• Journal of Microbiology and Biotechnology
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• v.27 no.11
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• pp.1983-1993
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• 2017

Salmonella enterica subsp. enterica serovar Typhimurium, one of the most common foodborne pathogens, is transmitted mainly through contaminated food derived from infected animals. In this study, S. Typhimurium ST1120, an isolate from pig feces in Korea, was subjected to whole-genome analysis to understand its genomic features associated with virulence. The genome of ST1120 was found to have a circular chromosome of 4,855,001 bp (GC content 52.2%) and a plasmid of 6,863 bp (GC content 46.0%). This chromosome was predicted to have 4,558 open reading frames (ORFs), 17 pseudogenes, 22 rRNA genes, and 86 tRNA genes. Its plasmid was predicted to have three ORFs. Comparative genome analysis revealed that ST1120 was phylogenetically close to S. Typhimurium U288, a critical isolate in piggery farms and food chains in Europe. In silico functional analysis predicted that the ST1120 genome harbored multiple genes associated with virulence and stress resistance, including Salmonella pathogenicity islands (SPIs containing SPI-1 to SPI-5, SPI-13, and SPI-14), C63PI locus, ST104 prophage locus, and various antibiotic resistance genes. In accordance with these analysis results, ST1120 showed competence in invasion and survival abilities when it was added to host cells. It also exhibited robust resistance against antibiotics in comparison with other S. Typhimurium strains. This is the first report of the complete genome sequence of S. Typhimurium isolated from swine in Korea. Comparative genome analysis between ST1120 and other Salmonella strains would provide fruitful information toward understanding Salmonella host specificity and developing control measures against S. Typhimurium infection.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.30 no.3
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• pp.408-412
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• 1997

The cytogenetic analysis of river puffer, Takifugu obscurus belongs to Family Tetraodontidae, was performed. The chromosome number of T. obscurus was 44 and the fundamental number was 64. Heteromorphic sex chromosomes were not found. The mean cellular size and nuclear size were $11.01\times7.95{\mu}m$ and $4.05\times3.15{\mu}m$, respectively. The mean surface area and volume in cell and nucleus were $68.76{\mu}m^2\;and\;366.00{\mu}m^3,\;10.06{\mu}m^2\;and\;21.36{\mu}m^3$, respectively. The number of erythrocyte of both female and male was $12\~13\times10^5/m\ell$. Gill tissues from diploid individuals had cells with one or two nucleoli. These cytogenetic studies should be used for cytotaxonomy and as a valuable estimation of polyploidy to come in T. obscurus.

• Korean Journal of Ichthyology
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• v.30 no.2
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• pp.71-74
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• 2018

The karyotype analysis of an endangered freshwater fish, Microphysogobio koreensis, was performed to obtain basic data for phylogenetic information. To carry out our study, 4 specimens were collected in Seomjingang River and Nakdongang River and its kidney was treated by flame-drying method. The chromosome number of this species demonstrated 50 diploid chromosomes, with two populations of M. koreensis not significantly different. The karyotype revealed 2n=26m+24sm, consisting of 26 metacentric (m) and 24 submetacentric (sm) chromosomes with the total fundamental arm number determined as FN=100. Total arm length and arm ratio of the chromosomes were $1.44{\sim}2.68{\mu}m$ and 1.27~2.27, respectively. The karyotype of M. koreensis was first reported in this study.

• Journal of Aquaculture
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• v.22 no.1
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• pp.74-78
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• 2009

Backcross hybridization between Korean bullhead Pseudobagrus fulvidraco female and Korean bullhead P. fulvidraco $\times$ Ussurian bullhead Leiocassis ussuriensis hybrid male was performed, and early viability and karyotype of the backcross hybrids were examined along with their parental species. Mean fertilization rate (86.8%), hatching success (70.7%) and early survival rate (76.4%) of backcross hybrids were similar with those found in the maternal species, the Korean bullhead. From the chromosome analysis, modal chromosome numbers of Korean bullhead, Ussurian bullhead, their hybrid and backcross hybrid were the same as 2n = 52. However, their karyotypes were different among genotypes. The karyotype of backcross hybrid was 22 metacentric + 18 submetacentacentric + 12 acrocentric chromosomes.

