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Osteopathia striata with cranial sclerosis, Wilms' tumor and the WTX gene

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World Journal of Medical genetics 2014年第2期4卷 34-38页

作者： Elisa Cattaneo Sara Ciceri Natascia Liberati Paolo Radice Luigi Tarani Angelo Selicorni Daniela Perotti UOS Pediatric Genetic UnitPediatric Department MBBM FoundationS Gerardo Hospital20900 Monza Italy Molecular bases of genetic Risk and genetic Testing Unit Department of Preventive and Predictive Medicine Fondazione IRCCS Istituto Nazionale dei Tumori20133 Milano Italy Department of Pediatrics Policlinico Umberto I Sapienza University00186 Roma Italy

Osteopathia striata with cranial sclerosis(OSCS, OMIM#300373) is an X-linked dominant sclerosing bone dysplasia that shows a distinct phenotype in females and males. In 2009, Zandra Jenkins et al found that germline mutations in the FAM123 B /WTX /AMER1 gene, mapped to chromosome Xq11.2, cause both the familial and sporadic forms of OSCS. Intriguingly, the WTX gene was already known as a putative tumor suppressor gene, since in 2007 Rivera et al had reported inactivating WTX mutations in Wilms' tumor(WT), the most frequent renal tumor of childhood. Here we review the heterogeneous clinical presentation of OSCS patients and the involvement of WTX anomalies in OSCS and in WT.

关键词： Osteopathia striata with cranial sclerosis Wilms’ tumor WTX Mutation genetics

The evolution of tea spatial agglomeration in China:An analysis based on different geographical scales

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Journal of Mountain Science 2018年第12期15卷 2590-2602页

作者： LIU Han-chu FAN Jie ZENG Yu-xi WANG Wen-zhao Key laboratory of Regional Sustainable DevelopmentModeling ChineseAcademy of SciencesBeijing 100101China Institute of C-eography Science andNatural Resources Research ChineseAcademy of SciencesBeIjing 100101China University of Chinese Academy of Sciences Beijing 10049China National Key laboratory of Crop genetic Improvement and National Center of Plant Gene Research (Wuhan) Huazhong Agricultural UniversityWuhan 430070China

The spatial agglomeration of agricultural production is conducive to reducing planting costs, increasing production efficiency and improving product quality. It is an important way to promote the transformation and upgrad of tea industry and realize the modernization of China's tea industry. This study used Gini coefficient and spatial autocorrelation analysis to explore the characteristics of tea spatial agglomeration in China from three geographical scales: regional level, provincial level and prefecture level from the year 2005 to 2015. The results indicated that there was a significant scale effect on the tea spatial agglomeration. The agglomeration degree increased from the regional level, provincial level to prefecture level. The types of spatial agglomeration evolution of the three scales were Ushaped, continuous diffusion, and continuous agglomeration. The spatial autocorrelation of tea production could only be found at the prefecture level. Meanwhile, at the prefecture scale, we could not only reveal the pattern changes at the regional and provincial levels, but also identify tea production agglomeration regions. Compared with the large scale, the small scale could reveal the characteristics of tea spatial agglomeration in more details. Factors such as natural resource endowments, cost factor, technological advancement, agglomeration economy, and agricultural policy influenced the evolution of tea spatial agglomeration from different geographical scales. Finally, from the perspectives of spatial transfer of tea production, promoting spatial agglomeration, building tea production bases, and breaking administrative boundaries, we proposed several policy suggestions for optimizing the spatial layout of tea production.

关键词： Tea production Spatial agglomeration Geographic scale Driving Factors China

A population for genome-wide association studies(GWAS) of root traits in oilseed rape(Brassic napus L.)

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A population for genome-wide association studies(GWAS) of ro...

Sequence Polymorphisms and Phylogenetic Relationships of hina Gene in Wild Barley from Tibet, China

第十四届全国植物基因组学大会

作者： Xiaohua Wang Yanling Chen Guangda Ding Fangsen Xu Tingdong Fu Lei Shi Bin Yi National Key laboratory of Crop genetic Improvement Huazhong Agricultural University

Genome-wide associate studies(GWAS) have been employed to reveal the genetic bases of some important complex agronomic traits in crops,such as kernel,plant height,flowering time and root number in the germination stag... 详细信息

关键词： genome-wide association studies(GWAS) oilseed rape root traits Single Nucleotide Polymorphism(SNP) phosphorus

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Agricultural Sciences in China 2008年第7期7卷 796-803页

作者： YANG Shi-dong WEI Yu-ming QI Peng-fei ZHENG You-liang Triticeae Research Institute Sichuan Agricultural University Ya＇an 625014 P..R.China Key laboratory of Crop genetic Resources and Improvement in Southwest China Ministry of Education/Sichuan Agricultural University Ya＇an 625014 P.R. China

The hina gene encodes a HINA protein in seeds of barley （Hordeum vulgare）, which was known to affect the grain hardness. 171 hina gene sequences from Tibetan wild barley accessions and worldwide were characterized. Across 1 452 nucleotides of 171 hina genes, 152 SNPs were detected, giving an average frequency of one SNP per 9.5 bases. There were 93 singleton variable sites （the nucleotide polymorphism only observed in a single accession）, 59 polymorphic sites （the polymorphisms found in two or more accessions） and 8 indels. A total of 18 haplotypes were defined, and most of the barley accessions shared one gene haplotype. H. spontaneum had a wider haplotype distribution. Through the analysis of median-joining network of the 18 haplotypes, 4 haplotype groups were found, which were testified by neighbor-joining tree based on the complete sequence alignment. Extremely low level of hina gene diversity was observed in Tibetan wild barley accessions, indicating that Tibet is unlikely a center of origin for cultivated barley.

