• 한국어류학회지
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• 제18권2호
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• pp.65-77
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• 2006

우리나라 주요 담수 어종인 미꾸라지(Misgurnus mizolepis)를 실험 모델로 이용하여 실험적으로 설정한 고온 노출($32^{\circ}C$)에 특이적으로 반응하는 유전자들을 cDNA microarray 분석을 통해 탐색하였다. 미꾸라지 간조직 expressed sequence tag (EST) 데이터베이스 분석을 통해 1,124개의 unigene들을 선발하여 제작한 cDNA microarray을 이용하여 $23^{\circ}C$ 및 $32^{\circ}C$에 4주간 노출된 실험어의 간(liver)조직의 전사 발현 양상을 3반복 분석하였다. 다양한 유전자군이 $32^{\circ}C$ 고온 노출에 전사 발현의 증감 또는 감소 양상을 보였으며 $23^{\circ}C$에 비해 $32^{\circ}C$군에서 2배 이상의 발현 증가를 보인 클론들은 총 93종류로서 에너지 대사, 단백질 대사, 면역/항산화 기능, 세포골격 및 구조, 물질수송 및 세포 신호전달등에 관여하는 단백질들을 암호화하는 유전자들이었고 최대 15배 이상의 전사발현이 관찰되었다. 반면 고온 노출군에서 유의적인 발현 감소(50% 이하)를 보인 유전자들(n=85) 역시 탐색되어 상기 단백질 분류군외에 vitellogenin 전구체들 및 리보좀 단백질류에서 특이적인 전사활성의 저하가 관찰되었고, vitellogenin 유전자에서 가장 많은 mRNA 수준의 감소가 관찰되었다.

• 생명과학회지
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• 제16권7호
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• pp.1188-1194
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• 2006

노년에 나타나는 정신병적 증상의 가장 흔한 원인 질환으로 만성적이고 서서히 악화되는 진행성이면, 기억력, 사고력, 학습능력 및 판단력 등의 손상을 포함한 인지기능의 장애이다. 고령화 사회가 도래하면서 노인성 치매환자가 매년 급격히 늘고 있으며 매년 수만 명이 노인성치매에 걸려 본인뿐 아니라 가족까지도 많은 고통에 시달리고 있다. 특히 노인성 치매의 경우는 환자 본인의 문제가 아니라 젊은 노동력을 환자의 보호자로 필요함으로 국가적 노동력의 손실로 이어지고 있다. 현재 연구에서 우리는 노인성 치매와 transposable elements와의 상호관계를 밝히기 위하여 공개된 유전자 데이터베이스에서 EST (expressed sequence tags)를 이용하여 생물정보학적 인 분석방법과 프로그램을 이용하여 치매의 원인으로 추정되는 후보유전자들을 찾아내었다. 이러한 분석을 통하여 치매환자에서 transposable elements의 발현으로 인해 유전자의 발현에 변화를 가지는 98개의 후보 유전자를 찾아내었다. 노인성질환인 치매와 transposable elements의 분석방법을 이용하면 치매의 원인을 규명하는데 많은 도움이 될 것이다.

• BMB Reports
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• 제34권6호
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• pp.559-565
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• 2001

