分子系统学分析平台的建立和应用

分子系统学建立在实验和计算的基础之上。DNA快速测序技术的普及为分子系统学家提供了大量数据，而序列分析技术则是探索数据发现知识的重要工具。在基因组时代，随着大量模式生物完整基因组序列的获得，分子系统学正面临着前所未有的机遇和挑战。一方面，生命之树计划有助于确定新的模式生物和开展相应的基因组计划;另一方面，模式生物的基因组计划有助于阐明它们之间的进化关系和基因组的进化模式。更为重要的是，分子系统学序列分析技术已经发展成为探索与整合基因组数据的强有力工具，从而在生命科学中发挥重要作用。事实上，分子系统学和基因组学的相互渗透正在形成一门崭新的交叉学科——系统发育基因组学。 为了奠定分子系统学研究中信息管理和数据分析工作的坚实基础，我们建立了分子系统发育分析平台。该平台为研究人员提供专业数据库服务和数据分析技术支持，以及相关的网络资源。 分子系统发育分析平台包括了3个专业数据库。第一个是DNA凭证标本数据库。该数据库中的记录包括了7项字段：英文科名、中文科名、物种拉丁名、采集人、采集号、采集地和采集时间。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括3491条标本记录。第二个是引物数据库。PCR引物是分子系统学实验的重要条件之一。该数据库中的记录包括3项字段：引物名称、序列内容和退火温度。用户可以通过设定单个或多个字段的取值进行检索。截止2004年6月1日，该数据库共包括170条用于扩增植物细胞核、叶绿体和线粒体基因组DNA序列的引物记录。第三个是生物计算数据库。该数据库为研究人员提供传输和保存序列分析数据和结果文件的服务。 为了确保数据库的安全性和使用性，我们开发了数据库的接口和检索工具，以及系统管理员和用户资格认证程序。通过前者，使用者可以进行数据的上传、下载、管理和检索等操作。而后者则是对不同使用者身份和权限进行设定。管理员的权限高于用户，主要负责本系统的日常维护和管理工作，以及对新增管理员和用户进行资格认证。 分析技术支持旨在帮助用户快速掌握常用的系统发育分析方法，进行有效的数据分析，从复杂的统计学算法和计算机程序中解放出来，将精力集中于计算结果的生物学解释。在该部分中，我们首先简要介绍了常用的分析方法，并且针对分子系统学中的不同问题提供了相应的解决方案。这些问题包括：系统发育重建、替代速率和分歧时间的估计、祖先分布区的重建、性状进化假说的检验、以及密码子水平适应性进化的检测。我们特别强调了似然比检验和贝叶斯推测作为方法论上的重要进展在分子系统学中所发挥的关键作用。本部分还包括大量常用的分子系统学程序或软件包及其快速使用说明和命令模块。下载安装之后，用户即可按照说明使用命令模块进行数据分析。 此外，该平台还提供了一些常用的网络资源地址，如生物信息中心、分子进化和系统发育实验室、专业期刊和相关数据库等。 最后还给出了4个应用实例，即针对特定分子系统学问题的解决方案和初步的分析结果。 第一个例子说明系统发育重建方法的应用。为了确定杨梅科的系统学位置，对6种DNA序列和叶绿体trnL-F区内的间隔性状进行了分析。单个分析表明这6种序列之间在系统学信息上存在显著差异。叶绿体基因组序列的合并分析强烈支持杨梅科和（木麻黄科，（桦木科，核果桦科））的姐妹群关系，而间隔性状的存在能够充分提高其分辨率和支持率。 第二个例子说明如何推测历史生物地理学过程。我们对壳斗目8科25属植物叶绿体基因组的trnL-F、matK、rbcL和atpB的合并序列进行了最大简约分析，得到唯一的最大简约树。基于该系统树和25属植物的地理分布数据，采用扩散－替代分析方法重建了系统树每个节点上的祖先分布区，推测了壳斗目的分布历史。结果表明，壳斗目的历史生物地理学过程由3次替代事件和20次扩散事件组成。其中最重要的替代事件是由于冈瓦纳大陆和劳亚大陆分离所导致的南青冈科及其姐妹群之间的分化。另外，在壳斗科和核心高等金缕梅类中多次发生从欧亚大陆到北美洲、甚至南美洲的平行扩散事件。 第三个例子说明如何估计分歧时间。我们仍然使用扩散－替代分析中所用的最大简约树作为分析的依据，并根据等级制似然比检验确定的最优替代模型对该系统树的支长进行了最大似然优化。似然比检验表明，该系统树不服从分子钟假说。我们以冈瓦纳大陆和劳亚大陆分离的地质事件和5个属的最早化石记录作为标定点，采用罚分似然法在没有分子钟的条件下估计了壳斗目的科间分歧时间。结果表明，绝大多数科间分歧事件都发生在白垩纪。 第四个例子说明如何检测密码子水平的适应性进化。分支间可变选择压力模型的似然比检验表明SARS冠状病毒的S基因在跨种传播过程中发生了正选择。

