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Evolution related genes of salt tolerance in rice revealed by McDonald-Kreitman Test
Jie Yu,Tae-Sung Kim,Kyu-Won Kim,Yong-Jin Park 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07
Salt is the major factor limiting crop productivity in saline soils. Development of genetic basis of high salt-tolerant rice is necessary to satisfy urgent needs in rice breeding. In this study, 295 rice accessions from a Korean authentic core set were used to identify the evolution associated genes regarding salt tolerance. By using McDonald-Kreitman Test (MKT), we detected orthologous genes in rice (Oryza sativa) using Brachypodium as an outgroup to investigate fast evolved genes that express differentially based on distinct phenotypic groups. Three groups which represented the salt sensitive (group 1), salt medium tolerant (group 2) and salt tolerant (group 3) were separated and each group was examined with the outgroup in neutral and non-neutral polymorphism together with the divergence levels. Total 53 fast evolutionary genes that have a positive selection with FDR ≤ 0.05 were found in the three groups. Among them, 15, 31 and 7 genes were included exclusively in group 1, 2 and 3, respectively. Annotation of these genes showing the predicted functions were checked. Two genes were found to be related to high salt tolerance based on the previous studies. Besides, association study of the candidate gene alleles and salt tolerance phenotype was carried out, indicating that these genes were correlated with salt tolerance. All these result support that using this type of evolution study, we may find some important candidate genes which are related to important traits in rice, such as the salt tolerance, providing important information for future gene based molecular breeding and functional analysis in rice.
Jie Yu,Tae-Sung Kim,Yong-Jin Park 한국육종학회 2014 한국육종학회 심포지엄 Vol.2014 No.07
Salt toxicity is the major factor limiting crop productivity in saline soils. Rice is an important staple food crop of nearly half of the world population and is well known to be a salt sensitive crop. The completion and enhanced annotations of rice genome sequence has provided the opportunity to study functional genomics of rice. With the rapid development of the biotechnology techniques, we can use more accurate and reliable methods to study the mechanism and function in different stress conditions. In present study, 295 rice accessions of diverse origin were re-sequenced and used for genome-wide association study (GWAS) with several germination-related traits, including germination percentage (GP), germination energy (GE), germination rate (GR), germination index (GI), salt tolerance index (STI) in salt tolerant germination stage. Phenotyping of the rice accessions were carried out at 200mM NaCl to screen salt tolerance levels. GWAS was applied to detect the associated genes related to salt tolerance in rice germination stage. Variations and haplotypes of the associated genes were detected and correlation between the phenotypes and genotypes were validated using qRT-PCR.
Choi, Yong-Woo;Kim, Sun-Mi;Jin, Xiong-Jie;Kwak, Ji-Yeong;Jung, Ju-Yang;Mun, Jun-II;Lim, Hong-Seok 중앙대학교 의과대학 의과학연구소 2012 中央醫大誌 Vol.37 No.1/2
The use of drug eluting stent (DES) has been increased in recent years because of its ability to inhibit neointimal proliferation. However, it may affect the normal healing process of the vessel wall after vascular injury and may be associated with coronary artery aneurysm formation in rare cases. We report a case of angiographic spontaneous resolution of coronary aneurysm developed after implantation of sirolimus-eluting coronary stent at the left anterior descending artery, diagonal branch, and left circumflex artery. But, there was discrepancy between intravascular ultrasound (IVUS) and coronary angiographic findings. IVUS demonstrated no significant shrinkage of maximal external elastic membrane (EEM) compared to earlier examination but echogenic tissue was filled in the free space between the stent and EEM at the stented segments where the angiographic resolution of the aneurysm occurred. We found out that an angiographic resolution of coronary aneurysm does not always guarantee real shrinkage of vessel wall, and fill-up of aneurismal space with thrombus or tissue could be an important mechanism of spontaneous resolution of DES related coronary aneurysm. Optimal treatment could be decided based on longer-term follow-up of patients which provide more accurate characterization of the consequences of DES-related aneurysm.
