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Li-hua Xie,Xin Quan,Jie Zhang,Yan-yan Yang,Run-hong Sun,Ming-cong Xia,Bao-guo Xue,Chao Wu,Xiao-yun Han,Ya-nan Xue,Li-rong Yang 한국식물병리학회 2019 Plant Pathology Journal Vol.35 No.1
Gaeumannomyces graminis var. tritici is a soil borne pathogenic fungus associated with wheat roots. The accurate quantification of gene expression during the process of infection might be helpful to understand the pathogenic molecular mechanism. However, this method requires suitable reference genes for transcript normalization. In this study, nine candidate reference genes were chosen, and the specificity of the primers were investigated by melting curves of PCR products. The expression stability of these nine candidates was determined with three programs-geNorm, Norm Finder, and Best Keeper. TUBβ was identified as the most stable reference gene. Furthermore, the exopolygalacturonase gene (ExoPG) was selected to verify the reliability of TUBβ expression. The expression profile of ExoPG assessed using TUBβ agreed with the results of digital gene expression analysis by RNA-Seq. This study is the first systematic exploration of the optimal reference genes in the infection process of Gaeumannomyces graminis var. tritici.
Ying-Hua Li,Yin-Yin Wang,Shan Zhong,Zhi-Li Rong,Yong-Ming Ren,Zhi-Yong Li,Shu-Ping Zhang,Zhi-Jie Chang,Li Liu 한국분자세포생물학회 2009 Molecules and cells Vol.27 No.1
Ligand-dependent or independent oligomerization of receptor protein tyrosine kinase (RPTK) is often an essential step for receptor activation and intracellular signaling. The novel oncogene with kinase-domain (NOK) is a unique RPTK that almost completely lacks an ectodomain, expresses intracellularly and activates constitutively. However, it is unknown whether NOK can form oligomer or what function oligomerization would have. In this study, two NOK deletion mutants were generated by either removing the ectodomain (NOKECD) or including the endodomain (NOK-ICD). Co-immunoprecipitation demonstrated that the transmembrane (TM) domain of NOK was essential for its intermolecular interaction. The results further showed that NOK aggregated more closely as lower order oligomers (the dimer- and trimer-sized) than either deletion mutant did since NOK could be cross-linked by both Sulfo-EGS and formaldehyde, whereas either deletion mutant was only sensitive to Sulfo-EGS. Removing the NOK TM domain (NOK-ICD) not only markedly promoted higher order oligomerization, but also altered the subcellular localization of NOK and dramatically elevated the NOK-mediated constitutive activation of extracellular signal-regulated kinase (ERK). Moreover, NOK-ICD but not NOK or NOKECD was co-localized with the upstream signaling molecule RAS on cell membrane. Thus, TM-mediated intermolecular contacting may be mainly responsible for the constitutive activation of NOK and contribute to the autoinhibitory effect on RAS/MAPK signaling.
이영화(Rong Hua Li),박성희(Sung-Hee Park),김진수(Jin Soon Kim),류근호(Keon Ho Ryu) 한국정보과학회 2002 한국정보과학회 학술발표논문집 Vol.29 No.2Ⅰ
현재 생명 정보는 웹 상에서 다양한 포맷으로 배포되고 있다. 이러한 생명 정보 분석으 위한 데이터베이스나 시스템마다 이질적인 포맷을 지원하고 있기 때문에 각 시스템에서 이용되는 포맷들간의 변환이 필요하다. 이러한 생명 정보의 포맷 변환은 1대1의 파서를 구현하여 진행되고 있으며 1:1 파서의 구현에는 많은 시간과 비용이 소모된다. 따라서, 이 논문에서는 생명 정보를 XML로 표현하고 이질적인 포맷간의 매핑 정보를 데이터베이스에 저장한다. 이러한 매핑 정보를 XML의 스타일 시트로 나타내어 최종적으로 원하는 포맷으로 변환한다. 이렇게 포맷 변환에 XML 기술을 이용함으로써 파서를 구현할 필요가 없이 매핑 정보를 스타일 시트로 기술하면 되기 때문에 구현이 용이하며, 원시 소스가 변경되었을 때 소스 전체를 수정할 필요가 없이 수정한 필드의 매핑 정보만 수정하고 그에 따라서 XML을 수정하면 되기 때문에 원시 소스 변경의 영향을 많이 받지 않는다.
