Allele-specific copy number profiling by next-generation DNA sequencing

The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual''s colon cancer.     

The expression level of anthocyanidin synthase determines the anthocyanin content of crabapple (<Emphasis Type="Italic">Malus</Emphasis> sp.) petals

In addition to contributing to the coloration of plant organs and their defense against herbivores, the consumption of anthocyanins in the human diet has a number of health benefits. Crabapple (Malus sp.) represents a valuable experimental model system to research the mechanisms and regulation of anthocyanin accumulation, in part due to the often vivid and varied petal and leaf coloration that is exhibited by various cultivars. The enzyme anthocyanidin synthase (ANS) plays a pivotal role in anthocyanin biosynthesis; however, the relationship between ANS expression and petal pigmentation has yet to be established in crabapple. To illuminate the mechanism of anthocyanin accumulation in crabapple petals, we evaluated the expression of two crabapple ANS allelic genes (McANS-1 and McANS-2) and the levels of anthocyanins in petals from cultivars with dark red (‘Royalty’) and white (‘Flame’) petals, as well as another (‘Radiant’) whose petals have an intermediate pink color. We determined that the expression of McANS in the three cultivars correlated with the variation of anthocyanin accumulation during different petal developmental stages. Furthermore, transgenic tobacco plants constitutively overexpressing one of the two McANS genes, McANS-1, had showed elevated anthocyanin accumulation and a deeper red coloration in their petals than those from untransformed control lines. In conclusion, we propose that McANS are responsible for anthocyanin accumulation during petal coloration in different crabapple cultivars.     

假单胞菌GP72 rpeB突变株的构建及其对吩嗪类抗生素合成的调控

[目的]绿针假单胞菌GP72是一株可生产吩嗪类抗生素吩嗪-1-羧酸(PCA)及2-羟基吩嗪(2-OH-PHZ)的生防假单胞菌.RpeA/RpeB双元调控系统是其双元调控系统中的一组,本文旨在研究这一系统中的应答调控子(RR)RpeB对于PCA及2-OH-PHZ的生物合成影响.[方法]通过生物信息学分析获得了rpeA/rpeB双元调控系统的序列,并从GP72中扩增出rpeB基因,通过同源重组技术构建卡那霉素抗性片段插入突变rpeB的突变菌株GP72BN.利用发酵实验、rpeB基因回补实验及荧光定量PCR实验,验证rpeB对于吩嗪类抗生素合成及相关基因表达的调控作用.[结果]在KMB培养基中,rpeB突变株的PCA产量下降为野生型的49.5％,2-OH-PHZ产量下降为野生型的67.3％.rpeB基因的回补可以在一定程度上回复PCA及2-OH-PHZ的产量.荧光定量PCR实验结果表明,rpeB突变株中群体感应系统基因phzI/phzR及吩嗪合成基因簇基因phzE转录水平均显著下调,而PCA转化为2-OH-PHZ的修饰基因phzO转录水平变化不显著.[结论]RpeB正调控PCA与2-OH-PHZ合成途径的表达.RpeB很可能是通过调控群体感应基因phzI/phzR和phz基因簇的表达,从而影响PCA的合成,并间接调控其衍生物2-OH-PHZ的合成.