• Asian-Australasian Journal of Animal Sciences
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• 제18권9호
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• pp.1237-1241
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• 2005

Mannose-P-dolichol utilization defect 1 (MPDU1) gene is required for utilization of the mannose donor MPD in synthesis of both lipid-linked oligosaccharides (LLOs) and glycosylphosphatidylinositols (GPI) which are important for functions such as protein folding and membrane anchoring. The full length cDNA of the porcine MPDU1 was determined by in silico cloning and rapid amplification of cDNA ends (RACE). The deduced amino acid showed 91% identity to the corresponding human sequence with five predicted transmembrane regions. RT-PCR was performed to detect its expression pattern in five tissues and results showed that it is expressed ubiquitously among the tissues checked. A single nucleotide substitution resulting in the amino acid change (137 Tyr-137 His) was detected within exon 5. Allele frequencies in six pig breeds showed distinctive differences between those Chinese indigenous pigs breeds and European pigs. Using the pig/rodent somatic cell hybrid panel (SCHP), we mapped the porcine MPDU1 gene to SSC12, which is consistent with the comparative mapping result as conservative syntenic groups presented between human chromosome 17 and pig chromosome 12.

• 한국콘텐츠학회논문지
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• 제11권1호
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• pp.193-201
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• 2011

본 연구에서는 디지털 미디어아트의 몰입과 상호작용적 특성에 따른 관객과 작품 사이의 '닫힌 관계'로써의 '열린 상호작용성'을 넘어, 인공생명(Artificial Life) 예술에 이르러 더욱 진화된 상호작용성에 관해 고찰한다. 이를 위해 생물학 및 계산과학을 비롯한 다양한 학문의 성과에 따른 인공생명 이론을 살펴보고, 인공생명의 자율성과 창발적 행동을 인공생명 예술적 맥락과 연결되는 특성으로 분석하였다. 특히 인공생명 예술을 공인하는 역할을 하고 있는 'VIDA : Art and Artificial Life International Awards'에서 선정된 예술 작품들 중 환경과 상호작용하는 인공생명 예술 작품과 외부 세계에서 개체로 살아 움직이는 인공생명 예술 작품들을 중심으로 분석하여, 관객과 작품 간의 감성적 주체로써의 관계와 나아가 기술과 인간이 맺는 공생과 공진화의 다양한 층위의 관계성에 대해 이해하고자 하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.13-16
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• 2000

Microorganisms have been widely employed for the production of useful bioproducts including primary metabolites such as ethanol, succinic acid, acetone and butanol, secondary metabolites represented by antibiotics, proteins, polysaccharides, lipids and many others. Since these products can be obtained in small quantities under natural condition, mutation and selection processes have been employed for the improvement of strains. Recently, metabolic engineering strategies have been employed for more efficient production of these bioproducts. Metabolic engineering can be defined as purposeful modification of cellular metabolic pathways by introducing new pathways, deleting or modifying the existing pathways for the enhanced production of a desired product or modified/new product, degradation of xenobiotics, and utilization of inexpensive raw materials. Metabolic flux analysis and metabolic control analysis along with recombinant DNA techniques are three important components in designing optimized metabolic pathways, This powerful technology is being further improved by the genomics, proteomics, metabolomics and bioinformatics. Complete genome sequences are providing us with the possibility of addressing complex biological questions including metabolic control, regulation and flux. In silico analysis of microbial metabolic pathways is possible from the completed genome sequences. Transcriptome analysis by employing ONA chip allows us to examine the global pattern of gene expression at mRNA level. Two dimensional gel electrophoresis of cellular proteins can be used to examine the global proteome content, which provides us with the information on gene expression at protein level. Bioinformatics can help us to understand the results obtained with these new techniques, and further provides us with a wide range of information contained in the genome sequences. The strategies taken in our lab for the production of pharmaceutical proteins, polyhydroxyalkanoate (a family of completely biodegradable polymer), succinic acid and me chemicals by employing metabolic engineering powered by genomics, proteomics, metabolomics and bioinformatics will be presented.

