Satellyptus: analysis and database of microsatellites from ESTs of Eucalyptus

The main goal of our research was to search for SSRs in the Eucalyptus EST FORESTs database (using a software for mining SSR-motifs). With this objective, we created a database for cataloging Eucalyptus EST-derived SSRs, and developed a bioinformatics tool, named Satellyptus, for finding and analyzing microsatellites in the Eucalyptus EST database. The search for microsatellites in the FORESTs database containing 71,115 Eucalyptus EST sequences (52.09 Mb) revealed 20,530 SSRs in 15,621 ESTs. The SSR abundance detected on the Eucalyptus ESTs database (29% or one microsatellite every four sequences) is considered very high for plants. Amongst the categories of SSR motifs, the dimeric (37%) and trimeric ones (33%) predominated. The AG/CT motif was the most frequent (35.15%) followed by the trimeric CCG/CGG (12.81%). From a random sample of 1,217 sequences, 343 microsatellites in 265 SSR-containing sequences were identified. Approximately 48% of these ESTs containing microsatellites were homologous to proteins with known biological function. Most of the microsatellites detected in Eucalyptus ESTs were positioned at either the 5 or 3 end. Our next priority involves the design of flanking primers for codominant SSR loci, which could lead to the development of a set of microsatellite-based markers suitable for marker-assisted Eucalyptus breeding programs.

Clinical and microbiological performance of resin-modified glass-ionomer liners after incomplete dentine caries removal

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Delimiting genetic units in Neotropical toads under incomplete lineage sorting and hybridization

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Updated Brazilian database on food carotenoids: Factors affecting carotenoid composition

This article updates the Brazilian database on food carotenoids. Emphasis is on carotenoids that have been demonstrated important to human health: alpha-carotene, beta-carotene, beta-cryptoxanthin, lycopene, lutein and zeaxanthin. The sampling and sample preparation strategies and the analytical methodology are presented. Possible sources of analytical errors, as well as the measures taken to avoid them, are discussed. Compositional variation due to such factors as variety/cultivar, stage of maturity, part of the plant utilized, climate or season and production technique are demonstrated. The effects of post-harvest handling, preparation, processing and storage of food on the carotenoid composition are also discussed. The importance of biodiversity is manifested by the variety of carotenoid sources and the higher levels of carotenoids in native, uncultivated or semi-cultivated fruits and vegetables in comparison to commercially produced crops. (C) 2008 Elsevier B.V. All rights reserved.

Relational learning in children with deafness and cochlear implants

This four-experiment series sought to evaluate the potential of children with neurosensory deafness and cochlear implants to exhibit auditory-visual and visual-visual stimulus equivalence relations within a matching-to-sample format. Twelve children who became deaf prior to acquiring language (prelingual) and four who became deaf afterwards (postlingual) were studied. All children learned auditory-visual conditional discriminations and nearly all showed emergent equivalence relations. Naming tests, conducted with a subset of the: children, showed no consistent relationship to the equivalence-test outcomes.. This study makes several contributions: to the literature on stimulus equivalence. First; it demonstrates that both pre- and postlingually deaf children-can: acquire auditory-visual equivalence-relations after cochlear implantation, thus demonstrating symbolic functioning. Second, it directs attention to a population that may be especially interesting for researchers seeking to analyze the relationship. between speaker and listener repertoires. Third, it demonstrates the feasibility of conducting experimental studies of stimulus control processes within the limitations of a hospital, which these children must visit routinely for the maintenance of their cochlear implants.

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.

An integrated database on ticks and tick-borne zoonoses in the tropics and subtropics with special reference to developing and emerging countries

Tick-borne zoonoses (TBZ) are emerging diseases worldwide. A large amount of information (e.g. case reports, results of epidemiological surveillance, etc.) is dispersed through various reference sources (ISI and non-ISI journals, conference proceedings, technical reports, etc.). An integrated database-derived from the ICTTD-3 project (http://www.icttd.nl)-was developed in order to gather TBZ records in the (sub-)tropics, collected both by the authors and collaborators worldwide. A dedicated website (http://www.tickbornezoonoses.org) was created to promote collaboration and circulate information. Data collected are made freely available to researchers for analysis by spatial methods, integrating mapped ecological factors for predicting TBZ risk. The authors present the assembly process of the TBZ database: the compilation of an updated list of TBZ relevant for (sub-)tropics, the database design and its structure, the method of bibliographic search, the assessment of spatial precision of geo-referenced records. At the time of writing, 725 records extracted from 337 publications related to 59 countries in the (sub-)tropics, have been entered in the database. TBZ distribution maps were also produced. Imported cases have been also accounted for. The most important datasets with geo-referenced records were those on Spotted Fever Group rickettsiosis in Latin-America and Crimean-Congo Haemorrhagic Fever in Africa. The authors stress the need for international collaboration in data collection to update and improve the database. Supervision of data entered remains always necessary. Means to foster collaboration are discussed. The paper is also intended to describe the challenges encountered to assemble spatial data from various sources and to help develop similar data collections.

A Fast Large Scale Iris Database Classification with Optimum-Path Forest Technique: A Case Study

Majority of biometric researchers focus on the accuracy of matching using biometrics databases, including iris databases, while the scalability and speed issues have been neglected. In the applications such as identification in airports and borders, it is critical for the identification system to have low-time response. In this paper, a graph-based framework for pattern recognition, called Optimum-Path Forest (OPF), is utilized as a classifier in a pre-developed iris recognition system. The aim of this paper is to verify the effectiveness of OPF in the field of iris recognition, and its performance for various scale iris databases. This paper investigates several classifiers, which are widely used in iris recognition papers, and the response time along with accuracy. The existing Gauss-Laguerre Wavelet based iris coding scheme, which shows perfect discrimination with rotary Hamming distance classifier, is used for iris coding. The performance of classifiers is compared using small, medium, and large scale databases. Such comparison shows that OPF has faster response for large scale database, thus performing better than more accurate but slower Bayesian classifier.

Use of a semantically grained database system for distribution and control within design environments

This paper presents a technique to share the data stored in an object-oriented database aimed at designing environments. This technique shares data between two related databases, called the Original and Product databases, and is composed of three processes: data separation, evolution and integration. Whenever a block of data needs to be shared, it is spread into both databases, resulting in a block on the original database, and another into the Product database, with special links between them controlled by the Object Manager. These blocks do not need to be maintained identical during the evolution phase of the sharing process. Six types of links were defined, and by choosing one, the designer control the evolution and reintegration of the block in both databases. This process uses the composite object concept as the unit of control. The presented concepts can be applied to any data model with support to composite objects.