Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis.

Rubisco is responsible for the fixation of CO2 into organic compounds through photosynthesis and thus has a great agronomic importance. It is well established that this enzyme suffers from a slow catalysis, and its low specificity results into photorespiration, which is considered as an energy waste for the plant. However, natural variations exist, and some Rubisco lineages, such as in C4 plants, exhibit higher catalytic efficiencies coupled to lower specificities. These C4 kinetics could have evolved as an adaptation to the higher CO2 concentration present in C4 photosynthetic cells. In this study, using phylogenetic analyses on a large data set of C3 and C4 monocots, we showed that the rbcL gene, which encodes the large subunit of Rubisco, evolved under positive selection in independent C4 lineages. This confirms that selective pressures on Rubisco have been switched in C4 plants by the high CO2 environment prevailing in their photosynthetic cells. Eight rbcL codons evolving under positive selection in C4 clades were involved in parallel changes among the 23 independent monocot C4 lineages included in this study. These amino acids are potentially responsible for the C4 kinetics, and their identification opens new roads for human-directed Rubisco engineering. The introgression of C4-like high-efficiency Rubisco would strongly enhance C3 crop yields in the future CO2-enriched atmosphere.

Comparing Governmental Agendas: Evolution of the Prioritization of Issues in the USA and Spain

This paper is the first step in a long term project investigating policy stability and change in Spain from an agenda setting perspective and comparing the Spanish policy agenda to that of other advanced democracies. Here we begin to compare the allocation of issue attention in Spain and the USA by comparing the substance of annual President and Prime Minister speeches from 1982 to 2005. Existing research argues that the public agenda has become more crowded, competitive and volatile in recent years. We find that in both countries there has been a transformation of the political agenda towards an increasing diversity of issues. However, most of the volatility in executive attention seems to be explained by salient events rather than by issue crowding. We conclude by discussing some limitations of executive speeches as a measure of governmental issue attention and directions for future research.

A glycine-arginine domain in control of the human MRE11 DNA repair protein.

Human MRE11 is a key enzyme in DNA double-strand break repair and genome stability. Human MRE11 bears a glycine-arginine-rich (GAR) motif that is conserved among multicellular eukaryotic species. We investigated how this motif influences MRE11 function. Human MRE11 alone or a complex of MRE11, RAD50, and NBS1 (MRN) was methylated in insect cells, suggesting that this modification is conserved during evolution. We demonstrate that PRMT1 interacts with MRE11 but not with the MRN complex, suggesting that MRE11 arginine methylation occurs prior to the binding of NBS1 and RAD50. Moreover, the first six methylated arginines are essential for the regulation of MRE11 DNA binding and nuclease activity. The inhibition of arginine methylation leads to a reduction in MRE11 and RAD51 focus formation on a unique double-strand break in vivo. Furthermore, the MRE11-methylated GAR domain is sufficient for its targeting to DNA damage foci and colocalization with gamma-H2AX. These studies highlight an important role for the GAR domain in regulating MRE11 function at the biochemical and cellular levels during DNA double-strand break repair.

Congenital and nursing effects on the evolution of Schistosoma mansoni infection in mice

Modification of the immune response to schistosomal infection in children or offspring born to mother R infected with Schistosoma mansoni has been demonstrated in human and in experimental schistosomiasis. One of the hypothesis to explain this fact could be the transfer of circulating antigens and antibodies from mother to foetus through the placenta or from mother to child by milk. The results of this spontaneous transference are controversial in the literature. In an attempt to investigate these questions, we studied one hundred and twenty offspring (Swiss mice), sixty born to infected-mothers (group A) and sixty born to non-infected mothers (group B). These were percutaneously infected with 50 cercariae/mouse, and divided in six sub-groups (20 mice/sub-group), according to the following schedule: after birth (sub-groups A.I and B.I), 10 days old (sub-groups A.II and B.II) and 21 days old (sub-groups A.III and B.III). After the exposure period, the young mice returned to their own mothers for nursing. Six weeks later, the mice were killed. We obtained the following results: 1) There is transference of antibody to cercariae (CAP), adult worms (SWAP) and egg antigens (SEA) from the infected mothers to the offspring, probably through placenta and milk; 2) Offspring born to infected mothers exhibit much less coagulative hepatic necrosis and show a lower number of eggs in the small intestine and a less intense and predominant exsudative stage of the hepatic granulomas when compared with the exsudative-productive stage of the control groups. The findings suggest that congenital and nursing factors can interfere on the development of the schistosomiasis infection, causing an hyporesponse to the eggs.