• Korean Chemical Engineering Research
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• 제44권1호
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• pp.97-105
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• 2006

본 연구에서는 대장균 내에서 L-threonine의 생합성에 영향을 미치는 저해제들에 대한 모사 연구를 위하여 L-aspartate에서 L-threonine까지의 아미노산 생합성 대사 네트워크를 문헌 및 데이터베이스를 통해 구축하였다. 또한 L-threonine 생합성에 영향을 미치는 저해제들을 수학적으로 모델링하여 효소 반응식에 적용시켰다. 모사 연구를 위해 초기 농도값을 L-aspartate 5 mM, ATP 5 mM, NADPH 2 mM으로 설정하고 저해제의 농도 변화에 따른 세포내 대사 물질들의 농도변화를 확인하였다. 그 결과 저해제 L-lysine, L-methionine, L-glutamate는 저해제 농도 변화에 따라 대사 물질들의 농도 변화가 없었다. 그러나 저해제 L-serine, L-cysteine 그리고 L-threonine의 경우 저해제의 농도 변화에 따라 세포내 대사물질들의 농도 곡선이 서로 다른 결과를 얻었다. 대장균 내에서 소비되어진 L-aspartate의 농도는 세포 내 생성되는 L-threonine과는 관련이 없었고, 생성되는 L-threonine의 농도는 세포 내에 축적된 D,L-aspartic ${\beta}$-semialdehyde에 반비례하였다.

• 한국식품영양과학회지
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• 제41권3호
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• pp.396-401
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• 2012

열무김치로부터 김치유산균을 분리하고 프로바이오틱스로 이용 가능한 균주를 선발하기 위하여 인체의 장관과 유사한 인체장모델시스템(SHIMS)을 이용한 in silico 실험을 수행하였다. 열무김치에서 분리한 5종과 표준균주 12종에 대해 내산성 및 내담즙산성을 시험하여 생존율이 높은 2종의 균주를 선발하였다. 선발한 균주를 SHIMS에서 시험하여 가장 높은 생존율을 나타낸 균주의 16S rRNA를 분석한 결과 Leu. mesenteroides로 동정되었으며 이 김치유산균을 Leu. mesenteroides K01으로 명명하였다. 이 균주는 SHIMS에서 생존율이 높았기 때문에 프로바이오틱스로 다양하게 이용할 가치가 있다고 판단된다.

• Journal of Microbiology and Biotechnology
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• 제26권12호
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• pp.2030-2035
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• 2016

Bacillus cereus causes food-borne illness through contaminated foods; therefore, its pathogenicity and genome sequences have been analyzed in several studies. We sequenced and analyzed B. cereus strain FORC_021 isolated from a sashimi restaurant. The genome sequence consists of 5,373,294 bp with 35.36% GC contents, 5,350 predicted CDSs, 42 rRNA genes, and 107 tRNA genes. Based on in silico DNA-DNA hybridization values, B. cereus ATCC $14579^T$ was closest to FORC_021 among the complete genome-sequenced strains. Three major enterotoxins were detected in FORC_021. Comparative genomic analysis of FORC_021 with ATCC $14579^T$ revealed that FORC_021 harbored an additional genomic region encoding virulence factors, such as putative ADP-ribosylating toxin, spore germination protein, internalin, and sortase. Furthermore, in vitro cytotoxicity testing showed that FORC_021 exhibited a high level of cytotoxicity toward INT-407 human epithelial cells. This genomic information of FORC_021 will help us to understand its pathogenesis and assist in managing food contamination.

