Biology subjects

Negi, R.

Publications and source records attributed to Negi, R..

3 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

A Deep Learning Approach to Detecting Temporal Characteristics of Cortical Regions

One view of the neocortical architecture is that every region functions based on a universal computational principle. Contrary to this, we postulated that each cortical region has its own specific algorithm and functional properties. This idea led us to hypothesize that unique temporal patterns should be associated with each region, with the functional commonalities and variances among regions reflecting in the temporal structure of their neural signals. To investigate these hypotheses, we employed deep learning to predict electrodes locations in the macaque brain using single-channel ECoG signals. To do this, we first divided the brain into seven regions based on anatomical landmarks, and trained a deep learning model to predict the electrode location from the ECoG signals. Remarkably, the model achieved an average accuracy of 33.6%, significantly above the chance level of 14.3%. All seven regions exhibited above-chance prediction accuracy. The models feature vectors identified two main clusters: one including higher visual areas and temporal cortex, and another encompassing the remaining other regions.These results bolster the argument for unique regional dynamics within the cortex, highlighting the diverse functional specializations present across cortical areas.

neuroscience↗

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↗