Draft genome sequence of Miniimonas arenae KCTC 19750^T isolated from sea sand

박수제,Park, Soo-Je The Microbiological Society of Korea 2019 미생물학회지 Vol.55 No.3

Actinobacteria 문 Beutenbergiaceae 과에 속하는 Miniimonas arenae KCTC $19750^T$는 해양모래에서 분리되었다. 본 연구에서는 KCTC $19750^T$의 비완전 유전체를 보고한다. 본 유전체는 3,402,690 bp의 크기와 73.6%의 평균 G + C 함량을 지니고 있으며, 2,947개의 단백질 코딩 유전자, 2개의 ribosomal RNA 및 44개의 transfer RNA로 구성되어 있다. 또한, 삼투압과 관련된 유전자를 포함하고 있다. 본 유전체 서열의 가용성은 Miniimonas 속의 유일한 구성원으로KCTC $19750^T$에 대한 더 많은 이해를 제공할 것이다. Miniimonas arenae KCTC $19750^T$ belonging to family Beutenbergiaceae of the phylum Actinobacteria was isolated from sea sand. I report here the draft genome sequence of strain KCTC $19750^T$. The draft genome comprises a size of 3,402,690 bp, a mean G + C content of 73.6%, 2,957 coding sequences, 2 ribosomal RNA genes, and 44 transfer RNA genes. Also, we found that genes involved in osmotic stress response were identified in its genome. The availability of the genome sequences will provide a more understanding of strain KCTC $19750^T$ as a unique member of the genus Miniimonas.

Microeukaryotic Diversity in Marine Environments, an Analysis of Surface Layer Sediments from the East Sea

박수제,Byoung-Joon Park,Vinh Hoa Pham,Dae-No Yoon,김시관,이성근 한국미생물학회 2008 The journal of microbiology Vol.46 No.3

Molecular techniques, based on clone library of 18S rRNA gene, were employed to ascertain the diversity of microeukaryotic organisms in sediments from the East Sea. A total of 261 clones were recovered from surface sediments. Most of the clone sequences (90%) were affiliated with protists, dominated by Ciliates (18%) and Dinoflagellates (19%) of Alveolates, phototrophic Stramenopiles (11%), and Cercozoa (20%). Many of the clones were related to uncultivated eukaryotes clones retrieved from anoxic environments with several highly divergent 18S rRNA gene sequences. However, no clones were related to cultivated obligate anaerobic protists. Protistan communities between subsurface layers of 1 and 9 cm shared 23% of total phylotypes which comprised 64% of total clones retrieved. Analysis of diversity indices and rarefaction curve showed that the protistan community within the 1 cm layer exhibited higher diversity than the 9 cm layer. Our results imply that diverse protists remain to be uncovered within marine benthic environments.

현무암 석분 슬러지를 재활용한 인공경량골재의 물성개선을 위한 폐유리분말과 탄산칼슘의 활용

박수제,이성은,최희복 한국건축시공학회 2014 한국건축시공학회지 Vol.14 No.3

This study was carried out to investigate the manufacturability of artificial lightweight aggregate as a way torecycle basalt powder sludge, which is a waste produced during the manufacturing process of basalt in Jeju. Powderedwaste glasses and calcium carbonate are used to improve the characteristics of manufactured artificial lightweightaggregate. Especially, considering the complex factors of basalt powder sludge, powdered waste glasses, and sinteringmethod, the amount of calcium carbonate is appropriate at the 9 wt.% in order to improve the intumescent oflightweight aggregate. Also, the amount of powdered waste glasses is effective with using less than 50 wt.% andapplying the direct sintering method at the same time on decreasing the absorption of lightweight aggregate. Furthermore, in order to manufacture artificial lightweight aggregate of high quality with a low specific gravity andlow water absorption, it is considered to be more effective to apply the direct sintering method after the surface ofartificial lightweight aggregate is covered with powdered waste glasses. 본 연구는 최근 제주도 지역내 현무암 가공과정에서 발생되는 폐기물인 석분슬러지를 재활용하기 위한 방안으로서, 인공경량골재의 제조가능성에 대해 실험하였다. 또한,현무암 석분 슬러지로 제조된 인공경량골재의 물성을 개선하기 위해 폐유리분말과 탄산칼슘이 사용되었다. 현무암 석분 슬러지와 폐유리분말 그리고 소성방법의 복합적인 요인을 고려할 때 경량골재 내부의 발포성 향상을 위해서 탄산칼슘의 양은 9 wt.%가 적당하였다. 또한, 제조된 인공경량골재의 흡수율을 저하시키기 위해서는 폐유리분말은 50 wt.%이내로 사용함과 동시에 직화소성의 방법을 적용하는 것이 더 효과적이다. 좀 더 낮은 비중과 흡수율을 가진 고품질의 인공경량골재를 성형하기 위해서는성형된 경량골재의 표면에 폐유리분말을 도포한 후 그 시료를 직화소성법으로 소성하는 것이 더 효과적일 것으로판단된다.

