• Genomics & Informatics
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• v.19 no.4
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• pp.46.1-46.11
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• 2021

Moringa oleifera is nowadays raising as the most preferred medicinal plant, as every part of the moringa plant has potential bioactive compounds which can be used as herbal medicines. Some bioactive compounds of M. oleifera possess potential anti-cancer properties which interact with the apoptosis protein p53 in cancer cell lines of oral squamous cell carcinoma. This research work focuses on the interaction among the selected bioactive compounds derived from M. oleifera with targeted apoptosis protein p53 from the apoptosis pathway to check whether the bioactive compound will induce apoptosis after the mutation in p53. To check the toxicity and drug-likeness of the selected bioactive compound derived from M. oleifera based on Lipinski's Rule of Five. Detailed analysis of the 3D structure of apoptosis protein p53. To analyze protein's active site by CASTp 3.0 server. Molecular docking and binding affinity were analyzed between protein p53 with selected bioactive compounds in order to find the most potential inhibitor against the target. This study shows the docking between the potential bioactive compounds with targeted apoptosis protein p53. Quercetin was the most potential bioactive compound whereas kaempferol shows poor affinity towards the targeted p53 protein in the apoptosis pathway. Thus, the objective of this research can provide an insight prediction towards M. oleifera derived bioactive compounds and target apoptosis protein p53 in the structural analysis for compound isolation and in-vivo experiments on the cancer cell line.

• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

• Journal of Ginseng Research
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• v.46 no.6
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• pp.750-758
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• 2022

Background: Mild cognitive impairment (MCI) is a transitional condition between normality and dementia. Ginseng is known to have effects on attenuating cognitive deficits in neurogenerative diseases. Ginsenosides are the main bioactive component of ginseng, and their protein targets have not been fully understood. Furthermore, no thorough analysis is reported in ginsenoside-related protein targets in MCI. Methods: The candidate protein targets of ginsenosides in brain tissues were identified by drug affinity responsive target stability (DARTS) coupled with label-free liquid chromatography-mass spectrometry (LC-MS) analysis. Network pharmacology approach was used to collect the therapeutic targets for MCI. Based on the above-mentioned overlapping targets, we built up a proteineprotein interaction (PPI) network in STRING database and conducted gene ontology (GO) enrichment analysis. Finally, we assessed the effects of ginseng total saponins (GTS) and different ginsenosides on mitochondrial function by measuring the activity of the mitochondrial respiratory chain complex and performing molecular docking. Results: We screened 2526 MCI-related protein targets by databases and 349 ginsenoside-related protein targets by DARTS. On the basis of these 81 overlapping genes, enrichment analysis showed the mitochondria played an important role in GTS-mediated MCI pharmacological process. Mitochondrial function analysis showed GTS, protopanaxatriol (PPT), and Rd increased the activities of complex I in a dose-dependent manner. Molecular docking also predicted the docking pockets between PPT or Rd and mitochondrial respiratory chain complex I. Conclusion: This study indicated that ginsenosides might alleviate MCI by targeting respiratory chain complex I and regulating mitochondrial function, supporting ginseng's therapeutic application in cognitive deficits.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.4
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• pp.238-246
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• 2005

Rice yield and protein content have been shown to be highly variable across paddy fields. In order to characterize this spatial variability of rice within a field, two-year experiments were conducted in 2002 and 2003 in a large-scale rice field of $6,600m^2$ In year 2004, an experiment was conducted to know if variable rate treatment (VRT) of N fertilizer, that was prescribed for site-specific management at panicle initiation stage, could reduce spatial variation in yield and protein content of rice while increasing yield compared to conventional uniform N topdressing (UN, 33kg N/ha at PIS) method. VRT nitrogen prescription for each grid was calculated based on the nitrogen (N) uptake (from panicle initiation to harvest) required for target rice protein content of $6.8\%$, natural soil N supply, and recovery of top-dressed N fertilizer. The required N uptake for target rice protein content was calculated from the equations to predict rice yield and protein content from plant growth parameters at panicle initiation stage (PIS) and N uptake from PIS to harvest. This model· equations were developed from the data obtained from the previous two-year experiments. The plant growth parameters for the calculation of the required N were predicted non-destructively by canopy reflectance measurement. Soil N supply for each grid was obtained from the experiment of year 2003, and N recovery was assumed to be $60\%$ according to the previous reports. The prescribed VRT N ranged from 0 to 110kg N/ha with an average of 57kg/ha that was higher than 33 kg/ha of UN. The results showed that VRT application successfully worked not only to reduce spatial variability of rice yield and protein content but also to increase rough rice yield by 960kg/ha. The coefficient of variation (CV) for rice yield and protein content was reduced significantly to $8.1\%$ and $7.1\%$ in VRT from $14.6\%$ and $13.0\%$ in UN, respectively. And also the average protein content of milled rice in VRT showed very similar value of target protein content of $6.8\%$. In conclusion the procedure used in this paper was believed to be reliable and promising method for reducing within-field spatial variability of rice yield and protein content. However, inexpensive, reliable, and fast estimation methods of natural N supply and plant growth and nutrition status should be prepared before this method could be practically used for site-specific crop management in large-scale rice field.

