Pramod Kumar Yadav

Glycine max is a worldwide leading economic crop and its seeds are deepening with proteins and oils which supply food and sustenance to all being. Various amounts of alimentary constituents are racked up in the G. max seed in the period of its ontogenesis. Thus, grasping the regulation of biological functions during seed enlargement belong to the basics for crop enhancement. The gene regulatory characteristics of miRNAs in G. max attracted us to focus on its target gene prediction, gene ontology (GO) analysis and expression pattern to their miRNA target genes, which suggest significant involvement in the development of G. max seed. Seven miRNAs have been found from the differential gene expression analysis of development stage 0–4 mm vs. 12–16 mm of G. max seed on the statistical parameter of p value ≤ 0.05 by computational-based microarray data analysis for miRNA target gene prediction. The miRNA target prediction analysis showed total 23 genes that were cleaved from 6 miRNAs, and computationally validated by identifying t-plots of miRNA targets using CleaveLand tool. GO results confirmed that the differentially expressed target genes could be classified into 20 molecular function categories, 73 biological process categories, and 10 cell components categories. On the basis of GO results, two genes were found to be significantly involved in the developmental process of G.max seed. The first miRNA target gene Glyma.01g119500 was predicted to annotate for embryo development ending in seed dormancy, seed dormancy, seed maturation, and seed germination. The second miRNA target gene Glyma.15g005300 was found to be involved in the regulation of seed germination. The Soybean eFP browser analysis suggests that the gene Glyma.01g119500 and Glyma.15g005300 reaches its maximum expression level of 35.88 and 26.6 respectively in the Soybean data source. The present study provides an avenue to explore more genomic and proteomic information about G. max seed developmental stage-specific miRNA target genes.

The Glycine max seed is an ultimate source of protein worldwide and plays the crucial role in crop development. This made us curious to insight the developmental stages of G. max seed at the genomic level with computational based microarray data analysis. The data analysis explored 10453 and 6085 significant DEGs from 0 to 4 mm vs. 12 to 16 mm and 4–8 mm vs. 8–12 mm stage, respectively and based on log2 FC, 407 & 2342 DEGs were regulating high expression and 340 & 1414 DEGs were low in expression at the 0–4 mm vs.12–16 mm and 4–8 mm vs. 8–12 mm stage, respectively. Gene symbols for DEGs has recognized and identified that, 7 DEGs from 0–4 mm vs. 12–16 mm stage were coding for miRNAs. Gene classification searched 2 & 4 highly enriched groups of genes from up-down regulated DEGs of 0–4 mm vs. 12–16 mm stage, respectively and 19 & 6 groups of genes from up-down regulated DEGs of 4–8 mm vs. 8–12 mm stage that were showing functional similarities. Analysis for functional characterization has found that 38% & 36% DEGs were annotating for BP, 42% & 67% DEGs were for CC and 53% & 46% DEGs were for MF in up-down regulated DEGs of 0–4 mm vs. 12–16 mm stage, respectively. For up-down regulated DEGs of 4–8 mm vs. 8–12 mm stage has drawn and 8% &10% DEGs were indicating BP, 4% & 3% for CC and 15% & 23% DEGs were annotating for MF, respectively. Top ten highly regulated genes with the ID 11998843, 11855572, 12189716, etc. from stage 0–4 mm vs. 12–16 mm were annotating 10 BP, 6 MF and 6 CC. While, up-regulated DEGs with the ID Gma.10969.1.S1_at, GmaAffx.92715.1.S1_s_at, etc. were annotating 19 MF, 7 BP and one term from CC for stage 4–8 mm vs. 8–12 mm. These analyses would be helpful in the further characterization of interesting candidate genes that involve in the seed development of G. max.

Trichomonas vaginalis causes the trichomoniasis, in women and urethritis and prostate cancer in men. Its genome draft published by TIGR in 2007 presents many unusual genomic and biochemical features like, exceptionally large genome size, the presence of hydrogenosome, gene duplication, lateral gene transfer mechanism and the presence of miRNA. To understand some of genomic features we have performed a comparative analysis of metabolic pathways of the T. vaginalis with other 22 significant common organisms. Enzymes from the biochemical pathways of T. vaginalis and other selected organisms were retrieved from the KEGG metabolic pathway database. The metabolic pathways of T. vaginalis common in other selected organisms were identified. Total 101 enzymes present in different metabolic pathways of T. vaginalis were found to be orthologous by using BLASTP program against the selected organisms. Except two enzymes all identified orthologous enzymes were also identified as paralogous enzyme...

