Relating simulation studies by provenance—Developing a family of Wnt signaling models

For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one. A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To answer this question, we need to identify entities and activities that contributed to the development of a simulation model. Therefore, we exploit the provenance data model, PROV-DM, of the World Wide Web Consortium and, building on previous work, continue developing a PROV ontology for simulation studies. Based on a case study of 19 Wnt/β-catenin signaling models, we identify crucial entities and activities as well as useful metadata to both capture the provenance information from individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, a web application for inserting and querying provenance information. Our specialization of PROV-DM contains the entities Research Question, Assumption, Requirement, Qualitative Model, Simulation Model, Simulation Experiment, Simulation Data, and Wet-lab Data as well as activities referring to building, calibrating, validating, and analyzing a simulation model. We show that most Wnt simulation models are connected to other Wnt models by using (parts of) these models. However, the overlap, especially regarding the Wet-lab Data used for calibration or validation of the models is small. Making these aspects of developing a model explicit and queryable is an important step for assessing and reusing simulation models more effectively. Exposing this information helps to integrate a new simulation model within a family of existing ones and may lead to the development of more robust and valid simulation models. We hope that our approach becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models.     

Cloning and expression analysis of a water stress-induced gene from Brassica oleracea.

Plant growth and productivity are greatly affected by water stress, such as drought and salinity. Here we report on the cloning and expression analysis of a water stress-induced gene from Brassica oleracea (designated as BoWS, GenBank accession number AY571333) by rapid amplification of cDNA ends (RACE). The full-length cDNA of BoWS consisted of 594 bp and contained a 285 bp open reading frame (ORF) encoding a 95-amino-acid protein. The deduced protein had a calculated molecular mass of 10.53 kDa and an isoelectric point of 6.93. The sequence similarity and comparative analysis showed that BoWS was 84% identical to Arabidopsis thaliana putative water stress-induced protein (GenBank accession number AAM67282). Southern blot analysis indicated that BoWS was a low-copy gene. Northern blot analysis revealed that the expression of BoWS was upregulated by abscisic acid (ABA), mannitol, NaCl, drought, salicylic acid (SA) and hydrogen peroxide (H(2)O(2)). Our results indicate that BoWS is extremely related to the water-deficit stress in B. oleracea.     

抗癌胚抗原免疫毒素生物学功能的研究

为了研究免疫毒素发挥生物学作用的全过程,构建了两种不同形式的基于假单胞菌外毒素(Pseudomonas exotoxin A,PE)的抗癌胚抗原（carcinoembryonic antigen, CEA）免疫毒素CEA(Fv)/PE38/KDEL和PE35/CEA(Fv)/KDEL.用流式细胞术经间接免疫荧光法测定免疫毒素的抗原结合活性.免疫毒素的内化(internalization)通过间接免疫荧光标记的方法在激光共聚焦显微镜下进行检测,采用流式细胞术进行免疫毒素内化的定量分析.细胞凋亡采用FITC-annexin V/PI双荧光染色方法进行分析.用噻唑蓝(MTT)法测定免疫毒素的靶细胞杀伤功能.对两种形式的免疫毒素在各个功能阶段的性质进行研究和比较,全面展现了免疫毒素发挥生物学功能的过程及各个生物作用过程之间的相互影响,为详尽的机制研究和免疫毒素的进一步优化改造提供了重要的依据.     

Water-borne seed transport and seed deposition during flooding in a small river-valley in Northern Germany

Water-borne seed transport and seed deposition during flooding were studied in the Upper Eider river (N-Germany) by direct sampling of the rivers seed content with aquatic seed traps and by analysing the number of deposited seeds on sedimentation mats which were exposed near the river on the soil surface during a flooding period of approx. three weeks.The number of seeds which were transported at the surface of the river Eider was continuously analysed by four aquatic seed traps for a period of 20 weeks (July–December 2000). To test the capture rate of these traps, a recapture experiment with colour marked seeds of Helianthus annuus L. was carried out. During the investigation period approx. 9000 seeds of 76 species were captured by the four aquatic seed traps. The number of trapped seeds varied both spatially (across the river profile) and temporally. Considering this variation and the capture rate of the traps, the water-borne seed transport was estimated to be 3139 seeds per week and meter of the river profile.The seed deposition during a flood in early spring 2002 was analysed by using 20 sedimentation mats. To distinguish effects of seed dispersal into patches from outside from seed rearrangement within patches, the water-borne seed transport was excluded from one half of the mats by fencing them with a woven fabric which was permeable for water but not for floating seeds. Outside of the exclosures 152 viable seeds of 26 species were deposited on the sedimentation mats while only one single seedling was found on mats from which water-borne seed transport was excluded.The results demonstrate that hydrochorous dispersal processes might play an important role in connecting otherwise fragmented populations in periodically flooded habitats along rivers.     

