Display and analysis of electrophysiological data under WindowsMMM

Conclusion Windows represents an attractive environment in which to implement a data analysis program. This environment benefits from a number of tools and programs that allow manipulation and analysis data interactively. Windows also has networking facilities that enable analysis of data from any microcomputer connected to the network. This approach leads to more efficient use of electrophysiological set-ups. Object-oriented development tools provide new opportunities to develop applications for neuroscientists and should facilitate sharing independently designed algorithms.     

Web-based applications for building, managing and analysing kinetic models of biological systems

Mathematical modelling and computational analysis play an essentialrole in improving our capability to elucidate the functionsand characteristics of complex biological systems such as metabolic,regulatory and cell signalling pathways. The modelling and concomitantsimulation render it possible to predict the cellular behaviourof systems under various genetically and/or environmentallyperturbed conditions. This motivates systems biologists/bioengineers/bioinformaticiansto develop new tools and applications, allowing non-expertsto easily conduct such modelling and analysis. However, amonga multitude of systems biology tools developed to date, onlya handful of projects have adopted a web-based approach to kineticmodelling. In this report, we evaluate the capabilities andcharacteristics of current web-based tools in systems biologyand identify desirable features, limitations and bottlenecksfor further improvements in terms of usability and functionality.A short discussion on software architecture issues involvedin web-based applications and the approaches taken by existingtools is included for those interested in developing their ownsimulation applications.      

Transposon tools: worldwide landscape of intellectual property and technological developments

DNA transposons are considered to be good candidates for developing tools for genome engineering, insertional mutagenesis and gene delivery for therapeutic purposes, as illustrated by the recent first clinical trial of a transposon. In this article we set out to highlight the interest of patent information, and to develop a strategy for the technological development of transposon tools, similar to what has been done in many other fields. We propose a patent landscape for transposon tools, including the changes in international patent applications, and review the leading inventors and applicants. We also provide an overview of the potential patent portfolio for the prokaryotic and eukaryotic transposons that are exploited by spin-off companies. Finally, we discuss the difficulties involved in tracing relevant state-of-the-art of articles and patent documents, based on the example of one of the most promising transposon systems, including all the impacts on the technological development of transposon tools.     

环境微生物宏基因组学研究中的生物信息学方法

高通量测序技术的发展促进了组学技术在环境微生物研究中的广泛应用,而宏基因组学是目前最为关键和成熟的组学方法。生物信息学在微生物宏基因组学研究中具有至关重要的作用。它贯穿于宏基因组学的数据收集和存储、数据处理和分析等各个阶段,既是宏基因组学推广的最大瓶颈,也是目前宏基因组学研究发展的关键所在。本文主要介绍和归纳了目前在高通量宏基因组测序中常用的生物信息学分析平台及其重要的信息分析工具。未来几年之内,测序成本的下降和测序深度的增加将进一步增大宏基因组学研究在数据存储、数据处理和数据挖掘层面的难度,因此相应生物信息学技术与方法的研究和发展也势在必行。近期内我们应该首先加强基础性分析和存储平台的建设以方便普通环境微生物研究者使用,同时针对目前生物信息分析的瓶颈步骤和关键任务重点突破,逐步发展。     

Alternative reagents to antibodies in imaging applications

Antibodies have been indispensable tools in molecular biology, biochemistry and medical research. However, a number of issues surrounding validation, specificity and batch variation of commercially available antibodies have prompted research groups to develop novel non-antibody binding reagents. The ability to select highly specific monoclonal non-antibody binding proteins without the need for animals, the ease of production and the ability to site-directly label has enabled a wide variety of applications to be tested, including imaging. In this review, we discuss the success of a number of non-antibody reagents in imaging applications, including the recently reported Affimer.     

A reliable epoxy resin mixture and its application in routine biological transmission electron microscopy

Although there are many papers in the literature on materials and procedures for the embedding of tissue for transmission electron microscopy (TEM), most recent publications have emphasized techniques for specialized applications. Although these may in many cases also be suitable for routine applications in addition to the specialized applications for which they were developed, this may not be clear from the literature. This paper describes the formulation and suggested procedures for the use of an epoxy resin mixture which has been routinely used by novice and experienced workers with success for a wide variety of biological TEM investigations in a multi-user multi-disciplinary EM facility. Results are given of the use of this embedding medium in the investigation of a variety of tissue types.     

