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Cindy Huang, Vichetra Sam, Sophie Du, Tuan Le, Anthony Fletcher, William Lau, Kathleen Meyer, Esther Asaki, Da Wei Huang, Calvin Johnson
The third-generation sequencing technology, PacBio, has shown an ability to sequence the HIV virus amplicons in their full length. The long read of PaBio offers a distinct advantage to comprehensively understand the virus evolution complexity at quasispecies level (i.e. maintaining linkage information of variants) comparing to the short reads from Illumina shotgun sequencing. However, due to the highnoise nature of the PacBio reads, it is still a challenge to build accurate contigs at high sensitivity. Most of previously developed NGS assembly tools work with the assumption that the input reads are fairly accurate, which is largely true for the data derived from Sanger or Illumina technologies...
2018: Bioinformation
Francesco Chiappelli
Health care is optimized when the best evidence base (BEB) is translated into policies whose effectiveness can be verified. Bioinformation disseminates BEB and is critical to translational health care. The survival of all prokaryotes and eukaryotes, including mammals, and ultimately our species, depends upon their ability to adapt to changes in their micro-environmental milieu and to the challenges of their surrounding macro-environment. Disturbances in the organism's macro-environment, such as the stressful stimuli derived from environmental changes akin to the current climate crisis, alter its physiological, cytological, biological, epigenetic and molecular microenvironment, and trigger concerted allostatic responses to regain homeostasis...
2018: Bioinformation
Rupesh Kumar Mohapatra, Satyabrata Nanda
Chitinases are glycoside hydrolase (GH) family of proteins having multifaceted roles in plants. It is of interest to identify and characterize chitinase-encoding genes from the popular bulbous plant onion ( Allium cepa L.). We have used the EST sequences for onion chitinases to elucidate its functional features using sequence, structure and functional analysis. These contigs belong to the GH19 chitinases family according to domain architecture analysis. They have highly conserved chitinase motifs including motifs exclusive to plant chitinases as implied using the MEME based structural characterization...
2018: Bioinformation
Radha Verma, B S Balaji, Aparna Dixit
Jasminum mesnyi Hance (yellow jasmine, Family Oleaceae) belongs to an important subclass of Jasminum family whose biological significance is under explored. The current study pertains to isolation of various solvent extracts fractions and their anti-bacterial effects on the Gram-positive and Gram-negative bacterial pathogens. Ethanolic extract of J. mesnyi Hance leaves was subjected to further partitioning using different solvents with increasing polarity to get different solvent fractions. Different extracts were analysed for their phytochemical constitutents and were evaluated for their antibacterial activity against a number of diseases causing bacteria...
2018: Bioinformation
Mohd Babu Khan, Bhagath Kumar Palaka, Tuleshwori Devi Sapam, Naidu Subbarao, Dinakara Rao Ampasala
Acetyl-cholinesterase enzyme (AChE) is a known target for identifying potential inhibitors against Alzheimer diseases (AD). Therefore, it is of interest to screen AChE with the CNS-BBB database. An AChE enzyme is a member of hydrolase family is activated by acetylcholine (ACh), so, targeting the AChE enzyme with the potential inhibitor may block the binding of the ACh. In this study we carried out virtual screening of drug-like molecules from Chemical Diversity Database particularly CNS-BBB compounds, to identify potential inhibitors using Glide docking program...
2018: Bioinformation
Ipsita Das, Hrishikesh Mishra, Prafulla K Khodiar, Pradeep K Patra
Sickle cell disease (SCD) is life-threatening hemoglobinopathy prevalent in India, Sub-Saharan Africa and Middle East. Inflammation plays a pivotal role in disease process and involves intricate interaction among leukocytes, platelets, sickle erythrocytes and vascular endothelium. Available disease modifying therapies are hydroxyl-urea and blood transfusion. Therefore, it is of interest to develop improved pharmacological agents for SCD. We report up-regulated genes in steady state and vaso-occlusive crisis using analysis of gene expression data obtained by microarray experiment for SCD as potential targets...
2018: Bioinformation
Luis Jaramillo, David Tarazona, Kelly Levano, Marco Galarza, Omar Caceres, Maximilian Becker, Heinner Guio
The emergence of multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB) strains is a major health problem for high Tuberculosis (TB) incidence countries. Therefore, it is of interest to identify antibiotic resistant bacteria by mismatch detection using DNA hybridization. We generated PCR products for five genes (rpoB, inhA, katG, gyrA and rrs) associated with drug resistance TB from MDR and XDR Mycobacterium tuberculosis (MTB) DNA samples. These were hybridized to PCR products from MTB H37Rv (pansusceptible laboratory strain) to generate DNA hetero-duplex products, which was digested by Detection Enzyme (GeneArt Genomic Cleavage Detection Kit) and visualized by agarose gel electrophoresis...
