Evolution of proteins after whole-genome duplication

Evolution of proteins after whole-genome duplicationGene and genome duplication are considered major mechanisms in the creation of newfunctions in genomes, or in the refinement of networks by the division of function amongmore genes. In animals, the best demonstrated whole genome duplication occurred at theorigin of Teleost fishes. This makes fishes an ideal model to study the consequences ofgenome duplication, particularly since we have a good sampling of genome sequences,abundant functional information, and a very well studied outgroup: the tetrapodes (includinghuman). More specifically, I studied the consequences of duplication on proteins usingevolutionary models to infer adaptive events. I analysed the influence of positive selection invertebrate genes, by contrasting singleton genes and duplicated genes. The conclusion of theanalyses was threefold: (i) positive selection affects diverse phylogenetic branches anddiverse gene categories during vertebrate evolution; (ii) it concerns only a small proportion ofsites (1%-5%); and (iii) whole genome duplication had no detectable impact on theprevalence of this positive selection.I also studied evolution at the amino acid level with different methods to detect functionalshifts (covarion process and constant-but-different process). As in my previous research, Ifound similar numbers of functional shifts between duplicates and between orthologs.The accepted framework for studies of molecular evolution is that orthologs share the samefunction, whereas the function of paralogs diverges. This framework gives a special place togene duplication in evolution, as the main mechanism for generating novelty. With myprevious results showing that duplication and speciation are not so different, we investigatedthe literature to question the evidence for similar or divergent evolution of gene function afterduplication relative to speciation genes. This led us to propose a more rigorous design offuture studies of gene duplication.Finally, based on my automated protocol, we built a database of positive selection invertebrates' genes, Selectome. This database is freely available on the web and will helpfuture evolutionary as well as biochemical studies.

Blood lymphocyte subsets in rats with adjuvant arthritis

To determine the phenotype of peripheral blood lymphocytes during the time-course of adjuvant arthritis (AA) to detect alterations that could be involved in the pathogenesis of the arthritic process. METHODS--Phenotype analysis was performed on days 7, 14, 21, 28, 42, 56 and 70 after arthritis induction using monoclonal antibodies to CD5, CD4 and CD8 subsets, and flow cytometry. The proportion of activated lymphocytes and lymphocytes was also assessed with monoclonal antibodies to IL-2R (CD25), to Ia antigen and by polyclonal antibodies to rat Ig. RESULTS--Adjuvant arthritis produced leukocytosis with neutrophilia. Rats with AA showed a marked increase in the number of both CD4+ and CD8+ cells. The ratio CD4/CD8 decreased because the rise in CD8+ cells was more pronounced than the increase in CD4+ cells. Changes in lymphocyte counts showed two well-defined periods: the first, from day 14 to day 28, during which the inflammation of the joints reached a maximum and changes in lymphocyte subsets were more pronounced, that is, there was a threefold increase in CD8+ lymphocytes over normal counts, and the second, from day 42 to day 70, in which modified parameters improved considerably but remained different from controls. CONCLUSION--Alterations were detected in the phenotype of peripheral blood lymphocytes in AA, which provides an additional marker of disease activity.

In vivo T-lymphocyte tolerance in the absence of thymic clonal deletion mediated by hematopoietic cells.

Thymic negative selection renders the developing T-cell repertoire tolerant to self-major histocompatability complex (MHC)/peptide ligands. The major mechanism of induction of self-tolerance is thought to be thymic clonal deletion, ie, the induction of apoptotic cell death in thymocytes expressing a self-reactive T-cell receptor. Consistent with this hypothesis, in mice deficient in thymic clonal deletion mediated by cells of hematopoietic origin, a twofold to threefold increased generation of mature thymocytes has been observed. Here we describe the analysis of the specificity of T lymphocytes developing in the absence of clonal deletion mediated by hematopoietic cells. In vitro, targets expressing syngeneic MHC were readily lysed by activated CD8(+) T cells from deletion-deficient mice. However, proliferative responses of T cells from these mice on activation with syngeneic antigen presenting cells were rather poor. In vivo, deletion-deficient T cells were incapable of induction of lethal graft-versus-host disease in syngeneic hosts. These data indicate that in the absence of thymic deletion mediated by hematopoietic cells functional T-cell tolerance can be induced by nonhematopoietic cells in the thymus. Moreover, our results emphasize the redundancy in thymic negative selection mechanisms.

