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Fereshteh Izadi, Hamid Najafi Zarrini, Ghaffar Kiani, Nadali Babaeian Jelodar
A Gene Regulatory Network (GRN) is a collection of interactions between molecular regulators and their targets in cells governing gene expression level. Omics data explosion generated from high-throughput genomic assays such as microarray and RNA-Seq technologies and the emergence of a number of pre-processing methods demands suitable guidelines to determine the impact of transcript data platforms and normalization procedures on describing associations in GRNs. In this study exploiting publically available microarray and RNA-Seq datasets and a gold standard of transcriptional interactions in Arabidopsis, we performed a comparison between six GRNs derived by RNA-Seq and microarray data and different normalization procedures...
2016: Bioinformation
Imane Sabaouni, Brigitte Vannier, Ahmed Moussa, Azeddine Ibrahimi
CD36 is a multifunctional membrane-type receptor glycoprotein that reacts with oxidized low-density lipoprotein and long-chain fatty acid (LCFA). However, much remains to be understood about the molecular mechanism of the cardio-myopathy observed in CD36-KO mice. In this study, we identify different genes pathways involved in response to CD36 cardio-myopathy phenotype by identifying the differences among biological processes, molecular pathways and networks of interactions that emerge from knocking CD3 and using different bioinformatics tools such as STRING, GeneMANIA and Cytoscape...
2016: Bioinformation
Ranjith Kumavath, Manan Azad, Pratap Devarapalli, Sandeep Tiwari, Shreya Kar, Debmalya Barh, Vasco Azevedo, Alan Prem Kumar
Aromatase (CYP19A1) the key enzyme of estrogen biosynthesis, is often deregulated in breast cancer patients. It catalyzes the conversion of androgen to estrogen, thus responsible for production of estrogen in human body. However, it causes over-production of estrogen which eventually leads to proliferation of breast cancer cells. Identification of new small molecule inhibitors targeted against CYP19A1 therefore, facilitates to increase drug sensitivity of cancer cells. In this scenario, the present study aims to identify new molecules which could block or suppress the activity of aromatase enzyme by molecular docking studies using Schrödinger-Maestro v9...
2016: Bioinformation
Hanumalal Nunavath, Chandrasekhar Banoth, Venkateswar Rao Talluri, Bhima Bhukya
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...
2016: Bioinformation
Mahesha Nand, Priyanka Maiti, Ragini Pant, Madhulata Kumari, Subhash Chandra, Veena Pande
Non-small cell lung cancer (NSCLC) is the most dominating and lethal type of lung cancer triggering more than 1.3 million deaths per year. The most effective line of treatment against NSCLC is to target epidermal growth factor receptor (EGFR) activating mutation. The present study aims to identify the novel anti-lung cancer compounds form nature against EGFR 696-1022 T790M by using in silico approaches. A library of 419 compounds from several natural resources was subjected to pre-screen through machine learning model using Random Forest classifier resulting 63 screened molecules with active potential...
2016: Bioinformation
Padmanabhan Mahadevan
The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Hundreds of tools have been developed to analyze biological sequence data. However, only some of these tools are user-friendly to biologists. Several of these tools that have been successfully used to analyze adenovirus genomes are described here...
2016: Bioinformation
Ajijur Rehman, Salman Akhtar, Mohd Haris Siddiqui, Usman Sayeed, Syed Sayeed Ahmad, Jamal M Arif, M Kalim A Khan
4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) is an important enzyme needed for the biosynthesis of lysine and many more key metabolites in Mycobacterium tuberculosis (Mtb). Inhibition of DHDPS is supposed to a promising therapeutic target due to its specific role in sporulation, cross-linking of the peptidiglycan polymers and biosynthesis of amino acids. In this work, a known inhibitor-based similarity search was carried out against a natural products database (Super Natural II) towards identification of more potent phyto-inhibitors...
