PSMD: An extensive database for pan‐species microsatellite investigation and marker development

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.     

基于生态足迹法的闽三角城市群生态安全评价

生态安全已经成为时下研究的热点问题,而生态足迹法(Ecological Footprint)是评价区域生态安全的重要方法之一。然而,目前鲜有应用改良后的生态足迹方法探讨海湾型城市群生态足迹以及生态安全状态的成果。鉴于此,论文以闽三角城市群为研究区,以NPP数据反映现实生物量,采用"国家公顷"实现产量因子区域化,测算2010—2015年的区域生态足迹、生态承载力、生态赤字以及生态压力指数,评价区域生态安全状态。结果表明:2010—2015年间,闽三角城市群的生态足迹快速增长,其中泉州与漳州增长迅速,而厦门则略有下降;区域总体生态承载力缓慢下降;城市群大部分区域呈现生态赤字且越发严重,其中厦门最为严重,泉州次之,漳州相对较轻;城市群生态压力指数持续增长,生态安全等级升高,与生态赤字情况总体相符,生态安全问题亟需解决。有助于拓展与丰富生态足迹与生态安全研究的视角与案例,并为城市群可持续发展提供科学依据和决策支撑。     

Decoupling Analysis of Four Selected Countries

We examine decoupling conditions of domestic extraction of materials, energy use, and sulfur dioxide (SO₂) emissions from gross domestic product (GDP) for two BRIC (Brazil, Russia, India and China) countries (i.e., China and Russia) and two Organisation for Economic Co‐operation and Development (OECD) countries (Japan and the United States) during 2000–2007, using a pair of decoupling indicators for resource use (D_r) and waste emissions (D_e) and the decoupling chart, which can distinguish between absolute decoupling, relative decoupling, and non‐decoupling. We find that (1) during 2000–2007, decoupling between environmental indicators and GDP was higher in the two OECD countries as compared with the two BRIC countries. The key reason is that these countries were in different development stages with different economic growth rates. (2) Changes in environmental policies can significantly influence the degree of decoupling in a country. (3) China, Japan, and the United States were more successful in decoupling SO₂ emissions from GDP than in decoupling material and energy use from GDP. The main reason is that, unlike resource use, waste emissions (e.g., SO₂ emissions) can be reduced by effective end‐of‐pipe treatment. (4) The decoupling indicator is different from the changing rate of resource use and waste emissions. If two countries have different GDP growth rates, even though they may have similar values using the decoupling indicator, they may show different rates of change for resource use and waste emissions.     

中国栝楼属(Trichosanthes L.)花粉形态的研究

本文系统地研究了我国栝楼属30种及分布于日本的多裂栝楼的花粉形态,观察了各种花粉在光学显微镜及扫描电镜下的形态特征.同时通过花粉形态的研究,验证了在分类上本属所分各组的合理性。并观察了栝楼族另一属植物油瓜的花粉,探讨了二属之间的亲缘关系。由于本属植物多数为药用,而花粉形态特征为本属药材真伪的鉴别提供了依据。     

Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.     

抗炎性细胞因子与抑郁症

细胞因子假说是关于抑郁症发病机理的重要假说,为探讨抑郁症的发病机理和临床治疗方法提供了新方向.细胞因子分为前炎性细胞因子和抗炎性细胞因子.前炎性细胞因子与抑郁症的发病密切相关,而抗炎性细胞因子可能具有抗抑郁的作用.本文着重综述抗炎性细胞因子与抑郁症的关系.抗炎性细胞因子如白介素10、白介素1受体拮抗剂、白介素4、白介素13、转化生长因子β和脂联素等,在抑郁症中表达下降;补充外源抗炎性细胞因子则具有一定的抗抑郁作用.抗炎性细胞因子可通过拮抗前炎性细胞因子的作用,并与MAPK信号通路、神经递质和糖皮质激素相互作用而参与到抑郁症中.抗抑郁药能使抗炎性细胞因子的表达上升,这可能是药物起效的机制之一.抗炎策略在抑郁症的治疗中有重要应用前景.     

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

Background

Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases.

Methods

To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria.

Results

Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features.

Conclusion

Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.

     

刚毛柽柳S-腺苷甲硫氨酸合成酶(ThSAMS)基因的克隆及表达分析

通过对刚毛柽柳转录组分析,克隆获得了一条与S-腺苷甲硫氨酸合成酶(SAMS)基因同源性高的基因,命名为ThSAMS。序列分析结果表明:ThSASM基因全长cDNA为1185bp,编码394个氨基酸,编码蛋白相对分子质量为97.85kDa,理论等电点为5.02。通过生物信息学分析表明,ThSASM基因编码的氨基酸与其他物种SAMS基因编码的氨基酸具有很高的同源性,其中与枣的同源性最高,达95%。实时荧光定量PCR(quantitativereal-timePCR,qRT-PCR)分析表明,ThSASM表达受NaCl、聚乙二醇(PEG)和ABA处理做出应答,暗示ThSASM可能参与了刚毛柽柳对盐和干旱的胁迫应答,为进一步研究SAMS基因在植物胁迫应答中的功能及作用机制提供了参考依据。     

农作物遗传多样性农家保护的现状及前景

农作物地方品种的有效保护是农业生物多样性的可持续利用的基础。由于现代农业的集约化生产方式使大量农作物地方品种被少数高产改良品种所取代,造成农作物基因库的严重“基因流失”（genetic erosion)。农家保护是在农业生态系统中进行的动态保护,被保护的生物多亲性可在其生境中继续进化而产生新的遗传变异,在而是农业生物多样性就地保护的重要途径。然而,尽管人们对作物品种资源农家保护的兴趣不断增长,也有大量有关农家的保护的研究和案例分析,但目前为止还没有比较成功的农家保护实例报道。因此,对农家保护的机制及科学问题进行深入的研究,并寻求一条新的途径来充分发挥农家保护应有的作用,显得格外重要。利用生物多样性布局的水稻混合间栽的生产模式,不仅解决了病害控制的问题,而且也保护了水稻地方品种的多样性。这种混合间栽的生物多样性布局和生产方式可能成为农保护的一条新途径。