合成生物学中不依赖限制性内切酶的分子克隆策略

随着合成生物学的兴起和发展,基因克隆和DNA大片段组装成为了常规操作。利用人工智能和液体操作机器人进行高通量的DNA组装和功能筛选已被广泛应用。传统的依赖于限制性内切酶识别位点的克隆技术对序列有选择性、步骤繁琐、实验人员的培训周期长,不利于以流水线形式进行工程化使用,已经逐步在生物工程领域内被淘汰。文中论述了一系列适于机械化操作的新一代分子克隆技术,即不依赖基因序列和连接反应克隆方法、Gibson组装、聚合酶环形延伸克隆、细胞裂解物体外无痕连接和细胞体内组装克隆。对这些方法的建立、基本原理及应用前景等方面进行了总结,并对其优缺点进行了比较。     

Miniaturization of polymerase chain reaction

Polymerase chain reaction (PCR) is one of the most widely used analytical tool and is an important module that would benefit from being miniaturized and integrated onto diagnostic or analytical chips. There are potentially two different approaches for the miniaturization of the PCR module: chamber-type and flow-type micro-PCR. These miniaturized PCRs have distinct characteristics and advantages. In this article, we review the necessity of micro-PCR, the materials for the chip fabrication, the surface modification, and characteristics of the two types of micro-PCR. The motivation underlying the development of micro-PCR, the advantages and disadvantages of the various materials used in fabrication and the surface modification methods will be discussed. And finally, the precise features of the two different types of micro-PCR will be compared.     

Chemical language models for de novo drug design: Challenges and opportunities

Generative deep learning is accelerating de novo drug design, by allowing the generation of molecules with desired properties on demand. Chemical language models – which generate new molecules in the form of strings using deep learning – have been particularly successful in this endeavour. Thanks to advances in natural language processing methods and interdisciplinary collaborations, chemical language models are expected to become increasingly relevant in drug discovery. This minireview provides an overview of the current state-of-the-art of chemical language models for de novo design, and analyses current limitations, challenges, and advantages. Finally, a perspective on future opportunities is provided.     

A component-based software environment for visualizing large macromolecular assemblies

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.     

A guide to the genomics of ecological speciation in natural animal populations

Interest in ecological speciation is growing, as evidence accumulates showing that natural selection can lead to rapid divergence between subpopulations. However, whether and how ecological divergence can lead to the buildup of reproductive isolation remains under debate. What is the relative importance of natural selection vs. neutral processes? How does adaptation generate reproductive isolation? Can ecological speciation occur despite homogenizing gene flow? These questions can be addressed using genomic approaches, and with the rapid development of genomic technology, will become more answerable in studies of wild populations than ever before. In this article, we identify open questions in ecological speciation theory and suggest useful genomic methods for addressing these questions in natural animal populations. We aim to provide a practical guide for ecologists interested in incorporating genomic methods into their research programs. An increased integration between ecological research and genomics has the potential to shed novel light on the origin of species.     

Semantic Web Service provision: a realistic framework for Bioinformatics programmers

Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework ('MobyServlet') that very simply allows an existing Java application to conform to the MOBY-S semantic Web Services protocol. Using an existing Java program for codon-pair bias determination as an example, we enumerate the steps required for MOBY-S compliance. With minimal programming effort, such a deployment has the advantages of: (1) wider exposure to the user community by automatic inclusion in all MOBY-S client programs and (2) automatic interoperability with other MOBY-S services for input and output. Complex on-line analysis will become easier for biologists as more developers adopt MOBY-S. AVAILABILITY: The framework and documentation are freely available from the Java developer's section of http://www.biomoby.org/.     

Supervisory control theory applied to swarm robotics

Currently, the control software of swarm robotics systems is created by ad hoc development. This makes it hard to deploy these systems in real-world scenarios. In particular, it is difficult to maintain, analyse, or verify the systems. Formal methods can contribute to overcome these problems. However, they usually do not guarantee that the implementation matches the specification, because the system’s control code is typically generated manually. Also, there is cultural resistance to apply formal methods; they may be perceived as an additional step that does not add value to the final product. To address these problems, we propose supervisory control theory for the domain of swarm robotics. The advantages of supervisory control theory, and its associated tools, are a reduction in the amount of ad hoc development, the automatic generation of control code from modelled specifications, proofs of properties over generated control code, and the reusability of formally designed controllers between different robotic platforms. These advantages are demonstrated in four case studies using the e-puck and Kilobot robot platforms. Experiments with up to 600 physical robots are reported, which show that supervisory control theory can be used to formally develop state-of-the-art solutions to a range of problems in swarm robotics.     

