• 한국축산시설환경학회지
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• 제21권3호
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• pp.93-98
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• 2015

The objective of this study was to review application of next-generation sequencing (NGS) to investigate microbiome in the livestock sector. Since the 16S rRNA gene is used as a phylogenetic marker, unculturable members of microbiome in nature or managed environments have been investigated using the NGS technique based on 16S rRNA genes. However, few NGS studies have been conducted to investigate microbiome in the livestock sector. The 16S rRNA gene sequences obtained from NGS are classified to microbial taxa against the 16S rRNA gene reference database such as RDP, Greengenes and Silva databases. The sequences also are clustered into species-level OTUs at 97% sequence similarity. Microbiome similarity among treatment groups is visualized using principal coordinates analysis, while microbiome shared among treatment groups is visualized using a venn diagram. The use of the NGS technique will contribute to elucidating roles of microbiome in the livestock sector.

• BMB Reports
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• 제37권2호
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• pp.148-152
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• 2004

A new molecular-baiting method was studied by retrieving targeted gene fragments from an oligonucleotide microarray bait after hybridization. To make the microarray bait, 70-mer oligonucleotides that were designed to specifically represent the SSA1 gene of Saccharomyces cerevisiae were printed on the slide. Samples of the Saccharomyces cerevisiae mRNA were extracted and labeled by the RD-PCR (Restriction Display PCR) method using the Cy5-labelled universal primer, then applied for hybridization. The sample fragments that hybridized to the microarray were stripped, and the eluted cDNAs were retrieved and cloned into the pMD 18-T vector for transformation, plasmid preparation, and sequencing. BLAST searching of the GenBank database identified the retrieved fragments as being identical to the SSA1 gene (from 2057-2541bp). A new method is being established that can retrieve the sample fragments using an oligo-microarray-bait.

• 대한한의학방제학회지
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• 제29권4호
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• pp.267-275
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• 2021

Objectives : Previously, we reported that compound K isolated from fermented ginseng by Aspillus oryzae has a wide biochemical and pharmacological effect, including anti-cancer activity in prostate cancer PC-3 cells. Despite these findings, its signaling pathway and gene expression pattern are not clearly understood. Methods : To confirm the gene expression study of treated with compound K in PC-3 cells, a cDNA microarray chip composed of 44K human cDNA probes was used. MTT assay, western blot analysis, propidium iodide staining, and annexin V/propidium iodide staining were analyzed. Results : We confirmed the differences of gene expression profiles. Then, we analyzed with the cell cycle arrest, cell death and cell proliferation related genes using DAVID database. Conclusions : Our finding should be useful for understanding genome-wide expression patterns of compound K-mediated cell cycle arrest toward induction of cell death and be helpful for finding future cancer therapeutic targets for prostate cancer cells.

• 한국미생물·생명공학회지
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• 제52권2호
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• pp.163-178
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• 2024

Pan-genome analysis is used to interpret genome heterogeneity and diversification of bacterial species. Here, we present pan-genome analysis of 22 strains of Enterococcus mundtii. The GenBank file of E. mundtii strains that have been isolated from different sources i.e., human fecal matter, soil, leaf, dairy products, and insects was downloaded from National Center for Biotechnology Information (NCBI) database and analyzed using BPGA-1.3.0 (Bacterial Pan Genome Analysis) pipeline. Out of a total, 4503 gene families, 1843 belongs to the core genes whereas 1,762 gene families represent the accessory genes and 898 gene families depict the unique genes among all the selected genomes. Majority of the core genes belongs to the categories of Metabolism (37.83%) and Information storage & processing (29.84%) whereas unique genes belongs to the category of Information storage & processing (48.08%). Further, accessory genes are almost equally present in both functional categories i.e. Information storage & processing and Metabolism (34.34% and 32.27% respectively). Further, subset analysis on the basis of the origin of isolates exhibits presence and absence of exclusive gene families. The observation suggests that even closely related strains of a species show extensive disparity in genome owing to their ability to adapt to a specific environment.

