棕头鸥线粒体基因组全序列测定与分析

基于长距PCR扩增及保守引物步移法测定并注释了棕头鸥(Larus brunnicephalus)的线粒体基因组全序列。结果表明,棕头鸥线粒体基因组全长16 769 bp,GenBank登录号JX155863。基因含量和排列次序与红原鸡一致,包含13个蛋白编码基因、22个tRNA、2个rRNA和一个D-loop区(控制区)。除COI基因以GTG、ND3基因以ATT为起始密码子外,其余11个蛋白质编码基因均以ATG起始。11个蛋白质编码基因以典型的完全终止密码子AGG、TAG、TAA或AGA终止,COIII和ND4基因为不完全终止密码子T。预测了22个tRNA基因的二级结构,发现tRNASer(AGN)缺少DHU臂,tRNAPhe的TψC臂出现第4种排列形式。预测的棕头鸥12S和16S rRNA二级结构分别包括4个结构域47个茎环和6个结构域60个茎环。其他鸟类控制区发现的F-box、E-box、D-box、C-box、B-box、Bird similarity-box和CSB-boxes(1-3)也存在于棕头鸥中,预测了控制区H链复制起始序列OH和双向复制起始序列LSP/HSP。系统发育分析支持将棕头鸥划归为面具鸥族(Masked gulls)。     

利用线粒体16S rRNA基因全序列分析直翅目主要类群的系统发生关系

为了构建稳健的直翅目主要类群间的系统发生关系并探讨16S rRNA基因序列在构建直翅目昆虫不同分类阶元系统发生关系时的可行性、功效以及性能,文章测定了直翅目4总科9科18种昆虫的16S rRNA基因全序列,联合已知该基因全序列的其他40种昆虫,构建了直翅目主要类群之间的系统发生关系,并分析了16SrRNA基因全序列的系统发生性能和功效。结果表明,直翅目昆虫的16S rRNA基因全长平均为1 310 bp;除生活方式特化的蚤蝼总科和蝼蛄总科的地位无法确定外,直翅目其他主要类群系统发生关系比较稳定;蝗总科下除了斑翅蝗科和槌角蝗科外,剑角蝗科、斑腿蝗科、网翅蝗科都不是单系群,且用不同的方法构建的系统发生树中聚类情况完全一致,各科间遗传距离差异不大,建议将其合为一科;锥头蝗科、瘤锥蝗科和癞蝗科间的遗传距离差异也不大;在构建系统发生树时,16S rRNA基因环区的信息量要比茎区的大;16S rRNA基因可以构建可靠的直翅目属与种水平和目与亚目高级阶元的系统发生关系,但对科和总科阶元缺乏足够的分辨力。     

Population genetic structure and historical demography of the ground beetle Pheropsophus jessoensis from the Tsinling-Dabashan Mountains, central China based on mitochondrial DNA analysis

The population genetic structure and demographic history of the ground beetle Pheropsophus jessoensis (Coleoptera: Carabidae) from the Tsinling-Dabashan Mountains, central China were estimated using the mtDNACol-tRNALeu-mtDNAColl region as a molecular marker. 184 individuals from 25 local populations, were collected. The haplotype diversity (H(d)) of total and each individual sampled population was high, and was accompanied by lower nucleotide diversity (P(i)). AMOVA analysis suggested that most of the variation was within populations (92.17%), while differentiation of among populations only contributed 7.83% to the total. Mantel test results showed significant correlation between the pairwise calculated genetic distance and pairwise calculated geographical distance of the populations (R(xy) = 0.360529, P = 0.00001 < 0.01), indicating the presence of isolationby-distance. No phylogeographic structure was found within the Tsinling-Dabashan Mountains region. Statistical phylogeographic analysis indicated that the contemporary populations are derived from multiple ancestral-refugial source populations. Gene flow calculated through the N(m) was high between many pairs of populations, which was probably due to ancient vicariance and subsequent rapid expansion of populations. The results of neutral test, mismatch distribution analyses, and Bayesian Skyline Plot (BSP) analysis together indicated a sudden demographic expansion. The estimated expansion time of individual haplogroup and the whole sampled population were 0.012-0.278 Myr, and a sudden expansion was identified between 0.05 Myr to 0.01 Myr by BSP. The postglacial population expansion might lead to the lack of phylogeographic structure.     

