Cartographic analysis of woodlice fauna of the former USSR

An inventory of the woodlice fauna of the former USSR yielded 190 species, 64 of them were recorded from the territory of Russia. According to the cartographic analysis, the limits of distribution of epigean terrestrial isopods over the area, excluding mountains, is explained by temperature. No woodlice records were found outside the isocline of 120 days a year with the mean daily air temperature >10°C. The highest species diversity was found between the isoclines of 180 and 210 days. These areas correspond to forest-steppe and steppe zones.     

InvertNet: a new paradigm for digital access to invertebrate collections

InvertNet, one of the three Thematic Collection Networks (TCNs) funded in the first round of the U.S. National Science Foundation's Advancing Digitization of Biological Collections (ADBC) program, is tasked with providing digital access to ~60 million specimens housed in 22 arthropod (primarily insect) collections at institutions distributed throughout the upper midwestern USA. The traditional workflow for insect collection digitization involves manually keying information from specimen labels into a database and attaching a unique identifier label to each specimen. This remains the dominant paradigm, despite some recent attempts to automate various steps in the process using more advanced technologies. InvertNet aims to develop improved semi-automated, high-throughput workflows for digitizing and providing access to invertebrate collections that balance the need for speed and cost-effectiveness with long-term preservation of specimens and accuracy of data capture. The proposed workflows build on recent methods for digitizing and providing access to high-quality images of multiple specimens (e.g., entire drawers of pinned insects) simultaneously. Limitations of previous approaches are discussed and possible solutions are proposed that incorporate advanced imaging and 3-D reconstruction technologies. InvertNet couples efficient digitization workflows with a highly robust network infrastructure capable of managing massive amounts of image data and related metadata and delivering high-quality images, including interactive 3-D reconstructions in real time via the Internet.     

The Littorina sequence database (LSD)--an online resource for genomic data

We present an interactive, searchable expressed sequence tag database for the periwinkle snail Littorina saxatilis, an upcoming model species in evolutionary biology. The database is the result of a hybrid assembly between Sanger and 454 sequences, 1290 and 147,491 sequences respectively. Normalized and non-normalized cDNA was obtained from different ecotypes of L. saxatilis collected in the UK and Sweden. The Littorina sequence database (LSD) contains 26,537 different contigs, of which 2453 showed similarity with annotated proteins in UniProt. Querying the LSD permits the selection of the taxonomic origin of blast hits for each contig, and the search can be restricted to particular taxonomic groups. The database allows access to UniProt annotations, blast output, protein family domains (PFAM) and Gene Ontology. The database will allow users to search for genetic markers and identifying candidate genes or genes for expression analyses. It is open for additional deposition of sequence information for L. saxatilis and other species of the genus Littorina. The LSD is available at http://mbio-serv2.mbioekol.lu.se/Littorina/.     

蛋白质相互作用数据库及其应用

对蛋白质相互作用及其网络的了解不仅有助于深入理解生命活动的本质和疾病发生的机制,而且可以为药物研发提供靶点.目前,通过高通量筛选、计算方法预测和文献挖掘等方法,获得了大批量的蛋白质相互作用数据,并由此构建了很多内容丰富并日益更新的蛋白质相互作用数据库.本文首先简要阐述了大规模蛋白质相互作用数据产生的3种方法,然后重点介绍了几个人类相关的蛋白质相互作用公共数据库,包括HPRD、BIND、 IntAct、MINT、 DIP 和MIPS,并概述了蛋白质相互作用数据库的整合情况以及这些数据库在蛋白质相互作用网络构建上的应用.     

Raccoon ecology database: A resource for population dynamics modelling and meta-analysis

The value of scientific studies increases and is extended when their data are stored in a manageable and accessible format. This is demonstrated through development of a raccoon ecology database (REDB) to store, manage and disseminate available peer-reviewed and unpublished data on raccoon (Procyon lotor) biology, ecology and raccoon rabies, including citations for data sources. Over 800 documents were identified and citations for them entered into the database as literature references. Approximately 1000 trait values were entered from almost 200 of these sources. These data included estimates of population density, survival rates, rabies incubation period, litter size, body weight, dispersal distance and home-range size, often by age or sex class. Each datum is linked to a citation for its source, and to information about location and land use in the study area, time of year the study was undertaken, sample size, and variance. The relational database design enables querying and easy updating and manipulation of data.

