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Search Results: 1 - 10 of 5399 matches for " HEE JONG KOH "
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Development of New CAPS/dCAPS and SNAP Markers for Rice Eating Quality
PUJI LESTARI,HEE JONG KOH
HAYATI Journal of Biosciences , 2013,
Abstract: Rice eating quality traits are very complex and essential to be evaluated not only through physicochemical analysis and sensory test but also by PCR-based marker approach. To date, simple markers based on single nucleotide polymorphism (SNP) discovery to evaluate eating quality of cooked rice are still limited. Thus, the aims of this study were to develop PCR-based markers, called SNAP (single nucleotide amplified polymorphism) as alternative markers of cleaved amplified polymorphic sequence/derived cleaved amplified polymorphic sequence (CAPS/dCAPS). Four primer pairs specific to targeted alleles (CAPS/dCAPS and SNAP) of four loci were successfully designed based on the discovered SNPs according to the eating quality-QTL and searching genomic database. The primer pairs were able to identify alleles corresponding loci among indica and japonica varieties with diverse palatability (overall eating quality). There was consistent allele pattern produced by SNAP and CAPS/dCAPS for the same base mutation. The SNAP marker for rice eating quality trait could be easily assayed by standard agarose gel electrophoresis, allowing to increase the advantage of genotyping methods. Moreover, the SNAP markers together with our previous developed markers which were recommended as applicable marker set for evaluation of rice eating quality, will facilitate as marker-assisted selection for rice breeding program.
A label-free quantitative shotgun proteomics analysis of rice grain development
Joohyun Lee, Hee-Jong Koh
Proteome Science , 2011, DOI: 10.1186/1477-5956-9-61
Abstract: Proteins were extracted from rice grains 10, 20, and 30 days after flowering, as well as from fully mature grains. By merging all of the identified proteins in this study, we identified 4,172 non-redundant proteins with a wide range of molecular weights (from 5.2 kDa to 611 kDa) and pI values (from pH 2.9 to pH 12.6). A Genome Ontology category enrichment analysis for the 4,172 proteins revealed that 52 categories were enriched, including the carbohydrate metabolic process, transport, localization, lipid metabolic process, and secondary metabolic process. The relative abundances of the 1,784 reproducibly identified proteins were compared to detect 484 differentially expressed proteins during rice grain development. Clustering analysis and Genome Ontology category enrichment analysis revealed that proteins involved in the metabolic process were enriched through all stages of development, suggesting that proteome changes occurred even in the desiccation phase. Interestingly, enrichments of proteins involved in protein folding were detected in the desiccation phase and in fully mature grain.This is the first report conducting comprehensive identification of rice grain proteins. With a label free shotgun proteomic approach, we identified large number of rice grain proteins and compared the expression patterns of reproducibly identified proteins during rice grain development. Clustering analysis, Genome Ontology category enrichment analysis, and the analysis of composite expression profiles revealed dynamic changes of metabolisms during rice grain development. Interestingly, we detected that proteins involved in glycolysis, TCA-cycle, lipid metabolism, and proteolysis accumulated at higher levels in fully mature grain compared to grain developing stages, suggesting that the accumulation of these proteins during the desiccation stage may be associated with the preparation of proteins required in germination.Rice is an important model plant because of its importance as a f
Comparison of Sasang Constitutional Medicine, Traditional Chinese Medicine and Ayurveda
Jong Yeol Kim,Duong Duc Pham,Byung Hee Koh
Evidence-Based Complementary and Alternative Medicine , 2011, DOI: 10.1093/ecam/neq052
Abstract: Sasang constitutional medicine (SCM), traditional Chinese medicine (TCM) and Ayurveda are three different forms of Asian traditional medicine. Although these traditions share a lot in common as holistic medicines, the different philosophical foundations found in each confer distinguishing attributes and unique qualities. SCM is based on a constitution-based approach, and is in this way relatively more similar to the Ayurvedic tradition than to the TCM, although many of the basic SCM theories were originally derived from TCM, a syndrome-based medicine. SCM and TCM use the same botanical materials that are distributed mainly in the East Asian region, but the basic principles of usage and the underlying rationale are completely different from each other. Meanwhile, the principles of the Ayurvedic use of botanical resources are very similar to those seen in SCM, but the medicinal herbs used in Ayurveda generally originate from the West Asian region which displays a different spectrum of flora.
