• Journal of Life Science
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• v.34 no.4
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• pp.254-263
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• 2024

Korean jang is a food made using fermented soybeans, and the typical products include gochujang (GO), doenjang (DO), cheonggukjang (CH), and ganjang (GA). In this study, 16S rRNA metagenome analysis was performed on a total of 200 types of GO, DO, CH, and GA using next-generation sequencing to analyze the microbial community of fermented soybean foods and compare taxonomic (biomarker) differences. Alpha diversity analysis showed that in the CHAO index, the species richness index tended to be significantly higher compared to the DO and GA groups (p<0.001). The results of the microbial distribution analysis of the GO, DO, CH, and GA products showed that at the order level, Bacillales was the most abundant in the GO, DO, and CH groups, but Lactobacillales was most abundant in the GA group. Linear discriminant analysis effect (LEfSe) analysis was used to identify biomarkers at the family and species levels. Leuconostocaceae, Thermoactinomycetaceae, Bacillaceae, and Enterococcaceae appeared as biomarkers at the family level, and Bacillus subtilis, Kroppenstedtia sanguinis, Bacillus licheniformis, and Tetragenococcus halophilus appeared at the species level. Permutational multivariate analysis of variance (PERMANOVA) analysis showed that there was a significant difference in the microbial community structure of the GO, DO, CH, and GA groups (p=0.001), and the microbial community structure of the GA group showed the greatest difference. This study clarified the correlation between the characteristics of Korean fermented foods and microbial community distribution, enhancing knowledge of microorganisms participating in the fermentation process. These results could be leveraged to improve the quality of fermented soybean foods.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.217-225
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• 2021

The family Platycephalidae is a taxonomic group of economically important demersal flathead fishes that predominantly occupy tropical or temperate estuaries and coastal environments of the Indo-Pacific oceans and the Mediterranean Sea. In this study, we for the first time analyzed the complete mitochondrial genome (mitogenome) of the flathead Platycephalus cultellatus Richardson, 1846 from Vietnam by Next Generation Sequencing method. Its mitogenome was 16,641 bp in total length, comprising 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The gene composition and order of the mitogenome were identical to those of typical vertebrates. The phylogenetic trees were reconstructed based on the concatenated nucleotide sequence matrix of 13 PCGs and the partial sequence of a DNA barcoding marker, cox1 in order to determine its molecular phylogenetic position among the order Scorpaeniformes. The phylogenetic result revealed that P. cultellatus formed a monophyletic group with species belonging to the same family and consistently clustered with one nominal species, P. indicus, and two Platycephalus sp. specimens. Besides, the cox1 tree confirmed the taxonomic validity of our specimen by forming a monophyletic clade with its conspecific specimens. The mitogenome of P. cultellatus analyzed in this study will contribute valuable information for further study on taxonomy and phylogeny of flatheads.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.386-398
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• 2020

Wheat is one of the world's top three crops and is an important staple crop, accounting for 20% of the nutrient calories consumed by the world's population. However, due to its complex heterogeneous hexaploid chromosomes and vast genome of approximately 16 Gb, compared to those of other crops, molecular biology and biotechnology studies on wheat are lacking. In recent years, wheat genome analysis has been performed using the latest next-generation sequencing technology so that useful genes can be easily obtained, and wheat biotechnology research is accelerating in various fields. In this review, wheat transformation, an indispensable technique for developing new functional biotech wheat by revealing the function of wheat genes, is described in detail. In addition, the latest research results for overcoming plant diseases, abiotic stresses, and wheat-related diseases that are difficult to solve by classical breeding through wheat transformation and biotechnology are described.

