Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes

We present evidence supporting the notion that codon usage (CU) compatibility between foreign genes and recipient genomes is an important prerequisite to assess the selective advantage of imported functions, and therefore to increase the fixation probability of horizontal gene transfer (HGT) events. This contrasts with the current tendency in research to predict recent HGTs in prokaryotes by assuming that acquired genes generally display poor CU. By looking at the CU level (poor, typical, or rich) exhibited by putative xenologs still resembling their original CU, we found that most alien genes predominantly present typical CU immediately upon introgression, thereby suggesting that the role of CU amelioration in HGT has been overemphasized. In our strategy, we first scanned a representative set of 103 complete prokaryotic genomes for all pairs of candidate xenologs (exported/imported genes) displaying similar CU. We applied additional filtering criteria, including phylogenetic validations, to enhance the reliability of our predictions. Our approach makes no assumptions about the CU of foreign genes being typical or atypical within the recipient genome, thus providing a novel unbiased framework to study the evolutionary dynamics of HGT.     

Myosin flexibility: structural domains and collective vibrations

The movement of the myosin motor along an actin filament involves a directed conformational change within the cross-bridge formed between the protein and the filament. Despite the structural data that has been obtained on this system, little is known of the mechanics of this conformational change. We have used existing crystallographic structures of three conformations of the myosin head, containing the motor domain and the lever arm, for structural comparisons and mechanical studies with a coarse-grained elastic network model. The results enable us to define structurally conserved domains within the protein and to better understand myosin flexibility. Notably they point to the role of the light chains in rigidifying the lever arm and to changes in flexibility as a consequence of nucleotide binding.     

Modelling age‐ and density‐structured reproductive biology and seasonal survival of Apanteles galleriae Wilkinson (Hym., Braconidae)

Abstract: The biology of Apanteles galleriae Wilkinson, an important biological control agent of wax moths, is well described in the literature. We developed models simulating the functional response of fecundity and female progeny proportion of adult females as a function of age, host and/or parasitoid density to integrate current knowledge. Daily pattern of age‐related fecundity and female progeny proportion of different parasitoids was also examined. We investigated the effect of sex, mating status and seasonal time on adult longevity. We derived survival data of females in two different seasonal periods. We found that 50% of adult life span is important for an efficient fecundity. The patterns of host and/or parasitoid density‐dependent fecundity and sex ratio varied considerably. The highest fecundity and female progeny proportion occurred with one parasitoid and one female equivalent host. Longevity of adults was affected by sex and month periods, but mating status did not affect their longevity. Female survival was greater between December and May relative to June and November. Our results indicated that age, host and parasitoid density, and the timing of rearing influenced the life processes of parasitoids.     

Infection, reinfection, and vaccination under suboptimal immune protection: epidemiological perspectives

The SIR (susceptible-infectious-resistant) and SIS (susceptible-infectious-susceptible) frameworks for infectious disease have been extensively studied and successfully applied. They implicitly assume the upper and lower limits of the range of possibilities for host immune response. However, the majority of infections do not fall into either of these extreme categories. We combine two general avenues that straddle this range: temporary immune protection (immunity wanes over time since infection), and partial immune protection (immunity is not fully protective but reduces the risk of reinfection). We present a systematic analysis of the dynamics and equilibrium properties of these models in comparison to SIR and SIS, and analyse the outcome of vaccination programmes. We describe how the waning of immunity shortens inter-epidemic periods, and poses major difficulties to disease eradication. We identify a "reinfection threshold" in transmission when partial immunity is included. Below the reinfection threshold primary infection dominates, levels of infection are low, and vaccination is highly effective (approximately an SIR model). Above the reinfection threshold reinfection dominates, levels of infection are high, and vaccination fails to protect (approximately an SIS situation). This association between high prevalence of infection and vaccine failure emphasizes the problems of controlling recurrent infections in high-burden regions. However, vaccines that induce a better protection than natural infection have the potential to increase the reinfection threshold, and therefore constitute interventions with a surprisingly high capacity to reduce infection where reduction is most needed.     

Potential Effects of Climate Warming on Fish Habitats in Temperate Zone Lakes with Special Reference to Lake 239 of the Experimental Lakes Area (ELA), North-Western Ontario

We used simple statistics (e.g. mean temperature, degree days, cumulative volume days) to describe present thermal habitats for cool water (yellow perch, Perca flavescens) and cold water (lake trout, Salvelinus namaycush) fish of a small boreal lake. We then modelled changes in the vertical and temporal extent of these habitats under various scenarios of climatic change that included increases in air temperature of 2°C, 4°C, and 9°C, and positive and negative deviations from present levels of 10% in solar radiation and relative humidity, and 20% in wind speed and the lake water extinction coefficient. Model simulations indicated pronounced changes in the temporal and vertical availability of fish thermal niche space. These changes were mainly driven by the large increases in mean mixed layer temperatures that corresponded to 85% of the increases in air temperature, but, in particular, changes in light attenuation also resulted in some non-linear, unexpected effects in the distribution and seasonal availability of thermal niche space. As expected, classical lake trout thermal habitat (5–15°C) was progressively reduced and almost disappeared in littoral areas in spring and early summer. Perch thermal niche space expanded for air temperature increases of up to 4°C, but largely disappeared for the 9°C increase. We discuss changes in thermal habitat with regard to the life history of lake trout and yellow perch, and include other determinants of fish habitat to evaluate the potential of these species for long-term ecological success under climatic warming.     

