Retention Modelling of Phenoxy Acid Herbicides in Reversed-Phase HPLC under Gradient Elution.

Phenoxy acid herbicides are used worldwide and are potential contaminants of drinking water. Reversed phase high-performance liquid chromatography (RP-HPLC) is commonly used to monitor phenoxy acid herbicides in water samples. RP-HPLC retention of phenoxy acids is affected by both mobile phase composition and pH, but the synergic effect of these two factors, which is also dependent on the structure and pKa of solutes, cannot be easily predicted. In this paper, to support the setup of RP-HPLC analysis of phenoxy acids under application of linear mobile phase gradients we modelled the simultaneous effect of the molecular structure and the elution conditions (pH, initial acetonitrile content in the eluent and gradient slope) on the retention of the solutes. In particular, the chromatographic conditions and the molecular descriptors collected on the analyzed compounds were used to estimate the retention factor k by Partial Least Squares (PLS) regression. Eventually, a variable selection approach, Genetic Algorithms, was used to reduce the model complexity and allow an easier interpretation. The PLS model calibrated on the retention data of 15 solutes and successively tested on three external analytes provided satisfying and reliable results.

Authentication of an Italian PDO hazelnut ("Nocciola Romana") by NIR spectroscopy.

Common hazelnuts are widely present in human diet all over the world, and their beneficial effects on the health have been extensively investigated and demonstrated. Different in-depth researches have highlighted that the harvesting area can define small variations in the chemical composition of the fruits, affecting their quality. As a consequence, it has become relevant to develop methodologies which would allow authenticating and tracing hazelnuts. In the light of this, the present work aims to develop a non-destructive method for the authentication of a specific high-quality Italian hazelnut, "Nocciola Romana," registered with a protected designation of origin (PDO). Thus, different samples of this fruit have been analyzed by near-infrared (NIR) spectroscopy and then classification models have been built, in order to distinguish between the PDO fruits and the hazelnuts not coming from the designated region. In particular, two different classification approaches have been tested, a discriminant one, partial least squares-discriminant analysis, and a class-modeling one, soft independent modeling of class analogies. Both methods led to very high prediction capability in external validation on a test set (classification accuracy in one case, and sensitivity and specificity in the other, all higher than 92%), suggesting that the proposed methodologies are suitable for a rapid and non-destructive authentication of the product.

MetaBase--the wiki-database of biological databases.

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

miSolRNA: A tomato micro RNA relational database.

BACKGROUND: The economic importance of Solanaceae plant species is well documented and tomato has become a model for functional genomics studies. In plants, important processes are regulated by microRNAs (miRNA). DESCRIPTION: We describe here a data base integrating genetic map positions of miRNA-targeted genes, their expression profiles and their relations with quantitative fruit metabolic loci and yield associated traits. miSolRNA provides a metadata source to facilitate the construction of hypothesis aimed at defining physiological modes of action of regulatory process underlying the metabolism of the tomato fruit. CONCLUSIONS: The MiSolRNA database allows the simple extraction of metadata for the proposal of new hypothesis concerning possible roles of miRNAs in the regulation of tomato fruit metabolism. It permits i) to map miRNAs and their predicted target sites both on expressed (SGN-UNIGENES) and newly annotated sequences (BAC sequences released), ii) to co-locate any predicted miRNA-target interaction with metabolic QTL found in tomato fruits, iii) to retrieve expression data of target genes in tomato fruit along their developmental period and iv) to design further experiments for unresolved questions in complex trait biology based on the use of genetic materials that have been proven to be a useful tools for map-based cloning experiments in Solanaceae plant species.

Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits.

With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.