Tools and collaborative environments for bioinformatics research

Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies.     

Seasonal variation of natural products in European trees

The present review gives an overview about the status of research on seasonal variation of natural products in European trees. Due to their different life forms, gymnosperms, deciduous angiosperms, and evergreen angiosperms are reviewed separately. Besides trying to give an overview about the existing newer literature, the review tries to define some repetitively found trends and discusses some possible explanations for these trends. Moreover, open research questions are highlighted and some suggestions for future studies are given. These suggestions encompass both subjects and desirable quality standards with regards to experimental designs. The reviewed publications are mainly focused on leaves, some on fruits, and some on barks and twigs. Phenolics, including phenolic acids and flavonoids of different types as well as tannins, are the most often studied compound class; additionally, some papers assess seasonal variation of alkaloids, diterpenes, essential oils, lignans, simple organic acid, secoiridoids, and stilbenoids.     

Sequence-based analysis of enzymatically amplified DNA fragments by mutation detection techniques.

The accurate analysis of molecular variation is important in a range of disciplines of parasitology. Although conventional DNA techniques have overcome some of the limitations of traditional approaches, some can be relatively expensive and/or cumbersome to use when large sample sizes require analysis, and some cannot accurately resolve or define nucleotide variation. Using selected examples of applications to parasites, Robin Gasser and Xingquan Zhu discuss some PCR-based mutation detection techniques and their advantages over conventional analytical methods.     

Parallel and nonparallel aspects of ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

Parallel (or convergent) evolution provides strong evidence for a deterministic role of natural selection: similar phenotypes evolve when independent populations colonize similar environments. In reality, however, independent populations in similar environments always show some differences: some nonparallel evolution is present. It is therefore important to explicitly quantify the parallel and nonparallel aspects of trait variation, and to investigate the ecological and genetic explanations for each. We performed such an analysis for threespine stickleback (Gasterosteus aculeatus) populations inhabiting lake and stream habitats in six independent watersheds. Morphological traits differed in the degree to which lake-stream divergence was parallel across watersheds. Some aspects of this variation were correlated with ecological variables related to diet, presumably reflecting the strength and specifics of divergent selection. Furthermore, a genetic scan revealed some markers that diverged between lakes and streams in many of the watersheds and some that diverged in only a few watersheds. Moreover, some of the lake-stream divergence in genetic markers was associated within some of the lake-stream divergence in morphological traits. Our results suggest that parallel evolution, and deviations from it, are primarily the result of natural selection, which corresponds in only some respects to the dichotomous habitat classifications frequently used in such studies.     

蛋白质晶体的优化生长

蛋白质晶体的优化生长是获得高质量蛋白质晶体, 进而得到高精度晶体结构的有效途径.针对不同的晶体生长方法,已尝试了不同的优化手段,这对改善某些蛋白质晶体的质量显示了明显的成效.然而,鉴于蛋白质晶体生长的多样性与复杂性,这些方面均未发展成为实用的技术.文章综述了这类研究进展,分析了各手段的利弊,并指出了应着重解决的问题.     

Neuropsychology: time out of mind.

We have always known that some form of clock is needed to measure time. It now seems that a variety of different neural clocks are involved in determining our temporal perceptions, some specialised for shorter and some for longer durations.     

A practical guide to molecular dating

Molecular dating has now become a common tool for many biologists and considerable methodological improvements have been made over the last few years. However, the practice of estimating divergence times using molecular data is highly variable among researchers and it is not straightforward for a newcomer to the field to know how to start. Here I provide a brief overview of the current state-of-the-art of molecular dating practice. I review some of the important choices that must be made when conducting a divergence time analysis, including how to select and use calibrations and which relaxed clock model and program to use, with a focus on some practical aspects. I then provide some guidelines for the interpretation of results and briefly review some alternatives to molecular dating for obtaining divergence times. Last, I present some promising developments for the future of the field, related to the improvement of the calibration process.     

Modeling the Citation Network by Network Cosmology

Citation between papers can be treated as a causal relationship. In addition, some citation networks have a number of similarities to the causal networks in network cosmology, e.g., the similar in-and out-degree distributions. Hence, it is possible to model the citation network using network cosmology. The casual network models built on homogenous spacetimes have some restrictions when describing some phenomena in citation networks, e.g., the hot papers receive more citations than other simultaneously published papers. We propose an inhomogenous causal network model to model the citation network, the connection mechanism of which well expresses some features of citation. The node growth trend and degree distributions of the generated networks also fit those of some citation networks well.     