Rapid evolution of cancer/testis genes on the X chromosome.

BACKGROUND: Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT proteins elicit an antigenic response in cancer patients, has established a role for this class of genes as targets in immunotherapy regimes. Many families of CT genes have been identified in the human genome, but their biological function for the most part remains unclear. While it has been shown that some CT genes are under diversifying selection, this question has not been addressed before for the class as a whole. RESULTS: To shed more light on this interesting group of genes, we exploited the generation of a draft chimpanzee (Pan troglodytes) genomic sequence to examine CT genes in an organism that is closely related to human, and generated a high-quality, manually curated set of human:chimpanzee CT gene alignments. We find that the chimpanzee genome contains homologues to most of the human CT families, and that the genes are located on the same chromosome and at a similar copy number to those in human. Comparison of putative human:chimpanzee orthologues indicates that CT genes located on chromosome X are diverging faster and are undergoing stronger diversifying selection than those on the autosomes or than a set of control genes on either chromosome X or autosomes. CONCLUSION: Given their high level of diversifying selection, we suggest that CT genes are primarily responsible for the observed rapid evolution of protein-coding genes on the X chromosome.

Quantification of clenbuterol at trace level in human urine by ultra-high pressure liquid chromatography-tandem mass spectrometry.

Clenbuterol is a β2 agonist agent with anabolic properties given by the increase in the muscular mass in parallel to the decrease of the body fat. For this reason, the use of clenbuterol is forbidden by the World Anti-Doping Agency (WADA) in the practice of sport. This compound is of particular interest for anti-doping authorities and WADA-accredited laboratories due to the recent reporting of risk of unintentional doping following the eating of meat contaminated with traces of clenbuterol in some countries. In this work, the development and the validation of an ultra-high pressure liquid chromatography coupled to electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) method for the quantification of clenbuterol in human urine is described. The analyte was extracted from urine samples by liquid-liquid extraction (LLE) in basic conditions using tert butyl-methyl ether (TBME) and analyzed by UHPLC-MS/MS with a linear gradient of acetonitrile in 9min only. The simple and rapid method presented here was validated in compliance with authority guidelines and showed a limit of quantification at 5pg/mL and a linearity range from 5pg/mL to 300pg/mL. Good trueness (85.8-105%), repeatability (5.7-10.6% RSD) and intermediate precision (5.9-14.9% RSD) results were obtained. The method was then applied to real samples from eighteen volunteers collecting urines after single oral doses administration (1, 5 and 10μg) of clenbuterol-enriched yogurts.

An outbreak of american cutaneous leishmaniasis (Leishmania braziliensis braziliensis) in a periurban area of Rio de Janeiro city, Brazil: clinical and epidemiological studies

From July 1984 to September 1986, 105 cases of American cutaneous leishmaniasis were studied in a locality closely situated to an urbanized area of the city of Rio de Janeiro, Brazil. Settement in this area was established at least 20 years ago but the first cases were noted six months prior to the beginning of this study. Cases were almost exlusively cutaneous and ulcerated, with one to six months of evolution. Montenegro's skin tests were positive in all cases and anti-Leishmania antibodies were detected by indirect immunofluorescence test in 74.3% of the patients. Parasites were demonstrated in 69.5% of cases. Domestic animals were easily found infected; 32% of the examined dogs and 30.8% of the examined equines were positive to the presence of Leishmania in cutaneous ulcerated lesions. Parasite isolates from human, dog andequines were immunologically characterized and identified as L. b. braziliensis. 73,0% of the sandfly population were Lutzomyia intermedia mainly caught on human baits and on domestic animals. Our observations suggest that this is an area of recent established L. b. braziliensis infection and that transmission probably occurs indoors or outdoors close to the houses.

