Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes

Our environment is stressed with a load of heavy and toxic metals. Microbes, abundant in our environment, are found to adapt well to this metal-stressed condition. A comparative study among five Cupriavidus/Ralstonia genomes can offer a better perception of their evolutionary mechanisms to adapt to these conditions. We have studied codon usage among 1051 genes common to all these organisms and identified 15 optimal codons frequently used in highly expressed genes present within 1051 genes. We found the core genes of Cupriavidus metallidurans CH34 have a different optimal codon choice for arginine, glycine and alanine in comparison with the other four bacteria. We also found that the synonymous codon usage bias within these 1051 core genes is highly correlated with their gene expression. This supports that translational selection drives synonymous codon usage in the core genes of these genomes. Synonymous codon usage is highly conserved in the core genes of these five genomes. The only exception among them is C. metallidurans CH34. This genomewide shift in synonymous codon choice in C. metallidurans CH34 may have taken place due to the insertion of new genes in its genomes facilitating them to survive in heavy metal containing environment and the co-evolution of the other genes in its genome to achieve a balance in gene expression. Structural studies indicated the presence of a longer N-terminal region containing a copper-binding domain in the cupC proteins of C. metallidurans CH3 that helps it to attain higher binding efficacy with copper in comparison with its orthologs.     

捕食者有无限时滞效应的两种群系统的全局渐近稳定性

本文用Liapunov泛函方法研究捕食者有无限时滞效应的捕食-被捕食系统的平衡状态的稳定性．文章提供了判定系统的平衡状态全局渐近稳定的简单条件,不要求积分核指数衰减.     

The unusually slow relaxation kinetics of the folding-unfolding of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus

In order to understand the thermodynamic and kinetic basis of the intrinsic stability of proteins from hyperthermophiles, the folding-unfolding reactions of cysteine-free pyrrolidone carboxyl peptidase (Cys142/188Ser) (PCP-0SH) from Pyrococcus furiosus were examined using circular dichroism (CD) and differential scanning calorimetry (DSC) at pH 2.3, where PCP-0SH exists in monomeric form. DSC showed a strong dependence of the shape and position of the unfolding profiles on the scan rate, suggesting the stability of PCP-0SH under kinetic control. On DSC timescales, even at a scan rate of 1 deg. C/hour, heat denaturation of PCP-0SH was non-equilibrium. However, over a long period of incubation of the heat-denatured PCP-0SH at pre-transition temperatures, it refolded completely, indicating reversibility with very slow relaxation kinetics. The rates of refolding of the heat-denatured PCP-0SH determined from the time-resolved DSC and CD spectroscopic progress curves were found to be similar within experimental error, confirming the mechanism of refolding to be a two-state process. The equilibrium established with a relaxation time of 5080 seconds (at t(m)=46.5 degrees C), which is unusually higher than the relaxation times observed for mesophilic and hyperthermophilic proteins. The long relaxation time may lead to the apparent irreversibility of an unfolding process occurring on the DSC experiment timescale. The refolding rate (9.8 x 10(-5) s(-1)) peaked near the t(m) (=46.5 degrees C), whereas the stability profile reached maxima (11.8 kJ mol(-1)) at 17 degrees C. The results clearly indicate the unusual mode of protein destabilization via a drastic decrease in the rate of folding at low pH and still maintaining a high activation energy barrier (284 kJ mol(-1)) for unfolding, which provides an effective kinetic advantage to unusually stable proteins from hyperthermophiles.     

金钟藤入侵群落的种间联结及生态位特征

金钟藤(Decalobanthus boisianus)是林业有害植物, 其暴发生长和扩散对森林生态系统造成了严重破坏。本文以海南岛48个金钟藤典型分布群落为研究对象, 用方差比率法和贡献定律法探究群落的稳定性; 用χ ²统计量、联结系数(AC)、共同出现百分率(PC)、Ochiai指数和Dice指数分析金钟藤与伴生物种的种间联结关系; 用生态位宽度、生态位相似性系数和生态位重叠指数研究群落中各物种的生态位特征, 以期为金钟藤生物防治的植物物种筛选提供借鉴。结果表明: (1)金钟藤所在48个群落共有156种伴生植物, 其中大戟科、茜草科、桑科、无患子科和樟科植物占优势; (2)群落中优势物种呈正联结关系, 植物种类累积倒数百分比与累积相对频度交点坐标为(44.53, 55.47), 远离稳定交点坐标(20, 80), 说明群落处于不稳定状态; (3)金钟藤与芳槁润楠(Machilus suaveolens)、黄椿木姜子(Litsea variabilis)、岭南山竹子(Garcinia oblongifolia)、显脉杜英(Elaeocarpus dubius)、鸭脚木(Schefflera octophylla)和银柴(Aporusa dioica)都紧密关联, 说明金钟藤与这些物种的资源利用方式较相似; (4)金钟藤的生态位宽度最大, 与伴生物种间的生态位重叠度较高, 但伴生物种间的生态位重叠度较低。金钟藤的入侵导致群落处于不稳定状态, 并与伴生物种间存在激烈的竞争关系。因此, 建议在金钟藤已入侵的群落中大量栽种芳槁润楠、黄椿木姜子、显脉杜英、鸭脚木和银柴, 以遏制其蔓延; 大量栽种翻白叶树(Pterospermum heterophyllum)、海南菜豆树(Radermachera hainanensis)、九节(Psychotria rubra)和肉实树(Sarcosperma laurinum)用于金钟藤入侵群落的植被恢复。     