To select or to weigh: a comparative study of linear combination schemes for superparent-one-dependence estimators

We conduct a large-scale comparative study on linearly combining superparent-one-dependence estimators (SPODEs), a popular family of seminaive Bayesian classifiers. Altogether, 16 model selection and weighing schemes, 58 benchmark data sets, and various statistical tests are employed. This paper's main contributions are threefold. First, it formally presents each scheme's definition, rationale, and time complexity and hence can serve as a comprehensive reference for researchers interested in ensemble learning. Second, it offers bias-variance analysis for each scheme's classification error performance. Third, it identifies effective schemes that meet various needs in practice. This leads to accurate and fast classification algorithms which have an immediate and significant impact on real-world applications. Another important feature of our study is using a variety of statistical tests to evaluate multiple learning methods across multiple data sets.

Evidence for oxygen-island formation on Al(111): Cluster-model theory and x-ray photoelectron spectroscopy

The O 1s x-ray photoelectron spectroscopy spectrum for Al(111)/O at 300 K shows two components whose behavior as a function of time and variation of detection angle are consistent with either (a) a surface species represented by the higher binding-energy (BE) component and a subsurface species represented by the lower BE component, or (b) small close-packed oxygen islands with the interior atoms represented by the lower BE component and the perimeter atoms by the higher BE component. We have modeled both situations using ab initio Hartree-Fock wave functions for clusters of Al and O atoms. For an O atom in a threefold site, it was found that a below-surface position gave a higher O 1s BE than an above-surface position, incompatible with interpretation (a). This change in the O 1s BE could arise because the bond for O to Al may have a more covalent character when the O is below the surface than when it is above the surface. We present evidence consistent with this view. An O adatom island with all the O atoms in threefold sites gives calculated O 1s BE's which are significantly higher for the perimeter O atoms. Further, the results for an isolated O island without the Al substrate present also give higher BE¿s for the perimeter atoms. Both these results are consistent with interpretation (b). Published scanning-tunneling-microscopy data supports the suggestion that the chemisorbed state consists of small, close-packed islands, whereas the presence of two vibrational modes in high-resolution electron-energy-loss spectroscopy data has been interpreted as representing surface and subsurface oxygen atoms. In light of the present results, we suggest that a vibrational interpretation in terms of interior and perimeter adatoms should be considered.

Evidence for two different bonding mechanisms of Al on Si(111)

By means of the ab initio cluster-model approach, we present theoretical evidence for two different mechanisms of bonding of atomic Al to Si(111). On the atop site (T1) the interaction of atomic Al to Si(111) is characteristic of an ionic bond whereas interaction above the threefold eclipsed site (T4) leads to the formation of a typical covalent bond. Moreover, both sites have a similar interaction energy if electronic correlation effects are included. While the conclusions regarding the nature of the chemisorption bond in the two sites do not depend either on the cluster-model size, the kind of embedding hydrogen atoms used, or the quality of the wave function (Hartree-Fock or configuration interaction), the chemisorption energy depends strongly on the wave function used. In fact, inclusion of correlation energy is necessary to properly describe the interaction energies.

Cellular distribution of Hsp70 expression in rat skeletal muscles. Effects of moderate exercise training and chronic hypoxia.

