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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Korea Genome Organization
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Volume 8, Issue 4 - Dec 2010
Volume 8, Issue 3 - Sep 2010
Volume 8, Issue 2 - Jun 2010
Volume 8, Issue 1 - Mar 2010
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A Comparative Analysis of Monofunctional Biosynthetic Peptidoglycan Transglycosylase (MBPT) from Pathogenic and Non-pathogenic Bacteria
Baker, Andrew T. ; Takahashi, Natsumi ; Chandra, Sathees B. ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 63~69
DOI : 10.5808/GI.2010.8.2.063
Monofunctional biosynthetic peptidoglycan transglycosylase (MBPT) catalyzes the formation of the glycan chain in bacterial cell walls from peptidoglycan subunits: N-acetylglucosamine (NAG) and acetylmuramic acid (NAM). Bifunctional glycosyltransferases such as the penicillin binding protein (PBP) have peptidoglycan glycosyltransferase (PGT) on their C terminal end which links together the peptidoglycan subunits while transpeptidase (TP) on the N terminal end cross-links the peptide moieties on the NAM monosaccharide of the peptide subunits to create the bacterial cell wall. The singular function of MBPT resembles the C terminal end of PBP as it too contains and utilizes a similar PGT domain. In this article we analyzed the infectious and non infectious protein sequences of MBPT from 31 different strains of bacteria using a variety of bioinformatic tools. Motif analysis, dot-plot comparison, and phylogenetic analysis identified a number of significant differences between infectious and non-infectious protein sequences. In this paper we have made an attempt to explain, analyze and discuss these differences from an evolutionary perspective. The results of our sequence analysis may open the door for utilizing MBPT as a new target to fight a variety of infectious bacteria.
In Silico Study of Human Gap Junction Beta-2 Protein by Homology Modeling
Shehzadi, Abida ; Masood, Khalid ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 70~75
DOI : 10.5808/GI.2010.8.2.070
Asp66his, Asp54Lys, and Asp50Asn are mutations in connexin 26 that are observed in the clinic and give rise to autosomal dominant syndromes. They are the result of point mutations in the human gap junction
gene. In order to investigate the structural mechanism of Bart-Pumphrey Syndrome, Keratitis-Ichthyosis-Deafness Syndrome, and Vohwinkel Syndrome, homology modeling was carried out. Asp66 has direct contact with Asn62 by two hydrogen bonds in the wild-type protein, and in Asp66His, the biggest change observed is a tremendous energy increase caused by hydrogen bond breakage to Asn62. Shifts in the side chain and new hydrogen bond formation are observed for Lys54 compared to the wild-type protein (Asn54) and result in closer contact to Val84. Asp50Asn causes a significant decrease in bond energy, and residual charge reversal repels the ion and metabolites and, hence, inhibits their transportation. Such perturbations are likely to be a factor contributing to abnormal functioning of ion channels, resulting cell death and disease.
No Association between Copy Number Variation of the TCRB Gene and the Risk of Autism Spectrum Disorder in the Korean Population
Yang, So-Young ; Yim, Seon-Hee ; Hu, Hae-Jin ; Kim, Soon-Ae ; Yoo, Hee-Jeong ; Chung, Yeun-Jun ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 76~80
DOI : 10.5808/GI.2010.8.2.076
Although autism spectrum disorder (ASD) has been thought to have a substantial genetic background, major contributing genes have yet to be identified or successfully replicated. Immunological dysfunction has been suggested to be associated with ASD, and T cell-mediated immunity was considered important for the development of ASD. In this study, we analyzed 163 ASD subjects and 97 normal controls by genomic quantitative PCR to evaluate the association between the copy number variation of the 7q34 locus, harboring the TCRB gene, and ASDs. As a result, there was no significant difference of the frequency distribution of TCRB copy numbers between ASD cases and normal controls. TCRB gene copy numbers ranged from 0 to 5 copies, and the frequency distribution of each copy number was similar between the two groups. The proportion of the individuals with <2 copies of TCRB was 52.8% (86/163) in ASD cases and 57.1% (52/91) in the control group (p=0.44). The proportion of individuals with >2 copies of TCRB was 11.7% (19/163) in ASD cases and 12.1% (11/91) in the control group (p=0.68). After the effects of sex were adjusted by logistic regression, ORs for individuals with <2 copies or >2 copies showed no significant difference compared with the diploid copy number as reference (n=2). Although we could not see the positive association, our results will be valuable information for mining ASD-associated genes and for exploring the role of T cell immunity further in the pathogenesis of ASD.
