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Kyungha Lee,Seong Hee Bhoo,Sang‑Won Lee,Man‑Ho Cho 한국응용생명화학회 2024 Applied Biological Chemistry (Appl Biol Chem) Vol.67 No.-
Rhododendrons produce a variety of methoxyflavonoids, including rarely found 3-methoxyflavonoids and 5-methoxyflavonoids. It was thus suggested that they have a series of regiospecific flavonoid O-methyltransferases (FOMTs). The 18 Class II O-methyltransferase (OMT) genes were retrieved from the Rhododendron delavayi genome, designating them as RdOMTs. A comprehensive biochemical characterization of RdOMTs was performed to identify functional FOMTs. The FOMT activity of recombinant RdOMTs was assayed with flavonoid substrates of different subclasses. Among the examined RdOMTs, RdOMT3, RdOMT10, and RdOMT12 showed FOMT activity for diverse flavonoids. In particular, RdOMT3 consumed only flavonols as a substrate. Structural analyses of the methylated products demonstrated that RdOMT3, RdOMT10, and RdOMT12 catalyze regiospecific methylation of flavonoids at the 3’/5’-, 3-, and 4’-hydroxyl groups, respectively. Their broad substrate spectrum and different regiospecificity suggest that these RdOMTs contribute to the formation of complex methoxyflavonoids in R. delavayi. Bioconversion of flavonoids using E. coli harboring each RdOMT demonstrated that RdOMT3, RdOMT10, and RdOMT12 are useful tools for the biotechnological production of valuable methoxyflavonoids, including the rarely found 3-methoxyflavonoids. Rhododendrons produce a variety of methoxyflavonoids, including rarely found 3-methoxyflavonoids and 5-methoxyflavonoids. It was thus suggested that they have a series of regiospecific flavonoid O -methyltransferases (FOMTs). The 18 Class II O -methyltransferase (OMT) genes were retrieved from the Rhododendron delavayi genome, designating them as RdOMTs. A comprehensive biochemical characterization of RdOMTs was performed to identify functional FOMTs. The FOMT activity of recombinant RdOMTs was assayed with flavonoid substrates of different subclasses. Among the examined RdOMTs, RdOMT3, RdOMT10, and RdOMT12 showed FOMT activity for diverse flavonoids. In particular, RdOMT3 consumed only flavonols as a substrate. Structural analyses of the methylated products demonstrated that RdOMT3, RdOMT10, and RdOMT12 catalyze regiospecific methylation of flavonoids at the 3'/5'-, 3-, and 4'-hydroxyl groups, respectively. Their broad substrate spectrum and different regiospecificity suggest that these RdOMTs contribute to the formation of complex methoxyflavonoids in R. delavayi . Bioconversion of flavonoids using E. coli harboring each RdOMT demonstrated that RdOMT3, RdOMT10, and RdOMT12 are useful tools for the biotechnological production of valuable methoxyflavonoids, including the rarely found 3-methoxyflavonoids.
A Study on Support Vectors of Least Squares Support Vector Machine
Seok, Kyungha,Cho, Daehyun 한국통계학회 2003 Communications for statistical applications and me Vol.10 No.3
LS-SVM(Least-Squares Support Vector Machine) has been used as a promising method for regression as well as classification. Suykens et al.(2000) used only the magnitude of residuals to obtain SVs(Support Vectors). Suykens' method behaves well for homogeneous model. But in a heteroscedastic model, the method shows a poor behavior. The present paper proposes a new method to get SVs. The proposed method uses the variance of noise as well as the magnitude of residuals to obtain support vectors. Through the simulation study we justified excellence of our proposed method.
Lee Kyungha,Cho Man-Ho,Kim Mi-Ju,Bhoo Seong-Hee 한국미생물·생명공학회 2024 Journal of microbiology and biotechnology Vol.34 No.6
Protein-specific antibodies are essential for various aspects of protein research, including detection, purification, and characterization. When specific antibodies are unavailable, protein tagging is a useful alternative. Small epitope tags, typically less than 10 amino acids, are widely used in protein research due to the simple modification through PCR and reduced impact on the target protein's function compared to larger tags. The 2B8 epitope tag (RDPLPFFPP), reported by us in a previous study, has high specificity and sensitivity to the corresponding antibody. However, when attached to the C-terminus of the target protein in immunoprecipitation experiments, we observed a decrease in detection signal with reduced immunity and low protein recovery. This phenomenon was not unique to 2B8 and was also observed with the commercially available Myc tag. Our study revealed that Cterminal tagging of small epitope tags requires the addition of more than one extra amino acid to enhance (restore) antibody immunities. Moreover, among the amino acids we tested, serine was the best for the 2B8 tag. Our findings demonstrated that the interaction between a small epitope and a corresponding paratope of an antibody requires an extra amino acid at the C-terminus of the epitope. This result is important for researchers planning studies on target proteins using small epitope tags.
Mass spectrometry-based ginsenoside profiling: Recent applications, limitations, and perspectives
Hyun Woo Kim,Dae Hyun Kim,Byeol Ryu,You Jin Chung,Kyungha Lee,Young Chang Kim,Jung Woo Lee,Dong Hwi Kim,Woojong Jang,Woohyeon Cho,Hyeonah Shim,Sang Hyun Sung,Tae-Jin Yang,Kyo Bin Kang The Korean Society of Ginseng 2024 Journal of Ginseng Research Vol.48 No.2
Ginseng, the roots of Panax species, is an important medicinal herb used as a tonic. As ginsenosides are key bioactive components of ginseng, holistic chemical profiling of them has provided many insights into understanding ginseng. Mass spectrometry has been a major methodology for profiling, which has been applied to realize numerous goals in ginseng research, such as the discrimination of different species, geographical origins, and ages, and the monitoring of processing and biotransformation. This review summarizes the various applications of ginsenoside profiling in ginseng research over the last three decades that have contributed to expanding our understanding of ginseng. However, we also note that most of the studies overlooked a crucial factor that influences the levels of ginsenosides: genetic variation. To highlight the effects of genetic variation on the chemical contents, we present our results of untargeted and targeted ginsenoside profiling of different genotypes cultivated under identical conditions, in addition to data regarding genome-level genetic diversity. Additionally, we analyze the other limitations of previous studies, such as imperfect variable control, deficient metadata, and lack of additional effort to validate causation. We conclude that the values of ginsenoside profiling studies can be enhanced by overcoming such limitations, as well as by integrating with other -omics techniques.