Evaluation of a Fosmid-Clone-Based Microarray for Comparative Analysis of Swine Fecal Metagenomes

박수제,김동환,정만영,김소정,김홍익,김양훈,채종찬,이성근 한국미생물학회 2012 The journal of microbiology Vol.50 No.4

Glass slide arrayed with fosmid clone DNAs generated from swine feces as probes were fabricated and used as a metagenome microarray (MGA). MGA appeared to be specific to their corresponding target genomic fragments. The detection limit was 10 ng of genomic DNA (ca. 106 bacterial cells) in the presence of 1000 ng of background DNA. Linear relationships between the signal intensity and the target DNA (20–100 ng) were observed (r2=0.98). Application of MGA to the comparison of swine fecal metagenomes suggested that the microbial community composition of swine intestine could be dependent on the health state of swine.

북극 Svalbard 지역 해양 퇴적물의 고세균 amoA 유전자의 다양성 분석

박수제,이성근,Park, Soo-Je,Rhee, Sung-Keun 한국미생물학회 2014 미생물학회지 Vol.50 No.2

북극지역은 지구온난화로 인하여 생태계에 큰 영향을 받고 있다. 본 연구는 북극 Svalbard 지역에서 육지 빙하의 해빙(ice melt)의 영향을 받는 해양퇴적층에서 질산화 과정에 핵심역할을 하는 고세균의 질산화유전자(ammonia monooxygenase, AMO)의 공간적 분포의 변화를 조사하였다. 해빙으로 인한 퇴적물 퇴적속도와 고세균 AMO의 alpha subunit를 코딩하는 amoA 유전자와의 관계를 클론라이브러리 분석을 통하여 분석하였다. 육지와 근접하여 퇴적속도가 가장 빠른 정점(188)에서 고세균 amoA 유전자의 다양성이 육지에서 비교적 먼 지역의 정점(176과 184)에 비해 현저히 낮음을 알 수 있었다. 3 정점의 고세균 amoA 유전자 클론들의 평균 아미노산 서열의 상동성은 94%(염기서열 91%)로 나타났다. 176과 184 정점에서 분석된 고세균 amoA 유전자 클론들 중 약 45%가 Nitosopumilus clade와 근연관계에 있는 반면, 188 지역의 경우 낮은 염농도에서 발견되는 Nitrosoarchaeaum clade와 근연관계에 있는 클론들이 발견되었다. 토양 고세균유래 amoA 유전자는 육지에 근접하여 해빙에 의한 영향을 가장 많이 받는 188정점에서만 발견이 되었다. 본 연구를 통하여, 해빙으로 인하여 육지로부터 운반되는 퇴적물의 량이 증가함에 따라, 해양퇴적층의 질소순환관련 미생물 군집에 변화가 유발되는 것으로 추정되며, 고세균의 amoA 유전자가 해양퇴적층 질소순환생태계 변화의 지표로 이용될 수 있음을 알 수 있었다. The ecosystem of the Arctic region has been increasingly affected by global warming. Archaeal ammonia monooxygenase alpha subunit coding gene (amoA) which is a key enzyme for nitrification was used to investigate the effect of runoff water of ice melt on microbial community of nitrogen cycle. The archaeal amoA genes at coastal area of Svalbard, Arctic region were PCR-amplified and sequenced after clone library construction. Analysis of archaeal amoA gene clone libraries suggested that the station 188 which is in the vicinity to the area of runoff water harbor lower ammonia-oxidizing archaeal diversity than the station 176 and 184. The average amino acid sequence identity within all archaeal amoA gene clones was 94% (with 91% nucleotide sequence identity). While all the clones of the station 188 were affiliated with Nitrosoarchaeaum clade containing strains isolated from low-salinity and terrestrial environments, about 45% of total clones of the station 176 and 184 were related to marine Nitosopumilus clade. Interestingly, other typical archaeal amoA gene clones of thaumarchaeal I.1b clade frequently retrieved from terrestrial environments was identified at station 188. Microbial community of nitrogen cycle in marine sediment might be affected by input of sediments caused by runoff glacier melt waters.

