• Genomics & Informatics
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• 제3권2호
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• pp.61-65
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• 2005

Comparing 231 genes on chimpanzee chromosome 22 with their orthologous on human chromosome 21, we have found that 15 orthologs have indels within their coding sequences. It was rather surprising that significant number of genes have changed by indel, despite the shorter time since their divergence and led us hypothesize that indels and structural changes may represent one of the major mechanism of proteome evolution in the higher primates. Human T-complex protein 10 like (TCP 10L) is a representative having indel within its coding sequence. Gene structure of human TCP10L compared with chimpanzee TCP10L gene showed 16 base pair difference in genomic DNA. As a result of the indel, frame shift mutation occurs in coding sequence (CDS) and human TCP10L express longer polypeptide of 21 amino acid residues than that of chimpanzee. Our prediction found that the indel may affect to dramatic change of secondary protein structure between human and chimpanzee TCP10L. Especially, the structural changes in the C-terminal region of TCP10L protein may affect on the interacting potential to other proteins rather than DNA binding function of the protein. Through these changes, TCP10L might influence gene expression profiles in liver and testis and subsequently influence the physiological changes required in primate evolution.

• BMB Reports
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• 제43권2호
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• pp.79-90
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• 2010

Mouse models are crucial for the functional annotation of human genome. Gene modification techniques including gene targeting and gene trap in mouse have provided powerful tools in the form of genetically engineered mice (GEM) for understanding the molecular pathogenesis of human diseases. Several international consortium and programs are under way to deliver mutations in every gene in mouse genome. The information from studying these GEM can be shared through international collaboration. However, there are many limitations in utility because not all human genes are knocked out in mouse and they are not yet phenotypically characterized by standardized ways which is required for sharing and evaluating data from GEM. The recent improvement in mouse genetics has now moved the bottleneck in mouse functional genomics from the production of GEM to the systematic mouse phenotype analysis of GEM. Enhanced, reproducible and comprehensive mouse phenotype analysis has thus emerged as a prerequisite for effectively engaging the phenotyping bottleneck. In this review, current information on systematic mouse phenotype analysis and an issue-oriented perspective will be provided.

• Journal of Computing Science and Engineering
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• 제4권4호
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• pp.291-312
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• 2010

The last decades a large amount of research has been done in the genomics domain which has and is generating terabytes, if not exabytes, of information stored globally in a very fragmented way. Different databases use different ways of storing the same data, resulting in undesired redundancy and restrained information transfer. Adding to this, keeping the existing databases consistent and data integrity maintained is mainly left to human intervention which in turn is very costly, both in time and money as well as error prone. Identifying a fixed conceptual dictionary in the form of a conceptual model thus seems crucial. This paper presents an effort to integrate the mutational data from the established genomic data source HGMD into a conceptual model driven database HGDB, thereby providing useful lessons to improve the already existing conceptual model of the human genome.

• 대한의생명과학회지
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• 제4권2호
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• pp.129-135
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• 1998

Cytochrome P45O 2El (CYP2El)의 retropseudogene이 사람에 존재하는지 확인하기 위해 혈액에서 분리한 DNA를 주형으로 한 polymerase chain reaction (PCR)을 수행하였다. Primer는 CYP2E1 유전자를 기초하여 여러개 제작하되 적절한 조합에 따라 정상유전자와 retropseudogene이 동시에 증폭될 수 있도록 고안하였다. 본 실험의 결과 그동안 예상은 되었지만 DNA차원에서 미처확인되지 못하였던 CYP2E1의 retropseudogene을 직접 증폭해낼 수 있었다. 세부 구조는 Southern blotting과 DNA 염기서열 결정에서 최종 분석되었다. PCR 반응으로 증폭된 부분에서는 염기서열이 mRNA와 완전히 일치하고 있는 점으로 미루어서 CYP2E1의 retropseudogene은 비교적 최근에 발생했을 것으로 추정되었다.

• Genomics & Informatics
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• 제9권4호
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• pp.152-160
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• 2011