Incorporating heuristic information into ant colony optimization for epistasis detection

Epistasis has been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for epistasis detection, genome-wide association study remains a challenging task: it makes the search space excessively huge while solution quality is excessively demanded. In this study, we introduce an ant colony optimization based algorithm, AntMiner, by incorporating heuristic information into ant-decision rules. The heuristic information is used to direct ants in the search process for improving computational efficiency and solution accuracy. During iterations, chi-squared test is conducted to measure the association between an interaction and the phenotype. At the completion of the iteration process, statistically significant epistatic interactions are ordered and then screened by a post-procedure. Experiments of AntMiner and its comparison with existing algorithms epiMODE, TEAM and AntEpiSeeker are performed on both simulation data sets and real age-related macular degeneration data set, under the criteria of detection power and sensitivity. Results demonstrate that AntMiner is promising for epistasis detection. In terms of detection power, AntMiner performs best among all the other algorithms on all cases regardless of epistasis models and single nucleotide polymorphism size; compared with AntEpiSeeker, AntMiner can obtain better detection power but with less ants and iterations. In terms of sensitivity, AntMiner is better than AntEpiSeeker in detecting epistasis models displaying marginal effects but it has moderate sensitivity on epistasis models displaying no marginal effects. The study may provide clues on heuristics for further epistasis detection. The software package is available online at https://sourceforge.net/projects/antminer/files/.     

丹参2 酮戊二酸依赖性双加氧酶基因克隆及表达分析

以商洛紫花丹参为材料,对其转录组序列SRA020132进行Blast分析,采用PCR技术克隆得到丹参2-酮戊二酸依赖性双加氧酶基因Sm2-ODD1,GenBank登录号为JN935923。Sm2-ODD1基因全长1 365bp,包含3个外显子和2个内含子;cDNA全长1 189bp,读码框951bp,编码316个氨基酸残基;预测的编码蛋白具有2-酮戊二酸依赖性双加氧酶中结合2-酮戊二酸和亚铁离子的"H-T-D"、"H-X"和"R-Y-S"保守基序以及"果冻状"空间结构。表达分析显示,Sm2-ODD1在丹参各个器官都表达,但表达水平具有组织特异性,在根中表达量最高,在叶中表达量最低;该基因表达明显受到MeJA、GA3和ABA的诱导,可能参与了丹参萜类代谢下游途径。     

青海省石栖蝗属一新种（直翅目：网翅蝗科）

记述采自青海省河卡山地区石栖蝗属1新种,即青海石栖蝗Saxetophilus qinghaiensis sp.nov.,该新种近似于甘肃石栖蝗Saxetophilus gansuensis Wang et al.,2006及米氏石栖蝗Saxetophilus mistshenkoi Naumovitsh,1988。主要区别为:1)前胸背板沟后区侧隆线间最宽处为其长度的3.30-3.75倍(♂)或3.00-3.60倍(♀);2)中胸腹板侧叶间中隔宽大于侧叶最宽处。附有石栖蝗属分种检索表。新种的模式标本保存于陕西师范大学动物研究所昆虫标本室。     

中国四川拟大磨蚱属一新种记述（直翅目：蚱总科：短翼蚱科)

记述采自四川峨嵋山拟大磨蚱属 Macromotettixoides 1新种,即波股拟大磨蚱 Macromotettixoides undulatifemura sp. nov.。该新种因其前胸背板后半部具网状纹;前、中足股节下缘明显呈波状,前足形成2个突起,中足形成3个突起区别于属内其它种。模式标本保存在陕西师范大学动物所标本室。     

云南省突眼蚱属一新种（直翅目：蚱科）

记述采自云南省突眼蚱属 1 新种,即龙陵突眼蚱 Ergatettix longlingensis sp. nov.。该新种近似于拟齿股突眼蚱。主要区别为:1)触角着生于复眼下缘之下;2)前胸背板沟前区侧隆线略收缩;3)前胸背板后突到达后足股节顶端;4)后翅到达后突顶端;5)后足股节上侧中隆线具二叶状突;6)后足股节下侧外面非黑色;7)后足胫节暗褐色。文中附有中国突眼蚱属分种检索表。模式标本现保存于陕西师范大学动物研究所昆虫标本室。     

基于响应面法从连翘叶中提取连翘酯苷A和连翘苷的工艺优化

采用响应面分析法优化连翘叶中连翘酯苷A和连翘苷的最佳提取工艺条件,在单因素实验基础上,采用Box-Behnken中心组合设计原理研究液料比、乙醇浓度、浸提时间、浸提温度4个因素对连翘酯苷A得率和连翘苷得率的影响.利用Design Expert 8.0.5 b分析确定最佳提取工艺,根据实际条件,得到连翘酯苷A和连翘苷的最佳提取工艺为:乙醇浓度53％、提取温度74℃、浸提时间为53 min、液料比30 mL/g.回归模型预测最优条件下连翘酯苷A得率为7.53％,连翘苷得率为3.03％,验证值分别为7.56％,3.09％,与预测值的相对误差分别为0.4％,2.0％.     

红托竹荪多糖抗氧化活性的研究

本文采用DPPH自由基、羟自由基及超氧阴离子自由基体系对红托竹荪多糖的抗氧化活性进行了研究,并同Vc和BHT进行了比较.结果表明,在0.2～1.2 mg/mL质量浓度范围内,红托竹荪多糖对DPPH自由基、羟自由基、超氧阴离子自由基的半数清除率(EC50)值分别为1.468、2.580和2.330,抗氧化活性稍强于BHT,但弱于VC.