GMODWeb: a web framework for the generic model organism database

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from .     

Four New Species of Rhagovelia (Heteroptera: Veliidae) from Minas Gerais (Brazil), with a Key to the Regional Species of the angustipes Complex

Four new species of Rhagovelia, R. ochroischion, R. turmalis, R. sbolos, and R. trianguloides, are described from Minas Gerais, Brazil, along with the previously unknown female of R. triangula Drake. A key to the Rhagovelia species of the angustipes complex known from Minas Gerais and adjacent areas is provided.     

The Human PAX6 Mutation Database.

The Human PAX6 Mutation Database contains details of 94 mutations of the PAX6 gene. A Microsoft Access program is used by the Curator to store, update and search the database entries. Mutations can be entered directly by the Curator, or imported from submissions made via the World Wide Web. The PAX6 Mutation Database web page at URL http://www.hgu.mrc.ac.uk/Softdata/PAX6/ provides information about PAX6, as well as a fill-in form through which new mutations can be submitted to the Curator. A search facility allows remote users to query the database. A plain text format file of the data can be downloaded via the World Wide Web. The Curation program contains prior knowledge of the genetic code and of the PAX6 gene including cDNA sequence, location of intron/exon boundaries, and protein domains, so that the minimum of information need be provided by the submitter or Curator.     

ASAP: automated sequence annotation pipeline for web-based updating of sequence information with a local dynamic database

The automated sequence annotation pipeline (ASAP) is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible resources and maintenance of a local database. The system allows easy use of the output from one search as the input for a new search, as well as the filtering of results. The database is used to store formats and parameters and information for parsing data from web sites. The database permits easy updating of format information should a site modify the format of a query or of a returned web page.     

Phylogeography of Plathymenia reticulata (Leguminosae) reveals patterns of recent range expansion towards northeastern Brazil and southern Cerrados in Eastern Tropical South America

Little is known about past vegetation dynamics in Eastern Tropical South America (ETSA). Here we describe patterns of chloroplast (cp) DNA variation in Plathymenia reticulata, a widespread tree in the ETSA Atlantic Forest and Cerrado biomes, but not found in the xeromorphic Caatinga. Forty one populations, comprising 220 individuals, were analysed by sequencing the trnS‐trnG and trnL‐trnL‐trnF cpDNA regions. Combined, they resulted in 18 geographically structured haplotypes. The central region of the sampling area, comprising Minas Gerais and Goiás Brazilian states, is a centre of genetic diversity and probably the most longstanding area of the distribution range of the species. In contrast, populations from northeastern Brazil and the southern Cerrados showed very low diversity levels, almost exclusively with common haplotypes which are also found in the central region. Coupled with a long‐branched star‐like network, these patterns suggest a recent range expansion of P. reticulata to those regions from central region sources. The recent origin of the species (in the early Pleistocene) or the extinction of some populations due to drier and cooler climate during the last glacial maximum could have been responsible for that phylogeographic pattern. The populations from northeastern Brazil originated from two colonization routes, one eastern (Atlantic) and one western (inland). Due to its high diversity and complex landscape, the central region, especially central‐north Minas Gerais (between 15°–18° S and 42°–46° W), should be given the highest priority for conservation.     

Bromeliaceae diversity and conservation in Minas Gerais state,Brazil

Field work and data from herbaria collections (2686 records) representing 283 taxa (265 species and 18 infraspecific taxa) of Bromeliaceae occurring at Minas Gerais state, southeastern Brazil, were analyzed in order to obtain distribution and diversity information, and to determine IUCN (The World Conservation Union) conservation status for each taxon. A map containing 1° × 1° grid cells was used to identify priority areas for new research collections, areas of high species diversity, and Bromeliaceae conservation status. A clear decrease in Bromeliaceae diversity is observed between the eastern and the western portions of Minas Gerais, and low floristic similarities were found between neighboring grid cells. The rocky mountains of Cadeia do Espinhaço are considered the most important area for Bromeliaceae endemics. From the 283 taxa of Bromeliaceae that occur at Minas Gerais, 118 (42%) are considered threatened, and 124 taxa (44% of the total) do not occur inside any protected area. The region of the Quadrilátero Ferrífero in the southern portion of the Cadeia do Espinhaço is the most threatened, and urgent strategies for conservation of this rich Bromeliaceae flora are needed. Northeastern Minas Gerais, particularly the rocky outcrops or inselbergs located in the Jequitinhonha and Mucuri rivers drainage basins need additional collection efforts and conservation actions focused on these saxicolous taxa.     

