• Korean Journal of Environment and Ecology
• /
• v.25 no.4
• /
• pp.470-478
• /
• 2011

Aster altaicus var. uchiyamae is on the list of endangered species in Korea. Using amplified fragment length polymorphism (AFLP) markers, we investigated the genetic diversity within and among four populations (Guram, Dori Island, Samhap, and Danyang) of A. altaicus var. uchiyamae. We also present the collecting strategies that most efficiently capture the genetic diversity of A. altaicus var. uchiyamae. Four AFLP primer combinations produced a total of 936 bands, of which 934 (99.8%) were polymorphic. A high level of genetic diversity (PPB = 45.3%, h = 0.104, I = 0.168, hs = 0.108) was recognized within the populations of A. altaicus var. uchiyamae. A low degree of genetic differentiation ($G_{ST}$ = 0.075, ${\theta}^B$ = 0.079) was detected among the populations. In addition, analysis of molecular variance (AMOVA) showed that genetic variation was greater within populations (91%) than among populations (9%). These results indicate that the high rate of gene flow has played an important role in forming the present populations of A. altaicus var. uchiyamae. According to maximization strategy, 17, 16, and 11 individuals captured all of the genetic variation in Dori Island, Samhap, and Guram population, respectively. The determination the minimum population size of A. altaicus var. uchiyamae in terms of the genetic information is critical and thereby gain reliable decision support for ex situ conservation of the endangered species, A. altaicus var. uchiyamae.

• Proceedings of the Korea Water Resources Association Conference
• /
• 2008.05a
• /
• pp.1634-1638
• /
• 2008

하천의 2차원 흐름 해석, 유사이동 해석, 오염확산 해석을 위한 유체의 수치해석법에는 유한요소법, 유한차분법, 유한차분법의 변형인 유한체적법, 경계적분법 등이 있다. 유체에 대한 수치해석 기법으로 전통적으로 가장 많이 사용되고 있는 방법은 유한차분법이지만, 비구조적 요소망(unstructured mesh)을 이용하여 복잡한 형상을 표현하기가 상대적으로 용이한 유한요소법이 다양한 형태의 하천 해석에는 더욱 적합할 것이다. 본 연구에서는 비구조적 요소망을 advanced front method를 이용하여 생성해 보았다. Advanced front method는 해석하고자 하는 영역에 적절한 절점들을 생성한 후 삼각 요소망을 구성하는 grid based advanced front method와 절점들을 생성하지 않고 해석 영역에 삼각 요소를 바로 구성하는 element based advanced front method로 나눌 수 있다. Grid based advanced front method에서 해석 영역에 적절한 절점을 생성하는 방법으로는 일반적인 격자 구조의 절점 생성 방법을 적용하였으며 경계와의 거리가 가까운 절점은 생성되지 않으며, 삼각 요소를 구성할 때에는 두 개의 인접 절점을 비교하여 최적의 삼각 요소를 구성하게 된다. 단 두 개의 인접 절점만을 비교함으로서 비교적 빠른 시간 안에 최적의 삼각 요소망을 구성할 수 있다. 삼각 요소망을 생성한 후에는 Laplacian smoothing을 이용하여 삼각 요소망의 형질을 개선하였다. Element based advanced front method는 외부 경계에서부터 시작된 Front가 내부 영역으로 확대되어지며 각 Front에서 적절한 절점을 직접 생성하여 바로 삼각 요소를 구성하게 된다. Front에서 생성된 절점은 인접 절점들이 있는지 검색하여 인접 절점이 있다면 생성된 절점은 삭제되어지며 인접 절점이 삼각 요소를 위한 나머지 한 점으로 채택되어진다. Front는 외부 경계와 교차되어지지 않아야 하며 또한 연속된 Front를 효율적으로 관리하기 위해 list 자료 구조를 활용하였다.

