Condition‐dependent expression of pre‐ and postcopulatory sexual traits in guppies

Female choice can impose persistent directional selection on male sexually selected traits, yet such traits often exhibit high levels of phenotypic variation. One explanation for this paradox is that if sexually selected traits are costly, only the fittest males are able to acquire and allocate the resources required for their expression. Furthermore, because male condition is dependent on resource allocation, condition dependence in sexual traits is expected to underlie trade‐offs between reproduction and other life‐history functions. In this study we test these ideas by experimentally manipulating diet quality (carotenoid levels) and quantity in the guppy (Poecilia reticulata), a livebearing freshwater fish that is an important model for understanding relationships between pre‐ and post‐copulatory sexually selected traits. Specifically, we test for condition dependence in the expression of pre‐ and postcopulatory sexual traits (behavior, ornamentation, sperm traits) and determine whether diet manipulation mediates relationships among these traits. Consistent with prior work we found a significant effect of diet quantity on the expression of both pre‐ and postcopulatory male traits; diet‐restricted males performed fewer sexual behaviors and exhibited significant reductions in color ornamentation, sperm quality, sperm number, and sperm length than those fed ad libitum. However, contrary to our expectations, we found no significant effect of carotenoid manipulation on the expression of any of these traits, and no evidence for a trade‐off in resource allocation between pre‐ and postcopulatory episodes of sexual selection. Our results further underscore the sensitivity of behavioral, ornamental, and ejaculate traits to dietary stress, and highlight the important role of condition dependence in maintaining the high variability in male sexual traits.     

Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (F_ST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes.     

Ontogenic variation in response of Brassica campestris L. to cadmium toxicity

Abstract

Rapeseed (Brassica campestris L.) cv Pusa Gold plants, exposed to different cadmium (Cd) levels (0, 25, 50 and 100 mg kg^?1 soil) in greenhouse, pot culture experiment, were analyzed with reference to distribution of metal, accumulation of biomass and the degree of growth stage Cd-sensitivity. A significant maximum decrease in plant biomass was observed at Cd-exposed flowering stage followed by pre-flowering and post-flowering stages. Activities of enzymatic antioxidants such as superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX) and glutathione reductase (GR) differentially increased; while, the concentrations of non-enzymatic antioxidants such as ascorbic acid (AsA) and glutathione (GSH) drastically decreased in plants exposed to Cd at various growth stages. However, the concentrations of GSH and AsA decreased maximally in plant groups exposed to Cd at their flowering stage. The maximum Cd-accumulation occurred in roots followed by leaves and stem. Various Cd levels inhibited also the contents of plant nutrients such as nitrogen (N), phosphorous (P), potassium (K) and sulfur (S) in leaves. The present endeavor hence concludes the existence of close relationships among growth parameters, Cd-sensitivity of phenological stages of the crop and the components of antioxidant system in rapeseed plants exposed at various growth stages.     

Novel Natural Allelic Variations at the Rht-1 Loci n Wheat

Plant height is an important agronomic trait. Dramatic increase in wheat yield during the ＂green revolution＂ is mainly due to the widespread utilization of the Reduced height （Rht）-1gene. We analyzed the natural allelic variations of three homoeologous loci Rht-A1, Rht-B1, and Rht-D1 in Chinese wheat （Triticum aestivum L.） micro-core collections and the Rht-B1/D1 genotypes in over 1,500 bred cultivars and germplasms using a modified EcoTILLING. We identified six new Rht-A1 allelic variations （Rht-Alb-g）, eight new Rht-B1 allelic variations （Rht-Blh-o）, and six new Rht-D1 allelic variations （Rht-Dle-j）. These allelic variations contain single nucleotide polymorphisms （SNPs） or small insertions and deletions in the coding or uncoding regions, involving two frame-shift mutations and 15 missenses. Of which, Rht-Dle and Rht-Dlh resulted in the loss of interactions of GID1-DELLA-GID2, Rht-Blicould increase plant height. We found that the Rht-Blh contains the same SNPs and 197 bp fragment insertion as reported in Rht-Blc. Further detection of Rht-Blh in Tibet wheat germplasms and wheat relatives indicated that Rht-Blc may originate from Rht-Blh. These results suggest rich genetic diversity at the Rht-1 loci and provide new resources for wheat breeding.     

