Integrated population modeling reveals the impact of climate on the survival of juvenile emperor penguins

Early‐life demographic traits are poorly known, impeding our understanding of population processes and sensitivity to climate change. Survival of immature individuals is a critical component of population dynamics and recruitment in particular. However, obtaining reliable estimates of juvenile survival (i.e., from independence to first year) remains challenging, as immatures are often difficult to observe and to monitor individually in the field. This is particularly acute for seabirds, in which juveniles stay at sea and remain undetectable for several years. In this work, we developed a Bayesian integrated population model to estimate the juvenile survival of emperor penguins (Aptenodytes forsteri), and other demographic parameters including adult survival and fecundity of the species. Using this statistical method, we simultaneously analyzed capture–recapture data of adults, the annual number of breeding females, and the number of fledglings of emperor penguins collected at Dumont d'Urville, Antarctica, for the period 1971–1998. We also assessed how climate covariates known to affect the species foraging habitats and prey [southern annular mode (SAM), sea ice concentration (SIC)] affect juvenile survival. Our analyses revealed that there was a strong evidence for the positive effect of SAM during the rearing period (SAMR) on juvenile survival. Our findings suggest that this large‐scale climate index affects juvenile emperor penguins body condition and survival through its influence on wind patterns, fast ice extent, and distance to open water. Estimating the influence of environmental covariates on juvenile survival is of major importance to understand the impacts of climate variability and change on the population dynamics of emperor penguins and seabirds in general and to make robust predictions on the impact of climate change on marine predators.     

体外多酶分子机器的现状和最新进展

体外多酶分子机器遵循所设计的多酶催化路径,将若干种纯化或部分纯化的酶元件进行合理的优化与适配,高效地在体外将特定的底物转化为目标化合物。体外多酶分子机器反应系统呈现元件化和模块化的特点,在设计、组装和调控方面具有较高的自由度。近年来,体外多酶分子机器在实现反应过程的精准调控和提高产品得率方面的优势逐渐体现,展示了其在生物制造领域重要的应用潜力。对体外多酶分子机器的相关研究已成为合成生物学的一个重要分支领域,日益受到广泛的关注。文中系统地综述了基于酶元件/模块的体外多酶分子机器的构建策略,以及改善该分子机器中酶元件/模块之间适配性的研究进展,并分析了该生物制造平台的发展前景与挑战。     

Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs

Interactions of transmembrane helices play a crucial role in the folding and oligomerisation of integral membrane proteins. In order to uncover novel sequence motifs mediating these interactions, we randomised one face of a transmembrane helix with a set of non-polar or moderately polar amino acids. Those sequences capable of self-interaction upon integration into bacterial inner membranes were selected by means of the ToxR/POSSYCCAT system. A comparison between low/medium-affinity and high-affinity sequences reveals that high-affinity sequences are strongly enriched in phenylalanine residues that are frequently observed at the − 3 position of GxxxG motifs, thus yielding FxxGxxxG motifs. Mutation of Phe or GxxxG in selected sequences significantly reduces self-interaction of the transmembrane domains without affecting their efficiency of membrane integration. Conversely, grafting FxxGxxxG onto unrelated transmembrane domains strongly enhances their interaction. Further, we find that FxxGxxxG is significantly over-represented in transmembrane domains of bitopic membrane proteins. The same motif contributes to self-interaction of the vesicular stomatitis virus G protein transmembrane domain. We conclude that Phe stabilises membrane-spanning GxxxG motifs. This is one example of how the role of certain side-chains in helix-helix interfaces is modulated by sequence context.     

基于多目标灰色局势决策的三峡库区防护林类型空间优化配置

基于2007年Landsat TM遥感影像和影响防护林的主导环境因子,对三峡库区的森林立地进行分类,并通过选取水源涵养量、生物量和林分生产力3个指标,利用多目标灰色局势决策模型对库区现有的针叶林、阔叶林、针阔混交林和灌木林4种防护林类型进行空间优化配置.结果表明： 2007年,三峡库区森林立地可划分为40种类型;空间配置优化后,研究区针叶林、阔叶林、针阔混交林和灌木林的面积比例分别为32.55%、29.43%、34.95%和3.07%.与优化前相比,优化后针叶林和灌木林的面积比例分别减少了8.79%和28.55%,阔叶林和针阔混交林分别增加了10.23%和27.11%.通过防护林类型的空间优化,三峡库区整体的水源涵养能力、生物量和林分生产力分别增加14.09×10⁸ m³、0.35×10⁸ t和1.08×10⁶ t.     

A platform to standardize,store, and visualize proteomics experimental data

With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database （IPED） as a platform for managing proteomics experimental data （both process and result data）. IPED is based on the schema of the Proteome Experimental Data Repository （PEDRo）, and complies with the General Proteomics Standard （GPS） drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform： the IPED client editor, IPED server software, and IPED web interface. The client editor collects experimental data and generates an extensible markup language （XML） data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database; and the web interface displays experimental results, to provide a convenient graphic representation of data. Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community. In its current release, IPED is available at http：//www. biosino.org/iped2.     