• Molecules and Cells
• /
• v.39 no.4
• /
• pp.330-336
• /
• 2016

Long non-coding RNAs (lncRNAs) are involved in multiple cellular events, as well as in tumorigenesis. Colon cance-rassociated transcript-1 (CCAT1) gene encodes an lncRNA whose over-activation was observed in an expanding list of primary human solid tumors and tumor cell lines, however its biological roles in acute myeloid leukaemia (AML) has not been reported yet at present. In this study, the aberrant upregulation of CCAT1 was detected in French-American-British M4 and M5 subtypes of adult AML patients. By gain- and loss-of-function analysis, we determined that CCAT1 repressed monocytic differentiation and promoted cell growth of HL-60 by sequestering tumor suppressive miR-155. Accordingly, a significant decrease in miR-155 level was detected in AML patients. Reintroduction of miR-155 into HL-60 cells restored monocytic maturation and repressed cell proliferation. Furthermore, CCAT1 could up-regulated c-Myc via its competing endogenous RNA (ceRNA) activity on miR-155. In conclusion, these results revealed new mechanism of lncRNA CCAT1 in AML development, and suggested that the manipulation of CCAT1 expression could serve as a potential strategy in AML therapy.

• Journal of Environmental Science International
• /
• v.24 no.8
• /
• pp.1085-1099
• /
• 2015

The purposes of this study were to suggest the methodology to select prior areas in the environmental pollution survey for livestock excreta (EPSLE) as well as to elucidate the validity of the methodology. In this study, the prior areas in the EPSLE were determined by examining the number of compost facilities categorized according to the three levels of size including the basin, the sub-basin and the watershed, respectively, based on the data from "Annual Nation-wide Pollution Sources Survey (2012)". The results suggested that the list of prior basins were Nakdong, Geum, Youngsan and Han river basins in order. Also, it was examined that the prior sub-basins in the four river basins including Nakdong, Geum, Youngsan and Han rivers were Naesung Stream, Geumgang Gongju, Juam Dam and Namhan Downstream, respectively. The prior watersheds in the sub-basins of Naesung stream, Geumgang Gongju, Juam Dam and Namhan Downstream were Seocheon Downstream, Geum Stream, Gyeombaek Suwipyo and Yanghwa Stream, respectively. The validity of the methodology used in this study was elucidated by analyzing the correlation of the number of compost facilities with the concentrations of T-N and T-P observed in the end-points of sub-basins. The results of correlation analysis showed that the concentrations of T-N and T-P increased with the number of compost facilities. Specifically, there was the stronger correlation between the number of compost facilities and the concentrations of T-N than that for T-P. Consequently, it was proved that the methodology used in this work was valid and rational for the selection of prior areas in environmental pollution survey for EPSLE.

• Molecular & Cellular Toxicology
• /
• v.1 no.4
• /
• pp.224-229
• /
• 2005

Cirsii Japonici Herba (CJH) extract has been used for hundreds of years in Asian countries as a treatment for pollutant, radiation, and alcohol-induced liver damage. The reducing effect of CJH on hydrogen peroxide-induced reactive oxygen species (ROS) production, the main cause of cell damage or death, was evaluated using the HepG2 cell line. Cell survival was determined using MTS assay. The viability of cells treated with CJH was not significantly different from oxidative-stressed HepG2 cells. A dose-dependent inhibitory effect by CJH on ROS production was shown in oxidative-stressed cells using the $H_{2}DCFDA$ assay. To identify candidate genes responsible for the anti-oxidative effects of CJH on HepG2 cells, an oligonucleotide microarray analysis was performed. The expressions of five genes were decreased, whereas nineteen genes were up-regulated in CJH plus hydrogen peroxide treated cells, compared to only hydrogen peroxide treated cells. Among them, the expression of 5 genes was decreased in hydrogen peroxide treatment when compared to control. These genes are known to regulate cell survival and progression. On the other hand, it was shown that its main compounds were not a sylimarin or its analogs. The list of differentially expressed genes may provide further insight on the action and mechanism behind the anti-oxidative effects of Cirsii Japonici Herba.

