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OALib Journal期刊

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Presentación
Signes-Codoer, Juan
Al-Qantara : Revista de Estudios Arabes , 2013,
Abstract: Not available No disponible
Why Should We Care About Molecular Coevolution?
Francisco M. Codoer,Mario A. Fares
Evolutionary Bioinformatics , 2008,
Abstract: Non-independent evolution of amino acid sites has become a noticeable limitation of most methods aimed at identifying selective constraints at functionally important amino acid sites or protein regions. The need for a generalised framework to account for non-independence of amino acid sites has fuelled the design and development of new mathematical models and computational tools centred on resolving this problem. Molecular coevolution is one of the most active areas of research, with an increasing rate of new models and methods being developed everyday. Both parametric and nonparametric methods have been developed to account for correlated variability of amino acid sites. These methods have been utilised for detecting phylogenetic, functional and structural coevolution as well as to identify surfaces of amino acid sites involved in protein-protein interactions. Here we discuss and briefl y describe these methods, and identify their advantages and limitations.
Reducing the false positive rate in the non-parametric analysis of molecular coevolution
Francisco M Codoer, Shirley O'Dea, Mario A Fares
BMC Evolutionary Biology , 2008, DOI: 10.1186/1471-2148-8-106
Abstract: Here we test the effect that variations on the MSA properties have over the sensitivity of non-parametric methods to detect coevolution. We test the effect that the size of the MSA (number of sequences), mean pairwise amino acid distance per site and the strength of the coevolution signal have on the ability of non-parametric methods to detect coevolution. Our results indicate that all three factors have significant effects on the accuracy of non-parametric methods. Further, introducing statistical filters improves the sensitivity and increases the statistical power of the methods to detect functional coevolution. Statistical analysis of the physico-chemical properties of amino acid sites in the context of the protein structure reveals striking dependencies among amino acid sites. Results indicate a covariation trend in the hydrophobicities and molecular weight characteristics of amino acid sites when analysing a non-redundant set of 8000 protein structures. Using this biological information as filter in coevolutionary analyses minimises the false positive rate of these methods. Application of these filters to three different proteins with known functional domains supports the importance of using biological filters to detect coevolution.Coevolutionary analyses using non-parametric methods have proved difficult and highly prone to provide spurious results depending on the properties of MSAs and on the strength of coevolution between amino acid sites. The application of statistical filters to the number of pairs detected as coevolving reduces significantly the number of artifactual results. Analysis of the physico-chemical properties of amino acid sites in the protein structure context reveals their structure-dependent covariation. The application of this known biological information to the analysis of covariation greatly enhances the functional coevolutionary signal and removes historical covariation. Simultaneous use of statistical and biological data is instrumenta
The Fittest versus the Flattest: Experimental Confirmation of the Quasispecies Effect with Subviral Pathogens
Francisco M Codoer,José-Antonio Darós,Ricard V Solé,Santiago F Elena
PLOS Pathogens , 2006, DOI: 10.1371/journal.ppat.0020136
Abstract: The “survival of the fittest” is the paradigm of Darwinian evolution in which the best-adapted replicators are favored by natural selection. However, at high mutation rates, the fittest organisms are not necessarily the fastest replicators but rather are those that show the greatest robustness against deleterious mutational effects, even at the cost of a low replication rate. This scenario, dubbed the “survival of the flattest”, has so far only been shown to operate in digital organisms. We show that “survival of the flattest” can also occur in biological entities by analyzing the outcome of competition between two viroid species coinfecting the same plant. Under optimal growth conditions, a viroid species characterized by fast population growth and genetic homogeneity outcompeted a viroid species with slow population growth and a high degree of variation. In contrast, the slow-growth species was able to outcompete the fast species when the mutation rate was increased. These experimental results were supported by an in silico model of competing viroid quasispecies.
Mutational dynamics of murine angiogenin duplicates
Francisco M Codoer, Silvia Alfonso-Loeches, Mario A Fares
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-310
Abstract: We analysed the phylogenetic asymmetries between the different Ang gene copies in mouse and rat in the context of vertebrate Ang phylogeny. This analysis shows strong evidence in support of accelerated evolution in some Ang murine copies (mAng). This acceleration is not due to non-functionalisation because constraints on amino acid replacements remain strong. We identify many of the amino acid sites involved in signal localization and nucleotide binding by Ang to have evolved under diversifying selection. Compensatory effects of many of the mutations at these paralogs and their key structural location in or nearby important functional regions support a possible functional shift (functional divergence) in many Ang copies. Similarities between 3D-structural models for mAng copies suggest that their divergence is mainly functional.We identify the main evolutionary dynamics shaping the variability of Angiogenin in vertebrates and highlight the plasticity of this protein after gene duplication. Our results suggest functional divergence among mAng paralogs. This puts forward mAng as a good system candidate for testing functional plasticity of such an important protein while stresses caution when using mouse as a model to infer the consequences of mutations in the single Ang copy of humans.Angiogenin (Ang) is a 14 kDa protein that belongs to the pancreatic ribonuclease A (RNase) superfamily [1-3], and is involved in angiogenesis by inducing the formation of blood vessels [3,4]. Ang is over-expressed in tumoral cancer cells [5] and inhibition of Ang function through protein-protein interactions blocks the establishment, progression and metastasis in mice [6-11]. Ang may function as a tRNA-specific ribonuclease that binds to actin on the surface of endothelial cells; once bound, angiogenin is translocated to the nucleus, promoting the endothelial invasiveness necessary for blood vessel formation. The biomedical importance of this protein has been recently pinpointed by studi
Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life
Lothar Wissler, Francisco M Codoer, Jenny Gu, Thorsten BH Reusch, Jeanine L Olsen, Gabriele Procaccini, Erich Bornberg-Bauer
BMC Evolutionary Biology , 2011, DOI: 10.1186/1471-2148-11-8
Abstract: In our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marina and P. oceanica) and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis.These results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence.Lambers and co-authors summarized the uniqueness of seagrasses as follows: "Aquatic angiosperms are perhaps comparable to whales: They returned to the water, preserving some features of terrestrial organisms" [1]. The monocotyledonous seagrasses represent, in fact, a polyphyletic group of plants that can live underwater in fully marine environments. At least three independent seagrass lineages, but no other angiosperm species, have evolved to a life in the marine environment [2,3].Seagrasses consist of about 60 species, most of which superficially resemble terrestrial grasses of the family Poaceae in that they have long, narrow leaves and grow in large meadows. Seagrasses belong to the order of Alismatales which includes 11 families of aquatic-freshwater species and 4 families that are fully marine. The marine families include the Posidoniaceae, Zosteraceae, Hydrocharitaceae, and Cymodoceaceae, and have originated in the Cretaceous period [2]. Phylogenetic analysis of members of the entire order, based on the plastid gene encoding for RuBi
New factors of cardiometabolic risk in severely obese children: influence of pubertal status Nuevos factores de riesgo cardiometabólico en ni os con obesidad severa: influencia del estado puberal
P. Codoer-Franch,R. Murria-Estal,M. Tortajada-Girbés,C. del Castillo-Villaescusa
Nutrición Hospitalaria , 2010,
Abstract: The aim of this prospective study was to evaluate the utility of new biochemical markers to assess cardiometabolic risk in severely obese children and adolescents. A total of 107 subjects aged 7 to 14 years, were clinically assessed and anthropometric measures and percentage of fat mass by single frequency bioimpedance analysis were recorded. Of these, 44 were non-overweight and 63 severely obese (body mass index Z-score >2.5) which were stratified by Tanner stages. To estimate the metabolic risk the following variables were considered for analysis: Waist circumference/height >0.5, fasting glucose >100 mg/dL, triglycerides >110 mg/dL, HDL-C <40 mg/dL, and systolic or diastolic blood pressure >95th percentile for age and gender. Fasting insulinemia, apoprotein A1 and B, high-sensitive C-reactive protein, alanine aminotransferase, homocysteine, and folic and uric acids were determined. In severely obese children, metabolic risk was present more frequently in mid puberty. The normalized anthropometric parameters with respect to 50th percentile for age and gender did not differ in the presence of metabolic risk. Insulin resistance was an independent determinant of metabolic risk, adjusted by Tanner stages. Elevated high-sensitive C-reactive protein was noted without any effect of metabolic risk or pubertal stage. Homocysteine, apoprotein B, and alanine aminotransferase values increased with metabolic risk and were not influenced by puberty. Although insulin resistance remains the main factor influencing metabolic risk, biochemical markers as homocysteine, apoprotein B, and alanine aminotransferase, may be useful for identifying severe obese pubertal subjects particularly prone to comorbidities. El objetivo de este estudio prospectivo ha sido evaluar la utilidad de nuevos marcadores bioquímicos para evaluar el riesgo cardiometabólico en ni os y adolescentes extremadamente obesos. Un total de 107 sujetos de entre 7 a 14 a os, se valoraron clínicamente registrando sus medidas antropométricas y el porcentaje de masa grasa mediante bioimpedancia. De ellos, 44 presentaban un peso normal para su edad y género y 63 estaban gravemente obesos (puntuación Z del índice de masa corporal > 2,5), los cuales fueron estratificados por estadios de Tanner. Para valorar el riesgo metabólico se consideraron las siguientes variables: Circunferencia cintura/altura> 0,5, glucosa en ayunas >100 mg/dL, triglicéridos >110 mg/dL, HDL-C <40 mg/dL y presión arterial sistólica o diastólica > percentil 95 para edad y género. Se determinaron la insulinemia en ayunas, apoproteinas A1 y B, pr
Identidade e economia (I): espelhamento, pertencimento, individualidade
Codo, Wanderley;
Psicologia: Teoria e Pesquisa , 2002, DOI: 10.1590/S0102-37722002000300009
Abstract: considering identity like a social construction of equalities and differences we notice the logical demand to the construction of equivalence in the process of identities formation, what enable us to inquire about relations between identity and economy, based on the assumption that both of theoretical territories are based on exchange relationships between the social agents evolved. observing comparatively the economical development across the history and evolution of the possibilities of identities expression we postulate three different possible identities, witch we call, mirroring, belonging and individuality, corresponding to three different moments of economical development: tribes, slaveries and capitalism. possible implications of this theoretical framework are discussed.
Identidade e economia (I): espelhamento, pertencimento, individualidade
Codo Wanderley
Psicologia: Teoria e Pesquisa , 2002,
Abstract: Partindo de uma defini o de identidade como a constru o social de igualdades e diferen as, constatamos a necessidade lógica de constru o de equivalências para o processo de forma o da identidade. O que nos autoriza a investigar teoricamente os vínculos entre identidade e economia, baseado na constata o de que ambos os territórios se estruturam a partir das rela es de troca. Uma observa o comparada do desenvolvimento econ mico e da evolu o das identidades possíveis nos leva a postular três formas possíveis de constru o da identidade: Espelhamento, pertencimento e individualidade, que correspondem, por sua vez a três momentos de desenvolvimento das rela es de produ o: tribal, escravismo e capitalismo. As possíveis implica es teóricas destas formula es s o discutidas.
Saúde mental e trabalho: uma urgência prática
Wanderley Codo
Psicologia: Ciência e Profiss?o , 1988, DOI: 10.1590/s1414-98931988000200008
Abstract:
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