• Korean Journal of Medicinal Crop Science
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• v.22 no.5
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• pp.339-348
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• 2014

The transcriptomes of four ginseng accessions such as Cheonryang (Korean ginseng cultivar), Yunpoong (Korean ginseng cultivar), G03080 (breeding line of Korean ginseng), and P. quinquefolius (American ginseng) was characterized. As a result of sequencing, total lengths of the reads in each sample were 156.42 Mb (Cheonryang cultivar), 161.95 Mb (Yunpoong cultivar), 165.07 Mb (G03080 breeding line), and 166.48 Mb (P. quinquefolius). Using a BLAST search against the Phytozome databases with an arbitrary expectation value of 1E-10, over 20,000 unigenes were functionally annotated and classified using DAVID software, and were found in response to external stress in the G03080 breeding line, as well as in the Cheonryang cultivar, which was associated with the ion binding term. Finally, unigenes related to transmembrane transporter activity were observed in Cheonryang and P. quinquefolius, which involves controlling osmotic pressure and turgor pressure within the cell. The expression patterns were analyzed to identify dehydrin family genes that were abundantly detected in the Cheonryang cultivar and the G03080 breeding line. In addition, the Yunpoong cultivar and P. quinquefolius accession had higher expression of heat shock proteins expressed in Ricinus communis. These results will be a valuable resource for understanding the structure and function of the ginseng transcriptomes.

• The Journal of the Korea Contents Association
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• v.19 no.3
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• pp.365-374
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• 2019

Unlike benign tumors, malignant tumors are capable of metastasis, easy to relapse, poor survival, and low quality of life. In Korea, here is a tendency to treat the tumors collectively according to the General Principles of Cancer Chemotherapy(GPCC) of the Health Insurance Review & Assessment Service (HIRA). But recently, companion diagnostics(CDx) is recommended rather than unilateral medication because biomarker-based molecular diagnostics is possible to predict the drug response of patients before drug treatment. Not only domestic but also overseas Food and Drug Administratio (FDA) recommends the development of the CDx system at the stage of drug development to ensure the responsiveness and safety of medicines. In this study, I focused on the necessity of CDx development direction as well as CDx development status through literature review. Furthermore I also discussed CDx types according to the molecular diagnostic technology such as immunohistochemistry (IHC), polymerase chain reaction (PCR), in situ hybridization (ISH), and next-generation sequencing (NGS) not only in the approved CDx but also in the developing one by US FDA. And I suggested the technology issue of CDx development process such as a selection of molecular diagnostics at the time of release, a clear understanding of the CDx mechanism, and a convergence of drug with CDx development. The necessity of social insurance system also was proposed for CDx development.

• Korean Journal of Microbiology
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• v.53 no.1
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• pp.39-48
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• 2017

In order to evaluate the diversity of microbial population of Korean traditional Deonjang and Gochujang produced in Jeju, Jeonnam, and Jeonbuk province area, microbial communities were analyzed using next generation sequencing. In this result, the dominant bacteria of Deonjang in three area were Bacillus amyloliquefaciens, Tetragenococcus halophilus, and Bacillus was major dominant bacteria in Jeonnam (43.16%) and Jeonbuk (64.54%) area. But in Jeju area, Bacillus was 0.22%, which was significantly different from the other two. Equally, the dominant fungi of Deonjang in 3 area were Candida versatilis. Common fungus in Jeonnam and Jeonbuk area was Candida sp., respectively, 64.22% and 33.68% and Micor sp. was a common fungus in Jeonnam (15.66%) and Jeonbuk area (36.73%). But in Jeju area, Candida sp. and Zygosaccharomyces rouxii were dominant than mold. Bacillus subtilis, Bacillus licheniformis, and B. amyloliquenfaciens were the preminant bacteria in the traditional Gochujang in three regions. But there were no common dominant fungi in the 3 regions. Aspergillus sp. and Rhizopus sp. prevailed in Jeju and Jeonnam region, and Zygosaccharomycess rouxii predominanted in Jeonbuk area. These results suggested that the difference in the samples collected for the study were classified into similar groups according to the characteristics of each sample rather than regional characteristics.

