The effect of redundancy and neutrality in genetic search

An experimental study aimed at assessing the influence of redundancy and neutrality on the performance of an (1+1)-ES evolution strategy modeled using Markov chains and applied to NK fitness landscapes is presented. For the study, two families of redundant binary representations, one non-neutral family which is based on linear transformations and that allows the phenotypic neighborhoods to be designed in a simple and effective way, and the neutral family based on the mathematical formulation of error control codes are used. The results indicate whether redundancy or neutrality affects more strongly the behavior of the algorithm used.

Evaluation of fruit and seed diversity and characterization of carob (Ceratonia siliqua L.) cultivars in Algarve region

The genetic diversity of 15 carob ( Ceratonia siliqua L.) cultivars located in an experimental field from Algarve (Portugal) was evaluated over 7 years using 12 fruit and seed phenotypic characters, in order to characterize carob cultivars. The values of morphological traits obtained by cultiv ar were compared with those from other countries of the Mediterranean basin. Statistically significant differences were found between cultivars for al l characters which were examined, what indicates a high genetic diversity. The relationship among these characters was analyzed by principal component analysis (PCA) resulting in the separation of these cultivars classed in four groups (clusters I–IV) and in four ungrouped cultivars. A three dimension of the model was found to be significant and explained 74.5% of the total variation, in which the first component accounting for 34.6% of the total variation is dominated by fruit characters, while the second component is dominated by seed characters. Cultivars plotted on the left-lower quadrant on the space determined by principal components 1 and 2 are characterized by fruits with high seed yield more appropriated for industrial rentability. The correlation analyses established by cultivar provided a specific understanding about the way how fruit and seed characteristics correlate within each cultivar. This approach can be useful for the development of a breeding programme, aiming to increase the seed yield, seed thickness, individual and total seed weight by fruit, characteristics that are determinant to improve the industrial exploitation of carob.

Study of influence of regulatory polymorphisms of expression in development of breast cancer

The human genome has millions of genetics variants that can affect gene expression. These variants are known as cis-regulatory variants and are responsible for intra-species phenotypic differences and individual susceptibility to disease. One of the diseases affected by cis-regulatory variants is breast cancer. Breast cancer is one of the most common cancers, with approximately 4500 new cases each year in Portugal. Breast cancer has many genes mutated and TP53 has been shown to be relevant for this disease. TP53 is one of the most commonly mutated genes in human cancer and it is involved in cell cycle regulation and apoptosis. Previous work by Maia et al has shown that TP53 has differential allelic expression (DAE), which suggests that this gene may be under the influence of cis-regulatory variants. Also, its DAE pattern is totally altered in breast tumours with normal copy number. We hypothesized that cis-regulatory variants affecting TP53 may have a role in breast cancer development and treatment. The present work aims to identify the cis-regulatory variants playing a role in TP53 expression, using in silico, in vitro and in vivo approaches. By bioinformatic tools we have identified candidate cis-regulatory variants and predicted the possible transcription factor binding sites that they affect. By EMSA we studied DNA-protein interactions in this region of TP53. The in silico analysis allowed us to identified three candidate cis-regulatory SNPs which may affect the binding of seven transcription factors. However, the EMSA experiments have not been conclusive and we have not yet confirmed whether any of the identified SNPs are associated with gene expression control of TP53. We will carry out further experiments to validate our findings.

The downy mildew resistance locus Pp523 is located on chromosome C8 of Brassica oleracea L.

We have previously constructed a genetic map of Brassica oleracea L. containing the Pp523 locus that confers downy mildew resistance to adult plants. In this work, 44 SSR markers of reference for the Brassica C genome chromosomes were added to the map, allowing the nine major linkage groups to be assigned to the nine chromosomes of B. oleracea. Locus Pp523 was located on chromosome C8, and a locus determining flower colour was mapped to chromosome C3. In comparison with the first version of the map, the new map is denser and more compact. The available genomic information on B. oleracea was enriched with the chromosome location of two phenotypic traits and 421 DNA markers (RAPD, ISSR, AFLP, SCAR, BAC-end derived STS, SSR and other PCR markers). Conversely, the genomic information on B. oleracea chromosome C8 is being used as an additional tool for the map-based cloning of Pp523, the first gene for adult plant resistance to downy mildew precisely located to a specific chromosome of this crop species.