• Genomics & Informatics
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• v.3 no.4
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• pp.142-148
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• 2005

The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-${\alpha}$ receptor-1 gene (IFNAR1), an immuneresponse-related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that 'ISPP' amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following ${\alpha}$-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species-specific host-pathogen interaction in primate evolution.

• Clinical and Experimental Reproductive Medicine
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• v.40 no.4
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• pp.148-154
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• 2013

Objective: To compare the mouse oocyte vitrification outcomes of the CryoLogic vitrification method (CVM) and the conventional open method using a Cryotop. Two CVM methods (original CVM and modified CVM) were tested. Methods: Mature oocytes obtained from female BDF-1 mice were vitrified by two-step exposure to equilibrium and vitrification solutions. Three vitrification protocols were tested on three groups: the CVM-kit, modified CVM, and Cryotop groups. After exposure to the two solutions, the oocytes were vitrified. After warming, the oocytes were fertilized in vitro, and the embryo development was assessed. Blastomeres positive for caspase were counted using an in situ assay kit. The spindle morphology and chromosome configurations of warmed vitrified oocytes were also assessed. Results: The modified CVM and Cryotop groups showed similar developmental capacities, and similar proportions of cells with intact spindles and chromosome configurations. The modified CVM protocol was superior to the original CVM protocol for developmental competence and intact spindle preservation. However, the CVM group showed a relatively higher number of apoptotic cells in blastocysts. Conclusion: Closed vitrification using the modified CVM protocol may be used as an alternative to the conventional open method, but strategies to decrease apoptosis in the blastomere need to be investigated.

• Journal of Pharmacopuncture
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• v.19 no.3
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• pp.213-224
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• 2016

Objectives: Ginseng Rh2+ is enzyme-treated ginseng extract containing high amounts of converted ginsenosides, such as compound k, Rh2, Rg3, which have potent anticancer activity. We conducted general and genetic toxicity tests to evaluate the safety of ginseng Rh2+. Methods: An acute oral toxicity test was performed at a high-level dose of 4,000 mg/kg/day in Sprague-Dawley (SD) rats. A 14-day range-finding study was also conducted to set dose levels for the 90-day study. A subchronic 90-day toxicity study was performed at dose levels of 1,000 and 2,000 mg/kg/day to investigate the no-observed-adverse-effect level (NOAEL) of ginseng Rh2+ and target organs. To identify the mutagenic potential of ginseng Rh2+, we conducted a bacterial reverse mutation test (Ames test) using amino-acid-requiring strains of Salmonella typhimurium and Escherichia coli (E. coli), a chromosome aberration test with Chinese hamster lung (CHL) cells, and an in vivo micronucleus test using ICR mice bone marrow as recommended by the Korean Ministry of Food and Drug Safety. Results: According to the results of the acute oral toxicity study, the approximate lethal dose (ALD) of ginseng Rh2+ was estimated to be higher than 4,000 mg/kg. For the 90-day study, no toxicological effect of ginseng Rh2+ was observed in body-weight changes, food consumption, clinical signs, organ weights, histopathology, ophthalmology, and clinical pathology. The NOAEL of ginseng Rh2+ was established to be 2,000 mg/kg/day, and no target organ was found in this test. In addition, no evidence of mutagenicity was found either on the in vitro genotoxicity tests, including the Ames test and the chromosome aberration test, or on the in vivo in mice bone marrow micronucleus test. Conclusion: On the basis of our findings, ginseng Rh2+ is a non-toxic material with no genotoxicity. We expect that ginseng Rh2+ may be used as a novel adjuvant anticancer agent that is safe for long-term administration.

