• Molecules and Cells
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• v.28 no.2
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• pp.119-124
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• 2009

Anti cancer agent 5-FU (Fluoro Uracil) is a prodrug that can be metabolized and then activated to interfere with RNA and DNA homeostasis. However, the majority of administered 5-FU is known to be catabolized in vivo in the liver where Dihydropyrimidine dehydrogenase (DPD) is abundantly expressed to degrade 5-FU. The biological factors that correlate with the response to 5-FU-based chemotherapy have been proposed to include uridine phosphorylase (UPP), thymidine phosphorylase (TPP), p53 and microsatellite instability. Among these, the expression of UPP is known to be controlled by cytokines such as $TNF-{\alpha}$, IL1 and $IFN-{\gamma}$. Our preliminary study using a DNA microarray technique showed that basic fibroblast growth factor (bFGF) markedly induced the expression of UPP1 at the transcription level. In the present study, we investigated whether bFGF could modulate the expression of UPP1 in osteo-lineage cells and examined the sensitivity of these cells to 5-FU mediated apoptosis.

• The Korean Journal of Physiology and Pharmacology
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• v.3 no.5
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• pp.501-505
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• 1999

Tryptophan hydroxylase (TPH), the rate-limiting enzyme in serotonin biosynthesis, is primarily expressed in serotonergic neurons of the raphe nuclei. Simple tandem repeat polymorphisms, typically one to four nucleotides long, are tandemly repeated several times and often characterized by many alleles. To identify the presence of polymorphic repeats, we sequenced the 5'-upstream region of the mouse TPH gene. For the detection of any allelic variants, polymerase chain reaction, nonisotopic single-strand conformation polymophism, and DNA sequencing analyses of the tandem repeat sequences were performed using genomic DNA extracted from 60 ICR mice. Two dinucleotide repeats, $5'-(AC/TG)_{22}-3'$ and $5'-(GT/CA)_{17}3',$ were identified at approximately - 5.7 kb and - 3.4 kb upstream from the transcriptional initiation site of the mouse TPH gene, respectively. Minor allelic variants, $5'-(AC/TG)_{21}-3'$ and $5'-(GT/CA)_{18}-3',$ were observed in heterozygous pairs from 3 of 60 and 1 of 60 ICR mice, respectively. The identification of these microsatellites in the mouse TPH promoter raises the possibility that identical and/or other polymorphic sequences might exist in the upstream region of the human TPH gene.

• Genomics & Informatics
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• v.20 no.3
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• pp.35.1-35.9
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• 2022

Microsatellites or simple sequence repeats are motifs of 1 to 6 nucleotides in length present in both coding and non-coding regions of DNA. These are found widely distributed in the whole genome of prokaryotes, eukaryotes, bacteria, and viruses and are used as molecular markers in studying DNA variations, gene regulation, genetic diversity and evolutionary studies, etc. However, in vitro microsatellite identification proves to be time-consuming and expensive. Therefore, the present research has been focused on using an in-house built java pipeline to identify, analyse, design primers and find related statistics of perfect and compound microsatellites in the seven complete genome sequences of coronavirus, including the genome of coronavirus disease 2019, where the host is Homo sapiens. Based on search criteria among seven genomic sequences, it was revealed that the total number of perfect simple sequence repeats (SSRs) found to be in the range of 76 to 118 and compound SSRs from 01 to10, thus reflecting the low conversion of perfect simple sequence to compound repeats. Furthermore, the incidence of SSRs was insignificant but positively correlated with genome size (R² = 0.45, p > 0.05), with simple sequence repeats relative abundance (R² = 0.18, p > 0.05) and relative density (R² = 0.23, p > 0.05). Dinucleotide repeats were the most abundant in the coding region of the genome, followed by tri, mono, and tetra. This comparative study would help us understand the evolutionary relationship, genetic diversity, and hypervariability in minimal time and cost.

• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.28-28
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• 2003

Viable interspecific hybrids between yellowtail flounder (Pleuronectes ferrugineus, Store.) and winter flounder (Pleuronectes americanus, Walbaum) were produced by artificial insemination of yellowtail flounder eggs with winter flounder sperm. However, mean fertilization rate, hatching success and early survival up to 3 weeks post hatch were significantly lower than those of parental pure cross controls (P<0.01). Overall, cytogenetic traits (karyological analysis and estimation of cellular DNA contents using flow cytometry) of hybrid flounder were intermediate between the two parental species. Microsatellite assay was used to distinguish the parental genomes in the hybrids; in most cases, one allele was specific to each of the parents. Morphometrics assessed by body proportions indicated that hybrids generally displayed a morphology intermediate between the maternal and paternal species. Interspecific hybrids exhibited abnormal and retarded gonad development in both sexes based on histological analysis of gonads from adult fish. The sterility of the hybrids presents a significant advantage for their use in aquaculture, as potential escapees would not be capable of reproducing in the wild and contaminating natural stocks.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2006.11a
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• pp.84-85
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• 2006

This study was carried out to ascertain phylogenetic status of long-tail chicken which found recently in Korea and was presumed to be a kind of Korean Natives. 10 loci microsatellites were analysed for 449 birds of 11 groups and 2 region of mitochondrial DNA were sequenced for 135 birds of the same groups, that consist of 3 introduced breeds and 8 Korean Natives including 3 long-tail chicken. In mean numbers of alleles per locus(MNA) for microsatellites, long-tail chicken were smaller (2.60${\sim}$3.20) than the others, but in heterozygosities, were higher(0.4087${\sim}$0.5375) than others that were the same level of MNA. And in the neighbor joining bootstrap tree drawing by Nei's standard distance, they made a cluster with some Korean Native groups. All of the nucleotide sequences of mitochondrial cytochrome b gene and D-loop were classified into 23 haplotypes. In long-tail chicken, the haplotypes were 3 kinds, and were different among the groups (LTA, LTB and LTD). Resultly, it was supposed that 3 groups of the long-tail chicken be all a kind of Korean Natives.

• The Plant Pathology Journal
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• v.29 no.1
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• pp.10-16
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• 2013

Hevea brasiliensis is a natural source of rubber and an important plantation tree species in Malaysia. Leaf blight disease caused by Fusicoccum substantially reduces the growth and performance of H. brasiliensis. The aim of this study was to use a combination of both morphological characteristics and molecular data to clarify the taxonomic position of the fungus associated with leaf blight disease. Fusicoccum species were isolated from infected leaves collected from plantations at 3 widely separated locations - Selangor, Perak, and Johor states - in Peninsular Malaysia in 2010. All the isolates were identified according to their conidial patterns and DNA sequences generated from internal transcribed spacers (ITS1 and ITS2), the 5.8S rRNA, and an unknown locus (BotF15) containing microsatellite repeats. Based on taxonomic and sequence data, Neofusicoccum ribis was identified as the main cause of leaf blight disease in H. brasiliensis in commercial plantations in Malaysia. A pathogenicity trial on detached leaves further confirmed that N. ribis causes leaf blight disease. N. ribis is an important leaf pathogen, and its detection in Malaysia has important implications for future planting of H. brasiliensis.

• Animal cells and systems
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• v.2 no.2
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• pp.281-285
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• 1998

We examined Y chromosomal DNA polymorphisms at the DYS19 and DXYS5Y loci in a total of 480 unrelated male samples from the Korean population. All five common alleles were identified at the tetranucleotide microsatellite locus DYS19 in this study. The C allele was the most frequent (212/480), followed by D (136/480), B (75/480), E (36/480) and A (21/480) allele. The frequency of Y2 allele at the DXYS5Y locus was found to be 4.6% (22/480). Combining the allelic variation at these two loci resulted in a total of 9 combination haplotypes. The mean combination haplotype diversity wIns 0.72. Based on the results of these two loci, Korean and Japanese populations may share some common genetic structure that is rare or absent in the other ethnic groups. The genetic similarity between Korean and Japanese populations may be due to the large infusion of Y chromosomes through the Yayoi migration starting 2,300 years ago from Korea to Japan.