Successful Application of Evolutionary Algorithms in Engineering Design

Evolutionary or bionic strategies have proven to be powerful tools in many optimisation studies. Starting with some parent generations, producing sets of children, selecting the best children to be new parents yields impressive improvements of the objective when used with some experience and sufficient equipment. During some years of research the parameters of evolutionary optimisation have been investigated. Many successful applications showed where and how to use it. Especially in the case of objective functions with some or many local maxima, evolutionary approaches may propose solutions which gradient based optimisation would hardly find.When used with a large number of optimisation parameters, evolutionary methods seem to be superior to other strategies, as the chances to find good proposals within an acceptable number of trials and within affordable time are much higher.Nevertheless, evolutionary approaches like all optimisation methods require large numbers of studies of individual solutions. The computer power necessary to apply these strategies should not be underestimated. Even with today low cost and high availability of computers, the time to solve problems may be surprisingly long. So all ways of parallel processing, using single computers with many processors or clusters of many computers may speed up the time to do the optimisation.The basic terms of the method are outlined, some problems discussed, some examples given and some proposals made, how to use evolutionary methods in engineering optimisation. Finally some warnings are given trying to prevent potential users from non-realistic expectations. Optimisation is a difficult and consuming process. This holds for evolutionary optimisation as well.     

转基因抗虫作物对非靶标昆虫的影响

转基因抗虫作物自 1996年被批准商业化种植以来 ,它的抗虫性和经济效益已得到了普遍肯定 ,同时 ,转基因抗虫作物对非靶标生物的影响 ,如转基因抗虫作物的长期种植 ,是否会导致次要害虫上升为主要害虫 ,是否会影响有益昆虫 ,包括重要经济昆虫、捕食性和寄生性天敌以及重要蝶类的种类及种群数量 ,已成为转基因抗虫作物生态风险评估的重要内容。一些研究结果表明 ,转基因抗虫作物在对靶标害虫有效控制的同时 ,一些对杀虫蛋白不敏感的非靶标害虫有加重危害的趋势 ,由于种植转基因抗虫作物 ,减少了化学农药的使用 ,客观上也使非靶标害虫种群数量上升 ,这对转基因抗虫作物害虫综合治理提出了新的要求。靶标害虫数量的减少直接影响了害虫天敌种群数量 ,靶标害虫取食转基因抗虫作物后发育迟缓 ,也间接影响了天敌昆虫的生长发育 ,转基因抗虫作物的花粉或花蜜是一些重要经济昆虫如蜜蜂、熊蜂和一些寄生蜂 ,甚至捕食性天敌的食物来源 ,或花粉飘落到一些鳞翅目昆虫如家蚕或重要蝶类昆虫的寄主植物上 ,直接或间接对这些昆虫造成一定影响。目前大多数研究表明转基因抗虫作物对非靶标昆虫 ,特别是对有益昆虫没有明显的不利影响 ,也有研究报道认为对某些有益昆虫有一定的不良影响。这为深入开展转基因抗虫作物的生态安全     

侵染细胞质膜附近小泡的来源及其作用

箭舌豌豆根瘤幼龄侵染细胞的壁和质膜比较光滑,成熟侵染细胞与此不同,不仅细胞壁厚薄均,有较多的胞间连丝,而且质膜常常内陷形成各种突起,然后离质膜形成小泡。这些位于质膜附近的小泡体积较小,多呈圆形,既可单独存在,也可多个聚在一起。在向细胞中央移动中,有的小泡靠近细胞质膜,甚至与细菌周期融合,有的小泡不民附近的小液泡融合变为较大液泡,并常用降解程度不同的细菌位于其中,在衰老侵染细胞中,细胞壁附近有小泡,     

计算机视觉技术在植物学中的应用

介绍计算机视觉技术的定义、组成系统和发展状况,总结其在植物学中的应用,指出目前存在的问题以及需要重点解决的关键技术,为今后的深入研究提出了一些建议和方向。     

国外防治重症急性呼吸综合征的措施概况

目前重症急性呼吸综合征(SARS)的疫情仍处于不稳定状态,并且呈现蔓延之势,引起了全球的重视。为了有效地控制其流行,打赢与SARS的战争,包括中国在内的许多国家和地区纷纷采取了强有力的预防和治疗措施,竭尽全力将疫情控制在最小的范围之内。本通过介绍世界各国针对SARS所采取的行之有效的反应措施,了解一些相关情况及经验,以开阔我们的眼界,同时冀望对建立和完善我国在突发性传染病、环境灾难以及生化恐怖袭击等公共危机突发事件的应急反应机制上提供借鉴意义。     

Cognitive ability and sentience: which aquatic animals should be protected?