Xie, Li-hua,Quan, Xin,Zhang, Jie,Yang, Yan-yan,Sun, Run-hong,Xia, Ming-cong,Xue, Bao-guo,Wu, Chao,Han, Xiao-yun,Xue, Ya-nan,Yang, Li-rong The Korean Society of Plant Pathology 2019 Plant Pathology Journal Vol.35 No.1
Gaeumannomyces graminis var. tritici is a soil borne pathogenic fungus associated with wheat roots. The accurate quantification of gene expression during the process of infection might be helpful to understand the pathogenic molecular mechanism. However, this method requires suitable reference genes for transcript normalization. In this study, nine candidate reference genes were chosen, and the specificity of the primers were investigated by melting curves of PCR products. The expression stability of these nine candidates was determined with three programs-geNorm, Norm Finder, and Best Keeper. $TUB{\beta}$ was identified as the most stable reference gene. Furthermore, the exopolygalacturonase gene (ExoPG) was selected to verify the reliability of $TUB{\beta}$ expression. The expression profile of ExoPG assessed using $TUB{\beta}$ agreed with the results of digital gene expression analysis by RNA-Seq. This study is the first systematic exploration of the optimal reference genes in the infection process of Gaeumannomyces graminis var. tritici.
Han Li,Hua Cao,Rong‑pei Yu,Zhen Miao,Ji‑hua Wang,Su‑Ping Qu,Qiang Yuan,Shenchong Li 한국원예학회 2018 Horticulture, Environment, and Biotechnology Vol.59 No.3
Paphiopedilum pacific shamrock is an orchid with high ornamental value. Understanding the mechanisms responsible for leaf color in albino mutants is important for ornamental development and breeding. In this study, we compared the leaf photosynthetic pigment content and transcriptome of albino mutants ppa01 and wild-type P. pacific shamrock. Photosynthetic pigment in mutants was less than 2% of the wild type and chl a/b was 60% less than the wild type. Transcriptome sequencing yielded 6.27 Gb and 5.67 Gb clean data from the mutant and wild-type leaves, respectively. De novo assembly yielded 104,763 unigenes with 15,400 greater than 1 kb in length. In unigene expression analysis, 3170 differentially expressed genes (DEGs) were identified with 2231 (70.38% of total DEGs) down-regulated. Results from GO and KEGG enrichment analysis, KEGG pathway analysis and qPCR suggest that the reduction of chloroplast biosynthesis and division in the mutant was due to low expression levels of ppGLK1 and ppFtsz. Mutants were associated with fewer chloroplasts in leaf cells, abnormal chloroplast structures, impaired chlorophyll biosynthesis, and thus reduced total chlorophyll and carotenoid contents. Furthermore, down-regulated expression of ppNYC1 reduced transformation of chlorophyll b into chlorophyll a, leading to a chl a/b decline. The research will guide future studies of leaf pigment mutations and the breeding of P. pacific shamrock.
Chen, Peng,Wang, Xiu-Li,Ma, Zhong-Sen,Xu, Zhong,Jia, Bo,Ren, Jin,Hu, Yu-Xin,Zhang, Qing-Hua,Ma, Tian-Gang,Yan, Bing-Di,Yan, Qing-Zhu,Li, Yan-Lei,Li, Zhen,Yu, Jin-Yan,Gao, Rong,Fan, Na,Li, Bo,Yang, Jun Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.7
HMGN5 is a typical member of the HMGN (high mobility group nucleosome-binding protein) family which may function as a nucleosomal binding and transcriptional activating protein. Overexpression of HMGN5 has been observed in several human tumors but its role in tumorigenesis has not been fully clarified. To investigate its significance for human lung cancer progression, we successfully constructed a shRNA expression lentiviral vector in which sense and antisense sequences targeting the human HMGN5 were linked with a 9-nucleotide loop. Inhibitory effects of siRNA on endogenous HMGN5 gene expression and protein synthesis were demonstrated via real-time RT-PCR and western blotting. We found HMGN5 silencing to significantly inhibit A549 and H1299 cell proliferation assessed by MTT, BrdU incorporation and colony formation assays. Furthermore, flow cytometry analysis showed that specific knockdown of HMGN5 slowed down the cell cycle at the G0/G1 phase and decreased the populations of A549 and H1299 cells at the S and G2/M phases. Taken together, these results suggest that HMGN5 is directly involved in regulation cell proliferation in A549 and H1299 cells by influencing signaling pathways involved in cell cycle progression. Thus, our finding suggests that targeting HMGN5 may be an effective strategy for human lung cancer treatment.