Protein carboxyl O-methyltransferase (E.C.2.1.1.24) may play a role in the repair of aged protein that is spontaneously incorporated with isoaspartyl residues. The porcine brain carboxyl O-methyltransferase was cloned in the pET32 vector, and overexpressed in E.coh (BL21) that harbors pETPCMT, which encodes 227 amino acids, including tagging proteins at the N-terminus. The protein sequence of the cloned porcine brain PCMT (r-pbPCMT) shares a 98% identity with that of human erythrocyte PCMT and rat brain PCMT. It is 100% identical with that of bovine brain. The r-pbPCMT was purified using Ni-NTA affinity chromatography and digested by enterokinase in order to remove the protein tags. Then Superdex 75HR gel filtration chromatography was performed. The r-pbPCMT exhibited similar in vitro substrate specificities with the PCMT that was purified from porcine brain. The molecular weight of the enzyme was estimated to be 24.5 kDa on the SDS polyacrylamide gel electrophoresis. The $K_m$ value was $1.1{\times}10^{-7}\;M$ for S-adenosyl-L-methionine. S-adnosyl-L-homocysteine was a competitive type of inhibitor with the $K_i$ value of $1.38{\times}10^{-4}\;M$. The enzyme has optimal activity at pH 6.0 and $37^{\circ}C$. These results indicate that the expressed enzyme is functionally similar to the natural protein. It also suggests that it may be a suitable model to further understand the function of the mammalian enzyme.

• 한국발생생물학회지:발생과생식
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• 제19권4호
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• pp.227-234
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• 2015

The objective of this study was to investigate the expression of bovine luteum expressed sequence tags (ESTs), vascular endothelial growth factor (VEGF), and tumor necrosis factor receptor 1 (TNFR1) and the presence of functional ESTs in the bovine corpus luteum (CL) during different stages of the estrus cycle. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed a difference in the expression of ESTs during the CL stage. Concentration of ESTs in the CL tissue increased significantly from the mid-luteal stage and decreased thereafter. RT-PCR analysis showed higher levels of the EST genes in the CL of the mid-luteal stage than in other stages, and the same level of expression of VEGF. Immunohistochemistry analysis of the tissue from CL formation to regression showed low cytosol and aggregation of the nucleus. And activity caspase 3 (apoptosis detector) was most strongly detected in the CL1 stage of bovine. During the estrous cycle, the cytosol was magnified and differentiation of the nucleus was clearly manifested. The ESTs affected the CL, and the relationship between VEGF and TNFR1 played a pivotal role for CL development and activation, dependent on the stage of CL. These results suggest local production of ESTs, the presence of functional ESTs in the bovine CL, and that ESTs play a role in regulating the function of cell death in bovine CL.

• 한국자원식물학회지
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• 제19권1호
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• pp.174-179
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• 2006

본 연구에서는 인삼 잎으로부터 정제한 mRNA를 이용하여 cDNA library를 제작하였다. 이 cDNA library로 부터 349개의 에너지 대사 관련 유전자를 선발 하였다. 에너지 대사 관련 유전자의 평균 사이즈는 0.49 kb이며, 에너지 관련 유전자들의 세부 기능별 발현을 분석한 결과 aerobic respiration(48.4%), accessory proteins of electron transport and membrane associated energy conservation(17.2%), glycolysis and gluconeogenesis(3.4%), electron transport and membrane associated energy conservation(2.9%), respiration(2.0%), glycolysis methylglyoxal byp-ass(1.7%), metabolism of energy reserves(0.6%)와 alcohol fermentation(0.3%)의 분포를 보였다. 인삼 잎에서 발현되는 유전자중 가장 많이 발현된 Chlorophyll a/b binding protein of IhcII type I(36.6%), Photosystem II oxygen-evolving complex protein(6.6%) 등이 발현되었다.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2010년도 정기총회 및 추계학술발표회
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• pp.11-11
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• 2010

