大气颗粒物污染对土地覆盖变化的响应

土地利用-覆盖变化(LUCC)直接或间接影响颗粒物污染。了解颗粒物污染对LUCC的响应,对维护和改善生态环境具有重要的意义。基于卫星遥感技术,从广域的空间尺度分析颗粒物污染对LUCC的响应。使用MODIS数据分别提取与颗粒物污染相关性较高的城市用地、林地等土地利用类型,确定土地利用类型的变化趋势,利用长时间序列MODIS气溶胶光学厚度(AOD,Aerosol optical depth)产品分析颗粒物污染与土地利用类型的变化的相关性。以山东省青岛市、淄博市、济南市3个典型城市为例,研究了AOD随土地利用类型的变化趋势。同时,考虑并分析了颗粒物污染对土地利用变化响应的敏感性,以及城市区域变化对环境的影响。研究结果表明,不同的城市类型,由于决定环境变化主导因素的差异,颗粒物污染对LUCC的响应具有明显的差异。青岛市地区,由于受海洋影响显著,大气颗粒物污染与LUCC的相关性较低,如中度污染天气与林地的相关系数为-0.451;而淄博市和济南市的相关系数分别为-0.473、-0.507。     

高通量RNA甲基化测序数据处理与分析研究进展

随着高通量测序技术快速发展,Me RIP-seq(methylated RNA immunoprecipitation sequencing)测序技术开启了RNA表观遗传学研究新局面,能够在全基因组范围内描述RNA甲基化.从Me RIP-seq高通量数据中挖掘RNA甲基化模式,有助于揭示m RNA甲基化在调控基因表达、剪切等方面所发挥的潜在功能,有效指导癌症的干预治疗.本文从Me RIP-seq测序原理出发,较全面地综述Me RIP-seq数据处理和分析方法研究现状,并对其所面临的计算问题进行讨论和展望.     

Skipper genome sheds light on unique phenotypic traits and phylogeny

Background

Butterflies and moths are emerging as model organisms in genetics and evolutionary studies. The family Hesperiidae (skippers) was traditionally viewed as a sister to other butterflies based on its moth-like morphology and darting flight habits with fast wing beats. However, DNA studies suggest that the family Papilionidae (swallowtails) may be the sister to other butterflies including skippers. The moth-like features and the controversial position of skippers in Lepidoptera phylogeny make them valuable targets for comparative genomics.

Results

We obtained the 310 Mb draft genome of the Clouded Skipper (Lerema accius) from a wild-caught specimen using a cost-effective strategy that overcomes the high (1.6 %) heterozygosity problem. Comparative analysis of Lerema accius and the highly heterozygous genome of Papilio glaucus revealed differences in patterns of SNP distribution, but similarities in functions of genes that are enriched in non-synonymous SNPs. Comparison of Lepidoptera genomes revealed possible molecular bases for unique traits of skippers: a duplication of electron transport chain components could result in efficient energy supply for their rapid flight; a diversified family of predicted cellulases might allow them to feed on cellulose-enriched grasses; an expansion of pheromone-binding proteins and enzymes for pheromone synthesis implies a more efficient mate-recognition system, which compensates for the lack of clear visual cues due to the similarities in wing colors and patterns of many species of skippers. Phylogenetic analysis of several Lepidoptera genomes suggested that the position of Hesperiidae remains uncertain as the tree topology varied depending on the evolutionary model.

Conclusion

Completion of the first genome from the family Hesperiidae allowed comparative analyses with other Lepidoptera that revealed potential genetic bases for the unique phenotypic traits of skippers. This work lays the foundation for future experimental studies of skippers and provides a rich dataset for comparative genomics and phylogenetic studies of Lepidoptera.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1846-0) contains supplementary material, which is available to authorized users.     

Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus

Background

Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling.

Results

Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster.

Conclusions

Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1763-2) contains supplementary material, which is available to authorized users.     

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.     

伯克霍尔德氏菌ZYB002脂肪酶lipC24基因的克隆、表达及其酶学性质

【目的】克隆伯克霍尔德菌ZYB002菌株中的新型脂肪酶lip C24基因,测定其基本酶学性质,为后续深入研究该基因在菌株中的生理功能奠定基础。【方法】根据洋葱伯克霍尔德菌JK321菌株的全基因组DNA信息,直接设计引物从伯克霍尔德菌ZYB002菌株基因组中扩增出lip C24基因,并对之进行原核表达、重组蛋白的纯化及酶学性质分析。【结果】lip C24基因全长1317 bp,编码438个氨基酸残基;多肽链中具有保守五肽-G-X1-S-X2-G-序列;重组蛋白Lip C24的分子量为45 k Da;能有效水解各种对硝基苯酯,对中链脂肪酸的对硝基苯酯表现出偏爱性;其催化水解反应的最适温度为40℃,最适p H7.5;40℃下的半衰期为15.72 min,在p H 7.0-8.0的条件下,具有较好的稳定性。【结论】lip C24的编码产物为一个45 k Da蛋白,具有明显的脂肪酶活性,为中温中性脂肪酶。     

Inferring demographic structure with moccasin size data from the Promontory Caves,Utah

The moccasin assemblage Julian Steward recovered from the Promontory caves in 1930–31 provides a novel example in which material culture can be used to understand the structure of an AD thirteenth century population. Several studies shed light on the relationship between shoe size, foot size, and stature. We develop an anthropometric model for understanding the composition of the Promontory Cave population by using moccasin size as a proxy for foot size. We then predict the stature of the individual who would have worn a moccasin. Stature is closely related to age for children, subadults and adult males. Although there are predictable sex and age factors biasing moccasin discard practices, moccasin dimensions suggest a relatively large proportion of children and subadults occupied the Promontory caves. This bison and antelope hunting population appears to have thrived during its stay on Promontory Point. Am J Phys Anthropol 156:76–89, 2015 © 2014 Wiley Periodicals, Inc.     

Simultaneous electrochemical detection of multiple biomarkers using gold nanoparticles decorated multiwall carbon nanotubes as signal enhancers

In this work, a novel sandwich-type electrochemical immunosensor has been developed for simultaneous detection of carcinoembryonic antigen (CEA) and α-fetoprotein (AFP) based on metal ion labels. Gold nanoparticles decorated multiwall carbon nanotubes (AuNPs@MWCNTs) were used as carriers to immobilize secondary antibodies and distinguishable electrochemical tags of Pb²⁺ and Cd²⁺ to amplify the signals. Due to the intrinsic property of high surface-to-volume ratio, the AuNPs@MWCNTs could load numerous secondary antibodies and labels. Therefore, the multiplexed immunoassay exhibited good sensitivity and selectivity. Experimental results revealed that this sandwich-type immunoassay displayed an excellent linear response, with a linear range of 0.01 to 60 ng mL^–1 for both analytes and detection limits of 3.0 pg mL^–1 for CEA and 4.5 pg mL^–1 for AFP (at a signal-to-noise ratio of 3). The method was successfully applied for the determination of AFP and CEA levels in clinical serum samples.