关键词： Tibetan wild barley hina SNP haplotype median-joining network

Non-dormant Axillary Bud 1 regulates axillary bud outgrowth in sorghum

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Journal of Integrative Plant Biology 2018年第10期60卷 938-955页

作者： Jun Chen Limin Zhang Mengjiao Zhu Lijie Han Ya Lv Yishan Liu Pan Li Haichun Jing Hongwei Cai Department of Plant genetics Breeding and Seed ScienceChina Agricultural UniversityBeijing Key Laboratory of Crop Genetic ImprovementLaboratory of Crop Heterosis and UtilizationMOEBeijing 100193China Key laboratory of Plant Resources Institute of BotanyChinese Academy of SciencesBeijing 100093China Inner Mongolia Research Centre for Practaculture Chinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China Forage Crop Research Institute Japan Grassland Agricultural and Forage Seed Association388-5 HigashiakadaNasushiobaraTochigi 329-2742Japan

Tillering contributes to grain yield and plant architecture and therefore is an agronomically important trait in sorghum （Sorghum bicolor）. Here, we identified and functionally characterized a mutant of the Non- dormant Axillary Bud 1 （NAB1） gene from an ethyl methanesulfonate-mutagenized sorghum population. The nab1 mutants have increased tillering and reduced plant height. Map-based cloning revealed that NAB~ encodes a carotenoid-cleavage dioxygenase 7 （CCDT） orthologous to rice COryza sativa） HIGH-TILLERING DWARF1/ DWARF^7 and Arabidopsis thaliana MORE AXILLARY BRANCHING 3. NAB1 is primarily expressed in axillary nodes and tiller bases and NAB1 localizes to chloroplasts. The nab1 mutation causes outgrowth of basal axillary buds; removing these non-dormant basal axillary buds restoredthe wild-type phenotype. The tillering of nab1 plants was completely suppressed by exogenous application of the synthetic strigolactone analog GR24. Moreover, the nab1 plants had no detectable strigolactones and displayed stronger polar auxin transport than wild-type plants. Finally, RNA-seq showed that the expression of genes involved in multiple processes, including auxin-related genes, was significantly altered in nab1. These results suggest that NAB1 functions in strigolactone biosynthesis and the regulation of shoot branching via an interaction with auxin transport.

关键词： NAB Non-dormant Axillary Bud 1 regulates axillary bud outgrowth in sorghum Figure HTD

Structural basis for the specific single-stranded RNA recognition by designer pentatricopeptide repeat protein

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Structural basis for the specific single-stranded RNA recogn...

Differentially expressed microRNAs in sugarcane challenged by Sporisorium scitamineum and functional identification of their target gene

第五届中国结构生物学学术讨论会

作者： Ping Yin National Key laboratory of Crop genetic Improvement and National Centre of Plant Gene Research

As a large family of RNA binding proteins, pentatricopeptide repeat（PPR） proteins mediate multiple aspects of RNA metabolism in eukaryotes. Binding to their target single-stranded RNA（ss RNA） in a modular and base-specific fashion, PPR proteins can serve as designable modules for gene manipulation. However, the structural basis for nucleotide-specific recognition by designer PPR（d PPR） remains to be elucidated. Here we report four crystal structures of d PPR proteins in complex with their respective ss RNA-targets. The d PPR repeats are assembled into a right-handed superhelical spiral shell that embraces the ss RNA inside. Interactions between different PPR codes and RNA bases are observed at the atomic level, revealing the molecular basis for the modular and specific recognition patterns of the RNA bases U, C, A and G. These structures not only provide insights into the functional study of PPR proteins, but also pinpoint a pathway toward the potential design of synthetic sequence-specific RNA-binding proteins.

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Differentially expressed microRNAs in sugarcane challenged b...