• Korean Journal of Breeding Science
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• v.42 no.2
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• pp.144-150
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• 2010

The objective of this study was to map gene/QTL for photoblastism in a weedy rice (photoblastic rice: PBR) using DNA markers. Light-induced effect on germination of seeds was compared among three accessions (Oryza sativa L.), PBR, Milyang 23 and Ilpum. Results showed that PBR seeds started to show photoblastism during seed development, different from Ilpum and Milyang 23. Frequency distribution of germination in the F4 lines from crosses between Ilpum and PBR and, Milyang 23 and PBR revealed bimodal distributions suggesting that photoblastism was controlled by a few genes. Bulked segregant analysis using $F_4$ populations derived from the above two crosses was conducted to identify gene/QTL for photoblastism. Two QTL were identified on chromosomes 1 and 12 explaining 11.2 and 12.8% of the phenotypic variance, respectively. Two QTL were further mapped between two SSR markers, RM8260 and RM246 on chromosome 1, and between RM270 and 1103 on chromosome 12. It is noteworthy that two QTL for photoblastism were colocalized with the QTL for seed dormancy reported in the previous QTL studies. The clustering of two genes for photoblastism and dormancy possibly indicates that these regions constitute rice phytochrome gene clusters related to germination. Because PBR has a low degree of dormancy, a pleiotropic effect of a single gene controlling dormancy and photoblastism can be ruled out. The linked markers will provide the foundation for positional cloning of the gene.

• Journal of Microbiology and Biotechnology
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• v.29 no.6
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• pp.962-972
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• 2019

Non-typhoidal Salmonella (NTS) is one of the most frequent causes of bacterial foodborne illnesses. Considering that the main reservoir of NTS is the intestinal tract of livestock, foods of animal origin are regarded as the main vehicles of Salmonella infection. In particular, poultry colonized with Salmonella Typhimurium (S. Typhimurium), a dominant serotype responsible for human infections, do not exhibit overt signs and symptoms, thereby posing a potential health risk to humans. In this study, comparative genomics approaches were applied to two S. Typhimurium strains, ST1539 and ST1120, isolated from a duck slaughterhouse and a pig farm, respectively, to characterize their virulence and antimicrobial resistance-associated genomic determinants. ST1539 containing a chromosome (4,905,039 bp; 4,403 CDSs) and a plasmid (93,876 bp; 96 CDSs) was phylogenetically distinct from other S. Typhimurium strains such as ST1120 and LT2. Compared to the ST1120 genome (previously deposited in GenBank; CP021909.1 and CP021910.1), ST1539 possesses more virulence determinants, including ST64B prophage, plasmid spv operon encoding virulence factors, genes encoding SseJ effector, Rck invasin, and biofilm-forming factors (bcf operon and pefAB). In accordance with the in silico prediction, ST1539 exhibited higher cytotoxicity against epithelial cells, better survival inside macrophage cells, and faster mice-killing activity than ST1120. However, ST1539 showed less resistance against antibiotics than ST1120, which may be attributed to the multiple resistanceassociated genes in the ST1120 chromosome. The accumulation of comparative genomics data on S. Typhimurium isolates from livestock would enrich our understanding of strategies Salmonella employs to adapt to diverse host animals.

• Biomedical Science Letters
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• v.26 no.4
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• pp.368-375
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• 2020

Metabolic syndrome (MetS) is a disease that is accompanied by various metabolic related problems and refers to a disease in which various adult diseases occur along with obesity. These metabolic syndromes appear according to the individual's genetic background. APOA5-ZPR1-BUD13, a gene cluster belonging to chromosome 11q23.3, is well known for its risk of plasma triglycerides and coronary artery disease. Recently, the GWAS results for metabolic syndrome were published in Koreans. The results included the APOA5-ZPR1-BUD13, and the SNPs that first appeared in Koreans in the ZPR1 and BUD13 were also discovered. In this study, the reproducibility was investigated for the newly discovered ZPR1 (rs964184) and BUD13 (rs2075295, rs1558861) using The Health Examinees (HEXA) cohort and showed significance. In addition, BUD13 (rs117548857, rs10488698, rs149527022, rs10790162), ZPR1 (rs2075290, rs145796806, rs201247587), APOA5 (rs12791103, rs1263173, rs7396835, rs17520254) were additionally discovered and significant results were obtained. For the SNPs that showed significant results, the effect on protein expression and the effect of expression quantitative trait loci (eQTL) were also confirmed. This study is expected to contribute to the prevention and treatment of diseases with differences in onset based on individual genetic patterns as well as presenting the effect of genetic mutations in the APOA5-ZPR1-BUD13 on metabolic syndrome and blood lipid levels.