• Molecules and Cells
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• 제43권12호
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• pp.1011-1022
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• 2020

Cell type specification is a delicate biological event in which every step is under tight regulation. From a molecular point of view, cell fate commitment begins with chromatin alteration, which kickstarts lineage-determining factors to initiate a series of genes required for cell specification. Several important neuronal differentiation factors have been identified from ectopic over-expression studies. However, there is scarce information on which DNA regions are modified during induced pluripotent stem cell (iPSC) to neuronal progenitor cell (NPC) differentiation, the cis regulatory factors that attach to these accessible regions, or the genes that are initially expressed. In this study, we identified the DNA accessible regions of iPSCs and NPCs via the Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq). We identified which chromatin regions were modified after neuronal differentiation and found that the enhancer regions had more active histone modification changes than the promoters. Through motif enrichment analysis, we found that NEUROD1 controls iPSC differentiation to NPC by binding to the accessible regions of enhancers in cooperation with other factors such as the Hox proteins. Finally, by using Hi-C data, we categorized the genes that directly interacted with the enhancers under the control of NEUROD1 during iPSC to NPC differentiation.

• The Plant Pathology Journal
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• 제39권4호
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• pp.409-416
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• 2023

Bacterial leaf blight of carrots caused by Xanthomonas hortorum pv. carotae (Xhc) is an important worldwide seed-borne disease. In 2012 and 2013, symptoms similar to bacterial leaf blight were found in carrot farms in Jeju Island, Korea. The phenotypic characteristics of the Korean isolation strains were similar to the type strain of Xhc. Pathogenicity showed symptoms on the 14th day after inoculation on carrot plants. Identification by genetic method was multi-position sequencing of the isolated strain JJ2001 was performed using four genes (danK, gyrB, fyuA, and rpoD). The isolated strain was confirmed to be most similar to Xhc M081. Furthermore, in order to analyze the genetic characteristics of the isolated strain, whole genome analysis was performed through the next-generation sequencing method. The draft genome size of JJ2001 is 5,443,372 bp, which contains 63.57% of G + C and has 4,547 open reading frames. Specifically, the classification of pathovar can be confirmed to be similar to that of the host lineage. Plant pathogenic factors and determinants of the majority of the secretion system are conserved in strain JJ2001. This genetic information enables detailed comparative analysis in the pathovar stage of pathogenic bacteria. Furthermore, these findings provide basic data for the distribution and diagnosis of Xanthomonas hortorum pv. carotae, a major plant pathogen that infects carrots in Korea.

• Asian-Australasian Journal of Animal Sciences
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• 제31권6호
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• pp.791-797
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• 2018

Objective: Trimethylation of histone 3 (H3) at 4th lysine N-termini (H3K4me3) in gene promoter region was the universal marker of active genes specific to cell lineage. On the contrary, coexistence of trimethylation at 27th lysine (H3K27me3) in the same loci-the bivalent H3K4m3/H3K27me3 was known to suspend the gene transcription in germ cells, and could also be inherited to the developed stem cell. In galline species, throughout example of H3K4m3 and H3K27me3 ChIP-seq analysis was still not provided. We therefore designed and demonstrated such procedures using ChIP-seq and mRNA-seq data of chicken follicular mesenchymal cells and male germ cells. Methods: Analytical workflow was designed and provided in this study. ChIP-seq and RNA-seq datasets of follicular mesenchymal cells and male germ cells were acquired and properly preprocessed. Peak calling by Model-based analysis of ChIP-seq 2 was performed to identify H3K4m3 or H3K27me3 enriched regions ($Fold-change{\geq}2$, $FDR{\leq}0.01$) in gene promoter regions. Integrative genomics viewer was utilized for cellular retinoic acid binding protein 1 (CRABP1), growth differentiation factor 10 (GDF10), and gremlin 1 (GREM1) gene explorations. Results: The acquired results indicated that follicular mesenchymal cells and germ cells shared several unique gene promoter regions enriched with H3K4me3 (5,704 peaks) and also unique regions of bivalent H3K4m3/H3K27me3 shared between all cell types and germ cells (1,909 peaks). Subsequent observation of follicular mesenchyme-specific genes-CRABP1, GDF10, and GREM1 correctly revealed vigorous transcriptions of these genes in follicular mesenchymal cells. As expected, bivalent H3K4m3/H3K27me3 pattern was manifested in gene promoter regions of germ cells, and thus suspended their transcriptions. Conclusion: According the results, an example of chicken H3K4m3/H3K27me3 ChIP-seq data analysis was successfully demonstrated in this study. Hopefully, the provided methodology should hereby be useful for galline ChIP-seq data analysis in the future.

