American Journal of Biotechnology and Bioinformatics


Research Article of American Journal of Biotechnology and Bioinformatics The intravarietal relationship among different accessions of Dolichos biflorus was checked based on protein profiling using SDS-PAGE Smita Srivastava, Prem Kumar Dantu Plant Biotechnology Laboratory, Department of Botany, Dayalbagh Educational Institute (Deemed University) Dayalbagh, Agra, India In this study, the phylogenetic relationship within the selected Eleven Indian (Dolichos biflorus (horse gram) varieties was analyzed for total soluble seed protein. Twenty-five bands were documented through SDS PAGE based on 100 seed weight of each variety and were studied for genetic diversity. Jaccard’s similarity matrix was acquired and used in UPGMA cluster analysis based on the polymorphism generated by the presence (1) or absence (0) of protein bands. Thus, the dendrogram showed four major groups that corre-spond to an earlier study on polymorphisms of 11 accessions of Indian Dolichos. Signifi-cant correspondence between the clustering pattern and the pedigree was observed; thus, a high genetic diversity could be kept within the Dolichos varieties. A similarity matrix among the targeted genotypes and phylogenetic analysis is considered a unique feature in the present work. Therefore, the current investigation was carried out to analyse Protein diversity of unexplored  Dolichos   genotypes at the molecular level, construct a dendro-gram based on similarity band matrix and generate efficiency in genetic divergence analy-sis among  Dolichos. This study underlines the importance of using genetic diversity based in the Dolichos breeding program. Keywords: Cluster analysis; Dolichos biflorus; Dendrogram; Seed proteins; SDS-PAGE; ...


Research Article of American Journal of Biotechnology and Bioinformatics ANTIMICROBIAL RESISTANCE AND FORMATION OF BIOFILM IN CLINICS ISOLATES CAUSERS OF INFECTIONS RELATED TO HEALTH CARE Francisco Henrique da Silva, Sivoneide Maria da Silva, Bárbara de Azevedo Ramos, Maria Betânia Melo de Oliveira, Maria Tereza dos Santos Correia, Márcia Vanusa da Silva Biochemistry Department, Federal University of Pernambuco, Recife, Pernambuco, Brazil Healthcare-related infections (HAI) represent a great risk to their victims and are an increasing cost to the clinical and therapeutic setting. The fast increase in microbial resistance to antibiotics in the hospital environment decreases drug effectiveness, increases length of stay, and increases the cost of treatment. Besides that, it may result in premature death as a direct consequence of unsafe health practices, according to the World Health Organization. In this context, the present study aimed to evaluate microbial resistance and biofilm formation in isolates of clinical interest. The methodology used was based on the analysis and identification of clinical isolates of Enterococcus faecalis, Enterococcus faecium, Proteus mirabilis and Providencia stuartii, performed by the Vitek® 2 Compact automated system (bioMérieux) and confirmed by obtaining mass spectrum in MALDI-TOF apparatus. Autoflex III Mass Spectrometer which were compared with MALDI Biotyper version 3.1 database. Microbial resistance was evaluated by Minimum Inhibitory Concentration (MIC) and biofilm formation of these isolates by violet crystal method, Congo Red Agar and optical microscopy. As results, it was observed that all isolates tested were compatible with identification by MALDI-TOF. In addition, of all isolates tested, 83.3% had higher resistance to the antibiotic Ampicillin (AMP) and 58.3% showed resistance to Ciprofloxacin (CIP), ranging from Resistant Multidrug (MDR) to Extensively Drug Resistant (XDR), by various other antibiotics. All microorganisms presented biofilm formation ranging from moderate to strong, in which the strong ones represented 66.6% of isolates. It was observed that ...

Molecular Docking and Pharmacophore-Based Virtual Screening of Novel Inhibitors for HCV NS5B RNA-Dependent RNA Polymerase Enzyme from Crude Sesame Essential Oil.

Research Article of American Journal of Biotechnology and Bioinformatics Molecular Docking and Pharmacophore-Based Virtual Screening of Novel Inhibitors for HCV NS5B RNA-Dependent RNA Polymerase Enzyme from Crude Sesame Essential Oil. Lukeman A.J Shittu 1, 2*, Abiodun M. Jinadu 2, Remilekun K. Shittu 3, Solomon A. Shittu2. 1.Department of Anatomical Sciences, University of Abuja, Gwagwalada, Abuja, Nigeria. 2.Research and Development Department, Jireh Laboratories International LLC, P. O. Box 1813, Alief Texas, 77411, USA. 3.Department of Microbiology, Jireh International Laboratory, P. O. Box 882, Gwagwalada, Abuja, Nigeria. Concern has been expressed worldwide about the rising prevalence of HCV induced acute hepatitis and chronic liver diseases with associated cirrhosis and liver cancers. However, the available synthetic drugs are ineffective for all the HCV genotypes especially in genotype-1 patients with about 40% viral response rates and numerous side effects. Besides, the availability of veritable bioinformatics tools which includes molecular docking and virtual screening studies have shown that computational generated models nowadays assists in modern drug design and development of novel and more potent inhibitors through the understanding of protein (receptors) -ligand (drugs) interaction mechanisms. Non-structural proteins especially the 5B (NS5B) is an RNA-dependent RNA polymerase implicated in the synthesis and replication of the HCV RNA; and has been a potential target for its inhibitory activities. Due to the paucity of knowledge, we aimed to determine the differential inhibitory activity of essential oils present in the crude Sesame leaves extracts on HCV-NS5B RNA dependent RNA polymerase. Using in-silico studies- a Microsoft pharmacophore-based virtual screening and molecular docking tools on the iGEMDOCK vs 2.0 software was used to dock the essential oil ligands on the generated HCV NS5B (PDB ID: 4EO6) RNA-dependent RNA polymerase protein. GC-MS of the leaves confirmed carboxylic acids and phenolic groups in the essential oils especially some potent antioxidants like alpha-linolenic acid, ...

