Browsing by Issue Date, starting with "2007"
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- The evolution of protein complexes by duplication of homomeric interactionsPublication . Pereira Leal, J.B.; Levy, E.D.; Kamp, C.; Teichmann, S.A.BACKGROUND: Cellular functions are accomplished by the concerted actions of functional modules. The mechanisms driving the emergence and evolution of these modules are still unclear. Here we investigate the evolutionary origins of protein complexes, modules in physical protein-protein interaction networks. RESULTS: We studied protein complexes in Saccharomyces cerevisiae, complexes of known three-dimensional structure in the Protein Data Bank and clusters of pairwise protein interactions in the networks of several organisms. We found that duplication of homomeric interactions, a large class of protein interactions, frequently results in the formation of complexes of paralogous proteins. This route is a common mechanism for the evolution of complexes and clusters of protein interactions. Our conclusions are further confirmed by theoretical modelling of network evolution. We propose reasons for why this is favourable in terms of structure and function of protein complexes. CONCLUSION: Our study provides the first insight into the evolution of functional modularity in protein-protein interaction networks, and the origins of a large class of protein complexes.
- Mapping of quantitative trait loci using the skew-normal distributionPublication . Fernandes, Elisabete; Pacheco, António; Penha-Gonçalves, CarlosIn standard interval mapping (IM) of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. When this assumption of normality is violated, the most commonly adopted strategy is to use the previous model after data transformation. However, an appropriate transformation may not exist or may be difficult to find. Also this approach can raise interpretation issues. An interesting alternative is to consider a skew-normal mixture model in standard IM, and the resulting method is here denoted as skew-normal IM. This flexible model that includes the usual symmetric normal distribution as a special case is important, allowing continuous variation from normality to non-normality. In this paper we briefly introduce the main peculiarities of the skew-normal distribution. The maximum likelihood estimates of parameters of the skew-normal distribution are obtained by the expectation-maximization (EM) algorithm. The proposed model is illustrated with real data from an intercross experiment that shows a significant departure from the normality assumption. The performance of the skew-normal IM is assessed via stochastic simulation. The results indicate that the skew-normal IM has higher power for QTL detection and better precision of QTL location as compared to standard IM and nonparametric IM.
- Allelic penetrance approach as a tool to model twolocusPublication . Sepúlveda, Nuno; Paulino, Carlos Daniel; Carneiro, Jorge; Penha-Gonçalves, CarlosMany binary phenotypes do not follow a classical Mendelian inheritance pattern. Interaction between genetic and environmental factors is thought to contribute to the incomplete penetrance phenomena often observed in these complex binary traits. Several two-locus models for penetrance have been proposed to aid the genetic dissection of binary traits. Such models assume linear genetic effects of both loci in different mathematical scales of penetrance, resembling the analytical framework of quantitative traits. However, changes in phenotypic scale are difficult to envisage in binary traits and limited genetic interpretation is extractable from current modeling of penetrance. To overcome this limitation, we derived an allelic penetrance approach that partitioned incomplete penetrance into the alleles controlling the phenotype and into the genetic background and environmental factors. We applied this approach to formulate dominance and recessiveness in a single biallelic locus and to model different genetic mechanisms for the joint action of two biallelic loci. We fit the models to data on the susceptibility of mice following infections with Listeria monocytogenes and Plasmodium berghei. These models gain in genetic interpretation, because they specify the alleles that are responsible for the genetic (inter)action and their genetic nature (dominant or recessive), and predict genotypic combinations determining the phenotype. Further, we show via computer simulations that the proposed models produce penetrance patterns not captured by traditional twolocus models. This approach provides a new analysis framework for dissecting mechanisms of interlocus joint action in binary traits using genetic crosses.
- Controlling excludability in the evolution of cooperationPublication . Dionisio, F.; Gordo, I.Background: A tragedy of the commons arises if individuals cannot protect their future use of a depletable resource, and individual fitness increases if individuals exploit the resource at rates beyond sustainability. Natural selection then forces the individuals to diminish, perhaps even to destroy, their resource. One way to protect future use is privatization - that is, locally excluding rivals from the resource. Another is to reduce rivalry among individuals by restricting exploitation rates.
- Total and functional parasite specific IgE responses in Plasmodium falciparum-infected patients exhibiting different clinical statusPublication . Duarte, J.; Deshpande, P.; Guiyedi, V.; Mecheri, S.; Fesel, C.; Cazenave, P.A.; Mishra, G.C.; Kombila, M.; Pied, S.Blood samples were collected from controls and P. falciparum-infected patients before treatment on the day of hospitalization (day 0) in India and, in addition, on days 7 and 30 after treatment in Gabon. Total IgE levels were determined by ELISA and functional P. falciparum-specific IgE were estimated using a mast cell line RBL-2H3 transfected with a human Fcε RI α-chain that triggers degranulation upon human IgE cross-linking. Mann Whitney and Kruskall Wallis tests were used to compare groups and the Spearman test was used for correlations. Total IgE levels were confirmed to increase upon infection and differ with level of transmission and age but were not directly related to the disease phenotype. All studied groups exhibited functional parasite-specific IgEs able to induce mast cell degranulation in vitro in the presence of P. falciparum antigens. Plasma IgE levels correlated with those of IL-10 in uncomplicated malaria patients from Gabon. In Indian patients, plasma IFN-γ , TNF and IL-10 levels were significantly correlated with IgE concentrations in all groups.