• Journal of Applied Biological Chemistry
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• 제63권3호
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• pp.189-195
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• 2020

The soybean (Glycine max L.), also known as the soya bean, is an economically important legume species. Pathogens are always major threats for soybean cultivation. Several pathogens negatively affect soybean production. The soybean is also known as a susceptible host to many viruses. Recently, we carried out systematic analyses to identify viruses infecting soybeans using soybean transcriptome data. Our screening results showed that only few soybean transcriptomes contained virus-associated sequences. In this study, we further carried out bioinformatics analyses using a soybean flower bud transcriptome for virus identification, genome assembly, and single nucleotide variations (SNVs). We assembled the genome of Soybean yellow common mosaic virus (SYCMV) isolate China and revealed two SNVs. Phylogenetic analyses using three viral proteins suggested that SYCMV isolate China is closely related to SYCMV isolates from South Korea. Furthermore, we found that replication and mutation of SYCMV is relatively low, which might be associated with flower bud tissue. The most interesting finding was that SYCMV was not detected in the cytoplasmic male sterility (CMS) line derived from the non-CMS line that was severely infected by SYCMV. In summary, in silico analyses identified SYCMV from the soybean flower bud transcriptome, and a nearly complete genome of SYCMV was successfully assembled. Our results suggest that the low level of virus replication and mutation for SYCMV might be associated with plant tissues. Moreover, we provide the first evidence that male sterility might be used to eliminate viruses in crop plants.

• Journal of Microbiology and Biotechnology
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• 제20권10호
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• pp.1403-1414
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• 2010

Aspergillus awamori BTMFW032, isolated from sea water, produced tannase as an extracellular enzyme under submerged culture conditions. Enzymes with a specific activity of 2,761.89 IU/mg protein, a final yield of 0.51%, and a purification fold of 6.32 were obtained after purification through to homogeneity, by ultrafiltration and gel filtration. SDS-PAGE analyses, under nonreducing and reducing conditions, yielded a single band of 230 kDa and 37.8 kDa, respectively, indicating the presence of six identical monomers. A pI of 4.4 and a carbohydrate content of 8.02% were observed in the enzyme. The optimal temperature was found to be $30^{\circ}C$, although the enzyme was active in the range of $5-80^{\circ}C$. Two pH optima, pH 2 and pH 8, were recorded, although the enzyme was instable at a pH of 8, but stable at a pH of 2.0 for 24 h. Methylgallate recorded maximal affinity, and $K_m$ and $V_{max}$ were recorded at $1.9{\times}10^{-3}$M and 830 ${\mu}Mol$/min, respectively. The impacts of a number of metal salts, solvents, surfactants, and other typical enzyme inhibitors on tannase activity were determined in order to establish the novel characteristics of the enzyme. The gene encoding tannase, isolated from A. awamori, was found to be 1.232 kb, and nucleic acid sequence analysis revealed an open reading frame consisting of 1,122 bp (374 amino acids) of one stretch in the -1 strand. In silico analyses of gene sequences, and a comparison with reported sequences of other species of Aspergillus, indicate that the acidophilic tannase from marine A. awamori differs from that of other reported species.

• BMB Reports
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• 제40권1호
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• pp.95-99
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• 2007

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

• 대한한방내과학회지
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• 제41권6호
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• pp.1078-1088
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• 2020

Objective: The purpose of this study was to investigate the effect of amorfrutin of licorice for Type2 diabetes mellitus. Method: The PubMed, CNKI, Wanfang, OASIS, NDSL, J-STAGE, and CiNii databases were searched from the beginning of the search to September 20, 2020, with no limits on language. Extractions and selections from the literature were made by two authors. The study included in vivo experiments with amorfrutins in high-fat diet-induced obesity C57BL/6 mice and leptin receptor-deficient db/db mice and in silico studies. Results & Conclusion: Four studies were finally selected. We confirmed that amorfrutin treatment considerably improved insulin sensitivity and glucose tolerance and reduced plasma insulin and glucose. Amorfrutins bind to and selectively activate Peroxisome Proliferator-Activated Receptor Gamma (PPARγ), which plays an important role in glucose metabolism. Amorfrutins also strongly bind to the glucagon receptor (GCGR) and work as antagonist. Using the amorfrutins from licorice could therefore be helpful in treating type2 diabetes mellitus.