Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

Transdermal enhancement through rat skin of luciferase plasmid DNA loaded in elastic nanovesicles

Transdermal absorption of luciferase plasmid (pLuc) was enhanced by loading in elastic cationic liposomes and niosomes and the application of iontophoresis or the stratum corneum (SC) stripping method. Cationic liposomes (DPPC/Chol/DDAB at a 1:1:1 molar ratio) and niosomes (Tween61/Chol/DDAB at a 1:1:0.5 molar ratio) were prepared by the freeze-dried empty liposomes method. The elastic vesicles were prepared by hydrating the lipid or surfactant film by 25% of ethanol instead of distilled water. Gel electrophoresis of all nanovesicles showed the 100% pLuc entrapment efficiency. All nanovesicles loaded with pLuc showed larger vesicular sizes than the nonloaded vesicles of about 1.4 times for liposomes and 1.7 times for niosomes. The nanovesicles loaded with pLuc demonstrated less positive zeta potential than the nonloaded vesicles. The pLuc loaded in elastic vesicles kept at 4 ± 2 and 27 ± 2°C for 8 weeks gave the remaining pLuc of about 70 and 60% for liposomes and 85 and 73% for niosomes, respectively. For nonelastic vesicles kept at 4 ± 2°C, 56 and 61% of the remaining pLuc were observed for liposomes and niosomes, respectively, while at 27 ± 2°C, all pLuc were degraded. The deformability indices of the elastic liposomes and niosomes loaded with the pLuc were 16.64 ± 2.92 and 20.72 ± 0.82, whereas the nonelastic vesicles gave 9.35 ± 0.09 and 10.08 ± 0.12, respectively. Transdermal absorption through rat skin pretreated with SC stripping or treated with iontophoresis of pLuc loaded in nanovesicles by vertical Franz diffusion cells was investigated at 37°C. The cells were stopped and the skin and the receiving solution were withdrawn at 1, 3, and 6 hours and the pLuc contents in the stripped SC, whole skin (viable epidermis and dermis; VED), and the receiving solution were assayed by the modified gel electrophoresis and gel documentation. Without the SC stripping technique or iontophoresis, the pLuc loaded and nonloaded in nonelastic cationic liposomes or niosomes were not found in SC, VED, and receiving solution. The fluxes in the whole skin of pLuc loaded in nonelastic liposomes and niosomes with SC stripping and iontophoresis at 6 hours gave 2.73 ± 0.46 and 3.83 ± 0.73, and 7.01 ± 1.22 and 9.60 ± 1.31 g/cm²/h, respectively, while pLuc loaded in elastic liposomes and niosomes without the SC stripping and iontophoresis at 6 hours showed 2.79 ± 0.09 and 2.84 ± 0.04 g/cm²/h, respectively. The pLuc loaded in elastic niosomes or in nonelastic niosomes with iontophoresis was found in the receiving solution with a higher amount than that loaded in elastic liposomes or nonelastic liposomes with iontophoresis. The fluxes in the receiving solution of pLuc loaded in nonelastic liposomes and niosomes with iontophoresis at 6 hours were 6.71 ± 0.31 and 8.82 ± 0.28 g/cm²/h, respectively. For elastic liposomes and niosomes, the fluxes of the loaded pLuc in the receiving solution were the same, at about 1.9 g/cm²/h. Although pLuc loaded in nonelastic niosomes with iontophoresis gave the highest delivery of the plasmid in VED and receiving solution, a more promising applicable approach for gene delivery has been suggested to be the elastic niosomal systems, since no equipment is required.     

Hierarchical Perception of Stimuli During Case Construction in the Bagworm Moth Eumeta crameri (Lepidoptera: Psychidae)

We studied case construction behavior of bagworm moth, Eumeta crameri (Lepidoptera: Psychidac) in the host plant, Acacia nilotica, at two sites. At the time of the study, Site A had 1-year-old A. nilotica saplings only, whereas Site B had full grown trees. The larva of bagworm moth used either thorns or cut-twigs or both as the materials for building its case. It renovated its case three times, and during each instance it increased the volume of its case by replacing older thorns or cut-twigs by newer and longer ones. However, it exhibited a spectacular predilection for thorns, irrespective of the sites, during the first-instar stage of its development. Thereafter, at Site A it used exclusively cut-twigs, whereas at Site B it preferably used thorns provided they were available in the range of the required length and within the threshold distance. It appears that the bagworm has an ability to process thorn length and distance signals hierarchically to fulfill its priority, that is, case building. Thus it optimizes time and energy expenditures during the period of its larval growth leading to pupation by toggling its preference between thorns and cut-twigs.     

蛋白质相互作用数据库及其应用

对蛋白质相互作用及其网络的了解不仅有助于深入理解生命活动的本质和疾病发生的机制，而且可以为药物研发提供靶点.目前，通过高通量筛选、计算方法预测和文献挖掘等方法,获得了大批量的蛋白质相互作用数据，并由此构建了很多内容丰富并日益更新的蛋白质相互作用数据库.本文首先简要阐述了大规模蛋白质相互作用数据产生的3种方法，然后重点介绍了几个人类相关的蛋白质相互作用公共数据库，包括HPRD、BIND、 IntAct、MINT、 DIP 和MIPS，并概述了蛋白质相互作用数据库的整合情况以及这些数据库在蛋白质相互作用网络构建上的应用.     