- Low frequency of CD4(+) CD25(+) Treg in SLE patients: a heritable trait associated with CTLA4 and TGF gene variantsPublication . Barreto, M.; Ferreira, RC.; Lourenço, L.; Moraes-Fontes, MF.; Santos, E.; Alves, M.; Carvalho, C.; Martins, B.; Andreia, R.; Viana, JF.; Vasconcelos, C.; Mota-Vieira, L.; Ferreira, C.; Demengeot, J.; Vicente, AM.Background: CD4(+)CD25(+) regulatory T cells play an essential role in maintaining immune homeostasis and preventing autoimmunity. Therefore, defects in Treg development, maintenance or function have been associated with several human autoimmune diseases including Systemic Lupus Erythematosus (SLE), a systemic autoimmune disease characterized by loss of tolerance to nuclear components and significantly more frequent in females.
- Selection against males in Caenorhabditis elegans under two mutational treatmentsPublication . Manoel, D; Carvalho, S; Phillips, PC; Teotónio, HWithin populations with mixed mating systems, selfing is expected to be favoured over outcrossing unless a countervailing process such as severe inbreeding depression is present. In this study, we consider the relationship between the expression of deleterious alleles and the maintenance of outcrossing in the nematode species, Caenorhabditis elegans. This species is characterized by an androdioecious breeding system composed of males at low frequency and self-fertilizing hermaphrodites that can only outcross via males. Here, we find that experimentally increasing the mutational load in four different isogenic wild isolates using 10 generations of Ethylmethane sulphonate (EMS) and UV irradiation mutagenesis significantly diminishes the cost of males. Males are maintained at higher frequencies in mutagenized versus non-mutagenized populations. Nevertheless, males still tend to be driven to low frequencies within isolates that are known to be prone to lose males. Further, we determine the viability effects of a single round of mutagen exposure and find that, for EMS, outcrossing overcomes the almost completely recessive and nearly lethal effects generated. We briefly interpret our results in light of current evolutionary theory of outcrossing rates.
- The reinfection threshold regulates pathogen diversity: the case of influenzaPublication . Gokaydin, D.; Oliveira-Martins, J. B.; Gordo, I.; Gomes, M. G. M.The awareness that pathogens can adapt and evolve over relatively short time-scales is changing our view of infectious disease epidemiology and control. Research on the transmission dynamics of antigenically diverse pathogens is progressing and there is increasing recognition for the need of new concepts and theories. Mathematical models have been developed considering the modelling unit in two extreme scales: either diversity is not explicitly represented or diversity is represented at the finest scale of single variants. Here, we use an intermediate approach and construct a model at the scale of clusters of variants. The model captures essential properties of more detailed systems and is much more amenable to mathematical treatment. Specificities of pathogen clusters and the overall potential for transmission determine the reinfection rates. These are, in turn, important regulators of cluster dynamics. Ultimately, we detect a reinfection threshold (RT) that separates different behaviours along the transmissibility axis: below RT, levels of infection are low and cluster substitutions are probable; while above RT, levels of infection are high and multiple cluster coexistence is the most probable outcome
- The reinfection threshold regulates pathogen diversity: the case of influenzaPublication . Gokaydin, D.; Oliveira-Martins, J.B.; Gordo, I.; Gomes, M.G.M.The awareness that pathogens can adapt and evolve over relatively short time-scales is changing our view of infectious disease epidemiology and control. Research on the transmission dynamics of antigenically diverse pathogens is progressing and there is increasing recognition for the need of new concepts and theories. Mathematical models have been developed considering the modelling unit in two extreme scales: either diversity is not explicitly represented or diversity is represented at the finest scale of single variants. Here, we use an intermediate approach and construct a model at the scale of clusters of variants. The model captures essential properties of more detailed systems and is much more amenable to mathematical treatment. Specificities of pathogen clusters and the overall potential for transmission determine the reinfection rates. These are, in turn, important regulators of cluster dynamics. Ultimately, we detect a reinfection threshold (RT) that separates different behaviours along the transmissibility axis: below RT, levels of infection are low and cluster substitutions are probable; while above RT, levels of infection are high and multiple cluster coexistence is the most probable outcome.
- Drug resistance in tuberculosis - a reinfection modelPublication . Rodrigues, P.; Gomes, M. G. M.; Rebelo, C.There is increasing recognition that reinfection is an important component of TB transmission. Moreover, it has been shown that partial immunity has significant epidemiological consequences, particularly in what concerns disease prevalence and effectiveness of control measures. We address the problem of drug resistance as a competition between two types of strains of Mycobacterium tuberculosis: those that are sensitive to anti-tuberculosis drugs and those that are resistant. Our objective is to characterise the role of reinfection in the transmission of drug-resistant tuberculosis. The long-term behaviour of our model reflects how reinfection modifies the conditions for coexistence of sensitive and resistant strains. This sets the scene for discussing how strain prevalence is affected by different control strategies. It is shown that intervention effectiveness is highly sensitive to the baseline epidemiological setting.