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.

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.

Poincaré plot indexes of heart rate variability: Relationships with other nonlinear variables

The Poincaré plot for heart rate variability analysis is a technique considered geometrical and non-linear, that can be used to assess the dynamics of heart rate variability by a representation of the values of each pair of R-R intervals into a simplified phase space that describes the system's evolution. The aim of the present study was to verify if there is some correlation between SD1, SD2 and SD1/SD2 ratio and heart rate variability nonlinear indexes either in disease or healthy conditions. 114 patients with arterial coronary disease and 65 healthy subjects underwent 30. minute heart rate registration, in supine position and the analyzed indexes were as follows: SD1, SD2, SD1/SD2, Sample Entropy, Lyapunov Exponent, Hurst Exponent, Correlation Dimension, Detrended Fluctuation Analysis, SDNN, RMSSD, LF, HF and LF/HF ratio. Correlation coefficients between SD1, SD2 and SD1/SD2 indexes and the other variables were tested by the Spearman rank correlation test and a regression analysis. We verified high correlation between SD1/SD2 index and HE and DFA (α1) in both groups, suggesting that this ratio can be used as a surrogate variable. © 2013 Elsevier B.V.

Testing search strategies for systematic reviews in the Medline literature database through PubMed

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

The Automatic Mapping of Princeton WordNet Lexical-Conceptual Relations onto the Brazilian Portuguese WordNet Database

Princeton WordNet (WN.Pr) lexical database has motivated efficient compilations of bulky relational lexicons since its inception in the 1980's. The EuroWordNet project, the first multilingual initiative built upon WN.Pr, opened up ways of building individual wordnets, and interrelating them by means of the so-called Inter-Lingual-Index, an unstructured list of the WN.Pr synsets. Other important initiative, relying on a slightly different method of building multilingual wordnets, is the MultiWordNet project, where the key strategy is building language specific wordnets keeping as much as possible of the semantic relations available in the WN.Pr. This paper, in particular, stresses that the additional advantage of using WN.Pr lexical database as a resource for building wordnets for other languages is to explore possibilities of implementing an automatic procedure to map the WN.Pr conceptual relations as hyponymy, co-hyponymy, troponymy, meronymy, cause, and entailment onto the lexical database of the wordnet under construction, a viable possibility, for those are language-independent relations that hold between lexicalized concepts, not between lexical units. Accordingly, combining methods from both initiatives, this paper presents the ongoing implementation of the WN.Br lexical database and the aforementioned automation procedure illustrated with a sample of the automatic encoding of the hyponymy and co-hyponymy relations.