• Genomics & Informatics
• /
• 제16권3호
• /
• pp.75-77
• /
• 2018

Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization. Text corpus for this journal annotated with various levels of linguistic information would be a valuable resource as the process of information extraction requires syntactic, semantic, and higher levels of natural language processing. In this study, we publish our new corpus called GNI Corpus version 1.0, extracted and annotated from full texts of Genomics & Informatics, with NLTK (Natural Language ToolKit)-based text mining script. The preliminary version of the corpus could be used as a training and testing set of a system that serves a variety of functions for future biomedical text mining.

• Genomics & Informatics
• /
• 제6권3호
• /
• pp.99-109
• /
• 2008

Protein phosphorylation at tyrosine residues is a key regulatory event that modulates insulin signal transduction. We studied the PTPN1 gene with regard to susceptibility to Korean type 2 diabetes mellitus (T2DM) and its related quantitative traits. A total of seven SNPs [g.36171G>A (rs941798), g.58166G>A (rs3787343), g.58208A>G (rs2909270), g.64840C>T (rs754118), g.69560C>G (rs6020612), g.69866G>A (rs718050), and g.69934T>G (rs3787343)] were selected based on frequency (>0.05), linkage disequilibrium (LD) status, and haplotype tagging status. We studied the seven SNPs in 483 unrelated patients with type 2 diabetes (age: $64{\pm}2.8$ years, onset age: $56{\pm}8.1$ years; 206 men, 277 women) and 1138 nondiabetic control subjects (age: $64{\pm}2.9$; 516 men, 622 women). The SNP rs941798 had protective effects against T2DM with an odds ratio of 0.726 (C.I. $0.541{\sim}0.975$) and p-value=0.034, but none of the remaining six SNPs was associated with T2DM. Also, rs941798 was associated with blood pressure, HDL cholesterol, insulin sensitivity. rs941798 also has been associated with T2DM in previous reports of Caucasian-American and Hispanic-American populations. This is the first report that shows an association between PTPN1 and T2DM in the Korean as well as Asian population.

• Journal of Microbiology and Biotechnology
• /
• 제26권2호
• /
• pp.263-269
• /
• 2016

Temperate phages have been suggested to carry virulence factors and other lysogenic conversion genes that play important roles in pathogenicity. In this study, phage TEM123 in wild-type Staphylococcus aureus from food sources was analyzed with respect to its morphology, genome sequence, and antibiotic resistance conversion ability. Phage TEM123 from a mitomycin C-induced lysate of S. aureus was isolated from foods. Morphological analysis under a transmission electron microscope revealed that it belonged to the family Siphoviridae. The genome of phage TEM123 consisted of a double-stranded DNA of 43,786 bp with a G+C content of 34.06%. A bioinformatics analysis of the phage genome identified 43 putative open reading frames (ORFs). ORF1 encoded a protein that was nearly identical to the metallo-β-lactamase enzymes that degrade β-lactam antibiotics. After transduction to S. aureus with phage TEM123, the metallo-β-lactamase gene was confirmed in the transductant by PCR and sequencing analyses. In a β-lactam antibiotic susceptibility test, the transductant was more highly resistant to β-lactam antibiotics than S. aureus S133. Phage TEM123 might play a role in the transfer of β-lactam antibiotic resistance determinants in S. aureus. Therefore, we suggest that the prophage of S. aureus with its exotoxin is a risk factor for food safety in the food chain through lateral gene transfer.

• Journal of Microbiology and Biotechnology
• /
• 제5권1호
• /
• pp.1-5
• /
• 1995

A genomic DNA of alkaliphilic bacterium, Micrococcus sp. Y-l, was analysed using the physical mapping method of pulsed-field gel electrophoresis (PFGE). Five restriction enzymes of Sspl, Hpal, Xbal, Ndel or EcoRI, which recognize the Adenine-Thymine-rich sequences of genomic DNA, were used for the generation of few (7 to 20) distinctly separate fragments, with average sizes in the range of 200～500 kb. However, the sites for Notl and SfiI, 8 base-recognizing enzymes, were highly frequent. The genome size of this strain was determined to be 4 mega base pairs (Mb) from restriction fragments separated by PFGE. This is the first case of restriction mapping in alkaliphilic bacterium.

• 한국유전체학회:학술대회논문집
• /
• 한국유전체학회 2002년도 The 11th Korea Genome Conference
• /
• pp.49.1-49.1
• /
• 2002

• ALGAE
• /
• 제31권2호
• /
• pp.137-154
• /
• 2016

Next generation sequencing (NGS) technologies have revolutionized many areas of biological research due to the sharp reduction in costs that has led to the generation of massive amounts of sequence information. Analysis of large genome data sets is however still a challenging task because it often requires significant computer resources and knowledge of bioinformatics. Here, we provide a guide for an uninitiated who wish to analyze high-throughput NGS data. We focus specifically on the analysis of organelle genome and metagenome data and describe the current bioinformatic pipelines suited for this purpose.

