A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.

Impact of stressful life event on the global functioning outcome after an assertive community treatment

Background: Assertive community treatment (ACT) was reported to be an effective treatment to improve global functioning of ultra-high risk (UHR) adolescents. However, the infl uence of stressful life event (SLE) was not extensively studied which represent our objective. Method: The SLE (encompassing adoption, migration, family member's deceased, sexual or physical abuse, etc.) of 20 UHR adolescents, treated with an ACT model, were rated. 10 adolescents having 0 to 1 SLE (mainly parents' divorce; low SLE group) were compared 10 adolescents with 2 to 5 SLE (high SLE group). The adolescents were assessed at baseline and after treatment with the Health of Nation Outcome Scale for Children and Adolescents (HoNOSCA). The HoNOSCA allowed rating different diffi culties such as behavior, symptoms, disorders and social. Results: First, results on the whole sample indicated signifi cant improvement after ACT (compared to baseline) on the total (P = .04), symptoms (P = .025) and social (P = .009) scores of the HoNOSCA. Second, the improvement on the HoNOSCA's score of the high SLE group were signifi cantly higher for the total (P = .016), symptoms (P = .019) and behavior (P = .033) scores compared to the low SLE group. Discussion/Conclusion: Globally, ACT seems to be an appropriate treatment to enhance global functioning and more specifi cally the social and symptoms diffi culties of UHR adolescents. Additionally, UHR adolescents with a high numbers of SLE were observed to have a better benefi t of the ACT on global, symptoms and behavioral diffi culties.

Niche, distribution and global change : modeling insights into biogeography and conservation biology Olivier Broennimann