A general robot control system for automatic chemical analysis

Advances in instrumentation have led to increasing interest in automatic chemical analyses. Unfortunately, the potential flexibility of robot systems can often not be exploited because of complex programming languages and poor user-interface. These factors generally limit the use of laboratory robots to a few repetitive tasks. This paper describes the development of a general robot control system for automatic chemical analysis. The program is written in Turbo Pascal and Visual Basic and runs in the Microsoft Windows environment. The analytical workspace is designed by selection of an object's icon followed by its desired orientation. Positioning of this object is then performed using a ‘drag and drop’ procedure. The robotic procedure is set-up by selection of items of apparatus and their associated actions. The performance of the system is demonstrated by the determination for caffeine in tablet formulations using a continuous dilution and calibration scheme.     

阵列光镊与微流控芯片技术的结合与应用

在生物医学研究领域中,阵列光镊与微流控芯片的结合已经成为进行细胞操纵、转移以及少量细胞样品分选等方面最有希望的方法之一。光镊技术对样品具有非接触弹性控制、无机械损伤、可无菌操作等优势,以及微流控芯片分析的高效、多功能、微型化、低成本等优势,成为芯片实验室(Lab-on-a-Chip)的重要研究方面。该文概述了阵列光镊技术的形成与研究现状以及微流控芯片技术的发展与应用现状,分析了在不同阵列光镊形成方法下结合微流控芯片可实现的功能与应用,并对其发展趋势进行了展望。     

Uridine natural products: Challenging targets and inspiration for novel small molecule inhibitors

Nucleoside derivatives, in particular those featuring uridine, are familiar components of the nucleoside family of bioactive natural products. The structural complexity and biological activities of these compounds have inspired research from organic chemistry and chemical biology communities seeking to develop novel approaches to assemble the challenging molecular targets, to gain inspiration for enzyme inhibitor development and to fuel antibiotic discovery efforts. This review will present recent case studies describing the total synthesis and biosynthesis of uridine natural products, and de novo synthetic efforts exploiting features of the natural products to produce simplified scaffolds. This research has culminated in the development of complementary strategies that can lead to effective uridine-based inhibitors and antibiotics. The strengths and challenges of the juxtaposing methods will be illustrated by examining select uridine natural products. Moreover, structure–activity relationships (SAR) for each natural product-inspired scaffold will be discussed, highlighting the impact on inhibitor development, with the aim of future uridine-based small molecule expansion.     

Component Partitioning Under Demand and Capacity Uncertainty in Printed Circuit Board Assembly

This paper considers the problem of configuring a printed circuit board (PCB) assembly line experiencing uncertainty in demand and capacity. The PCB assembly process involves a single line of automatic placement machines, a variety of board types, and a number of component types. The line is set up only once, at the beginning of a production cycle, to eliminate setups between board types. Using this strategy, the line therefore can assemble all different types of PCBs without feeder changes. The problem then becomes to partition component types to the different machines in the hope of processing all boards quickly with a good workload balance. In this paper, the board demands and machine breakdowns are random but follow some probability distribution, which can be predicted from past observations of the system. We formulate this problem as a stochastic mixed-integer programming formulation with the objective of minimizing the expected makespan for assembling all PCBs during a production cycle. The results obtained indicate significant improvement over the existing methods. We hope that this research will provide more PCB assembly facilities with models and techniques to hedge against variable forecasts and capacity plans     

Phase4: automatic evaluation of database search methods

It has become standard to evaluate newly devised database search methods in terms of sensitivity and selectivity and to compare them with existing methods. This involves the construction of a suitable evaluation scenario, the execution of the methods, the assessment of their performances, and the presentation of the results. Each of these four phases and their smooth connection usually imposes formidable work. To relieve the evaluator of this burden, a system has been designed with which evaluations can be effected rapidly. It is implemented in the programming language Python whose object-oriented features are used to offer a great flexibility in changing the evaluation design. A graphical user interface is provided which offers the usual amenities such as radio- and checkbuttons or file browsing facilities.     