Rat hindlimb muscles constitutively express the inducible heat shock protein 72 (Hsp70), apparently in proportion to the slow myosin content. Since it remains controversial whether chronic Hsp70 expression reflects the overimposed stress, we investigated Hsp70 cellular distribution in fast muscles of the posterior rat hindlimb after (1) mild exercise training (up to 30 m/min treadmill run for 1 h/day), which induces a remodeling in fast fiber composition, or (2) prolonged exposure to normobaric hypoxia (10%O(2)), which does not affect fiber-type composition. Both conditions increased significantly protein Hsp70 levels in the skeletal muscle. Immunohistochemistry showed the labeling for Hsp70 in subsets of both slow/type 1 and fast/type 2A myofibers of control, sedentary, and normoxic rats. Endurance training increased about threefold the percentage of Hsp70-positive myofibers (P < 0.001), and changed the distribution of Hsp70 immunoreactivity, which involved a larger subset of both type 2A and intermediate type 2A/2X myofibers (P < 0.001) and vascular smooth muscle cells. Hypoxia induced Hsp70 immunoreactivity in smooth muscle cells of veins and did not increase the percentage of Hsp70-positive myofibers; however, sustained exposure to hypoxia affected the distribution of Hsp70 immunoreactivity, which appeared detectable in a very small subset of type 2A fibers, whereas it concentrated in type 1 myofibers (P < 0.05) together with the labeling for heme-oxygenase isoform 1, a marker of oxidative stress. Therefore, the chronic induction of Hsp70 expression in rat skeletal muscles is not obligatory related to the slow fiber phenotype but reveals the occurrence of a stress response.

Are patients at nutritional risk more prone to complications after major urological surgery?

PURPOSE: The nutritional risk score is a recommended screening tool for malnutrition. While a nutritional risk score of 3 or greater predicts adverse outcomes after digestive surgery, to our knowledge its predictive value for morbidity after urological interventions is unknown. We determined whether urological patients at nutritional risk are at higher risk for complications after major surgery than patients not at nutritional risk. MATERIALS AND METHODS: We performed a prospective observational study in consecutive patients undergoing major surgery. A priori sample calculation resulted in a study cohort of 220 patients. Interim analysis was planned after 110 patients. The nutritional risk score was assessed preoperatively by a specialized study nurse. Nutritional care was standardized in all patients. Postoperative complications were defined previously using the standardized Dindo-Clavien classification. The primary end point was 30-day morbidity. Univariate and multivariate analysis was performed to identify predictors of complications. RESULTS: The study was discontinued due to significant results after interim analysis. A total of 125 patients were included in analysis from June 2011 to June 2012 and 15 were excluded because of incomplete data. Of 51 patients at nutritional risk 38 (74%) presented with at least 1 complication compared to 28 of 59 controls (47%). Patients at nutritional risk were at threefold risk for complications on univariate and multivariate analysis (OR 3.3, 95% CI 1.3-8.0). Cystectomy was the only other predictor of morbidity (OR 10, 95% CI 2-48). CONCLUSIONS: Patients at nutritional risk are more prone to complications after major urological procedures. Whether this increased morbidity can be reversed by perioperative nutritional support should be studied.

The ArgR regulatory protein, a helper to the anaerobic regulator ANR during transcriptional activation of the arcD promoter in Pseudomonas aeruginosa.

Pseudomonas aeruginosa, when deprived of oxygen, generates ATP from arginine catabolism by enzymes of the arginine deiminase pathway, encoded by the arcDABC operon. Under conditions of low oxygen tension, the transcriptional activator ANR binds to a site centered 41.5 bp upstream of the arcD transcriptional start. ANR-mediated anaerobic induction was enhanced two- to threefold by extracellular arginine. This arginine effect depended, in trans, on the transcriptional regulator ArgR and, in cis, on an ArgR binding site centered at -73.5 bp in the arcD promoter. Binding of purified ArgR protein to this site was demonstrated by electrophoretic mobility shift assays and DNase I footprinting. This ArgR recognition site contained a sequence, 5'-TGACGC-3', which deviated in only 1 base from the common sequence motif 5'-TGTCGC-3' found in other ArgR binding sites of P. aeruginosa. Furthermore, an alignment of all known ArgR binding sites confirmed that they consist of two directly repeated half-sites. In the absence of ANR, arginine did not induce the arc operon, suggesting that ArgR alone does not activate the arcD promoter. According to a model proposed, ArgR makes physical contact with ANR and thereby facilitates initiation of arc transcription.

