• Molecules and Cells
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• v.43 no.12
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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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• v.39 no.4
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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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• v.31 no.6
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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.

• Korean Journal of Environment and Ecology
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• v.36 no.1
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• pp.1-29
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• 2022

This study surveyed the Mt. Teomo·Hyeolgu and surrounding areas in Ganghwa Island, located in Ganghwa-gun, Incheon, to identify vascular flora and alien plants to be used as basic data for systematic management of the remarkable plants and biodiversity conservation. The survey was carried out 13 times from March 2019 to October 2020. The identified vascular flora of Mt.Teomo·Hyeolgu was 101 families, 321 genera, 517 species, 13 subspecies, 38 varieties, 5 forms, and 573 taxa. They accounted for about 12.35% of a total of 4,641 taxa of vascular plants in Korea. The identified Northern lineage plants, endemic plants, and rare plants on the Korean Peninsula as designated by IUCN were 68 taxa, 10 taxa, and 9 taxa, respectively. 69 taxa were classified as floristic target species. Three taxa, including Maui sedge [Carex thunbergii var. appendiculata (Trautv. & C.A.Mey.) Ohwi] were identified s Class IV and 14 taxa, including Violet Stanavoi clematis (Clematis fusca var. violacea Maxim.) were identified as Class III. The naturalized plants that appeared in the study site were 63 taxa, including daisy fleabane [Erigeron annuus(L.) Pers.], common ragweed [Ambrosia artemisiifoliaL.] and Canadian fleabane [Conyza canadensis(L.) Cronquist]. The above three species were found to have spread throughout Ganghwa Island and surrounding areas such as Seokmo Island, Gyodong Island, and Gimpo city. As introduced disturbing plants like prickly lettuce [Lactuca scariola L.], bur cucumber [Sicyos angulatus L.] and field dock [Rumex acetosella L.] have been newly reported in the Mt. Teomo·Hyeolgu area, mid- to long-term conservation measures should be established for native plants, such as remarkable plants, and also management measures like physical removal should be prepared at an early stage.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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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.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.11
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• pp.102-108
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• 2020

This study was conducted to investigate the genetic diversity and genetic taxonomic relationships between Korean native black goat (KNBG) populations and crossbred goats. The 45,658 common single nucleotide polymorphisms present in the KNBG strain and crossbred goat were used for the analysis. The expected and observed heterozygosity (which can be indicators of genetic diversity) were in the order of crossbred, Gyeongsang National University, Jangsu, then the Tongyeong strains. The variance component represents the degree of genetic diversity between groups. The highest variance (19.98 %) was between the Dangjin and Gyeongsang National University strains. The lowest variance (8.87 %) was between the Jangsu and Tongyeong strains. In addition, the genetic distance between the populations showed that Jangsu and Tongyeong formed one branch (they were very similar genetically). The Dangjin and the Gyeongsang National University strains appeared to form a second branch. Furthermore, the crossbred formed one branch with the Dangjin and the Gyeongsang National University strains. Therefore, the results of this study can be used as basic data to reduce unnecessary inbreeding and genetic resource flow between the KNBG populations. The basic data indicates the uniqueness of the genetic resources of the domestic lineage. These findings provide a basis for differentiating KNBG and Crossbred goats to use to improve the desirable characteristics of this species.

• Animal cells and systems
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• v.12 no.4
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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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• v.46 no.3
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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.

• Korean Journal of Environmental Biology
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• v.42 no.1
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• pp.95-126
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• 2024

In this study, we investigated the vertical distribution and vascular plants on Joryeongsan Mountain in Baekdudaegan, Korea. The results of four field surveys from April to September 2023 identified a total of 552 taxa, representing 491 species, ten subspecies, 43 varieties, six forms, and two hybrids in 314 genera and 101 families. The elevational distribution ranges of 360 taxa of vascular plants were also identified. Among them, 19 taxa were endemic to Korea, and two taxa were rare plants. The floristic target plants amounted to 100 taxa, specifically two taxa of grade V, seven taxa of grade IV, 25 taxa of grade III, 33 taxa of grade II, and 33 taxa of grade I. Seventy-eight taxa were northern lineage plants. In all, 29 taxa of alien plants were recorded in the investigated area, with a naturalized index of 5.3% and an urbanization index of 7.4%. Two plants disturbed the ecosystem. Species richness along the elevation showed a reversed double-hump shape with peaks at low, mid, and high elevations. The results of a cluster analysis showed a high degree of similarity between adjacent elevation sections, except in lowlands. Detrended Correspondence Analysis ordination also supported distinct groups by elevation. Warmth index values ranged from 62.1℃·month to 92.9℃·month on Joryeongsan Mountain. Our results provide primary data on vascular plants and valuable information on the current distribution ranges of plant species on Joryeongsan Mountain. These data could serve as a baseline for comparing species shifts at elevations under future climate changes.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.5
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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.