Discovery of immune related factors in Fenneropenaeus chinensis by annotation of ESTs

A total of 10446 expressed sequence tags (ESTs) are obtained by a large-scale sequencing of a cDNA library from cephalothorax of adult Fenneropenaeus chinensis. An EST analysis platform was built up based on local computers and bioinformatic techniques were used to annotate these ESTs in order to promptly find possible functional genes, especially for immune related factors. About 4% of the ESTs show similarity to the coding sequences of such factors, including lectin, serine protease, serpin, lysozyme, etc. These ESTs provide a partial profile of the immune system in F. chinensis and useful information for further study on these genes.

Finite Element Analysis of Deformed Legs of Offshore Platform Structures

The element stiffness matrix of the equivalent beam or pipe element of the deformed leg of the platform is derived by the finite element method. The stresses and displacements of some damaged components are calculated, and the numeri-cal solutions agree well with those obtained by the fine mesh finite element method. Finally, as an application of this method, the stresses of some platform structures are calculated and analyzed.

Hill Instability Analysis Of Tlp Tether Subjected To Combined Platform Surge And Heave Motions

This paper presents the Hill instability analysis of Tension Leg Platform (TLP) tether it, deep sea. The 2-D nonlinear beam model which is Undergoing Coupled axial and transverse vibrations, is applied. The governing equations are reduced to nonlinear Hill equation by use of the Galerkin's method and the modes superposition principle. The Hill instability charted Lip to large parameters is obtained. An important parameter M is defined and can he expressed as the functions of tether length, the platform surge and heave motion amplitudes. Some example studies are performed for various environmental conditions. The results demonstrate that the nonlinear coupling between the axial and transverse vibrations has a significant effect on the response of structure.. It needs to be considered for the accurate dynamic analysis of long TLP tether subjected to the combined platform surge and heave motions.

Nonlinear analysis of pile foundation jacket platform

In this paper, the nonlinear collapse of the BOHAI-8 pile foundation jacket platform has been analyzed. The ultimate load and collapse process of two computational models of the structure are given. One model is of fixed support whose length is eight times the pile leg diameter and the other considers the nonlinearity of the soil-pile interaction.

Governing Equations and Numerical Solutions of Tension Leg Platform with Finite Amplitude Motion

It is demonstrated that when tension leg platform (TLP) moves with finite amplitude in waves, the inertia force, the drag force and the buoyancy acting on the platform are nonlinear functions of the response of TLP. The tensions of the tethers are also nonlinear functions of the displacement of TLP. Then the displacement, the velocity and the acceleration of TLP should be taken into account when loads are calculated. In addition, equations of motions should be set up on the instantaneous position. A theoretical model for analyzing the nonlinear behavior of a TLP with finite displacement is developed, in which multifold nonlinearities are taken into account, i.e., finite displacement, coupling of the six degrees of freedom, instantaneous position, instantaneous wet surface, free surface effects and viscous drag force. Based on the theoretical model, the comprehensive nonlinear differential equations are deduced. Then the nonlinear dynamic analysis of ISSC TLP in regular waves is performed in the time domain. The degenerative linear solution of the proposed nonlinear model is verified with existing published one. Furthermore, numerical results are presented, which illustrate that nonlinearities exert a significant influence on the dynamic responses of the TLP.

