http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
무척추동물의 NGS 데이터 분석용 PANM 데이터베이스 업데이트 (Version Ⅳ)
상민규,박지은,송대권,정준양,홍찬의,김용태,황희주,강세원,박소영,이준상,한연수,박홍석,이용석 한국패류학회 2021 The Korean Journal of Malacology Vol.37 No.1
The PANM database (Protostome DB) was first established in 2015 as a public database platform aimed at the efficient annotation of next-generation sequencing (NGS) data of species belonging to Mollusks. It was updated to version 2 in 2016 and version 3 established in 2019, with a total of 11,615,243 protein sequences. The PANM DB version 4 was updated by integrating the protein sequences of Arthropoda, Nematoda, and Mollusca registered in NCBI from the update to PANM DB v3 until February 2021. The PANM DB v4 accounts for only about 4% of the NCBI-nr database but significantly reduces the Invertebrates’ NGS data annotation time.
멸종위기야생동물 Ⅱ급 Satsuma myomphala (거제외줄달팽이) 의 argrinine kinase 유전자를 이용한 계통학적 분석
상민규,황희주,정종민,박지은,송대권,정준양,박소영,박홍석,조용훈,이종대,이준상,이용석,강세원 한국패류학회 2020 The Korean Journal of Malacology Vol.36 No.2
Arginine kinase (AK) belongs to the phosphagen kinase (PK) super family group of enzyme that has an essential role in maintaining energy homeostasis by catalyzing the re-phosphorylation of ADP. The AK gene is used for phylogenetic analysis in arthropods, mollusks, and Nematoda, and has been reported to branch in the Phylum unit. Satsuma myomphala has been reported as an indigenous species in Northeast Asia, including Korea and Japan. Particularly in Korea, it was registered as an endangered wildlife class 2 in 2017. Therefore, the preservation of species and securing genetic resources became more important. The genetic resources of S. myomphala registered on the NCBI GenBank have only six nucleotides and two proteins registered. The AK sequence was extracted from the RNAseq data which was obtained from Illumina Hiseq 2500 platfrom. After sequencing, de novo assembly and clustering, 103,774 unigenes were generated. Through annotation step by using the PANM database and BLAST program, we obtained AK sequence of 354 amino acid residues containing a 1,062 bp coding region. The AK sequence was verified using the BLAST program in the NCBI nr database, and phylogenetic analysis with the AK sequences of Gastropoda, Bivalvia, and Cephalopoda registered in NCBI was conducted. A phylogenetic dendrogram was generated using the MEGA program, and we confirmed the phylogenetic relationships. In addition, the 2D and 3D structures of the AK gene were predicted.
Metallothionein 유전자를 기초로 한 멸종위기 육상 달팽이 Satsuma myomphala (거제외줄달팽이) 의 분자계통학적 연구
상민규,강세원,황희주,정종민,송대권,민혜린,박지은,하희철,이현준,홍찬의,박소영,안영모,박영수,박홍석,한연수,이준상,이용석 한국패류학회 2016 The Korean Journal of Malacology Vol.32 No.4
Metallothionein (MT) family of metal-binding proteins are involved in maintaining homeostasis and heavy metal poisoning. Recently, MT has been considered as a biomarker that can identify a particular species, very similar to the use of cytochrome oxidase I (COI) gene. Satsuma myomphala species of land snails have been reported from North-East Asia, including South Korea and Japan. In particular, the land snail species have been known from only a limited area of Geoje Island, Gyeongsangnam-do province of South Korea. Genetic studies of S. myomphala has been limited with only 6 nucleotide, 2 protein registered on the NCBI server. For elucidating the genetic information of S. myomphala, we conducted RNA sequencing analysis using Illumina HiSeq 2500 next-generation platform. We screened the MT gene from the RNA-Seq database to confirm the molecular phylogenetic relationship. After sequencing, the de novo analysis and clustering generated 103,774 unigenes. After annotation against PANM database using BLAST program, we obtained MT sequence of 74 amino acid residues containing the coding region of 222 bp. Based on this sequence, we found about 53 sequences using the BLAST program in NCBI nr database. Using ClustalX alignment, Maximum-Likehood Tree of MEGA program, we confirmed the molecular phylogenetic relationships that showed similarity with mollusks such as Helix pomatia and H. aspersa, Megathura crenulata.