Development of Optimal Breeding Pigs Using DNA Marker Information
Kim, Sang-Wook ; Roh, Jung-Gun ; Cho, Yang-Il ; Choi, Bong-Hwan ; Kim, Tae-Hun ; Kim, Jong-Joo ; Kim, Kwan-Suk ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 81~85
DOI : 10.5808/GI.2010.8.2.081
The aim of the study was to investigate pig reference families, generated from Korean native pigs (KNP) that were crossed with Yorkshire (YS) breeds, which were used to evaluate genetic markers to select breeding animals with superior pork quality. A set of five candidate genes (PRKAG3, MC4R, CAST, ESR, and PRLR ) was analyzed for association with pork quality traits. PRKAG3 (I199V) SNP genotypes were significantly associated with muscle moisture, protein, and fat contents. The MC4R D298N polymorphism was significantly associated with meat tenderness and color traits. The CAST polymorphism was significantly associated with muscle moisture and crude protein traits. These three genes have been associated with pork quality traits in other pig populations, and some of our results are consistent with earlier studies. In addition, two reproductive candidate genes (ESR and PRLR ) did not have significant associations. These results suggest that further study is warranted to investigate and develop more DNA markers associated with pork quality in our KNP-crossed pig families.
Non-Synteny Regions in the Human Genome
Lee, Ki-Chan ; Kim, Sang-Soo ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 86~89
DOI : 10.5808/GI.2010.8.2.086
Closely related species share large genomic segments called syntenic regions, where the genomic elements such as genes are arranged co-linearly among the species. While synteny is an important criteria in establishing orthologous regions between species, non-syntenic regions may display species-specific features. As the first step in cataloging human- or primate- specific genomic elements, we surveyed human genomic regions that are not syntenic with any other non-primate mammalian genomes sequenced so far. Based on the data compiled in Ensembl databases, we were able to identify 10 such regions located in eight different human chromosomes. Interestingly, most of these highly human- or primate- specific loci are concentrated in subtelomeric or pericentromeric regions. It has been reported that subtelomeric regions in human chromosomes are highly plastic and filled with recently shuffled genomic elements. Pericentromeric regions also show a great deal of segmental duplications. Such genomic rearrangements may have caused these large human- or primate- specific genome segments.
AKAPDB: A-Kinase Anchoring Proteins Database
Kim, In-Sil ; Lim, Kyung-Joon ; Han, Bok-Ghee ; Chung, Myung-Guen ; Kim, Kyu-Won ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 90~93
DOI : 10.5808/GI.2010.8.2.090
A-kinase-anchoring proteins (AKAPs) are scaffold proteins which compartmentalize protein kinase A (PKA, cAMP-dependent protein kinase) and other enzymes to specific subcellular sites. The spatiotemporal control of these enzymes by AKAPs is important for cellular function like cell growth and development etc. Hence, it is important to understand the basic function of AKAPs and their functional domains. However, diverse names, function, cellular localizations and many members of AKAPs increase difficulties when researchers search appropriate AKAPs for their experimental purpose. Nevertheless, there was no previous AKAPs-related database regardless of their important cellular functions and difficulty of finding appropriate AKAPs. So, we developed AKAPs database (AKAPDB), which contains their sequence information, functions and other information derived from prediction programs and other databases. Therefore, we propose that AKAPDB can be an important tool to researchers in the related fields. AKAPDB is available via the internet at http://plaza3.snu.ac.kr/akapdb/.
Java DOM Parsers to Convert KGML into SBML and BioPAX Common Exchange Formats
Lee, Kyung-Eun ; Jang, Myung-Ha ; Rhie, A-Rang ; Thong, Chin Ting ; Yang, San-Duk ; Park, Hyun-Seok ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 94~96
DOI : 10.5808/GI.2010.8.2.094
Integrating various pathway data collections to create new biological knowledge is a challenge, for which novel computational tools play a key role. For this purpose, we developed the Java-based conversion modules KGML2SBML and KGML2BioPAX to translate KGML (KEGG Markup Language) into a couple of common data exchange formats: SBML (Systems Biology Markup Language) and BioPAX (Biological Pathway Exchange). We hope that our work will be beneficial for other Java developers when they extend their bioinformatics system into SBML- or BioPAX-aware analysis tools. This is part of our ongoing effort to develop an ultimate KEGG-based pathway enrichment analysis system.
A Simple GUI-based Sequencing Format Conversion Tool for the Three NGS Platforms
Rhie, A-Rang ; Yang, San-Duk ; Lee, Kyung-Eun ; Thong, Chin Ting ; Park, Hyun-Seok ;
Genomics & Informatics, volume 8, issue 2, 2010, Pages 97~99
DOI : 10.5808/GI.2010.8.2.097
To allow for a quick conversion of the proprietary sequence data from various sequencing platforms, sequence format conversion toolkits are required that can be easily integrated into workflow systems. In this respect, a format conversion tool, as well as quality conversion tool would be the minimum requirements to integrate reads from different platforms. We have developed the Pyrus NGS Sequencing Format Converter, a simple software toolkit which allows to convert three kinds of Next Generation Sequencing reads, into commonly used fasta or fastq formats. The converter modules are all implemented, uniformly, in Java GUI modules that can be integrated in software applications for displaying the data content in the same format.