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Cellular Serpents and Dreaming Spires:New Frontiers in Arginine and Pyrimidine Biology

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Journal of Genetics and genomics 2014年第10期41卷 561-565页

作者： Gabriel N.Aughey mr Y.Tastan Ji-Long Liu MRC Functional genomics Unit Department of Physiology Anatomy and Genetics University of Oxford Oxford OX1 3PT United Kingdom

The International Conference on Arginine and Pyrimidines （ICAP） had its origin as an arginine workshop organised by a group of microbiologists led by Werner Maas in 1972 （Rubio, 2003）. The shared requirement of carbamoyl phosphate in both arginine and pyrimidine metabolism led to a natural association of researchers working in both fields.

关键词： Cellular Serpents and Dreaming Spires ICAP

Genetic diversity for mycorrhizal symbiosis and phosphate transporters in rice

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Journal of Integrative Plant Biology 2015年第11期57卷 969-979页

作者： Kwanho Jeong Nicolas Mattes Sheryl Catausan Joong Hyoun Chin Uta Paszkowski Sigrid Heuer Southern Cross Plant Science Southern Cross University International Rice Research Institute(IRRI) Crop and Environmental Sciences Division Seoul National University College of Agriculture and Life SciencesPlant Genomics and Breeding Institute University of Cambridge Department of Plant Sciences Australian Center For Plant Functional genomics(ACPFG)

Phosphorus （P） is a major plant nutrient and developing crops with higher P-use efficiency is an important breeding goal. In this context we have conducted a comparative study of irrigated and rainfed rice varieties to assess genotypic differences in colonization with arbuscular mycorrhizal （AM） fungi and expression of different P trans- porter genes. Plants were grown in three different soil samples from a rice farm in the Philippines. The data show that AM symbiosis in all varieties was established after 4 weeks of growth under aerobic conditions and that, in soil derived from a rice paddy, natural AM populations recovered within 6 weeks. The analysis of AM marker genes （AM1, AM3, AM14） and P transporter genes for the direct Pi uptake （PT2, PT6） and AM-mediated pathway （PTll, PT13） were largely in agreement with the observed root AM colonization providing a useful tool for diversity studies. Interestingly, delayed AM colonization was observed in the aus-type rice varieties which might be due to their different root structure and might confer an advantage for weed competition in the field. The data further showed that P-starvation induced root growth and expression of the high-affinity P transporter PT6 was highest in the irrigated variety IR66 which a]so maintained grain yield under P-deficient field conditions.

关键词： Mycorrhiza P deficiency tolerance phosphatetransporters rice roots

Genetic association between the polymorphism of cytosolicPLA2 gene family and schizophrenia

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Frontiers of Medicine 2010年第1期4卷 101-105页

作者： Qiong YU Xiang-Fei MENG Jie-Ping SHI Ya-Qin YU department of Epidemiology and Biostatistics Center of Medical GenomicsSchool of Public HealthJilin UniversityChangchun 130021China

Abnormal phospholipid metabolism in the brain plays an important role in neuropsychiatric *** A2(PLA2)is a crucial element for normal neuro-physiological *** study aims to investi-gate the genetic association between the polymorphism of cytosolic phospholipase A2(cPLA2)family genes and schizophrenia among Han Chinese in the northern part of *** polymerase chain reaction-based ligase detec-tion reaction(PCR-LDR)was applied to detect the genotype ten single nucleotide polymorphisms(SNPs)of cPLA2 family genes among 201 pedigrees consisting of fathers,mothers and affected offsprings with *** pedigrees were collected from 2000 to *** relative risk(HRR)test,transmission disequili-brium test(TDT),haplotype transmission analysis and multiple locus analysis were conducted to analyze the genotyping *** genotypic frequency of cPLA2 gene did not deviate from Hardy-Weinberg equilibrium either in case or control *** and TDT showed that the ten SNPs were not associated with schizophrenia(P>0.05).Analysis for haplotype transmission showed that no haplotype system was associated with schizophrenia(P>0.05).The conditioning on allele(COA)and conditioning on gene(COG)tests showed disease associations with the haplotype of rs2162886-rs1668589,rs891014-rs1668589 and rs2307279-rs7542180(χ2=6.913,P=0.032;χ2=8.393,P=0.015;χ2=8.447,P=0.038).Our data suggest that many loci in the cPLA2 family genes may be associated with schizophrenia.

关键词： schizophrenia cytosolic phospholipase A2 ligase detection reaction polymorphism

Synthetic genomes engineered by SCRaMbLEing

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Science China(Life Sciences) 2018年第8期61卷 975-977页

作者： Feng Zhang Daniel F.Voytas department of Plant and Microbial Biology University of Minnesota Center for Precision Plant genomics University of Minnesota department of Genetics Cell Biology and Development University of Minnesota Center for Genome Engineering University of Minnesota

The ability to design and synthesize the genome of a living organism marks one of the most significant achievements in synthetic biology. The first synthetic genomes were those of bacteria （Gibson et al., 2010; Hutchison et al., 2016）, but an international consortium of scientists is now undertaking the ambitious task of designing and synthesizing the entire genome of Saccharornayces cerevisiae, a eukaryotic single-celled yeast （Dymond et al., 2011; Kannan and Gibson, 2017）. One feature of the redesigned yeast genome, called Saccharomyces cerevisiae 2.0 or Sc2.0, is the ability to in-duce novel genetic variation.

