The Mitochondrial Genome of the Threespot WrasseHalichoeres trimaculatus (Perciformes, Labridae)

오대주,정용환 한국유전학회 2008 Genes & Genomics Vol.30 No.2

To characterize the mitochondrial genome of the threespot wrasse Halichoeres trimaculatus (Perciformes, Labridae), we cloned and sequenced the complete mitochondrial DNA. The H. trimaculatus mitochondrial genome is 16,621 base pairs (bp) in length and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control regions, as found in the mitochondrial genomes of other bony fishes. Most of the H. trimaculatus genes are encoded on the L-strand, whereas the nicotinamide adenine dinucleotide dehydrogenase (ND) 6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser-UCN, Glu, and Pro) genes are encoded on the H-strand. Two reading-frame overlaps were found on the same strand: ATPase subunit (ATP) 8 and 6 overlapped by ten nucleotides, and ND4L and ND4 overlapped by seven nucleotides. The L-strand replication origin (31 bp) was located between tRNA-Asn and tRNA-Cys genes in the H. trimaculatus mitochondrial genome. The control region, which spans 861 bp, is located between tRNA-Pro and tRNA-Phe that shows consistency with its location as other bony fishes. Within this sequence, we identified several domain sequences such as a termination associated sequence and the conserved sequence blocks 1, 2, 3 as well as D box domains. These results provide basic information for comparative mitochondrial DNA in the genus Labridae along with further consideration on molecular phylogeny and biogeographic studies in the Halichoeres species. To characterize the mitochondrial genome of the threespot wrasse Halichoeres trimaculatus (Perciformes, Labridae), we cloned and sequenced the complete mitochondrial DNA. The H. trimaculatus mitochondrial genome is 16,621 base pairs (bp) in length and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control regions, as found in the mitochondrial genomes of other bony fishes. Most of the H. trimaculatus genes are encoded on the L-strand, whereas the nicotinamide adenine dinucleotide dehydrogenase (ND) 6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser-UCN, Glu, and Pro) genes are encoded on the H-strand. Two reading-frame overlaps were found on the same strand: ATPase subunit (ATP) 8 and 6 overlapped by ten nucleotides, and ND4L and ND4 overlapped by seven nucleotides. The L-strand replication origin (31 bp) was located between tRNA-Asn and tRNA-Cys genes in the H. trimaculatus mitochondrial genome. The control region, which spans 861 bp, is located between tRNA-Pro and tRNA-Phe that shows consistency with its location as other bony fishes. Within this sequence, we identified several domain sequences such as a termination associated sequence and the conserved sequence blocks 1, 2, 3 as well as D box domains. These results provide basic information for comparative mitochondrial DNA in the genus Labridae along with further consideration on molecular phylogeny and biogeographic studies in the Halichoeres species.

The Complete Mitochondrial DNA Sequence of the Jeju Salamander, Hynobius quelpaertensis, and the Phylogenetic Relationships among the Hynobiidae

오대주,장민호,오홍식,정용환 한국유전학회 2007 Genes & Genomics Vol.29 No.3

We sequenced and characterized the complete mitochondrial genome of the Jeju salamander Hynobius quelpaertensis (Caudata, Hynobiidae). This genome, consisting of 16,407 base pairs (bp), encoded genes for 13 protein-coding genes, two ribosomal RNAs, 2 transfer RNAs, and a noncoding control region as found in other vertebrates. Most of genes from H. quelpaertensis were encoded on the H-strand, while the ND6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser-UCN, Glu, and Pro) genes were encoded on the L-strand. Al mitochondrial protein-coding genes began with an ATG start codon except for CO1, which started with the GTG. Open reading frame of H. quelpaertensis ended with TAA (ND2, CO1, ATPase 8, ATPase 6, ND3, and ND4L), TAG (ND1), AGA (ND6) or incomplete stop codons, TA (CO3, ND5, and CytB) or T (CO2 and ND4). The origin of L-strand replication in H. quelpaertensis was located in a cluster of five tRNA genes (WANCY) and was 36 nucleotides in length. A major noncoding region betwen the tRNA-Pro and tRNA-Phe genes (806 bp) was considered to be the control region. Within this sequence, we identified a conserved sequence block characteristic of this region. Acording to the maximum likelihod analyses, the Jeju salamander was grouped with H. leechi, which showed a 100% bootstrap support for their divergence. However, the homologous identity of 13 protein-coding genes ranged from 89 to 93%. These findings are useful for infering the biogeographic and phylogenetic studies within the Hynobiidae family, and in particular, the Hynobius species in Korea.