Physicochemical bases for protein folding,dynamics,and protein-ligand binding

中国作物学会——2015年学术年会

作者： Yuye Zhang Yachun Su Ning Huang Jinlong Guo Hui Ling Feng Liu Weihua Su Qibin Wu Youxiong Que Liping Xu Key laboratory of Sugarcane Biology and genetic Breeding Fujian Agriculture and Forestry UniversityMinistry of Agriculture

Two sugarcane varieties,Yacheng 05-179(smut resistant)and ROC 22(smut susceptible),were used as the plant *** buds challenged by *** at 48 hours after inoculation(hpi)were taken as treatment group and those treated by water as the control *** used high-throughput HiSeq sequencing technology to analyze the differentially expressed microRNAs in sugarcane challenged by *** at 48 hpi,then small RNA sequences were annotated and the differentially expressed miRNAs were *** results showed that the number of known miRNAs was 264 in ROC 22control,263 in ROC 22 treatment,260 in Yacheng 05-179 control and 262 in Yacheng 05-179 treatment,respectively,while the corresponding number of novel miRNAs in each sample was 137,140,111 and *** addition,the statistical analysis of base distribution of novel miRNAs showed that most of the first point bases of 21 nt and 22 nt in novel miRNA sequences that had more contents in plants were U,and eleven loci bases of candidate miRNAs sequence tended to be *** ROC22,we identified 231 expressed known *** them,35 known miRNAs were significantly differentially expressed(|log2-ratio|>1,P1,P<0.05)in between treatment and control *** these 11 miRNAs,2 were expression up-regulated and 9 were expression down-regulated,and the highest difference ratio of expression quantity was up to 2.1 between control group and treatment ***,most of significant differentially expressed know miRNAs in ROC 22 and Yacheng 05-179 were the same with l

关键词： Sugarcane Sporisorium scitamineum High-throughput sequencing Differentially expressed miRNAs Function prediction of target genes qRT-PCR

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Science China(Life Sciences) 2014年第5期57卷 287-302页

作者： LI HuiMin XIE YueHui LIU CiQuan LIU ShuQun School of Mathematics and Computer Science Yunnan University of Nationalities laboratory for Conservation and Utilization of Bio-Resources & Key laboratory for Microbial Resources of Ministry of Education Yunnan University Teaching and Research Section of Computer Department of Basic MedicalKunming Medical University Southwest Biological Diversity laboratory Kunming Branch of Chinese Academy of Sciences Key laboratory for Animal genetic Diversity and Evolution of High Education in Yunnan Province

Proteins are essential parts of living organisms and participate in virtually every process within cells. As the genomlc sequences for increasing number of organisms are completed, research into how proteins can perform such a variety of functions has become much more intensive because the value of the genomic sequences relies on the accuracy of understanding the encoded gene products. Although the static three-dimensional structures of many proteins are known, the functions of proteins are ulti- mately governed by their dynamic characteristics, including the folding process, conformational fluctuations, molecular mo- tions, and protein-ligand interactions. In this review, the physicochemical principles underlying these dynamic processes are discussed in depth based on the free energy landscape （FEL） theory. Questions of why and how proteins fold into their native conformational states, why proteins are inherently dynamic, and how their dynamic personalities govern protein functions are answered. This paper will contribute to the understanding of structure-function relationship of proteins in the post-genome era of life science research.

关键词： free energy landscape entropy-enthalpy non-complementarity ruggedness driving force thermodynamics kinetics

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Association between low molecular polypeptide 7 single nucleotide polymorphism and response to therapy in hepatitis C virus infection

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World Journal of Hepatology 2013年第3期5卷 97-103页

作者： Moataza H Omran Basma E Fotouh Samar S Youssef Noha E Ibrahim Wael Nabil EL-Sayed M Mahdy Wafaa G Shosha Mostafa K El-Awady Microbial Biotechnology Department Genetic Engineering Division National Research Center Chemistry Department Faculty of Science Helwan University

AIM: To investigate the relationship between low molecular polypeptide-7 (LMP-7) gene polymorphism and response to interferon (IFN) therapy in chronic hepatitis C virus (HCV) patients. METHODS: LMP-7 polymorphism at codon 49 with nucleotide substitution from A to C was amplified in 104 chronic HCV patients of genotype 4. The amplicons were digested with restriction endonuclease Bsm I and the produced restriction fragment length polymorphism was analyzed. Patients received IFN + regional blood volume therapy for 48 wk and the frequency of thissingle nucleotide polymorphism (SNP) was statistically correlated with treatment response. The exclusion criteria for these patients were stated by the national health program for treating viral hepatitis. Main exclusion criteria included co-infection with hepatitis B virus or schistosomiasis, thyroid dysfunction, uncontrolled diabetes mellitus, history of long term drug or alcohol intake and autoimmune hepatitis. Multivariate analyses were done to correlate LMP-7 SNP plus several factors such as age, gender, weight, serum alpha-fetoprotein (AFP) and alanine aminotransferase levels, liver activity, fibrosis score and viral load with response to therapy. RESULTS: The data presented in this study clearly demonstrated statistically significant differences between sustained virological response (SVR) (defined as the absence of HCV RNA levels in the patient's sera at least 6 mo after discontinuation of treatment) and non-response (NR) (where HCV RNA levels in the patient's sera never become undetectable for 6 mo during or after treatment). Variables were described as odds ratio with 95%CI. The data were considered significant if P values were ≤ 0.05; highly significant if P < 0.01 and very highly significant if P < 0.001. Current data showed that 91.7% of patients carrying LMP-7 C/C allele were associated with SVR, while the other two genotypes C/A and A/A were associated with NR patients, 83.3% and 64.3% respectively, showing that g

关键词： Hepatitis C virus Interferon therapy Low molecular mass polypeptide Host gene Single nucleotide polymorphism