• Bulletin of the Korean Chemical Society
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• 제35권3호
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• pp.845-850
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• 2014

The rapid development of shotgun proteomics is paving the way for extensive proteome profiling, while providing extensive information on various post translational modifications (PTMs) that occur to a proteome of interest. For example, the current phosphoproteomic methods can yield more than 10,000 phosphopeptides identified from a proteome sample. Despite these developments, it remains a challenging issue to pinpoint the true phosphorylation sites, especially when multiple sites are possible for phosphorylation in the peptides. We developed the Phospho-UMC filter, which is a simple method of localizing the site of phosphorylation using unique mass classes (UMCs) information to differentiate phosphopeptides with different phosphorylation sites and increase the confidence in phosphorylation site localization. The method was applied to large scale phosphopeptide profiling data and was demonstrated to be effective in the reducing ambiguity associated with the tandem mass spectrometric data analysis of phosphopeptides.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2008년도 한국컴퓨터종합학술대회논문집 Vol.35 No.1 (C)
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• pp.217-221
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• 2008

생명공학 기술의 발달로 지놈 프로젝트를 통해 인간 초파리 등 여러 종의 유전체 정보가 밝혀 졌다. 그러나 Post-Genome 연구에 있어서 매우 중요한 생물체인 멍게(Ciona intestinalis)와 성게(Strongylocentrotus purpuratus)의 유전체 서열은 현재 공개되어 있으나 염기서열의 연속성(continuity)에는 심각한 문제점이 존재하고 있다. 이들은 염기서열에 변이가 많은 다염기변이 유전체(polymorphic genomes)로 그 특성이 반영되지 않은 전통적인 Whole Genome Shotgun Sequencing(WGSS)방법을 사용였기 때문이다. 이와 같은 다염기변이 유전체 서열 분석은 시스템 생물학이나 비교 유전체학 등의 후발 연구에 기초가 되므로 매우 중요하다. 본 논문에서는 다염기변이 유전체에 대해 알아보고 서열 조립 알고리즘의 기본이 되는 서열 정렬 툴들 중 가장 많이 사용되는 FASTA, BLAST, BLAT에 대해 분석하여 봄으로써 다염기변이 유전체에 적합한 서열 조립 전략 수립을 위해 고려해야 하는 사항들을 논의해 본다.

• Journal of Microbiology and Biotechnology
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• 제14권1호
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• pp.74-80
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• 2004

Aspergillus fumigatus is one of the most common fungi in the human environment, both in-doors and out-doors. It is the main causative agent of invasive aspergillosis, a life-threatening mycosis among immunocompromised patients. The genome has been sequenced by an international consortium, including the Wellcome Trust Sanger Institute (U.K.) and The Institute for Genomic Research (TIGR, U.S.A.), and a ten times whole genome shotgun sequence assembly has been made publicly available. In this study, we identified tricarboxylic acid (TCA) cycle enzymes of A. fumigatus by comparative analysis with four other fungal species. The open reading frames showed high amino acid sequence similarity with the other fungal citric acid enzymes and well-conserved functional domains. All genes present in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, and Neurospora crassa were also found in A. fumigatus. In addition, we identified four A. fumigatus genes coding for enzymes in the glyoxylate shunt, which may be required for fungal virulence. The architecture of multi-gene encoded enzymes, such as isocitrate dehydrogenase, 2-ketoglutarate, succinyl-CoA synthetase, and succinate dehydrogenase was well conserved in A. fumigatus. Furthermore, our results show that genes of A. fumigatus can be detected reliably using GlimmerM.

• 한국전자통신학회논문지
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• 제10권2호
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• pp.233-238
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• 2015

본 논문에서는 FTV(Free-viewpoint TV) 서비스에서, 몰입도를 향상시킬 수 있는 유효 잡음 이용 입체 음향효과 방법을 제안한다. 농구장에서 초지향성 마이크 및 무선 마이크를 사용하여 선수와 심판의 연속적인 음향 정보를 획득함으로써 주파수 스펙트럼을 관찰하였으며, 스펙트럼을 분석하여 시청자가 Zoom-in을 할 경우, 유효 주파수 여부를 판단하였다. 따라서 FTV 서비스에서 시청자가 피사체를 향해 Zoom-in 시, 제거대상이었던 잡음을 활용할 필요가 있음을 제시하였다. 본 연구는 향후 FTV의 입체 음향 연구에 활용될 것으로 기대된다.

• Journal of Korean Dental Science
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• 제16권1호
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• pp.35-46
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• 2023

Purpose: Culture-based methods for microbiological diagnosis and antibiotic susceptibility tests have limitations in the management of orofacial infections. We aimed to profile pus microbiota and identify antibiotic resistance genes (ARGs) using a culture-independent approach. Materials and Methods: Genomic DNA samples extracted from the pus specimens of two patients with orofacial abscesses were subjected to shotgun sequencing on the NovaSeq system. Taxonomic profiling and prediction of ARGs were performed directly from the metagenomic raw reads. Result: Taxonomic profiling revealed obligate anaerobic polymicrobial communities associated with infections of odontogenic origins: the microbial community of Patient 1 consisted of one predominant species (Prevotella oris 74.6%) with 27 minor species, while the sample from Patient 2 contained 3 abundant species (Porphyromonas endodontalis 33.0%; P. oris 31.6%; and Prevotella koreensis 13.4%) with five minor species. A total of 150 and 136 putative ARGs were predicted in the metagenome of each pus sample. The coverage of most predicted ARGs was less than 10%, and only the CfxA2 gene identified in Patient 1 was covered 100%. ARG analysis of the seven assembled genome/metagenome datasets of P. oris revealed that strain C735 carried the CfxA2 gene. Conclusion: A metagenomics-based approach is useful to profile predominantly anaerobic polymicrobial communities but needs further verification for reliable ARG detection.

