Analysis of chickpea gene co-expression networks and pathways during heavy metal stress

Pseudomonas putida is widely used as a biocontrol agent, however, mechanisms by which it initiates the plants’ defenseresponse remains obscure. To gain an insight into the molecular changes that occur in plants upon plant growth-promotingrhizobacteria colonization, root transcriptome analysis by using a microarray was performed in rice using P. putida RRF3 (arice rhizosphere isolate). Data analysis revealed a differential regulation of 61 transcripts (48 h post-treatment), of which,majority corresponded to defense response, cell wall modification and secondary metabolism. Seven genes encodingsalicylic acid (SA) responsive pathogenesis-related proteins were up-regulated significantly (fold change ranges from 1 to4), which suggests that RRF3 has a profound impact on a SA-mediated defense signaling mechanism in rice. Investigationsperformed at later stages of RRF3 colonization by real-time polymerase chain reaction and high-performance liquidchromatography (HPLC) analysis confirmed the above results, demonstrating RRF3 as a potent biocontrol agent. Further,the impact of RRF3 colonization on root exudation, in particular, exudation of SA was investigated by HPLC. However,analysis revealed RRF3 to have a negative impact on root exudation of SA. Overall, this study shows that P. putida RRF3immunizes the rice plants by re-organizing the root transcriptome to stimulate plant defense responses (‘priming’), andsimultaneously protects itself from the primed plants by altering the rhizosphere chemical constituents.

Interaction network analysis of YBX1 for identification of therapeutic targets in adenocarcinomas

Human Y-box binding protein-1 (YBX1) is a member of highly conserved cold-shock domain protein family, which isinvolved in transcriptional as well as translational regulation of many genes. Nuclear localization of YBX1 has beenobserved in various cancer types and it’s overexpression has been linked to adverse clinical outcome and poor therapyresponse, but no diagnostic or therapeutic correlation has been established so far. This study aimed to identify differentiallyexpressed novel genes among the interactors of YBX1 in different cancer types. Analysis of RNA-Seq data for colorectal,lung, prostate and stomach adenocarcinoma identified 39 unique genes, which are differentially expressed in the fouradenocarcinoma types. Gene-enrichment analysis for the differentially expressed genes from individual adenocarcinomawith focus on unique genes resulted in a total of 57 gene sets specific to each adenocarcinoma. Gene ontology forcommonly expressed genes suggested the pathways and possible mechanisms through which they affect each adenocarcinoma type considered in the study. Gene regulatory network constructed for the common genes and network topologywas analyzed for the central nodes. Here 12 genes were found to play important roles in the network formation; amongthem, two genes FOXM1 and TOP2A were found to be in central network formation, which makes them a common targetfor therapeutics. Furthermore, five common differentially expressed genes in all adenocarcinomas were also identified.