• Korean Journal of Medicinal Crop Science
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• v.27 no.2
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• pp.75-85
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• 2019

Background: Medicinal plants are widely used in Asia. They have proven to be an invaluable asset in modern drug discovery and their demand has been steadily increasing across various industries. Methods and Results: Using 4,867 valid patents related to 12 oriental medicinal plants of 10 country groups, the growth and development potential of patents was evaluated. The cites per patent (CPP) and patent family size (PFS) indices were used to evaluate the market capability and technological level of the collected patents. Meanwhile, the patent impact index (PII) and technology strength (TS) were used to compare the technological competitiveness of patents among various technology types and markets. Both CPP and PFS indices showed that magnolia-vine and balloon flower have numerous core or original patents. Furthermore, an increase in both PII and TS indices was observed. A newly designed intellectual property multi-layer (IPM) model predicted that the medicine, genome and cosmetic categories have a high possibility of patent application growth. Conclusions: The IPM model can be used to provide the scope of particular technology fields for patent development. In addition, this study can assist patents to advance in the international market and guide the development of a national industrial strategy.

• Genomics & Informatics
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• v.21 no.1
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• pp.5.1-5.13
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• 2023

Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.273-273
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• 2022

The increasing number of Westernized eating patterns based on wheat flour in Korea has led to an increase in the rate of diseases such as obesity and diabetes, which has become a social problem. Wheat consumption is increasing due to changes in eating habits, but domestic wheat has low price competitiveness and has stagnated recently, so it is necessary to secure new resources to differentiate from imported wheat. Resistant starch, a newly created resource in domestic wheat, can act as a prebiotic similar to dietary fiber in the body, inducing microbial changes in the gut and having beneficial effects on metabolic syndrome. Wheat research on resistant starch was carried out based on the breeding of high amylose. A genome-wide association study (GWAS) was used to perform SNP identification and expression analysis related to wheat amylose through phenotype and genotype. 561 wheat core collection gene sources were investigated for amylose content in wheat, and related genes were extracted and analyzed. In the GWAS analysis, the model formulas BLIMK, FarmCPU, GLM, MLM, and MLMM were used to derive results such as QQ plots and Manhattan plots through phenotypic data. Among these models, BLAST was conducted to find the association between the SNPs identified using FarmCPU and genes related to starch, and 15 were found. Using the identified markers, it becomes easier to develop and browse related wheat cultivars according to their amylose content.

• Journal of Microbiology and Biotechnology
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• v.34 no.2
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• pp.296-305
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• 2024

Peach tree gummosis is a botanical anomaly distinguished by the secretion of dark-brown gum from the shoots of peach trees, and Botryosphaeria dothidea has been identified as one of the fungal species responsible for its occurrence. In South Korea, approximately 80% of gummosis cases are linked to infections caused by B. dothidea. In this study, we isolated microbes from the soil surrounding peach trees exhibiting antifungal activity against B. dothidea. Subsequently, we identified several bacterial strains as potential candidates for a biocontrol agent. Among them, Bacillus velezensis KTA01 displayed the most robust antifungal activity and was therefore selected for further analysis. To investigate the antifungal mechanism of B. velezensis KTA01, we performed tests to assess cell wall degradation and siderophore production. Additionally, we conducted reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis based on whole-genome sequencing to confirm the presence of genes responsible for the biosynthesis of lipopeptide compounds, a well-known characteristic of Bacillus spp., and to compare gene expression levels. Moreover, we extracted lipopeptide compounds using methanol and subjected them to both antifungal activity testing and high-performance liquid chromatography (HPLC) analysis. The experimental findings presented in this study unequivocally demonstrate the promising potential of B. velezensis KTA01 as a biocontrol agent against B. dothidea KACC45481, the pathogen responsible for causing peach tree gummosis.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.317-327
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• 2008

Phytocystatins, which are inhibitors of plant cysteine peptidases, are involved in the regulation of protein turnover and in the defense against insect pests and pathogens. Extensive searches in the Brassica rapa genome allowed the prediction of at least eight different phytocystatin genes on seven chromosomes in the B. rapa genome. Structure comparisons based on alignments of the all BrCYS ($\underline{B}$. $\underline{r}apa$ $phyto{\underline{cys}}tatin$) proteins using the CLUSTALW program revealed conservation of the three consensus motifs known to interact with the active site of cysteine peptidases. According to the phylogenetic analysis based on the deduced amino acid sequences, the eight BrCYS proteins were divided into several clusters related to the orthologous phytocystatin. The predicted three-dimensional structure models of the eight BrCYS proteins demonstrate that all of these proteins are similar to the reported crystal structure of oryzacystatin-I (OC-I). Digital northern and RT-PCR analyses indicated that the eight BrCYS genes exhibit different expression patterns in B. rapa tissues and respond differently to abiotic stimuli. The differences in gene structure and expression between the eight BrCYS genes suggest that these proteins may play diverse physiological roles in B. rapa and may interact with cysteine peptidases through different mechanisms.

