Secondary structure prediction for complete rDNA sequences (18S, 5.8S,and 28S rDNA) of Demodex folliculorum, and comparison of divergent domains structures across Acari

According to base pairing, the rRNA folds into corresponding secondary structures, which contain additional phylogenetic information. On the basis of sequencing for complete rDNA sequences (18S, ITS1, 5.8S, ITS2 and 28S rDNA) of Demodex, we predicted the secondary structure of the complete rDNA sequence (18S, 5.8S, and 28S rDNA) of Demodex folliculorum, which was in concordance with that of the main arthropod lineages in past studies. And together with the sequence data from GenBank, we also predicted the secondary structures of divergent domains in SSU rRNA of 51 species and in LSU rRNA of 43 species from four superfamilies in Acari (Cheyletoidea, Tetranychoidea, Analgoidea and Ixodoidea). The multiple alignment among the four superfamilies in Acari showed that, insertions from Tetranychoidea SSU rRNA formed two newly proposed helixes, and helix c3-2b of LSU rRNA was absent in Demodex (Cheyletoidea) taxa. Generally speaking, LSU rRNA presented more remarkable differences than SSU rRNA did, mainly in D2, D3, D5, D7a, D7b, D8 and D10.     

Whole genome comparison of six Crocosphaera watsonii strains with differing phenotypes

Crocosphaera watsonii, a unicellular nitrogen‐fixing cyanobacterium found in oligotrophic oceans, is important in marine carbon and nitrogen cycles. Isolates of C. watsonii can be separated into at least two phenotypes with environmentally important differences, indicating possibly distinct ecological roles and niches. To better understand the evolutionary history and variation in metabolic capabilities among strains and phenotypes, this study compared the genomes of six C. watsonii strains, three from each phenotypic group, which had been isolated over several decades from multiple ocean basins. While a substantial portion of each genome was nearly identical to sequences in the other strains, a few regions were identified as specific to each strain and phenotype, some of which help explain observed phenotypic features. Overall, the small‐cell type strains had smaller genomes and a relative loss of genetic capabilities, while the large‐cell type strains were characterized by larger genomes, some genetic redundancy, and potentially increased adaptations to iron and phosphorus limitation. As such, strains with shared phenotypes were evolutionarily more closely related than those with the opposite phenotype, regardless of isolation location or date. Unexpectedly, the genome of the type‐strain for the species, C. watsonii WH8501, was quite unusual even among strains with a shared phenotype, indicating it may not be an ideal representative of the species. The genome sequences and analyses reported in this study will be important for future investigations of the proposed differences in adaptation of the two phenotypes to nutrient limitation, and to identify phenotype‐specific distributions in natural Crocosphaera populations.     

Educational performance of native and immigrant children from various countries of origin

Mostly due to the lack of suitable data, cross-national research on the integration of migrant pupils is still scarce. We aim to fill this gap by addressing the question of the extent to which native and first- and second-generation migrants from various regions of origin, living in thirteen different countries of destination, differ in their scholastic ability. Using the PISA 2003 data, we focus primarily on the impact of origin and destination effects on the scholastic achievement of migrants.

The results indicate that family characteristics and origin and destination effects can offer a significant contribution to the explanation of difference in scholastic knowledge between natives and first- and second-generation migrants. However, certain primary origin and destination effects, as well as interactions between these and family characteristics, remain significant and substantive after controlling for family characteristics, suggesting serious integration problems in the case of migrants from a few regions of origin in some European countries of destination.     

The New Paradox in Marine Scientific Research: Regulating the Potential Environmental Impacts of Conducting Ocean Science

Concerns about the negative effects of marine scientific research are in clear juxtaposition to the beneficial role that scientific knowledge plays in enhancing the understanding of the oceans and protecting the marine environment. This presents a regulatory paradox that is examined in this article in light of the legal framework in the 1982 United Nations Convention on the Law of the Sea. The article traces how these general principles in the Convention are elaborated in soft law instruments for the promotion of environmentally sustainable research practices. It also looks at an example of state practice in this area by examining regulatory measures instituted in the Canadian Endeavour Hydrothermal Vent Marine Protected Area.     

陷阱法和Winkler法调查土壤节肢动物多样性比较:以千岛湖岛屿封闭生境研究为例

陷阱法和Winkler法是调查土壤动物的两种常规方法,然而这两种方法的调查效率各有优劣。本研究于2010年秋季,在千岛湖中心湖区选取了15个面积不同的岛屿,同时采用Winkler法和陷阱法采集岛屿上的土壤节肢动物,在岛屿这一封闭生境中比较两种方法收集土壤节肢动物的效率。结果表明,两种方法捕获土壤动物类群丰富度差异不显著,但多样性指数差异极显著。Winkler法对常规土壤节肢动物类群的采集效率优于陷阱法,尤其对运动较缓慢、活动范围较小的土壤节肢动物类群的采集具有优势;陷阱法则更优于采集运动能力较强、活动范围较大的类群。基于样方的稀疏曲线结果说明,Winkler法能用少量样方快速获取研究区域的土壤节肢动物群落基本组成,推荐在面积较小的岛屿上使用;而在面积较大的岛屿上使用陷阱法能够获取更多的类群。ChaoJaccard相似性系数比较则显示两种方法所取的土壤节肢动物相似性在大型岛屿上差异较大,说明大样本数据的采集需要两种方法同时使用能够提高数据的完整性和可靠性。本研究的结果为土壤节肢动物研究的方法选择提供了数据支持,具有一定的实际应用性。     

