• Journal of Microbiology and Biotechnology
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• 제27권11호
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• pp.1983-1993
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• 2017

Salmonella enterica subsp. enterica serovar Typhimurium, one of the most common foodborne pathogens, is transmitted mainly through contaminated food derived from infected animals. In this study, S. Typhimurium ST1120, an isolate from pig feces in Korea, was subjected to whole-genome analysis to understand its genomic features associated with virulence. The genome of ST1120 was found to have a circular chromosome of 4,855,001 bp (GC content 52.2%) and a plasmid of 6,863 bp (GC content 46.0%). This chromosome was predicted to have 4,558 open reading frames (ORFs), 17 pseudogenes, 22 rRNA genes, and 86 tRNA genes. Its plasmid was predicted to have three ORFs. Comparative genome analysis revealed that ST1120 was phylogenetically close to S. Typhimurium U288, a critical isolate in piggery farms and food chains in Europe. In silico functional analysis predicted that the ST1120 genome harbored multiple genes associated with virulence and stress resistance, including Salmonella pathogenicity islands (SPIs containing SPI-1 to SPI-5, SPI-13, and SPI-14), C63PI locus, ST104 prophage locus, and various antibiotic resistance genes. In accordance with these analysis results, ST1120 showed competence in invasion and survival abilities when it was added to host cells. It also exhibited robust resistance against antibiotics in comparison with other S. Typhimurium strains. This is the first report of the complete genome sequence of S. Typhimurium isolated from swine in Korea. Comparative genome analysis between ST1120 and other Salmonella strains would provide fruitful information toward understanding Salmonella host specificity and developing control measures against S. Typhimurium infection.

• 한국지능시스템학회논문지
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• 제21권5호
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• pp.575-580
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• 2011

맞춤형 의료에 대한 기대가 커지면서 분자생물학적인 의료정보의 분석이 중요해지고 있다. 유전자 발현 데이터는 생명현상의 분자생물학적 동태을 보여주는 대표적인 데이터이다. 유전자 발현 데이터의 분석을 통해서 유전자 발현 수준에서의 특정 질병의 발병, 전이, 재발 등을 예측하기 위한 마커에 대한 관심이 많다. 두 개의 대조적인 관심 집단을 식별하는 유전자를 찾기 위해 통계적인 방법 등이 이용되어 왔다. 이 논문에서는 여러 유전자의 조합을 통해서 집단을 식별할 수 있는 후보 마커를 찾는 의사결정트리 기반 방법을 제안한다. 제안한 방법에서는 수치적인 유전자의 발현값을 세 개의 범주값으로 이산화시키고, 유전자 발현값을 해당 범주값뿐만 아니라 범주값의 부정값을 허용할 수 있도록 한다. 한편, 마커로 활용하기 위해서는 소수의 유전자만을 사용하는 것이 바람직하기 때문에, 마커에 소속할 유전자의 개수를 제한하여 마커를 찾도록 한다.

• Genomics & Informatics
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• 제14권3호
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• pp.78-84
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• 2016

Extranodal natural killer (NK)/T-cell lymphoma, nasal type (NKTCL), is a malignant disorder of cytotoxic lymphocytes of NK or T cells. It is an aggressive neoplasm with a very poor prognosis. Although extranodal NKTCL reportedly has a strong association with Epstein-Barr virus, the molecular pathogenesis of NKTCL has been unexplored. The recent technological advancements in next-generation sequencing (NGS) have made DNA sequencing cost- and time-effective, with more reliable results. Using the Ion Proton Comprehensive Cancer Panel, we sequenced 409 cancer-related genes to identify somatic mutations in five NKTCL tissue samples. The sequencing analysis detected 25 mutations in 21 genes. Among them, KMT2D, a histone modification-related gene, was the most frequently mutated gene (four of the five cases). This result was consistent with recent NGS studies that have suggested KMT2D as a novel driver gene in NKTCL. Mutations were also found in ARID1A, a chromatin remodeling gene, and TP53, which also recurred in recent NGS studies. We also found mutations in 18 novel candidate genes, with molecular functions that were potentially implicated in cancer development. We suggest that these genes may result in multiple oncogenic events and may be used as potential bio-markers of NKTCL in the future.

