• Journal of Species Research
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• 제5권1호
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• pp.188-200
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• 2016

During recent screening to discover indigenous prokaryotic species in South Korea, a total of 31 bacterial strains assigned to the class Gammaproteobacteria were isolated from a variety of environmental samples including soil, tidal flat, freshwater, seawater, and plant roots. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust phylogenetic clade with the closest species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 31 species have been described in South Korea; therefore 5 species of 3 genera in the order Alteromonadales, 11 species of 3 genera in the order Pseudomonadales, 8 species of 6 genera in the order Enterobacteriales, 2 species of 1 genera in the order Vibrionales, 1 species of 1 genera in the order Oceanospirillales, 3 species of 3 genera in the order Xanthomonadales, and 1 species in the order Spongiibacter_o within the Gammaproteobacteia are reported for proteobacterial species found in South Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are also described in the species description section.

• Journal of Species Research
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• 제6권2호
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• pp.91-100
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• 2017

Five bacterial strains, ES10-3-3-1, KKM10-2-2-1, Ant11, JM10-4-1-3, and KMS4-11 assigned to the genus Deinococcus were isolated from soil samples collected from Namyangju-si in Gyeonggi-do, Gangnam-gu and Dongdaemun-gu in Seoul, Korea. In addition, four bacterial strains, KKM10-2-7-2, JM10-2-5, JM10-2-6-2, and KKM10-2-3 assigned to the genus Hymenobacter were isolated from soil samples collected from Gangnam-gu and Dongdaemun-gu in Seoul, in South Korea. The five Deinococcus species were Gram-stain positive, pink-pigmented, and short-rod or coccus shaped. The four Hymenobacter species were Gram-stain negative, red-pigmented, and short-rod shaped. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ES10-3-3-1, KKM10-2-2-1, Ant11, JM10-4-1-3, and KMS4-11 were most closely related to Deinococcus citri $NCCP-154^T$ (with 99.8% similarity), Deinococcus grandis DSM $12784^T$ (99.0%), Deinococcus marmoris DSM $12784^T$ (98.8%), Deinococcus claudionis $PO-04-19-125^T$ (98.7%), and Deinococcus radioresistens $8A^T$ (99.8%), respectively. KKM10-2-7-2, JM10-2-5, JM10-2-6-2, and KKM10-2-3 were most closely related to Hymenobacter algoricola $VUG-A23a^T$ (99.1% similarity), Hymenobacter elongatus $VUG-A112^T$ (99.1% similarity), Hymenobacter gelipurpurascens $Txg1^T$ (99.1% similarity), and Hymenobacter psychrotolerans $Tibet-IIU11^T$ (99.3% similarity), respectively. These nine species have never been reported in Korea; thus, five Deinococcus species are reported in the family Deinococcaceae, order Deinococcales, class Deinococci, phylum Deinococcus-Thermus and four Hymenobacter species are reported in the family Cytophagaceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes.

• Journal of Species Research
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• 제6권2호
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• pp.141-153
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• 2017

During an investigation of the biodiversity of bacterial species in Korea, we discovered many indigenous prokaryotic species. A total of 39 bacterial strains in the class Alphaproteobacteria were isolated from various environmental samples collected from marine organisms, sea water, fresh water, tap water, mud flats, activated sludge, mineral water, tidal flats, soil and decayed plants. From the high 16S rRNA gene sequence similarity (>98.7%) and formation of robust phylogenetic clades with the most closely related species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that any of these 39 Alphaproteobacteria species have been described in Korea. Specifically, 18 species in 11 genera in the order Sphingomonadales, 11 species in 10 genera in the order Rhizobiales, two species in two genera in the order Caulobacterales, six species in six genera in the order Rhodobacterales and two species in two genera in the order Rhodospirillales were found in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

• Journal of Species Research
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• 제6권2호
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• pp.129-140
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• 2017