Geografia literària dels Països Catalans. El cas de la comarca d' Osona

La literatura ha estat, històricament, una forma de vivència i de coneixença del territori. En aquest sentit, el projecte Geografia literària dels Països Catalans esdevé una proposta de redescoberta de pobles, ciutats i comarques, de recuperació i fixació en la memòria d’espais, indrets, cases, monuments, edificis patrimonials o llocs mítics que han estat el centre d’interès dels nostres escriptors d’ençà dels trobadors i Ramon Llull fins als nostres dies. Per tot plegat, aquest treball té un triple objectiu: en primer lloc, donar a conèixer la iniciativa Geografia literària dels Països Catalans; en segon lloc, proposar-ne un marc teòric, i, per acabar, analitzar, específicament, alguns dels espais literaris que es localitzen a la comarca d’Osona.

Manipulation of salicylate content in Arabidopsis thaliana by the expression of an engineered bacterial salicylate synthase.

Salicylic acid (SA) plays a central role as a signalling molecule involved in plant defense against microbial attack. Genetic manipulation of SA biosynthesis may therefore help to generate plants that are more disease-resistant. By fusing the two bacterial genes pchA and pchB from Pseudomonas aeruginosa, which encode isochorismate synthase and isochorismate pyruvate-lyase, respectively, we have engineered a novel hybrid enzyme with salicylate synthase (SAS) activity. The pchB-A fusion was expressed in Arabidopsis thaliana under the control of the constitutive cauliflower mosaic virus (CaMV) 35S promoter, with targeting of the gene product either to the cytosol (c-SAS plants) or to the chloroplast (p-SAS plants). In p-SAS plants, the amount of free and conjugated SA was increased more than 20-fold above wild type (WT) level, indicating that SAS is functional in Arabidopsis. P-SAS plants showed a strongly dwarfed phenotype and produced very few seeds. Dwarfism could be caused by the high SA levels per se or, perhaps more likely, by a depletion of the chorismate or isochorismate pools of the chloroplast. Targeting of SAS to the cytosol caused a slight increase in free SA and a significant threefold increase in conjugated SA, probably reflecting limited chorismate availability in this compartment. Although this modest increase in total SA content did not strongly induce the resistance marker PR-1, it resulted nevertheless in enhanced disease resistance towards a virulent isolate of Peronospora parasitica. Increased resistance of c-SAS lines was paralleled with reduced seed production. Taken together, these results illustrate that SAS is a potent tool for the manipulation of SA levels in plants.

Approximate polytope ensemble for one-class classification

In this work, a new one-class classification ensemble strategy called approximate polytope ensemble is presented. The main contribution of the paper is threefold. First, the geometrical concept of convex hull is used to define the boundary of the target class defining the problem. Expansions and contractions of this geometrical structure are introduced in order to avoid over-fitting. Second, the decision whether a point belongs to the convex hull model in high dimensional spaces is approximated by means of random projections and an ensemble decision process. Finally, a tiling strategy is proposed in order to model non-convex structures. Experimental results show that the proposed strategy is significantly better than state of the art one-class classification methods on over 200 datasets.

Assessment of insecticide resistance in eggs and neonate larvae of Cydia pomonella (Lepidoptera: Tortricidae)