诱集植物在农业中的应用研究进展与展望

全世界每年因病虫害导致严重的农业经济损失, 为了减少病虫害的发生, 实际生产中通常使用大量化学农药, 然而农药的大量施用, 不仅造成环境污染和农产品安全问题, 还会使病虫害产生抗药性, 天敌种群受损, 从而导致病虫害爆发日益严重。种植诱集植物是一种环境友好型病虫害防控方法, 该方法主要是通过诱集植物吸引虫害和降低病害, 从而减少病虫害对主栽作物的危害, 达到保护主栽作物的目的, 最终减少农业上化学农药的使用。根据诱集植物自身特性, 将其分为五种主导作用类型: 传统诱集植物、致死型诱集植物、基因工程型诱集植物、生物辅助控制型诱集植物、化学信息素辅助作用型诱集植物等, 根据种植和利用方式, 将其分为: 围种诱集、间种诱集、连作诱集、与其它方式结合等。尽管关于诱集植物的研究已有近160年历史, 但有关高效诱集植物的筛选、诱集植物与主栽作物的优化配置模式与配套种植技术、诱集植物对靶标病虫害的作用机理、诱集植物在农业生产中的生态风险评估等仍不清楚, 且诱集植物仍具有较大开发潜力和应用价值, 如(1)开发应用诱集植物的环境污染修复功能及相关技术; (2)开发应用诱集植物的景观生态与休闲旅游功能及相关技术; (3)开发利用诱集植物对土壤的养分转化与固持提升功能(如固氮、固碳、固土功能等)、生物质能源功能、节能减排功能及相关技术; (4)开发应用诱集植物及其废弃物的经济产品功能及其可持续生产技术。论文综述了近年来国内外有关诱集植物的相关研究与实践应用, 旨在为诱集植物在农业生产中进行病虫害防治研究和应用提供相关参考。     

Trait biogeography of marine copepods – an analysis across scales

Functional traits, rather than taxonomic identity, determine the fitness of individuals in their environment: traits of marine organisms are therefore expected to vary across the global ocean as a function of the environment. Here, we quantify such spatial and seasonal variations based on extensive empirical data and present the first global biogeography of key traits (body size, feeding mode, relative offspring size and myelination) for pelagic copepods, the major group of marine zooplankton. We identify strong patterns with latitude, season and between ocean basins that are partially (c. 50%) explained by key environmental drivers. Body size, for example decreases with temperature, confirming the temperature‐size rule, but surprisingly also with productivity, possibly driven by food‐chain length and size‐selective predation. Patterns unrelated to environmental predictors may originate from phylogenetic clustering. Our maps can be used as a test‐bed for trait‐based mechanistic models and to inspire next‐generation biogeochemical models.     

Whole genome DNA methylation profiling of oral cancer in ethnic population of Meghalaya,North East India reveals novel genes

Oral Squamous Cell Carcinoma (OSCC) is a serious and one of the most common and highly aggressive malignancies. Epigenetic factors such as DNA methylation have been known to be implicated in a number of cancer etiologies. The main objective of this study was to investigate physiognomies of Promoter DNA methylation patterns associated with oral cancer epigenome with special reference to the ethnic population of Meghalaya, North East India. The present study identifies 27,205 CpG sites and 3811 regions that are differentially methylated in oral cancer when compared to matched normal. 45 genes were found to be differentially methylated within the promoter region, of which 38 were hypermethylated and 7 hypomethylated. 14 of the hypermethylated genes were found to be similar to that of the TCGA-HNSCC study some of which are TSGs and few novel genes which may serve as candidate methylation biomarkers for OSCC in this poorly characterized ethnic group.     

Estimability of migration survival rates from integrated breeding and winter capture–recapture data

Long‐distance migration is a common phenomenon across the animal kingdom but the scale of annual migratory movements has made it difficult for researchers to estimate survival rates during these periods of the annual cycle. Estimating migration survival is particularly challenging for small‐bodied species that cannot carry satellite tags, a group that includes the vast majority of migratory species. When capture–recapture data are available for linked breeding and non‐breeding populations, estimation of overall migration survival is possible but current methods do not allow separate estimation of spring and autumn survival rates. Recent development of a Bayesian integrated survival model has provided a method to separately estimate the latent spring and autumn survival rates using capture–recapture data, though the accuracy and precision of these estimates has not been formally tested. Here, I used simulated data to explore the estimability of migration survival rates using this model. Under a variety of biologically realistic scenarios, I demonstrate that spring and autumn migration survival can be estimated from the integrated survival model, though estimates are biased toward the overall migration survival probability. The direction and magnitude of this bias are influenced by the relative difference in spring and autumn survival rates as well as the degree of annual variation in these rates. The inclusion of covariates can improve the model's performance, especially when annual variation in migration survival rates is low. Migration survival rates can be estimated from relatively short time series (4–5 years), but bias and precision of estimates are improved when longer time series (10–12 years) are available. The ability to estimate seasonal survival rates of small, migratory organisms opens the door to advancing our understanding of the ecology and conservation of these species. Application of this method will enable researchers to better understand when mortality occurs across the annual cycle and how the migratory periods contribute to population dynamics. Integrating summer and winter capture data requires knowledge of the migratory connectivity of sampled populations and therefore efforts to simultaneously collect both survival and tracking data should be a high priority, especially for species of conservation concern.     

The role of predators and parasites in controlling populations ofEarias insulana,heliothis armigera andBemisia tabaci on cotton in the Syrian Arab Republic

Studies on the relationship between insect pests and their predators and parasites were conducted in the Syrian cotton agro-ecosystem from 1980 up to 1983.Earias insulana (Boisduval) was found to be the most damaging pest, whileHeliothis armigera (Hübner) was not an annual returning problem. Among the entomophagous insects found, coccinellids were most numerous during the months June and July and the hemipterous predators were more abundant during August and September. When predator numbers were reduced with insecticide applications, a significant increase in the bollworm populations occurred, resulting in significant reductions in seed cotton yields. Parasites were relatively not important for the control of lepidopterous pests on cotton. Egg and larva populations ofE. insulana andH. armigera were parasitized byTrichogramma spp. andHabrobracon brevicornis Wesmael respectively. Populations ofBemisia tabaci (Gennadius) were heavily parasitized byEretmocerus mundus Mercet.