• 한국환경생태학회지
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• 제36권1호
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• pp.1-29
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• 2022

본 연구는 인천광역시 강화군에 위치한 퇴모·혈구산의 관속식물상과 강화도 및 주변 지역의 외래식물 등을 파악하여, 조사된 식물들의 체계적인 관리와 생물다양성 보전을 위한 기초자료로 활용하기 위하여 조사를 실시하였다. 조사는 2019년 3월부터 2020년 10월까지 총 13회에 걸쳐 실시되었다. 퇴모·혈구산 일대의 관속식물상은 총 101과 321속 517종 13아종 38변종 5품종 573분류군으로 파악되었다. 이는 우리나라 관속식물 총 4,641분류군의 약 12.35%로 나타났다. 퇴모·혈구산에서 확인된 한반도 북방계식물은 청나래고사리 등 68분류군, 한반도 특산식물은 늦둥굴레 등 10분류군, IUCN 지정 희귀식물은 께묵 등 총 9분류군이 확인되었다. 식물구계학적 특정식물은 총 69분류군으로 파악되었다. IV등급은 뚝사초 등 3분류군, III등급은 종덩굴 등 14분류군이 확인되었다. 연구 대상지에서 출현한 귀화식물은 개망초, 돼지풀, 망초 등 63분류군으로 확인되었다. 개망초, 돼지풀, 망초 3종은 강화도뿐만 아니라 주변 지역인 석모도, 교동도 김포 등에도 전방위적으로 확산된 것으로 파악되었다. 그리고 가시상추, 가시박, 애기수영 등 생태계교란식물이 퇴모·혈구산에 처음으로 보고되어 퇴모·혈구산 내 특기할만한 식물 등 자생식물에 대해 중장기적인 보전 대책을 수립하고 정기적으로 물리적인 제거 등의 관리방안 대책을 조기에 마련하여야 할 것이다.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 춘계학술대회 및 임시총회
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• pp.55-55
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• 2015

Rust is one of the most destructive diseases on economically important plants such as agricultural and horticultural crops, as well as forest trees [1]. Chemical treatment is the most effective means to control rust, but use of the chemical fungicides involves inevitable risks to human health and environment [2]. Unfortunately, biocontrol is currently impracticable for rust disease management [3]. It is necessary to exploit biocontrol agents to help prevent rust diseases. As a fundamental research for future development of biocontrol agents for rusts, biodiversity of hyperparasites occurring on rust fungi was investigated. During 2006-2010, 197 fungal isolates of the rust hyperparasites were collected and isolated from various combinations of mycohosts and plant hosts in many regions of Korea. Based on morphological and molecular data, they were identified as 8 genera and 12 species. Besides, phylogenetic relationships between the hyperparasites and related taxa were inferred. A total of 114 isolates of Pseudovirgaria were obtained from rust pustules of Phragmidium spp. and Pucciniastrum agrimoniae infecting rosaceous plants. Phylogenetic analysis using multigene sequences revealed a high level of genetic variability among many isolates of Pseudovirgaria and close correlation between the isolates and mycohosts. Only two species of Pseudovirgaria, P. hyperparasitica and P. grisea are often difficult to distinguish by their morphological similarity, but on the molecular basis they were clearly differentiated from each other. There had been no previous record of P. grisea outside Europe, but the present study has proved its presence in Korea. Among six distinct groups (five of P. hyperparasitica and one of P. grisea) within the Pseudovirgaria isolates, each lineage of P. hyperparasitica was closely associated with specific mycohosts and thus might have cospeciated with their mycohosts, which probably led to coevolution. Although P. grisea possesses a host preference for Phragmidium species occurring on Rubus, it was not specific for a mycohost. P. grisea seems to evolve in the direction of having a broad mycohost range. Seventeen isolates of Verticillium-like fungi were isolated from rust sori. Based on morphological data and DNA sequence analysis, the isolates were identified as three Lecanicillium species, viz. L. attenuatum, Lecanicillium sp. 1, Lecanicillium sp. 2, and V. epiphytum. The unidenified two species of Lecanicillium appear to be previously unknown taxa. Sixty-six isolates of miscellaneous hyphomycetes belonging to 6 species of 5 genera were obtained from pustules of rust fungi. On the basis of morphological and molecular analyses, the miscellaneous hyphomycetes growing on rusts were identified as Acrodontium crateriforme, Cladophialophora pucciniophila, Cladosporium cladosporioides, Phacellium vossianum, Ramularia coleosporii, and R. uredinicola.

