基于质谱的BLAST方法在金鱼胚胎蛋白质鉴定中的应用

未知基因组及蛋白质序列数据库有限的物种的蛋白质组学分析是当前一些非模式生物物种蛋白质组学研究领域的瓶颈之一.基于同源性搜索的BLAST方法（MS BLAST）,是近年新发展起来的一种用于未知基因组的蛋白质鉴定的搜索工具,已成功应用于许多未知基因组物种的蛋白质鉴定.SPITC化学辅助方法是本实验室建立的一种改进的de novo质谱测序方法.采用MS BLAST方法对经Mascot软件数据库搜索未能鉴定到的19个金鱼胚胎蛋白质进行鉴定,其中12个蛋白质是直接测序后进行MS BLAST搜索得到的结果,另外7个蛋白质是联合MS BLAST和SPITC衍生方法得到的鉴定结果.实验结果证明,采用MS BLAST方法进行蛋白质的跨物种鉴定具有可行性和可靠性,给蛋白质的跨物种鉴定提供了一条新的途径.     

Social networks predict patch discovery in a wild population of songbirds

Animals use social information in a wide variety of contexts. Its extensive use by individuals to locate food patches has been documented in a number of species, and various mechanisms of discovery have been identified. However, less is known about whether individuals differ in their access to, and use of, social information to find food. We measured the social network of a wild population of three sympatric tit species (family Paridae) and then recorded individual discovery of novel food patches. By using recently developed methods for network-based diffusion analysis, we show that order of arrival at new food patches was predicted by social associations. Models based only on group searching did not explain this relationship. Furthermore, network position was correlated with likelihood of patch discovery, with central individuals more likely to locate and use novel foraging patches than those with limited social connections. These results demonstrate the utility of social network analysis as a method to investigate social information use, and suggest that the greater probability of receiving social information about new foraging patches confers a benefit on more socially connected individuals.     

Hand searching versus pitfall trapping: how to assess biodiversity of ground beetles (Coleoptera: Carabidae) in high altitude equatorial Andes?

The use of ground beetles (Coleoptera: Carabidae) as bioindicators of environmental change depends on the reliability and the effectiveness of the sampling methods. Those that have been tested in the temperate zone and in tropical forests still await experimentation in tropical high-altitude environments. For the first time, pitfall trapping and hand searching have been compared in Ecuadorian páramo above 4000 m a.s.l., in terms of practical effectiveness. The study was performed on six volcanoes and was based on the comparison of 28 sampling sessions (pitfall trapping and hand searching) performed along two different elevational belts [lower superpáramo (LSP) and upper superpáramo (USP)]. Analyses of sampling sessions showed that detected species richness is slightly higher with hand searching than with pitfall trapping, regardless of the elevation. Additionally, hand searching is more time-effective than pitfall trapping. The performance of the sampling method slightly varies when species assemblage composition is analysed in relation to elevational belts. In the LSP, hand searching and pitfall trapping should be simultaneously used to obtain exhaustive inventories of carabid biodiversity, since different species are likely to be collected by each method. In the USP, hand searching and pitfall trapping efficiency is very similar, but hand searching allows to collect a slightly larger number of species. Lastly, the sample-based rarefaction curves showed that four temporal replicates are mandatory to obtain a robust dataset and an exhaustive inventory of the true species richness and species assemblages composition. Our findings suggest a combined use of hand searching and pitfall trapping in the LSP, while both methods can be used alone for surveying carabids in the USP. Furthermore, hand searching is recommended if the aim is to obtain an inventory of species diversity, whereas pitfall trapping seems more convenient for fine grain ecological and comparative studies.     