基于生态位构建的n-种群集合种群动态分析

生态位构建是指任何有机体具有的对环境的修复作用,其可能对集合种群的动态与分布产生深刻的影响.尝试性的将生态位构建概念引入集合种群的续存与动态这一复杂问题的研究中,建立了具有生态位构建作用的多物种集合种群的数学模型.模拟结果表明:随着生态位构建能力的增强,种群的续存能力和平衡态大小都有所增加;在此过程中,生态序的变化具有一定的规律性,分别呈现灭绝数为零的 1、 3、 5、 7和 9的协同演化.     

Collagen gene construction and evolution

Summary Collagen genes appear to have been assembled by the tandem repetition of homologous primary (9 base pair), secondary (54 base pair), and tertiary (702 base pair) modules. In vertebrate interstitial collagen genes many of the secondary modules are separated by introns, but in invertebrate collagen genes the non-coding sequences lie near the ends of supposed tertiary modules and are therefore about 702 (54×13) base pairs apart. The genes for vertebrate interstitial collagens (types I–III) seem to have been constructed by the tandem repetition of five tertiary modules, three of which were subsequently shortened by internal deletions. This shortening of the gene resulted in the non-integral relationship between the period of the fibrils and the length of the molecules of vertebrate collagens, and was therefore responsible for the mechanical properties of the completed product. Comparisons of the amino acid sequences of various collagens indicate that the main types of collagen evolved about 800–900 million years ago, a date that agrees well with the fossil record of primitive Metazoa.     

The plant cell pressure probe

The pressure probe is a micro manometer for the simultaneous direct recording and manipulation of plant cell hydrostatic pressure. It is used to map in space and time the turgor pressures of individual cells within tissues and organs of intact plants. This is used to study the hydraulic architecture of tissues, tissue movement and the responses of tissues to water stress. The approach can be augmented by simultaneous measurement of individual cell osmotic pressure. This permits the hydraulic driving forces across selectively permeable membranes and walls to be assessed fully. By manipulating manually the pressure, cell wall elasticity and its properties can also be mapped. Under some conditions this can be extended to plastic behaviour.     

Uses and Conservation of Plant Species in a National Park—A Case Study of Ben En, Vietnam

Uses and Conservation of Plant Species in a National Park—A Case Study of Ben En, Vietnam. This paper surveys the use of wild and cultivated plants by local people in Ben En National Park, Vietnam, and analyzes its impact on the conservation status of some of the utilized species. A total of 208 species used for a range of nonmedicinal purposes are listed. See Hoang et al. (2008a) for 230 medicinal plants used in the park. Most species are used for food. The use of plants contributes very significantly to the livelihood of local people in the park, but the current use patterns are not sustainable and would lead to local extinction of rare and endangered species if no additional conservation measures are introduced. Men collect nonmedicinal plants more often than women. A total of 38 useful plant species are commercialized, and contribute 12% of the average income of individual households. Bamboo shoots of Schizostachyum funghomii (Poaceae) are the most important for income generation. The monetary equivalent of noncommercialized useful plants probably far exceeds the value of the traded plant products. Plant use is independent of the ethnicity of the different populations living in the park. Larger households make use of a greater variety of useful plant species than small families. Abundant species in the forest have a higher use index (UI) than less common species. Out of the 208 useful species, as many as 27 were found to be endangered locally, many more than the 11 or 8 endangered species included in national or global red lists. Currently, useful plants, especially important timber trees, are more abundant in the less disturbed parts of the park, far away from the villages, indicating the pressures of illegal logging and harvesting near villages on the ecosystems.     

用海建设项目海洋生态损失补偿评估方法及应用

海洋生态补偿是一种防止海洋生态破坏、增强和促进海洋生态系统良性发展的环境政策,是用海者履行海洋资源有偿使用责任,对因开发利用海洋资源造成的海洋生态价值损失进行的货币化补偿。基于快速化、定量化和差别化补偿评估原则,编制了山东近海海域生态价值基准值表、生态损害系数表以及补偿系数表,建立了一种新的用海建设项目海洋生态损失补偿评估方法体系,包括占用海域和邻近影响海域的海洋生物资源和海洋生态系统服务两个方面的海洋生态价值损失补偿评估。针对2016年山东省5个典型用海项目,核算了其需要缴纳的海洋生态补偿资金,并与旧标准《山东省海洋生态损害赔偿和损失补偿评估方法》(DB37/T 1448—2009)的评估结果进行了对比。结果表明,按照本评估方法,用海企业需要缴纳的生态补偿资金会不同程度地提高,这将有利于用海企业增强资源有偿使用意识,引导企业理性用海,市场经济条件下这有利于海洋资源的优化配置,提高用海效率;另外,按照产业政策不同、受影响海域的生态脆弱性不同对用海建设项目造成的海洋生态损失进行差别化补偿,使得海洋生态补偿标准的评估结果更加科学合理。目前,该方法已经应用于山东海域7个沿海地市9个海区的海洋生态损失补偿评估中,被新发布的山东省地方标准《用海建设项目海洋生态损失补偿评估技术导则》(DB37/T 1448—2015)吸收采用。该评估方法可为海洋管理部门的生态资本核算、生态补偿核算、环评审批和发放许可证提供科学基础,对我国海洋生态环境保护和海洋经济绿色发展以及生态补偿制度实施具有积极推动作用。