• Proceedings of the Korean Society of Crop Science Conference
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• 2005.08a
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• pp.57-74
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• 2005

Rice yield and protein content have been shown to be highly variable across paddy fields. In order to characterize this spatial variability of rice within a field, the two-year experiments were conducted in 2002 and 2003 in a large-scale rice field of $6,600m^2$ In year 2004, an experiment was conducted to know if prescribed N for site-specific fertilizer management at panicle initiation stage (VRT) could reduce spatial variation in yield and protein content of rice while increasing yield compared to conventional uniform N topdressing (UN, ,33 kg N/ha at PIS) method. The trial field was subdivided into two parts and each part was subjected to UN and VRT treatment. Each part was schematically divided in $10\times10m$ grids for growth and yield measurement or VRT treatment. VRT nitrogen prescription for each grid was calculated based on the nitrogen (N) uptake (from panicle initiation to harvest) required for target rice protein content of $6.8\%$, natural soil N supply, and recovery of top-dressed N fertilizer. The required N uptake for target rice protein content was calculated from the equations to predict rice yield and protein content from plant growth parameters at panicle initiation stage (PIS) and N uptake from PIS to harvest. This model equations were developed from the data obtained from the previous two-year experiments. The plant growth parameters for this calculation were predicted non-destructively by canopy reflectance measurement. Soil N supply for each grid was obtained from the experiment of year 2003, and N recovery was assumed to be $60\%$ according to the previous reports. The prescribed VRT N ranged from 0 to 110kg N/ha with average of 57kg/ha that was higher than 33kg/ha of UN. The results showed that VRT application successfully worked not only to reduce spatial variability of rice yield and protein content but also to increase rough rice yield by 960kg/ha. The coefficient of variation (CV) for rice yield and protein content was reduced significantly to $8.1\%\;and\;7.1\%$ in VRT from $14.6\%\;and\;13.0\%$ in UN, respectively. And also the average protein content of milled rice in VRT showed very similar value of target protein content of $6.8\%$. Although N use efficiency of VRT compared to UN was not quantified due to lack of no N control treatment, the procedure used in this paper for VRT estimation was believed to be reliable and promising method for managing within-field spatial variability of yield and protein content. The method should be received further study before it could be practically used for site-specific crop management in large-scale rice field.

• Molecules and Cells
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• v.38 no.6
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• pp.475-481
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• 2015

Programmable nucleases, which include zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and RNA-guided engineered nucleases (RGENs) repurposed from the type II clustered, regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system are now widely used for genome editing in higher eukaryotic cells and whole organisms, revolutionising almost every discipline in biological research, medicine, and biotechnology. All of these nucleases, however, induce off-target mutations at sites homologous in sequence with on-target sites, limiting their utility in many applications including gene or cell therapy. In this review, we compare methods for detecting nuclease off-target mutations. We also review methods for profiling genome-wide off-target effects and discuss how to reduce or avoid off-target mutations.

• Journal of Korean Home Economics Education Association
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• v.29 no.3
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• pp.77-88
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• 2017

