• 생태와환경
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• 제55권4호
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• pp.352-359
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• 2022

국내 서식하는 수서 생물(식물플랑크톤, 동물플랑크톤, 저서대형무척추동물, 어류)에 대한 eDNA 연구에 주요 이용되는 유전자인 12S rRNA와 16S rRNA, 18S rRNA, COI, CYTB를 대상으로 속(Genus) 수준의 등록 현황을 조사하였다. 그 결과 식물플랑크톤과 동물플랑크톤은 18S rRNA에서 가장 높은 등록 속 비율을 보였으며, 저서무척추동물은 COI에서 가장 높은 등록 속 비율을 확인하였다. 어류에서는 18S rRNA를 제외한 모든 유전자에서 90%에 가까운 높은 비율을 보였다. 분류군에 따른 우점 생물의 상위 20속에 대한 유전자 등록 현황은 식물플랑크톤은 18S rRNA에서 19속이, 저서무척추동물은 COI에서 18개 속이 등록되어 있었다. 어류에서는 12S rRNA, 16S rRNA, CYTB에서 상위 20의 모든 유전자 염기서열이 존재함을 확인하였다. 본 자료 분석을 통하여 각 분류군별 eDNA 연구에 적합한 유전자 데이터베이스의 양적인 정보를 파악하였다.

• Journal of Animal Science and Technology
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• 제62권2호
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• pp.121-140
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• 2020

Anaerobic fungi habitat in the gastrointestinal tract of foregut fermenters or hindgut fermenters and degrade fibrous plant biomass through the hydrolysis reactions with a wide variety of cellulolytic enzymes and physical penetration through fiber matrix with their rhizoids. To date, seventeen genera have been described in family Neocallimasticaceae, class Neocallimastigomycetes, phylum Neocallimastigomycota and one genus has been described in phylum Neocallimastigomycota. In National Center for Biotechnology Information (NCBI) database (DB), 23,830 nucleotide sequences and 59,512 protein sequences have been deposited and most of them were originated from Piromyces, Neocallimastix and Anaeromyces. Most of protein sequences (44,025) were acquired with PacBio next generation sequencing system. The whole genome sequences of Anaeromyces robustus, Neocallimastix californiae, Pecoramyces ruminantium, Piromyces finnis and Piromyces sp. E2 are available in Joint Genome Institute (JGI) database. According to the results of protein prediction, average Isoelectric points (pIs) were ranged from 5.88 (Anaeromyces) to 6.57 (Piromyces) and average molecular weights were ranged from 38.7 kDa (Orpinomyces) to 56.6 kDa (Piromyces). In Carbohydrate-Active enZYmes (CAZY) database, glycoside hydrolases (36), carbohydrate binding module (11), carbohydrate esterases (8), glycosyltransferase (5) and polysaccharide lyases (3) from anaerobic fungi were registered. During four decades, 1,031 research articles about anaerobic fungi were published and 444 and 719 articles were available in PubMed (PM) and PubMed Central (PMC) DB.

• 생명과학회지
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• 제19권5호
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• pp.639-643
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• 2009

배추는 재배 온도에 따라 수확량과 품질에 많은 영향을 받을 수 있다. 고온 스트레스 저항성 배추품종 육성을 위해 본 연구는 스트레스 저항성에 관련이 있다고 알려진 trehalose 유전자 관련 다형성 마커를 개발하였다. 아라비돕시스 trehalose 합성 유전자와 유사한 총 28개의 배추 EST를 NCBI database에서 찾고 고온에 상대적으로 약한 지부품종과 고온에 잘 견디는 품종인 권심을 대상으로 다형성을 조사하였다. 이 중 10개의 EST에서 insertion/deletion 또는 single nucleotide polymorphism을 발견하여 이를 바탕으로 쉽게 이용이 가능한 10개의 다형성 PCR 마커를 개발하였다. 본 연구에서 개발된 trehalose 분자마커는 앞으로 배추 작물에서 환경 스트레스 저항성과 유전적 연관성을 확인하는데 이용될 수 있고 MAS를 이용한 품종육성에 이용될 수 있다고 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제26권8호
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• pp.1144-1151
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• 2013

In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below $E^{-10}$ using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4) were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below $10^{-5}$. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2019년도 춘계학술대회
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• pp.35-35
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• 2019

Aster spathulifolius Maxim. is belongs to the Asteraceae family which is distributed only in Korea and Japan. It is recognize as a traditionally medicinal plants and economically valuable in ornamental field. However, among the Asteraceae family, the Aster genus, which is lacks in genomic resources and information of molecular function. Therefore, we used high throughput RNA-sequencing transcriptome data of the A. spathulifolius to know molecular level function. DeNovo assembly produced 98,660 unigene with N50 value 1126 bp. Unigenes was performed to analyses the functional annotation against NCBI database like plant database of nucleotide (Nt) and non-redundant protein (Nr), Pfam, Uniprot, KEGG and Transcriptional factor (TF). In addition, Distribution of SSR markers also analyzed for future perfectives. Further, Comparing with other two Asteraceae family species like, Karelinia caspica and Chrysanthemum morifolium to the A. spathulifolius shows the number of gene that regulated in internal and external stress respectively salt-tolerant and heat and drought stress to understand the molecular basis related to the different environments stress.

