Papers by Venkateswara Talluri
Computational Biology and Chemistry, Jun 1, 2019
Structural prediction, whole exome sequencing and molecular dynamics simulation confirms p.G118D ... more Structural prediction, whole exome sequencing and molecular dynamics simulation confirms p.G118D somatic mutation of PIK3CA as functionally important in breast cancer patients,
Gene Reports, Sep 1, 2020
Abstract Breast cancer is the most commonly diagnostic cancer and the leading cause of cancer dea... more Abstract Breast cancer is the most commonly diagnostic cancer and the leading cause of cancer death in females. An important gene PIK3CA is known for playing the important role in breast cancer pathogenesis. In this study, we carried out RNA sequencing of cancer and normal samples of a breast cancer patient positive for PIK3CA G118D somatic mutation to identify the potential targets through differential gene expression and alternative splicing of genes. RNA sequencing of cancer and normal samples was carried out using Illumina Hiseq 2500. Sequencing reads were mapped with the human reference genome hg19 using algorithm implemented in STAR. Cuffdiff of Cufflinks was used to identify differentially expressed genes (DEGs) and rMATS was used to identify differentially alternative splicing (DASs) events. Functional enrichment and pathway analysis was carried out using DAVID database. Overall, the cancer sample resulted in the identification of a total of 322 DEGs; 64% of them were down regulated and 36% were up-regulated. Skipping Exon (SE) was found to be most common alternative splicing (AS) event and accounted for 73% of all the AS events. The important cancer genes showing AS include PIK3CA, MUTYH, PALB2, NTRK1, DNMT3A. The GO annotation revealed very important biological processes associated with DAS including cell death, apoptosis, response to stress, cell differentiation. We also obtained very interesting pathways using the KEGG pathway database including TNF signaling pathway, estrogen signaling pathway, ErbB signaling pathway and cAMP signaling pathway. We conclude that splicing alterations would be a great source to elucidate the potential biomarkers for breast cancer treatment.
Microorganisms for sustainability, 2020
Journal of Cellular Biochemistry, May 25, 2017
† This article has been accepted for publication and undergone full peer review but has not been ... more † This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as
Punica granatum L (Pomegranate) is cultivated in India and throughout the tropical and subtropica... more Punica granatum L (Pomegranate) is cultivated in India and throughout the tropical and subtropical regions of the world for its delicious and highly nutritive fruits. Apart from fruits, alkaloids present in the stem bark are used in treating dysentery and diarrhea. The clonal propagation of Pomegranate is by cuttings and air layering. These methods are time consuming and the number of plants obtained is few. Seed propagation has resulted in lot of variation producing inferior seedlings. This resulted in the scarcity of elite Pomegranate plant material for the large-scale cultivation. Modern biotechnological techniques like micropropagation helps to produce large quantity of quality, disease free, clonal plant material those are true to type in quality, in a shorter period and in limited space. Present study was undertaken to establish and standardize media composition, cultural conditions and growth requirements influencing the large-scale in vitro propagation of elite Pomegranate species using nodal explants.
Gene, 2013
P bodies are 100-300 nm sized organelles involved in mRNA silencing and degradation. A total of 6... more P bodies are 100-300 nm sized organelles involved in mRNA silencing and degradation. A total of 60 human proteins have been reported to localize to P bodies. Several human SNPs contribute to complex diseases by altering the structure and function of the proteins. Also, SNPs alter various transcriptional binding, splicing and miRNA regulatory sites. Owing to the essential functions of P bodies in mRNA regulation, we explored computationally the functional significance of SNPs in 7 P body components such as XRN1, DCP2, EDC3, CPEB1, GEMIN5, STAU1 and TRIM71. Computational analyses of non-synonymous SNPs of these components was initiated using well utilized publicly available software programs such as the SIFT, followed by PolyPhen, PANTHER, MutPred, I-Mutant-2.0 and PhosSNP 1.0. Functional significance of noncoding SNPs in the regulatory regions were analysed using FastSNP. Utilizing miRSNP database, we explored the role of SNPs in the context that alters the miRNA binding sites in the above mentioned genes. Our in silico studies have identified various deleterious SNPs and this cataloguing is essential and gives first hand information for further analysis by in vitro and in vivo methods for a better understanding of maintenance, assembly and functional aspects of P bodies in both health and disease.
