High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

Hybridisation and diversification in the adaptive radiation of clownfishes.

BackgroundThe importance of hybridisation during species diversification has long been debated among evolutionary biologists. It is increasingly recognised that hybridisation events occurred during the evolutionary history of numerous species, especially during the early stages of adaptive radiation. We study the effect of hybridisation on diversification in the clownfishes, a clade of coral reef fish that diversified through an adaptive radiation process. While two species of clownfish are likely to have been described from hybrid specimens, the occurrence and effect of hybridisation on the clade diversification is yet unknown.ResultsWe generate sequences of three mitochondrial genes to complete an existing dataset of nuclear sequences and document cytonuclear discordance at a node, which shows a drastic increase of diversification rate. Then, using a tree-based jack-knife method, we identify clownfish species likely stemming from hybridisation events. Finally, we use molecular cloning and identify the putative parental species of four clownfish specimens that display the morphological characteristics of hybrids.ConclusionsOur results show that consistently with the syngameon hypothesis, hybridisation events are linked with a burst of diversification in the clownfishes. Moreover, several recently diverged clownfish lineages likely originated through hybridisation, which indicates that diversification, catalysed by hybridisation events, may still be happening.

Effect of irrigation water and processing on the microbial quality of lettuces produced and sold on markets in Dakar (Senegal)

The aim of this survey is to assess the microbiological impact of irrigation water on lettuces produced on two urban agricultural sites and sold on markets; 6 and 7%, respectively, of lettuces coming from the sites of Pikine and Patte d'Oie were Salmonella spp. positive. Lettuces irrigated with shallow groundwater (''Ceanes'' water) were more contaminated (8% at both Pikine and Patte d'Oie sites) compared to those irrigated with wastewater (4% at Pikine) or well water (5% at Patte d'Oie). As for the lettuces in marketplaces, their contamination seems to depend on the type of treatment occurring before sale. Lettuces previously washed in the ``Ceanes'' were more contaminated than those rinsed with tap water at the marketplace. Salmonella spp. have been isolated from all marketplaces. However, the rates of contamination in markets surrounding Patte d'Oie are higher (9 and 11% at Grand Yoff and Dalifort) than those surrounding Pikine (4 and 2% at Zinc and Sham) or Rufisque, the control (2%). Our results confirm that the reuse of wastewater in irrigation is an alternative to animal manure. Its risk of microbial contamination can be significantly reduced by washing the vegetables with tap water before they are sold. Copyright (C) 2010 John Wiley & Sons, Ltd.

Twenty-year trends in the prevalence of Down syndrome and other trisomies in Europe: impact of maternal age and prenatal screening.

This study examines trends and geographical differences in total and live birth prevalence of trisomies 21, 18 and 13 with regard to increasing maternal age and prenatal diagnosis in Europe. Twenty-one population-based EUROCAT registries covering 6.1 million births between 1990 and 2009 participated. Trisomy cases included live births, fetal deaths from 20 weeks gestational age and terminations of pregnancy for fetal anomaly. We present correction to 20 weeks gestational age (ie, correcting early terminations for the probability of fetal survival to 20 weeks) to allow for artefactual screening-related differences in total prevalence. Poisson regression was used. The proportion of births in the population to mothers aged 35+ years in the participating registries increased from 13% in 1990 to 19% in 2009. Total prevalence per 10 000 births was 22.0 (95% CI 21.7-22.4) for trisomy 21, 5.0 (95% CI 4.8-5.1) for trisomy 18 and 2.0 (95% CI 1.9-2.2) for trisomy 13; live birth prevalence was 11.2 (95% CI 10.9-11.5) for trisomy 21, 1.04 (95% CI 0.96-1.12) for trisomy 18 and 0.48 (95% CI 0.43-0.54) for trisomy 13. There was an increase in total and total corrected prevalence of all three trisomies over time, mainly explained by increasing maternal age. Live birth prevalence remained stable over time. For trisomy 21, there was a three-fold variation in live birth prevalence between countries. The rise in maternal age has led to an increase in the number of trisomy-affected pregnancies in Europe. Live birth prevalence has remained stable overall. Differences in prenatal screening and termination between countries lead to wide variation in live birth prevalence.

Prevalence of thinness in children and adolescents in the Seychelles: comparison of two international growth references.