Carbon isotopic record of terrestrial ecosystems spanning the Late Miocene extinction of Oreopithecus bambolii, Baccinello Basin (Tuscany, Italy)

Oreopithecus bambolii is a Late Miocene hominoid with an extensive fossil record in the Baccinello Basin (Tuscany, Italy), and was the only western European hominoid to survive a major extinction event ca. 9.6 Ma (millions of years ago). Oreopithecus lived in the insular Tusco-Sardinian paleobioprovince, where it evolved many unique anatomical specializations that make it important for understanding the mechanisms and history of Late Miocene hominoid evolution. The eventual extinction of Oreopithecus and its associated fauna ca. 6.5 Ma has generally been attributed to interaction with species that arrived from continental Europe following tectonic collision of the Tusco-Sardinian province with mainland Italy, but palynological, paleontological, and sedimentological records indicate an environmental shift toward more variable climate across the extinction event.To explore the possibility of environmental change as a contributing factor in the extinction of Oreopithecus, we developed a stable carbon and oxygen isotope record from organic matter in paleosols from the Baccinello Basin. These data show very low temporal and spatial variability (indicating plant ecosystem stability through time and space) and provide no evidence for ecologically significant changes in floral composition spanning the extinction event, suggesting that environmental change was not an underlying cause for the extinction of Oreopithecus and its associated fauna. The carbon isotope values fall entirely within the range of isotopic variability for modern plants following the C₃ photosynthetic pathway (trees, shrubs, cool-season grasses), indicating that C₄ vegetation (warm-season grasses) was not an important component of biomass. When corrected for temporal variation in the carbon isotopic composition of atmospheric carbon dioxide, the paleosol carbon isotope values are consistent with predicted values based on modern plants and the Baccinello palynoflora, supporting the reliability of paleosol isotopic records as paleoecological proxies.     

基于物种多样性与生物量关系的草地群落稳定性对全球变暖的响应研究进展

全球变暖背景下物种多样性和生物量的空间变化格局及其对温度升高的响应是生态学研究的热点内容,是探究群落稳定性响应全球变暖的关键.物种分布是多个生态过程相互作用的产物,温度升高通过改变群落关键种的作用影响物种多样性,从而改变群落稳定性.关于草地群落稳定性对全球变暖的响应过程,国内外学者的相关研究存在很大差异.该文作者结合自...     

A broad range of Fab stabilities within a host of therapeutic IgGs

Although the functional properties of IgGs are well known, little has been published concerning the stability of whole IgG molecules. Stability is, however, a requirement for the development of antibodies for therapeutic or diagnostic applications. The hypervariable antigen-binding region (Fv) is responsible for stability variations between IgGs of identical subclass. To determine the range of stabilities that may be expected for human(ized) antibodies, differential scanning calorimetry was performed on 17 human(ized) antibodies from various in-house programs. The antigen-binding fragments (Fabs) of these antibodies exhibited thermal unfolding transitions with midpoints (T(M)s) varying from 57 to 82 degrees C. Antibodies with very low Fab stabilities were found to aggregate and express poorly. Fab instability was often associated with high levels of uncommonly observed amino acids or CDR loop lengths particularly within the variable heavy chain domain. Overall, the study provides a thermostability range for IgGs and suggests possible stability guidelines for developing antibody diagnostics or therapeutics.     

Exploring the interplay of stability and function in protein evolution

A new split β‐lactamase assay promises experimental testing of the interplay of protein stability and function. Proteins are sufficiently stable to act effectively within cells. However, mutations generally destabilize structure, with effects on free energy that are comparable to the free energy of folding. Assays of protein functionality and stability in vivo enable a quick study of factors that influence these properties in response to targeted mutations. These assays can help molecular engineering but can also be used to target important questions, including why most proteins are marginally stable, how mutations alter structural makeup, and how thermodynamics, function, and environment shape molecular change. Processes of self‐organization and natural selection are determinants of stability and function. Non‐equilibrium thermodynamics provides crucial concepts, e.g., cells as emergent energy‐dissipating entities that do work and build their own parts, and a framework to study the sculpting role of evolution at different scales.     

The effect of falling height on muscle activity and foot motion during landings

The aims of this study were: (a) to examine the effect of falling height on the kinematics of the tibiotalar, talonavicular and calcaneocuboid joints and (b) to study the influence of falling height on the muscle activity of the leg during landings. Six female gymnasts (height: 1.63±0.04 m, weight: 58.21±3.46 kg) participated in this study. All six gymnasts carried out barefoot landings, falling from 1.0, 1.5 and 2.0 m height onto a mat. Three genlocked digital high speed video cameras (250 Hz) captured the motion of the left shank and foot. Surface electromyography (EMG) was used to measure muscle activity (1000 Hz) from five muscles (gastrocnemius medialis, tibialis anterior, peroneus longus, vastus lateralis and hamstrings) of the left leg. The kinematics of the tibiotalar, talonavicular and calcaneocuboid joints were studied. The lower-leg and the foot were modelled by means of a multi-body system, comprising seven rigid bodies. The falling height does not show any influence on the kinematics neither of the tibiotalar nor of the talonavicular joints during landing. The eversion at the calcaneocuboid joint increases with increasing falling height. When augmenting falling height, the myoelectric activity of the muscles of the lower limb increases as well during the pre-activation phase as during the landing itself. The muscles of the lower extremities are capable of stabilizing the tibiotalar and the talonavicular joints actively, restricting their maximal motion by means of a higher activation before and after touchdown. Maximal eversion at the calcaneocuboid joint increases about 52% when landing from 2.0 m.