Quantitative analysis of DNA array autoradiographs

DNA arrays and chips are powerful new tools for gene expression profiling. Current arrays contain hundreds or thousands of probes and large scale sequencing and screening projects will likely lead to the creation of global genomic arrays. DNA arrays and chips will be key in understanding how genes respond to specific changes of environment and will also greatly assist in drug discovery and molecular diagnostics. To facilitate widespread realization of the quantitative potential of this approach, we have designed procedures and software which facilitate analysis of autoradiography films with accuracy comparable to phosphorimaging devices. Algorithms designed for analysis of DNA array autoradiographs incorporate 3-D peak fitting of features on films and estimation of local backgrounds. This software has a flexible grid geometry and can be applied to different types of DNA arrays, including custom arrays.     

An efficient algorithm for minimal primer set selection

SUMMARY: We have developed U-PRIMER, a primer design program, to compute a minimal primer set (MPS) for any given set of DNA sequences. The U-PRIMER algorithm, which uses automatic variable fixing and automatic redundant constraint elimination to tackle the binary integer programming problem associated with the MPS selection problem. The program has been tested successfully with 32 adipocyte development-related genes and 9 TB-specific genes to obtain their respective MPSs. AVAILABILITY: A free copy of U-PRIMER implemented in C++ programming language is available from http://www.u-vision-biotech.com     

Technical issues in using robots to reproduce joint specific gait

Reproduction of the in vivo motions of joints has become possible with improvements in robot technology and in vivo measuring techniques. A motion analysis system has been used to measure the motions of the tibia and femur of the ovine stifle joint during normal gait. These in vivo motions are then reproduced with a parallel robot. To ensure that the motion of the joint is accurately reproduced and that the resulting data are reliable, the testing frame, the data acquisition system, and the effects of limitations of the testing platform need to be considered. Of the latter, the stiffness of the robot and the ability of the control system to process sequential points on the path of motion in a timely fashion for repeatable path accuracy are of particular importance. Use of the system developed will lead to a better understanding of the mechanical environment of joints and ligaments in vivo.     

Word sense disambiguation in the biomedical domain: an overview.

There is a trend towards automatic analysis of large amounts of literature in the biomedical domain. However, this can be effective only if the ambiguity in natural language is resolved. In this paper, the current state of research in word sense disambiguation (WSD) is reviewed. Several methods for WSD have already been proposed, but many systems have been tested only on evaluation sets of limited size. There are currently only very few applications of WSD in the biomedical domain. The current direction of research points towards statistically based algorithms that use existing curated data and can be applied to large sets of biomedical literature. There is a need for manually tagged evaluation sets to test WSD algorithms in the biomedical domain. WSD algorithms should preferably be able to take into account both known and unknown senses of a word. Without WSD, automatic metaanalysis of large corpora of text will be error prone.     

蛋白质点阵/芯片技术的新进展

蛋白质点阵/芯片技术是分子生物学技术的重要进展,在功能蛋白质组研究方面具有广阔的潜在应用价值.目前发展起来的印迹蛋白微阵列、分子扫描技术和传感器生物芯片质谱,将应用于药靶检测、疾病诊断、蛋白质结构鉴定和/或蛋白质之间的相互作用分析等方面,具有分析速度快、效率高、样品消耗少等特点,将成为生命科学与医学领域新的研究工具.     

筛选差异表达基因方法的新进展

了解不同细胞或同类细胞在不同发育阶段、不同生理状态下的基因表达状况,可以为研究生命活动过程提供重要信息。以差别筛选、削减杂交等基本方法为出发点,研究基因表达差异的方法不断完善,先后出现了DDRT—PCR、RDA、SSH、cDNA微阵列(基因芯片)、基因表达的系统分析(SAGE)等技术。本着重对这些方法的优缺点及改进进行论述和评介,并对技术的发展趋势进行了分析。     

几种新型生物芯片的研究进展

随着生物芯片技术的迅速发展,一些新型生物芯片,如生物电子芯片、凝胶元件微阵列芯片、药物控释芯片、毛细管电泳或层析芯片、PCR芯片及生物传感芯片等应运而生,这些芯片不同于常规的分子微阵列芯片,而是以各种结构微阵列为基础,用于分子杂交与扩增,以检测突变、分析多态性及测序,通过电泳及层析分离生物样品,控制药物释放以治疗疾病,作为生物传感器检测分子行为等,具有分析速度快、效率高、样品消耗少等特点,将成为生命科学与医学领域的新工具.