Competition, predation and interspecific synchrony in cyclic small mammal communities

Although competition and predation are considered to be among the most important biotic processes influencing the distribution and abundance of species in space and time, the relative and interactive roles of these processes in communities comprised of cyclically fluctuating populations of small mammals are not well known. We examined these processes in and among populations of field voles, sibling voles, bank voles and common shrews in western Finland, using spatially replicated trapping data collected four times a year during two vole cycles (1987–1990 and 1997–1999). Populations of the four species exhibited relatively strong interspecific temporal synchrony in their multiannual fluctuations. During peak phases, we observed slight deviations from close temporal synchrony: field vole densities peaked at least two months earlier than those of either sibling voles or bank voles, while densities of common shrews peaked even earlier. The growth rates of all four coexisting small mammal species were best explained by their own current densities. The growth rate of bank vole populations was negatively related to increasing densities of field voles in the increase phase of the vole cycle. Apart from this, no negative effects of interspecific density, direct or delayed, were observed among the vole species. The growth rates of common shrew populations were negatively related to increasing total rodent (including water voles and harvest mice) densities in the peak phase of the vole cycle. Sibling voles appeared not to be competitively superior to field voles on a population level, as neither of these Microtus voles increased disproportionately in abundance as total rodent density increased. We suggest that interspecific competition among the vole species may occur, but only briefly, during the autumn of peak years, when the total available amount of rodent habitat becomes markedly reduced following agricultural practices. Our results nonetheless indicate that interspecific competition is not a strong determinant of the structure of communities comprised of species exhibiting cyclic dynamics. We suggest that external factors, namely predation and shortage of food, limit densities of vole populations below levels where interspecific competition occurs. Common shrews, however, appear to suffer from asymmetric space competition with rodents at peak densities of voles; this may be viewed as a synchronizing effect.     

广东金山温泉沉积物中原核与真核微生物多样性初步分析

[目的]本研究旨在采用不同的PCR引物对广东省恩平市金山温泉的高温水底沉积物微生物多样性进行初步的分析.[方法]采用改进的玻璃珠法抽提温泉沉积物中环境基因组DNA,通过对用4对引物分别扩增得到的原核微生物16S rRNA基因和真核微生物ITS序列的分析,将所得到的数据与国际基因数据库GenBank进行相似性比较并构建系统发育树.[结果]研究发现原核类群G的 14个优势克隆中7个都属于蛭弧菌属(Bdellovibrio).与它们最相似的序列是从海洋中分离到的两个菌株 Bacteriovorax sp. NE1 (EF092445)和Bdellovibrio sp. JS5 (AF084859),相似性分别为96%和99%.原核类群X的4个序列主要属于蓝细菌类群,其中JS-X2与在美国黄石公园温泉发现的Uncultured Cyanobacterium (L35331)有95%的相似性,并且与已经全基因组测序的嗜热蓝细菌聚球藻Thermosynechococcus elongatus BP-1 (47118315)有89%的相似性.真核类群Z有三个类群,分别是Penicillium sp.,Lodderomyces sp.和Gloeotinia sp..其中大部分序列与青霉属相似性在88%～ 90%之间.[结论]所得到的结果显示金山温泉中的微生物多样性十分丰富.     

放线菌药物资源开发面临的问题与对策

放线菌药物的开发已取得了极其辉煌的成就, 对医疗事业的发展和人类健康做出了重大贡献。然而, 随着放线菌药物资源的长期开发和利用, 也面临诸多问题。如: 包袱沉重, 去重复难度极大, 因而投资周期长、耗资巨, 风险大; 药物开发赶不上病原菌抗药性的增加及不断出现的新疾病; 虽然未知放线菌甚多, 但发现难度大。为此, 提出了从化学、菌种和基因三方面开展放线菌药物研究的应对策略, 以解决限制放线菌药物资源持续利用和发展的瓶颈。     

Fluorescence detection of amino acids in the postcleavage conversions for manual sequencing of a peptide

A modified Edman degradation method where fluorescent derivatives of amino acids were generated from the postcleavage products of a peptide is described. In the method, the target peptide was applied onto double glass fiber membranes in a small filter disk (4 mm i.d.) and then treated with small amounts of reagents for the manual sequencing of the peptide. The anilinothiazolinone (ATZ) of N-terminus amino acid residue after the isolation from the solid-phase membranes was reacted with a primary amine, 4-(1′-cyanoisoindolyl)aniline (CIA), to form a more stable and sensitive fluorescent derivative, phenylthiocarbamoyl-CIA. An average yield of 85% was obtained in neutral pH conditions for the CIA reaction. The ATZ-CIA-amino acids were separated by reversed-phase liquid chromatography and detected by fluorometry. The lower limits of the detection for amino acids after the Edman degradation were 0.16 to 0.52 pmol (signal/noise ratio = 3) on the column. The sensitivity was approximately 10 times higher than ultraviolet absorbance detection of phenylthiohydantoin products in the conventional Edman degradation. The suitability of the method was demonstrated by the sensitive manual sequencing of insulin chain B composed of 30 amino acids.     

In situ delipidation of low-density lipoproteins in capillary electrochromatography yields apolipoprotein B-100-coated surfaces for interaction studies

An electrochromatographic method was developed for the in situ delipidation of intact low-density lipoprotein (LDL) particles immobilized on the inner wall of a 50-μm inner diameter silica capillary. In this method, the immobilized LDL particles were delipidated with nonionic surfactant Nonidet P-40 at pH 7.4 and 25 °C, resulting in an apolipoprotein B-100 (apoB-100)-coated capillary surface. The mobility of the electroosmotic flow marker dimethyl sulfoxide gave information about the surface charge, and the retention factors of β-estradiol, testosterone, and progesterone were informative of the surface hydrophobicity. The calculated distribution coefficients of the steroids produced specific information about the affinity interactions of the steroids, with capillary surfaces coated either with intact LDL particles or with apoB-100. Delipidation with Nonidet P-40 resulted in a strong decrease in the hydrophobicity of the LDL coating. Atomic force microscopy images confirmed the loss of lipids from the LDL particles and the presence of apoB-100 protein coating. The in situ delipidation of LDL particles in capillaries represents a novel approach for the isolation of immobilized apoB-100 and for the determination of its pI value. The technique requires extremely low quantities of LDL particles, and it is simple and fast.