• 한국산학기술학회논문지
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• 제21권11호
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• pp.102-108
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• 2020

본 연구는 국내 재래흑염소 집단 (당진 계통, 장수 계통, 통영 계통 및 경상대 계통)과 교잡종 염소 집단의 유전적 다양성 및 유전적 유연관계를 조사하기 위해 수행되었다. 각 집단에 존재하는 공통 SNP 45,658개를 이용하여 분석에 이용하였다. 유전적 다양성의 지표가 될 수 있는 기대, 관측 이형접합도는 교잡종, 경상대, 장수, 통영 계통 순으로 나타났다. 집단 사이의 유전적 다양성 정도를 나타내는 분산 성분은 당진과 경상대 계통 사이에서 19.98%로 가장 높게 나타났으며, 장수와 통영 계통 사이에서 8.87%로 가장 낮게 나타났다. 또한, 집단 사이의 유전적 거리는 장수, 통영 계통에서 하나의 분지를 형성하였으며, 당진, 경상대 계통이 하나의 분지로 나타냈다. 또한, 교잡종 집단은 당진, 경상대 계통과 하나의 분지를 이루는 것으로 나타났다. 따라서 본 연구 결과는 국내 계통 간의 불필요한 근친교배와 유전자원 흐름을 줄이기 위한 기초자료 및 국내 재래흑염소 유전자원의 고유성을 나타내는 기초자료로 활용이 가능할 것으로 사료된다.

• Animal cells and systems
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• 제12권4호
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• pp.269-277
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• 2008

Siberian flying squirrel, an endangered species in South Korea, is distributed through major mountain regions of South Korea. The number of Siberian flying squirrel(Pteromys volans) in South Korea has decreased and their habitats are fragmented and isolated because of anthropogenic activities. So far no molecular genetic data has, however, been available for their conservation and management. To obtain better information concerning genetic diversity and phylogenetic relationships of the Siberian flying squirrel in South Korea, we examined 14 individuals from South Korea, 7 individuals from Russia, and 5 individuals from northeastern China along with previously published 29 haplotypes for 1,140 bp of the mtDNA cytochrome b gene. The 14 new individuals from South Korea had 7 haplotypes which were not observed in the regions of Russia and Hokkaido. The level of genetic diversity(0.616%) in the South Korean population was lower than that in eastern Russia(0.950%). The geographical distribution of mtDNA haplotypes and reduced median network confirmed that there are three major lineages of Siberian flying squirrel, occupying; Far Eastern, northern Eurasia, and the island of Hokkaido. The South Korean population only slightly distinct from the Eurasia, and eastern Russian population, and is part of the lineage Far Eastern. Based on these, we suggest that the South Korean population could be considered to belong to one partial ESU(Far Eastern) of three partial ESUs but a different management unit. However, the conservation priorities should be reconfirmed by nuclear genetic marker and ecological data.

• Journal of Ecology and Environment
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• 제46권3호
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• pp.259-272
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• 2022