Bioinformation, Dec 31, 2015
Increase in obesity rates and obesity associated health issues became one of the greatest health ... more Increase in obesity rates and obesity associated health issues became one of the greatest health concerns in the present world population. With alarming increase in obese percentage there is a need to design new drugs related to the obesity targets. Among the various targets linked to obesity, pancreatic lipase was one of the promising targets for obesity treatment. Using the in silico methods like structure based virtual screening, QikProp, docking studies and binding energy calculations three molecules namely zinc85531017, zinc95919096 and zinc33963788 from the natural database were reported as the potential inhibitors for the pancreatic lipase. Among them zinc95919096 presented all the interactions matching to both standard and crystal ligand and hence it can be further proceeded to drug discovery process. BIOINFORMATION
Springer eBooks, 2016
Indiscriminate use of chemical pesticides in agriculture and allied sectors have contributed to s... more Indiscriminate use of chemical pesticides in agriculture and allied sectors have contributed to soil, water and environmental pollution leading not only to human and animal illnesses but also biodiversity loss. The late 1980s, thus, opened new avenues for alternative pest management practices. Biopesticides derived from biological sources were tried, and, over the years, they have become an integral part of pest management practices, thereby minimizing the use of chemical pesticides. However, to protect the farmers, registration requirement of biopesticides has been made mandatory to ensure safety to human health, beneficial non-target organisms and environment. Countries promoting biopesticides constitute various regulatory bodies including committees/ boards/special authorities in order to oversee the regulatory affairs for biopesticides. These regulatory bodies formulate the dossier requirements for biopesticides and update the dossiers from time to time based on local and international needs. Robust and stringent but user-friendly regulatory norms would ensure availability of quality and safe biopesticide formulations.
International journal of acarology, Feb 17, 2022
Rasayan journal of Chemistry, 2021
Due to the widespread use of medicinal plant products in the pharmaceutical and biotechnology fie... more Due to the widespread use of medicinal plant products in the pharmaceutical and biotechnology field, phytochemical analysis of medicinal plants has become an important and challenging task. Analytical techniques including liquid chromatography coupled with mass spectrometry were found to be an important technique in the analysis of complex bioactive constituents. The present study was aimed at bioactive constituent analysis from select Indian medicinal plants viz., Pongamia pinnata, Dodonea viscosa, Gardenia resinifera and Gymnospora emarginata by (HR)-LCMS (High Resolution-Liquid Chromatography Mass Spectrometry) analysis. The present study confirms presence of important therapeutic secondary metabolites including alkaloids (Hydroxycotinine), Flavonoids (Apiin, Genkwanin, Kaempherol), Coumarin (Lomatin), Carboxylic acid (Quinic acid) and Phenolic compounds (Isoliquiritigenin) in the select Indian medicinal plants.
Bioinformation, 2016
The present study explains computational methods to design thermostable horseradish peroxidase en... more The present study explains computational methods to design thermostable horseradish peroxidase enzyme using the crystal structure available from Protein Data Bank (PDB ID: 6ATJ). Multiple mutations were introduced to the original enzyme and developed a model by using Modeler9.14. After designing the model functional effect was confirmed in terms of protein ligand binding by molecular docking using Autodock 4.2. The implementation of modeling steps is demonstrated in the context of performing mutations for particular amino acid residue on the ligand pocket of the horseradish peroxidase, to derive the desired ligand binding properties. The docking investigation of modelled HRP with Quercetindihydroxide using Autodock 4.2 software that six amino acid residues, P139, H42, A31, L174, A38, and G169 are involved in hydrogen bonding. More importantly, it provides insight into understanding and properly interpreting the data produced by these methods. The 3D model was docked with Quercetindi...
Genomics, 2012
In the present study, nsSNPs in EPHX1, GSTT1, GSTM1 and GSTP1 genes were screened for their funct... more In the present study, nsSNPs in EPHX1, GSTT1, GSTM1 and GSTP1 genes were screened for their functional impact on concerned proteins and their plausible role in breast cancer susceptibility. Initially, SNPs were retrieved from dbSNP, followed by identification of potentially deleterious nsSNPs using PolyPhen and SIFT. Functional analysis was done with SNPs3D, SNPs&GO and MutPred methods. Prediction and evaluation of the functional impact on the 3D structure of proteins were performed with Swiss PDB viewer and NOMAD-Ref servers. On analysis, 13 nsSNPs were found to be highly deleterious and damaging to the protein structure, of which 6 nsSNPs, rs45549733, rs45506591 and rs4986949 of GSTP1, rs72549341 and rs148240980 of EPHX1 and rs17856199 of GSTT1 were predicted to be potentially polymorphic. It is therefore hypothesized that the 6 identified nsSNPs may alter the detoxification process and elevate carcinogenic metabolite accumulation thus modifies the risk of breast cancer susceptibility in a group of women.