Nutritional adequacy of Target patterns in Dietary Guidance System were evaluated. Study subjects were 18 Target patterns designed for 2 children groups, 4 adolescent and 4 adult male and female groups in Dietary Reference Intakes for Koreans 2015. Nutrients examined were 4 macro-nutrients(protein, fat, carbohydrate, and dietary fiber), 5 minerals(Ca, P, Fe, Na, and K), and 5 vitamins(vitamin A, thiamin, riboflavin, niacin, and vitamin C). Energy and nutrients contents were calculated based upon assigned multiples of single serving in Target pattern and Representative Food Composition Table by Excel program. Among the 18 Target patterns, only 5 were mean adequacy ratio(MAR) of 1.0, fulfilled the expectations of Dietary Guidance System. Protein and Na contents were more than dietary reference intakes(DRI) in all 18 Target patterns. Dietary fiber, Ca, and K were deficient nutrient in 15, 10, and 9 Target patterns, respectively. The units of vitamin A were not same in Target pattern and DRI, retinol equivalent(RE) in Target pattern and retinol activity equivalent(RAE) in DRI. When calculate RE content of vitamin A in Target pattern to RAE content, 15 Target patterns did not reach to DRI of vitamin A. The Target pattern of elderly women showed the lowest mean adequacy ratio(MAR), 7 nutrients were less than DRI, need to be revised. Average energy contribution ratio of protein, fat, and carbohydrate were 16.04%, 24.35%, and 60.91%, respectively, fulfilled the adequate acceptable macro-nutrient distribution range(AMDR). To improve the nutritional inadequacy of dietary fiber, Ca, K, and vitamin A in Target pattern, effective mean may be the increasing vegetable group assignment. Also decreasing the meat fish egg legume group assignment in some Target pattern may be the way of preventing of protein overconsumption. The energy in adequate amount for condiment use also need to be considered.

• Molecules and Cells
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• v.37 no.9
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• pp.691-698
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• 2014

SCYL1-BP1 is thought to function in the p53 pathway through Mdm2 and hPirh2, and mutations in SCYL1-BP1 are associated with premature aging syndromes such as Geroderma Osteodysplasticum; however, these mechanisms are unclear. Here, we report significant alterations in miRNA expression levels when SCYL1-BP1 expression was inhibited by RNA interference in HEK293T cells. We functionally characterized the effects of potential kernel miRNA-target genes by miRNA-target network and protein-protein interaction network analysis. Importantly, we showed the diminished SCYL1-BP1 dramatically reduced the expression levels of EEA1, BMPR2 and BRCA2 in HEK293T cells. Thus, we infer that SCYL1-BP1 plays a critical function in HEK293T cell development and directly regulates miRNA-target genes, including, but not limited to, EEA1, BMPR2, and BRCA2, suggesting a new strategy for investigating the molecular mechanism of SCYL1-BP1.

• Biodesign
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• v.6 no.4
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• pp.100-102
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• 2018

Autophagy is a degradation pathway that targets many cellular components and plays a particularly important role in protein degradation and recycling. This process is very complex and several proteins participate in this process. One of them, P62/SQSTM1, is related to the N-end rule and induces protein degradation through autophagy. The P62/SQSTM1 makes a huge oligomer, and this oligomerization is known to play an important role in its mechanism. This oligomerization takes two steps. First, the PB1 domain of P62/SQSTM1 makes the base oligomer, and then, when the ligand binds to the ZZ domain of P62/SQSTM1, it induces a higher oligomer by the disulfide bond of the two cysteines. To understand the oligomerization mechanism of P62/SQSTM1, we need to know the dimerization of the PB1 domain. In this study, crystals of PB1 dimer were made and the crystals were diffracted by X-ray to collect usable data up to 3.2A. We are analyzing the structure using the molecular replacement (MR) method.

• Journal of Microbiology and Biotechnology
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• v.30 no.12
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• pp.1919-1926
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• 2020

CRISPR interference (CRISPRi) has been developed as a transcriptional control tool by inactivating the DNA cleavage ability of Cas9 nucleases to produce dCas9 (deactivated Cas9), and leaving dCas9 the ability to specifically bind to the target DNA sequence. CRISPR/Cas9 technology has limitations in designing target-specific single-guide RNA (sgRNA) due to the dependence of protospacer adjacent motif (PAM) (5'-NGG) for binding target DNAs. Reportedly, Cas9-NG recognizing 5'-NG as the PAM sequence has been constructed by removing the dependence on the last base G of PAM through protein engineering of Cas9. In this study, a dCas9-NG protein was engineered by introducing two active site mutations in Cas9-NG, and its ability to regulate transcription was evaluated in the gal promoter in E. coli. Analysis of cell growth rate, D-galactose consumption rate, and gal transcripts confirmed that dCas9-NG can completely repress the promoter by recognizing DNA targets with PAM of 5'-NGG, NGA, NGC, NGT, and NAG. Our study showed possible PAM sequences for dCas9-NG and provided information on target-specific sgRNA design for regulation of both gene expression and cellular metabolism.