Viral envelope glycoprotein processing by proprotein convertases.

The proprotein convertases (PCs) are a family of nine mammalian enzymes that play key roles in the maintenance of cell homeostasis by activating or inactivating proteins via limited proteolysis under temporal and spatial control. A wide range of pathogens, including major human pathogenic viruses can hijack cellular PCs for their own purposes. In particular, productive infection with many enveloped viruses critically depends on the processing of their fusion-active viral envelope glycoproteins by cellular PCs. Based on their crucial role in virus-host interaction, PCs can be important determinants for viral pathogenesis and represent promising targets of therapeutic antiviral intervention. In the present review we will cover basic aspects and recent developments of PC-mediated maturation of viral envelope glycoproteins of selected medically important viruses. The molecular mechanisms underlying the recognition of PCs by viral glycoproteins will be described, including recent findings demonstrating differential PC-recognition of viral and cellular substrates. We will further discuss a possible scenario how viruses during co-evolution with their hosts adapted their glycoproteins to modulate the activity of cellular PCs for their own benefit and discuss the consequences for virus-host interaction and pathogenesis. Particular attention will be given to past and current efforts to evaluate cellular PCs as targets for antiviral therapeutic intervention, with emphasis on emerging highly pathogenic viruses for which no efficacious drugs or vaccines are currently available.

Condicions socioecològiques de la riera d'Arbúcies pel retorn de la llúdriga (Lutra lutra)

La llúdriga (Lutra lutra) va desaparèixer de la conca de la Tordera a causa de la pressió humana sobre ella i el seu hàbitat. Recentment les seves poblacions s’estan recuperant a las conques nord de Catalunya. En aquest context es presenta els resultats dels anàlisis dels requeriments socioecològics de la llúdriga en l’afluent del riu Tordera de la riera d’Arbúcies: qualitat del bosc de ribera, valoració de la contaminació de l’aigua i l’anàlisi de les poblacions d’ictiofauna, a més de l’estimació de l’espècie més abundant. L’evolució de l’ús i cobertes del sòl del sòl mostren que existeix una tendència augment en las masses forestals, zones urbanitzades i infraestructures; també una disminució del camps de cultiu, fruiters i vinyes. La qualitat del bosc de ribera es va valorar a partir del l’índex QBR, obtenint que la màxima qualitat es localitza en el tram alt, disminuint a mesura que s’apropa a la desembocadura al Tordera. La contaminació de l’aigua a estat valorada, per una banda analitzant la qualitat biològica a partir dels índexs IPS i BMWPC, obtenint que la qualitat de l’aigua disminueix a mesura que transcorre riu avall, segons l’IPS. Amb el BMWPC es troba que existeix una recuperació de la qualitat de l’aigua en l’últim tram. Per altra banda s’han analitzat el compostos químics que afecten a la llúdriga, obtenint que les concentracions d’aquest no són rellevants a l’aigua. S’ha analitzat l’estructura de la població d’ictiofauna present, trobant que el Barbus meridionalis és l’espècie més abundant en tots el trams, a més d’augmentar en captures a mesura que l’aigua s’apropa al aiguabarreig amb la Tordera. S’ha estimat la biomassa present d’aquesta espècie, concloent que es suficient per mantenir una població no gaire densa de llúdrigues, inferior a 0,15 individus per kilòmetre de riu.

