全球气候变暖胁迫下的雅鲁藏布江流域植被覆盖度变化驱动机制探讨

为了解雅鲁藏布江流域内植被变化对气候变化响应的时空差异性,引入重心模型,分析和探讨了2002-2014年雅鲁藏布江流域植被的变化特点与气候因子的相关性。结果表明,植被的NDVI(归一化植被指数,Normalized difference vegetation index)重心与降水重心年际迁移方向具有正相关性。雅鲁藏布江流域的月植被NDVI受前0-1月降水影响最大,而不同季节植被的NDVI对降水影响表现出一定的滞后性,其中春季和冬季的植被NDVI均与前一季的降水呈现正相关性。该流域中乔木、灌木对降水反应的滞后性比草本植物要大;生长季的温度变化与植被的生长具有相关性。植被NDVI与月均温的正相关性达到最大的时间段差异较大。因此,植被NDVI和气候因子间的时空异质性研究对于雅鲁藏布江流域的生态环境保护具有重要意义。     

Performance comparison of four exome capture systems for deep sequencing

Background

Recent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen’s SeqCap EZ v3.0, Agilent’s SureSelect v4.0, Illumina’s TruSeq Exome, and Illumina’s Nextera Exome, all applied to the same human tumor DNA sample.

Results

Each capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content.

Conclusions

We show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-449) contains supplementary material, which is available to authorized users.     

三江源区生态系统和土壤保持服务对未来气候变化的响应特征

气候变化条件下的生态系统响应特征对生态系统服务的提升和生态环境保护具有重要意义。现有气候变化评估多以全球或区域大尺度研究为主,不适合局地小尺度。以2015年为基准,根据局地特征改进了综合顺序分类系统（CSCS）,模拟了未来不同温室气体排放模式下三江源地区自然植被分布,同时分析了植被覆盖度及土壤保持功能的时空变化。研究结果表明：①在2080年的不同排放情境下,三江源地区的降水和气温增长主要发生在生长季（5—9月）和半湿润地区,其中,高排放情境的增幅最大（42.21 mm和4.93℃）;②三江源地区潜在自然植被主要由草地转化为森林,植被覆盖度和土壤保持服务在不同排放情境下均呈现由西北向东南增加的趋势,与水热规律一致,其中高排放情境的增幅最大,低排放最小;③ 利用三江源地区原生裸地演替特点和多年NPP改进的CSCS模型,模拟精度提高了24%。研究成果为局地小尺度生态系统气候响应特征提供了必要的手段和规律认识。     

岷江上游暗针叶林采伐迹地人工混交林群落结构

对四川岷江上游高山峡谷区暗针叶林采伐迹地年龄为２０－４０年的人工混交林群落结构进行了研究,结果是：（１）群落中各层次物种盖度的大小相互影响,相互制约,而林下（各）层次物种盖度的大小主要取决于其上（各）层盖度（或郁闭度）的大小,（２）人工重建的群落所能容纳的物种数及物种在群落中的分布状况主要取决于乔木物种郁工,海拔高度及经营强度。（３）群落中出现大量的耐荫植物,先锋灌丛植物已被抑制或淘汰,（４）乔木     

Next generation genome-wide association tool: design and coverage of a high-throughput European-optimized SNP array

The success of genome-wide association studies has paralleled the development of efficient genotyping technologies. We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using an approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom system. The new array provides a valuable addition to the repertoire of tools for large scale genome-wide association studies.     

Microbial metabolomics: toward a platform with full metabolome coverage

Achieving metabolome data with satisfactory coverage is a formidable challenge in metabolomics because metabolites are a chemically highly diverse group of compounds. Here we present a strategy for the development of an advanced analytical platform that allows the comprehensive analysis of microbial metabolomes. Our approach started with in silico metabolome information from three microorganisms-Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae-and resulted in a list of 905 different metabolites. Subsequently, these metabolites were classified based on their physicochemical properties, followed by the development of complementary gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry methods, each of which analyzes different metabolite classes. This metabolomics platform, consisting of six different analytical methods, was applied for the analysis of the metabolites for which commercial standards could be purchased (399 compounds). Of these 399 metabolites, 380 could be analyzed with the platform. To demonstrate the potential of this metabolomics platform, we report on its application to the analysis of the metabolome composition of mid-logarithmic E. coli cells grown on a mineral salts medium using glucose as the carbon source. Of the 431 peaks detected, 235 (=176 unique metabolites) could be identified. These include 61 metabolites that were not previously identified or annotated in existing E. coli databases.     

Simultaneous confidence intervals for a success probability and intraclass correlation,with an application to screening mammography

This paper provides asymptotic simultaneous confidence intervals for a success probability and intraclass correlation of the beta‐binomial model, based on the maximum likelihood estimator approach. The coverage probabilities of those intervals are evaluated. An application to screening mammography is presented as an example. The individual and simultaneous confidence intervals for sensitivity and specificity and the corresponding intraclass correlations are investigated. Two additional examples using influenza data and sex ratio data among sibships are also considered, where the individual and simultaneous confidence intervals are provided.     

Adjusting estimative prediction limits

This note presents a direct adjustment of the estimative predictionlimit to reduce the coverage error from a target value to third-orderaccuracy. The adjustment is asymptotically equivalent to thoseof Barndorff-Nielsen & Cox (1994, 1996) and Vidoni (1998).It has a simpler form with a plug-in estimator of the coverageprobability of the estimative limit at the target value.