It is of scientific and practical interest to consider the levels of cognitive ability in animals, which animals are sentient, which animals have feelings such as pain and which animals should be protected. A sentient being is one that has some ability to evaluate the actions of others in relation to itself and third parties, to remember some of its own actions and their consequences, to assess risk, to have some feelings and to have some degree of awareness. These abilities can be taken into account when evaluating welfare. There is evidence from some species of fish, cephalopods and decapod crustaceans of substantial perceptual ability, pain and adrenal systems, emotional responses, long- and short-term memory, complex cognition, individual differences, deception, tool use, and social learning. The case for protecting these animals would appear to be substantial. A range of causes of poor welfare in farmed aquatic animals is summarised.     

Neuronal basis of behavior

In addition to describing behavior in terms of neuronal properties and interconnections, some studies are using these well defined neuronal circuits to see how the circuits interact, how they develop, and how they are modified by experience, hormones and neuromodulators. The ready availability of computers and computational techniques has helped in some efforts, as have improvements in physiological and morphological techniques. The major insights, however, still come from experiments that ask clear and direct questions. This review highlights some of the promising approaches and suggests some general features of how neuronal circuits produce behavior.     

我国煤矿矿山医疗救护工作的SWOT分析

运用SWOT方法分析了目前我国矿山医疗救护工作的整体优势，认识到当前矿山医疗救护工作创新能力不足是面临的主要劣势，剖析了创新发展的机遇和一些结构性威胁，并提出了相应的发展策略。     

Is 'big biology' a commercial enterprise?

Big projects in biology - such as the human genome project and a number of related and ensuing enterprises - require big funding. A new tradition is growing in which some types of basic research take place within commercial organizations. This article reviews some of the reasons for this and some of the key players, in the USA, Europe and Japan, and highlights some issues to be considered when deciding whether particular research belongs in a company rather than an academic setting.     

Insects on the brink of a major discontinuity

Population surges and local extinctions are not uncommon among insects. In response to climatic changes in the past, insects have often shifted their ranges. This long-term range shifting and the vagaries of short-term weather makes reserve selection unrealistically rigid for many species. Although some insect species are surviving in reserves, others have disappeared from such small areas because of adverse weather. In contrast, many other insects depend on localized disturbance for survival. In response to anthropogenic disturbance, some native insects have become more abundant and widespread, such as Orthoptera in response to grazing and burning, and some Odonata in response to aquatic weeds and water impoundment. The effect of some exotic invasive insects on some native ecosystems is of major concern. Human-induced insect population crashes and species extinctions are becoming more common and widespread, and exacerbated by the synergistic effect of the various local impacts with global changes. A major insect population and species extinction discontinuity is beginning to take place. Yet, there is also an increase in range and abundance of some other insects. The world is becoming increasingly species-poorer and more homogenous in its insect fauna.     

植物对荒漠生境的趋同适应

植物体的表型特征是其基因与生态因子二者共同作用的结果,生活在荒漠生境中的植物由于遭受相同的自然选择压力,在外部形态、内部结构、生活史特征、生理特性、次生代谢产物的合成以及大分子物质的诱导产生等诸多表型方面均表现出高度趋同的现象。随着研究手段的改善,对植物趋同适应的研究已逐渐深入到了分子水平。研究荒漠生境中植物的趋同适应对于人们深刻地认识和理解植物与环境间的相互关系及其分子基础,以及利用功能基因改良重要作物的抗逆性等将会产生深远的影响;对极端干旱环境下特殊次生代谢产物的定向发现及重要先导化合物的筛选等有着重大的指导意义;同时对我国的西部开发及干旱区的生态恢复亦有重要的参考价值。     

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. III. An evaluation of pectinase and amylase isoenzymes for species characterization

Polyacrylamide gel electrophoresis of extracellular pectinase and amylase isozymes of 170 mainly terverticillate Penicillium strains was undertaken. The data were coded and subjected to numerical analysis. Variation in intensity of isozymes was observed in repeat analyses of some strains, although most were consistent. Variation was also observed between some representative strains of species. P. viridicatum was more variable than P. brevicompactum and P. hordei for intensity of pectinase activity. There was a correlation between the grouping of the strains on the basis of the isozymes and the species concepts only in some cases. The method proved useful for the identification of strains producing intense activity which provided clear patterns, for example, P. brevicompactum and P. chrysogenum and to a lesser extent P. solitum var. crustosum and P. hordei. The method was also exclusionary in that some species were restricted to a particular cluster or subcluster. Amylase patterns confirmed that strains referred to as single species are not all homogeneous genetically, and that some strains are not simply haploid homokaryons. The genetic heterogeneity of the strains explains some of the problems in the systematics of the terverticillate penicillia.