RESUME Les évidences montrant que les changements globaux affectent la biodiversité s'accumulent. Les facteurs les plus influant dans ce processus sont les changements et destructions d'habitat, l'expansion des espèces envahissantes et l'impact des changements climatiques. Une évaluation pertinente de la réponse des espèces face à ces changements est essentielle pour proposer des mesures permettant de réduire le déclin actuel de la biodiversité. La modélisation de la répartition d'espèces basée sur la niche (NBM) est l'un des rares outils permettant cette évaluation. Néanmoins, leur application dans le contexte des changements globaux repose sur des hypothèses restrictives et demande une interprétation critique. Ce travail présente une série d'études de cas investiguant les possibilités et limitations de cette approche pour prédire l'impact des changements globaux. Deux études traitant des menaces sur les espèces rares et en danger d'extinction sont présentées. Les caractéristiques éco-géographiques de 118 plantes avec un haut degré de priorité de conservation sont revues. La prévalence des types de rareté sont analysées en relation avec leur risque d'extinction UICN. La revue souligne l'importance de la conservation à l'échelle régionale. Une évaluation de la rareté à échelle globale peut être trompeuse pour certaine espèces car elle ne tient pas en compte des différents degrés de rareté que présente une espèce à différentes échelles spatiales. La deuxième étude test une approche pour améliorer l'échantillonnage d'espèces rares en incluant des phases itératives de modélisation et d'échantillonnage sur le terrain. L'application de l'approche en biologie de la conservation (illustrée ici par le cas du chardon bleu, Eryngium alpinum), permettrait de réduire le temps et les coûts d'échantillonnage. Deux études sur l'impact des changements climatiques sur la faune et la flore africaine sont présentées. La première étude évalue la sensibilité de 227 mammifères africains face aux climatiques d'ici 2050. Elle montre qu'un nombre important d'espèces pourrait être bientôt en danger d'extinction et que les parcs nationaux africains (principalement ceux situé en milieux xériques) pourraient ne pas remplir leur mandat de protection de la biodiversité dans le futur. La seconde étude modélise l'aire de répartition en 2050 de 975 espèces de plantes endémiques du sud de l'Afrique. L'étude propose l'inclusion de méthodes améliorant la prédiction des risques liés aux changements climatiques. Elle propose également une méthode pour estimer a priori la sensibilité d'une espèce aux changements climatiques à partir de ses propriétés écologiques et des caractéristiques de son aire de répartition. Trois études illustrent l'utilisation des modèles dans l'étude des invasions biologiques. Une première étude relate l'expansion de la laitue sáuvage (Lactuca serriola) vers le nord de l'Europe en lien avec les changements du climat depuis 250 ans. La deuxième étude analyse le potentiel d'invasion de la centaurée tachetée (Centaures maculosa), une mauvaise herbe importée en Amérique du nord vers 1890. L'étude apporte la preuve qu'une espèce envahissante peut occuper une niche climatique différente après introduction sur un autre continent. Les modèles basés sur l'aire native prédisent de manière incorrecte l'entier de l'aire envahie mais permettent de prévoir les aires d'introductions potentielles. Une méthode alternative, incluant la calibration du modèle à partir des deux aires où l'espèce est présente, est proposée pour améliorer les prédictions de l'invasion en Amérique du nord. Je présente finalement une revue de la littérature sur la dynamique de la niche écologique dans le temps et l'espace. Elle synthétise les récents développements théoriques concernant le conservatisme de la niche et propose des solutions pour améliorer la pertinence des prédictions d'impact des changements climatiques et des invasions biologiques. SUMMARY Evidences are accumulating that biodiversity is facing the effects of global change. The most influential drivers of change in ecosystems are land-use change, alien species invasions and climate change impacts. Accurate projections of species' responses to these changes are needed to propose mitigation measures to slow down the on-going erosion of biodiversity. Niche-based models (NBM) currently represent one of the only tools for such projections. However, their application in the context of global changes relies on restrictive assumptions, calling for cautious interpretations. In this thesis I aim to assess the effectiveness and shortcomings of niche-based models for the study of global change impacts on biodiversity through the investigation of specific, unsolved limitations and suggestion of new approaches. Two studies investigating threats to rare and endangered plants are presented. I review the ecogeographic characteristic of 118 endangered plants with high conservation priority in Switzerland. The prevalence of rarity types among plant species is analyzed in relation to IUCN extinction risks. The review underlines the importance of regional vs. global conservation and shows that a global assessment of rarity might be misleading for some species because it can fail to account for different degrees of rarity at a variety of spatial scales. The second study tests a modeling framework including iterative steps of modeling and field surveys to improve the sampling of rare species. The approach is illustrated with a rare alpine plant, Eryngium alpinum and shows promise for complementing conservation practices and reducing sampling costs. Two studies illustrate the impacts of climate change on African taxa. The first one assesses the sensitivity of 277 mammals at African scale to climate change by 2050 in terms of species richness and turnover. It shows that a substantial number of species could be critically endangered in the future. National parks situated in xeric ecosystems are not expected to meet their mandate of protecting current species diversity in the future. The second study model the distribution in 2050 of 975 endemic plant species in southern Africa. The study proposes the inclusion of new methodological insights improving the accuracy and ecological realism of predictions of global changes studies. It also investigates the possibility to estimate a priori the sensitivity of a species to climate change from the geographical distribution and ecological proprieties of the species. Three studies illustrate the application of NBM in the study of biological invasions. The first one investigates the Northwards expansion of Lactuca serriola L. in Europe during the last 250 years in relation with climate changes. In the last two decades, the species could not track climate change due to non climatic influences. A second study analyses the potential invasion extent of spotted knapweed, a European weed first introduced into North America in the 1890s. The study provides one of the first empirical evidence that an invasive species can occupy climatically distinct niche spaces following its introduction into a new area. Models fail to predict the current full extent of the invasion, but correctly predict areas of introduction. An alternative approach, involving the calibration of models with pooled data from both ranges, is proposed to improve predictions of the extent of invasion on models based solely on the native range. I finally present a review on the dynamic nature of ecological niches in space and time. It synthesizes the recent theoretical developments to the niche conservatism issues and proposes solutions to improve confidence in NBM predictions of the impacts of climate change and species invasions on species distributions.

