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Michael Sekula, Somnath Datta, Susmita Datta
There exist numerous programs and packages that perform validation for a given clustering solution; however, clustering algorithms fare differently as judged by different validation measures. If more than one performance measure is used to evaluate multiple clustering partitions, an optimal result is often difficult to determine by visual inspection alone. This paper introduces optCluster, an R package that uses a single function to simultaneously compare numerous clustering partitions (created by different algorithms and/or numbers of clusters) and obtain a "best" option for a given dataset...
2017: Bioinformation
Sathish Sankar, Mageshbabu Ramamurthy, Balaji Nandagopal, Gopalan Sridharan
Hantavirus cardiopulmonary syndrome in North America is caused by Sin Nombre virus (SNV) and poses a public health problem. We identified T-cell epitopes restricted to HLA alleles commonly seen in the N. American population. Nucleocapsid (N) protein is 428 aminoacid in length and binds to RNA and functions also as a key molecule between virus and host cell processes. The predicted epitopes from N protein that bind to class I MHC were analyzed for human proteasomes cleavage, TAP efficiency, immunogenicity and antigenicity...
2017: Bioinformation
Sunanda Baidya, Rasel Das, Md Golam Kabir, Md Arifuzzaman
Cervical cancer accounts for about two-thirds of all cancer cases linked etiologically to Human Papilloma Virus (HPV). 15 oncogenic HPV types can cause cervical cancer, of which HPV16 and HPV18 combinedly account for about 70% of it. So, effective epitope design for the clinically relevant HPV types 16 and 18 would be of major medical benefit. Here, a comprehensive analysis is carried out to predict the epitopes against HPV types 16 and 18 through "reverse vaccinology" approach. We attempted to identify the evolutionarily conserved regions of major capsid protein (L1) as well as minor capsid protein (L2) of HPV and designed epitopes within these regions...
2017: Bioinformation
Soumitra Polley, Soham Seal, Avisek Mahapa, Biswanath Jana, Anindya Biswas, Sukhendu Mandal, Debabrata Sinha, Keya Sau, Subrata Sau
Cyclophilins, a class of peptidyl-prolyl cis-trans isomerase (PPIase) enzymes, are inhibited by cyclosporin A (CsA), an immunosuppressive drug. Staphylococcus aureus Newman, a pathogenic bacterium, carries a gene for encoding a putative cyclophilin (SaCyp). SaCyp shows significant homology with other cyclophilins at the sequence level. A three-dimensional model structure of SaCyp harbors a binding site for CsA. To verify whether SaCyp possesses both the PPIase activity and the CsA binding ability, we have purified and investigated a recombinant SaCyp (rCyp) using various in vitro tools...
2017: Bioinformation
Subramaniam Sivakumar, Palanivel Anitha, Balsubramanian Ramesh, Gopal Suresh
Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. The accumulation of Malathion in environment is the biggest threat to the environment because of its toxicity. Malathion is lethal to beneficial insects, snails, micro crustaceans, fish, birds, amphibians, and soil microorganisms...
2017: Bioinformation
Shaista Khan, Mohd Imran, Mohammed Imran, Nuzhat Pindari
A total of 50 Candida isolates were isolated and identified from clinical specimens and these were tested for resistance to various antifungal drugs. It was observed multi-drug resistance in all candida isolates by 84%, 62%, 60%, 76%, 46, 30%, and 22% against fluconazole, clotrimazole, Amphotericin B, itraconazole, ketoconazole, miconazole and nystatin tested respectively. The isolates, which were found to be resistant to antifungal drugs were selected and subjected to antifungal testing against six ethanolic plants, extract namely Azadiracta indica, Allium sativum, Cordia dichotoma Ocimum sanctum, Syzygium cumini and Trigonella foenum grecum...
2017: Bioinformation
Yahya Hobani, Ahmed Jerah, Anil Bidwai
Interaction of curcumin (CUR) with the enzyme dihydrofolate reductase (DHFR) was studied by molecular docking using AutoDock 4.2 as the docking software application. AutoDock 4.2 software serves as a valid and acceptable docking application to study the interactions of small compounds with proteins. Interactions of curcumin with DHFR were compared to those of methotrexate (MTX), a known inhibitor of the enzyme. The calculated free energy of binding (ΔG binding) shows that curcumin (ΔG = -9.02 kcal/mol; Ki = 243 nM) binds with affinity comparable to or better than MTX (ΔG = -8...
