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.     

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.     

Error catastrophe in and the evolution of the protein synthesizing machinery

The theory of the propagation of errors in the system of enzymes translating genetic information proposed earlier is developed further. It is shown that if initially for some of these enzymes the normal molecules are more than, for some less than, and for some equal to the erroneous ones, the evolution of the system can lead to many asymptotic conditions including error catastrophe and complete recovery from errors.     

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.     

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.     

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.     

Emerging data on the use of anti-tumor necrosis factor-alpha medications in pregnancy

Anti-tumor necrosis factor (TNF) α medications are used for the treatment of a number of autoimmune diseases. Evaluation of pregnancy safety for these medications is complicated by the contribution of the underlying maternal disease to adverse pregnancy outcomes, such as preterm delivery and reduced birth weight. Placental transport of these medications is thought to be minimal in the first trimester, thereby providing some reassurance regarding theoretical risks for congenital malformations. Available human exposure data are sparse; however, to date there has been no convincing evidence to support an increased risk for a specific pattern of major congenital malformations with any of the drugs in this group for which some data is currently available. As a result of the improvement of symptoms during pregnancy in some women with autoimmune diseases, it may be possible to discontinue treatment before or shortly after conception. However, in some cases the benefits of treatment and concerns for disease flares in pregnancy have warranted continued treatment during pregnancy. Because of the relatively long half-life of these medications, and theoretical concerns for immune compromise of the infant following exposure in the latter two trimesters, some clinicians recommend discontinuation of treatment in the third trimester to avoid potentially prolonged infant exposure in the postpartum period. Currently ongoing controlled cohort studies for some of the TNF blocker medications will help to provide more definitive answers for clinicians and patients. Birth Defects Research (Part A) 94:607-611, 2012. ? 2012 Wiley Periodicals, Inc.     

Fungicidal and herbicidal activities of berberine related alkaloids

The 23 quaternary and tertiary protoberberines related to berberine were tested for in vitro and/or in vivo fungicidal and herbicidal activities. Among the compounds tested, there was some activity observed with some of only the protoberberinium salts, but not sufficiently strong or broad spectrum for agrochemical use. From the structure-activity point of view, some features can be pointed out.     

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.     

Experimental oil exposure of Ascophyllum nodosum (L.) Le Jolis

The effect of weathered, crude oil on Ascophyllum nodosum was tested in an outdoor experiment and in a laboratory experiment. Adult A. nodosum plants which were exposed to oil in an outdoor basin for 3 days showed reduced growth for a certain period of time, after which growth recovered. Also, some necrotic damage was observed. Three-week-old and 1-year-old germlings placed under the adult plants showed no significant reduction in number compared to control plants. In the laboratory experiment some of the 1-month-old germlings were initially exposed to oil for 6 min, some for 1 h, some for 3 h and some for 5 h. After 3 weeks in running, filtered water oil-exposed germlings had reached the same length as those in the control groups, and no effect of exposing the germlings to oil for different lengths of time at the start of the experiment was found. The results indicate that a limited oil pollution of weathered, crude oil may reduce growth and biomass of adult plants for a certain period of time. However, this need not be detrimental to a population with good recruitment from germlings or vegetative shoots growing under a dense canopy layer.     

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     

血液制品病毒灭活及去除工艺进展

随着医学科学的进步和大众生活水平的提高,血液制品的安全性愈来愈受到关注。为了提高血液制品的安全性,国家食品药品监督管理局发布的相关指导原则要求生产工艺要具有一定的去除/灭活部分病毒能力,生产过程中应有特定的去除/灭活病毒方法。我们对几种适用于血液制品的病毒灭活方法及病毒去除工艺进行综述,以期对生产及科研提供参考。     

Ciliate evolution: The ribosomal phylogenies of the tetrahymenine ciliates

Summary We have assembled and analyzed nucleotide sequences for several different rRNA components from tetrahymenine ciliates. These include previously published and some new 5S and 5.8S rRNAs for a total of 18 species. We also report sequences for some 30 species obtained by primer extension analysis of a region near the 5′ end of the 23S rRNAs (region 580). Phylogenetic trees have been constructed for these species, utilizing heuristics (shifting ditypic site analysis) described in a companion paper. The trees based on these sequences are consistent with each other and with those based on longer sequences of the 17S rRNA. They show the tetrahymenines to consist of a number of distinctive clusters of species. The clusters (ribosets) are homogeneous with respect to certain life history characteristics, especially the mode of mating type determination, but are inhomogeneous with respect to some morphological and life history features, such as cyst formation and adaptations to parasitism or carnivory. Using the same molecular data, we also begin to explore the relationships of the tetrahymenines to some other ciliate taxa and to some other protists.     

Conference retrospective: An appropriate modeling infrastructure for cancer research

Presentations and discussions at the symposium illustrate some general issues in biomedical modeling for cancer research. Given the motivations for modeling and assumptions concerning who should be involved in the modeling process, one can identify some basic needs to be met in supports to modelers. These concern both the models themselves and ways of presenting them to users. In conclusion, some thoughts are offered on economic and educational issues that may affect the infusion of modeling into biomedical research.     