Genomic tools and cDNA derived markers for butterflies

The Lepidoptera have long been used as examples in the study of evolution, but some questions remain difficult to resolve due to a lack of molecular genetic data. However, as technology improves, genomic tools are becoming increasingly available to tackle unanswered evolutionary questions. Here we have used expressed sequence tags (ESTs) to develop genetic markers for two Müllerian mimic species, Heliconius melpomene and Heliconius erato. In total 1363 ESTs were generated, representing 330 gene objects in H. melpomene and 431 in H. erato. User-friendly bioinformatic tools were used to construct a nonredundant database of these putative genes (available at http://www.heliconius.org), and annotate them with blast similarity searches, InterPro matches and Gene Ontology terms. This database will be continually updated with EST sequences for the Papilionideae as they become publicly available, providing a tool for gene finding in the butterflies. Alignments of the Heliconius sequences with putative homologues derived from Bombyx mori or other public data sets were used to identify conserved PCR priming sites, and develop 55 markers that can be amplified from genomic DNA in both H. erato and H. melpomene. These markers will be used for comparative linkage mapping in Heliconius and will have applications in other phylogenetic and genomic studies in the Lepidoptera.     

Vibrio natriegens: an ultrafast-growing marine bacterium as emerging synthetic biology chassis

The marine bacterium Vibrio natriegens is the fastest-growing non-pathogenic bacterium known to date and is gaining more and more attention as an alternative chassis organism to Escherichia coli. A recent wave of synthetic biology efforts has focused on the establishment of molecular biology tools in this fascinating organism, now enabling exciting applications – from speeding up our everyday laboratory routines to increasing the pace of biotechnological production cycles. In this review, we seek to give a broad overview on the literature on V. natriegens, spanning all the way from its initial isolation to its latest applications. We discuss its natural ecological niche and interactions with other organisms, unveil some of its extraordinary traits, review its genomic organization and give insight into its diverse metabolism – key physiological insights required to further develop this organism into a synthetic biology chassis. By providing a comprehensive overview on the established genetic tools, methods and applications we highlight the current possibilities of this organism, but also identify some of the gaps that could drive future lines of research, hopefully stimulating the growth of the V. natriegens research community.     

Hybrid Models and Biological Model Reduction with PyDSTool

The PyDSTool software environment is designed to develop, simulate, and analyze dynamical systems models, particularly for biological applications. Unlike the engineering application focus and graphical specification environments of most general purpose simulation tools, PyDSTool provides a programmatic environment well suited to exploratory data- and hypothesis-driven biological modeling problems. In this work, we show how the environment facilitates the application of hybrid dynamical modeling to the reverse engineering of complex biophysical dynamics; in this case, of an excitable membrane. The example demonstrates how the software provides novel tools that support the inference and validation of mechanistic hypotheses and the inclusion of data constraints in both quantitative and qualitative ways. The biophysical application is broadly relevant to models in the biosciences. The open source and platform-independent PyDSTool package is freely available under the BSD license from http://sourceforge.net/projects/pydstool/. The hosting service provides links to documentation and online forums for user support.     

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope prediction methods depends on a community consensus on the data and metrics utilized to develop and evaluate such tools. A workshop, sponsored by the National Institute of Allergy and Infectious Disease (NIAID), was recently held in Washington, DC to discuss the current state of the B-cell epitope prediction field. Many of the currently available tools were surveyed and a set of recommendations was devised to facilitate improvements in the currently existing tools and to expedite future tool development. An underlying theme of the recommendations put forth by the panel is increased collaboration among research groups. By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools.     

XmMol: An X11 and motif program for macromolecular visualization and modeling

XmMol is a desktop tool designed to provide both interactive molecular graphics on X11 displays and easy interface with external applications. A kernel provides an interactive wire-frame display of macromolecules. It supports depth cueing, 3D clipping, and stereo. Various representations, coloring, and labeling modes are proposed. Docking and interactive back-bone deformation tools are also supported. Communication protocols allow the user to develop new external features or to use XmMol as a visualization tool for external numerical programs.     

In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells

Regulation of protein activity is central to the complexity of life. The ability to regulate protein activity through exogenously added molecules has biotechnological/biomedical applications and offers tools for basic science. Such regulation can be achieved by establishing a means to modulate the specific activity of the protein (i.e. allostery). An alternative strategy for intracellular regulation of protein activity is to control the amount of protein through effects on its production, accumulation, and degradation. We have previously demonstrated that the non-homologous recombination of the genes encoding maltose binding protein (MBP) and TEM1 β-lactamase (BLA) can result in fusion proteins in which β-lactamase enzyme activity is allosterically regulated by maltose. Here, through use of a two-tiered genetic selection scheme, we demonstrate that such recombination can result in genes that confer maltose-dependent resistance to β-lactam even though they do not encode allosteric enzymes. These 'phenotypic switch' genes encode fusion proteins whose accumulation is a result of a specific interaction with maltose. Phenotypic switches represent an important class of proteins for basic science and biotechnological applications in vivo.     