• 정보처리학회논문지D
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• 제16D권3호
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• pp.327-338
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• 2009

마이크로어레이 데이터는 유전자의 집합이 어떠한 조건 혹은 샘플의 집합 하에서 얼마나 발현되는지를 수치화한 2차원 행렬 데이터이다. 바이클러스터는 마이크로어레이의 샘플의 부분 집합과 이 샘플 부분 집합 하에서 일정한 증감 패턴을 보이는 유전자의 부분 집합을 말한다. 이렇게 같은 패턴을 보이는 유전자의 부분 집합은 일정한 정도의 유의 수준으로 비슷한 기능을 한다고 말할 수 있다. 따라서 바이클러스터링 알고리즘은 같은 기능에 연관된 유전자의 집합과, 이 기능이 발현되고 있는 조건의 집합을 밝혀내는데 있어서 매우 유용하다. 본 논문에서는 다항식 시간 복잡도를 유지하면서, 높은 기능적 상관관계를 가지는 바이클러스터를 밝혀 낼 수 있는 알고리즘을 제안한다. 이 알고리즘은 1) 마이크로어레이 데이터에 심한 노이즈가 있을 경우 패턴으로 인식하지 못하는 기존 알고리즘과 달리, 노이즈 레벨이 심하더라도 거시적으로 비슷한 모양을 보이는 패턴을 찾아내는 방식을 이용하여 숨어있는 패턴들을 찾아낼 수 있고, 2) 바이클러스터 상호간에 오버랩을 허용하며, 또한 다양성이 보장되는 복수의 바이클러스터를 찾아내며, 3) 찾아진 유전자 부분 집합의 기능적 상관관계가 매우 높은 특성을 지니고, 4) 유전자 및 샘플의 순서와 상관없이 결정적인(deterministic) 결과를 도출한다. 또한 본 논문에서는 알고리즘이 찾아낸 바이클러스터의 기능적 상관관계의 정도와, 비교 알고리즘이 찾아낸 바이클러스터의 기능적 상관관계의 정도를 유전자 온톨로지(Gene Ontology)를 통해서 측정함으로써 비교하고 있다.

• 한국미생물·생명공학회지
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• 제48권2호
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• pp.230-235
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• 2020

The global evolution of antibiotic resistance has threatened the efficacy of available treatment options with ravaging impacts observed in developing countries. As a result, investigations into the prevalence of antibiotic resistance and the role of plasmids are crucial. In this study, we investigated the presence and distribution of bla_TEM and gyrA genes, plasmid profiles, and the antimicrobial susceptibility pattern of Salmonella strains isolated from raw meat and stool sources across Niger State, Nigeria. Ninety-eight samples, comprising 72 raw meat and 26 stool samples, were screened for Salmonella spp. The antimicrobial susceptibility of Salmonella isolates to 10 commonly used antimicrobial agents was determined using the KirbyBauer disc diffusion method. Isolates were further analyzed for plasmids, in addition to PCR amplification of beta-lactamase (bla_TEM) and gyrA genes. A total of 31 Salmonella spp. were isolated, with 22 from raw meat (70.97%) and 9 from stool (29.03%). Salmonella spp. with multiple resistance patterns to ceftazidime, cefuroxime, ceftriaxone, erythromycin, ampicillin, cloxacillin, and gentamicin were detected. Ofloxacin and ciprofloxacin were found to be the most effective among the antibiotics tested, with 67.7% and 93.5% susceptible isolates, respectively. Nine (29.03%) isolates harbored plasmids with molecular sizes ranging between 6557 bp and 23137 bp. PCR amplification of gyrA was detected in 1 (3.23%) of the 31 isolates while 28 isolates (90.32%) were positive for bla_TEM. This study shows the incidence of antibiotic resistance in Salmonella isolates and the possible role of plasmids; it also highlights the prevalence of ampicillin resistance in this local population.

• Journal of Microbiology and Biotechnology
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• 제32권9호
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• pp.1110-1119
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• 2022

Fe-S clusters are versatile and essential cofactors that participate in multiple and fundamental biological processes. In Escherichia coli, the biogenesis of these cofactors requires either the housekeeping Isc pathway, or the stress-induced Suf pathway which plays a general role under conditions of oxidative stress or iron limitation. In the present work, the Fe-S cluster assembly Isc and Suf systems of acidophilic Bacteria and Archaea, which thrive in highly oxidative environments, were studied. This analysis revealed that acidophilic microorganisms have a complete set of genes encoding for a single system (either Suf or Isc). In acidophilic Proteobacteria and Nitrospirae, a complete set of isc genes (iscRSUAX-hscBA-fdx), but not genes coding for the Suf system, was detected. The activity of the Isc system was studied in Leptospirillum sp. CF-1 (Nitrospirae). RT-PCR experiments showed that eight candidate genes were co-transcribed and conform the isc operon in this strain. Additionally, RT-qPCR assays showed that the expression of the iscS gene was significantly up-regulated in cells exposed to oxidative stress imposed by 260 mM Fe₂(SO₄)₃ for 1 h or iron starvation for 3 h. The activity of cysteine desulfurase (IscS) in CF-1 cell extracts was also upregulated under such conditions. Thus, the Isc system from Leptospirillum sp. CF-1 seems to play an active role in stressful environments. These results contribute to a better understanding of the distribution and role of Fe-S cluster protein biogenesis systems in organisms that thrive in extreme environmental conditions.