关键词：合成生物学染色体设计国际协会真核细胞基因变化有机体科学家

Intracellular compartmentation of CTP synthase in Drosophila

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Journal of Genetics and genomics 2010年第5期37卷 281-296页

作者： Ji-Long Liu Medical Research Council Functional genomics Unit,department of Physiology,Anatomy and Genetics,University of Oxford,Oxford,OX1 3QX,United Kingdom Medical Research Council Functional genomics Unit Department of Physiology Anatomy and Genetics University of Oxford Oxford OX1 3QX United Kingdom

Compartmentation is essential for the localization of biological processes within a eukaryotic cell. ATP synthase localizes to organelles such as mitochondria and chloroplasts. By contrast, little is known about the subcellular distribution of CTP synthase, the critical enzyme in the production of CTP, a high-energy molecule similar to ATP. Here I describe the identification of a novel intracellular structure con- taining CTP synthase, termed the cytoophidium, in Drosophila cells. I find that cytoophidia are present in all major cell types in the ovary and exist in a wide range of tissues such as brain, gut, trachea, testis, accessory gland, salivary gland and lymph gland. In addition, I find CTP synthase-containing cytoophidia in other fruit fly species. The observation of compartmentation of CTP synthase now permits a broad range of questions to be addressed concerning not only the structure and function of cytoophidia but also the organization and regulation of CTP synthesis.

关键词： CTP synthase cytoophidium Drosophila organelle cilium oogenesis

Role of Peroxisome Proliferator-Activated Receptor Gamma in Glucose-induced Insulin Secretion

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Acta Biochimica et Biophysica Sinica 2006年第1期38卷 1-7页

作者： Ze-Kuan XU~(1,2),Neng-Guin CHEN~1,Chang-Yan MA~1,Zhuo-Xian MENG~1,Yu-Jie SUN~1,and Xiao HAN~(1*) ~1 Key Laboratory of Human Functional genomics of Jiangsu Province,department of Biochemistry and Molecular Biology, Nanjing Medical University,Nanjing 210029,China ~2 department of Normal Surgery,the First Affiliated Hospital of Nanjing Medical University,Nanjing 210029,China Key Laboratory of Human Functional genomics of Jiangsu Province Department of Biochemistry and Molecular Biology Nanjing Medical University Nanjing 210029 China department of Normal Surgery the First Affiliated Hospital of Nanjing Medical University Nanjing 210029 China

Peroxisome proliferator-activated receptor (PPAR) isoforms (α and γ) are known to beexpressed in pancreatic islets as well as in insulin-producing cell *** of PPAR have been shoWn toenhance glucose-induced insulin secretion in rat pancreatic ***,their effect on insulin secretionis still *** understand the molecular mechanism by which PPAR7 exerts its effect on glucose-induced insulin secretion,we examined the endogenous activity of PPAR isoforms,and studied the PPARyfunction and its target gene expression in INS-1 *** found that:(1)endogenous PPARγ was activatedin a ligand-dependent manner in INS-1 cells;(2)overexpression of PPARy in the absence of PPARγ ligandsenhanced glucose-induced insulin secretion,which indicates that the increased glucose-induced insulin secretionis a PPARγ-mediated event;(3)the addition of both PPARγ and retinoid X receptor (RXR) ligands showed asynergistic effect on the augmentation of reporter activity,suggesting that the hetero-dimerization of PPAR7and RXR is required for the regulation of the target genes;(4)PPARs upregulated both the glucose transporter2 (GLUT2) and Cbl-associated protein (CAP) genes in INS-1 *** findings suggest an importantmechanistic pathway in which PPARγ enhances glucose-induced insulin secretion by activating the expressionof GLUT2 and CAP genes in a ligand-dependent manner.

关键词： PPARγ ligand glucose-induced insulin secretion glucose transporter 2 Cb1-associated protein

Genetic polymorphism of mitochondrial DNA HVS-I and HVS-II of Chinese Tu ethnic minority group

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Journal of Genetics and genomics 2008年第4期35卷 225-232页

作者： Feng Chen Yajun Deng Yonghui Dang Bo Zhang Haofang Mu Xiaoguang Yu Lin Li Chunxia Yan Teng Chen department of Forensic Science Xi＇an Jiaotong University School of Medicine Shaanxi 710061 China Key Laboratory of Forensic Medicine Ministry of Health Xi＇an Jiaotong University Shaanxi 710061 China Beijing genomics Institute Chinese Academy of Sciences Beijing 100029 China Center of Forensic Sciences Beijing Genomics Institute Chinese Academy of Sciences Beijing 101300 China