• 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.

• 한국산림과학회지
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• 제83권1호
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• pp.6-11
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• 1994

경상남도(慶尙南道) 일대(一帶)에서 채집(採集)한 수렵조수류(狩獵鳥獸類) 4종(種)에 대한 중금속(重金屬)을 분석(分析)한 결과(結果), 일반적(一般的)으로 생체필수원소(生體必須元素)인 Fe, Zn, Cu의 농도(濃度) 수준은 국내(國內)의 비오염지역(非汚染地域)에서 채집(採集) 발표(發表)된 산림(山林) 조수류(鳥獸類) 및 수금류(水禽類)에 대한 분석결과(分析結果)와 비슷한 수준을 보이고 있는 것으로 나타났으나 오염원소(汚染元素)인 Pb와 Cd는 일부조직(一部組織)에서 백그라운드레벨을 넘어 높은 농도(濃度)를 나타내었다. 특(特)히 Pb의 경우 정상적(正常的)인 조직분포(組織分布) 패턴과는 달리 일부(一部) 근육조직(筋肉組織)에서 높은 농도(濃度)로 검출(檢出)되었으며 이것은 포획당시 산탄(霰彈)(Pb 탄알)에 의한 오염(汚染)인 것으로 판단(判斷)되었다. 또한 산탄(霰彈)에 오염(汚染)된 근육조직(筋肉組織)은 Pb 농도(濃度)가 높아 식용(食用)으로 부적합(不適合)한 것으로 평가(評價)되었으며 국민건강(國民健康) 측면(側面)에서 볼 때 앞으로 이에 관(關)한 연구(硏究)가 시급(時急)한 실정에 있다고 하겠다.

• 한국미생물·생명공학회지
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• 제14권2호
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• pp.161-168
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• 1986

E. coli-S. cerevisiae shuttle vector인 plasmid YRp7을 이용하여 B. amyloliquefaciens의 $\alpha$-amylase gene을 E. coli 내에 cloning하였다. 이때 제한 효소 Sau 3 AI에 의해 얻어진 $\alpha$-amylase gene의 크기는 약 1.95kb정도였으며 E. coli내에서 비교적 안정하게 유지되고 발현되었다. 재조합 plasmid p-EA24를 함유한 E. coli는 B. amyloliquefaciens의 약 65% 정도의 $\alpha$-amylase를 생성하였으며, 최적온도, pH, CaCl$_2$의 영향등 $\alpha$-amylase의 효소학적인 성질을 비교 조사해 본 결과 B. amyloliquefaciens의 $\alpha$-amylase와 동일하였다. 또한 E. coli에서 생성된 $\alpha$-amylase로 70% 정도가 periplasmic space에 존재하였으며 나머지는 세포 내부에 존재함을 알았다.

• 한국미생물·생명공학회지
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• 제14권2호
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• pp.155-160
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• 1986

E. coli-Yeast shuttle vector YEp 13에 B. amyloliquefaciens의 $\alpha$-amylase gene을 cloning하여 얻은 hybrid plasnidlasmid를 E. coli를 숙주세포로 하여 형질을 발현시켰다. 형질전환주의 $\alpha$-amylase 활성 측정 결과, B. amyloliquefaciens에 대해 20-30%의 상대 활성도를 나타내었다. 형질전환주의 경우 생성된 $\alpha$-amylase의 60-65%가 periplasm에 축적되었으며 세포 외부로의 분비는 없었다. Hybrid DNA를 agarose-gel 전기영동으로 조사한 결과 그 크기가 다른 다수의 hybrid DNA가 확인되었으며 pHA28의 plasmid (a)(Fig.3)에서만 $\alpha$-amylase 활성을 나타내는 것으로 밝혀졌다 pHA28의 plasmid(a)의 크기가 YEp 13 plasmid DNA보다 작은 것은 YEp13 plasmid에서 yeast gene부분이 deletion된 결과로 추측되었다.

• Journal of Microbiology and Biotechnology
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• 제30권2호
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• pp.259-270
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• 2020

Listeria monocytogenes is a gram-positive, facultative anaerobe food pathogen responsible for the listeriosis that mostly occurs during the low-temperature storage of a cold cut or dairy products. To understand the systemic response to a wide range of growth temperatures, L. monocytogenes were cultivated at a different temperature from 10℃ to 42℃, then whole cell proteomic analysis has been performed both exponential and stationary cells. The specific growth rate increased proportionally with the increase in growth temperature. The maximum growth rate was observed at 37℃ and was maintained at 42℃. Global protein expression profiles mainly depended on the growth temperatures showing similar clusters between exponential and stationary phases. Expressed proteins were categorized by their belonging metabolic systems and then, evaluated the change of expression level in regard to the growth temperature and stages. DnaK, GroEL, GroES, GrpE, and CspB, which were the heat&cold shock response proteins, increased their expression with increasing the growth temperatures. In particular, GroES and CspB were expressed more than 100-fold than at low temperatures during the exponential phase. Meanwhile, CspL, another cold shock protein, overexpressed at a low temperature then exponentially decreased its expression to 65-folds. Chemotaxis protein CheV and flagella proteins were highly expressed at low temperatures and stationary phases. Housekeeping proteins maintained their expression levels constant regardless of growth temperature or growth phases. Most of the growth related proteins, which include central carbon catabolic enzymes, were highly expressed at 30℃ then decreased sharply at high growth temperatures.