• Journal of Plant Biotechnology
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• v.45 no.1
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• pp.17-29
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• 2018

This study was conducted to investigate a morphological trait in 294 rice accessions including Korean breeding lines. We also carried out a genome-wide association study (GWAS) to detect significant single nucleotide polymorphism markers and candidate genes affecting major agronomic traits. A Manhattan plot analysis of GWAS using morphological traits showed that phenotypic and statistical significance was associated with a chromosome in each group. The significance of SNPs that were detected in this study was investigated by comparing them with those found previously studied QTL regions related to agronomic traits. As a result, SNP (S8-19815442), which is significant with regard to leaf angle, was located in the known QTL regions. To observe gene mutations related to leaf angle in a candidate gene, Os08g31950, its sequences were compared with sequences in previously selected rice varieties. In Os08g31950, a single nucleotide mutation occurred in one region. To compare relative RNA expression levels of candidate gene Os08g31950, obtained from GWAS analysis of 294 rice accessions and related to lateral leaf angle, we investigated relative levels by selecting 10 erect leaf angle varieties and 10 horizontal leaf angle varieties and examining real-time PCR. In Os08g31950, a high level of expression and various expression patterns were observed in all tissues. Also, Os08g31950 showed higher expression levels in the erect leaf angle variety group and higher expression rates in the leaf than in the root. The candidate gene detected through GWAS would be useful in developing new rice varieties with improved yield potential through future molecular breeding.

• Korean Journal of Microbiology
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• v.44 no.3
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• pp.186-192
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• 2008

For the development of specific and effective basic genetic materials to inhibit replication of hepatitis C virus (HCV), HCV genome-targeting trans-splicing aptazyme, which activity is allosterically regulated by a specific ligand, was developed. The aptazyme was designed to be comprised of sequence of RNA aptamer to the ligand, communication module sequence which can transfer structural transition for inducing ribozyme activity upon binding the ligand to the aptamer, and trans-splicing ribozyme targeting +199 nt of HCV IRES. Especially, when the aptamer and the communication module was inserted at both P6 and P8 catalytic domain of the specific ribozyme, allosteric activity of the aptazyme was the most induced. The aptazyme was shown to induce activity of trans-splicing reaction specifically and efficiently only in the presence of the specific ligand, but neither in the absence of any ligand nor in the presence of control ligand. This aptazyme can be used as a specific and effective genetic agent against HCV, and a tool for the isolation of anti-HCV lead compounds.

• Korean Journal of Plant Resources
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• v.34 no.4
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• pp.278-286
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• 2021

Efficient in vitro regeneration system is essential for the successful crop breeding of soybean (Glycine max (L.) Merr.) using the new biotechnology. The genotype of donor plants strongly influences the establishment of tissue culture system. Therefore, the screening of genotypes with excellent tissue culture ability is very important for soybean genetic improvement. In this study, we report the tissue culture efficiency of 21 soybean cultivars belong to Korean soybean core-collection and two foreign cultivars (Jack and Maverick). The Kwangan, Anpyeong and Seonam are share close genetic relationship in 21 cultivars and these three cultivars were observed the high frequency of germination and regeneration. Furthermore, the high tissue culture abilities were also observed in the Williams 82 used in reference genome sequencing and the two foreign cultivars. The transformation of pBAtc:tRNA with bar gene was performed by Agrobacterium tumefaciens in the cultivars with high tissue culture ability. Transformation of the bar gene was identified by PCR analysis in Kwangan, Pungwon, Seonam, and Maverick. Our results provide useful information for the breeding of various soybean cultivars by plant biotechnology such as, genome editing.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.3
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• pp.320-333
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• 2019

Objective: The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods: In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results: The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion: Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.

• The Plant Pathology Journal
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• v.34 no.1
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• pp.11-22
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• 2018

Type VI secretion system (T6SS) has been discovered in a variety of gram-negative bacteria as a versatile weapon to stimulate the killing of eukaryotic cells or prokaryotic competitors. Type VI secretion effectors (T6SEs) are well known as key virulence factors for important pathogenic bacteria. In many Burkholderia species, T6SS has evolved as the most complicated secretion pathway with distinguished types to translocate diverse T6SEs, suggesting their essential roles in this genus. Here we attempted to detect and characterize T6SSs and potential T6SEs in target genomes of plant-associated and environmental Burkholderia species based on computational analyses. In total, 66 potential functional T6SS clusters were found in 30 target Burkholderia bacterial genomes, of which 33% possess three or four clusters. The core proteins in each cluster were specified and phylogenetic trees of three components (i.e., TssC, TssD, TssL) were constructed to elucidate the relationship among the identified T6SS clusters. Next, we identified 322 potential T6SEs in the target genomes based on homology searches and explored the important domains conserved in effector candidates. In addition, using the screening approach based on the profile hidden Markov model (pHMM) of T6SEs that possess markers for type VI effectors (MIX motif) (MIX T6SEs), 57 revealed proteins that were not included in training datasets were recognized as novel MIX T6SE candidates from the Burkholderia species. This approach could be useful to identify potential T6SEs from other bacterial genomes.