Identification of drought stress-responsive genes in rice (Oryza sativa) by meta-analysis of microarray data

Meta-analysis provides a systematic access to the previously studied microarray datasets that can recognize several common signatures of stresses. Three different datasets of abiotic stresses on rice were used for meta-analysis. These microarray datasets were normalized to regulate data for technical variation, as opposed to biological differences between the samples. A t-test was performed to recognize the differentially-expressed genes (DEGs) between stressed and normal samples. Gene ontology enrichment analysis revealed the functional distribution of DEGs in different stressed conditions. Further analysis was carried out using software RICE NET DB and divided into three different categories: biological process (homoiothermy and protein amino acid phosphorylation), cellular component (nucleus and membrane), and molecular function (zinc ion binding ad DNA binding). The study revealed that 5686 genes were constantly expressed differentially in Oryza sativa (2089 upregulated and 3597 downregulated). The lowest P value (P = 0.003756) among upregulated DEGs was observed for naringenin, 2-oxoglutrate 3-dioxygenase protein. The lowest P value (P = 0.002866816) among the downregulated DEGs was also recorded for retrotransposon protein. The network constructed from 48 genes revealed 10 hub genes that are connected with topological genes. These hub genes are stress responsive genes that may also be regarded as the marker genes for drought stress response. Our study reported a new set of hub genes (reference genes) that have potentially significant role in development of stress tolerant rice

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.

Isolated abscess in superior rectus muscle in a child.

Pyomyositis is a primary bacterial infection of striated muscles nearly always caused by Staphylococcus aureus. Development of the intramuscular abscess involving the extra‑ocular muscles (EOMs) remains an extremely rare process. We herein present a case of isolated EOM pyomyositis involving superior rectus muscle in a 2‑year male child who was referred with complaints of swelling in left eye (LE) and inability to open LE since last 1‑month. Orbital computed tomography (CT) scan showed a well‑defined, hypo‑dense, peripheral rim‑enhancing lesion in relation to left superior rectus muscle suggestive of left superior rectus abscess. The abscess was drained through skin approach. We concluded that pyomyositis of EOM should be considered in any patient presenting with acute onset of orbital inflammation and characteristic CT or magnetic resonance imaging features. Management consists of incision and drainage coupled with antibiotic therapy.