Comparison of Sequence with Cluster based analysis for molecular properties and composition of Glutathione Peroxidase family proteins

Research Article of American Journal of Biotechnology and Bioinformatics Comparison of Sequence with Cluster based analysis for molecular properties and composition of Glutathione Peroxidase family proteins Shailesh Kumar1*, Sumit Govil2, Vikram Kumar1 ICMR-National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research, P 33 CIT Road, Scheme XM< Beliaghata, Kolkata 700010, West Bengal, India Glutathione peroxidase (GPx) is very important protein helps in eradication of exogenous materials from the body of human reported to do the same work in other organisms. The selenocysteine amino acid contributes to the structure of this protein. Here a comparative study on sequence based methods and property based methods is carried out on all curated sequences of Glutathione Peroxidase for Human. Swiss Prot database was explored and only 65 protein of GPx family was obtained out of which 18 curated sequences were used for further analysis. Sequence based Distance method of Multiple Sequence Analysis is used for finding similar groups. Then all 18 sequences were studied for number of cleavage sites analysis followed by hierarchical clustering which represents cleavage sites based similar groups. Further, these sequences were computed to find amino acid composition and various properties like theoretical PI, Instability Index, Alipahtic Index and Hydropathy, followed by Hierarchical clustering. The interesting fact obtained in this study is that on comparison with the cleavage sites based clustering and amino acid composition with properties based clustering is having similar type of groups. These similar groups are having no relation sequence based methods groups. Hence, we conclude that for finding functional similarity between various sequences clustering of property based methods are more reliable as compared to sequence based methods phylogenetic methods. Keywords: Glutathione Peroxidase; computational analysis; hierarchical clustering; curated; hydropathy ...

Dr. Yousif Mohamed Y. Abdallah
Professor (Assistant), Radiological Science and Medical Imaging Department, College of Applied Medical Sciences, Majmaah University, Majmaah, Saudi Arabia

Dr. Indrasena R Kummetha
University of California San Diego (UCSD), Department of Pediatrics, 9500 Gilman Drive, MC 0762, BRF-11, Room NO:2220, San Diego, California, 92093, USA

Dr. Ayman EL Sabagh
Assistant professor, agronomy department, faculty of agriculture, kafresheikh university, Egypt; visiting scientist at Field Crops Department ,Faculty of Agriculture , Cukurova University, Turkey

Dr. Moustafa M. Zeitoun
Professor, Department of Animal Production, Faculty of Agriculture, University of Alexandria, El-Shatby, Alexandria, Egypt; Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University

Dr. Zhiqiang Hou
Senior Research Associate, Center for Alzheimer’s and Neurodegenerative Diseases, UT Southwestern Medical Center, Dallas, TX 75390

Dr. Suban K Sahoo
Assistant Professor, Department of Applied Chemistry, S.V. National Institute of Technology (SVNIT) Ichchanath, Surat, Gujrat-395 007, INDIA

Dr. Elsayed Ibrahim Elagamy
Professor of Immunology, Department of Applied Medical Sciences, College of Community (Unaizah), Qassim University, Kingdom of Saudi Arabia.

Dr. Mustafa SEVINDIK
Institute of Science and Technology, Akdeniz University

Dr. Celal Bal
Gaziantep University Oguzeli Vocaitonal School and Higher Education

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1.Lukeman A.J Shittu, Abiodun M Jinadu, Remilekun K. Shittu, Solomon A. Molecular Docking and Pharmacophore-Based Virtual Screening of Novel Inhibitors for HCV NS5B RNA-Dependent RNA Polymerase Enzyme from Crude Sesame Essential Oil. American Journal of Biotechnology and Bioinformatics, 2018; 2:7. DOI: 10.28933/ajobb-2018-04-1601 
2.Sumallya Karmakar et al.,. Surveillance of enteric parasites in an infectious diseases hospital, Kolkata, India. American Journal of Biotechnology and Bioinformatics, 2017; 1:5 . DOI: 10.28933/ajobb-2017-09-2805 

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American Journal of Biotechnology and Bioinformatics