2017: Bioinformation
Gunjan Mishra, Deepak Sehgal, Jayaraman K Valadi
Antimicrobial peptides are host defense peptides being viewed as replacement to broad-spectrum antibiotics due to varied advantages. Hepatitis is the commonest infectious disease of liver, affecting 500 million globally with reported adverse side effects in treatment therapy. Antimicrobial peptides active against hepatitis are called as anti-hepatitis peptides (AHP). In current work, we present Extratrees and Random Forests based Quantitative Structure Activity Relationship (QSAR) regression modeling using extracted sequence based descriptors for prediction of the anti-hepatitis activity...
2017: Bioinformation
Soumya Sharma, Sarika Jaiswal, Sunil Archak
Enhanced Disease Susceptibility1 (EDS1) is a nucleo-cytoplasmic protein, known to be a key regulator of plant basal defense and effector-triggered immunity. Sequence of a single copy brinjal EDS1 gene (SmEDS1) was mined from draft brinjal genome assembly. The extracted sequence was found to be incomplete and polished with the help of transcriptome sequence data. Full-length SmEDS1 gene is 4.5kb long having three exons that coded for 1.8kb mRNA. SmEDS1 protein is a 602 amino acid long protein consisting of Lipase3 and EP domain regions...
2017: Bioinformation
Jerrine Joseph, Raj Bhaskaran, Muthusamy Kaliraj, Muthiyah Muthuswamy, Arumugam Suresh
The development of shrimp aquaculture has been severely affected by viral diseases resulting in a huge economic burden to the industry. White spot disease (WSD) has caused severe mortality in farmed shrimp in many countries. Globally aquaculture industries face huge economic losses due to rapid spread of White Spot Syndrome Virus (WSSV) disease that can cause 100% mortality in a short period of 3-10 days. In the present study in order to prevent the spread of WSSV disease in shrimps, the receptor, PmRab7 has been chosen as the drug target...
2017: Bioinformation
Ashvini Desai, Inamul Hasan Madar, Amjad Hussain Asangani, Hussain Al Ssadh, Iftikhar Aslam Tayubi
Polycystic ovary syndrome (PCOS) is endocrine system disease which affect women ages 18 to 44 where the women's hormones are imbalance. Recently it has been reported to occur in early age. Alteration of normal gene expression in PCOS has shown negative effects on long-term health issues. PCOS has been the responsible factor for the infertility in women of reproductive age group. Early diagnosis and treatment can improve the women's health suffering from PCOS. Earlier Studies shows correlation of PCOS upon insulin resistance with significant outcome, Current study shows the linkage between PCOS with obesity and non-obese patients...
2017: Bioinformation
Jessica Marklevitz, Laura K Harris
Antibiotic resistant Staphylococcus aureus is a major public health concern effecting millions of people annually. Medical science has documented completely untreatable S. aureus infections. These strains are appearing in the community with increasing frequency. New diagnostic and therapeutic options are needed to combat this deadly infection. Interestingly, around 50% of the proteins in S. aureus are annotated as hypothetical. Methods to select hypothetical proteins related to antibiotic resistance have been inadequate...
2017: Bioinformation
Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani
Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. Here, we present a new method to augment regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity...
2017: Bioinformation
Azita Sahni, Mohammadreza Hajjari, Jamshid Raheb, Ali Mohammad Foroughmand, Morteza Asgari
Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Previous studies have indicated that rprA can increase the tolerance to Kanamycin in RcsB-deficient Escherichia coli K-12 following osmotic shock. The current study aims to clone and over-express the non-coding RNA rprA in E.coli and investigate its effect on the bacterial resistance to Kanamycin without any osmotic shock...