Metallothionein 유전자에 기초한 산민달팽이 (Incilaria fruhstorferi) 의 분자계통분석 연구
상민규,황희주,강세원,박승환,박소영,정종민,박지은,민혜린,이준상,한연수,박홍석,원란,이용석 한국패류학회 2017 The Korean Journal of Malacology Vol.33 No.4
Metallothionein (MT) family is a metal binding protein that is involved in maintaining homeostasis in the body and detoxifying against heavy metal poisoning. Recently, MT has been studied as a biomarker, same as a cytochrome oxidase I (COI) gene, that can identify species of various organisms. Incilaria fruhstorferi is a large slug that is distributed in Jeju Island, Chuncheon, Busan, and Deokjeokdo. The genetic information of I. fruhstorferi registered in the NCBI (53 nucleotides and 21 proteins) is indicative of the organism’s study should be needed. The researchers conducted a transcriptome study using the Illumina HiSeq 2500 Next Generation Sequencing Platform for the genetic analysis of I. fruhstorferi and obtained the MT gene of I. fruhstorferi. Molecular phylogenetic analysis was carried out using the MT gene of I. fruhstorferi, confirming the similarity with molluscs belonging to Stylommatophora such as Nesiohelix samarangae, Arianta arbustorum, Helix aspersa and H. pomatia.
상민규,황희주,정종민,박지은,송대권,정준양,강세원,한연수,이용석,박소영 한국패류학회 2020 The Korean Journal of Malacology Vol.36 No.1
With the help of Next-Generation Sequencing (NGS) technology, comprehensive genomic and transcriptomic studies have been conducted by researchers working on mollusks around the world. Base on March 2020 data at the GOLD database, 237,877 genetic projects have been registered. It shows that these results are about 4 times higher than the data reported in 2015, meaning that the genetic projects have been steadily conducted with various species. Among them, a total of 71 cases were registered for mollusks (37 cases of bivalves, 28 cases of gastropoda, and 6 cases of cephalopoda). The genome project for mollusks has increased by about 30 cases compared to 2015, mainly in the United States and China. Besides, analysis of the genetic resources registered in the NCBI for ten years indicated that the genome projects have quadrupled depending on the type of database. In case of sequence read archive (SRA) database, 18,476 mollusks-related genomic studies (about 34.7 TB) have been registered. About 66 GB of data was registered by 2010, and also about 32,532 GB was registered from 2011 to 2019, meaning that there is a 500-fold increase over the decade. Taken together, it is expected that genomic research on mollusks will have many advantages such as the preemption of genetic resources.
상민규(Min-Gyu Sang),이남경(Nam-Kyoung Lee),신용혁(Yong-Hyuk Shin),이철웅(Chulung Lee),오영진(Young-Jin Oh) 한국컴퓨터정보학회 2021 韓國컴퓨터情報學會論文誌 Vol.26 No.12
본 연구에서는 부유식 해상풍력발전의 운영 및 유지보수에 필요한 체계적인 정비계획 수립을 위해 최적화기법을 활용한 수리 모형을 제안하고자 한다. 주간 단위로 선박과 기술자를 운용하는 계획정비와 고장정비 작업의 배정에 혼합정수계획법(Mixed Integer Linear Programming, MILP)을 도입하였다. 본 연구의 최적화 모델을 활용한 사례연구에서는 선박과 기술자의 투입 규모가 유지정비 비용에 미치는 영향을 확인하였으며 1년간 정비계획 수립에서 더 나아가 정비작업별 상세스케줄링까지 연계되는 단계적 최적화 방법론을 함께 제시하였다. 세부적으로는 기상 데이터와 정비 데이터를 활용한 발전량 손실을 비가동 비용으로 반영하여 정비 우선순위를 선정하였으며, 이를 통해 국내 실정에 맞는 해상풍력단지의 유지보수 전략을 제시할 수 있을 것으로 기대한다. In this paper, we propose operations and maintenance (O&M) planning approach for floating offshore wind farm using the mathematical optimization. To be specific, we present a MILP (Mixed Integer Linear Programming that suggests the composition of vessels, technicians, and maintenance works on a weekly basis. We reflect accessibility to wind turbines based on weather data and loss of power generation using the Jensen wake model to identify downtime cost that vary from time to time. This paper also includes a description of two-stage approach for maintenance planning & detailed scheduling and numeric analysis of the number of vessels and technicians on the O&M cost. Finally, the MILP model could be utilized in order to establish the suitable and effective maintenance planning reflecting domestic situation.
