Biology subjects

Joshi, C.

Publications and source records attributed to Joshi, C..

4 recordsLinked to original sources

bioRxiv2018

Sonic stimulation, and low power microwave radiation can modulate bacterial virulence towards Caenorhabditis elegans

Caenorhabditis elegans worms infected with different pathogenic bacteria were subjected to sonic treatment to investigate whether such sound treatment can exert any therapeutic effect on the infected worms. Sonic therapy corresponding to 400 Hz, and the divine sound om were found to confer protective effect on this nematode worm in face of bacterial infection, particularly that caused by Serratia marcescens or Staphylococcus aureus. The observed effect seemed to occur due to influence of sound on bacteria, and not on the worm. In addition to this, effect of microwave exposure on bacterial virulence was also investigated, wherein microwave exposure was found to reduce virulence of S. aureus towards C. elegans.

microbiology↗

bioRxiv2018

Assessing key decisions for transcriptomic data integration in biochemical networks

MotivationTo gain insights into complex biological processes, genome-scale data (e.g., RNA-Seq) are often overlaid on biochemical networks. However, many networks do not have a one-to-one relationship between genes and network edges, due to the existence of isozymes and protein complexes. Therefore, decisions must be made on how to overlay data onto networks. For example, for metabolic networks, these decisions include (1) how to integrate gene expression levels using gene-protein-reaction rules, (2) the approach used for selection of thresholds on expression data to consider the associated gene as \"active\", and (3) the order in which these steps are imposed. However, the influence of these decisions has not been systematically tested.\n\nResultsWe compared 20 decision combinations using a transcriptomic dataset across 32 tissues and showed that definition of which reaction may be considered as active is mainly influenced by thresholding approach used. To determine the most appropriate decisions, we evaluated how these decisions impact the acquisition of tissue-specific active reaction lists that recapitulate organ-system tissue groups. These results will provide guidelines to improve data analyses with biochemical networks and facilitate the construction of context-specific metabolic models.\n\nContactnlewisres@ucsd.edu

systems biology↗

bioRxiv2017

Anti-infective potential of a quorum modulatory polyherbal extract (Panchvalkal) against certain pathogenic bacteria

Anti-infective potential of a polyherbal ayurvedic formulation namely panchvalkal was assayed against three pathogenic bacteria. This formulation was found to exert quorum-modulatory effect on Chromobacterium violaceum, Serratia marcescens, and Staphylococcus aureus at 250-750 g/mL. Besides altering production of the quorum sensing-regulated pigments in these bacteria, the test formulation also had in vitro effect on antibiotic susceptibility, catalase activity and hemolytic potential of the pathogens. In vivo assay confirmed the protective effect of this panchvalkal formulation on Caenorhabditis elegans, when challenged with the pathogenic bacteria. Repeated exposure of S. aureus to panchvalkal did not induce resistance in this bacterium. To the best of our awareness, this the first report on quorum-modulatory potential of panchvalkal formulation, validating the anti-infective potential and moderate prebiotic property of this polyherbal preparation.

microbiology↗

bioRxiv2017

Frequency-dependent response of Chromobacterium violaceum to sonic stimulation, and altered gene expression associated with enhanced violacein production at 300 Hz

Chromobacterium violaceum was subjected to sonic (100-2000 Hz) stimulation, and the effect on its cell yield and quorum sensing regulated pigment (violacein) production was investigated. Sound corresponding to the 300 Hz was found to promote (by 1.52 fold) violacein production the most, with only marginal impact on cell yield. Whole transcriptome analysis revealed that a total of 342 genes (i.e. 4.63% of whole genome) were significantly up-regulated in the sonic stimulated culture. Enhanced violacein production in the sound stimulated culture seems to have stemmed from enhanced expression of the genes involved in glucose metabolism through pentose phosphate pathway, resulting in increased availability of erythrose-4-phosphate, to be used for synthesis of tryptophan, the precursor for violacein synthesis. Multiple ribosomal subunit genes, enzyme coding genes, and those associated with secretion/transport were up-regulated owing to sonic stimulation. This study is a good demonstration of the ability of sound waves to alter bacterial metabolism.

microbiology↗