Latitudinal gradient in the taxonomic composition of parasite communities

Although latitudinal gradients in diversity have been well studied, latitudinal variation in the taxonomic composition of communities has received less attention. Here, we use a large dataset including 950 surveys of helminth endoparasite communities in 650 species of vertebrate hosts to test for latitudinal changes in the relative contributions of trematodes, cestodes, nematodes and acanthocephalans to parasite assemblages. Although the species richness of helminth communities showed no consistent latitudinal variation, their taxonomic composition varied as a function of both host type and latitude. First, trematodes and acanthocephalans accounted for a higher proportion of species in helminth communities of fish, whereas nematodes achieved a higher proportion of the species in communities of bird and especially mammal hosts. Second, the proportion of trematodes in helminth communities of birds and mammals increased toward higher latitudes. Finally, the proportion of nematodes per community increased toward lower latitudes regardless of the type of host. We present tentative explanations for these patterns, and argue that new insights in parasite community ecology can be gained by searching for latitudinal gradients not only in parasite species richness, but also in the taxonomic composition of parasite assemblages.     

Explicit model for searching behavior of predator

The authors present an approach for explicit modeling of spatio-temporal dynamics of predator-prey community. This approach is based on a reaction-diffusion-adjection PD (prey dependent) system. Local kinetics of population is determined by logistic reproduction function of prey, constant natural mortality of predator and Holling type 2 trophic function. Searching behavior of predator is described by the advective term in predator balance equation assuming the predator acceleration to be proportional to the prey density gradient. The model was studied with zero-flux boundary conditions. The influence of predator searching activity on the community dynamics, in particular, on the emergence of spatial heterogeneity, has been investigated by linear analysis and numerical simulations. It has been shown how searching activity may effect the persistence of species, stabilizing predator-prey interactions at very low level of pest density. It has been demonstrated that obtaining of such dynamic regimes does not require the use of complex trophic functions.     

Neural control of salivary glands in ixodid ticks

Studies of tick salivary glands (SGs) and their components have produced a number of interesting discoveries over the last four decades. However, the precise neural and physiological mechanisms controlling SG secretion remain enigmatic. Major studies of SG control have identified and characterized many pharmacological and biological compounds that activate salivary secretion, including dopamine (DA), octopamine, γ-aminobutyric acid (GABA), ergot alkaloids, pilocarpine (PC), and their pharmacological relatives. Specifically, DA has shown the most robust activities in various tick species, and its effect on downstream actions in the SGs has been extensively studied. Our recent work on a SG dopamine receptor has aided new interpretations of previous pharmacological studies and provided new concepts for SG control mechanisms. Furthermore, our recent studies have suggested that multiple neuropeptides are involved in SG control. Myoinhibitory peptide (MIP) and SIFamide have been identified in the neural projections reaching the basal cells of acini types II and III. Pigment-dispersing factor (PDF)-immunoreactive neural projections reach type II acini, and RFamide- and tachykinin-immunoreactive projections reach the SG ducts, but the chemical nature of the latter three immunoreactive substances are unidentified yet. Here, we briefly review previous pharmacological studies and provide a revised summary of SG control mechanisms in ticks.     

Propolis of stingless bees: A phytochemist's guide through the jungle of tropical biodiversity

BackgroundStingless bees (Meliponini), like honeybees Apis mellifera, collect plant resins in order to produce propolis (cerumen, geopropolis). This type of propolis has long been used in traditional medicine in Mexico, Brazil, Argentina, India, and Vietnam, as a remedy for improving health and treating various diseases. The scientific and commercial interest in stingless bee propolis has been steadily increasing over the last few years. The new and growing knowledge in this field requires systematising, as a basis for further work. Recent reviews of Meliponini propolis deal only with the South American and Mesoamerican species, while reviews of the Asian, Australian and African species are missing. Furthermore, the chemical composition has not been thoroughly reviewed since 2007.PurposeThis review summarises and discusses the available data about the chemical composition of propolis from the stingless bee species (Meliponinae) of the Americas, Asia and Australia, published after 2007. The published information on the biological action of chemically characterised Meliponini propolis, and of individual constituents, is addressed. The plant sources of this propolis are also considered.Conclusion and perspectivesChemical studies of Meliponini propolis has resulted in the discovery of new natural molecules, some of them with valuable bioactivity. Moreover, finding known molecules in propolis stimulates the study of their pharmacological properties. The enormous chemical variability of stingless bee propolis is a challenge to chemists, entomologists and pharmacologists. It is essential to perform pharmacological studies with only chemically characterised propolis of stingless bees. Further studies are required to chemically characterise and scientifically support the medicinal properties of stingless bee propolis and to clarify the potential for its commercial use. This could lead to increased prices for Meliponinae propolis and provide an additional source of income for farmers in rural communities with most serious social needs.     