The relational data model is presented, as is its application in further developing an individual-based, spatially-explicit population model of raccoon rabies. Using information queried from the REDB benefits model development by: i) assessing the appropriateness of input parameter values, ii) providing sources for citing input values, iii) parameterising the model to different geographic regions, iv) enabling meta-analyses for evaluating model structure, as well as further contributing to parameterisation at specific locations, and v) providing biologically appropriate parameter input values for model sensitivity testing. The REDB is a useful research resource that will increase in value with ongoing inclusion of data from future raccoon and raccoon rabies studies and serves as a model for database design and research applications to other species. The database and an empty database for use with other species are available online (http://redb.nrdpfc.ca).     

Characterization of new microsatellite markers derived from sequence databases for the emu (Dromaius novaehollandiae)

The emu (Dromaius novaehollandiae), a member of ratite family, is native to Australia and has been introduced to other countries worldwide. In this work, 10 polymorphic microsatellite loci were isolated and characterized for emu from public sequences. Polymorphism was surveyed in 22 individuals from two different populations kept in captivity. Between two and 11 alleles were found per locus, and the observed heterozygosity ranged from 0.05 to 0.85, in accordance with expectations. These markers will be useful as tools for detecting levels of genetic variation, reconstructing pedigrees (for quantitative genetic analysis) and identifying markers associated to fitness traits in emu populations.     

Remote access to ACNUC nucleotide and protein sequence databases at PBIL

The ACNUC biological sequence database system provides powerful and fast query and extraction capabilities to a variety of nucleotide and protein sequence databases. The collection of ACNUC databases served by the Pôle Bio-Informatique Lyonnais includes the EMBL, GenBank, RefSeq and UniProt nucleotide and protein sequence databases and a series of other sequence databases that support comparative genomics analyses: HOVERGEN and HOGENOM containing families of homologous protein-coding genes from vertebrate and prokaryotic genomes, respectively; Ensembl and Genome Reviews for analyses of prokaryotic and of selected eukaryotic genomes. This report describes the main features of the ACNUC system and the access to ACNUC databases from any internet-connected computer. Such access was made possible by the definition of a remote ACNUC access protocol and the implementation of Application Programming Interfaces between the C, Python and R languages and this communication protocol. Two retrieval programs for ACNUC databases, Query_win, with a graphical user interface and raa_query, with a command line interface, are also described. Altogether, these bioinformatics tools provide users with either ready-to-use means of querying remote sequence databases through a variety of selection criteria, or a simple way to endow application programs with an extensive access to these databases. Remote access to ACNUC databases is open to all and fully documented (http://pbil.univ-lyon1.fr/databases/acnuc/acnuc.html).     

The value of georeferenced collection records for predicting patterns of mosquito species richness and endemism in the Neotropics

Abstract.  1. Determining large-scale distribution patterns for mosquitoes could advance knowledge of global mosquito biogeography and inform decisions about where mosquito inventory needs are greatest.
2. Over 43 000 georeferenced records are presented of identified and vouchered mosquitoes from collections undertaken between 1899 and 1982, from 1853 locations in 42 countries throughout the Neotropics. Of 492 species in the data set, 23% were only recorded from one location, and Anopheles albimanus Wiedemann is the most common species.
3. A linear log–log species–area relationship was found for mosquito species number and country area. Chile had the lowest relative density of species and Trinidad-Tobago the highest, followed by Panama and French Guiana.
4. The potential distribution of species was predicted using an Ecological Niche Modelling (ENM) approach. Anopheles species had the largest predicted species ranges, whereas species of Deinocerites and Wyeomyia had the smallest.
5. Species richness was estimated for 1° grids and by summing predicted presence of species from ENM. These methods both showed areas of high species richness in French Guiana, Panama, Trinidad-Tobago, and Colombia. Potential hotspots in endemicity included unsampled areas in Panama, French Guiana, Colombia, Belize, Venezuela, and Brazil.
6. Argentina, The Bahamas, Bermuda, Bolivia, Cuba, and Peru were the most under-represented countries in the database compared with known country species occurrence data. Analysis of species accumulation curves suggested patchiness in the distribution of data points, which may affect estimates of species richness.
7. The data set is a first step towards the development of a global-scale repository of georeferenced mosquito collection records.