• International Journal of Industrial Entomology and Biomaterials
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• 제31권2호
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• pp.62-69
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• 2015

The Asian cavity-nesting honeybee, Apis cerana (Hymenoptera: Apidae), has been extensively studied for its biogeography and genetic diversity, but the molecules utilized in past studies were mainly ~90 bp long mitochondrial non-coding sequences, located between $tRNA^{Leu}$ and COII. Thus, additional molecular markers may enrich our understanding of the biogeography and genetic diversity of this valuable bee species. In this study, we reviewed the public genome database to find introns of cDNA sequences, with the assumption that these introns may have less evolutionary constraints. The six introns selected were subjected to preliminary tests. Thereafter, two introns, titled White gene and MRJP9 gene, were selected. Sequencing of 552 clones from 184 individual bees showed a total of 222 and 141 sequence types in the White gene and MRJP9 gene introns, respectively. The sequence divergence ranged from 0.6% to 7.9% and from 0.26% to 17.6% in the White gene and the MRJP9 introns, respectively, indicating higher sequence divergence in both introns. Analysis of population genetic diversity for 16 populations originating from Korea, China, Vietnam, and Thailand shows that nucleotide diversity (π) ranges from 0.003117 to 0.025837 and from 0.016541 to 0.052468 in the White gene and MRJP9 introns, respectively. The highest π was found in a Vietnamese population for both intron sequences, whereas the nine Korean populations showed moderate to low sequence divergence. Considering the variability and diversity, these intron sequences can be useful as non-mitochondrial DNA-based molecular markers for future studies of population genetics.

• Asian-Australasian Journal of Animal Sciences
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• 제20권3호
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• pp.328-333
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• 2007

Carboxypeptidase E (CPE) plays an important role in the regulation of the body fat content. Therefore, it has been suggested as candidate gene for traits related to meat quality in beef cattle. This study was conducted to identify single nucleotide polymorphisms (SNPs) in the CPE gene and to investigate association of SNP marker with carcass and meat quality traits in Korean cattle. Three SNPs were identified in the intron 4 (A309G SNP and C445T SNP) and exon 5 (C601T SNP) of the CPE gene by sequence analyses of CPE cDNA and genomic DNA samples. The sequences have been deposited in GenBank database with accession numbers AY970664 and AY970663. Genotyping of the gene-specific SNP marker was carried out using the PCR-RFLP with restriction enzymes DdeI for C445T SNP and NlaIII for C601T SNP. The frequencies of C and T alleles were 0.43 and 0.57 for C445T SNP and 0.42 and 0.58 for C601T SNP, respectively. Statistical analysis indicated that the C445T SNP showed a significant effect (p<0.05) on marbling score (MS) and breeding value of backfat thickness (BF-EBV), respectively. Animals with the CT genotype showed higher marbling score and backfat thickness than those with the TT genotype. This marker also showed a significant dominance effect for the MS and BF-EBV (p<0.05). However, no significant associations were observed between C601T SNP genotypes and all traits examined. The results suggest that the CPE gene may be used as a marker for carcass traits in Korean cattle.

• Journal of Ginseng Research
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• 제29권4호
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• pp.167-175
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• 2005

The $Ca^{2+}-activated$ chloride channel (CLCA) was activated by ginseng total saponin (GTS) in Xenopus oocytes. The reverse transcription PCR (RT-PCR) method was performed with gene specific primers on oocytes. The gene specific primers were deduced from spleen cDNA in expressed sequence tags (EST) database showing high homology to the mouse CLCA. Full length of cDNA sequence was completed by linkage of several 5' and 3'-half cDNA fragments have been sequenced. We named the full cDNA to oCLCA transiently. The oCLCA gene encodes a protein of 911 amino acids with $48.9\%$ identity overall to that of mouse CLCA (mCLCA4). A predicted oCLCA amino acids sequence shows the molecular weight of 108 kDa and has four or more transmembrane domains, and also the one hydrophobic C­terminal domain. oCLCA gene was expressed ubiquitously in various tissues included oocytes, also interfered in oocytes by siRNA for oCLCA. Here, we suggest that oCLCA is a endogenous chloride channel gene in oocytes. We are studying for the identification of oCLCA gene and further physiological research.

• 한국잠사학회:학술대회논문집
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• 한국잠사학회 1997년도 Progress and Future Development of Sericultural Science and Technology 40th Anniversary Commemoration Symposium
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• pp.23-49
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• 1997

