Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at http://www.penbase.immunaqua.com, has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature. (c) 2005 Elsevier Ltd. All rights reserved.

attB site disruption in marine Actinomyces sp M048 via DNA transformation of a site-specific integration vector

An efficient conjugation method has been developed for the marine Actinomyces sp. isolate M048 to facilitate the genetic manipulation of the chandrananimycin biosynthesis gene cluster. A phi C31-derived integration vector pIJ8600 containing oriT and attP fragments was introduced into strain M048 by bi-parental conjugation from Escherichia coli ET12567 to strain M048. Transformation efficiency was (6.38 +/- 0.41) x 10(-5) exconjugants per recipient spore. Analysis of eight exconjugants showed that the plasmid pIJ8600 was stably integrated at a single chromosomal site (attB) of the Actinomyces genome. The DNA sequence of the attB was cloned and shown to be conserved. The results of antimicrobial activity analysis indicated that the insertion of plasmid pIJ8600 seemed to affect the biosynthesis of antibiotics that could strongly inhibit the growth of E. coli and Mucor miehei (Tu284). HPLC-MS analysis of the extracts indicated that disruption of the attB site resulted in the complete abolition of chandrananimycin A-C production, proving the identity of the gene cluster. Instead of chandrananimycins, two bafilomycins were produced through disruption of the attB site from the chromosomal DNA of marine Actinomyces sp. M048.

Genesis of Th-230 excess in basalts from mid-ocean ridges and ocean islands: Constraints from the global U-series isotope database and major and rare earth element geochemistry

Based on Th-230-U-238 disequilibrium and major element data from mid-ocean ridge basalts (MORBs) and ocean island basalts (OIBs), this study calculates mantle melting parameters, and thereby investigates the origin of Th-230 excess. (Th-230/U-238) in global MORBs shows a positive correlation with Fe-8, P (o), Na-8, and F-melt (Fe-8 and Na-8 are FeO and Na2O contents respectively after correction for crustal fractionation relative to MgO = 8 wt%, P (o)=pressure of initial melting and F (melt)=degree of melt), while Th-230 excess in OIBs has no obvious correlation with either initial mantle melting depth or the average degree of mantle melting. Furthermore, compared with the MORBs, higher (Th-230/U-238) in OIBs actually corresponds to a lower melting degree. This suggests that the Th-230 excess in MORBs is controlled by mantle melting conditions, while the Th-230 excess in OIBs is more likely related to the deep garnet control. The vast majority of calculated initial melting pressures of MORBs with excess Th-230 are between 1.0 and 2.5 GPa, which is consistent with the conclusion from experiments in recent years that D (U)> D (Th) for Al-clinopyroxene at pressures of > 1.0 GPa. The initial melting pressure of OIBs is 2.2-3.5 GPa (around the spinel-garnet transition zone), with their low excess Ra-226 compared to MORBs also suggesting a deeper mantle source. Accordingly, excess Th-230 in MORBs and OIBs may be formed respectively in the spinel and garnet stability field. In addition, there is no obvious correlation of K2O/TiO2 with (Th-230/U-238) and initial melting pressure (P (o)) of MORBs, so it is proposed that the melting depth producing excess Th-230 does not tap the spinel-garnet transition zone. OIBs and MORBs in both (Th-230/U-238) vs. K2O/TiO2 and (Th-230/U-238) vs. P (o) plots fall in two distinct areas, indicating that the mineral phases which dominate their excess Th-230 are different. Ce/Yb-Ce curves of fast and slow ridge MORBs are similar, while, in comparison, the Ce/Yb-Ce curve for OIBs shows more influence from garnet. The mechanisms generating excess Th-230 in MORBs and OIBs are significantly different, with formation of excess Th-230 in the garnet zone only being suitable for OIBs.