Hypertension is the major factor of most death and high blood pressure (BP) can lead to stroke, myocardial infarction and cardiac failure. Moreover, hypertension is strongly correlated with body mass index (BMI). Although the exact causes of hypertension are still unclear, some of genetic loci were discovered from genome-wide association study (GWAS). Therefore, it is essential to study genetic variation for finding more genetic factor affecting hypertension. The purpose of our study is to conduct a CNV association study for hypertension-related traits, BP and BMI, in Korean individuals. We identified 2,206 CNV regions from 3,274 community-based Korean participants using the Affymetrix Genome-Wide Human SNP Array 6.0 platform and performed a logistic regression analysis of CNVs with two hypertension-related traits, BP and BMI. Moreover, the 4,692 participants in an independent cohort were selected for respective replication analyses. GWAS of CNV identified two loci encompassing previously known hypertension-related genes: LPA (lipoprotein) on 6q26, and JAK2 (Janus kinase 2) on 9p24, with suggestive p-values (0.0334 for LPA and 0.0305 for JAK2 ). These two positive findings, however, were not evaluated in the replication stage. Our result confirmed the conclusion of CNV study from the WTCCC suggesting weak association with common diseases. This is the first study of CNV association study with BP and BMI in Korean population and it provides a state of CNV association study with common human diseases using SNP array.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2004년도 춘계학술발표대회
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• pp.173-175
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• 2004

단백질체(Proteome)이란 말은 어원적으로 단백질(protein)에 전체란 뜻을 가진 어미(-body, -some)가 연결된 합성어로 주어진 순간에 세포나 조직이 발현하는 모든 단백질의 총체를 의미하고 이를 연구하는 학문은 Proteomics라 일컫는다. 2001년 2월 International Human Genome Project에 의해 human genome sequence가 밝혀짐으로써 유전체 연구는 일단락 완성되었지만, 염기서열만 가지고는 이 유전자 산물의 기능을 알 수 없었고, 이것이 전사되고 최종적으로 완벽한 모양이 갖추어진 단백질을 분석해야만 그 기능을 알 수 있었다. (중략)

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2-1
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• pp.97-99
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• 2003

With advances in determining the entire DNA sequence of the human genome, it is now critical to systematically identify the function of a number of genes in the human genome. These biological problems, especially those in human diseases including cancer, should be addressed in human cells in which genetic approaches have been extremely difficult to implement. To overcome this, my efforts have focused on the development of a novel “chemical genetic/genomic approach” that uses small molecules to “probe and identify” the function of genes in specific biological process or pathway in human cells. (omitted)

• Interdisciplinary Bio Central
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• 제4권4호
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• pp.11.1-11.8
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• 2012

Genes that are indispensable for survival are referred to as essential gene. Due to the momentous significance of these genes for cellular activity they can be selected potentially as drug targets. Here in this study, an essential gene for Streptococcus suis was predicted using coherent statistical analysis and powerful genome comparison computational method. At first the whole genome protein scatter plot was generated and subsequently, on the basis of statistical significance, a reference genome was chosen. The parameters set forth for selecting the reference genome was that the genome of the query (Streptococcus suis) and subject must fall in the same genus and yet they must vary to a good degree. Streptococcus pneumoniae was found to be suitable as the reference genome. A whole genome comparison was performed for the reference (Streptococcus pneumoniae) and the query genome (Streptococcus suis) and 14 conserved proteins from them were subjected to a screen for potential essential gene property. Among those 14 only one essential gene was found to be with impressive similarity score between reference and query. The essential gene encodes for a type of 'Clp protease'. Clp proteases play major roles in degrading misfolded proteins. Results found here should help formulating a drug against Strptococcus suis which is responsible for mild to severe clinical conditions in human. However, like many other computational studies, the study has to be validated furthermore through in vitro assays for concrete proof.

• Asian Pacific Journal of Cancer Prevention
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• 제13권2호
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• pp.599-606
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• 2012

The characterization of the whole genome of human papillomavirus type 16 (HPV16) from cervical cancer specimens with multiple infections in comparison with single infection samples as the oncogenic potential of the virus may differ. Cervical carcinoma specimens positive for HPV16 by PCR and INNO-LiPA were randomly selected for whole genome characterization. Two HPV16 single infection and six HPV16 multiple infection specimens were subjected to whole genome analysis by using conserved primers and subsequent sequencing. All HPV16 whole genomes from single infection samples clustered in the European (E) lineage while all multiple infection specimens belonged to the non-European lineage. The variations in nucleotide sequences in E6, E7, E2, L1 and Long control region (LCR) were evaluated. In the E6 region, amino acid changes at L83V were related to increased cancer progression. An amino acid variation N29S within the E7 oncoprotein significantly associated with severity of lesion was also discovered. In all three domains of the E2 gene non synonymous mutations were found. The L1 region showed various mutations which may be related to conformation changes of viral epitopes. Some transcription factor binding sites in the LCR region correlated to virulence were shown on GRE/1, TEF-1, YY14 and Oct-1. HPV16 European variant prone to single infection may harbor a major variation at L83V which significantly increases the risk for developing cervical carcinoma. HPV16 non-European variants prone to multiple infections may require many polymorphisms to enhance the risk of cervical cancer development.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2006년도 The 15th Korean Genome Organization Conference KOGO 2006 Annual Meeting
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• pp.51-51
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• 2006