An efficient and convenient microwave-assisted chemical synthesis of (thio)xanthones with additional in vitro and in silico characterization

Xanthones and their thio-derivatives are a class of pleiotropic compounds with various reported pharmacological and biological activities. Although these activities are mainly determined in laboratory conditions, the class itself has a great potential to be utilized as promising chemical scaffold for the synthesis of new drug candidates. One of the main obstacles in utilization of these compounds was related to the difficulties in their chemical synthesis. Most of the known methods require two steps, and are limited to specific reagents not applicable to a large number of starting materials. In this paper a new and improved method for chemical synthesis of xanthones is presented. By applying a new procedure, we have successfully obtained these compounds with the desired regioselectivity in a shorter reaction time (50s) and with better yield (>80%). Finally, the preliminary in vitro screenings on different bacterial species and cytotoxicity assessment, as well as in silico activity evaluation were performed. The obtained results confirm potential pharmacological use of this class of molecules.     

Phytochemistry and biological properties of <Emphasis Type="Italic">Aristotelia chilensis</Emphasis> a Chilean blackberry: a review

Aristotelia chilensis (Mol.) Stuntz, commonly called Maqui, is known for its pharmacological uses in traditional medicine of native Mapuche communities in Chile. It is reported to have excellent medicinal properties that help to cure chronic diarrhea, dysentery, throat diseases, intestinal tumors, fever, wounds healing, and scars. Pharmacologically, fruits and leaves of Maqui have been investigated for antioxidant, antidiabetic, and antiviral activities. The current high demand of natural antioxidants has placed Maqui as one of the most over-exploited species in Chile. This review analyzes the information collected from the published research articles, and highlights the phytochemical and pharmacological aspects of A. chilensis. The information will be useful to develop new strategies of sustainable use of the species to generate new formulations with therapeutic and economical value in the future.     

Snake venom: From fieldwork to the clinic: Recent insights into snake biology, together with new technology allowing high-throughput screening of venom, bring new hope for drug discovery

Snake venoms are recognized here as a grossly under-explored resource in pharmacological prospecting. Discoveries in snake systematics demonstrate that former taxonomic bias in research has led to the neglect of thousands of species of potential medical use. Recent discoveries reveal an unexpectedly vast degree of variation in venom composition among snakes, from different species down to litter mates. The molecular mechanisms underlying this diversity are only beginning to be understood. However, the enormous potential that this resource represents for pharmacological prospecting is clear. New high-throughput screening systems offer greatly increased speed and efficiency in identifying and extracting therapeutically useful molecules. At the same time a global biodiversity crisis is threatening the very snake populations on which hopes for new venom-derived medications depend. Biomedical researchers, pharmacologists, clinicians, herpetologists, and conservation biologists must combine their efforts if the full potential of snake venom-derived medications is to be realized.     

Male versus female mate searching in fiddler crabs: a comparative analysis

We present a comparative analysis of mate searching in fiddlercrabs, genus Uca. Several ecological factors determine whichsex will search for mates and how complex male signaling willbe. Female searching is most tightly correlated with matingin male burrows. Female searching is associated with high burrowdensity, small body size, and large soil size. These factors explain variation in a female's need for male-defended incubationsites. Female searching also is correlated with short eyestalks.In species in which females search for mates, males use a morecomplex mate attraction signal than in species in which malessearch.     