• 한국육종학회지
• /
• 제43권2호
• /
• pp.103-114
• /
• 2011

In recent years, genomic resources and information have accumulated at an ever increasing pace, in many plant species, through whole genome sequencing, large scale analysis of transcriptomes, DNA markers and functional studies of individual genes. Well-characterized species within key plant taxa, co-called "model systems", have played a pivotal role in nucleating the accumulation of genomic information and databases, thereby providing the basis for comparative genomic studies. In addition, recent advances to "Next Generation" sequencing technologies have propelled a new wave of genomics, enabling rapid, low cost analysis of numerous genomes, and the accumulation of genetic diversity data for large numbers of accessions within individual species. The resulting wealth of genomic information provides an opportunity to discern evolutionary processes that have impacted genome structure and the function of genes, using the tools of comparative analysis. Comparative genomics provides a platform to translate information from model species to crops, and to relate knowledge of genome function among crop species. Ultimately, the resulting knowledge will accelerate the development of more efficient breeding strategies through the identification of trait-associated orthologous genes and next generation functional gene-based markers.

• Journal of Microbiology and Biotechnology
• /
• 제19권11호
• /
• pp.1301-1305
• /
• 2009

The evolution of living organisms occurs via a combination of highly complicated processes that involve modification of various features such as appearance, metabolism and sensing systems. To understand the evolution of life, it is necessary to understand how each biological feature has been optimized in response to new environmental conditions and interrelated with other features through evolution. To accomplish this, we constructed contents-based trees for a two-component system (TCS) and metabolic network to determine how the environmental communication mechanism and the intracellular metabolism have evolved, respectively. We then conducted a comparative analysis of the two trees using ARACNE to evaluate the evolutionary and functional relationship between TCS and metabolism. The results showed that such integrated analysis can give new insight into the study of bacterial evolution.

• Journal of Plant Biotechnology
• /
• 제42권3호
• /
• pp.161-167
• /
• 2015

고구마는 척박한 환경에서도 생육이 가능한 세계 7대 농작물로 식량뿐만 아니라 사료용, 전분 등의 산업용으로도 중요하다. 최근 고구마는 항산화물질, 식이섬유질 등을 고함유하는 건강식품으로 각광을 받고 있다. 그러나 고구마 유전체 해독에 관한 연구는 고구마의 중요도에 비해 많이 이루어지지 않고 있다. 본 총설의 목적은 고구마 유전체 연구 동향분석을 통하여 유전체 해독 연구의 효율성 증대 및 유용형질 유전자의 실용화 연구를 위한 기반구축을 모색하는데 있다. 최근 NGS 분석을 통한 동식물 유전체해독이 급진적으로 많이 이루어지고 있다. 고구마 유전체 해독의 경우는 다배수성 문제와 이질유전체 문제로 유전체 완전해독 연구가 이루어지지 않고 있으며 반면 전사체 분석 연구는 활발히 이루어지고 있는 실정이다. 최근 2015년 일본 연구자들에 의해 2배체 고구마의 유전체 해독 초안이 보고되었다. 한중일 고구마 연구협의회(Trilateral Research Association of Sweetpotato, TRAS)에 의해 6배체 고구마 Xushu 18의 유전자지도 작성 및 유전체 해독 연구가 2014년부터 이루어지고 있다. 빌게이츠재단(Bill & Melinda Gates Foundation)은 사하라사막 남쪽 아프리카지역의 기근과 영양문제를 해결하기 위해 고구마 유전체 기반 분자육종을 위한 분자도구 개발에 관한 프로젝트를 미국을 중심으로 한 컨소시엄을 구성하여 출범하였다. 고구마 유전체 해독과정 중에 분석된 고구마 엽록체 유전체 분석을 통하여 진화학적 해석연구가 이루어지고 있다. 본 총설을 통하여 고구마 유전체 해독 연구동향을 살펴보았다. 이러한 연구 동향 분석은 고구마의 생산성 및 기능성 향상 등의 실용화 연구를 수행하는 연구자들에게 최근의 연구현황을 제공할 수 있을 것이며 세계적인 식량, 에너지, 환경문제의 해결에 크게 기여 할 것으로 생각된다.

• 한국생물공학회:학술대회논문집
• /
• 한국생물공학회 2003년도 생물공학의 동향(XIII)
• /
• pp.783-784
• /
• 2003