基于多源遥感数据的景观格局及预测研究

以TM、中巴资源卫星和环境与灾害监测预报小卫星等遥感影像为数据源,利用ENVI 4.7、ARCGIS 9.2、IDRISI 15等软件,研究了西安市辖区的景观特征与空间格局,预测了未来的景观变化,提出了景观格局预测的数据转化和多距离空间分析的精简步骤.结果表明:研究区的景观本底是一个由林地和耕地构成的复合景观基质,建设用地在研究时段内呈现持续增加趋势,且2004-2011年间的增加量高于2000-2004年间的增加量;林地面积略有降低,林地和草地总面积略呈增长趋势,水域和未利用地面积变化较小.研究时段内的景观破碎化程度在降低,林地景观的连通性增强了,耕地的降低了.各景观类型在所设定的最大预期研究尺度下均呈现显著的聚集空间格局;各年和各景观类型之间的聚集、随机和离散的临界阈值差别相对比较大;水域和未利用地的空间聚集强度明显高于耕地、林地、草地和城乡建设用地;耕地和草地空间分布存在一个异质性最大的特征尺度,且均出现了聚集分布、随机分布和离散分布3种分布格局,以2011年最为明显.利用景观指数法和多距离空间聚类分析方法研究景观格局特征的效果要比单一的景观指数法较理想.CA-Markov模型模拟的结果基本能够反映未来的景观格局状况.     

家域研究进展

家域是动物行为学和保护生物学的重要概念之一,它在动物对资源环境的适应与选择,种群密度及社会关系等生态学过程研究中有着重要的作用.对家域的内涵、特征、估算方法(包括取样方法,样本含量,位点数据自相关,模型评价等)等方面进行阐述,总结了家域估算模型的发展过程及发展方向,评述了3种主要家域估算模型的优势与不足,并结合最新的理论和应用,对未来的研究方向提出建议.     

基于Holdridge和CCA分析的中国生态地理分区的比较

在前人工作基础上,对中国自然地理要素与生态地理区域的关系进行了综合分析,采用全国地形、土壤、气候、植被及遥感植被指数等数据,综合分析中国范围生态地理区域的分异规律,制订了生态地理分区的初步方案,并建立了相应的地理信息系统.基于Holdridge模型和CCA分析划分中国生态地理分区,建立了分区的指标体系,得到中国生态分区的大致界线,初步总结了各生态地理分区的地形、植被、气候等综合自然地理特征,完成对中国区域生态地理分区的划分.基于CCA分析的生态地理的分区,不仅结合自然区划和生态地理两种方法,而且加入了生态群落和遥感数据的综合应用.结果显示,由于受到模型适用性及数据误差的原因,基于CCA分析的结果比Holdridge模型的结果更合理一些.     

Gene delivery by lentivirus vectors

The capacity to efficiently transduce nondividing cells, shuttle large genetic payloads, and maintain stable long-term transgene expression are attributes that have brought lentiviral vectors to the forefront of gene delivery vehicles for research and therapeutic applications in a clinical setting. Our discussion initiates with advances in lentiviral vector development and how these sophisticated lentiviral vectors reflect improvements in safety, regarding the prevention of replication competent lentiviruses (RCLs), vector mobilization, and insertional mutagenesis. Additionally, we describe conventional molecular regulatory systems to manage gene expression levels in a spatial and temporal fashion in the context of a lentiviral vector. State of the art technology for lentiviral vector production by transient transfection and packaging cell lines are explicitly presented with current practices used for concentration, purification, titering, and determining the safety of a vector stock. We summarize lentiviral vector applications that have received a great deal of attention in recent years including the generation of transgenic animals and the stable delivery of RNA interference molecules. Concluding remarks address some of the successes in preclinical animals, and the recent transition of lentiviral vectors to human clinical trials as therapy for a variety of infectious and genetic diseases.     

Production, purification and partial enzymatic and molecular characterization of a laccase from the wood-rotting ascomycete Xylaria polymorpha

The hard wood-colonizing ascomycete Xylaria polymorpha, that is seemingly lacking peroxidases, produces laccase as sole ligninolytic oxidoreductase. The fungus secreted the enzyme preferably during the growth in complex media based on tomato juice. Addition of 2,5-xylidine considerably stimulated laccase production (up to 14,000 U l⁻¹). The enzyme was purified to homogeneity by anion exchange and size exclusion chromatography and characterized by biochemical and molecular methods. Xylaria laccase has a molecular mass of 67 kDa, a pI of 3.1 and an absorption maximum at 605 nm that is characteristic for blue copper proteins. It oxidized all typical laccase substrates including ABTS, 2,6-dimethoxyphenol, guaiacol as well as syringaldazine (catalytic efficiencies 3 × 10³ to 7 × 10⁴ M⁻¹ s⁻¹). The deduced amino acid sequence of one amplified laccase gene sequence between the copper binding regions 1 and 3 showed a high level of identity to some other laccases from ascomycetes. Furthermore, the sequence of an internal peptide fragment of the purified laccase was identical with an amino acid sequence deduced from the nucleotide sequence of the laccase gene. Xylaria laccase was found to oxidize a non-phenolic β-O-4 lignin model compound in presence of 1-hydroxybenzotriazole into the corresponding keto-form. The results of this study show that – in addition to ligninolytic basidiomycetes – also wood-dwelling ascomycetes can produce high titers of laccase that may be involved in the oxidation of lignin.