Molecular population genetic analysis of Eriocheir japonica inhabiting Andeok Valley

오대주,고민희,양경식,정용환 국립중앙과학관 2023 Journal of Asia-Pacific Biodiversity Vol.16 No.1

Eriocheir japonica inhabits rivers flowing into the East Sea, South Sea, and the coastal waters of Jeju-do in South Korea, Japan, and Sakhalin. The larvae migrate to freshwater, mature, and move to estuaries to spawn. Jeju-do has habitats that prevent the migration of aquatic organisms. Populations with low within-group genetic diversity experience increased extinction risk. Industrialization causes climate change and also creates species extinctions. The goal of this study was to investigate the genetic diversity of E. japonica inhabiting Andeok Valley to elucidate their genetic stability and encourage future con servation plans. E. japonica samples used for the study were from the Andeok Valley in South Korea. One walking leg was used for DNA extraction. DNA was amplified using polymerase chain reaction to sequence mitochondrial cytochrome c oxidase subunit 1 (CO1) and cytochrome b (CytB) genes. Haplo type and sequence diversity analyses were performed. Sequencing results for CO1 and CytB genes included 658 and 651 base pairs, respectively. The median network analysis showed that the population inhabiting Andeok Valley had a genetically simple phylogenetic structure. This region pro vides simple habitat conditions, preventing gene transfer. The probability of extinction of E. japonica that inhabits Andeok Valley is markedly high

Complete Mitochondrial Genome of the Multicolorfin Rainbowfish Halichoeres poecilopterus (Perciformes, Labridae)

오대주,김지영,이정아,정용환 한국유전학회 2007 Genes & Genomics Vol.29 No.1

We cloned and sequenced the complete mitochondrial genome of the multicolorfin rainbowfish Halichoeres poecilopterus (Perciformes, Labridae). The complete 16,433 base pairs (bp) of the fish mitochondrial genome contained 22 tRNA, two rRNA, 13 protein-coding genes, and one noncoding control region, as found in the mitochondrial genomes of other bony fishes, with the gene order identical to that of typical vertebrates. Most of the genes of H. poecilopterus were encoded on the H-strand, whereas the NADH dehydrogenase subunits (ND) 6 and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser [UCN], Glu, and Pro) genes were encoded on the L-strand. For two pairs of genes, i.e., ATPase subunit (ATPase) 8 and 6 and ND4L and ND4, the reading frames overlapped by ten and seven nucleotides, respectively. The origin of L-strand replication in H. poecilopterus occurred in a cluster of five tRNA genes (WANCY) and was 38 nucleotides in length. The conserved motif (5′-GCGGG-3′) was found at the base of the stem within the tRNA-Cys gene. A major noncoding region between the tRNA-Pro and tRNA-Phe genes (761 bp) was considered to be the control region (D-loop). Within this sequence, we identified conserved sequence blocks 1 and 2, and D Box domains characteristic to this region. We provide the first evidence for the basic characteristics of the Halichoeres mitochondrial genome among the Labridae fishes.