2018: Bioinformation
Thakur Vikram, Pradeep Kumar
Hepatitis E viral infection is now emerging as a global health concern, which needs to be addressed. Mechanism of viral replication and release is attributed by the different genomic component of HEV. However, few proteins/domain like X and Y domain remain unexplored, so we aim to explore the physiochemical, structural and functional features of HEV ORF-1 X domain. Molecular modeling of the unknown X domain was carried out using Phyre2 and Swiss Model. Active ligand binding sites were predicted using Phyre2...
2018: Bioinformation
Rajhans Tyagi, Apoorv Tiwari, Alok Kumar Gupta, Sanjay Gupta
Finger millet is a calcium-rich cereal crop of the grass family. The transcriptome data for finger millet is available at NCBI. It is of interest to annotate and characterize starch synthase enzyme from finger millet transcriptome data. Starch synthase plays an important role in the elongation of glucan chains during the formation of starch. The starch synthase enzyme is characterized using three domains (Glyco_transf_5, Glycos_transf_1 and Glyco_trans_1_4). Binding sites for GLC (alpha-d-glucose), PLP (Pyridoxal-5'- phosphate), AMP (Adenosine monophosphate) and GOL (Glycerol) are found...
2018: Bioinformation
Lahmadi Ayoub, El-Aliani Aissam, Kasmi Yassine, Elantri Said, El Mzibri Mohammed, Aboudkhil Souad
Oleaeuropaea and Ficuscarica are widely used in traditional medicine for the treatment of cancer. Therefore, it is of interest to develop a QSAR model for screening proteasome inhibitors from plant source. Hence, a QSAR model was developed using multiple linear regressions; partial least squares regression and principal component regression methods. Results of QSAR modeling and docking demonstrate that compounds derived from both plants have great potentiality to be proteasome inhibitors. The developed QSAR model highlights a strong structure-effect relationship...
2018: Bioinformation
Mohankrishna Ghanta, Elango Panchanathan, Bhaskar Venkata Kameswara Subrahmanya Lakkakula, Anbumani Narayanaswamy, P A Abhinand, Stalin Antony
Soluble guanylate cyclase (sGC) is a type of lyase enzyme with profoundly increasing importance in treatments of cardiovascular and neurodegenerative disorders. Modulation of sGC activity demonstrated beneficial effects against Parkinson's disease by reducing glutamate excitotoxicity. It is of interest to evaluate the pharmacological activity of Momordica charantia phytoconstituent (DGalacturonic acid) and ODQ with catalytic domain of sGC enzyme, using Autodock version 4.2 programs. Docking results revealed the binding ability of ODQ at the allosteric sites of sGC...
2018: Bioinformation
Mohammad Nazmol Hasan, Zobaer Akond, Md Jahangir Alam, Anjuman Ara Begum, Moizur Rahman, Md Nurul Haque Mollah
The aim of toxicogenomic studies is to optimize the toxic dose levels of chemical compounds (CCs) and their regulated biomarker genes. This is also crucial in drug discovery and development. There are popular online computational tools such as ToxDB and Toxygates to identify toxicogenomic biomarkers using t-test. However, they are not suitable for the identification of biomarker gene regulatory dose of corresponding CCs. Hence, we describe a one-way ANOVA model together with Tukey's HSD test for the identification of toxicogenomic biomarker genes and their influencing CC dose with improved efficiency...
2018: Bioinformation
Gagandeep K Khurana, Poonam Vishwakarma, Niti Puri, Andrew Michael Lynn
Proteins of the SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptors) family play a significant role in all vesicular fusion events involved in endocytic and exocytic pathways. These proteins act as molecular machines that assemble into tight four-helix bundle complex, bridging the opposing membranes into close proximity forming membrane fusion. Almost all SNARE proteins share a 53 amino acid coiled-coil domain, which is mostly linked to the transmembrane domain at the C-terminal end...
