• Journal of Food Hygiene and Safety
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• v.39 no.3
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• pp.231-238
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• 2024

Vibrio parahaemolyticus is a major seafood-borne pathogen commonly detected in marine environments. In Korea, V. parahaemolyticus-induced foodborne illnesses account for 7.5% of bacterial pathogen-related food poisonings. Moreover, the amount of antimicrobial agents used in aquatic cultures is continuously increasing. In this study, we isolated V. parahaemolyticus from seafood samples and performed antimicrobial susceptibility tests using the microbroth dilution method. Furthermore, using whole-genome sequencing, we identified antimicrobial resistance genes, virulence genes, and sequence types (STs). We could isolate V. parahaemolyticus from 47 (59.5%) of the 79 seafood samples we purchased from retail markets in Seoul and Chungcheong provinces. Antimicrobial susceptibility tests revealed that 2 and all of the 47 isolates were ampicillin-resistant (4.3%) and susceptible to all tested antimicrobial agents (100%), respectively. The genotype analysis revealed that all isolates carried beta-lactam-, tetracycline-, and chloramphenicol-associated antimicrobial resistance genes. However, we could detect fosfomycin resistance only in one isolate. Concerning the virulence genes, we detected T3SS1 and T3SS2-associated genes in all and one isolate, respectively. However, we could not detect the tdh and trh genes. Of the 47 isolates, 17 belonged to 15 different STs, including ST 658 with 3 isolates. The rest 30 isolates were identified as 25 new STs. The results of this study support the need for operating a continuous monitoring system to prevent foodborne illnesses and the spread of antimicrobial resistance genes in V. parahaemolyticus.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.9
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• pp.1235-1243
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• 2015

The goat Capra hircus is one of several economically important livestock in China. Advances in molecular genetics have led to the identification of several single nucleotide variation markers associated with genes affecting economic traits. Validation of single nucleotide variations in a whole-transcriptome sequencing is critical for understanding the information of molecular genetics. In this paper, we aim to develop a large amount of convinced single nucleotide polymorphisms (SNPs) for Cashmere goat through transcriptome sequencing. In this study, the transcriptomes of Cashmere goat skin at four stages were measured using RNA-sequencing and 90% to 92% unique-mapped-reads were obtained from total-mapped-reads. A total of 56,231 putative SNPs distributed among 10,057 genes were identified. The average minor allele frequency of total SNPs was 18%. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Our follow up biological validation revealed that 64% of SNPs were true SNPs. Our results show that RNA-sequencing is a fast and efficient method for identification of a large number of SNPs. This work provides significant genetic resources for further research on Cashmere goats, especially for the high density linkage map construction and genome-wide association studies.

• Journal of Life Science
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• v.31 no.4
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• pp.410-417
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• 2021

Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, premapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.526-530
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• 2023

Here, we report the draft genome sequence of Latilactobacillus sakei subsp. sakei FBL10 isolated from Saeujeot (salted fermented shrimp). The draft genome consists of 2,285,672 bp with a G+C content of 41.1% and contains 2,282 coding genes. Genome analysis revealed that clusters associated with bacteriocin production were identified, in addition to several probiotic properties, such as stress resistance factors and aggregation. On the other hand, antibiotic resistance genes and virulence factors were not present. Pangenome analysis for 32 genomes showed 213 unique genes for FBL10 strain. These results demonstrate the beneficial properties of strain FBL10 as a putative probiotic.

• Journal of Korean Neurosurgical Society
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• v.63 no.5
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• pp.559-565
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• 2020

Objective : Conflicting results regarding SOX17 genes and the risk of intracranial aneurysms (IA) exist in the Korean population, although significant positive correlations were noted in genome-wide association studies in European and Japanese populations. Therefore, we aimed to investigate an association between SOX17 gene variants and IA using exome sequencing data. Methods : This study included 26 age-gender matched IA patients and 26 control subjects. The SOX17 gene variants identified from whole-exome sequencing data were examined. Genetic associations to estimate odds ratio (OR) and 95% confidence interval (CI) were performed using the software EPACTS. Results : The mean age of the IA and control groups were 51.0±9.3 years and 49.4±14.3 years, respectively (p=0.623). Seven variants of SOX17, including six single nucleotide polymorphisms and one insertion and deletion, were observed. Among these variants, rs12544958 (A>G) showed the most association with IA, but the association was not statistically significant (OR, 1.97; 95% CI, 0.81-4.74; p=0.125). Minor allele frequencies of the IA patients and controls were 0.788 and 0.653, respectively. None of the remaining variants were significantly associated with IA formation. Conclusion : No significant association between SOX17 gene variants and IA were noted in the Korean population. A large-scale exome sequencing study is necessary to investigate any Korean-specific genetic susceptibility to IA.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1030-1038
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• 2023

Lactiplantibacillus plantarum, previously named Lactobacillus plantarum, is a facultative, homofermentative lactic acid bacterium widely distributed in nature. Several Lpb. plantarum strains have been demonstrated to possess good probiotic properties, and Lpb. plantarum HOM3204 is a potential probiotic strain isolated from homemade pickled cabbage plants. In this study, whole-genome sequencing was performed to acquire genetic information and predict the function of HOM3204, which has a circular chromosome of 3,232,697 bp and two plasmids of 48,573 and 17,060 bp, respectively. Moreover, various oxidative stress-related genes were identified in the strain, and its antioxidant activity was evaluated in vitro and in vivo. Compared to reference strains, the intracellular cell-free extracts of Lpb. plantarum HOM3204 at a dose of 10¹⁰ colony-forming units (CFU)/ml in vitro exhibited stronger antioxidant properties, such as total antioxidant activity, 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate, superoxide dismutase activity, and glutathione (GSH) content. Daily administration of 10⁹ CFU Lpb. plantarum HOM3204 for 45 days significantly improved the antioxidant function by increasing the glutathione peroxidase activity in the whole blood and GSH concentration in the livers of D-galactose-induced aging mice. These results suggest that Lpb. plantarum HOM3204 can potentially be used as a food ingredient with good antioxidant properties.

• Genomics & Informatics
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• v.20 no.2
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• pp.21.1-21.14
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• 2022

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

• Molecules and Cells
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• v.39 no.12
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• pp.862-868
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• 2016

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and cross-bred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.5
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• pp.1737-1742
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• 2015

Background: Mitochondrial DNA (mtDNA) mutations have been shown to be associated with cancer. This study explored whether mtDNA mutations enhance cholangiocarcinoma (CCA) development in individuals. Materials and Methods: The whole mitochondrial genome sequences of 25 CCA patient tissues were determined and compared to those of white blood cells from the corresponding individuals and 12 healthy controls. The mitochondrial genome was amplified using primers from Mitoseq and compared with the Cambridge Reference Sequence. Results: A total of 161 mutations were identified in CCA tissues and the corresponding white blood cells, indicating germline origins. Sixty-five (40%) were new. Nine mutations, representing those most frequently observed in CCA were tested on the larger cohort of 60 CCA patients and 55 controls. Similar occurrence frequencies were observed in both groups. Conclusions: While the correspondence between the cancer and mitochondrial genome mutation was low, it is of interest to explore the functions of the missense mutations in a larger cohort, given the possibility of targeting mitochondria for cancer markers and therapy in the future.

• Genomics & Informatics
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• v.12 no.4
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• pp.165-170
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• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.