During a comprehensive investigation of indigenous prokaryotic species in Korea, a total 31 bacterial strains assigned to the class Alphaproteobacteria were isolated from diverse environmental habitats including freshwater, seawater, brackish water, ginseng soil, plant roots, natural caves, and tidal flats. Based on their high 16S rRNA gene sequence similarities(>99.1%) and formation of robust phylogenetic clades with the closest type species, each strain was assigned to an independent and predefined bacterial species. Because there were no published or official reports regarding the isolation of these 31 species in Korea, this study identified three species in two genera in the order Caulobacterales, 12 species in 10 genera in the order Rhodobacterales, three species in two genera in the order Rhizobiales, two species in two genera in the order Rhodospirillales and 11 species in seven genera, all in the order Sphingomonadaceae within the Alphaproteobacteria are reported as new alphaproteobacterial species in Korea. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

• 전자공학회논문지CI
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• 제45권4호
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• pp.27-33
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• 2008

유전자 발현 데이터의 분석 기법 중 무감독 학습 기반의 클러스터링 기법은 생물학적 변화와 진의 발현 정도를 이해하는데 자주 사용되는 방법이다. 생명공학 연구에 있어서 그래프 기반의 MCL 알고리즘은 그래프 내의 노드들을 클러스터링 하는 알고리즘으로 빠르고 효과적이다. 우리는 기존의 MCL 알고리즘을 개선하여 마이크로어레이 데이터에 적용시켰다. MCL 알고리즘 수행 시 inflation과 대각선 항의 두 요인을 조정하는 시뮬레이션을 실행하였으며, 마코브 행렬을 이용하여 변환하였다. 또한 개선된 MCL 알고리즘에서는 더 명확한 클래스를 구분하기 위하여 각 열의 평균을 구한 후 그 값을 임계치로 사용하였다. 따라서 수정된 알고리즘은 기존의 알고리즘들보다 정확도를 높일 수 있었다. 즉, 실제 실험 결과 기존에 알려진 클래스와 비교했을 때 평균 70%의 정확도를 보였다. 또한, 다른 클러스터링 기법, K-means 알고리즘, 계층적 클러스터링 그리고 SOM 알고리즘을 비교 분석하였으며, 그 결과 MCL 알고리즘이 다른 클러스터링 기법보다 더 좋은 결과를 보임을 알 수 있다.

• 생태와환경
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• 제50권1호
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• pp.70-78
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• 2017

화산습지는 경북 군위와 영천 경계의 산정 분지 (표고 644~780 m)에 위치한다. Z.-M. 학파의 식물사회학적 방법으로 현장 식생조사가 이루어졌고, 현존식생도가 제작되었다. 단위식생의 출현종의 행동양식은 피도와 상대기여도를 이용하여 분석하였다. 버드나무하위군락, 전형하위군락, 산돌배하위군락으로 이루어진 오리나무-백당나무군락이 처음으로 기재되었다. 오리나무 우점림에 대한 선행 기재단위식생 (오리나무-진퍼리새군락, 오리나무-일본갈매나무군집, 버드나무-신나무군집 등)과의 군락분류학적, 군락동태학적 대응성이 논의되었다. 본 군락은 오리나무군강(Alnetea japonicae)에 귀속되고 산간 계류 선상지에서의 분지상(分地狀) 범람원 습생림으로 규정되었다. 화산습지의 잠재자연식생이고 증거 식생형으로서 식생보존등급 [I]의 자연식생으로 평가되었다. 입지의 수리수문 환경조건의 극적인 변화(건생화 및 부영양화)로부터 국가적 보호 전략이 요구되었다.

• Molecules and Cells
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• 제28권5호
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• pp.447-453
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• 2009

The quorum sensing (QS) inhibitors that antagonize TraR, a receptor protein for N-3-oxo-octanoyl-L-homoserine lactones (3-oxo-C8-HSL), a QS signal of Agrobacterium tumefaciens were developed. The structural analogues of 3-oxo-C8-HSL were designed by in silico molecular modeling using SYBYL packages, and synthesized by the solid phase organic synthesis (SPOS) method, where the carboxamide bond of 3-oxo-C8-HSL was replaced with a nicotinamide or a sulfonamide bond to make derivatives of N-nicotinyl-L-homoserine lactones or N-sulfonyl-L-homoserine lactones. The in vivo inhibitory activities of these compounds against QS signaling were assayed using reporter systems and compared with the estimated binding energies from the modeling study. This comparison showed fairly good correlation, suggesting that the in silico interpretation of ligand-receptor structures can be a valuable tool for the pre-design of better competitive inhibitors. In addition, these inhibitors also showed anti-biofilm activities against Pseudomonas aeruginosa.