Song, Qing-Kun,Li, Jing,Huang, Rong,Fan, Jin-Hu,Zheng, Rong-Shou,Zhang, Bao-Ning,Zhang, Bin,Tang, Zhong-Hua,Xie, Xiao-Ming,Yang, Hong-Jian,He, Jian-Jun,Li, Hui,Li, Jia-Yuan,Qiao, You-Lin,Chen, Wan-Qin Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.22
Background: The study aimed to describe the age distribution of breast cancer diagnosis among Chinese females for comparison with the United States and the European Union, and provide evidence for the screening target population in China. Materials and Methods: Median age was estimated from hospital databases from 7 tertiary hospitals in China. Population-based data in China, United States and European Union was extracted from the National Central Cancer Registry, SEER program and GLOBOCAN 2008, respectively. Age-standardized distribution of breast cancer at diagnosis in the 3 areas was estimated based on the World Standard Population 2000. Results: The median age of breast cancer at diagnosis was around 50 in China, nearly 10 years earlier than United States and European Union. The diagnosis age in China did not vary between subgroups of calendar year, region and pathological characteristics. With adjustment for population structure, median age of breast cancer at diagnosis was 50~54 in China, but 55~59 in United States and European Union. Conclusions: The median diagnosis age of female breast cancer is much earlier in China than in the United States and the European Union pointing to racial differences in genetics and lifestyle. Screening programs should start at an earlier age for Chinese women and age disparities between Chinese and Western women warrant further studies.
Xiu-Shi Yang,Li-Li Wang,Xian-Rong Zhou,Shaomin Shuang,Zhi-Hua Zhu,Nan Li,Yan Li,Fang Liu,San-Cai Liu,Ping Lu,Guixing Ren,Chuan Dong 한국식품과학회 2013 Food Science and Biotechnology Vol.22 No.6
Quantitative detection of protein, fat, starch,and amino acids in foxtail millet using Fourier transformnear-infrared spectroscopy (NIRS) was investigated. Foxtail millet samples (n=259) were analyzed using NIRS. Spectral data were linearized with data from chemicalanalyses. Calibration models were established using apartial least-squares (PLS) algorithm with cross-validation. Optimized models were tested using external validation setsamples with coefficients of determination in the externalvalidation (R2val) of >0.90. Residual predictive deviation(RPD) values were nearly equal to or >2.5 for crudeprotein, alanine, aspartic acid, glutamic acid, isoleucine,leucine, and serine. However, for glycine, histidine,phenylalanine, proline, threonine, tyrosine, and valine, theR2val values were >0.83 and RPD values were nearly equalto or >2.0. For crude fat, total starch, arginine, and lysine,the R2val values were >0.70 and RPD values were >1.5. NIRS is a rapid determination tool for foxtail milletbreeding, and for quality control.
Li, Qiu-Wen,Lu, Can-Rong,Ye, Ming,Xiao, Wen-Hua,Liang, Jun Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.1
We conducted a case-control study in China to clarify the association between XRCC1-Arg399Gln polymorphism and HCC risk. A total of 150 cases and 158 controls were selected from the the Affiliated Hospital of Qingdao University from May 2008 to May 2010. XRCC1-Arg399Gln polymorphism was based upon duplex polymerase-chain-reaction with the confronting-two-pairprimer (PCR-CTPP) method. All analyses were performed using the STATA statistical package. A significantly increased risk was associated with the Arg/Gln genotype (adjusted OR 1.78, 95%CI=1.13-2.79) compared with genotype Arg/Arg. In contrast, the Gln/Gln genotype had non-significant increased risk of HCC with adjusted OR (95%CI) of 1.69 (0.93-2.66). A significant association was found between positive HBsAg and Arg/Gln, with an OR of 3.43 (95% CI=1.45-8.13). Patients carrying Gln/Gln genotypes showed significantly lower median survival than Arg/Arg genotypes (HR=1.38, 95% CI=1.04-1.84). Further Kaplan-Meier analysis showed decreased median survival in Arg/Gln+Gln/Gln genotype carriers in comparison to Arg/Arg carriers (HR=1.33, 95% CI=1.02-1.76). In conclusion, we observed that XRCC1-Arg399Cln polymorphism is associated with susceptibility to HCC, and XRCC1 Gln allele genotype showed significant prognostic associations.