Introgression browser: high‐throughput whole‐genome SNP visualization

Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker‐assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (iBrowser ), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi‐nucleotide polymorphisms (MNPs) and insertion–deletions (InDels). For data analysis iBrowser makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the iBrowser in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP‐free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of iBrowser makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes iBrowser a valuable breeding tool.     

SIRT1与肝细胞癌

肝细胞癌(hepatocellular carcinoma, HCC)是世界上最常见的癌症之一.然而,就目前现状而言,HCC的治疗效果还很有限.作为一个依赖于烟酰胺腺嘌呤二核苷酸(NAD+)的去乙酰化酶, SIRT1(silent mating type information regulation 2 homolog 1 )参与了代谢、应激反应、衰老以及肿瘤的演进等许多重要的生物学进程.临床研究显示,SIRT1在HCC患者中异常高表达,并可预测其不良预后;进一步的研究表明,SIRT1在HCC演进中发挥了关键作用,且作用范围广泛,分子机制复杂.这提示,SIRT1有望成为新的HCC治疗靶点和诊断、预后标志物.本文拟对SIRT1在HCC的演进和预后中的具体作用及其潜在分子机制作一总结,并就SIRT1作为肝癌治疗靶点和诊断、预后标志物的可行性做出探讨.     

印度-西太平洋胡椒鲷亚科鱼类DNA条形码及分子系统进化研究

为探讨COⅠ基因作为条形码在胡椒鲷亚科鱼类物种鉴定的可行性, 研究测定了胡椒鲷亚科8种鱼类51个个体线粒体COⅠ基因长度为651 bp的序列, 利用MEGA 5.0计算胡椒鲷亚科种内与种间的遗传距离, 基于最大似然法与贝叶斯法构建了系统进化树。结果显示: 胡椒鲷亚科鱼类种间平均遗传距离(0.142)显著大于种内平均遗传距离(0.003), 物种间遗传距离均大于Hebert推荐的物种鉴定最小种间遗传距离0.020(2%)。系统进化树上, 同一物种不同个体间均能形成独立的单系分支, 表明COⅠ基因可作为胡椒鲷亚科物种鉴定的有效条形码基因。研究同时揭示, 在形态分类上被认为是同种异名的两种胡椒鲷(条纹胡椒鲷与东方胡椒鲷)的COⅠ基因序列差异达到0.070, 有可能是两个独立的物种。此外, 在属级水平, 少棘胡椒鲷属与胡椒鲷属种类之间的平均遗传距离小于胡椒鲷属内部种间的遗传距离, 支持少棘胡椒鲷归属于胡椒鲷属的观点。       

龙葵上柑橘木虱存活观察与黄龙病检测

柑橘木虱Diaphorina citri是毁灭性病害黄龙病的媒介,其寄主范围比较严格,仅为芸香科内的一些植物。研究发现,在自然状态下,柑橘木虱成虫可在柑橘园中常见茄科Solanaceae杂草-龙葵Solanum nigrum上停留。对比试验显示,木虱成虫在龙葵上的存活期最长可达45 d,而在假臭草Eupatorium catarium、含水海绵和无水海绵上分别为24 d、9 d和2 d;通过实时荧光PCR检测发现部分龙葵叶片中含有黄龙病病原菌。这些非寄主植物可能有助于柑橘木虱躲避不良环境或长距离迁移扩散,成为柑橘木虱和黄龙病的潜在库源。     

Comparison of the Morphology Development of Polymer–Fullerene and Polymer–Polymer Solar Cells during Solution‐Shearing Blade Coating

In this work, the detailed morphology studies of polymer poly(3‐hexylthiophene‐2,5‐diyl) (P3HT):fullerene(PCBM) and polymer(P3HT):polymer naphthalene diimide thiophene (PNDIT) solar cell are presented to understand the challenge for getting high performance all‐polymer solar cells. The in situ X‐ray scattering and optical interferometry and ex situ hard and soft X‐ray scattering and imaging techniques are used to characterize the bulk heterojunction (BHJ) ink during drying and in dried state. The crystallization of P3HT polymers in P3HT:PCBM bulk heterojunction shows very different behavior compared to that of P3HT:PNDIT BHJ due to different mobilities of P3HT in the donor:acceptor glass. Supplemented by the ex situ grazing incidence X‐ray diffraction and soft X‐ray scattering, PNDIT has a lower tendency to form a mixed phase with P3HT than PCBM, which may be the key to inhibit the donor polymer crystallization process, thus creating preferred small phase separation between the donor and acceptor polymer.     

Nonparametric association analysis of bivariate left‐truncated competing risks data

We develop time‐varying association analyses for onset ages of two lung infections to address the statistical challenges in utilizing registry data where onset ages are left‐truncated by ages of entry and competing‐risk censored by deaths. Two types of association estimators are proposed based on conditional cause‐specific hazard function and cumulative incidence function that are adapted from unconditional quantities to handle left truncation. Asymptotic properties of the estimators are established by using the empirical process techniques. Our simulation study shows that the estimators perform well with moderate sample sizes. We apply our methods to the Cystic Fibrosis Foundation Registry data to study the relationship between onset ages of Pseudomonas aeruginosa and Staphylococcus aureus infections.     

ZAKβ antagonizes and ameliorates the cardiac hypertrophic and apoptotic effects induced by ZAKα

ZAK (sterile alpha motif and leucine zipper containing kinase AZK), a serine/threonine kinase with multiple biochemical functions, has been associated with various cell processes, including cell proliferation, cell differentiation, and cardiac hypertrophy. In our previous reports, we found that the activation of ZAKα signaling was critical for cardiac hypertrophy. In this study, we show that the expression of ZAKα activated apoptosis through both a FAS‐dependent pathway and a mitochondria‐dependent pathway by subsequently inducing caspase‐3. ZAKβ, an isoform of ZAKα, is dramatically expressed during cardiac hypertrophy and apoptosis. The interaction between ZAKα and ZAKβ was demonstrated here using immunoprecipitation. The results show that ZAKβ has the ability to diminish the expression level of ZAKα. These findings reveal an inherent regulatory role of ZAKβ to antagonize ZAKα and to subsequently downregulate the cardiac hypertrophy and apoptosis induced by ZAKα.     

小叶兜兰的果实生长和雌配子体发育

为了解濒危兰科植物小叶兜兰(Paphiopedilum barbigerum Tang et Wang)胚珠和雌配子体的发育过程,采用常规石蜡切片技术对其果实的生长动态进行了研究。结果表明,授粉后60~75 d的蒴果内种子数量迅速增加,到授粉后120 d时种子充满整个蒴果。授粉后40 d的胎座上分化形成多数由1层表皮细胞包被1列细胞的胚珠原基;授粉后60 d时位于胎座指状结构末端处紧靠表皮细胞下方的孢原细胞分化为大孢子母细胞。之后,大孢子母细胞经过减数分裂和有丝分裂最终形成成熟胚囊;授粉后135 d胚囊发育成熟,附着在胎座上的种子个体分化明显。小叶兜兰胚囊的发育类型为双孢子葱型,胚珠为倒生胚珠,薄珠心,单珠被,成熟胚囊为8核。这为小叶兜兰的生殖生物学及繁殖体系的建立提供理论依据。