BACKGROUND: : Thinness in children and adolescents is largely under studied, a contrast with abundant literature on under-nutrition in infants and on overweight in children and adolescents. The aim of this study is to compare the prevalence of thinness using two recently developed growth references, among children and adolescents living in the Seychelles, an economically rapidly developing country in the African region. METHOD: S: Weight and height were measured every year in all children of 4 grades (age range: 5 to 16 years) of all schools in the Seychelles as part of a routine school-based surveillance program. In this study we used data collected in 16,672 boys and 16,668 girls examined from 1998 to 2004. Thinness was estimated according to two growth references: i) an international survey (IS), defining three grades of thinness corresponding to a BMI of 18.5, 17.0 and 16.0 kg/m2 at age 18 and ii) the WHO reference, defined here as three categories of thinness (-1, -2 and -3 SD of BMI for age) with the second and third named "thinness" and "severe thinness", respectively. RESULTS: : The prevalence of thinness was 21.4%, 6.4% and 2.0% based on the three IS cut-offs and 27.7%, 6.7% and 1.2% based on the WHO cut-offs. The prevalence of thinness categories tended to decrease according to age for both sexes for the IS reference and among girls for the WHO reference. CONCLUSION: The prevalence of the first category of thinness was larger with the WHO cut-offs than with the IS cut-offs while the prevalence of thinness of "grade 2" and thinness of "grade 3" (IS cut-offs) was similar to the prevalence of "thinness" and "severe thinness" (WHO cut-offs), respectively.

Sex-related and non-sex-related comorbidity subtypes of tic disorders: a latent class approach.

BACKGROUND AND PURPOSE: Recent evidence suggests that there may be more than one Gilles de la Tourette syndrome (GTS)/tic disorder phenotype. However, little is known about the common patterns of these GTS/tic disorder-related comorbidities. In addition, sex-specific phenomenological data of GTS/tic disorder-affected adults are rare. Therefore, this community-based study used latent class analyses (LCA) to investigate sex-related and non-sex-related subtypes of GTS/tic disorders and their most common comorbidities. METHODS: The data were drawn from the PsyCoLaus study (n = 3691), a population-based survey conducted in Lausanne, Switzerland. LCA were performed on the data of 80 subjects manifesting motor/vocal tics during their childhood/adolescence. Comorbid attention-deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder, depressive, phobia and panic symptoms/syndromes comprised the selected indicators. The resultant classes were characterized by psychosocial correlates. RESULTS: In LCA, four latent classes provided the best fit to the data. We identified two male-related classes. The first class exhibited both ADHD and depression. The second class comprised males with only depression. Class three was a female-related class depicting obsessive thoughts/compulsive acts, phobias and panic attacks. This class manifested high psychosocial impairment. Class four had a balanced sex proportion and comorbid symptoms/syndromes such as phobias and panic attacks. The complementary occurrence of comorbid obsessive thoughts/compulsive acts and ADHD impulsivity was remarkable. CONCLUSIONS: To the best of our knowledge, this is the first study applying LCA to community data of GTS symptoms/tic disorder-affected persons. Our findings support the utility of differentiating GTS/tic disorder subphenotypes on the basis of comorbid syndromes.

Gut-derived signaling molecules and vagal afferents in the control of glucose and energy homeostasis.

PURPOSE OF REVIEW: The control of glucose and energy homeostasis, including feeding behaviour, is tightly regulated by gut-derived peptidic and nonpeptidic endocrine mediators, autonomic nervous signals, as well as nutrients such as glucose. We will review recent findings on the role of the gastrointestinal tract innervation and of portal vein glucose sensors; we will review selected data on the action of gastrointestinally released hormones. RECENT FINDINGS: The involvement of mechanosensory vagal afferents in postprandial meal termination has been clarified using mouse models with selective impairments of genes required for development of mechanosensory fibres. These activate central glucogen-like peptide-1/glucogen-like peptide-2 containing ascending pathways linking the visceroceptive brainstem neurons to hypothalamic nuclei. Mucosal terminals comprise the chemosensory vagal afferents responsive to postprandially released gastrointestinal hormones. The mechanism by which the hepatoportal glucose sensor stimulates glucose utilization by muscles was demonstrated, using genetically modified mice, to be insulin-independent but to require GLUT4 and AMP-kinase. This sensor is a key site of glucogen-like peptide-1 action and plays a critical role in triggering first phase insulin secretion. PeptideYY and ghrelin target intracerebral receptors as they are bidirectionally transported across the blood brain barrier. The anorectic functions of peripherally released peptideYY may however be mediated both via vagal afferents and intracerebral Y2 receptors in the brainstem and arcuate nucleus. SUMMARY: These recent findings demonstrate that the use of improved anatomical and physiological techniques and animal models with targeted gene modifications lead to an improved understanding of the complex role of gastrointestinal signals in the control of energy homeostasis.