노화가 경동맥 내막-중막두께의 변화에 미치는 영향

박수제,김인섭,임성훈,허영선,김상욱,김태호,김치정,류왕성,유언호 중앙대학교 의과대학 의과학연구소 1998 中央醫大誌 Vol.23 No.4

Atherosclerosis is a diffuse disease process that produce thickening of the vascular wall because of intimal deposition of lipid, fibrous tissue, and calcific material and is highly associated with cardiovascular and cerebrovascular diseases. An increased intimal-meterial thickness (IMT) of the carotid artery has been suggested to be an early feature of atherosckerotic disease. High resolution B-mode ultrasound has been demonstrated to be useful to detect early atherosclerosis and to follow progression or regression during interventions. The purpose of this study was to investigate the influence of age on IMT of the carotid artery in healthy Koreans. IMT of the carotid artery was measured in 140 subjects who no history of cardiovascular diseases. The sonographic investigation of extracranial carotid arteries was performed with a 7.5 MHz Duplex prode. Subjects were classified into three groups; Group Ⅰ: age 30-49(n=41), Group Ⅱ: age 50-69(n=56), Group Ⅲ: age 70 or older(n=43). The results were as follows. 1. IMT of the carotid artery was thickest at the carotid bifurcation, and followed in order by common carotid artery, internal carotid artery. 2. There were no significant differences between males and females of the same decades in the carotid IMT. 3. Mean of the maximum IMT measurements from the 12 walls was 0.45±0.11mm in group Ⅰ, 0.55±0.15 mm in group Ⅱ, and 0.71±0.25 mm in group Ⅲ. IMT of common carotid artery was 0.45±0.12 mm in group Ⅰ, 0.50±0.11 mm in group Ⅱ, and 0.68±0.23 mm in group Ⅲ. IMT of carotid bifucation was 0.50±0.12 mm in group Ⅰ, 0.65±0.22 mm in group Ⅱ, and 0.84±0.34 mm in group Ⅲ, respectively. 4. Carotid atherosclerosis was not shown in group Ⅰ, however, in group Ⅱ, 8 subjects(14%) had carotid atherosclerotic plaques, and 12 subjects(28%) of group Ⅲ showed significant atherosclerosis of the carotid arteries. The prevalence of atherosclerotic plaques in 140 subjects was about 14 %. In conclusion, out study has shown that IMT of the carotid artery is significantly increased with age. However, IMT of the carotid artery of healthy subjects in Korea was slightly thinner, compared with western countries. B-mode ultrasonography may provide a useful tool to identify subjects prone to develop atherosclerotic disease.

Draft genome sequence of Pseudoalteromonas sp. meg-B1 isolated from marine sediment

박수제,박세욱,Park, Soo-Je,Park, Sewook The Microbiological Society of Korea 2018 미생물학회지 Vol.54 No.3

Gammaproteobacteria에 속하는 Pseudoalteromonas sp. meg-B1을 제주도 해양 퇴적물로부터 분리하였다. 본 연구에서는 대략 4.15 Mb의 크기와 41.2%의 평균 G + C 함량을 가진 meg-B1 균주의 완전한 유전체를 보고한다. 유전체는 3,606개의 코딩 서열, 9개의 리보솜 RNA 및 94개의 전사 RNA 유전자가 존재하며, 한 개의 완전한 프로파지 영역이 발견되었다. 본 유전체는 해양환경에서 생존하기 위한 삼투화합성 용질합성과 관련된 유전자(예, choline dehydrogenase)들이 확인되었다. Pseudoalteromonas sp. meg-B1 belonging to Gammaproteobacteria was isolated from marine sediment in Jeju island. Here, we report the draft genome sequence of strain meg-B1 with a size of approximately 4.15 Mbp and a mean G + C content of 41.2%. The draft genome included 3,606 coding sequences, and 9 ribosomal RNA and 94 transfer RNA genes. In the draft genome, genes (e.g. choline dehydrogenase) involved in the accumulation of compatible solutes required for survival in marine environments have been identified.