第22种氨基酸和无义密码子的重新诠释

遗传密码字典的破译,通用性作为遗传密码的基本特点之一被人们认可.近年来的研究发现了一些例外.除线粒体使用一组密码子其含义有别于核基因之外,原先被认为仅用作终止信号的无义密码子在某些情况下可重新诠释,编码特定的氨基酸.在揭示了硒代半胱氨酸由UGA编码后,最近的研究表明,在某些古细菌和真细菌中,无义密码子UAG可重新诠释,编码组成蛋白质的第22种天然氨基酸——吡咯赖氨酸.     

Yeast as an efficient biocatalyst for the production of lipid-derived flavours and fragrances

Responding to consumer' demand for natural products, biotechnology is constantly seeking new biocatalysts. In the field of hydrophobic substrate degradation, some yeast species known some years ago as non-conventional, have acquired their right to be considered as good biocatalysts. These Candida, Yarrowia, Sporobolomyces ... are now used for themselves or for their lipases in processes to produce flavours and fragrances. In this paper we present some examples of use of these biocatalysts to generate high-value compounds and discuss the new trends related to progress in the development of molecular tools or the mastering of the redox characteristics of the medium.     

脑内微透析采样技术及其在神经科学中的应用

作为一种新的在体化学采样技术,脑内微透析引起了神经科学家的关注。它与迅速发展起来的高灵敏度的微量分析技术相结合,实现了对体内细胞外环境中化学物质变化的动态监测,从而在神经科学领域获得应用。本系统地介绍了这一新技术的原理和方法,并扼要地介绍了一这一技术在神经科学中的应用及其取得的新进展,并结合本实验室的工作经验,对该技术存在的一些问题进行了讨论。     

Immunolocalization of cysteine proteinases (cathepsins) and cysteine proteinase inhibitors (salarin and salmon kininogen) in Atlantic salmon,Salmo salar

Tissue localization of cysteine proteinases (cathepsins) and their inhibitors (salarin, salmon kininogen) was performed in tissues of the Atlantic salmon. In skin, both epidermis and dermis were strongly stained by antisera against salarin and salmon kininogen. In epidermis the intercellular space seemed to be heavily stained (salarin). In kidney, the inhibitors were mainly localized to the interstitial capillaries. Also, some epithelial cells of the tubules (salarin) and some cells of the interstitium were stained. Mostly, the staining had a diffuse cytoplasmic localization. In the liver some hepatocytes were strongly positive for salarin and salmon kininogen. Purified fish cysteine proteinase inhibitors were not found to inhibit the growth of fish pathogenic bacteria and viruses. In the trunk kidney cathepsins B and L were localized in epithelial cells of the tubules (proximal part) and in cells of the interstitium. Mostly, the staining showed a prominent lysosomal localization. In head kidney large macrophage-like cells were positively stained for cathepsin B. The staining was localized to granula/vacuoles in the cytoplasm. In the liver, some hepatocytes were strongly stained and some were less strongly positive for cathepsin B and L. Mostly, the hepatocytes showed lysosomal staining. Cathepsin L was found in some big macrophage-like cells in the spleen. Mucosal epithelial cells of the esophagus and intestine seemed to be strongly stained for cathepsin B and L. The results show that cathepsins and their inhibitors are specifically and widely distributed in the Atlantic salmon skin indicating that they perform some biologically important and specific but so far unknown functions.     

肿瘤放化综合治疗中的靶向研究

放化疗综合应用是癌症治疗中的常用方法。研究表明,放化疗综合应用可以有效地控制杀伤肿瘤,但过程中对正常细胞的毒副作用严重制约着放化疗的剂量和疗效。如何在有效杀伤肿瘤细胞的同时减轻放化疗综合应用中对正常细胞的毒副作用已经成为探索更好的治疗策略的关键。随着研究的不断深入,各种相关的新药和新治疗思路层出不穷,比如针对肿瘤发生及代谢过程的靶向类新药、用于辐射增敏的新的基因靶点等都已进入研究者的视线。另外,近年来关于肿瘤细胞中药物转运蛋白的研究也为综合治疗靶点寻找提供了一定依据。本文根据当前研究现状,着重总结近年来放化疗综合治疗靶向研究在上述几方面的一些新进展。     

肿瘤放化综合治疗中的靶向研究

放化疗综合应用是癌症治疗中的常用方法。研究表明,放化疗综合应用可以有效地控制杀伤肿瘤,但过程中对正常细胞的毒副作用严重制约着放化疗的剂量和疗效。如何在有效杀伤肿瘤细胞的同时减轻放化疗综合应用中对正常细胞的毒副作用已经成为探索更好的治疗策略的关键。随着研究的不断深入,各种相关的新药和新治疗思路层出不穷,比如针对肿瘤发生及代谢过程的靶向类新药、用于辐射增敏的新的基因靶点等都已进入研究者的视线。另外,近年来关于肿瘤细胞中药物转运蛋白的研究也为综合治疗靶点寻找提供了一定依据。本文根据当前研究现状,着重总结近年来放化疗综合治疗靶向研究在上述几方面的一些新进展。