Protein Disulfide Isomerase-Like Protein 1-1 Controls Endosperm Development through Regulation of the Amount and Composition of Seed Proteins in Rice
Yeon Jeong Kim, Song Yion Yeu, Bong Soo Park, Hee-Jong Koh, Jong Tae Song, Hak Soo Seo
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0044493
Abstract: Protein disulfide isomerase (PDI) is a chaperone protein involved in oxidative protein folding by acting as a catalyst and assisting folding in the endoplasmic reticulum (ER). A genome database search showed that rice contains 19 PDI-like genes. However, their functions are not clearly identified. This paper shows possible functions of rice PDI-like protein 1-1 (PDIL1-1) during seed development. Seeds of the T-DNA insertion PDIL1-1 mutant, PDIL1-1Δ, identified by genomic DNA PCR and western blot analysis, display a chalky phenotype and a thick aleurone layer. Protein content per seed was significantly lower and free sugar content higher in PDIL1-1Δ mutant seeds than in the wild type. Proteomic analysis of PDIL1-1Δ mutant seeds showed that PDIL1-1 is post-translationally regulated, and its loss causes accumulation of many types of seed proteins including glucose/starch metabolism- and ROS (reactive oxygen species) scavenging-related proteins. In addition, PDIL1-1 strongly interacts with the cysteine protease OsCP1. Our data indicate that the opaque phenotype of PDIL1-1Δ mutant seeds results from production of irregular starch granules and protein body through loss of regulatory activity for various proteins involved in the synthesis of seed components.
Proteomic and biochemical analyses reveal the activation of unfolded protein response, ERK-1/2 and ribosomal protein S6 signaling in experimental autoimmune myocarditis rat model
Joo Chung, Hee Choi, Soo Kim, Kwan Hong, Soo Min, Myung Nam, Chan Kim, Young Ho Koh, Jong Seo
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-520
Abstract: By performing unbiased 2-dimensional electrophoresis of protein extracts from control rat heart tissues and EAM rat heart tissues, followed by nano-HPLC-ESI-QIT-MS, 67 proteins were identified from 71 spots that exhibited significantly altered expression levels. The majority of up-regulated proteins were confidently associated with unfolded protein responses (UPR), while the majority of down-regulated proteins were involved with the generation of precursor metabolites and energy metabolism in mitochondria. Although there was no difference in AKT signaling between EAM rat heart tissues and control rat heart tissues, the amounts and activities of extracellular signal-regulated kinase (ERK)-1/2 and ribosomal protein S6 (rpS6) were significantly increased. By comparing our data with the previously reported myocardial proteome of the Coxsackie viruses of group B (CVB)-mediated myocarditis model, we found that UPR-related proteins were commonly up-regulated in two murine myocarditis models. Even though only two out of 29 down-regulated proteins in EAM rat heart tissues were also dysregulated in CVB-infected rat heart tissues, other proteins known to be involved with the generation of precursor metabolites and energy metabolism in mitochondria were also dysregulated in CVB-mediated myocarditis rat heart tissues, suggesting that impairment of mitochondrial functions may be a common underlying mechanism of the two murine myocarditis models.UPR, ERK-1/2 and S6RP signaling were activated in both EAM- and CVB-induced myocarditis murine models. Thus, the conserved components of signaling pathways in two murine models of acute myocarditis could be targets for developing new therapeutic drugs or methods aimed at treating enigmatic myocarditis.Myocarditis is an inflammatory heart disease with a wide variety of symptoms that range from mild dyspnea to cardiogenic death [1]. Although viral infection is thought to be the most common cause of acute myocarditis in humans, myocarditis is