This is a progress report of rice biotechnology including development of gene transformation system, gene cloning and molecular mapping in rice. The scope of the research was focused on the connection between conventional breeding and biotech-researches. Plant transformation via Agrobacterium or particle bombardment was developed to introduce one or several genes to recommended rice cultivars. Two chimeric genes containing a maize ribosome inactivating protein gene (RIP) and a gerbicide resistant gene (bar) were introduced to Nipponbare, a Japonica cultivar, and transmitted to Korean cultivars. The homozygous progenies of herbicide resistant transgenic plant showed good fertility and agronomic characters. To explore the genetic resourses in rice, over 8,000 cDNA clones from immature rice seed have been isolated and sequenced. About 13% of clones were identified as enzymes related to metabolic pathway. Among them, twenty clones have high homology with genes encoding enzymes in the photorespiratory carbon cycle reaction. Up to now about 100 clones were fully sequenced and registered at EMBL and GenBank. For the mapping of quantitative tarits loci (QTL) and eternal recombinant inbred population with 164 F13 lines (MGRI) was developed from a cross between Milyang 23 and Gihobyeo, Korean rice cultivars. After construction of fully saturated RFLP and AFLP map, quantitative traits using MGRI population were analyzed and integrated into the molecular map. Eighty seven loci were determined with 27 QTL characters including yield and yield components on rice chromosomes. Map based cloning was also tried to isolate semi-dwarf (sd-1) gene in rice. A DNA probe, RG 109, the most tightly linked to sd-1 gene was used to screen from bacterial artifical chromosome (BAC) libraries and five over lapping clones presumably containing sd-1 gene were isolated. Rice genetic database including results of biotech reasearch and classical genetics is provided at Korea Rice Genome Server which is accessible with world wide web (www) browser. The server provides rice cDNA sequences and map informations linked with phenotypic images.

• Journal of Animal Science and Technology
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• 제46권2호
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• pp.155-164
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• 2004

이 연구는 gene-trap construct를 가지고 있는 배양세포로부터 trap gene을 확인하고 클로닝한 다음 이러한 세포를 이용하여 복제 지브라물고기를 만들기 위해 수행되어졌다. 본 연구에서 gene-trap과 연관된 복제 지브라물고기가 성공적으로 만들어졌다. 본 실험에서 두 종류의 백터(SA/GFP-TP와 Neo-TP)가 사용되었다. 이들 벡터에 의해 전이된 모든 종류의 세포는 항생제에 의해 선별을 하여 분석에 이용하였다. SA/GFP-TP에 의해 전이된 세포의 경우, 단일세포상에서 GFP 발현도가 낮아 본 연구에서 동물복제에 사용되지 않았으며, Neo-TP에 의해 전이된 세포주가 복제실험에 이용되었다. Neo-TP 세포에 의한 복제실험 결과, 총 1179개의 핵치환 난으로부터 44(3.7%) 개의 배자가 포배기에 도달하였으며, 8(0.8%) 개의 배자가 부화시기에 이르렀다. 그리고 3마리는 성숙단계에 이르렀으며, 이중 1마리에서 정상적으로 gene-trap 전이가 이루어짐을 Southern blot 분석을 통해 확인되었다.

• 한국산학기술학회논문지
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• 제21권7호
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• pp.312-320
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• 2020

본 연구의 목적은 Ribosomal Database Project에서 공적으로 활용 가능한 16S rRNA 유전자 시퀀스들의 메타분석을 통해 반추위 고세균의 계통발생 다양성을 조사하는 것이다. 총 8,416개의 시퀀스가 Ribosomal Database Project(출시버전 11, 업데이트 5)로부터 회수되었고, taxonomy tree를 구축하는데 사용되었다. Species 수준의 OTUs가 97% sequence 유사성 기준으로 QIIME 프로그램을 사용하여 분석되었다. 총 8,416개의 시퀀스 중에서 8,412개의 시퀀스는 총 3개의 문으로 분류되었고, 나머지 4개의 시퀀스는 어떤 알려진 문으로 분류되지 못했다. Euryarchaeota는 가장 우점하는 문으로, 전체 고세균 시퀀스의 99.8%를 차지하였다. 이 중에서 차례로 Methanobrevibacter가 65.4%, Methanosphaera가 10.4%, Methanomassillicoccus가 10.4%, Methanomicrobium가 7.9%, Methanobacterium가 1.9%, Methanimicrococcus가 0.5%, Methanosarcina가 0.1%, Methanoculleus가 0.1%를 차지하였다. V2와 V3 영역으로 자른 7,544개의 시퀀스는 493개의 OTUs로 분류되었다. 총 493 OTUs 중에서 단지 17개만 우점하였고, 총 7,544 시퀀스 중 1% 이상을 차지하였다. 본 연구는 반추동물로 부터 메탄발생에 크게 기여하는 반추위 우점 메탄생성균 분석에 대한 향후 연구를 인도하는데 도움을 주고, 사료나 가축품종이 달라져도 이러한 메탄생성균을 억제하는 메탄저감제를 개발하는데 도움을 줄 것이다.