We analyzed the two hypervariable segments HVS-I and HVS-II of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes, Comparing with Anderson sequence, 79 polymorphic loci in HVS-I and 40 in HVS-II were found in Chinese Tu ethnic minority group mtDNA sequences, and 90 and 64 haplotypes were then defined. Haplotype diversity and the mean pairwise differences were 0.9903±0.0013 and 5.7785 in HVS-I, and 0.9777±0.0013 and 3.5819 in HVS-II, respectively. By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-I, we defined some new types of sequence variations. We also compared the relationship between Tu population and other populations using mtDNA HVS-I sequences. According to Rst genetic distances, the phylogenetic tree showed that the Tu population, the Xi＇an Han population, the Chinese Korean, and the Mongol ethnic group were in a clade. This indicated a close genetic relationship between them. There were far relations between the Tu population and other Chinese southern Han populations, Siberian, European, African, and other foreign populations. The results suggest that Tu population has a multi-origin and has also merged with other local populations.

关键词： mtDNA HVS-I HVS-II Chinese Tu ethnic minority group population genetics

Developmental staging of male murine embryonic gonad by SAGE analysis

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Journal of Genetics and genomics 2009年第4期36卷 215-227页

作者： Tin-Lap Lee Yunmin Li Diana Alba Queenie R Vong Shao-Ming Wu Vanessa Baxendale Owen M. Rennert Yun-Fai Chris Lau Wai-Yee Chan Section on Developmental genomics Laboratory of Clinical Genomics Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD 20892 USA department of Medicine VA Medical Center University of California San Francisco CA 94121 USA department of Pediatrics Biochemistry Molecular & Cellular Biology Georgetown University Washington DC 20007 USA

Despite the identification of key genes such as Sry integral to embryonic gonadal development, the genomic classification and identification of chromosomal activation of this process is still poorly understood. To better understand the genetic regulation of gonadal development, we performed Serial Analysis of Gene Expression （SAGE） to profile the genes and novel transcripts, and an average of 152,000 tags from male embryonic gonads at E10.5 （embryonic day 10.5）, E11.5, E12.5, E13.5, E15.5 and E17.5 were analyzed. A total of 275,583 non-singleton tags that do not map to any annotated sequence were identified in the six gonad libraries, and 47,255 tags were mapped to 24,975 annotated sequences, among which 987 sequences were uncharacterized. Utilizing an unsupervised pattern identification technique, we established molecular staging of male gonadal development. Rather than providing a static descriptive analysis, we developed algorithms to cluster the SAGE data and assign SAGE tags to a corresponding chromosomal position; these data are displayed in chromosome graphic format. A prominent increase in global genomic activity from E10.5 to E17.5 was observed. Important chromosomal regions related to the developmental processes were identified and validated based on established mouse models with developmental disorders. These regions may represent markers for early diagnosis for disorders of male gonad development as well as potential treatment targets.

关键词： SAGE transcriptome male gonads gene tag novel transcripts cluster analysis chromosome transcription hotspot

Improving genomic predictions by correction of genotypes from genotyping by sequencing in livestock populations

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Journal of Animal Science and Biotechnology 2019年第2期10卷 283-292页

作者： Xiao Wang Mogens SandΦ Lund Peipei Ma Luc Janss Haja N.Kadarmideen Guosheng Su Center for Quantitative Genetics and genomics Department of Molecular Biology and GeneticsAarhus UniversityTjeleDenmark School of Agriculture and Biology Shanghai Jiaotong UniversityShanghaiChina.

Background: Genotyping by sequencing(GBS) is a robust method to genotype markers. Many factors can influence the genotyping quality. One is that heterozygous genotypes could be wrongly genotyped as homozygotes,dependent on the genotyping depths. In this study, a method correcting this type of genotyping error was demonstrated. The efficiency of this correction method and its effect on genomic prediction were assessed using simulated data of livestock ***: Chip array(Chip) and four depths of GBS data was simulated. After quality control(call rate ≥ 0.8 and MAF ≥ 0.01), the remaining number of Chip and GBS SNPs were both approximately 7,000, averaged over 10 replicates. GBS genotypes were corrected with the proposed method. The reliability of genomic prediction was calculated using GBS, corrected GBS(GBSc), true genotypes for the GBS loci(GBSr) and Chip data. The results showed that GBSc had higher rates of correct genotype calls and higher correlations with true genotypes than GBS. For genomic prediction, using Chip data resulted in the highest reliability. As the depth increased to 10, the prediction reliabilities using GBS and GBSc data approached those using true GBS data. The reliabilities of genomic prediction using GBSc data were 0.604, 0.672, 0.684 and 0.704 after genomic correction, with the improved values of 0.013, 0.009, 0.006 and 0.001 at depth = 2, 4, 5 and 10, ***: The current study showed that a correction method for GBS data increased the genotype accuracies and, consequently, improved genomic predictions. These results suggest that a correction of GBS genotype is necessary, especially for the GBS data with low depths.

关键词： Genomic prediction Genotype correction Genotyping by sequencing Simulation