中国东北地区水稻主要栽培品种的遗传多样性分析
玄英实,姜文洙,刘宪虎,程正海,Hee-Jong Koh,元东林
植物遗传资源学报 , 2010,
Abstract: 利用68对SSR引物对91份粳稻品种进行了遗传多样性分析。研究结果,共检测到293个等位基因,平均4.3个;平均多态信息含量(PIC)为0.313,变动范围为0.022~0.825。RM333和RM206的等位基因数最多,分别为14、10;且PIC也最高,分别为0.825、0.805。聚类和群体差异分析结果表明,东北三省水稻品种的遗传基础狭窄。黑龙江省和吉林省、黑龙江省和日本、吉林省和日本水稻品种间遗传距离都很小,分别为0.083、0.084.0.090,而辽宁省水稻品种遗传基础与吉林省、黑龙江省有一些差异。9个地理来源的品种聚类结果,可分为5个大类群,黑龙江省、吉林省、日本和韩国形成第Ⅰ类群;北京和辽宁省归为第Ⅱ类群;中国台湾、云南省、美国分别为第Ⅲ、第Ⅳ和第Ⅴ类群。东北三省作为重要的粳稻生产基地,但遗传基础非常狭窄,要克服遗传脆弱性应从地理位置较远的国家或地区收集更丰富的遗传资源。
Molecular Aspect of Good Eating Quality Formation in Japonica Rice
Ming-Mao Sun,Sailila E. Abdula,Hye-Jung Lee,Young-Chan Cho,Long-Zhi Han,Hee-Jong Koh,Yong-Gu Cho
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018385
Abstract: The composition of amylopectin is the determinant of rice eating quality under certain threshold of protein content and the ratio of amylose and amylopectin. In molecular biology level, the fine structure of amylopectin is determined by relative activities of starch branching enzyme (SBE), granule-bound starch synthase (GBSS), and soluble starch synthase (SSS) in rice grain under the same ADP-Glucose level. But the underlying mechanism of eating quality in molecular biology level remains unclear. This paper reports the differences on major parameters such as SNP and insertion-deletion sites, RNA expressions, and enzyme activities associated with eating quality of japonica varieties. Eight japonica rice varieties with significant differences in various eating quality parameters such as palatability and protein content were used in this experiment. Association analysis between nucleotide polymorphism and eating quality showed that S12 and S13 loci in SBE1, S55 in SSS1, S58 in SSS2A were significantly associated with apparent amylose content, alkali digestion value, setback viscosity, consistency viscosity, pasting temperature, which explained most of the variation in apparent amylose content, setback viscosity, and consistency viscosity; and explained almost all variations in alkali digestion value and pasting temperature. Thirty-five SNPs and insertion-deletions from SBE1, SBE3, GBSS1, SSS1, and SSS2A differentiated high or intermediate palatability rice varieties from low palatability rice varieties. Correlation analysis between enzyme activities and eating quality properties revealed that SBE25 and SSS15/W15 were positively correlated with palatability, whereas GBSS10 and GBSS15 were negatively correlated. Gene expressions showed that SBE1 and SBE3 expressions in high palatability varieties tended to be higher than middle and low palatability varieties. Collectively, SBE1, SBE3, SSS1, and SSS2A, especially SBE1 and SBE3 could improve eating quality, but GBSS1 decreased eating quality. The results indicated the possibility of developing high palatability cultivars through modification of key genes related to japonica rice eating quality formation in starch biosynthesis.