Estimating the null distribution to adjust observed confidence levels for genome-scale screening

In a novel approach to the multiple testing problem, Efron (2004, Journal of the American Statistical Association 99, 96-104; 2007a Journal of the American Statistical Association 102, 93-103; 2007b, Annals of Statistics 35, 1351-1377) formulated estimators of the distribution of test statistics or nominal p-values under a null distribution suitable for modeling the data of thousands of unaffected genes, nonassociated single-nucleotide polymorphisms, or other biological features. Estimators of the null distribution can improve not only the empirical Bayes procedure for which it was originally intended, but also many other multiple-comparison procedures. Such estimators in some cases improve the proposed multiple-comparison procedure (MCP) based on a recent non-Bayesian framework of minimizing expected loss with respect to a confidence posterior, a probability distribution of confidence levels. The flexibility of that MCP is illustrated with a nonadditive loss function designed for genomic screening rather than for validation. The merit of estimating the null distribution is examined from the vantage point of the confidence-posterior MCP (CPMCP). In a generic simulation study of genome-scale multiple testing, conditioning the observed confidence level on the estimated null distribution as an approximate ancillary statistic markedly improved conditional inference. Specifically simulating gene expression data, however, indicates that estimation of the null distribution tends to exacerbate the conservative bias that results from modeling heavy-tailed data distributions with the normal family. To enable researchers to determine whether to rely on a particular estimated null distribution for inference or decision making, an information-theoretic score is provided. As the sum of the degree of ancillarity and the degree of inferential relevance, the score reflects the balance conditioning would strike between the two conflicting terms. The CPMCP and other methods introduced are applied to gene expression microarray data.     

Experimental conditions affecting functional comparison of highly active glutathione transferases

Glutathione transferases (GSTs, EC 2.5.1.18) possess multiple functions and have potential applications in biotechnology. Direct evidence of underestimation of activity of human GST A3-3 and porcine GST A2-2 measured at submicromolar enzyme concentrations is reported here for the first time. The combination of time-dependent and enzyme concentration-dependent loss of activity and the choice of the organic solvent for substrates were found to cause irreproducibility of activity measurements of GSTs. These effects contribute to high variability of activity values of porcine GST A2-2 and human Alpha-class GSTs reported in the literature. Adsorption of GSTs to surfaces was found to be the main explanation of the observed phenomena. Several approaches to improved functional comparison of highly active GSTs are proposed.     

以兽类为例探讨我国陆生野生动物疫病监管中面临的问题与对策

近年来, 新型冠状病毒、SARS病毒和鼠疫等新发和再发性动物源疫病多是由兽类及其媒介携带的病原生物直接或间接感染而引发的, 不仅对人类健康和生态系统平衡造成了重大威胁, 而且威胁全球公共卫生安全、粮食安全和生物安全。结合我国重要陆生兽类疫源疫病发生的新情况和新特点, 本文重点总结了我国以陆生野生及非野生兽类(家畜为主)为重点的24种重要人兽共患病的监管情况, 并对这些疫源疫病的监管空缺进行了分析。由于病原生物的种类多及其感染传播方式多样, 我国人间和动物间疫情呈现多发态势, 新发和再发疫病防控面临严峻挑战。从目前情况来看, 我国重要野生动物疫源疫病呈现为多部门、多层监管的局面。全球化贸易剧增、非法猎杀、非法交易、违法违规养殖、滥食野生动物陋习、检疫环节失察等导致了当前我国野生动物疫源疫病的传染源头和传播链错综复杂, 加剧了人类与野生动物所携带的病原接触、感染和传播的风险。极端气候或灾害事件频发以及对新发再发传染病的认知不足导致难以从源头做好疫病防控。针对上述问题, 本文提出了从源头加强基础研究和全链条监管来积极防范陆生野生动物疫病疫情的对策和建议。     

《本草图经》建州产植物药图考证

《本草图经》所附药图中标明为福建产的药物有22种,其中建州(今属福建南平地区)产有3种,分别为建州天门冬、建州前胡、建州栀子。对其药图及文字记载进行考证,认为建州天门冬应为今之百合科植物天门冬[Asparagus cochinchinensis (Lour.) Merr.],建州前胡应为今之伞形科植物隔山香[Ostericum citriodorum (Hance) Yuan et Shan],建州栀子应为今之茜草科植物栀子(Gardenia jasminoides Ellis)。     

《本草图经》兴化军防己的本草考证

对《本草图经》中兴化军防己的附图及文字记载进行本草考证,探究其原植物品种。通过古今文献考证和植物学比较研究,从植物形态、药材性状、产地分布及性味功用等方面进行分析,认为《本草图经》中的兴化军防己应为今之防己科植物木防己[Cocculus orbiculatus (L.) DC.],为防己类中药的古今品种沿革及基原考证提供参考。