Quantifying rates of landscape evolution and tectonic processes by thermochronology and numerical modeling of crustal heat transport using PECUBE

PECUBE is a three-dimensional thermal-kinematic code capable of solving the heat production-diffusion-advection equation under a temporally varying surface boundary condition. It was initially developed to assess the effects of time-varying surface topography (relief) on low-temperature thermochronological datasets. Thermochronometric ages are predicted by tracking the time-temperature histories of rock-particles ending up at the surface and by combining these with various age-prediction models. In the decade since its inception, the PECUBE code has been under continuous development as its use became wider and addressed different tectonic-geomorphic problems. This paper describes several major recent improvements in the code, including its integration with an inverse-modeling package based on the Neighborhood Algorithm, the incorporation of fault-controlled kinematics, several different ways to address topographic and drainage change through time, the ability to predict subsurface (tunnel or borehole) data, prediction of detrital thermochronology data and a method to compare these with observations, and the coupling with landscape-evolution (or surface-process) models. Each new development is described together with one or several applications, so that the reader and potential user can clearly assess and make use of the capabilities of PECUBE. We end with describing some developments that are currently underway or should take place in the foreseeable future. (C) 2012 Elsevier B.V. All rights reserved.

Are glutamate and lactate increases ubiquitous to physiological activation? A (1)H functional MR spectroscopy study during motor activation in human brain at 7Tesla.

Recent studies at high field (7Tesla) have reported small metabolite changes, in particular lactate and glutamate (below 0.3μmol/g) during visual stimulation. These studies have been limited to the visual cortex because of its high energy metabolism and good magnetic resonance spectroscopy (MRS) sensitivity using surface coil. The aim of this study was to extend functional MRS (fMRS) to investigate for the first time the metabolite changes during motor activation at 7T. Small but sustained increases in lactate (0.17μmol/g±0.05μmol/g, p<0.001) and glutamate (0.17μmol/g±0.09μmol/g, p<0.005) were detected during motor activation followed by a return to the baseline after the end of activation. The present study demonstrates that increases in lactate and glutamate during motor stimulation are small, but similar to those observed during visual stimulation. From the observed glutamate and lactate increase, we inferred that these metabolite changes may be a general manifestation of the increased neuronal activity. In addition, we propose that the measured metabolite concentration increases imply an increase in ΔCMRO2 that is transiently below that of ΔCMRGlc during the first 1 to 2min of the stimulation.

Human babesiosis in Europe

Human babesiosis in Europe came to medical attention in 1957 and until now 19 cases have been reported, most of them due to Babesia divergens. The onset of the disease is characterized by hemoglobinuria, high fever and renal failure ensue rapidly. The patients were generally asplenic and resident in a rural area. Intraerythrocytic pleomorphic parasites (1-3 µm) observed in stained thin blood smears are essential for Genus diagnosis. Parasitemia varyed from 5 to 80% of red blood cells. Massive blood exchange transfusion (2-3 blood volumes) followed by intravenous clindamycine (3-4 times daily) and oral quinine (600 mg base, 3 times daily) were successfully used in the treatment of three recent cases. Splenectomised individuals should be aware for prevention.