面向CIMS的多数据源互操作与开放分布处理系统———CIMS-MIODP的设计与实现

多数据源互操作与开放分布处理系统ＣＩＭＳ－ＭＩＯＤＰ是采用分布对象互操作与代理技术，实现面向ＣＩＭＳ的基于ＲＰＣ的远程对象访问ＲＯＡ（ＲｅｍｏｔｅＯｂｊｅｃｔＡｃｅｓ）功能和基于ＳＱＬ３的远程数据库访问ＲＤＡ（ＲｅｍｏｔＤａｔａｂａｓｅＡｃｅｓ）功能的系统，为ＣＩＭＳ环境下的信息集成与分布处理提供了不同层次的支持功能。本文讨论了ＣＩＭＳ－ＭＩＯＤＰ系统的主要设计和实现问题，包括基本模型、扩展服务和协议、对ＳＱＬ３的支持、系统实现结构等。

大规模多数据库系统的互操作机制

Sharing data among disparate databases has so far mostly been achieved through some form of ad-hoc schema integration. This approach becomes less tractable as the number of participating database increases. In this paper,we first present the primary problems to be resolved in large multidatabase systems and discuss the autonomy and heteroheneity of large multidatabase systems and then describe a coalition agent mechanism to implement large multidatabase systems interoperation.

人口统计信息空间可视化系统研究

Population research is a front area concerned by domestic and overseas, especially its researches on its spatial visualization and its geo-visualization system design, which provides a sound base for understanding and analysis of the regional difference in population distribution and its spatial rules. With the development of GIS, the theory of geo-visualization more and more plays an important role in many research fields, especially in population information visualization, and has been made the big achievements recently. Nevertheless, the current research is less attention paid to the system design for statistical-geo visualization for population information. This paper tries to explore the design theories and methodologies for statistical-geo-visualization system for population information. The researches are mainly focused on the framework, the methodologies and techniques for the system design and construction. The purpose of the research is developed a platform for population atlas by the integration of the former owned copy software of the research group in statistical mapping system. As a modern tool, the system will provide a spatial visual environment for user to analyze the characteristics of population distribution and differentiate the interrelations of the population components. Firstly, the paper discusses the essentiality of geo-visualization for population information and brings forward the key issue in statistical-geo visualization system design based on the analysis of inland and international trends. Secondly, the geo-visualization system for population design, including its structure, functionality, module, user interface design, is studied based on the concepts of theory and technology of geo-visualization. The system design is proposed and further divided into three parts: support layer, technical layer, user layer. The support layer is a basic operation module and main part of the system. The technical layer is a core part of the system, supported by database and function modules. The database module mainly include the integrated population database (comprises spatial data, attribute data and geographical features information), the cartographic symbol library, the color library, the statistical analysis model. The function module of the system consists of thematic map maker component, statistical graph maker component, database management component and statistical analysis component. The user layer is an integrated platform, which provides the functions to design and implement a visual interface for user to query, analysis and management the statistic data and the electronic map. Based on the above, China's E-atlas for population was designed and developed by the integration of the national fifth census data with 1:400 million scaled spatial data. The atlas illustrates the actual development level of the population nowadays in China by about 200 thematic maps relating with 10 map categories(environment, population distribution, sex and age, immigration, nation, family and marriage, birth, education, employment, house). As a scientific reference tool, China's E-atlas for population has already received the high evaluation after published in early 2005. Finally, the paper makes the deep analysis of the sex ratio in China, to show how to use the functions of the system to analyze the specific population problem and how to make the data mining. The analysis results showed that: 1. The sex ratio has been increased in many regions after fourth census in 1990 except the cities in the east region, and the high sex ratio is highly located in hilly and low mountain areas where with the high illiteracy rate and the high poor rate; 2. The statistical-geo visualization system is a powerful tool to handle population information, which can be used to reflect the regional differences and the regional variations of population in China and indicate the interrelations of the population with other environment factors. Although the author tries to bring up a integrate design frame of the statistical-geo visualization system, there are still many problems needed to be resolved with the development of geo-visualization studies.