Arginine Kinase를 이용한 대추귀고둥 (Ellobium chinense) 의 분자계통학적 분석
박지은,상민규,황희주,송대권,정준양,박소영,강세원,박홍석,한연수,이준상,이용석 한국패류학회 2020 The Korean Journal of Malacology Vol.36 No.3
In Korea, Ellobium chinense is one of the well-known small, air-breathing snails, and was registered as the endangered species in 2005. The number of E. chinense populations has rapidly declined in recent years. In this context, genetic information of E. chinense is needed for species conservation in the future. However, the registered genetic information of E. chinense in NCBI is only 55 nucleotides and 53 proteins. Thus, we sequenced an E. chinense cDNA library using the Illumina platform, and selected arginine kinase (AK) gene which has been used as a molecular phylogenetic marker. AK sequence of E. chinense was analyzed through bioinformatic programs, and the biological importance of E. chinense was discussed in conjuntion with molecular phylogenetic trees.
신용혁,상민규,이철웅 한국SCM학회 2023 한국SCM학회지 Vol.23 No.2
As the importance of eco-friendly energy increases worldwide, the demand for offshore wind power is gradually increasing, and accordingly, the importance of offshore wind power support port complexes is also increasing. However, compared to onshore wind power, the maintenance cost of offshore wind power is relatively high. For efficient power generation operation, a support port that can stably support maintenance is required. In this study, we propose a hydraulic model for selecting the optimal location for a maintenance support port that supports maintenance work among offshore wind power support port complexes. To solve the problem, Mixed Integer Linear Programming is introduced, and various port characteristics and meteorological requirements are reflected to enhance the realism of the model. It is expected that the results of this study will be able to suggest strategies suitable for the situation when developing large-scale offshore wind farms in Korea.
염주알다슬기 (Koreanomelania nodifila) 의 Arginine Kinase 유전자를 이용한 분자계통학적 분석
이혁,상민규,송대권,박지은,정준양,홍찬의,김용태,신현준,장이선,황희주,강세원,박소영,박홍석,이준상,한연수,이용석 한국패류학회 2023 The Korean Journal of Malacology Vol.39 No.4
Arginine kinases (AK) are known to be widely distributed in various invertebrates. It has an essential role in cellular energy metabolism. It regulates energy regulation and homeostasis in response to external stress. AK gene is used as a marker in invertebrate phylogenetic analysis. In this study, we verified whether AK can be used in molecular phylogenetic analysis. We sequenced Koreanomelania nodifila cDNA library using Illumina Hiseq 2000. The AK gene of K. nodifila was sequenced using the BLASTx program and PANM DB (v5.1). AK gene was used as a marker to molecular phylogenetic using the MEGA 11 maximum likelihood method. To analyze the 2D structure of the AK gene, the 2D structure was predicted using PSIPRED (v4.0). As a result, the AK gene ORF of K. nodifila is a total of 352 amino acids and AK gene is considered to be highly useful for molecular phylogenetic analysis of Mollusca.