Spanish Cydia pomonella (L.) field populations have developed resistance to several insecticide groups. Diagnostic concentrations were established as the LC90 calculated on a susceptible strain (S_Spain) for five and seven insecticides and tested on eggs and neonate larvae field populations, respectively. The three most relevant enzymatic detoxification systems (mixed-function oxidases (MFO), glutathione S-tranferases (GST) and esterases (EST)) were studied for neonate larvae. In eggs, 96% of the field populations showed a significantly lower efficacy when compared with the susceptible strain (S_Spain) and the most effective insecticides were fenoxycarb and thiacloprid. In neonate larvae, a significant loss of susceptibility to the insecticides was detected. Flufenoxuron, azinphos-methyl and phosmet showed the lowest efficacy, while lambda-cyhalothrin, alpha-cypermethrin and chlorpyrifos-ethyl showed the highest. Biochemical assays showed that the most important enzymatic system involved in insecticide detoxification was MFO, with highest enzymatic activity ratios (5.1–16.6 for neonates from nine field populations). An enhanced GST and EST activities was detected in one field population, with enzymatic activity ratios of threefold and fivefold for GST and EST, respectively, when compared with the susceptible strain. The insecticide bioassays showed that the LC90 used were effective as diagnostic concentrations. Measures of MFO activity alongside bioassays with insecticide diagnostic concentrations could be used as tools for monitoring insecticide resistance in neonate larvae of C. pomonella.

Une justice plus commerciale qu'industrielle ? Comparaison des attentes d'une « bonne justice » en Suisse

Le but de cet article est triple. D'abord, nous identifions les qualités d'une bonne justice en Suisse, telles que défi nies par les différents acteurs qui forment le tribunal au sens large (juges, gestionnaires de tribunaux, avocats, journalistes, politiciens). Deuxièmement, nous vérifions si ces qualités peuvent coexister avec les valeurs véhiculées par le monde managérial (NGP). Enfin, nous évaluons la manière dont elles cohabitent (hybridation, dominance des unes sur les autres, etc.). Pour ce faire, nous avons analysé une série d'entretiens (56) semi-structurés menés dans des tribunaux de première et seconde instance dans des cours civiles, administratives et criminelles, dans les trois régions linguistiques du pays. Les résultats montrent que les groupes d'acteurs interviewés ont des attentes relativement similaires et qu'elles ne semblent pas être incompatibles avec celles de l'univers managérial. Cependant, lorsqu'ils décrivent la bonne justice, les participants font plus souvent appel à des notions liées au monde commercial qu'au monde industriel contrairement à d'autres études menées auprès d'employés du secteur public suisse, mais dans la lignée de ceux du Québec. L'article ouvre la voie à des recherches ultérieures dont l'objectif sera de tester ces conclusions. Abstract The purpose of this paper is threefold. First, we identify the qualities of good justice in Switzerland, as defi ned by the various actors who form the tribunal in a broad sense (judges, court managers, lawyers, journalists, politicians). Second, we verify if these qualities are compatible with the values conveyed by the managerial universe (NPM). Finally, we evaluate how they coexist (hybridization, dominance over each other, etc.). To do this, we analysed a series of semi-structured interviews (56) conducted in tribunals of fi rst and second instance in civil, administrative,and criminal courts in the three linguistic regions of the country. The results show that the groups of actors interviewed have relatively similar expectations that do not seem to be incompatible with those of the managerial world. However, when describing good justice, the participants refer more frequently to concepts related to the commercial than the industrial world, contrary to other Swiss public servants but in line with those of Quebec, as uncovered by former studies. The article opens up the path to further research whose objective will be to test those conclusions.

High-density sex-specific linkage maps of a European tree frog (Hyla arborea) identify the sex chromosome without information on offspring sex.

Identifying homology between sex chromosomes of different species is essential to understanding the evolution of sex determination. Here, we show that the identity of a homomorphic sex chromosome pair can be established using a linkage map, without information on offspring sex. By comparing sex-specific maps of the European tree frog Hyla arborea, we find that the sex chromosome (linkage group 1) shows a threefold difference in marker number between the male and female maps. In contrast, the number of markers on each autosome is similar between the two maps. We also find strongly conserved synteny between H. arborea and Xenopus tropicalis across 200 million years of evolution, suggesting that the rate of chromosomal rearrangement in anurans is low. Finally, we show that recombination in males is greatly reduced at the centers of large chromosomes, consistent with previous cytogenetic findings. Our research shows the importance of high-density linkage maps for studies of recombination, chromosomal rearrangement and the genetic architecture of ecologically or economically important traits.