计算系统生物学:理论、方法及在药物研发中的应用

计算系统生物学是一个多学科交叉的新兴领域,旨在通过整合海量数据建立其生物系统相互作用的复杂网络。数据的整合和模型的建立需要发展合适的数学方法和软件工具,这也是计算系统生物学的主要任务。生物系统模型有助于从整体上理解生物体的内在功能和特性。同时,生物网络模型在药物研发中的应用也越来越受到制药企业以及新药研发机构的重视,如用于特异性药物作用靶点的预测和药物毒性评估等。该文简要介绍计算系统生物学的常见网络和计算模型,以及建立模型所用的研究方法,并阐述其在建模和分析中的作用及面临的问题和挑战。     

Expert systems and the pancreatic cancer problem: decision support in the pre-operative diagnosis

In this paper, after reviewing the main issue in artificial intelligence, decision support systems, medical decision-making, expert systems and some of their applications in medicine, we focus on the diagnostic aspect of pancreatic cancer. We briefly examine the most significant applications both from the oncological and from the diagnostic point of view. We discuss the medical problems mentioning incidence and mortality, aetiological factors and diagnosis, considering the roles of surgery and adjuvant therapies. Finally we justify the decision to develop an expert system in such a medical domain and discuss the SPES (Surgical Pancreatic Expert System) project, its parts dealing with the different medical phases of pancreatic cancer diagnosis and therapy: pre-operative, intra-operative and adjuvant therapies. In particular we discuss diagnostic aspects of pancreatic cancer disease, pointing out the aims of the project, methodologies, tools used and future developments.     

Proteomics in reproductive biology: Beacon for unraveling the molecular complexities

Proteomics, an interface of rapidly evolving advances in physics and biology, is rapidly developing and expanding its potential applications to molecular and cellular biology. Application of proteomics tools has contributed towards identification of relevant protein biomarkers that can potentially change the strategies for early diagnosis and treatment of several diseases. The emergence of powerful mass spectrometry-based proteomics technique has added a new dimension to the field of medical research in liver, heart diseases and certain forms of cancer. Most proteomics tools are also being used to study physiological and pathological events related to reproductive biology. There have been attempts to generate the proteomes of testes, sperm, seminal fluid, epididymis, oocyte, and endometrium from reproductive disease patients. Here, we have reviewed proteomics based investigations in humans over the last decade, which focus on delineating the mechanism underlying various reproductive events such as spermatogenesis, oogenesis, endometriosis, polycystic ovary syndrome, embryo development. The challenge is to harness new technologies like 2-DE, DIGE, MALDI-MS, SELDI-MS, MUDPIT, LC–MS etc., to a greater extent to develop widely applicable clinical tools in understanding molecular aspects of reproduction both in health and disease.     

Brave new (strept)avidins in biotechnology

Avidin and streptavidin are widely used in (strept)avidin-biotin technology, which is based on their tight biotin-binding capability. These techniques are exceptionally diverse, ranging from simple purification and labeling methods to sophisticated drug pre-targeting and nanostructure-building approaches. Improvements in protein engineering have provided new possibilities to develop tailored protein tools. The (strept)avidin scaffold has been engineered to extend the existing range of applications and to develop new ones. Modifications to (strept)avidins--such as simple amino acid substitutions to reduce biotin binding and alter physico-chemical characters--have recently developed into more sophisticated changes, including chimeric (strept)avidins, topology rearrangements and stitching of non-natural amino acids into the active sites. In this review, we highlight the current status in genetically engineered (strept)avidins and illustrate their versatility as advanced tools in the multiple fields of modern bioscience, medicine and nanotechnology.     

Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities

Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host–bacterial interface.     

Protein structural analysis as a tool for protein design

The analysis of known protein structures is a very valuable and indispensable tool for deciphering the complex rules relating sequence to structure in proteins. On the other hand, the design of novel proteins is certainly the most severe test of our understanding of such rules. In this report we describe our own attempt to develop appropriate tools for the investigation of known protein structure properties and their applications to the design of a novel, all β protein. The success of the design project is a demonstration of the usefulness of careful analysis of the data base of known protein structures. © 1994 John Wiley & Sons, Inc.     

Broadening the application of evolutionarily based genetic pest management

Insect- and tick-vectored diseases such as malaria, dengue fever, and Lyme disease cause human suffering, and current approaches for prevention are not adequate. Invasive plants and animals such as Scotch broom, zebra mussels, and gypsy moths continue to cause environmental damage and economic losses in agriculture and forestry. Rodents transmit diseases and cause major pre- and postharvest losses, especially in less affluent countries. Each of these problems might benefit from the developing field of Genetic Pest Management that is conceptually based on principles of evolutionary biology. This article briefly describes the history of this field, new molecular tools in this field, and potential applications of those tools. There will be a need for evolutionary biologists to interact with researchers and practitioners in a variety of other fields to determine the most appropriate targets for genetic pest management, the most appropriate methods for specific targets, and the potential of natural selection to diminish the effectiveness of genetic pest management. In addition to producing environmentally sustainable pest management solutions, research efforts in this area could lead to new insights about the evolution of selfish genetic elements in natural systems and will provide students with the opportunity to develop a more sophisticated understanding of the role of evolutionary biology in solving societal problems.