2018: Bioinformation
Mohammad Mahfuz Ali Khan Shawan, Md Ashraful Hasan, Raihana Yesmin, Tareq Hossan, Md Mozammel Hossain, Md Mahmudul Hasan, Afroza Parvin, Mahbubul Morshed, Nahiyan Mohammad Salauddin, Satya Ranjan Sarker, Md Nazibur Rahman, S M Badier Rahman
Whole genome sequences (DNA sequences) of four uncultured archeon clones (1B6:CR626858.1, 4B7:CR626856.1, 22i07:JQ768096.1 and 19c08:JQ768095.1) were collected from NCBI BioSample database for the construction of digital data on tRNA. tRNAscan-SE 2.0 and ENDMEMO tools were used to identify and sketch tRNA structure as well as calculate Guanine-Cytosine (GC) percentage respectively. Eight true/functional tRNAs were identified from above 4 sequences which showed cove score greater than 20% with no variable loop...
2018: Bioinformation
Neetu Singh Yadav, Devapriya Choudhury
Water-Dimethylsulfoxide (DMSO) and water-Acetonitrile (MeCN) binary mixtures at various molar ratios ranging from 0 to 1 are studied using Molecular Dynamics (MD) simulations. Hydration properties of water in different regions of MeCN/DMSO are investigated by using the statistical geometry approach. The obtained results reveal that in water-DMSO simulations both water and solvent molecules prefer to be in mixed cluster forms, depending upon the concentration of DMSO. While in case of water-MeCN mixtures, self-association of water and acetonitrile molecules, take place, showing microheterogeneity associated with the water- MeCN binary mixtures...
2018: Bioinformation
Paul Shapshak
The use of quantum computers and Artificial Intelligence (AI) is imperative for use in space exploration and astrobiology investigations. Considerable progress has been made since the commencement of origin of life laboratory and theoretical studies in the mid 20th century. However, the sheer amount of data amassed to date in all these studies including exoplanetary and astrobiological studies is enormous and increasing steadily. Thus, there is the need for AI and quantum computers. As AI develops, it will become crucial in the development of the statistical and database programs that are indispensable to analyze the huge quantity of cumulative data...
2018: Bioinformation
Debmalya Barh, Sandeep Tiwari, Ranjith N Kumavath, Preetam Ghosh, Vasco Azevedo
Lung cancer and pulmonary tuberculosis caused by Mycobacterium are two major causes of deaths worldwide. Tuberculosis linked lung cancer is known. However, the precise molecular mechanism of Mycobacterium associated increased risk of lung cancer is not understood. We report 45 common human miRNAs deregulated in both pulmonary tuberculosis and lung cancer. We show that sRNA_1096 and sRNA_1414 from M. tuberculosis have sequence homology with human mir-21. Hence, the potential role of these three small non-coding RNAs in rifampicin resistance in pulmonary tuberculosis is implied...
2018: Bioinformation
Atul Kumar Jaiswal, Syed Hussain Abbas Husaini, Amarjeet Kumar, Naidu Subbarao
By-products of fatty acid degradation are extensively utilized by Mycobacterium tuberculosis (Mtb) for lipid synthesis and energy production during the infection phase. Cholesterol from host is scavenged by Mtb to fulfill its metabolic requirements, evade host immunity and invade macrophages. Blocking cholesterol catabolic pathways leads to bacteriostasis. FadA5 (Acetyl-CoA acetyltransferase), a thiolase encoded by fadA5 (Rv3546) gene in Mtb, plays a crucial role in cholesterol aliphatic chain degradation. Hence, FadA5 is a potential target for designing antitubercular inhibitors...
2018: Bioinformation
Chowdhury Nilkanta, Angshuman Bagchi
The DNA-protein interactions play vital roles in the central dogma of molecular biology. Proper interactions between DNA and protein would lead to the onset of various biological phenomena like transcription, translation, and replication. However, the mechanisms of these well-known processes vary between prokaryotic and eukaryotic organisms. The exact molecular mechanisms of these processes are unknown. Therefore, it is of interest to report the comparative estimate of the different properties of the DNA binding proteins from prokaryotic and eukaryotic organisms...
2018: Bioinformation
Anuraj Nayarisseri, Poonam Singh, Sanjeev Kumar Singh
Biosurfactants are surface-active compounds produced by a wide range of microorganisms. They have both hydrophobic and hydrophilic domains and can decrease the surface tension and the interfacial tension of growth medium. Biosurfactants have different chemical structures like-lipopeptides, glycolipids, neutral lipids and fatty acids. They are biodegradable non-toxic biomolecules that show strong emulsification of hydrophobic compounds. They have the ability to form stable emulsions. The low water-solubility of these compounds restricts their availability to microorganisms...
2018: Bioinformation
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