DNA barcoding of Cymbidium by genome skimming: Call for next-generation nuclear barcodes

Cymbidium is an orchid genus that has undergone rapid radiation and has high ornamental, economic, ecological and cultural importance, but its classification based on morphology is controversial. The plastid genome (plastome), as an extension of plant standard DNA barcodes, has been widely used as a potential molecular marker for identifying recently diverged species or complicated plant groups. In this study, we newly generated 237 plastomes of 50 species (at least two individuals per species) by genome skimming, covering 71.4% of members of the genus Cymbidium. Sequence-based analyses (barcoding gaps and automatic barcode gap discovery) and tree-based analyses (maximum likelihood, Bayesian inference and multirate Poisson tree processes model) were conducted for species identification of Cymbidium. Our work provides a comprehensive DNA barcode reference library for Cymbidium species identification. The results show that compared with standard DNA barcodes (rbcL + matK) as well as the plastid trnH-psbA, the species identification rate of the plastome increased moderately from 58% to 68%. At the same time, we propose an optimized identification strategy for Cymbidium species. The plastome cannot completely resolve the species identification of Cymbidium, the main reasons being incomplete lineage sorting, artificial cultivation, natural hybridization and chloroplast capture. To further explore the potential use of nuclear data in identifying species, the Skmer method was adopted and the identification rate increased to 72%. It appears that nuclear genome data have a vital role in species identification and are expected to be used as next-generation nuclear barcodes.     

西伯利亚蝗抗菌肽基因的克隆及表达特性研究

[目的]扩增西伯利亚蝗Gomphocerus sibiricus抗菌肽(attacin)基因,并对其进行生物信息学分析,同时分析西伯利亚蝗不同组织中抗菌肽基因的差异表达.[方法]基于RACE技术从西伯利亚蝗中克隆得到抗菌肽,利用生物信息学软件对西伯利亚蝗抗菌肽的一级结构、二级结构、三级结构、系统进化和亚细胞定位进行分析.采用实时荧光定量PCR技术检测了西伯利亚蝗抗菌肽基因在马氏管、中肠、后肠、脂肪体和唾液腺中的相对表达量.[结果]克隆获得的抗菌肽基因的开放阅读框为282 bp,编码93个氨基酸,其编码蛋白预测理论分子量为9.98 ku,等电点为9.26.抗菌肽氨基酸序列中存在信号肽序列.基因定量分析显示,抗菌肽基因在西伯利亚蝗的中肠中表达量最高.[结论]attacin在西伯利亚蝗成虫不同组织中差异表达,提示其消化道在防御病原微生物的入侵中起着重要的作用.     

Association between the XRCC3 T241M polymorphism and risk of cancer: Evidence from 157 case–control studies

The T241M polymorphism in the X-ray cross-complementing group 3 (XRCC3) had been implicated in cancer susceptibility. The previous published data on the association between XRCC3 T241M polymorphism and cancer risk remained controversial. Hence, we performed a meta-analysis to investigate the association between cancer susceptibility and XRCC3 T241M (61,861 cases and 84,584 controls from 157 studies) polymorphism in different inheritance models. We used odds ratios with 95% confidence intervals to assess the strength of the association. Overall, significantly increased cancer risk was observed in any genetic model (dominant model: odds ration [OR] = 1.07, 95% confidence interval [CI] = 1.00–1.13; recessive model: OR = 1.15, 95% CI = 1.08–1.23; additive model: OR = 1.17, 95% CI = 1.08–1.28) when all eligible studies were pooled into the meta-analysis. In further stratified and sensitivity analyses, the elevated risk remained for subgroups of bladder cancer and breast cancer, especially in Caucasians. In addition, significantly decreased lung cancer risk was also observed. In summary, this meta-analysis suggests the participation of XRCC3 T241M in the susceptibility for bladder cancer and breast cancer, especially in Caucasians, and XRCC3 T241M polymorphism is associated with decreased lung cancer risk. Moreover, our work also points out the importance of new studies for T241M association in some cancer types, such as gastric cancer, colorectal cancer, and melanoma skin cancer, where at least some of the covariates responsible for heterogeneity could be controlled, to obtain a more conclusive understanding about the function of the XRCC3 polymorphism in cancer development.     

小麦旗叶高纯度质膜的提取及蛋白质组学双向电泳体系的建立

以生长到Feekes 8.5时期小麦旗叶为试验材料,通过差速离心结合两相法提取 并纯化质膜蛋白,进而在裂解液选择、SDS-PAGE胶浓度及蛋白质上样量等方面对质膜蛋白质双向电泳体系进行了优化.结果表明,采用6.4% PEG 3 350/Dextran T-500 (W/W)两相体系可以获得纯度高达87.9%质膜微囊. 经TCA-丙酮法裂解蛋白,以12% SDS-PAGE分离胶对900 μg质膜蛋白进行双向电泳,在2-DE图谱上可分辨出173个蛋白点. 建立了一套用于小麦旗叶高纯度质膜的提取方法及其蛋白质组学双向电泳体系.     