• Korean Journal of Microbiology
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• v.55 no.3
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• pp.268-273
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• 2019

The intestinal microbiomes vary according to the factors such environment, age and diet. The purpose of this study was to compare the gut microbial diversity between Korean infants receiving breast-fed milk and formula-fed milk. We analyzed microbial communities in stool samples collected from 80 Korean infants using next generation sequencing. Phylum level analysis revealed that microbial communities in both breast-fed infants group (BIG) was dominated by Actinobacteria ($74.22{\pm}3.48%$). Interestingly, the phylum Actinobacteria was dominant in formula-fed infants group A (FIG-A) at $73.46{\pm}4.12%$, but the proportions of phylum Actinobacteria were lower in formulafed infants group B and C (FIG-B and FIG-C) at $66.52{\pm}5.80%$ and $68.88{\pm}4.33%$. The most abundant genus in the BIG, FIG-A, FIG-B, and FIG-C was Bifidobacterium, comprising $73.09{\pm}2.31%$, $72.25{\pm}4.93%$, $63.81{\pm}6.05%$, and $67.42{\pm}5.36%$ of the total bacteria. Furthermore, the dominant bifidobacterial species detected in BIG and FIG-A was Bifidobacterium longum at $68.77{\pm}6.07%$ and $66.85{\pm}4.99%$ of the total bacteria. In contrast, the proportions of B. longum of FIG-B and FIG-C were $58.94{\pm}6.20%$ and $61.86{\pm}5.31%$ of the total bacteria. FIG-A showed a community similar to BIG, which may be due to the inclusion of galactooligosaccharide, galactosyllactose, synergy-oligosaccharide, bifidooligo and improvement material of gut microbiota contained in formula-milk. We conclude that 5-Bifidus factor contained in milk powder promotes the growth of Bifidobacterium genus in the intestines.

• KIPS Transactions on Computer and Communication Systems
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• v.2 no.2
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• pp.67-74
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• 2013

Approximate string matching problems have been studied in diverse fields. Recently, fast approximate string matching algorithms are being used to reduce the time and costs for the next generation sequencing. To measure the amounts of errors between two strings, we use a distance function such as the edit distance. Given two strings X(|X| = m) and Y(|Y| = n) over an alphabet ${\Sigma}$, the edit distance between X and Y is the minimum number of edit operations to convert X into Y. The edit distance between X and Y can be computed using the well-known dynamic programming technique in O(mn) time and space. The edit distance also can be computed using the Four-Russians' algorithm whose preprocessing step runs in $O((3{\mid}{\Sigma}{\mid})^{2t}t^2)$ time and $O((3{\mid}{\Sigma}{\mid})^{2t}t)$ space and the computation step runs in O(mn/t) time and O(mn) space where t represents the size of the block. In this paper, we present a parallelized version of the computation step of the Four-Russians' algorithm. Our algorithm computes the edit distance between X and Y in O(m+n) time using m/t threads. Then we implemented both the sequential version and our parallelized version of the Four-Russians' algorithm using CUDA to compare the execution times. When t = 1 and t = 2, our algorithm runs about 10 times and 3 times faster than the sequential algorithm, respectively.

• Tuberculosis and Respiratory Diseases
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• v.59 no.3
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• pp.250-256
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• 2005

Background : Fluoroquinolone drugs are an important anti-tuberculous agent for the treatment of multi-drug resistant tuberculosis. However, many drugs belonging to the fluoroquinolones have different cross resistance to each other. Methods : Sixty-three ofloxacin (OFX) resistant and 10 pan-susceptible M. tuberculosis isolates were selected, and compared for their cross resistance using a proportion method on Lowenstein-Jensen media, containing ofloxacin (OFX), ciprofloxacin (CIP), levofloxacin (LVX), moxifloxacin (MXF), gatifloxacin (GAT) and sparfloxacin (SPX), at concentrations ranging from 0.5 to $3{\mu}g/ml$. DNA extracted from the isolates was directly sequenced after amplifying from the gyrA and gyrB genes. Results : The 63 OFX resistant M. tuberculosis isolates showed complete cross resistance to CIP, but only 90.5, 44.4, 36.5 and 46.0% to LVX, MXF, GAT, and to SPX, respectively. Fifty-one of the isolates (81.0%) had point mutations in codons 88, 90, 91 and 94 in gyrA, which are known to be correlated with OFX resistance. The Gly88Ala, Ala90Valand Asp94Ala mutations in gyrA showed a tendency to be susceptible to MXF, GAT and SPX. Only 4 isolates had mutations in the gyrB gene, which did not affect the OFX resistance. Conclusion : About 60% of the OFX resistant M. tuberculosis isolates were susceptible to GAT, SPX and MXF. These fluoroquinolones may be useful in the treatment of TB patients showing OFX resistance.