ZFIQ: a software package for zebrafish biology

Rapid development, transparency and small size are the outstanding features of zebrafish that make it as an increasingly important vertebrate system for developmental biology, functional genomics, disease modeling and drug discovery. Zebrafish has been regarded as ideal animal specie for studying the relationship between genotype and phenotype, for pathway analysis and systems biology. However, the tremendous amount of data generated from large numbers of embryos has led to the bottleneck of data analysis and modeling. The zebrafish image quantitator (ZFIQ) software provides streamlined data processing and analysis capability for developmental biology and disease modeling using zebrafish model. AVAILABILITY: ZFIQ is available for download at http://www.cbi-platform.net.     

Estimating evolution of temporal sequence changes: a practical approach to inferring ancestral developmental sequences and sequence heterochrony

Developmental biology often yields data in a temporal context. Temporal data in phylogenetic systematics has important uses in the field of evolutionary developmental biology and, in general, comparative biology. The evolution of temporal sequences, specifically developmental sequences, has proven difficult to examine due to the highly variable temporal progression of development. Issues concerning the analysis of temporal sequences and problems with current methods of analysis are discussed. We present here an algorithm to infer ancestral temporal sequences, quantify sequence heterochronies, and estimate pseudoreplicate consensus support for sequence changes using Parsimov-based genetic inference [PGi]. Real temporal developmental sequence data sets are used to compare PGi with currently used approaches, and PGi is shown to be the most efficient, accurate, and practical method to examine biological data and infer ancestral states on a phylogeny. The method is also expandable to address further issues in developmental evolution, namely modularity.     

系统生物学——生命科学的新领域

系统生物学是继基因组学、蛋白质组学之后一门新兴的生物学交叉学科,代表21世纪生物学的未来.最近,系统生物学研究机构纷纷成立.在研究上,了解一个复杂的生物系统需要整合实验和计算方法.基因组学和蛋白质组学中的高通量方法为系统生物学发展提供了大量的数据.计算生物学通过数据处理、模型构建和理论分析,成为系统生物学发展的一个必不可缺、强有力的工具.在应用上,系统生物学代表新一代医药开发和疾病防治的方向.     

Systems approaches to understanding cell signaling and gene regulation

The age of 'omics' is upon us, and scientific papers that reflect this are starting to appear at an ever-increasing rate. The amount of information generated in any 'omics' program is daunting and often overwhelms plant scientists whose main interests relate to cell or developmental biology. For this revolution in data generation to have any impact in plant signaling studies, we must have great confidence in both the quality of the data and our ability to represent it in ways that are meaningful to general plant biologists. Systems biology has begun to address these issues and to provide examples in which the analysis of large data sets has led to biological insights into cell signaling and gene regulation.     

Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering

Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.     

Time warping of evolutionary distant temporal gene expression data based on noise suppression

Background  

Comparative analysis of genome wide temporal gene expression data has a broad potential area of application, including evolutionary biology, developmental biology, and medicine. However, at large evolutionary distances, the construction of global alignments and the consequent comparison of the time-series data are difficult. The main reason is the accumulation of variability in expression profiles of orthologous genes, in the course of evolution.     

The strategy concept and John Maynard Smith’s influence on theoretical biology

Here we argue that the concept of strategies, as it was introduced into biology by John Maynard Smith, is a prime illustration of the four dimensions of theoretical biology in the post-genomic era. These four dimensions are: data analysis and management, mathematical and computational model building and simulation, concept formation and analysis, and theory integration. We argue that all four dimensions of theoretical biology are crucial to future interactions between theoretical and empirical biologists as well as with philosophers of biology.     

Enhanced CellClassifier: a multi-class classification tool for microscopy images

Background  

Light microscopy is of central importance in cell biology. The recent introduction of automated high content screening has expanded this technology towards automation of experiments and performing large scale perturbation assays. Nevertheless, evaluation of microscopy data continues to be a bottleneck in many projects. Currently, among open source software, CellProfiler and its extension Analyst are widely used in automated image processing. Even though revolutionizing image analysis in current biology, some routine and many advanced tasks are either not supported or require programming skills of the researcher. This represents a significant obstacle in many biology laboratories.     

Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships

Evolutionary developmental biology ("evo-devo") has revolutionized evolutionary biology but has had relatively little impact on systematics. We show that similar large-scale developmental changes in distantly related lineages can dramatically mislead phylogenetic analyses based on morphological data. Salamanders are important model systems in many fields of biology and are of special interest in that many species are paedomorphic and thus never complete metamorphosis. A recent study of higher-level salamander phylogeny placed most paedomorphic families in a single clade based on morphological data. Here, we use new molecular and morphological data to show that this result most likely was caused by the misleading effects of paedomorphosis. We also provide a well-supported estimate of higher-level salamander relationships based on combined molecular and morphological data. Many authors have suggested that paedomorphosis may be problematic in studies of salamander phylogeny, but this hypothesis has never been tested with a rigorous phylogenetic analysis. We find that the misleading effects of paedomorphosis on phylogenetic analysis go beyond the sharing of homoplastic larval traits by paedomorphic adults, and the problem therefore is not solved by simply excluding suspected paedomorphic characters. Instead, two additional factors are critically important in causing paedomorphic species to be phylogenetically "misplaced": (1) the absence of clade-specific synapomorphies that develop during metamorphosis in nonpaedomorphic taxa and allow their "correct" placement and (2) parallel adaptive changes associated with the aquatic habitat of the larval stage. Our results suggest that the effects of paedomorphosis on phylogenetic analyses may be complex, difficult to detect, and can lead to results that are both wrong and statistically well supported by parsimony and Bayesian analyses.     

Evolving strategies for the incorporation of bioinformatics within the undergraduate cell biology curriculum

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum.     

The evolution of molecular biology into systems biology

Systems analysis has historically been performed in many areas of biology, including ecology, developmental biology and immunology. More recently, the genomics revolution has catapulted molecular biology into the realm of systems biology. In unicellular organisms and well-defined cell lines of higher organisms, systems approaches are making definitive strides toward scientific understanding and biotechnological applications. We argue here that two distinct lines of inquiry in molecular biology have converged to form contemporary systems biology.     

Apoptosis: a four-week laboratory investigation for advanced molecular and cellular biology students

Over the past decade, apoptosis has emerged as an important field of study central to ongoing research in many diverse fields, from developmental biology to cancer research. Apoptosis proceeds by a highly coordinated series of events that includes enzyme activation, DNA fragmentation, and alterations in plasma membrane permeability. The detection of each of these phenotypic changes is accessible to advanced undergraduate cell and molecular biology students. We describe a 4-week laboratory sequence that integrates cell culture, fluorescence microscopy, DNA isolation and analysis, and western blotting (immunoblotting) to follow apoptosis in cultured human cells. Students working in teams chemically induce apoptosis, and harvest, process, and analyze cells, using their data to determine the order of events during apoptosis. We, as instructors, expose the students to an environment closely simulating what they would encounter in an active cell or molecular biology research laboratory by having students coordinate and perform multiple tasks simultaneously and by having them experience experimental design using current literature, data interpretation, and analysis to answer a single question. Students are assessed by examination of laboratory notebooks for completeness of experimental protocols and analysis of results and for completion of an assignment that includes questions pertaining to data interpretation and apoptosis.     

Systems chemical biology

The increasing availability of data related to genes, proteins and their modulation by small molecules has provided a vast amount of biological information leading to the emergence of systems biology and the broad use of simulation tools for data analysis. However, there is a critical need to develop cheminformatics tools that can integrate chemical knowledge with these biological databases and simulation approaches, with the goal of creating systems chemical biology.     

组学技术在产油微生物中的应用

微生物油脂是未来燃料和食品用油的重要潜在资源.近年来,随着系统生物学技术的快速发展,从全局角度理解产油微生物生理代谢及脂质积累的特征成为研究热点.组学技术作为系统生物学研究的重要工具被广泛用于揭示产油微生物脂质高效生产的机制研究中,这为产油微生物理性遗传改造和发酵过程控制提供了基础.文中对组学技术在产油微生物中的应用概...     