Protective Effect of the Ethyl Acetate Fraction of Sargassum muticum against Ultraviolet B–Irradiated Damage in Human Keratinocytes
Mei Jing Piao,Weon Jong Yoon,Hee Kyoung Kang,Eun Sook Yoo,Young Sang Koh,Dong Sam Kim,Nam Ho Lee,Jin Won Hyun
International Journal of Molecular Sciences , 2011, DOI: 10.3390/ijms12118146
Abstract: The aim of this study was to investigate the cytoprotective properties of the ethyl acetate fraction of Sargassum muticum (SME) against ultraviolet B (UVB)-induced cell damage in human keratinocytes (HaCaT cells). SME exhibited scavenging activity toward the 1,1-diphenyl-2-picrylhydrazyl radicals and hydrogen peroxide (H 2O 2) and UVB-induced intracellular reactive oxygen species (ROS). SME also scavenged the hydroxyl radicals generated by the Fenton reaction (FeSO 4 + H 2O 2), which was detected using electron spin resonance spectrometry. In addition, SME decreased the level of lipid peroxidation that was increased by UVB radiation, and restored the level of protein expression and the activities of antioxidant enzymes that were decreased by UVB radiation. Furthermore, SME reduced UVB-induced apoptosis as shown by decreased DNA fragmentation and numbers of apoptotic bodies. These results suggest that SME protects human keratinocytes against UVB-induced oxidative stress by enhancing antioxidant activity in cells, thereby inhibiting apoptosis.
Proper Indication of BRAFV600E Mutation Testing in Fine-Needle Aspirates of Thyroid Nodules
Jieun Koh, Jong Rak Choi, Kyung Hwa Han, Eun-Kyung Kim, Jung Hyun Yoon, Hee Jung Moon, Jin Young Kwak
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064505
Abstract: Background The aim of this study was to evaluate the proper indication of adjunctive BRAFV600E mutation analysis at the time of ultrasound-guided fine-needle aspiration in the diagnosis of thyroid nodules. Methods This study included 518 nodules in 479 patients who underwent ultrasound-guided fine-needle aspiration with BRAFV600E mutation. We calculated and compared the diagnostic performances of cytology and cytology with BRAFV600E mutation analysis to detect malignancy among thyroid nodules according to ultrasound features and size. Results Sensitivity, negative predictive value, and accuracy of cytology with BRAFV600E mutation analysis were significantly higher than those of cytology alone in thyroid nodules with suspicious ultrasound features, regardless of size. Diagnostic performances did not show significant differences between cytology and cytology with BRAFV600E mutation analysis in nodules without any suspicious ultrasound features, regardless of size. Conclusion The BRAFV600E mutation analysis was a useful adjunctive diagnostic tool in the diagnosis of thyroid nodules with suspicious ultrasound features regardless of size.
Isolation and Characterization of a Dominant Dwarf Gene, D-h, in Rice
Rihua Piao, Sang-Ho Chu, Wenzhu Jiang, Yoye Yu, Yongmei Jin, Mi-Ok Woo, Joohyun Lee, Sunghan Kim, Hee-Jong Koh
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0086210
Abstract: Plant height is an important agronomic trait that affects grain yield. Previously, we reported a novel semi-dominant dwarfmutant, HD1, derived from chemical mutagenesis using N-methyl-N-nitrosourea (MNU) on a japonica rice cultivar, Hwacheong. In this study, we cloned the gene responsible for the dwarf mutant using a map-based approach. Fine mapping revealed that the mutant gene was located on the short arm of chromosome 1 in a 48 kb region. Sequencing of the candidate genes and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) analysis identified the gene, d-h, which encodes a protein of unknown function but whose sequence is conserved in other cereal crops. Real-time (RT)-PCR analysis and promoter activity assays showed that the d-h gene was primarily expressed in the nodes and the panicle. In the HD1 plant, the d-h gene was found to carry a 63-bp deletion in the ORF region that was subsequently confirmed by transgenic experiments to be directly responsible for the gain-of-function phenotype observed in the mutant. Since the mutant plants exhibit a defect in GA response, but not in the GA synthetic pathway, it appears that the d-h gene may be involved in a GA signaling pathway.
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