Tide-related Changes in mRNA Abundance of Aromatases and Estrogen Receptors in the Ovary and Brain of the Threespot Wrasse Halichoeres trimaculatus

오대주,허성표,Selma Bouchekioua,Yuki Takeuchi,Shingo Udagawa,Neelakanteswar Aluru,박용주,박지권,김세재,Thomas W. Moon,Mathilakath M. Vijayan,Akihiro Takemura 한국해양과학기술원 2018 Ocean science journal Vol.53 No.2

The threespot wrasse (Halichoeres trimaculatus; Family Labridae) is a common coral reef species of the Indo-Pacific Ocean. Given that this species spawns daily at high tide (HT), we hypothesized that endocrine changes in relation to gonadal development are synchronized with the tidal cycle. To test this, we examined the transcript abundance of two cytochrome P450 aromatases (cyp19a and cyp19b) and two estrogen receptors (erα and erβ) in the ovary and brain of this species in response to tidal change. When fish were collected around four tidal points [low tide (LT), flood tide (FT), high tide (HT), and ebb tide (ET)], gonadosomatic index and oocyte diameter increased around HT and FT, respectively. Ovulatory follicles were observed in ovaries around HT. Real-time quantitative polymerase-chain reaction revealed that mRNA abundance of cyp19a and erα, but not erβ, in the ovary increased around ET and HT, respectively. On the other hand, mRNA levels of cyp19b in the forebrain were significantly higher around FT. Increases of erα and erβ mRNA abundance around FT were observed in all areas of the brain and the midbrain, respectively. The changes in mRNA abundance of key genes involved in reproduction at specific tidal cycles, along with the development of the vitellogenic oocytes in the ovary, support our hypothesis that synchronization of endocrine changes to the tidal periodicity plays a role in the gonadal development of this species. We hypothesize that conversion of testosterone to E2 in the brain may be associated with the spawning behavior given that the wrasse exhibits group spawning with a territory-holding male around HT.

단메밀과 쓴메밀의 ITS 염기서열 기반 식별마커

오대주 ( Oh Dae-ju ),현호봉 ( Hyun Ho-bong ),임태준 ( Lim Tae-joon ),윤선아 ( Yoon Seon-a ),함영민 ( Ham Young-min ),윤원종 ( Yoon Weon-jong ),양우삼 ( Yang Woo-sam ),정용환 ( Jung Yong-hwan ) 한국유기농업학회 2018 韓國有機農業學會誌 Vol.26 No.4

We analyzed the nuclear ribosomal internal transcribed spacer (ITS) sequence of common buckwheat, Fagopyrum esculentum and tartary buckwheat, F. tataricum. The diversity of the nucleotides and haplotypes, Tajima’s D, and Fu’s Fs was analyzed and compared among the varieties of common buckwheat and tartary buckwheat. The diversity of nucleotides and haplotypes indicated that the buckwheat populations had undergone rapid population expansion but D and Fs did not support their expansion statistically. The phylogenetic analysis of ITS sequences did not clearly establish the phylogenetic relationships between the varieties of common buckwheat. The In/Del sequence of ITS-1 region could, therefore, be used as a DNA marker to distinguish raw or manufactured products derived from common buckwheat and tartary buckwheat.

Three new records of mushroom species from Hangyeong-Andeok Gotjawal, South Korea

이승학,오대주,윤원종,정용환 한국균학회 2023 韓國菌學會誌 Vol.51 No.3

This study introduces one specimen each of the genera Gymnopilus, Marasmius, and Mycenaas an unrecorded species found in the Hwasun Gotjawal and Jeju Gotjawal Provincial Parkof the Hangyeong-Andeok terrain, South Korea. Morphological analyses of macroscopic andmicroscopic features, and molecular analysis of the nuclear ribosomal internal transcribedspacer region were conducted to identify the specimens. Our results indicated that thenewly identified specimens were Gymnopilus dilepis, Marasmius tenuissimus, and Mycenaseminau. Here, we describe these newly identified mushroom species and provide baselinedata on their diversity in Gotjawal, South Korea.