The molecular evolution of trypanosomes.

The absence of a fossil record has meant that the evolution of protozoa has remained largely a matter for speculation. Recent advances in molecular biology and phylogenetic analysis, however, are allowing the 'history written in the genes' to be interpreted. Here, Jamie Stevens and Wendy Gibson review progress in reconstruction of trypanosome phylogeny based on molecular data from rRNA and protein-coding genes.     

Biology in the secondary science curriculum

The search for a model of balanced science has not so far been based on a detailed analysis of the nature and effects of the science curriculum. The present paper attempts to begin to fill the gap, from the perspective of biology, using data from the Assessment of Perform-ance Unit (APU). It is shown that, in England, the uptake of the subject as an option outstrips that of the other sciences, with pupils quoting its intrinsic interest as their motivation. Biology serves to attract to science pupils of all abilities and girls in particular. The other sciences are not so successful in this sphere. However, performance data show that the study of biology is not as effective in enhancing science performance as are the physical sciences.     

基于空间分析的保护生物学研究

 保护生物学家和生态学家早就认识到只有准确地辨识保护对象的空间位置、 范围、 及其相邻的关系(例如边缘)和连接度, 以及依存的地形和气候等生境条件, 才能发现生物种群和生境在空间的扩散与收缩、 增长与灭绝的动态, 揭示分布的格局, 从而系统、 全面地了解保护对象和生境的存在状态、 破碎程度和变化趋势, 进行有效的自然保护。 得益于新兴的空间分析技术, 保护生物学自20世纪90年代以来取得了很大的进步。基于空间分析的保护生物学研究是最近10年左右大力发展的新保护生物学的重要基础。 该文结合作者的研究工作,综述了基于空间分析的保护生物学项目, 探讨了保护生物学发展历史、 主要研究方法与应用、 以及今后的可能发展趋势。 在生物多样性的丰度和分布的空间解绎部分,通过综述世界保护监测中心的图解全球生物多样性的工作, 如国家尺度的生物多样性水平、 植物多样性的分布中心和维管束植物科的多样性等的空间分布 ,介绍了 Dobson等图示美国主要濒危植物、 鸟类、 鱼类和软体动物等4个主要类群在县(County) 为基本空间单位上分布的空间格局, 讨论了生物多样性空间解绎的意义。在第二部分用世界资源研究所的全球森林监测(Global forest watch)项目, 美国的国家保护缺失区分析(GAP analysis)项目, 美国林务局的无路自然区域(Roadless area)保护项目和加拿大自然审计(Nature audit)项目, 以及北美和东亚生物多样性空间分布的比较分析和生物入侵的空间分析等具体实例来说明生物多样性空间分布变化比较分析方法的应用。 过去20年来, 面向空间格局的生态学和保护生物学研究得到了快速的发展, 特别是空间格局的描述、 由地统计演变而成的空间统计、 地理信息系统、 基于个体(或栅格)的空间解绎模拟模型、 基于斑块(Patch)的种群理论及其发展(如复合种群理论, 源 汇模型等)等。在第三部分, 以美国森林破碎度空间格局分析和美国太平洋西北演替后期森林的空间格局分析为例, 介绍了空间格局分析在保护生物学中的应用。 同时介绍了澳大利亚保护生态学家Lindenmayer 和美国著名景观生态学家Franklin 2002年提出的模板(Matrix)保护理论,把保护的眼光不局限在面积不多而且分散的保护区中,应注意景观模板和保护区相邻的原生区域的综合保护, 这样将大大扩展保护的范围, 并且平衡保护与发展的关系。最后, 介绍了在保护生物学中已有一定应用的空间模型和模拟, 包括了空间解绎模型(Spatial explicit model)、 基于过程(Process-based)的空间模拟模型、 面向代理(Agent-based)的空间适应模拟模型(SWAM)以及与此有关的动态全球植被模型(DGVM)。 通过上面的讨论和综述, 预测一个新的保护生物学的分支: 空间保护生物学, 已经逐渐成熟问世, 这门基于现代信息技术和空间技术的新学科已经而且还将为全球生物多样性的研究和保育作出重大的贡献。