cavity without lesion induction, the diversity and composition of the gut microbiota were clearly altered by HFD as a sign of low-grade systemic inflammation. Thus, HFD alone might not establish a local inflammatory environment in the pelvic cavity, but it can contribute to further enhancing chronic inflammation, leading to the exacerbation of endometriosis-associated abdominal hyperalgesia following the establishment and progression of the disease.

physiology↗

bioRxiv2022

Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hot spots, functional patterns and molecule repurposing for monkey pox virus

Monkeypox is a viral zoonosis with symptoms that are reminiscent to those experienced in previous smallpox cases. GSAID databases (Global Initiative on Sharing Avian Influenza Data) was used to assess 630 genomes of MPXV. Six primary clades were inferred from the phylogenetic study, coupled with a lesser percentage in radiating clades. Individual clades that make up various nationalities may have formed as a result of a particular SNP hotspot type, which may have mutated in a particular population type. The most significant mutation, based on a mutational hotspot analysis, was found at G3729A and G5143A. The gene ORF138, which encodes the Ankyrin repeat (ANK) protein, was found to have the most mutations. This protein is known to mediate molecular recognition via protein-protein interactions. It was shown that 243 host proteins interacted with 10 monkeypox proteins identified as the hub proteins E3, SPI2, C5, K7, E8, G6, N2, B14, CRMB, and A41 through 262 direct connections. The interaction with chemokine system-related proteins provides further evidence that the human protein is being suppressed by the monkey pox virus in order to facilitate its survival against innate immunity. A few FDA-approved molecules were likely used as possible inhibitors after being researched for blocking F13, a significant envelope protein on the membrane of extracellular versions of virus. A total of 2500 putative ligands were docked individually with the F13 protein. The F13 protein and these molecules interaction may help prevent the monkey pox virus from spreading. As a result, after being confirmed by experiments, these putative inhibitors might have an impact on the activity of these proteins and be utilised in monkeypox treatments.

genomics↗

bioRxiv2021

Microbial ecology of sulfur biogeochemical cycling at a mesothermic hot spring atop Northern Himalayas, India

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/470874v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1dfd0d5org.highwire.dtl.DTLVardef@107811forg.highwire.dtl.DTLVardef@1ae4af6org.highwire.dtl.DTLVardef@1bb90a1_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Sulfur Related Prokaryotes (SRP) residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expand the phylogenetic breadth of these extraordinary sulfur metabolizing microorganisms, as well a their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on sulfur cycling genes through metagenomic analysis of sulfur (S) contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment and water were assigned to Proteobacteria as reflected from the RPKs (reads per kilobase) categorized into translation and ribosomal structure and biogenesis. Analysis of sequence similarity showed conserved pattern of both dsrAB genes (n=178) retrieved from all metagenomes while other sulfur disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of sulfur oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, we confirm that (i) SRBs belongs to{delta} -Proteobacteria occurring independent LGT of dsr genes to different and few novel lineages (ii) also, the oxidative and reductive dsr evolutionary time scale phylogeny, proved that the earliest (not first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score= 0.86; 0.98; 0.96) and Archaeoglobus fulgidus (TM score= 0.97; 0.98). We proposed that the genetic repertoire might provide the basis of studying time scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling and the complementary genes could be implemented in biotechnology and bioremediation applications.

microbiology↗

bioRxiv2020

Comparative Genomic Analysis of Rapidly Evolving SARS CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution

The Coronavirus Disease-2019 (COVID-19) that started in Wuhan, China in December 2019 has spread worldwide emerging as a global pandemic. The severe respiratory pneumonia caused by the novel SARS-CoV-2 has so far claimed more than 60,000 lives and has impacted human lives worldwide. However, as the novel SARS-CoV-2 displays high transmission rates, their underlying genomic severity is required to be fully understood. We studied the complete genomes of 95 SARS-CoV-2 strains from different geographical regions worldwide to uncover the pattern of the spread of the virus. We show that there is no direct transmission pattern of the virus among neighboring countries suggesting that the outbreak is a result of travel of infected humans to different countries. We revealed unique single nucleotide polymorphisms (SNPs) in nsp13-16 (ORF1b polyprotein) and S-Protein within 10 viral isolates from the USA. These viral proteins are involved in RNA replication, indicating highly evolved viral strains circulating in the population of USA than other countries. Furthermore, we found an amino acid addition in nsp16 (mRNA cap-1 methyltransferase) of the USA isolate (MT188341) leading to shift in amino acid frame from position 2540 onwards. Through the construction of SARS-CoV-2-human interactome, we further revealed that multiple host proteins (PHB, PPP1CA, TGF-{beta}, SOCS3, STAT3, JAK1/2, SMAD3, BCL2, CAV1 & SPECC1) are manipulated by the viral proteins (nsp2, PL-PRO, N-protein, ORF7a, M-S-ORF3a complex, nsp7-nsp8-nsp9-RdRp complex) for mediating host immune evasion. Thus, the replicative machinery of SARS-CoV-2 is fast evolving to evade host challenges which need to be considered for developing effective treatment strategies.

microbiology↗