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.     

What makes a mitochondrion?

Experimental analyses of the proteins found in the mitochondria of yeast, humans and Arabidopsis have confirmed some expectations but given some surprises and some insights into the evolutionary origins of mitochondrial proteins.     

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.     

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.     

About the theory of competing species

We review some typical features of the dynamics of systems of competing species, described by the Lotka-Volterra equations and give some new results concerning the coexistence of many species and the linear stability of equilibrium states. We also commenton some types of asymptotic behaviors for three-dimensional systems.     

Antibacterial substances from lichens

Crude extracts of many lichens and some lichen acids have considerable antibacterial activity, suggesting their possible value in chemotherapy and providing some justification for their folk-lore use in some countries against pulmonary disorders.     

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.     

On the HIV Incubation Distribution Under AZT Treatment

Assuming some general models for the HIV epidemic, in this paper I derive the HIV incubation distributions under AZT treatment. It is shown that under some conditions, these probability distributions are mixtures of some generalized Gamma distributions and products of generalized Gamma distributions.     

蜜露对天敌昆虫生长繁殖及搜寻行为的影响

已有研究表明:同翅目昆虫蜜露对一些天敌昆虫有着特殊的作用。一方面,蜜露可用来补充营养,从而促进天敌若虫死亡率下降、成虫寿命延长以及繁殖力提高;另一方面,蜜露作为天敌搜寻行为的信息物质。而人工蜜露在很多情况下对部分天敌也具有上述2方面的作用。文章就此内容的研究进展作一概述,以期促进蜜露在天敌昆虫人工饲养、害虫综合防治以及其他方面发挥作用。     

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.     

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,     

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.     

高阶线性泛函方程解的振动性

考虑一类高阶线性泛函方程解的振动性,我们获得一些新的振动准则.这些振动准则,推广或改进了一些文献中的某些结果.     

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.     

RANUNCULALES ‐ BUTTERCUPS,POPPIES AND THEIR RELATIVES

Lardizabalaceae belong to the well‐circumscribed order Ranunculales. Here we summarise modern knowledge about the relationships between the seven families in the order, some of which have major horticultural and agricultural importance. They include many familiar garden plants, some major weeds, some important and controversial crop plants and sources of medicines and poisons.     

具有放牧率的某些概周期生态模型

文［１］研究了具有放牧率的周期生态模型的周期解的存在性、唯一性与稳定性等问题．本文考虑更加广泛的生态模型,即具有放牧率的概周期生态系统的概周期解的存在性、稳定性,通过利用指数型二分性和不动点方法,得到一些新结果．     

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.     

Histochemical and electrophoretic studies of lactate dehydrogenase (LDH/E.C. 1.1.1.27/) activity in the rat liver following the administration of Biseptol 480 (co-trimoxazole)

The present experiments are stimulated by some reports suggesting disturbances in the liver metabolism after application of Biseptol 480. 10 a ago, Biseptol has been widely used in the treatment of some inflammatory states of the respiratory and urinary systems, the alimentary canal, the genitals, and of some bacterial skin infection. The examinations were carried out on 15 white male rats of Wistar strain which were treated by 80 mg of the sulphonamide Biseptol 480 for 7 consecutive days, by stomach tube. Histochemical activity of lactate dehydrogenase (LDH) and isoenzymatic composition of LDH were estimated in the liver's experimental sections. The results show a decrease of LDH activity in the liver tissue and the absence of LDH-5 and LDH-1 fractions in the experimental electrophoregrams. They confirm some authors' supposition of some disturbances in the liver metabolism following application of Biseptol 480.     

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.     

侧根的发生及其激素调控

本文概述了侧根发生及其植物激素调控的研究进展。侧根的发生起源于特定的中柱 鞘细胞,其发生过程可简单地分为侧根发生的起始、侧根原基的形成、侧根分生组织的形成和活化等几个关键时期。参与侧根发生调控的植物激素主要是生长素,它影响到侧根发生过程的各个时期。茉莉酸对侧根的发生也有一定的调控作用。