Influence of Individual Characteristics on Work Engagement and Job Stress in a Sample of National and Foreign Workers in Switzerland

In most Western postindustrial societies today, the population is aging, businesses are faced with global integration, and important migration flows are taking place. Increasingly work organizations are hiring crossnational and multicultural workteams. In this situation it is important to understand the influence of certain individual and cultural characteristics on the process of professional integration. The present study explores the links between personality traits, demographic characteristics (age, sex, education, income, and nationality), work engagement, and job stress. The sample consisted of 618 participants, including 394 Swiss workers (200 women, 194 men) and 224 foreigners living and working in Switzerland (117 women, 107 men). Each participant completed the NEO-FFI, the UWES, and the GWSS questionnaires. Our results show an interaction between age and nationality with respect to work engagement and general job stress. The levels of work engagement and job stress appear to increase with age among national wotkers, whereas they decrease among foreign workers. In addition, work engagement was negatively associated with Neuroticism and positively with the other four personality dimensions. Finally, job stress was positively associated with Neuroticism and Conscientiousness, and negatively associated with Extraversion. However, the strength of these relationships appeared to vary according to the worker's nationality, age, sex, education, and income.

Obesity markers and blood pressure in a sample of Portuguese children and adolescents.

Little information exists regarding the effect of several obesity markers on blood pressure (BP) levels in youth. Transverse study including 2494 boys and 2589 girls. Height, weight and waist were measured according to the international criteria and body fat (BF) by bioimpedance. BP was measured by an automated device. Hypertension was defined using sex-specific, age-specific and height-specific observation-points. Body mass index (BMI) and waist were positively related with systolic blood pressure (SBP) and diastolic blood pressure (DBP) and heart rate in both sexes, whereas the relationships with BF were less consistent. Stepwise linear regression analysis showed that BMI was positively related with SBP and DBP in both sexes, whereas BF was negatively related with SBP in both sexes and with heart rate in boys only; finally, waist was positively related with SBP in boys and heart rate in girls. Age and heart rate-adjusted values of SBP and DBP increased with BMI: for SBP, 117+/-1, 123+/-1 and 124+/-1 mmHg in normal, overweight and obese boys, respectively; corresponding values for girls were 111+/-1, 114+/-1 and 116+/-2 mmHg (mean+/-SE, P<0.001). Overweight and obese boys had an odds ratio for being hypertensive of 2.26 (95% confidence interval: 1.79-2.86) and 3.36 (2.32-4.87), respectively; corresponding values for girls were 1.58 (confidence interval 1.25-1.99) and 2.31 (1.53-3.50). BMI, not BF or waist, is consistently and independently related to BP levels in children; overweight and obesity considerably increase the risk of hypertension.

Gender difference in the response to an angiotensin-converting enzyme inhibitor and a diurectic in hypertensive patients of African descent

Résumé de la thèse en français Titre : Différence entre hommes et femmes dans la réponse à un inhibiteur de l'enzyme de conversion de l'angiotensine et un diurétique chez des patients hypertendus d'origine Africaine. Introduction: L'efficacité des inhibiteurs de l'enzyme de conversion de l'angiotensine (ACEI) dans le traitement de l'hypertension artérielle chez les patients africains est controversée. Objectif: Nous avons examiné la baisse de la tension artérielle ambulatoire (ABP) en réponse à un diurétique et un ACEI chez des patients hypertendus d'origine africaine et nous avons évalué les différentes caractéristiques déterminant l'efficacité du traitement. Méthodes: Etude en simple-aveugle randomisée, en crossover AB/BA. Arrangement Familles hypertendues d'origine africaine de la population générale des Seychelles. Participants : 52 patients (29 hommes et 23 femmes) sur 62 patients hypertendus éligibles ont été inclus. Le principal résultat était la mesure de la réponse de l'ABP à 20 mg de lisinopril (LIS) ou 25 mg d'hydrochlorothiazide (HCT) quotidiennement pendant quatre semaines. Résultats: Le jour, la réponse systolique/diastolique de l'ABP sous HCT était de 4.9 (95% intervalle de confiance (IC) 1.2-8.6)/3.6 (1.0-6.2) mm Hg pour les hommes et 12.9 (9.216.6)/6.3 (3.7-8.8) mm Hg pour les femmes. Sous LIS, la réponse était de 18.8 (15.022.5)/14.6 (12.0-17.1) mm Hg pour les hommes et de 12.4 (8.7-16.2)/7.7 (5.1-10.2) mm Hg pour les femmes. La nuit, la réponse systolique/diastolique sous HCT était de 5.0 (0.6-9.4)/2.7 ((-0.4)-5.7) mm Hg pour les hommes et de 11.5 (7.1-16.0)/5.7 (2.6-8.8) mm Hg pour les femmes, et sous LIS était de 18.7 (14.2-22.1)/15.4 (12.4-18.5) mm Hg pour les hommes et de 3.5 ((-1.0)-7.9)/2.3 ((-0.8)-5.4) mm Hg pour les femmes. L'analyse de régression linéaire multiple a montré que le sexe est un prédicteur indépendant de la réponse tensionnelle à l'HCT et au LIS. Conclusions : Les patients hypertendus d'origine africaine ont présenté une baisse tensionnelle plus grande en réponse au LIS qu'à l'HCT. Les hommes ont mieux répondu au LIS qu'à l'HCT alors que les femmes ont répondu de manière similaire aux deux traitements.