Nonlinear Dynamic Response of Tension Leg Platform

Tension Leg Platform (TLP) is a typical compliant offshore structure for oil exploitation in deep water. Most of the existing mathematical models for analyzing the dynamic response of TLP are based on explicit or implicit assumptions that displacements (translations and rotations) are small magnitude. Herein a theoretical method for analyzing the nonlinear dynamic behavior of TLP with finite displacement is developed, in which multifold nonlinearities are taken into account, i.e. finite displacement, coupling of the six degrees of freedom, instantaneous position, instantaneous wet surface, free surface effects and viscous drag force. Using this theoretical model, we perform the numerical analysis of dynamic response of a representative TLP. The comparison between the degenerative linear solution of the proposed nonlinear model and the published one shows good agreements. Furthermore, numerical results are presented which illustrate that nonlinearities exert a distinct influence on the dynamic responses of the TLP.

Experimental Research On Fatigue Property Of Steel Rubber Vibration Isolator For Offshore Jacket Platform In Cold Environment

Jacket platform is the most widely used offshore platform. Steel rubber vibration isolator and damping isolation system are often used to reduce or isolate the ice-induced and seismic-induced vibrations. The previous experimental and theoretical studies concern mostly with dynamic properties, vibration isolation schemes and vibration-reduction effectiveness analysis. In this paper, the experiments on steel rubber vibration isolator were carried out to investigate the compressive properties and fatigue properties in different low temperature conditions. The results may provide some guidelines for design of steel rubber vibration isolator for offshore platform in a cold environment, and for maintenance and replacement of steel rubber vibration isolator, and also for fatigue life assessment of the steel rubber vibration isolator. (C) 2009 Elsevier Ltd. All rights reserved.

Nonlinear Dynamic Responses of Tension Leg Platform with Slack-Taut Tether

The slack-taut state of tether is a particular Averse circumstance, which may influence the normal operation stale of tension leg platform (TLP). The dynamic responses of TLP with slack-taut tether are studied with consideration of several nonlinear factors introduced by large amplitude motions. The time histories of stresses of tethers of a typical TLP in slack-taut state are given. In addition, the sensitivities of slack to stiffness and mass are investigated by varying file stiffness of tether and mass of TLP. It is found that slack is sensitive to the mass of TLP. The critical culled surfaces (over which indicates the slack) for the increase of mass are obtained.

Nafion-graphene nanocomposite film as enhanced sensing platform for ultrasensitive determination of cadmium

In this work, an ultrasensitive platform for the detection of cadmium (Cd2+) combining the nafion-graphene nanocomposite film with differential pulse anodic stripping voltammetry (DPASV) analysis was presented. It is found that this sensing platform exhibits enhanced response to the determination of the Cd2+ and has been used to determine the Cd2+ in real sample with good recovery.

Microfluidic devices for the analysis of apoptosis

Apoptosis is the outcome of a metabolic cascade that results in cell death in a controlled manner. Due to its important role in maintaining balance in organisms, in mechanisms of diseases, and tissue homeostasis, apoptosis is of great interest in the emerging fields of systems biology. Research into cell death regulation and efforts to model apoptosis processes have become powerful drivers for new technologies to acquire ever more comprehensive information from cells and cell populations. The microfluidic technology promises to integrate and miniaturize many bioanalytical processes, which offers an alternative platform for the analysis of apoptosis. This review aims to highlight the recent developments of microfluidic devices in measuring the hallmarks as well as the dynamic process of cellular apoptosis. The potential capability and an outlook of microfluidic devices for the study of apoptosis are addressed.