Background: The Korean Peninsula exhibits a characteristic graded floral distribution, with northern (Manchurian flora) and southern (China-Japan-Korea flora) lineage species coexisting according to climatic and topographical characteristics. However, this distribution has been altered by climate change. To identify ecosystem changes caused by climate change and develop appropriate measures, the current ecological status of the entire Korean Peninsula should first be determined; however, analysis of the current floral distribution in North Korea has been hampered for political reasons. To overcome these limitations, this study constructed a database of floral distributions in both South and North Korea by integrating spatial information from the previously established National Ecological Survey in South Korea and geocoding data from the literature on biological distributions published in North Korea. It was then applied to analyze the current status and distribution characteristics of Manchurian and China-Japan-Korea plant species on the Korean Peninsula. Results: In total, 45,877 cases were included in the Manchurian and China-Japan-Korea floral distribution database. China-Japan-Korea species were densely distributed on Jeju-do and along the southern coast of the Korean Peninsula. The distribution density decreased as the latitude increased, and the distributions reached higher-latitude regions in the coastal areas compared with the inland regions. Manchurian species were distributed throughout North Korea, while they were densely distributed in the refugia formed in the high-elevation mountain regions and the Baekdudaegan in South Korea. In the current distribution of biomes classified according to the Whittaker method, subtropical and endemic species were densely distributed in temperate seasonal forest and woodland/shrubland biomes, whereas boreal species were densely distributed in the boreal forest biome Korean Peninsula, with a characteristic gradation of certain species distributed in the temperate seasonal forest biome. Factor analysis showed that temperature and latitude were the main factors influencing the distribution of flora on the Korean Peninsula. Conclusions: The findings reported herein on the current floral distribution trends across the entire Korean Peninsula will prove valuable got mitigating the ecological disturbances caused by ongoing climate change. Additionally, the gathered flora data will serve as a basis for various follow-up studies on climate change.

• 환경생물
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• 제42권1호
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• pp.95-126
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• 2024

본 연구는 백두대간 조령산의 관속식물과 고도별 수직분포 조사를 조사하였다. 2023년 4월부터 2023년 9월까지 총 4회에 걸쳐 조사한 결과, 관속식물은 101과 314속 491종 10아종 43변종 6품종 2교잡종의 총 552분류군이 확인되었다. 또한 우리는 관속식물 360분류군에 대해 고도별 분포범위를 구축하였다. 한반도 특산식물은 19분류군, 희귀식물은 2분류군이었다. 식물구계학적 특정식물은 총 100분류군으로 V등급에 2분류군, IV등급에 7분류군, III등급에 25분류군, II등급에 33분류군, I등급에 33분류군이 확인되었다. 북방계 식물은 78분류군, 외래식물은 29분류군이며, 귀화율 5.3%, 도시화지수 7.4%로 나타났다. 생태계교란식물은 2분류군이 확인되었다. 종 풍부도는 저지대와 중간 고도, 정상부에서 높은 패턴이 나타났다. 고도별 종 조성의 유사도는 저지대인 해발 200~300 m를 제외하고 인접한 고도구간일수록 유사성이 높게 나타났다. 조령산은 고도에 따라 62.1~92.9℃·month의 온도 범위를 보여주었다. 본 연구는 조령산 관속식물의 분포 자료로써 추후 기후변화에 따른 식물의 분포변화 연구를 위한 기초자료로 활용될 것이다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권5호
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• pp.2073-2080
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• 2015

Background: The human papillomavirus (HPV) and its variants show wide geographical distribution and have been reported to cause cervical lesions. With cervical neoplasia as the leading cancer in Indian women, the aim of the present study was to evaluate the multiple infection HPV type distribution and variant genotypes in cervical samples from the coastal Karnataka region, India. Materials and Methods: A total of 212 samples were screened by nested polymerase chain reaction using PGMY9/11 and GP5+/6+ primers. HPV positive samples were sequenced to identify the types and a phylogenetic tree was constructed using the neighbor-joining method. Results: Sequence analysis identified a total of 14 HPV types distributed in 20%, 73.3% and 82.5% of non-malignant, pre-malignant [low grade squamous intraepithelial lesion (LSIL) and high grade squamous intraepithelial lesion (HSIL)] and cervical cancer samples. The distribution of high risk HPV in cancer samples was HPV 16, 76.4%, HPV18, 11.7%, HPV81, 2.9%, HPV31, 1.4%, HPV35, 1.4% and HPV 45, 1.4%. Multiple infections were observed in 11.8% of tumor samples with HPV 16 contributing to 62.5% of cases. In non-malignant samples, 20% of HPV positive samples were detected with HPV16, 82.3%, HPV33, 5.8% and HPV58, 5.8% and very low incidence of multiple infections. Comparative phylogenetic analysis of HPV variants identified 9 HPV sequences as new papillomavirus species, predominantly classified as European lineage type. Conclusions: The findings for HPV infections associated with progression of cervical cancer in coastal Karnataka region and HPV variant analysis provide baseline data for prevention and HPV vaccination programs.