Heat shock protein 70 (Hsp70), a 70-kDa protein, also known as a molecular chaperone, is highly conserved. It plays a major role in cellular functions such as protein folding, regulation of protein degradation, translocation of proteins across membranes, receptor signaling, and protein assembly or disassembly. Vigna radiata is an important legume crop with available whole-genome sequence, but no such study on the HSP70 family is reported. A total of 32 V. radiate HSP70s (Vr-HSP70s) were identified and described. They are phylogenetically clustered into four subgroups. Vr-HSP70s show variations in intron/exon organization. This indicates that introns may play an essential role in gene regulating. The coexpression analysis of Vr-HSP70s revealed that these genes were involved in both abiotic and biotic stresses. Three cytoplasmic hub genes namely Vr-HSP70-C-14, Vr-HSP70-C-29, and Vr-HSP70-C-30 were found common in both stresses. Our findings provide directions for future studies to dissect functional analysis of Vr-HSP70s in response to abiotic and biotic stresses.

Legionellosis is a potentially fatal infectious disease caused by gram negative aerobic bacteria belonging to the genus Legionella. Over 90% of legionellosis cases are caused by Legionella pneumophila which is a thin, aerobic, pleomorphic, flagellated, non-spore forming bacteria. The emergence of drug resistance of L. pneumophila has led to the search for novel drug targets. In the present research work, computational analysis of metabolic pathways of the bacteria and host was performed to identify novel drug targets non-homologous to Homo sapiens. All enzymes involved in the metabolic pathways of L. pneumophila strain Paris were searched against the proteome of Homo sapiens using the BLASTp program and the threshold of E-value was set to as 0.001. Total 45 unique putative targets were identified and encoding genes of these targets were further searched in the DEG database to recognize the essentiality of genes. It was found that 37 encoding genes were essential for the survival of ...

... Pramod Kumar Yadav1,*, Raghvendra Sachan2, Shruti Tandon3, Satendra Singh1, B. Gautam1, R. Farmer1 and PA Jain1 1Department of ... first member of the TLR family identified was a Drosophila protein implicated in dorsoventral patterning during embryonal development8. ...

Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We report the predicted potential epitopes in the E7 antigen. We further describe the subsequent interaction of these linear epitope peptides with the human TMEM 50 A structural model using molecular docking. This data finds application in the development of components towards HPV associated disease prevention.

Human cytomegalovirus (HCMV), a ubiquitous and opportunistic pathogen, is a member of the Herpesviridae family of viruses. Infection with HCMV is generally asymptomatic, but naïve or immunosuppressed individuals, such as neonates, AIDS patients, and transplant recipients, often manifest serious disease. In the present work, MHC class-I, MHC class-II and B-cell epitopes for the envelope glycoprotein B (gB) of HCMV were predicted using the ProPred1, MHC2Pred and ABCpred servers respectively. The 3D structures of predicted epitopes were modeled using the HHpred server. In order to find the most relevant epitopes among all predicted T-cell epitopes, protein-protein docking was carried out for MHC-I and MHC-II receptors respectively. The energy score for every docked complex was calculated using the Hex 6.0 program. The lower energy score reveals higher binding affinity towards the receptor. It was found that the epitopes ‘YLFKRMIDL’ and ‘KYGDVVGVN’ possess highest binding affinity for M...

In 1990s, a new strain of methicillin resistant Staphylococcus aureus (MRSA) emerged in the community setting occurring among young healthy individuals with no exposure to the healthcare setting. The infections caused by these strains are called community-acquired MRSA (CA-MRSA). Skin and soft-tissue infections (SSTIs) are the most common type of CA-MRSA infection including furuncles, abscesses, folliculitis, impetigo, cellulitis, and more rarely, in cases of severe sepsis, necrotizing fascitis, and necrotizing pneumonia. Recently, fructose 1, 6 biphosphate aldolase-II (FBA) enzyme has been identified as potential drug target for CA-MRSA through metabolic pathways analysis. In the present work, phylogenetic analysis and computational proteomic analysis of FBA for CA-MRSA was carried out. The phylogenetic analysis results of FBA in CA-MRSA reveal that apart from various S. aureus strains, it is closely related to other pathogenic non-aureus staphylococcal species as well. In addition...

The traditional method of discovering drugs has always been a tedious process, consuming several years, huge man power and millions of dollars in order to come up with a single effective novel drug. Computer-aided drug design (CADD) represents more recent applications of computers as tools in the drug design process. CADD uses a variety of computational methods to identify novel compounds, design compounds for selectivity, efficacy and safety, and develop compounds into clinical trial candidates. Most common strategies used in drug designing are structure or target based drug designing (SBDD) and ligand or analogue based drug designing (LBDD). The approach used in CADD is dependent upon the amount of information that is available about the ligand and receptor. In structure based drug design approach one should have reliable 3-dimensional structural information for the receptor or the ligand-receptor complex which is available, as from X-ray diffraction, NMR or homology modeling tech...