• Korean Journal of Breeding Science
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• v.42 no.1
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• pp.23-27
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• 2010

The objective of this study was to map the gene for reduced embryo size in rice using DNA markers. The reduced embryo size mutant was induced from N-methyl-N-nitrosourea (MNU) treated Taichung 65. Genetic analysis revealed that the phenotype of the reduced embryo was controlled by a single recessive gene, designated as re-1. For mapping the gene controlling embryo size, an $F_2$ population was developed from a cross between the Korean Tongil-type, Milyang 23 (Oryza sativa ssp. indica) and the mutant. The ratio of $F_2$ seeds nearly fitted to 3:1 ratio, indicating that this phenotype was controlled by a single recessive gene. Bulked sergeant analysis was performed with SSR markers. The gene for the reduced embryo size was detected on chromosome 1. The gene was further mapped between two SSR markers, RM315 and RM265 on chromosome 1 (approximately 1.5 Mb interval). The linked markers will facilitate selection of this grain character in a breeding program and provide the foundation for positional cloning of this gene.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• v.3 no.1
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• pp.1-6
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• 2022

Among the 13 species of otters in the world, only one Eurasian otter (Lutra lutra) is found in South Korea. In the Korean Peninsula, otter pelts were historically valuable and expensive commodities used for international trade, and otters have long been poached as hunting animals. Recent rapid economic development in South Korea has increased habitat fragmentation and loss, creating a continuing threat to the natural environment. Otters live only in the area of rivers and streams as a family group and are territorial (linear habitat). Due to these limited conditions of otter habitat, the population size of otter is lower than that of onshore mammals. According to recent research, DNA analyses using microsatellite markers have shown that only approximately 7-21 otter individuals inhabit river systems for a length of 50-230 km. Korea's urban streams are associated with many threats that hinder otters from inhabiting them. Many areas around the urban streams are surrounded by high concrete riverbanks, and the risk of roadkill is also high. Nevertheless, ecological restoration projects in the urban rivers will contribute greatly to the stable inhabitation of otters. Detailed otter conservation strategies, such as the elimination of threat factors, improvement of habitat environment, and restoration of food resources and shelter, will provide a positive restoration effect on otter and river ecosystems as well.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.4
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• pp.2185-2193
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• 2016

Background: The pathogenesis of sporadic colorectal cancer (CRC) is influenced by the patient genetic background and environmental factors. Based on prior understanding, these are classified in two major pathways of genetic instability. Microsatellite instability (MSI) and CPG island methylator phenotype (CIMP) are categorized as features of the hypermethylated prototype, and chromosomal instability (CIN) is known to be indicative of the non-hypermethylated category. Secreted frizzled related protein 2 (SFRP2), APC1A in WNT signaling pathway and the DNA repair gene, O6-methylguanine-DNA methyltransferase (MGMT), are frequently hypermethylated in colorectal cancer. Detection of methylated DNA as a biomarker by easy and inexpensive methods might improve the quality of life of patients with CRC via early detection of cancer or a precancerous condition. Aim: To evaluate the rate of SFRP2 and MGMT hypermethylation in both polyp tissue and serum of patients in south Iran as compared with matched control normal population corresponding samples. Materials and Methods: Methylation-specific PCR was used to detect hypermethylation in DNA extracted from 48 polypoid tissue samples and 25 healthy individuals. Results: Of total polyp samples, 89.5% had at least one promoter gene hypermethylation. The most frequent methylated locus was SFRP2 followed by MGMT-B (81.2 and 66.6 percent respectively). Serologic detection of hypermethylation was 95% sensitive as compared with polyp tissue. No hypermethylation was detected in normal tissue and serum and its detection in patients with polyps, especially of serrated type, was specific. Conclusions: Serologic investigation for detection of MGMT-B, SFRP2 hypermethylation could facilitate prioritization of high risk patients for colonoscopic polyp detection and excision.