DNA barcoding is a new approach in comparative genomics of plants

DNA barcoding was proposed as a method for recognition and identification of eukaryotic species through comparison of sequences of a standard short DNA fragment—DNA barcode—from an unknown specimen to a library of reference sequences from known species. This allows identifying an organism at any stage of development from a very small tissue sample, fresh or conserved many years ago. Molecular identification of plant samples can be used in various scientific and applied fields. It would also help to find new species, which is particularly important for cryptogamic plants. An optimal DNA barcode region is a small fragment presented in all species of a major taxonomic group, having invariable nucleotide sequence in all members of the same species, but with sufficient variation to discriminate among the species. This fragment should be flanked by low-variable regions for use of universal primers in PCR for amplification and sequencing. The DNA barcode that is well established in animals is a sequence of a fragment of the mitochondrial cytochrome c oxidase gene CO1. However, searching for DNA barcode in plants proved to be a more challenging task. No DNA region universally suitable for all plants and meeting all of the necessary criteria has been found. Apparently, a multilocus or two-stage approach should be applied for this purpose. Several fragments of the chloroplast genome (trnH-psbA, matK, rpoC, rpoB, rbcL) in combinations of two or three regions were suggested as candidate regions with highest potential, but more representative samples should be examined to choose the best candidate. The possibility is discussed to use as DNA barcode internal transcribed spacers (ITS) of nuclear rRNA genes, which are highly variable, widely employed in molecular phylogenetic studies at the species level, but also have some limitations.     

Vicinity analysis: a methodology for the identification of similar protein active sites

Vicinity analysis (VA) is a new methodology developed to identify similarities between protein binding sites based on their three-dimensional structure and the chemical similarity of matching residues. The major objective is to enable searching of the Protein Data Bank (PDB) for similar sub-pockets, especially in proteins from different structural and biochemical series. Inspection of the ligands bound in these pockets should allow ligand functionality to be identified, thus suggesting novel monomers for use in library synthesis. VA has been developed initially using the ATP binding site in kinases, an important class of protein targets involved in cell signalling and growth regulation. This paper defines the VA procedure and describes matches to the phosphate binding sub-pocket of cyclin-dependent protein kinase 2 that were found by searching a small test database that has also been used to parameterise the methodology.     

Polyphenols in cerebral ischemia

Plant polyphenols are dietary components that exert a variety of biochemical and pharmacological effects. Recently, considerable interest has been focused on polyphenols because of their antioxidant, anti-inflammatory, and antiproliferative activities. Oxidative stress is thought to be a key event in the pathogenesis of cerebral ischemia. Overproduction of reactive oxygen species during ischemia/reperfusion could cause an imbalance between oxidative and antioxidative processes. Reactive oxygen species can damage lipids, proteins, and nucleic acids, thereby inducing apoptosis or necrosis. There is increasing evidence supporting the hypothesis that plant polyphenols can provide protection against neurodegenerative changes associated with cerebral ischemia. This article reviews the neuroprotective effects of plant extracts and their constituents that have been used in animal models of cerebral ischemia. The use of polyphenols as therapeutic agents in stroke has been suggested.     

Recent progress in phytochemistry,pharmacology and biotechnology of Astragalus saponins

Saponins are widely distributed among plant kingdom and possess a wide range of pharmacological properties. Genus Astragalus is the largest in the Fabaceae family, comprising more than 2,200 species spread over the Globe. Astragalus species have been used in traditional medicine of many countries as well as in the modern one. The main use in the folk medicine of the species is due to their saponin content. The paper is focused on the above mentioned group of compounds. Details on their structure, distribution, recent information on the pharmacological properties and biotechnology of Astragalus saponins will be summarized and thoroughly discussed.     