2016: Bioinformation
Sushanta Deb, Surajit Basak
Paenibacillus sp. 32O-W, which is attributed for biodesulfurization of petroleum, has 56.34% genomic G+C content. Correspondence analysis on Relative Synonymous Codon Usage (RSCU) of the Paenibacillus sp. 32O-W genome has revealed the two different trends of codon usage variation. Two sets of genes have been identified representing the two distinct pattern of codon usage in this bacterial genome. We have measured several codon usage indices to understand the influencing factors governing the differential pattern of codon usage variation in this bacterial genome...
2016: Bioinformation
Navneet Chauhan, Anuradha Gajjar, Syed Hussain Basha
Glycogen synthase kinase-3 (GSK-3) is a multitasking serine/threonine protein kinase, which is associated with the pathophysiology of several diseases such as diabetes, cancer, psychiatric and neurodegenerative diseases. Tideglusib is a potent, selective, and irreversible GSK-3 inhibitor that has been investigated in phase II clinical trials for the treatment of progressive supranuclear palsy and Alzheimer's disease. In the present study, we performed pharmacophore feature-based virtual screening for identifying potent targetspecific GSK-3 inhibitors...
2016: Bioinformation
Pankaj Kumar Singh, Akshay Singh, Deepak V Pawar, B N Devanna, Jyoti Singh, Vinay Sharma, Tilak R Sharma
Microsatellites have been widely utilized for molecular marker development. Codominant and multiallelic nature of these simple repeats have several advantages over other types of molecular markers. Their broad applicability in the area of molecular biology like gene mapping, genome characterization, genome evolution, and gene regulation has been reported in various crop plants, animals and fungi. Considering these benefits of the SSR markers, a MMDB (Magnaporthe oryzae Microsatellite Database) was developed to help in understanding about the pathogen and its diversity at strains level of a particular geographic region, which can help us to make a proper utilization of blast resistance genes in the region...
2016: Bioinformation
Sridharan Brindha, Jagadish Chandrabose Sundaramurthi, Devadasan Velmurugan, Savariar Vincent, John Joel Gnanadoss
Repurposing has gained momentum globally and become an alternative avenue for drug discovery because of its better success rate, and reduced cost, time and issues related to safety than the conventional drug discovery process. Several drugs have already been successfully repurposed for other clinical conditions including drug resistant tuberculosis (DR-TB). Though TB can be cured completely with the use of currently available anti-tubercular drugs, emergence of drug resistant strains of Mycobacterium tuberculosis and the huge death toll globally, together necessitate urgently newer and effective drugs for TB...
2016: Bioinformation
Laura K Harris
Acetolactate synthase (ALS) is a highly conserved protein family responsible for producing branched chain amino acids. In Methanocaldococcus jannaschii, two ALS proteins, MJ0277 and MJ0663 exist though variations in features between them are noted. Researchers are quick to examine MJ0277 homologs due to their increased function and close relationship, but few have characterized MJ0663 homologs. This study identified homologs for both MJ0277 and MJ0663 in all 15 Methanococci species with fully sequenced genomes...
2016: Bioinformation
Divya Shaji
Intrinsically Disordered Proteins (IDPs) lack a stable, three-dimensional structure under physiological conditions, yet they exhibit numerous biological activities. Protean segments (ProSs) are the functional regions of intrinsically disordered proteins that undergo disorder-to-order transitions upon binding to their partners. Example ProSs collected from the intrinsically disordered proteins with extensive annotations and literature (IDEAL) database. The interface of protean segments (ProSs) is classified into core, rim, and support, and analyzed their secondary structure elements (SSEs) based on the relative accessible surface area (rASA)...
2016: Bioinformation
Syed Hussain Basha, Abhishek Thakur, Firoz A Samad
Indoleamine-2,3-dioxygenase (IDO) an immunoregulatory enzyme and emerging as a new therapeutic drug target for the treatment of cancer. Carboranes, an icosahedral arrangement of eleven boron atoms plus one carbon atom with unique pharmacological properties such low toxicity, isosterism with phenyl ring and stability to hydrolysis. On the other hand, carboranes are known to increase the interaction of ligand with non-polar region of the protein provides an excellent platform to explore these carboranes towards designing and development of novel, potent and target specific drug candidates with further enhanced binding affinities...