The Korean ginseng, Panax ginseng C. A. Meyer is a popular medicinal herb in Araliaceae. Genetic map in crops provides valuable information for breeding, genetic and genomic researches. However, little information is available for construction of genetic map in ginseng. Up to now, we have produced large amounts of expressed sequence tags (ESTs) from four ginseng cultivars (37Mb, 49Mb, 39Mb, 47Mb from Gopoong, Gumpoong, Chunpoong and Yunpoong respectively using pyrosequencing technique and 5Mb from normalized full-length cDNA library of Chunpoong) to obtain comprehensive information of gene expression, and constructed EST database including ESTs from public database. Till now, we designed 261 SSR primer sets using EST sequences and identified 106 intergenic polymorphic markers. And 44 of the 106 showed polymorphisms among panax ginseng cultivars. Among 44 markers, 27 SSR polymorphic markers were inspected to 51 $F_2$ population from Yunpoong x Chunpoong, which showed good at the fitness of Mendellian segregation ratio 1:2:1. To enrich the number of markers, and thus construct high resolution genetic map which can be used as frame map for further genome sequencing. we are planning to develop large scale EST-derived SNP markers which are available in the F2 population. This study provides genetic information as well as foundation for ginseng researches such as genetics, genomics, breeding, and the final goal for whole genome sequencing. This study was supported by Technology Development Program for Agriculture and Forestry, Ministry for Food, Agriculture, Forestry and Fisheries, Republic of Korea (Grant No. 609001-051SB210).

• 농업과학연구
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• 제45권4호
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• pp.583-590
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• 2018

Genus Typha L. (Typhaceae; Cattail in common) is one of the hydrophytic plants found in semi-aquatic regions. About nine to 18 species of the genus exist all over the world. In Korea, the most commonly found cattail species are T. laxmanni and T. angustifolia. The aim of this study was to prepare a cDNA library and sequences and analyze expressed sequence tags (ESTs) from these species, T. laxmanni and T. angustifolia. In the case of T. laxmanni, we observed that 715 out of 742 ESTs had high quality sequences, whereas the remaining 27 ESTs were low quality sequences. In this study, we identified 77 contigs, 393 unassembled clones and 65.7% singletons. Furthermore, in the case of T. angustifolia, we recorded 992 high quality EST sequences, and by excluding 28 low quality sequences from among them, we retrieved 120 contigs, 348 unassembled clones and 48.9% singletons. The basic local alignment search tool (BLAST) and Kyoto encyclopedia of genes and genomes (KEGG) database results enabled us to identify the functional categories, i.e., molecular function (16.5%), biological process (22.2%) and cellular components (61.3%). In addition, between these two species, the no hits and anonymous genes were 4.2% and 11.7% and 6.2% and 11.2% in T. laxmanni and T. angustifolia, respectively, based on the BLAST results. The study concluded that they have certain species-specific genes. Hence, the results of this study on these two species could be a valuable resource for further studies.

• 원예과학기술지
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• 제31권6호
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• pp.772-781
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• 2013

본 연구의 목적은 상추(Lactuca sativa)의 expressed sequence tag(EST)로부터 simple sequence repeat(SSR) 마커를 개발하고, 개발된 EST-SSR 마커를 이용하여 상추의 3가지 야생종의 유전자원 9점과 61개의 유통품종을 식별하는 것이다. NCBI 데이터베이스로부터 총 81,330개의 상추 EST를 대상으로 SSR을 탐색하였고, 총 4,229개의 SSR을 발견하였다. SSR의 반복 motif 중 trinucleotide(59.12%, 2,500개)가 가장 많았고, 그 다음으로 dinucleotide(29.70%, 1,256개), hexanucleotide(6.62%, 280개) 순의 분포를 나타내었다. EST로부터 총 474개의 EST-SSR primers를 개발하였고, 이 중 267개의 primer를 9점의 유전자원과 61품종에 대한 유전적 다양성 평가에 활용하였다. 267개의 마커 중 47개의 EST-SSR 마커가 7개 품종 내에서 다형성을 보였으며, 이 중 다형성 정도와 반복 재현성 및 밴드의 선명성을 고려하여 26개의 EST-SSR 마커를 선발하였다. 최종 선발된 26개의 SSR 마커를 이용하여 70개 공시재료를 분석한 결과 대립유전자 수는 총 127개였으며, 최소 2개에서 9개의 분포를 나타내었으며 마커당 평균 대립유전자 수는 4.88개를 나타내었다. PIC평균값은 0.542로 나타났으며, 0.269-0.768의 범위를 나타내었다. 70개 공시재료의 유전적 거리는 0.05-0.94로 나타났으며, 유사도 지수 0.34를 기준으로 할 때 7개의 주요 그룹으로 나누어졌다. 26개의 EST-SSR 마커를 이용한 유전적 다양성 분석 결과 9점의 유전자원과 61개의 유통품종이 마커의 유전자형에 의해 모두 식별이 되었다. 본 연구를 통해 신규 개발된 EST-SSR 마커는 상추의 품종식별과 구별성, 균일성, 안정성 검정에 유용하게 활용될 수 있을 것으로 사료된다.