Three new species of Peristicta Hagen in Selys (Odonata: Zygoptera: Protoneuridae) from Brazil

Three new species of Peristicta Hagen in Selys from Brazil are described and illustrated: P. janiceae from Minas Gerais State (Diamantina, Gouvêa, Lagoa Santa, Serra do Cara?a, Serra do Cipó, Urobotanga), P. jalmosi from Goiás State (Chapada dos Veadeiros, Reserva da Universidade de Brasília) and Minas Gerais State (Urobotanga, Lagoa Santa, Ponte Nova, S?o Jo?o del Rey,) and P. muzoni from Mato Grosso State (Serra da Bodoquena). An identification key for males of Peristicta is presented.     

PRECIS: protein reports engineered from concise information in SWISS-PROT

MOTIVATION: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords.     

DEPD: a novel database for differentially expressed proteins

SUMMARY: The Differentially Expressed Protein Database was designed to store the output of comparative proteomics studies and provides a publicly available query and analysis platform for data mining. The database contains information about more than 3000 differentially expressed proteins (DEPs) manually extracted from the published literature, including relevant biological, experimental and methodological elements. Tools for visualization and functional analysis of DEPs are provided via a user-friendly webinterface. AVAILABILITY: http://protchem.hunnu.edu.cn/depd/.     

GOfetcher: a database with complex searching facility for gene ontology

MOTIVATION: An important contribution to the Gene Ontology (GO) project is to develop tools that facilitate the creation, maintenance and use of ontologies. Several tools have been created for communicating and using the GO project. However, a limitation with most of these tools is that they suffer from lack of a comprehensive search facility. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: 'Quick Search', 'Advanced Search' and 'Upload Files' for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating GO information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values and the extensible markup language (XML) format. The database is available at http://mcbc.usm.edu/gofetcher/.     

The MUSC DNA Microarray Database

SUMMARY: The Medical University of South Carolina (MUSC) DNA Microarray Database is a web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project/data management system, micro ArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser. In addition to serving as an online resource of gene expression data, the MUSC DNA Microarray Database is a model for other academic DNA microarray data repositories. AVAILABILITY: Browsing and downloading of MUSC DNA Microarray Database information can be done after registration at http://proteogenomics.musc.edu/pss/home.php.     

Genetic diversity of turmeric germplasm (Curcuma longa; Zingiberaceae) identified by microsatellite markers

Turmeric (Curcuma longa) is a triploid, vegetatively propagated crop introduced early during the colonization of Brazil. Turmeric rhizomes are ground into a powder used as a natural dye in the food industry, although recent research suggests a greater potential for the development of drugs and cosmetics. In Brazil, little is known about the genetic variability available for crop improvement. We examined the genetic diversity among turmeric accessions from a Brazilian germplasm collection comprising 39 accessions collected from the States of Goiás, Mato Grosso do Sul, Minas Gerais, S?o Paulo, and Pará. For comparison, 18 additional genotypes were analyzed, including samples from India and Puerto Rico. Total DNA was extracted from lyophilized leaf tissue and genetic analysis was performed using 17 microsatellite markers (single-sequence repeats). Shannon-Weiner indexes ranged from 0.017 (Minas Gerais) to 0.316 (S?o Paulo). Analyses of molecular variance (AMOVA) demonstrated major differences between countries (63.4%) and that most of the genetic diversity in Brazil is found within states (75.3%). Genotypes from S?o Paulo State were the most divergent and potentially useful for crop improvement. Structure analysis indicated two main groups of accessions. These results can help target future collecting efforts for introduction of new materials needed to develop more productive and better adapted cultivars.     