화순곶자왈 버섯 종 다양성 연구

이승학,오대주,윤원종,정용환 제주학회 2022 濟州島硏究 Vol.58 No.-

This study was conducted to provide the academic foundation for the mushroom species diversity studies on Hwasun Gotjawal, which has not been investigated compared to other Gotjawal in Jeju Island. It was performed for 8 months from April to November 2020, and a total of 16 investigations were performed twice a month. Mushrooms collected through the investigations were identified through the macroscopic characteristics and nucleotide sequencse analysis of the nuclear ribosome ITS region. As a result of the investigation, a total of 17 families, 25 genera, and 33 species of mushrooms were investigated. When examining the pattern of occurrence by family, the Polyporaceae accounted for the largest proportion with 7 species, followed by Hymenogastraceae with 3 species. In this investigation, no climate-sensitive biological indicator species were observed, and 10 biological resources that need to approve for overseas export were observed. In addition, Flammulina filiformis, which has not been officially reported in South Korea, was also observed. In this study, we described the morphological characteristics and phylogenetic tree analysis results and suggest the korean name of the mushrooms. 본 연구는 제주도 내 곶자왈 중 다른 곳에 비해 조사가 이루어지지 않은 화순곶자왈을 대상으로 버섯 종 다양성 연구의 학술적 토대를 마련하기 위해 수행되었다. 본 연구의 조사는 2020년 4월부터 11월까지 8개월간 수행되었으며, 매월 2회씩 총 16회 조사를 수행하였다. 조사를 통해 채집된 버섯들은 형태적인 특징과핵 리보솜 ITS구간의 염기서열 분석을 통해 동정하였다. 조사결과 총 17과 25속 33종의 버섯이 조사되었으며, 과 별 발생양상을 살펴봤을 때 구멍장이버섯과가 7종으로 가장 많은 비중을 차지하였고 Hymenogastraceae가 3종으로 그 다음 많은 비중을 차지하였다. 이번 조사에서는 기후변화 생물지표종이 관찰되지 않았으며, 국외 반출 승인 대상 생물자원은 10종 관찰되었다. 또한 국내에 정식으로 보고되지 않은 팽나무버섯 속 버섯인 Flammulina filiformis가 관찰되었으며, 본 연구에서는 해당 버섯의 형태적 특징과 계통수 분석 결과를 제시하고 국명을 신청하고자 한다.

까마귀쪽나무 열매 추출물의 골관절염 억제 효과

윤원종,송상목,오대주,고창식,윤선아,이용범,박대원,정용준,권정은,조영미,조주현,김창숙,강세찬,함영민 한국자원식물학회 2015 한국자원식물학회지 Vol.28 No.5

Osteoarthritis (OA) is a degenerative disease characterized by the progressive degradation of joint cartilage and is accompanied by secondary inflammation of synovial membranes. The purpose of this study describes a preliminary evaluation of the anti-inflammatory activity on test material of Litsea japonica. fruit (LJTM) Also, this study was to evaluate the effects of LJTM on the joint cartilage of rat with OA induced by monosodium iodoacetate (MIA). To study for anti-inflammatory agents effectively, we first examined the inhibitory effect of the LJTM on the production of pro-inflammatory factors and cytokines stimulated with lipopolysaccharide. We identified anti-nociceptive effects of the LJTM by using in vivo peripheral and central nervous pain models. In addition, the aim of this study was to evaluate the effects on mRNA expression of MMP-2, -3, -7, -9, -13, TIMP-1 and –2 in cartilage of OA. In the LJTM inhibited production of pro-inflammatory mediators (NO and PGE2) and pro-inflammatory cytokines (TNF-α and IL-6). In cartilage, Expression of MMPs and TIMPs mRNA was suppressed in LJTM treatment group than in the control group. This study suggests that LJTM are potential candidates as anti-inflammation and anti-osteoarthritis agents (painkillers) for the treatment of OA. 본 연구는 까마귀쪽나무 열매 70% 주정에탄올 추출물을 가지고 제작된 인체적용시험시료(LJTM)의 항염증 및 골관절염biomarker의 변화를 통한 관절건강 기능성식품을 개발하기 위하여 인체적용시험시료를 제작한 후 이에 대한 유효성분의 함량을 평가하고, 인체적용시험전에 그 효력이 유지됨을 확인하기 위하여 수행되었다. 본 연구에 사용된 시료 LJTM은 NO생성이 억제되는 농도에서 세포독성이 관찰되지 않았으며, TNF-α 와 IL-6 생성이 농도 의존적으로 억제되고 PGE2를 억제하였다. 또한 동물시험에서 골관절염의 biomarker인 MMP-2, 3, 7, 9 와 TIMP-1, 2에 대한 mRNA 발현이 농도 의존적으로 억제되었으며, 중추신경계 및 말초신경계에 의한 통증을 억제하는 것으로 평가되었다. 따라서 까마귀쪽나무 열매 70% 추출물이 함유된 인체적용시험시료(LJTM)는 골관절염과 진통억제에 우수한효과가 있는 것으로 확인되었다.