• Mycobiology
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• 제49권6호
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• pp.582-588
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• 2021

The interaction of mating pheromone and pheromone receptor from the B mating-type locus is the first step in the activation of the mushroom mating signal transduction pathway. The B mating-type locus of Lentinula edodes is composed of Bα and Bβ subloci, each of which contains genes for mating pheromone and pheromone receptor. Allelic variations in both subloci generate multiple B mating-types through which L. edodes maintains genetic diversity. In addition to the B mating-type locus, our genomic sequence analysis revealed the presence of a novel chromosomal locus 43.3 kb away from the B mating-type locus, containing genes for a pair of mating pheromones (PHBN1 and PHBN2) and a pheromone receptor (RCBN). The new locus (Bα-N) was homologous to the Bα sublocus, but unlike the multiallelic Bα sublocus, it was highly conserved across the wild and cultivated strains. The interactions of RcbN with various mating pheromones from the B and Bα-N mating-type loci were investigated using yeast model that replaced endogenous yeast mating pheromone receptor STE2 with RCBN. The yeast mating signal transduction pathway was only activated in the presence of PHBN1 or PHBN2 in the RcbN producing yeast, indicating that RcbN interacts with self-pheromones (PHBN1 and PHBN2), not with pheromones from the B mating-type locus. The biological function of the Bα-N locus was suggested to control the expression of A mating-type genes, as evidenced by the increased expression of two A-genes HD1 and HD2 upon the treatment of synthetic PHBN1 and PHBN2 peptides to the monokaryotic strain of L. edodes.

• 구강회복응용과학지
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• 제36권3호
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• pp.145-157
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• 2020

목적: 본 연구에서는 구강연조직재생에서 인간치은섬유아세포에 hydrophobically modified glycol chitosan (HGC) 기반 나노방출제어시스템을 적용 시 PI3K-AKT 신호전달의 세포생존 연관 유전자를 통해 trichloroacetic acid (TCA)와 epidermal growth factor (EGF)의 영향을 확인하고자 하였다. 연구 재료 및 방법: TCA와 EGF를 방출하는 나노방출제어시스템을 제작하였다. 실험군은 3가지 군으로 나누었다; 대조군(CON), TCA-담지형 나노방출제어시스템 투여군(EXP1), TCA-와 EGF- 담지형 나노방출제어시스템 투여군(EXP2). 인간치은섬유아세포 배양 후 PI3K-AKT 신호전달에 연관된 총 29개 유전자를 실시간 중합효소연쇄반응으로 분석했다. 일요인 분산분석 및 다중회귀분석이 사용되었다. 결과: 세포생존 관련 유전자들은 EXP1과 EXP2에서 상향조절되었다. 다중회귀분석에서는 ITGB1이 AKT1의 발현에 가장 영향력 있는 요소로 결정되었다. 결론: HGC기반 나노방출제어시스템을 통한 TCA와 EGF의 적용은 세포생존에 관한 신호전달을 상향 조절시킬 수 있다.

• Nutritional Sciences
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• 제6권4호
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• pp.229-231
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• 2003

New biochemical and genetic markers will be required to be more successful in the prevention of coronary heart disease. Postprandial lipid metabolism has received considerable attention since it was shown that postprandial triglyceride-rich lipoproteins are independently involved in the development of atherosclerosis. Multiple genes and environmental factors work in concert to alter these lipid. In this paper, postprandial lipemia, genetic variation and cardiovascular risk will be reviewed.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.113-117
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• 2005

In comparative genome analyses, synteny blocks play important roles for finding ortholog genes, reconstructing phylogenetic tree and predicting genome rearrangement events. In this paper, we propose a novel method to search biologically plausible synteny blocks not only from the viewpoint of finding highly preserved regions but also from the viewpoint of analyzing genome rearrangements. We have applied the method to our experiments on four fungal organisms, and succeeded to obtain some biologically interesting results.