Annotating the human genome

2 Abstract2.1 En françaisLe séquençage du génome humain est un pré-requis fondamental à la compréhension de la biologie de l'être humain. Ce projet achevé, les scientifiques ont dû faire face à une tâche aussi importante, comprendre cette suite de 3 milliards de lettres qui compose notre génome. Le consortium ENCODE (ENCyclopedia Of Dna Elements) fût formé comme une suite logique au projet du génome humain. Son rôle est d'identifier tous les éléments fonctionnels de notre génome incluant les régions transcrites, les sites d'attachement des facteurs de transcription, les sites hypersensibles à la DNAse I ainsi que les marqueurs de modification des histones. Dans le cadre de ma thèse doctorale, j'ai participé à 2 sous-projets d'ENCODE. En premier lieu, j'ai eu la tâche de développer et d'optimiser une technique de validation expérimentale à haut rendement de modèles de gènes qui m'a permis d'estimer la qualité de la plus récente annotation manuelle. Ce nouveau processus de validation est bien plus efficace que la technique RNAseq qui est actuellement en train de devenir la norme. Cette technique basée sur la RT-PCR, m'a notamment permis de découvrir de nouveaux exons dans 10% des régions interrogées. En second lieu j'ai participé à une étude ayant pour but d'identifier les extrémités de tous les gènes des chromosomes humains 21 et 22. Cette étude à permis l'identification à large échelle de transcrits chimères comportant des séquences provenant de deux gènes distincts pouvant être à une grande distance l'un de autre.2.2 In EnglishThe completion of the human genome sequence js the prerequisite to fully understand the biology of human beings. This project achieved, scientists had to face another challenging task, understanding the meaning of the 3 billion letters composing this genome. As a logical continuation of the human genome project, the ENCODE (ENCyclopedia Of DNA Elements) consortium was formed with the aim of annotating all its functional elements. These elements include transcribed regions, transcription binding sites, DNAse I hypersensitive sites and histone modification marks. In the frame of my PhD thesis, I was involved in two sub-projects of ENCODE. Firstly I developed and optimized an high throughput method to validate gene models, which allowed me to assess the quality of the most recent manually-curated annotation. This novel experimental validation pipeline is extremely effective, far more so than transcriptome profiling through RNA sequencing, which is becoming the norm. This RT-PCR-seq targeted-approach is likewise particularly efficient in identifying novel exons, as we discovered about 10% of loci with unannotated exons. Secondly, I participated to a study aiming to identify the gene boundaries of all genes in the human chromosome 21 and 22. This study led to the identification of chimeric transcripts that are composed of sequences coming form two distinct genes that can be map far away from each other.

Clinical follow-up of women infected with human papillomavirus-16, either alone or with other human papillomavirus types: identification of different risk groups.

OBJECTIVES: Evaluation of the clinical impact of multiple infections of the cervix by human papillomavirus, including human papillomavirus-16, compared with single human papillomavirus-16 infection. STUDY DESIGN: One hundred sixty-nine women were classified in 3 categories depending on their human papillomavirus profile: human papillomavirus-16 only, human papillomavirus-16 and low-risk type(s), and human papillomavirus-16 and other high-risk type(s). Cervical brush samples were analyzed for human papillomavirus DNA by polymerase chain reaction and reverse line blot hybridization. All women were evaluated with colposcopy during 24 months or more. Management was according to the Bethesda recommendations. RESULTS: Women infected with human papillomavirus-16 and other high-risk human papillomavirus type(s) presented more progression or no change in the grade of dysplasia, compared with women of the other groups (relative risk [RR], 1.39; 95% confidence interval [CI], 1.07-1.82; P = .02 at 6 months; RR, 2.10; 95% CI, 1.46-3.02; P < .001 at 12 months; RR, 1.82; 95% CI, 1.21-2.72; P = .004 at 24 months). CONCLUSION: Coinfection of women with human papillomavirus-16 and other high-risk human papillomavirus type(s) increases the risk of unfavorable evolution.

Characterization of the hemagglutinin receptor specificity and neuraminidase substrate specificity of clinical isolates of human influenza A viruses

Six clinical isolates of influenza A viruses were examined for hemagglutinin receptor specificity and neuraminidase substrate specificity. All of the viral isolates minimally passaged in mammalian cells demonstrated preferential agglutination of human erythrocytes enzymatically modified to contain NeuAc alpha 2,6Gal sequences, with no agglutination of cells bearing NeuAc alpha 2,3Gal sequences. This finding is consistent with the hemagglutination receptor specificity previously demonstrated for laboratory strains of influenza A viruses. The neuraminidase substrate specificities of the clinical isolates examined were also identical to that described for the N2 neuraminidase of recent laboratory strains of human influenza viruses. The H3N2 viruses all displayed the ability to release sialic acid from both alpha 2, 3 and alpha 2, 6 linkages. In addition, two clinical isolates of H1N1 viruses also demonstrated this dual neuraminidase substrate specificity, a characteristic which has not been previously described for the N1 neuraminidase. These results demonstrate that complementary hemagglutinin and neuraminidase specificities are found in recent isolates of both H1N1 and H3N2 influenza viruses.