• Molecules and Cells
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• 제28권6호
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• pp.529-536
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• 2009

Genome sequencing of the pig is being accelerated because of its importance as an evolutionary and biomedical model animal as well as a major livestock animal. However, information on expressed porcine genes is insufficient to allow annotation and use of the genomic information. A series of expressed sequence tags of 5' ends of five full-length enriched cDNA libraries (SUSFLECKs) were functionally characterized. SUSFLECKs were constructed from porcine abdominal fat, induced fat cells, loin muscle, liver, and pituitary gland, and were composed of non-normalized and normalized libraries. A total of 55,658 ESTs that were sequenced once from the 5′ ends of clones were produced and assembled into 17,684 unique sequences with 7,736 contigs and 9,948 singletons. In Gene Ontology analysis, two significant biological process leaf nodes were found: gluconeogenesis and translation elongation. In functional domain analysis based on the Pfam database, the beta transducin repeat domain of WD40 protein was the most frequently occurring domain. Twelve genes, including SLC25A6, EEF1G, EEF1A1, COX1, ACTA1, SLA, and ANXA2, were significantly more abundant in fat tissues than in loin muscle, liver, and pituitary gland in the SUSFLECKs. These characteristics of SUSFLECKs determined by EST analysis can provide important insight to discover the functional pathways in gene networks and to expand our understanding of energy metabolism in the pig.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.21-22
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• 2000

Expressed sequence tags (EFTs) are the partial segments of cDNA produced from 5 or 3 single-pass sequencing of cDNA clones, error-prone and generated in highly redundant sets. Advancement and expansion of Genomics made biologists to generate huge amount of ESTs from variety of organisms-human, microorganisms as well as plants, and the cumulated number of ESTs is over 5.3 million, As the EST data being accumulate more rapidly, it becomes bigger that the needs of the EST analysis tools for extraction of biological meaning from EST data. Among the several needs of EST analyses, the extraction of protein sequence or functional motifs from ESTs are important for the identification of their function in vivo. To accomplish that purpose the precise and accurate identification of the region where the coding sequences (CDSs) is a crucial problem to solve primarily, and it will be helpful to extract and detect of genuine CD5s and protein motifs from EST collections. Although several public tools are available for EST analysis, there is not any one to accomplish the object. Furthermore, they are not targeted to the plant ESTs but human or microorganism. Thus, to correspond the urgent needs of collaborators deals with plant ESTs and to establish the analysis system to be used as general-purpose public software we constructed the pipelined-EST analysis system by integration of public software components. The software we used are as follows - Phred/Cross-match for the quality control and vector screening, NCBI Blast for the similarity searching, ICATools for the EST clustering, Phrap for EST contig assembly, and BLOCKS/Prosite for protein motif searching. The sample data set used for the construction and verification of this system was 1,386 ESTs from human intrathymic T-cells that verified using UniGene and Nr database of NCBI. The approach for the extraction of CDSs from sample data set was carried out by comparison between sample data and protein sequences/motif database, determining matched protein sequences/motifs that agree with our defined parameters, and extracting the regions that shows similarities. In recent future, in addition to these components, it is supposed to be also integrated into our system and served that the software for the peptide mass spectrometry fingerprint analysis, one of the proteomics fields. This pipelined-EST analysis system will extend our knowledge on the plant ESTs and proteins by identification of unknown-genes.