2017: Bioinformation
Remya Krishnan, Achuthsankar S Nair, Pawan K Dhar
MicroRNAs (miRNAs) are small non-coding RNAs ~22 nucleotides long that do not encode for proteins but have been reported to influence gene expression in normal and abnormal health conditions. Though a large body of scientific literature on miRNAs exists, their network level profile linking molecules with their corresponding phenotypes, is less explored. Here, we studied a network of 191 human miRNAs reported to play a role in 30 human cardiac diseases. Our aim was to study miRNA network properties like hubness and preferred associations, using data mining, network graph theory and statistical analysis...
2017: Bioinformation
Madhulata Kumari, Subhash Chandra, Neeraj Tiwari, Naidu Subbarao
The Brucella melitensis methionyl-tRNA-synthetase (MetRSBm) is a promising target for brucellosis drug development. The virtual screening of large libraries of a drug like molecules against a protein target is a common strategy used to identify novel inhibitors. A High throughput virtual screening was performed to identify hits to the potential antibrucellosis drug target, MetRSBm. The best inhibitor identified from the literature survey was 1312, 1415, and 1430. In the virtual screening 56,400 compounds of ChEMBL antimycobacterial library, 1596 approved drugs, 419 Natural product IV library, and 2396 methionine analogous were docked and rescoring, identified top 10 ranked compounds as anti-mycobacterial leads showing G-scores -10...
2017: Bioinformation
Parth Sarthi Sen Gupta, Shyamashree Banerjee, Rifat Nawaz Ul Islam, Vishma Pratap Sur, Amal K Bandyopadhyay
Orthologous proteins, form due to divergence of parental sequence, perform similar function under different environmental and biological conditions. Amino acid changes at locus specific positions form hetero-pairs whose role in BLOCK evolution is yet to be understood. We involve eight protein BLOCKs of known divergence rate to gain insight into the role of hetero-pairs in evolution. Our procedure APBEST uses BLOCK-FASTA file to extract BLOCK specific evolutionary parameters such as dominantly used hetero-pair (D), usage of hetero-pairs (E), non-conservative to conservative substitution ratio (R), maximally-diverse residue (MDR), residue (RD) and class (CD) specific diversity...
2017: Bioinformation
Ayub Shaik, Vishnu Thumma, Aruna Kumari Kotha, Sandhya Kramadhati, Jalapathy Pochampally, Seshagiri Bandi
The functional inference of UniProtKB nitrate reductase enzyme (UniProtKB - P0AF33) through structural modeling is of interest in plant biology. Therefore, a homology model for UniProtKB variant of the enzyme was constructed using available data with the MODELER software tool. The model was further docked with five natural flavonoid structures such as hesperetin, naringenin, leucocyanidin, quercetin and hesperetin triacetate using the AUTODOCK (version 4.2) software tool. The structure aided molecular interactions of these flavonoids with nitrate reductase is documented in this study...
2016: Bioinformation
Narmataa Muthu, Su Yin Lee, Kia Kien Phua, Subhash Janardhan Bhore
Plants are very complex organisms that produce medicinally important natural products. The Star-fruit producing plant (Averrhoa carambola L.) is a species of woody plant in the family Oxalidaceae native to the Philippines, Indonesia, Malaysia, Vietnam, India, Bangladesh and Sri Lanka; but, cultivated in many parts of the world. Star-fruits are popular tropical fruits and used commonly in Ayurvedic and Traditional Chinese Medicines (TCM) in India, China, and Brazil to relieve ailments such as chronic headache, fever, cough, gastro-enteritis, diarrhoea, ringworm infections, and skin inflammations...
2016: Bioinformation
Aakrati Agarwal, Yashwanti Mudgil, Saurabh Pandey, Dhirendra Fartyal, Malireddy K Reddy
Eukaryotic translation initiation factor 4A (eIF4A) is an indispensable component of the translation machinery and also play a role in developmental processes and stress alleviation in plants and animals. Different eIF4A isoforms are present in the cytosol of the cell, namely, eIF4A1, eIF4A2, and eIF4A3 and their expression is tightly regulated in cap-dependent translation. We revealed the structural model of PgeIF4A2 protein using the crystal structure of Homo sapiens eIF4A3 (PDB ID: 2J0S) as template by Modeller 9...
2016: Bioinformation
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