宏蛋白质组学信息分析的基本策略及其挑战

宏蛋白质组学是一门新型科学,它运用质谱技术规模化地采集自然界微生物种群的蛋白质信息,并结合多种组学数据,开展微生物种群的遗传特征及其生物功能的研究.宏蛋白质组学的信息分析与传统蛋白质组学方法有较大的不同,亟需拓展新的分析思路.由于宏蛋白质组的研究对象是复杂度极高的微生物样品,因此,需要构建尽可能囊括样本中所含微生物的基因组信息的物种数据库.面对庞大的数据库,必须考虑到分析过程中所消耗的计算资源和鉴定结果的质控标准,因此,需要高度优化库容量、搜库、假阳性控制等参数.鉴于宏蛋白质组数据中广泛存在复杂的同源蛋白质序列,因此,需要充分利用NCBI数据库中的分类信息进行匹配,并运用LCA算法过滤处理才能将蛋白质有效地归组到物种.本文立足于宏蛋白质组学信息分析,从宏蛋白质组的数据库建立、蛋白质归并、生物学意义发掘等几个方面着手,对该领域的发展现状、面临挑战以及未来研究方向进行了评述.     

The tmRNA website.

tmRNA (10Sa RNA) has a central role in trans -translation, in which a peptide tag encoded in tmRNA is added to the abnormally short protein product of a broken mRNA, as a signal for proteolysis of the entire tagged protein. The tmRNA website was established in 1997 as a resource for phylogenetic considerations of tmRNA structure and function. Since then, three partial tmRNA sequences have been completed, and sequences from 13 more species have been identified. Forty-six species from 10 bacterial phyla and chloroplasts are now represented in the database. Provisional sequence alignments and predicted proteolysis tag sequences are provided, as well as a literature review and a guide to searching for new tmRNA sequences. The tmRNA website is accessible via WWW at a new URL: http://sunflower.bio.indiana.edu/kwilliam/tmRNA /home.html     

Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis

Spectral library searching has been recently proposed as an alternative to sequence database searching for peptide identification from MS/MS. We performed a systematic comparison between spectral library searching and sequence database searching using a wide variety of data to better demonstrate, and understand, the superior sensitivity of the former observed in preliminary studies. By decoupling the effect of search space, we demonstrated that the success of spectral library searching is primarily attributable to the use of real library spectra for matching, without which the sensitivity advantage largely disappears. We further determined the extent to which the use of real peak intensities and non-canonical fragments, both under-utilized information in sequence database searching, contributes to the sensitivity advantage. Lastly, we showed that spectral library searching is disproportionately more successful in identifying low-quality spectra, and complex spectra of higher- charged precursors, both important frontiers in peptide sequencing. Our results answered important outstanding questions about this promising yet unproven method using well-controlled computational experiments and sound statistical approaches.     

微卫星位点筛选方法综述

微卫星标记因其丰富的多态性和共显性等特点,已得到了广泛的应用.应用微卫星标记首先需要获得微卫星位点的序列信息,用来设计引物.获得微卫星位点的方法有多种,本文综述了获得和富集微卫星位点的常用方法.最简便、最省时的方法是从公共数据库(如EMBL、Genbank、EST数据库等)或已发表的文献中查找到微卫星位点,但只限于已经有序列数据发布的物种.第二种方法是种间转移扩增,即从相近物种的数据库中查找微卫星位点,或使用已有数据发表的遗传距离相近物种的微卫星标记.第三种方法是从基因组DNA中筛选微卫星位点,其中用于富集微卫星的方法有引物法、磁珠杂交法、尼龙膜杂交法以及RAPD技术法.     

Conditioning of appetitive behavior in the Hymenopteran parasitoid Microplitis croceipes

Work on insect learning has made ample use of conditioned behaviors in single learning tasks. Parasitic wasps are particularly suited to study more complex learning processes, as they alternate between host searching and foraging for sugar sources. We here describe a set of behaviors that unambiguously represents sugar feeding in the Hymenopteran parasitoid Microplitis croceipes (Cresson) (Hymenoptera: Braconidae). Furthermore, we demonstrate that this parasitoid can be conditioned to exhibit these behaviors in response to odor stimuli previously associated with feeding. In conjunction with a previously described ovipositor probing response in this species, our findings constitute the first instance in which multiple conditioned behaviors representing feeding and reproduction have been identified for one insect species. This provides a valuable tool for the study of multiple task learning.