• 한국패류학회지
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• 제30권4호
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• pp.429-431
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• 2014

본 연구를 통하여 연체동물 전용 BLAST 서버 (Version II)가 웹주소 http://www.malacol.or.kr/blast에 구축되었다. 연체동물을 대상으로 하는 연구에 있어 필요한 정보를 매우 빠르게 얻을 수 있었다. 본 시스템을 사용하여 앞으로도 많은 연구가 진행되어지길 바라며, 아울러 많은 연체동물 연구자들에게 많은 도움이 되리라고 사료된다.

• 원예과학기술지
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• 제29권2호
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• pp.116-122
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• 2011

본 연구에서는 지리산에서 자생하는 한국 특산종인 노각나무(Stewartia koreana Nakai)의 EST library를 제작하고 서열을 분석하였다. 노각나무의 유엽을 재료로 cDNA library 만들었고 1,392개의 cDNA에 대한 부분 서열 분석을 진행하였다. EST와 unigene 서열의 분석은 컴퓨터를 기반으로한 filtering과 수작업 그리고 NCBI의 BLAST 분석을 통해 수행하였다. 벡터 서열과 100bp 이하의 서열을 제거한 후 1,301개의 EST를 분석하였다. 전체 150개의 contig와 743개의 singleton을 분리하여 총 893개의 unigene을 분리해냈으며 서열 분석을 통해 95개의 microsatellite를 확인하였다. NCBI 데이터베이스의 BLASTX로 상동성을 검색한 결과 EST의 65%는 기능을 알고 있는 유전자와 11.6%의 EST는 아직까지 기능이 보고되지 않은 유전자와 높은 상동성을 보였다. 남아 있는 23.2%의 EST는 기존에 데이터베이스에 보고된 유전자와 상동성을 보이지 않는 유전자로 밝혀졌다. 다양한 데이터베이스를 기반으로 한 유사성 기반 기능 분석은 노각나무의 EST가 포도나무와 포플러와 높은 유사성을 보인 것을 확인하였다. 기능에 따른 분류에 있어 molecular function은 nucleotide binding, biological process는 transport, cellular component는 plastid가 가장 높은 비율로 나왔다. 본 연구를 통해 얻어진 EST 자료는 노각나무의 새로운 유전자원에 대한 연구의 기본 자료로 유용하게 활용될 것이다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권6호
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• pp.2489-2493
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• 2015

Background: Loss of heterozygosity (LOH) on chromosomal regions is crucial in tumor progression and this study aimed to identify genome-wide LOH in pancreatic cancer. Materials and Methods: Single-nucleotide polymorphism (SNP) profiling data GSE32682 of human pancreatic samples snap-frozen during surgery were downloaded from Gene Expression Omnibus database. Genotype console software was used to perform data processing. Candidate genes with LOH were screened based on the genotype calls, SNP loci of LOH and dbSNP database. Gene annotation was performed to identify the functions of candidate genes using NCBI (the National Center for Biotechnology Information) database, followed by Gene Ontology, INTERPRO, PFAM and SMART annotation and UCSC Genome Browser track to the unannotated genes using DAVID (the Database for Annotation, Visualization and Integration Discovery). Results: The candidate genes with LOH identified in this study were MCU, MICU1 and OIT3 on chromosome 10. MCU was found to encode a calcium transporter and MICU1 could encode an essential regulator of mitochondrial $Ca^{2+}$ uptake. OIT3 possibly correlated with calcium binding revealed by the annotation analyses and was regulated by a large number of transcription factors including STAT, SOX9, CREB, NF-kB, PPARG and p53. Conclusions: Global genomic analysis of SNPs identified MICU1, MCU and OIT3 with LOH on chromosome 10, implying involvement of these genes in progression of pancreatic cancer.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.80.2-81
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• 2003

Since hot peppers (Capsicum annuum L.) are getting reputation as an important source of vitamins, medicine and many other areas, consumption and cultivation is being increased in the world. In spite of this usefulness, so little attention has been given to the hot pepper plants. To date, less than 500 nucleotide sequences including redundancy has been identified in NCBI database. Therefore we started to EST sequencing project for initial characterization of the genome, because of the large genome size of hot pepper (2.7 3.3 ${\times}$ 109 bp), To date, a set of 10,000 non-redundant genes were identified by EST sequencing for microarray-based gene expression studies. At present, cDNA microarrays containing 4,685 unigene clones are used for hybridization labeled targets derived from pathogen infected and uninoculated leaf tissues. Monitoring of gene expression profiles of hot pepper interactions with soybean pustule pathogen (Xag；Xanthomonas axonopodis pv. glycine) will be presented.

• Parasites, Hosts and Diseases
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• 제47권2호
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• pp.103-107
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• 2009

The genus Acanthamoeba can cause severe infections such as granulomatous amebic encephalitis and amebic keratitis in humans. However, little genomic information of Acanthamoeba has been reported. Here, we constructed Acanthamoeba expressed sequence tags (EST) database (Acanthamoeba EST DB) derived from our 4 kinds of Acanthamoeba cDNA library. The Acanthamoeba EST DB contains 3,897 EST generated from amebae under various conditions of long term in vitro culture, mouse brain passage, or encystation, and downloaded data of Acanthamoeba from National Center for Biotechnology Information (NCBI) and Taxonomically Broad EST Database (TBestDB). The almost reported eDNA/genomic sequences of Acanthamoeba provide stand alone BLAST system with nucleotide (BLAST NT) and amino acid (BLAST AA) sequence database. In BLAST results, each gene links for the significant information including sequence data, gene orthology annotations, relevant references, and a BlastX result. This is the first attempt for construction of Acanthamoeba database with genes expressed in diverse conditions. These data were integrated into a database (http://www. amoeba.or.kr).