• Microbiology and Biotechnology Letters
• /
• v.26 no.1
• /
• pp.23-33
• /
• 1998

The entire sequence of a 4,214,810 bp genome of the Bacillus subtilis 168 has been determined by an international project, and the completion has been announced on July 19, 1997. For the sequencing project an international consortium was established and 25 European, 7 Japanese laboratories, 2 biotechnology companies, and our laboratory participated in the project. Within this framework we determined the complete nucleotide sequence of a 53,289 bp fragment upstream of the odhA gene (181 $^{\circ}$) of the B. subtilis 168 chromosome. On the basis of the published DNA sequences of the B. subtilis sspC and odhA genes, we obtained genomic fragments by plasmid rescue and long-range PCR. The sequenced fragment contains 56 putative open reading frames (designated yojA-yolI and 9 known genes (sspC, cge cluster, orfE5, orfRMl and odhA), in which we found many interesting features. In addition, the entire nucleotide sequence of a 53,289 bp region enabled us to revise the current genetic map of this region.

• Clinical and Experimental Reproductive Medicine
• /
• v.32 no.3
• /
• pp.269-277
• /
• 2005

Objectives: Previously, we sought to compile a list of genes expressed during early folliculogenesis by using cDNA microarray to investigate follicular gene expression and changes during primordialprimary follicle transition and development of secondary follicles (Yoon et al., 2005). Among those genes, a group of genes related to the cell size growth was characterized during the ovarian development in the present study. Methods: We determined ovarian expression pattern of six genes related to the cell size growth (cyr61, emp1, fhl1, socs2, wig1 and wisp1) and extended into CCN family (${\underline{c}}onnective$ tissue growth factor/${\underline{c}}ysteine$-rich 61/${\underline{n}}ephroblastoma$-overexpressed), ctgf, nov, wisp2, wisp3, including cyr61 and wisp1 genes. Expression of mRNA and protein according to the ovarian developmental stage was evaluated by in situ hybridization, and/or semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR), and immunohistochemistry, respectively. Results: Among 6 genes related to the cell size growth, cyr61 and wisp1 mRNA was detected only in oocytes in the postnatal day5 mouse ovaries. cyr61 mRNA expression was limited to the nucleolus of oocytes, while wisp1 was expressed in the cytoplasm and nucleolus of oocytes, except nucleus. cyr61 mRNA expression, however, was found in granulosa cells from secondary follicles. The rest 4 genes in the cell size growth group were detected in oocytes, granulosa and theca cells. Cyr61 and Wisp1 proteins were expressed in the oocyte cytoplasm from primordial follicle stage. Especially, Cyr61 protein was detected in pre-granulosa cells, Wisp1 protein was not. By using RT-PCR, we evaluated and decided that Cyr61 protein is produced by their own mRNA in pre-granulosa cells that was not detected by in situ hybridization. cyr61 and wisp1 genes are happen to be the CCN family members. The other members of CCN family were also studied, but their expression was detected in oocytes, granulose and theca cells. Conclusions: We firstly characterized the ovarian expression of genes related to the cell size growth and CCN family according to the early folliculogenesis. Cyr61 protein expression in the pre-granulosa cells is profound in meaning. Further functional analysis for cyr61 in early folliculogenesis is under investigation.

• Korean Journal of Ecology and Environment
• /
• v.55 no.4
• /
• pp.352-359
• /
• 2022

Recently, with the development of genetic technology, interest in environmental DNA (eDNA) to study biodiversity according to molecular biological approaches is increasing. Environmental DNA has many advantages over traditional research methods for biological communities distributed in the environment but highly depends on the established base sequence database. This study conducted a comprehensive analysis of the habitat status and classification at the genus level, which is mainly used in eDNA (12S rRNA, 16S rRNA, 18S rRNA, COI, and CYTB), focusing on Korean registration taxon groups (phytoplankton, zooplankton, macroinvertebrates, and fish). As a result, phytoplankton and zooplankton showed the highest taxa proportion in 18S rRNA, and macroinvertebrates observed the highest ratio in the nucleotide sequence database in COI. In fish, all genes except 18S rRNA showed a high taxon ratio. Based on the Korean registration taxon group, the gene construction of the top 20 genera according to bio density observed that most of the phytoplankton were registered in 18S rRNA, and the most significant number of COI nucleotide sequences were established in macroinvertebrates. In addition, it was confirmed that there is a nucleotide sequence for the top 20 genera in 12S rRNA, 16S rRNA, and CYTB in fish. These results provided comprehensive information on the genes suitable for eDNA research for each taxon group.