김치에서 분리한 Weizmannia coagulans KK7으로 발효한 당근 잎 추출물의 함염증 활성 연구

이윤지,고보람,현혜진,오대주,윤원종 한국응용과학기술학회 2022 한국응용과학기술학회지 Vol.39 No.6

In this study, the extracts of carrot (Daucus carota var. sativa) leaf fermented with Weizmannia coagulans KK7 strain were investigated for the anti-inflammatory activities and component changes. The KK7 strain was isolated from kimchi, a Korean fermented vegetable. The high-performance liquid chromatography was performed to analyze the changes in the components of the carrot leaf extracts before and after fermentation. It was confirmed that the content of luteolin, a kind of flavonoid, was significantly increased after fermentation. The anti-inflammatory activities of the carrot leaf extracts and the fermented carrot leaf extracts were evaluated by the inhibition of NO (nitric oxide) production in LPS-induced RAW 264.7 cells. The NO scavenging ability of the fermented carrot leaf extracts was higher than the other extracts. The protein expression of iNOS, an enzyme responsible for the NO production was significantly reduced in a concentration-dependent manner by treatment with the fermented carrot leaf extracts. In conclusion, we found that the anti-inflammatory effect of carrot leaf was increased by microbial fermentation, suggesting that carrot leaf generally discarded could be used as new food and cosmetic materials through fermentation. 본 연구에서는 김치로부터 분리한 유산균 Weizmannia coagulans KK7(KCTC19023P) 균주를이용하여 당근(Daucus carota var. sativa) 잎 추출물의 발효를 실시하고 얻은 생산물의 항염증 활성 및 성분변화를 확인하였다. 발효에 의한 당근 잎 추출물의 성분 변화를 확인하기 위하여 고성능 액체크로마토그래피를 이용하여 분석한 결과 발효 전과 비교하였을 때 발효 후에 플라보노이드의 일종인 루테올린(luteolin)의 함량이 현저히 증가하는 것을 확인할 수 있었다. 당근 잎 추출물과 발효 당근 잎 추출물의 항염 활성은 LPS에서 염증을 유발한 RAW 264.7 세포에서 NO (Nitric oxide) 생성 억제 효과로 확인하였다. 발효 당근 잎 추출물을 처리하였을 때 당근 잎 추출물 처리군에 비해 NO 생성이 상대적으로 억제되는것을 확인할 수 있었다. 발효 당근 잎 추출물 농도가 증가함에 따라 NO 생성 억제 효과도 유의적으로 증가 하였다. Western blot을 통해 염증반응에서 NO 생합성과 관련된 효소 iNOS의 발현을 확인한 결과 발효 당근 잎 추출물에서 단백질 발현이 농도 의존적으로 감소하는 것을 확인할 수 있었다. 이러한 실험 결과로부터 미생물 발효를 통해 당근 잎의 항염 효과가 증대된다는 것을 확인할 수 있었으며 이는 식품으로 거의 이용되지 않고 버려지는 당근 잎이 발효를 통해 새로운 식품 및 화장품 소재로 사용될 수 있음을 시사한다.