基于GIS的高速公路养护管理信息系统的设计与开发

China is experiencing a rapid development of highway ever since 1990s. By the end of 2004, the total length of the highway summed up to 33 thousand kilometers, ranking 2n in the world. After the open of highway, the accumulation of time and traffic causes the decrease of its capability. To ensure its good quality, security and operation functions, we should take some reasonable measures to maintain it periodically. At present, a big problem is that the traditional maintain measures can no longer meet the increasing requirements. Due to the characters of highway, the relationship of various maintenance data and geographic positions is even closer than any others. If we wan to improve the quality and efficiency of the maintenance work, particularly when there is need for decision-making, a great number of data that is related to geographic positions are absolutely necessary. Evidently, Geographical Information System (GIS) has incomparably advantages in dealing with these spatial information. As a result, a management system for highway maintenance work based on GIS became inevitable for the development of the maintenance of highway. The purpose of this paper is to establish a management system for highway maintenance work base on Geographical Information System (GIS), Global Positioning System (GPS) and spatial database, to manage all kinds of problems encountered in the work, and to provide support on information and methods. My study mainly includes: (1) Analysis on the current status of the maintenance and management work; overview on the history of domestic and international highway maintenance management systems; identifying the necessity and importance for establishing a management system for highway maintenance work based on GIS. (2) Based on the requirement analysis, I proposed a general design for this management system, and discussed the objective, design principles, framework, systematical structure and function design. (3) Outdoor data collection is not only a prime way to understand the current situation of the road, but also an important method for data update after the system is put into use. This paper also intends to establish a set of plan to collect data efficiently and precisely which is based on GIS and GPS technologies. (4) The maintenance management database is a supporting platform for various maintenance decision-makings. Such decisions need the support of a great amount of data, which would cause other problems, such as the diversity of the data source, difference of data formats. This paper also discussed how to deal with these problems and establish such a database. (5) To propose an approach to assess the condition of pavement, based on GIS and related maintenance models. Among all the maintenance models, the two for assessing and forecasting pavement condition are the most important and mature. This paper also analyzed these two models and introduced them in terms of the integration of models. (6) This paper took the Guangshen Highway for example, explaining how to realize a GIS for management of highway maintenance work.

Integration of ion-exchange chromatography fractionation with reversed-phase liquid chromatography-atmospheric pressure chemical ionization mass spectrometer and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for isolation and identification of compounds in Psoralea corylifolia

An approach for the separation and identification of components in a traditional Chinese medicine Psoralea corylifolia was developed. Ion-exchange chromatography (IEC) was applied for the fractionation of P corylifolia extract, and then followed by concentration of all the fractions with rotary vacuum evaporator. Each of the enriched fractions was then further separated on an ODS column with detection of UV absorbance and atmospheric pressure chemical ionization mass spectrometer (APCI/MS), respectively, and also analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) with matrix of oxidized carbon nanotubes. Totally more than 188 components in P. corylifolia extract were detected with this integrated approach, and 12 of them were preliminary identified according to their UV spectra and mass spectra performed by APCI/MS and MALDI-TOF/MS. The obtained analytical results not only demonstrated the powerful resolution of integration IEC fractionation with reversed-phase liquid chromatography (RPLC)-APCI/MS and MALDI-TOF/MS for analysis of compounds in a complex sample, but also exhibited the superiority of APCI/MS and MALDI-TOF/MS for identification of low-mass compounds, such as for study of traditional Chinese medicines (TCMs) and metabolome. (c) 2005 Published by Elsevier B.V.

Separation and detection of compounds in Honeysuckle by integration of ion-exchange chromatography fractionation with reversed-phase liquid chromatography-atmospheric pressure chemical ionization mass spectrometer and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis

A hyphenated method for the isolation and identification of components in a traditional Chinese medicine of Honeysuckle was developed. Ion-exchange chromatography (IEC) was chosen for the fractionation of Honeysuckle extract, and then followed by concentration of all the fractions with rotary vacuum evaporator. Each of the enriched fractions was then further analyzed by reversed-phase liquid chromatography-atmospheric pressure chemical ionization mass spectrometer (RPLC-APCI/MS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) with matrix of oxidized carbon nanotubes, respectively. It can be noted totally more than 117 components were detected by UV detector, APCI/MS and MALDI-TOF/MS in Honeysuckle extract except the, 145 components identified by MALDI-TOF/MS alone with this integrated approach, and 7 of them were preliminary identified according to their UV spectra and mass spectra performed by APCI/MS and MALDI-TOF/MS, respectively. The obtained analytical results not only indicated the approach of integration IEC fractionation with RPLC-APCI/MS and MALDI-TOF/MS is capable of analyzing complex samples, but also exhibited the potential power of the mass spectrometer in detection of low-mass compounds, such as traditional Chinese medicines (TCMs) and complex biological samples. (c) 2005 Elsevier B.V. All rights reserved.