디지털 PCR을 응용한 특정 amoA유전자를 가진 질산화 Archaea 동정

박병준,박수제,이성근,Park, Byoung-Jun,Park, Soo-Je,Rhee, Sung-Keun 한국미생물학회 2007 미생물학회지 Vol.43 No.3

Mesophilic Crenarchaeota have been known to be predominant among ammonia-oxidizing microorganisms in terrestrial and marine environments. In this study, we determined the archaeal phylotypes carrying specific amoA by combining digital PCR and multiplex-nested PCR. Analysis of samples in which amoA and 16S rRNA gene were amplified showed that amoA gene diversity was relatively higher than that of 16S rRNA gene. Nitrifying archaeal group I.1a was dominant over I.1b group of crenarchaota and euryarchaeota. This approach could be applied for interrelating a functional gene to a specific phylotype in natural environments. 해양 및 토양에서의 암모니아 산화는 세균에 비해 Crenarchaeota 그룹의 archaea에 의해 우세하게 일어나고 있음이 알려졌다. 서해 갯벌에서, 배양에 의존하지 알고, 특정 암모니아 산화유전자(amoA)를 가진 archaea을 동정하고자 디지털 PCR법을 응용한 nested PCR법을 개발하였다. amoA와 16S rRNA유전자가 동시에 증폭된 샘플의 분석결과, 16S rRNA유전자에 비해 amoA 유전자의 다양성 이 높았으며, I.1a 그룹의 crenarchaea가 I.1b 그룹의 crenarchaea보다 갯벌지역에서 암모니아 산화에 우점적으로 기여하고 있음을 알 수 있었다. 본 연구에서 시도된, 디지털 PCR과 multiplex-nested PCR을 접목한 접근법을 이용하면 특정 기능유전자를 가진 미생물을 환경에서 검증하는데 응용할 수 있을 것이다.

Genome sequence of Ochrobactrum anthropi AM3 isolated from compost

이승제,박수제,채종찬,Patil, Kishor Sureshbhai,Lee, Seung Je,Park, Soo-Je,Chae, Jong-Chan 한국미생물학회 2016 미생물학회지 Vol.52 No.4

단일 탄소원과 에너지원으로 리그닌을 이용하여 성장할 수 있는 Ochrobactrum anthropi AM3 균주를 퇴비로부터 분리하였다. 본 연구에서는 AM3 균주로부터 56.2% G+C 함량의 약 5.11 Mb 크기 유전체 염기서열을 결정하였으며 연구 결과는 Ochrobactrum속의 유전적 다양성과 리그닌 분해기작 연구를 위한 유전체 정보를 제공한다. Ochrobactrum anthropi AM3 was isolated for the ability to utilize lignin as a sole carbon and energy source from compost in South Korea. Here we report the 5.11 Mb draft genome of strain AM3 with a G+C content of 56.2%, which is helpful for understanding the genetic diversity among Ochrobactrum spp. and the mechanism of lignin degradation.

Complete genome sequence analysis of Photobacterium atrarenae GJH2-4 reveals its genetic capability for benzene degradation isolated from marine environment

김민지,박수제 한국미생물학회 2022 미생물학회지 Vol.58 No.3

The genus Photobacterium belongs to family Vibrionaceae, order Vibrionales, and phylum Pseudomonadota. It is known as a Gram-stain-negative and facultative aerobe that is motile. Members of the genus Photobacterium including pathogens have various life cycles. In this study, we isolated a strain GJH2-4 belonging to the genus Photobacterium from a marine sediment of Jeju Island, South Korea. Its complete genome sequence was found to have three circularized chromosomes. After de novo assembling, its total size and G + C content were about 5.41 Mb and 53.0%, respectively. The three chromosomes encoded 4,794 protein-coding sequences, 34 ribosomal RNAs, and 153 transfer RNA genes. Unexpectedly, the genome of strain GJH2-4 contained genes for benzene degradation, complete denitrification, dissimilatory nitrate reduction, assimilatory sulfate reduction, flagellar assembly, and vitamins biosynthesis based on its genetic functional characteristics. Furthermore, its genome encoded cytochrome cbb3 oxidases known to have a high affinity for oxygen. Finally, we discovered that strain GJH2-4 could contribute to nutrient cycling in their habitats. Our findings might facilitate a better understanding of various capabilities of species in genus Photobacterium.