A new species of <Emphasis Type="Italic">Orthophytum</Emphasis> (Bromeliaceae,Bromelioideae) from Minas Gerais,Brazil

Orthophytum vidaliorum, a new species from Minas Gerais, Brazil, is described and illustrated, and its relationship to Orthophytum itambense is discussed.     

A new species of Microlicia (Melastomataceae) from Brazil

A new species of the genusMicrolicia,M. flava, from the highland “campo rupestre” vegetation of Serra da Canastra National Park, São Roque de Minas, Minas Gerais, Brazil, is described and illustrated.     

Validation of the name <Emphasis Type="Italic">Microlicia petiolulata</Emphasis> (Melastomataceae), a new species from the Espinhaço Range,Minas Gerais,Brazil

A new species of Microlicia (Melastomataceae) from Diamantina, Minas Gerais, Brazil is described and illustrated and a conservation assessment based on IUCN criteria is given.     

Caseous lymphadenitis in sheep flocks of the state of Minas Gerais,Brazil: Prevalence and management surveys

Corynebacterium pseudotuberculosis is the etiologic agent of caseous lymphadenitis, which is a serious, economically important problem for sheep production. We examined the seroprevalence of infection by C. pseudotuberculosis and possible risk factors associated with caseous lymphadenitis in sheep herds of the state of Minas Gerais, Brazil. Samples were collected from 642 sheep from 97 farms. Sera of all of the sheep were tested with ELISA for antibodies against C. pseudotuberculosis. A questionnaire was applied to gather data on the farm, the sheep herd, the farmer, and individual animal data (breed, sex and age). This is the first sero-epidemiological survey for caseous lymphadenitis in sheep herds in Minas Gerais. We found a high real prevalence, much higher than that suggested from information obtained with the questionnaire, which points to the scarcity of vaccination against caseous lymphadenitis in the sample evaluated. Only a small proportion of the farmers declared that cases of this disease were present in their flocks. The frequency of seropositive sheep varied significantly with breed (χ² test, P = 0.021). Age group also significantly affected the percentage of seropositivity (χ² test, P = 0.049), the highest frequency being found in adult animals (more than 12 months old), when compared to the 5–12 months old group (χ² test, P = 0.021). The prevalence of infection with C. pseudotuberculosis in sheep in the state of Minas Gerais was estimated to be 70.9% (95% confidence interval (CI): 64.7–77.0%) and the prevalence of infected flocks being 95.9% (95% CI: 89.8–98.9%). We concluded that C. pseudotuberculosis infection is widely disseminated in sheep flocks in Minas Gerais and that caseous lymphadenitis control and eradication programs are necessary in this state.     

Variation in Aggressiveness Components in the Hemileia vastatrix Population in Brazil

The Pucciniomycete fungus Hemileia vastatrix causes leaf rust on coffee trees. The pathogen is responsible for considerable yield losses in susceptible coffee cultivars if appropriate management strategies are not implemented. Rapid spread and epidemics of rust fungi are usually associated with the emergence of new races of the pathogen that overcome resistance or with the emergence of more aggressive populations of the pathogen. In Brazil, coffee production is dominated by susceptible cultivars of Coffea arabica and Coffea canephora. We assessed aggressiveness in 46 populations of H. vastatrix from Minas Gerais and Espírito Santo, two of the most important coffee‐producing states in Brazil. We observed a significant difference in the incubation period between the populations from Minas Gerais and Espírito Santo when 183 single‐pustule isolates were inoculated onto Catuaí Vermelho IAC 44, a susceptible C. arabica cultivar. Variation in aggressiveness components was observed between and within localities. Isolates with longer incubation periods also tended to have longer latent periods, although there was only a low correlation between these two aggressiveness components (r² = 0.34, P = 2.2 × 10^?16). Low‐sporulating isolates also had significantly longer incubation and latent periods. The H. vastatrix population from Minas Gerais and Espírito Santo is structured by the formation of groups of individuals with differential level of aggressiveness. Our results indicate that the variation in aggressiveness of the Brazilian H. vastatrix population may be associated with the geographic coffee‐producing areas.     

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.