Extensive intragenic recombination and patterns of linkage disequilibrium at the CSN3 locus in European rabbit

Kappa-casein (CSN3) plays an important role in stabilising the Ca-sensitive caseins in the micelle. The European rabbit (Oryctolagus cuniculus) CSN3 has previously been shown to possess two alleles (A and B), which differ deeply in their intronic regions (indels of 100 and 1550 nucleotides in introns 1 and 4, respectively). Furthermore, a correlation between several reproductive performance traits and the different alleles was described. However, all these data were exclusively collected in rabbit domestic breeds, preventing a deeper understanding of the extensive polymorphism observed in the CSN3 gene. Additionally, the techniques available for the typing of both indel polymorphisms were until now not suitable for large-scale studies. In this report, we describe a simple, PCR-based typing method to distinguish rabbit CSN3 alleles. We analyse both ancient wild rabbit populations from the Iberian Peninsula and France, and the more recently derived English wild rabbits and domestic stocks. A new allele (C) showing another major indel (250 bp) in intron 1 was found, but exclusively detected in Iberian wild rabbits. In addition, our survey revealed the occurrence of new haplotypes in wild populations, suggesting that intragenic recombination is important in creating genetic diversity at this locus. This easy and low cost single-step PCR-based method results in an improvement over previous described techniques, can be easily set up in a routine molecular laboratory and would probably be a valuable tool in the management of rabbit domestic breeds

Quantification of reachable attractors in asynchronous discrete dynamics

Motivation: Models of discrete concurrent systems often lead to huge and complex state transition graphs that represent their dynamics. This makes difficult to analyse dynamical properties. In particular, for logical models of biological regulatory networks, it is of real interest to study attractors and their reachability from specific initial conditions, i.e. to assess the potential asymptotical behaviours of the system. Beyond the identification of the reachable attractors, we propose to quantify this reachability. Results: Relying on the structure of the state transition graph, we estimate the probability of each attractor reachable from a given initial condition or from a portion of the state space. First, we present a quasi-exact solution with an original algorithm called Firefront, based on the exhaustive exploration of the reachable state space. Then, we introduce an adapted version of Monte Carlo simulation algorithm, termed Avatar, better suited to larger models. Firefront and Avatar methods are validated and compared to other related approaches, using as test cases logical models of synthetic and biological networks. Availability: Both algorithms are implemented as Perl scripts that can be freely downloaded from http://compbio.igc.gulbenkian.pt/nmd/node/59 along with Supplementary Material.Comment: 19 pages, 2 figures, 2 algorithms and 2 table

Devolução do devoluto à comunidade: metodologia para intervenção em centros comerciais de Braga

Dissertação de mestrado em Cidade e TerritórioExistem no centro urbano de Braga v árias estruturas de concentração de comércio (centros e galerias comerciais construídos entre os anos 70 e 80 do Século XX) cujo insucesso est á visível no progressivo ou quase total abandono dos espaços das lojas e no fluxo residual de pessoas que as frequentam. Uma vez que a comunidade não encontra utilidade nas estruturas supracitadas, impõe-se uma reformulação crítica das suas características espaciais e programáticas atrav és da qualificação e transformação das valências designadas originalmente. Para complemento da reformulação, terão de ser simultaneamente revistos os pr óprios modos de gestão e de propriedade dos edifícios. Atrav és de uma análise de aprofundamento dos fenómenos que afectam as 18 estruturas comerciais identificadas na cidade, procura-se o desenvolvimento de um olhar específico e de produção de raciocínios críticos sobre elas, de modo a constituir uma metodologia de intervenção extensível a casos análogos aos estudados em Braga. O ensaio das medidas de remodelação espacial e programática num dos edifícios é demonstrativo não só da viabilidade dos centros e galerias comerciais devolutos para intervenção, como também da importância que essa pode ter na dinamização das respectivas envolventes, no contributo para a resolução de problemas funcionais locais e da pr ópria cidade, no combate à segregação social e geracional e, em suma, na sustentabilidade do edificado urbano.In Braga’s city center we can identify several commercial structures (shopping centres and commercial galleries built between the 70’s and the 80’s of the 20th century) whose functional failure is depicted in the progressive or almost total abandonment of its spaces and the residual flow of users. Once the community can’t find the referred structures useful it is ought to make an enlightened reformulation of their spacial and functional properties through qualification and transformation of the originally assigned purposes. The management and ownership concepts of these buildings must also be reviewed to ensure the extent of the reformulation. Through a deep analysis of the phenomena that affect the 18 commercial structures identified in this city, it is pretended to develop a specific way of looking and producing judgements about them, to generate an intervention method applicable to all the cases similar to the ones of Braga. The rehearsal of the spacial and functional improvements, in one of the buildings, shows the shopping centres and commercial galleries are improvable and the importance that action can have in the stimulation of the surrounding areas, the contribution to solve local and even global functional problems, the opposition to social and generational segregations and to assure the sustainability of the city