儿童急性淋巴细胞白血病特异性标记物的精准检测方法研究

目的：T细胞和免疫球蛋白重链基因重排是微小残留病灶水平的特异性标记物,而微小残留病灶的水平与儿童急性淋巴细胞白血病的复发强烈相关。应用传统的聚合酶链式反应方法来监测IgH／TCR基因重排不仅耗时、耗人力,而且敏感度较低。本研究旨在探索一种更为高效和敏感与实用的监测IgH／TCR基因重排的精准检测方法。方法：应用多重PCR技术检测26个患有急性淋巴细胞白血病的儿童的外周血样品中的标记物,这些儿童是在中国哈尔滨市最近两年内被诊断的患者。分别应用基因扫描和毛细血管电泳方法检测IgH（FRI,FRII,FRⅢ）／TCR（TCRB,TCRγ）基因重排和分析PCR产物的片段。结果：IgH／TCR基因重排和对IgH基因重排的阳性率分别为92．3％和75％,在26个病例中,4个复发病人的IgH的三个片段（FRI,FRII,FRⅢ）基因重排显示阳性。进一步分析显示复发与ign基因重排呈线性相关。结论：实验与临床应用表明,基因扫描这种方法对于IgH／TCR基因重排的检测是可靠的、实用的,因而可用于儿童急性淋巴细胞白血病的诊断和随访。     

纳米金-聚乙烯亚胺基因载体的制备

目的:基因方法治疗癌症近年来取得了很大的突破,因此基因载体的构建显得尤为重要.其中纳米基因载体合成简单,成本低廉,并能够包裹、浓缩、保护核苷酸使其免受核酸酶降解,因此纳米材料广泛地应用于基因输送.我们拟开展聚乙烯亚胺-纳米金基因载体的制备及其表征.方法:采用层层包裹技术制备基因载体,首先通过柠檬酸钠还原法制备纳米金颗粒后,应用11-巯基十一烷酸对金颗粒进行修饰,使其表面带有羧基,然后进一步将带有氨基的低分子量聚乙烯亚胺与羧基进行连接.应用动态光散射(DLS),紫外可见光谱(UV)和透射电子显微镜(TEM)对构建的纳米基因载体进行表征.结果:成功制备了聚乙烯亚胺-纳米金基因载体,检测表明每一步制备出的产物纳米尺寸在20-30nm之间,液体均匀稳定,分散系数(PDI)在0.2以下,Zeta电位测定表明,每步的产物电荷变化与外层包裹的反应物有关.尽管金颗粒外层包裹聚乙烯亚胺,但是总体上纳米载体尺寸没有发生太大的变化,TEM检测表明每一步形成了均匀的、单分散的、球状的纳米颗粒.结论:我们通过层层包裹技术成功制备了聚乙烯亚胺-纳米金基因载体,在进一步开展的生物活性的检测中,希望通过纳米载体的携带作用,将基因转染进靶细胞,从而检测相关基因对靶细胞的沉默作用,提高基因药物的应用,为开发新型基因药物提供基础.     

中国汉族人群CXCR2基因＋1235C/T多态与急性冠脉综合征的关联研究

目的：炎症反应在动脉粥样斑块变化的病理过程中发挥着重要的作用。本研究探讨CXCR2基因＋1235 C/T单核苷酸多态与中国汉族人群急性冠脉综合征发病的相关关系。方法：本研究采用聚合酶链反应-限制性片段长度多态性方法对675例急性冠脉综合征的患者和636例对照组进行检测,分析CXCR2基因＋1235 C/T单核苷酸多态的基因型和等位基因频率的分布情况,同时收集济南军区总医院心内科经冠脉造影证实为阳性的急性冠脉综合征患者360例及对照者360例,对上述关联分析的结果进行复制实验的印证。结果：CXCR2基因＋1235 C/T单核苷酸多态三种基因型（CC型,CT型和TT型）在急性冠脉综合征组分布频率分别为39.3%,45.3%和15.1%,在对照组分别为41.7%,47.2%和11.1%,CXCR2基因＋1235 C/T基因型和等位基因频率对照组和急性冠脉综合征组之间存在统计学差异（P〈0.05）。Logistic回归校正性别、年龄、体重指数、吸烟、高血压、高脂血症、糖尿病等冠心病的易患因素后,CXCR2基因＋1235 C/T多态与急性冠脉综合征的发病存在相关关系（P〈0.05）。结论：CXCR2基因＋1235 C/T多态与急性冠脉综合征发病存在相关关系,CXCR2基因＋1235 C/T多态可能是中国汉族人群急性冠脉综合征发病的独立危险因子。     