• Journal of Species Research
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• 제8권4호
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• pp.319-336
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• 2019

During an investigation of unrecorded prokaryotic species in Republic of Korea, a total of 53 bacterial strains belonging to the class Gammaproteobacteria were isolated from soil, seawater, tidal flats, rhizosphere, salt ponds, beach sand, urine, manure, sediment, and animal intestine (Russian grayling butterfly [Hipparchia autonoe], mouse [Mus musculus], and sea bass [Lateolabrax japonicus]). Strains were identified to species using the 16S rRNA gene sequence, showing high similarity (>98.7%) with the closest bacterial species and forming a robust clade in the neighbor-joining phylogenetic tree. The 53 strains of Gammaproteobacteria in this study have not been report previously in Korea. Therefore, we describe 27 genera of 16 families in 7 orders: 13 strains in the order Alteromonadales, 1 strain in the order Chromatiales, 11 strains in the order Enterobacterales, 7 strains in the order Oceanospirillales, 10 strains in the order Pseudomonadales, 8 strains in the order Vibrionales, and 3 strains in the order Xanthomonadales. Gram reaction, strain ID, isolation source, and morphological and basic biochemical characteristics are described for each species.

• Journal of Korean Biological Nursing Science
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• 제21권1호
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• pp.22-36
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• 2019

Purpose: Even though advanced heart failure (HF) severely affects the patient's health-related quality of life (HRQoL), there is little information regarding this issue. This review is aimed to describe the relevant clinical characteristics of patient with advanced HF and identify factors influencing HRQoL in these patients. Methods: Empirical articles were searched from electronic databases issued from January 2000 to June 2018 with using the key terms 'heart failure' and 'quality of life'. There were a total of 22 articles that met the inclusion criteria and were analyzed for this study. Results: First, nine studies among 22 studies clearly stated that their participants were samples of patients with advanced HF. Most reviewed studies showed the New York Heart Association (NYHA) class as the criteria for identifying advanced HF. Second, the level of HRQoL varied depending on the measurement tools utilized by the researchers. Third, the NYHA class, gender, and symptoms were mainly associated with HRQoL in patients with advanced HF. Also, nurse- or physician-led intervention, exercise, spiritual-focused intervention, and palliative care improved the HRQoL of the patients with advanced HF. Conclusion: This study found that the clear application of criteria for advanced HF and the development of advanced HF-specific HRQoL measurement was needed. Prospective studies should be considered for identifying differences in the levels and factors influencing HRQoL in patients with early stage or advanced HF to design patient-centered care.

• 수산해양기술연구
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• 제52권2호
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• pp.130-140
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• 2016

This study analyzed annual catch trend during 45 years and monthly catch of the least 10 years (2005~2014) for chub mackerel caught in the Korean coastal waters. To determine fishing status of chub mackerel, fork length measurements were conducted at least twice every week for 100 individuals randomly selected at the Busan Cooperative Fish Market from January of 2012 to December of 2014; and biological characteristics and proximate composition (moisture, protein, fat, ash) were analyzed by length class (I~IV) on a monthly basis from January to December of 2014. Monthly catch trend showed low level below 5,000 mt from February to July, whereas high level above 15,000 mt from October to December. For the period between 2012 and 2014, annual average catch proportion of juvenile were relatively high at 68.1%, 53.1% and 53.2% from January to April, before spawning season, while those were low at 21.5%, 20.7% and 29.12% from June to November. As for the change in the proximate composition per 100 g of muscle, protein and ash did not change much by seasons and length class, whereas fat and moisture contents showed large fluctuations and complementary relationship between the two factors. Regardless of length class, monthly average fat content, containing Omega-3, showed the lowest at 7.18 g in April and highest at 19.27 g in December, which exhibited 2.6 times difference from one another. Regardless of fishing seasons, fat content by length class were 19.06 g for the class I and 6.43 g for the class IV, which showed three times difference. Fat contents of the class I were high at 26.97 g and 27.19 g in November and December, while low at 8.37 g and 9.99 g in April and May. Especially, fat contents from January to May were 5.0 g, which was the lowest. Therefore, it is expected that consumer could indirectly contribute fisheries management through their understanding and wise consumption based on fishing status and fluctuation of proximate composition.