中国汉族人群(西安)STR基因扫描与遗传结构

选择9种STR基因位点和Amelogenin基因位点,以测序为基础,研究我国汉族人群STR遗传结构.采用基因自动测序仪建立了10个位点基因分析方法,通过对汉族群体的基因扫描、基因分型和遗传结构分析,获得了STR基因传递特征的大量基因遗传数据,在汉族人群DP为1.05×10-0,EPP为0.9998,为建立我国不同民族STR基因数据库、基因资源研究与保护奠定了基础,为生物考古、基因诊断、性别鉴定、个人识别,司法审判、侦察破案提供有力的科学依据.     

Identification and expression profile of a putative basement membrane protein gene in the midgut of <Emphasis Type="Italic">Helicoverpa armigera</Emphasis>

Background  

The midgut undergoes histolysis and remodeling during the larval to adult transition in holometabolous insects, but the molecular mechanisms underlying this process are not well understood.     

A case report of a 24-year-old male with a large hemorrhagic pericardial effusion

Although bloody pericardial effusion often suggests neoplasia, such an event is not rare in tuberculosis (TB), especially in those countries with a high TB disease burden. Meanwhile, TB accounts for 50% and greater than 90% of large pericardial effusions in human immunodeficiency virus (HIV)-negative and HIV-positive patients, respectively. Here we report a case of a 24-year-old HIV-negative male who presented with fever and hemorrhagic pericardial effusion. The patient was given presumptive anti-TB treatment before diagnosis was established. Eventually the patient responded well to the anti-TB treatment at the last follow-up and the diagnosis was confirmed by aspirated pericardial fluid culture on Lowenstein-Jensen (LJ) medium.     

The yeast chromatin remodeler RSC complex facilitates end joining repair of DNA double-strand breaks

Repair of chromosome double-strand breaks (DSBs) is central to cell survival and genome integrity. Nonhomologous end joining (NHEJ) is the major cellular repair pathway that eliminates chromosome DSBs. Here we report our genetic screen that identified Rsc8 and Rsc30, subunits of the Saccharomyces cerevisiae chromatin remodeling complex RSC, as novel NHEJ factors. Deletion of RSC30 gene or the C-terminal truncation of RSC8 impairs NHEJ of a chromosome DSB created by HO endonuclease in vivo. rsc30Delta maintains a robust level of homologous recombination and the damage-induced cell cycle checkpoints. By chromatin immunoprecipitation, we show recruitment of RSC to a chromosome DSB with kinetics congruent with its involvement in NHEJ. Recruitment of RSC to a DSB depends on Mre11, Rsc30, and yKu70 proteins. Rsc1p and Rsc2p, two other RSC subunits, physically interact with yKu80p and Mre11p. The interaction of Rsc1p with Mre11p appears to be vital for survival from genotoxic stress. These results suggest that chromatin remodeling by RSC is important for NHEJ.     

Activation of the checkpoint kinase Rad53 by the phosphatidyl inositol kinase-like kinase Mec1

Saccharomyces cerevisiae Rad53, the ortholog of mammalian Chk2, is an essential protein kinase in DNA damage and DNA replication checkpoint pathways. Consecutive phosphatidyl inositol kinase-like kinase (PIKK)-dependent and PIKK-independent steps in activation of Rad53 are key steps for controlling and transmitting diverse downstream responses to DNA damage. However, these activities have not been demonstrated in vitro in defined systems. Here, we have shown that enzymatically dephosphorylated purified Rad53 autoactivates in vitro through a phosphorylation-dependent mechanism. Kinetic analysis demonstrated that autophosphorylation results in a more than 9-fold increase in protein kinase activity. Autophosphorylation was Rad53 concentration-dependent, indicating that the reaction follows an intermolecular mechanism. DNA damage induced oligomerization of a subset of Rad53 molecules in vivo. At low concentrations of Rad53, preincubation of Rad53 with immune complexes containing the Mec1/Ddc2 complex can activate Rad53 kinase activity. Our findings showed that Mec1/Ddc2 complexes can directly activate Rad53 through a phosphorylation-dependent mechanism, and more generally, supported the hypothesis that PIKKs regulate Chk2 orthologs through phosphorylation. Moreover, this work has substantiated a model for PIKK-independent amplification of Rad53 activation (and by extension, activation of other Chk2 orthologs) mediated by inter-Rad53 phosphorylation.