( Hai Yan Zhao ),( Hui Ying Li ),( Jian Jin ),( Ji Zhe Jin ),( Long Ye Zhang ),( Mei Ying Xuan ),( Xue Mei Jin ),( Yu Ji Jiang ),( Hai Lan Zheng ),( Ying Shun Jin ),( Yong Jie Jin ),( Bum Soon Choi ) 대한내과학회 2021 The Korean Journal of Internal Medicine Vol.36 No.0
Background/Aims: Accumulating evidence indicates that L-carnitine (LC) protects against multiorgan damage through its antioxidant properties and preservation of the mitochondria. Little information is available about the effects of LC on renal fibrosis. This study examined whether LC treatment would provide renoprotection in a rat model of unilateral ureteral obstruction (UUO) and in vitro. Methods: Sprague-Dawley rats that underwent UUO were treated daily with LC for 7 or 14 days. The influence of LC on renal injury caused by UUO was evaluated by histopathology, and analysis of gene expression, oxidative stress, mitochondrial function, programmed cell death, and phosphatidylinositol 3-kinase (PI3K)/ AKT/forkhead box protein O 1a (FoxO1a) signaling. In addition, H<sub>2</sub>O<sub>2</sub>-exposed human kidney cells (HK-2) were treated with LC. Results: LC treatment inhibited expression of proinflammatory and profibrotic cytokines, and was followed by a significant attenuation of tubulointerstitial inflammation and fibrosis. The increased oxidative stress caused by UUO was associated with mitochondrial dysfunction and excessive apoptosis and autophagy via PI3K/AKT/FoxO1a-dependent signaling, and this was abrogated by administration of LC. In H<sub>2</sub>O<sub>2</sub>-exposed HK-2 cells, LC decreased intracellular production of reactive oxygen species, and suppressed expression of profibrotic cytokines and reduced the number of apoptotic cells. Conclusions: LC protects against the progression of tubulointerstitial fibrosis in an obstructed kidney.
Positively Selected Orthologous Genes Identified in Sesame (Sesamum indicum) by Deep Resequencing
( Jie Yu ),( Myeong-hyeon Min ),( Sang-ho Chu ),( Kyu-won Kim ),( Yong-jin Park ) 한국육종학회 2019 Plant Breeding and Biotechnology Vol.7 No.1
Sesame (Sesamum indicum L.) is the queen of oil seed crops and is cultivated widely in tropical and subtropical areas. The availability of the sesame genome sequence presents unprecedented opportunities for studying its genetics, genomics, and evolution. In this report, we conducted a genome resequencing-based identification of sesame orthologs; in total, 26,379 coding sequences (CDSs) were isolated. Using a reciprocal best hit, we ultimately identified a total of 639 orthologs sets after one-to-one orthologs extraction across seven Pentapetalae plant species. These orthologs were considered to be the most credible between the two species, and in sesame. Furthermore, we performed a branch model-based maximum likelihood estimation of dN/dS of the orthologs, resulting in the identification of 198 evolutionarily accelerated orthologs and 66 positively selected genes (P-value and FDR < 0.05). An enrichment analysis and protein interaction network suggested 19 genes with important functions of the orthologs specific in sesame development and domestication. The method we used here provides a case study for identifying orthologous genes between sesame and other plants species that are distributed in equilibrium phylogenetically, which can be used in other plants.
JIN, HAI-LAN,PIAO, YONG-JIE Chungcheong Mathematical Society 2015 충청수학회지 Vol.28 No.3
A continuous and non-decreasing function ${\psi}$ and another continuous function ${\phi}$ with ${\phi}(z)=0{\Leftrightarrow}z=0$ defined on $\mathbb{C}^+=\{x+yi:x,y{\geq}0\}$ are introduced, the ${\psi}-{\phi}$-contractive or expansive type conditions are considered, and the existence theorems of common fixed points for two mappings defined on a complex valued metric space are obtained. Also, Banach contraction principle and a fixed point theorem for a I-expansive type mapping are given on complex valued metric spaces.