International Journal of Acarology, 2022
ABSTRACT The present study evaluates the pathogenic efficacy of an entomopathogenic fungus, Metar... more ABSTRACT The present study evaluates the pathogenic efficacy of an entomopathogenic fungus, Metarhizium anisopliae s.l. (=M. anisopliae) against the red spider mite, Oligonychus coffeae damaging tea plants. Laboratory studies revealed that M. anisopliae s.l. was pathogenic on O. coffeae and exhibited 78% mortality. Evaluation of formulated 5% aqueous suspension (AS) of M. anisopliae (1000 ml containing 2 × 107 conidia/ml in 400 L of water/ha) against O. coffeae through micro-plot study revealed a maximum of 68.2% reduction in mite’s population in sprayed plots, as compared to Fenpyroximate (5% EC), where a 67.5% reduction in mite’s population was recorded. Furthermore, large-scale field trials with aqueous suspension of entomopathogen revealed that 1000 and 1200 ml doses of M. anisopliae s.l. 5%AS each in 400 L of water/ha significantly reduced O. coffeae’s population in the tea gardens of Dooars and Darjeeling regions, India. Metarhizium anisopliae s.l. was more effective than standard acaricides and was non-pathogenic to the beneficial insects present in the tea gardens. Metarhizium anisopliae s.l. 5%AS had no phytotoxic effect on the tea leaves, with acceptable organoleptic attributes. Thus, M. anisopliae s.l. isolate can be commercialized as an alternative natural acaricide to reduce the load of synthetic acaricides in the tea crop.
Additional file 1. Evaluation of phytotoxicity of M. anisopliae 5% AS on tea plants.
Shape based virtual screening and molecular docking towards designing novel pancreatic lipase inh... more Shape based virtual screening and molecular docking towards designing novel pancreatic lipase inhibitors
Drug Design, Development and Therapy, 2015
Background: Obesity is a progressive metabolic disorder in the current world population, and is c... more Background: Obesity is a progressive metabolic disorder in the current world population, and is characterized by the excess deposition of fat in the adipose tissue. Pancreatic lipase is one of the key enzymes in the hydrolysis of triglycerides into monoglycerides and free fatty acids, and is thus considered a promising target for the treatment of obesity. The present drugs used for treating obesity do not give satisfactory results, and on prolonged usage result in severe side effects. In view of the drastic increase in the obese population day-today , there is a greater need to discover new drugs with lesser side effects. Materials and methods: High-throughput virtual screening combined with e-pharmacophore screening and ADME (absorption, distribution, metabolism, and excretion) and PAINS (panassay interference compounds) filters were applied to screen out the ligand molecules from the ZINC natural molecule database. The screened molecules were subjected to Glide XP docking to study the molecular interactions broadly. Further, molecular dynamic simulations were used to validate the stability of the enzyme-ligand complexes. Finally, the molecules with better results were optimized for in vitro testing. Results: The screening protocols identified eight hits from the natural molecule database, which were further filtered through pharmacological filters. The final four hits were subjected to extra precision docking, and the complexes were finally studied with molecular dynamic simulations. The results pointed to the zinc 85893731 molecule as the most stable in the binding pocket, producing consistent H-bond interaction with Ser152 (G=-7.18). The optimized lead molecule exhibited good docking score, better fit, and improved ADME profile. Conclusion: The present study specifies zinc 85893731 as a lead molecule with higher binding score and energetically stable complex with pancreatic lipase. This lead molecule, along with its various analogs, can be further tested as a novel inhibitor against pancreatic lipase using in vitro protocols.
Computational Biology and Chemistry, 2019
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service... more This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Structural prediction, whole exome sequencing and molecular dynamics simulation confirms p.G118D somatic mutation of PIK3CA as functionally important in breast cancer patients
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Papers by Venkateswara Talluri