2016: Bioinformation
Mohammad Teimouri, Muhammad Junaid, Shoaib Saleem, Abbas Khan, Arif Ali
The contest of cancer couldn't be completed without novel drug with novel modes of action, improved efficacy and acceptable pharmacokinetic properties. Transcription factors are attractive targets to develop anti-cancerous drugs. 6-Gingerol, Anethol analogues, Capsaicinoids, Curcumin, Dibenzoylmethane, Diosgenin, Eugenol, Gambogic acid, Thymoquinone, Ursolic acid, Xanthohumol, Zerumbone are the promising nutraceuticals that help in the prevention of cancer. These nutraceuticals showed promising activity in invitro tests...
2016: Bioinformation
Mahendran Botlagunta, Bhulakshmi Kollapalli, Lavanya Kakarla, Siva Priya Gajarla, Sai Pujitha Gade, Chandra Lekha Dadi, Akhila Penumadu, Shaik Javeed
RNA helicase, DDX3 is a multifunctional enzyme and is known to be associated with several diseases like HIV progression, brain and breast cancer. Some of the ring expanded nucleoside compounds such as REN: NZ51, fused di imidazodiazepine ring (RK33), (Z)-3-(5- (3-bromo benzylidene)-4-oxo-2-thioxothiazolidin-3-yl)-N-(2- hydroxy phenyl) propanamide compound (FE15) have been documented to inhibit DDX3 helicase activity. However, synthesis of these drugs is limited to few research groups. Prevalence of literature study, we found that doxorubicin form strong hydrogen bond interactions with crystallized form of DDX3 using in-silico molecular docking approach...
2016: Bioinformation
Rupa Lavarti, Jayasree Ganugapati, Shirisa Ratcha, Lakshmana Ss Rao, Krovvidi Sr SivaSai
Peptides of Rv0679c a membrane protein of the cell envelope (16.6 KDa) of Mycobacterium tuberculosis (M. tb), inhibited entry of live bacilli into epithelial (A549) and macrophage (U937) cell lines in vitro, suggesting a possible role in invasion. Receptors associated with Rv0679c antigen entry into cell lines were not characterized. We are reporting that Rv0679c peptides could bind to Toll like receptors (TLRs), the principal class of pathogen recognition receptors on host cells (PRR) by docking studies. Peptide structures were predicted using PEP FOLD and docking of truncated peptides with TLR's was performed using Cluspro 2...
2016: Bioinformation
Hulikal Shivashankara Santosh Kumar, Vadlapudi Kumar
The inventory of proteins used in different kingdoms appears surprisingly similar in all sequenced eukaryotic genome. Protein domains represent the basic evolutionary units that form proteins. Domain duplication and shuffling by recombination are probably the most important forces driving protein evolution and hence the complexity of the proteome. While the duplication of whole genes as well as domain encoding exons increases the abundance of domains in the proteome, domain shuffling increases versatility, i...
2016: Bioinformation
Dyavegowda Padmashree, Narayanaswamy Ramachandraswamy
microRNAs (Small regulatory non-coding RNAs) have an important role in gene regulation and evolutionarily conserved molecules. Trichinella spiralis infect majority of species. Therefore, it is of interest to identify conserved miRNAs and their targets using sequences from EST, GSS and full length nucleotides obtained from NCBI against previously reported worm miRNAs. We identify 11 novel miRNAs in T. spiralis by using bioinformatics-homology based search. In addition, we predicted target mRNA genes form complementary base pair in seed region of miRNAs...
2016: Bioinformation
Abhishek Upadhyay, Vengatesen Thiyagarajan, Ying Tong
Oysters are economically and ecologically important bivalves, with its calcareous shell and delicious meat. The shell composition is a blend of inorganic crystals and shell proteins that form an organic matrix which protects the soft inner tissue of the oyster. The objective of the study was to compare the composition of organic matrix proteins (OMP) of two phylogenetically related species: the Hong Kong oyster (Crassostrea hongkongensis) and the Portuguese oyster (Crassostrea angulata) which differ in their shell hardness and mechanical properties...
2016: Bioinformation
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