解偶联蛋白-866G/A基因多态性与肥胖关联性的Meta分析

目的:近年来,关于UCP2-866G/A基因多态性与肥胖关系的研究较多,但各研究的结果不尽一致.本文拟采用Meta分析的方法,对已公开发表的有关UCP2-866G/A基因多态性与肥胖的研究进行系统综合定量分析,以期科学的评价UCP2-866G/A基因多态性与肥胖的关系.方法:本研究运用计算机检索万方全文数据库、中国知网、维普数据库、中国生物医学文献数据库、PubMed等数据库收集关于UCP2-866G/A基因多态性与肥胖相关的公开发表的文献,选择OR值及其95％CI作为Meta分析指标.利用Stata10.0软件对各研究结果进行异质性检验和效应值合并计算.结果:根据统一的纳入和剔除标准,纳入14篇文献,共有肥胖者5195例,对照组9735人.在总人群中,UCP2-866G/A位点A/G的OR=0.931 (95％CI:0.884-0.980),AA+GA/GG的OR=0.924 (95％CI:0.859-0.994),AA/GG的OR=0.886 (95％CI:0.797-0.985),GA/GG的OR=0.925 (95％CI:0.856-0.999),有统计学意义.在欧洲人群中,UCP2-866G/A位点A/G的OR=0.912 (95％CI:0.857-0.970),AA+GA/GG的OR=0.882 (95％CI:0.808-0.962),AA/GG的OR=0.846 (95％CI:0.743-0.963),GA/GG的OR=0.893(95％CI:0.814-0.980),有统计学意义.但在亚洲人群中均无统计学意义.结论:我们认为-866G/A基因多态性与欧洲人群的肥胖有关,与亚洲人群的肥胖无关.     

Gene regulatory network inference by point-based Gaussian approximation filters incorporating the prior information

Abstract

The extended Kalman filter (EKF) has been applied to inferring gene regulatory networks. However, it is well known that the EKF becomes less accurate when the system exhibits high nonlinearity. In addition, certain prior information about the gene regulatory network exists in practice, and no systematic approach has been developed to incorporate such prior information into the Kalman-type filter for inferring the structure of the gene regulatory network. In this paper, an inference framework based on point-based Gaussian approximation filters that can exploit the prior information is developed to solve the gene regulatory network inference problem. Different point-based Gaussian approximation filters, including the unscented Kalman filter (UKF), the third-degree cubature Kalman filter (CKF₃), and the fifth-degree cubature Kalman filter (CKF₅) are employed. Several types of network prior information, including the existing network structure information, sparsity assumption, and the range constraint of parameters, are considered, and the corresponding filters incorporating the prior information are developed. Experiments on a synthetic network of eight genes and the yeast protein synthesis network of five genes are carried out to demonstrate the performance of the proposed framework. The results show that the proposed methods provide more accurate inference results than existing methods, such as the EKF and the traditional UKF.

     

msap: a tool for the statistical analysis of methylation‐sensitive amplified polymorphism data

In this study msap, an R package which analyses methylation‐sensitive amplified polymorphism (MSAP or MS‐AFLP) data is presented. The program provides a deep analysis of epigenetic variation starting from a binary data matrix indicating the banding pattern between the isoesquizomeric endonucleases HpaII and MspI, with differential sensitivity to cytosine methylation. After comparing the restriction fragments, the program determines if each fragment is susceptible to methylation (representative of epigenetic variation) or if there is no evidence of methylation (representative of genetic variation). The package provides, in a user‐friendly command line interface, a pipeline of different analyses of the variation (genetic and epigenetic) among user‐defined groups of samples, as well as the classification of the methylation occurrences in those groups. Statistical testing provides support to the analyses. A comprehensive report of the analyses and several useful plots could help researchers to assess the epigenetic and genetic variation in their MSAP experiments. msap is downloadable from CRAN ( http://cran.r-project.org/ ) and its own webpage ( http://msap.r-forge.R-project.org/ ). The package is intended to be easy to use even for those people unfamiliar with the R command line environment. Advanced users may take advantage of the available source code to adapt msap to more complex analyses.