Volume 16, number 2
Editorial
New books
Forthcoming Events
Еuropean Medical Physics and Engineering Conference 2012
Bioinformatics
In silico Structural Prediction of E6 and E7 Proteins of Human Papillomavirus Strains by Comparative Modeling101-110
Satish Kumar, Lingaraja Jena, Vidya W. Bhomale, Sangeeta Daf
[ +/- abstract ][ full text ]
More than 200 different types of Human papillomavirus (HPV) are identified, 40 transmit extensively through sexual contacts affecting the genital tract. HPV strains have been etiologically linked to vaginal, vulvar, penile, anal, oral and cervical cancer (99.7%) as a result of mutations leading to cell transformations due to interference of E6 and E7 oncoproteins with p53 and pRB tumor suppressor genes respectively, besides other cellular proteins. As structures of E6 and E7 proteins are not available, the simultaneous structural analysis of E6 and E7 proteins of 50 different HPV strains was carried out in detail for prediction and validation, using bioinformatics tools. E6 and E7 proteins sequences were retrieved in FASTA format from NCBI and their structures predicted by comparative modeling using modeller9v6 software. Further, most of the HPV strains showed good stereochemistry results in most favored regions when subjected to PROCHECK analysis and subsequently each protein was validated using ProSA-web tool. The work carried out on comparing and exploring the structural variations in these oncogenic proteins might help in genome based drugs and vaccines designing, beyond their limitations.
In silico Sequence Analysis, Homology Modeling and Function Annotation of Ocimum basilicum Hypothetical Protein G1CT28_OCIBA111-118
Sobia Idrees, Shahid Nadeem, Samia Kanwal, Beenish Ehsan, Ayesha Yousaf, Sameera Nadeem, Muhammad Ibrahim Rajoka
[ +/- abstract ][ full text ]
Ocimum basilicum is commonly known as sweet basil and belongs to the Lamiaceae Family. Ocimum basilicum has great therapeutic benefits and can be used for lowering blood pressure, as an antispasmodic as well as cleansing the blood. In the present study, subcellular localization prediction suggested that it is a cytoplasmic protein. We predicted the 3D structure of protein using homology modeling as 3D structure prediction approach. 3D structure of the protein was determined using Protein Structure Prediction Server (PS)2 selecting MODELLER as 3D structure prediction method. Quality analysis of the model indicated that it is a reliable model. Furthermore, it was discovered that Ocimum basilicum hypothetical protein G1CT28_OCIBA is involved in two biological processes, oxidation reduction and metabolic process and the biochemical function of the protein is acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, catalytic activity and oxidoreductase.
Molecular Characterization of Wheat Genotypes Using SSR Markers119-128
Sheikh Arslan Sehgal, Rana Adnan Tahir, Muhammad Nawaz
[ +/- abstract ][ full text ]
Wheat (Triticum aestivum L.) rusts are the most destructive and widespread among all other diseases of wheat because of their wide distribution, and their capacity to form new races that can attack previously resistant cultivars which result in serious yield losses. The molecular characterization and genetic diversity of 20 wheat genotypes was investigated using 34 polymorphic Simple Sequence Repeats (SSR) screened primers. About thirty-one loci were found. Lr-19 gene was present in all 20 wheat genotypes that cause resistance against wheat rust. Shalimar-86 and Chakwal-86 showed the highest genetic diversity with SH-02 and Ufaq respectively, giving a 98.94% genetic similarity and a minimum genetic diversity was observed between Chakwal-50 and Bhakar which showed that they are 74% similar. The current research found that SSR makers could distinguish and characterize all of the genotypes, more screened primers could be used for study and for saturation of different regions in further research. The identification of rust resistant genes in Pakistani wheat germplasm will help in accelerating the breeding program in future, including pyramiding of different wheat resistant genes in wheat genotypes and varieties.
GasCan: A Novel Database for Gastric Cancer Genes and Primers129-134
Sobia Idrees, Shahid Nadeem, Beenish Ehsan, Muhammad Ibrahim Rajoka
[ +/- abstract ][ full text ]
GasCan is a specialized and unique database of gastric cancer protein encoding genes expressed in human and mouse. The features that make GasCan unique are the availability of gene information, availability of primers for each gene, and built in programmed sequence analysis facility that analyze gene sequences in database itself. Furthermore, DNA sequence analysis tool is provided that can be access freely. GasCan will expand in future to other species, genes and cover more useful information of other species. Flexible database design, expandability and easy access of information to all of the users are the main features of the database. The database is publicly available at http://www.gastric-cancer.site40.net.
Biomedical systems
Techniques to Assess Stationarity and Gaussianity of EEG: An Overview135-142
Fahrettin F. Gonen, Gleb V. Tcheslavski
[ +/- abstract ][ full text ]
Often, while analyzing naturally generated signals (such as speech, seismogram, electroencephalogram, etc.), questions of stationarity and Gaussianity (normality) arise. This paper presents a brief literature overview focused on different methods proposed for assessing stationarity and Gaussianity of electroencephalogram (EEG). Summaries of several methods are discussed.

Sponsored by National Science Fund of Bulgaria, Grant No DNP 03/32

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