A global marine sedimentary response to the end-Permian mass extinction: Examples from southern Turkey and the western United States

The end-Permian mass extinction greatly diminished marine diversity and brought about a whole-scale restructuring of marine ecosystems; these ecosystem changes also profoundly affected the sedimentary record. Data presented here, attained through facies analyses of strata deposited during the immediate aftermath of the end-Permian mass extinction (southern Turkey) and at the close of the Early Triassic (southwestern United States), in combination with a literature review, show that sedimentary systems were profoundly affected by: (1) a reduction in biotic diversity and abundance and (2) long-term environmental fluctuations that resulted from the end-Permian crisis. Lower Triassic strata display widespread microbialite and carbonate seafloor fan development and contain indicators of suppressed infaunal bioturbation such as flat-pebble conglomerates and wrinkle structures (facies considered unusual in post-Cambrian subtidal deposits). Our observations suggest that depositional systems, too, respond to biotic crises, and that certain facies may act as barometers of ecologic and environmental change independent of fossil assemblage analyses. Close investigation of facies changes during other critical times in Earth history may serve as an important tool in interpreting the ecology of metazoans and their environment.

Time invested in the global respiratory care of cystic fibrosis paediatrics patients.

INTRODUCTION: Respiratory therapy is a keystone of the treatment for cystic fibrosis (CF) lung disease, but it is time consuming. OBJECTIVES: We aimed to assess the total time spent on respiratory therapy, including chest physiotherapy (CPT) and physical activity (PA), as well as inhalation therapy (IT) and maintenance of materials (MM) to rationalise and optimise treatment. METHODS: A cross-sectional prospective study in a paediatric CF cohort. A questionnaire was developed to look at the time spent on respiratory care over 3 months. Enrolled in this study are all CF patients aged from 6 to 16 years (the exclusion criterion was lung transplantation). RESULTS: Of the 40 enrolled patients, 22 participated (13 boys and 9 girls), with a mean age of 11 years. The patients spent approximately 19.46 h per week (standard deviation ± 7.53, 8.00-35.25 h) on therapy: CPT (30.58%), IT (15.11%), PA (50%) and MM (4.32%), without statistical significance between sexes. CONCLUSION: In our cohort, CF patients spent an average of nearly 20 h a week in respiratory therapy, within a wide range of between 8 h to almost 36 h a week. PA consumes almost half of the time. Physicians have to take into consideration the burden of the treatment, to optimise the therapy.

Contribution of the Global Regulator Gene gacA to Persistence and Dissemination of Pseudomonas fluorescens Biocontrol Strain CHA0 Introduced into Soil Microcosms.

Structural and regulatory genes involved in the synthesis of antimicrobial metabolites are essential for the biocontrol activity of fluorescent pseudomonads and, in principle, amenable to genetic engineering for strain improvement. An eventual large-scale release of such bacteria raises the question of whether such genes also contribute to the persistence and dissemination of the bacteria in soil ecosystems. Pseudomonas fluorescens wild-type strain CHA0 protects plants against a variety of fungal diseases and produces several antimicrobial metabolites. The regulatory gene gacA globally controls antibiotic production and is crucial for disease suppression in CHA0. This gene also regulates the production of extracellular protease and phospholipase. The contribution of gacA to survival and vertical translocation of CHA0 in soil microcosms of increasing complexity was studied in coinoculation experiments with the wild type and a gacA mutant which lacks antibiotics and some exoenzymes. Both strains were marked with spontaneous resistance to rifampin. In a closed system with sterile soil, strain CHA0 and the gacA mutant multiplied for several weeks, whereas these strains declined exponentially in nonsterile soil of different Swiss origins. The gacA mutant was less persistent in nonrhizosphere raw soil than was the wild type, but no competitive disadvantage when colonizing the rhizosphere and roots of wheat was found in the particular soil type and during the period studied. Vertical translocation was assessed after strains had been applied to undisturbed, long (60-cm) or short (20-cm) soil columns, both planted with wheat. A smaller number of cells of the gacA mutant than of the wild type were detected in the percolated water and in different depths of the soil column. Single-strain inoculation gave similar results in all microcosms tested. We conclude that mutation in a single regulatory gene involved in antibiotic and exoenzyme synthesis can affect the survival of P. fluorescens more profoundly in unplanted soil than in the rhizosphere.

The global activator GacA of Pseudomonas aeruginosa PAO positively controls the production of the autoinducer N-butyryl-homoserine lactone and the formation of the virulence factors pyocyanin, cyanide, and lipase.

The global activator GacA, a highly conserved response regulator in Gram-negative bacteria, is required for the production of exoenzymes and secondary metabolites in Pseudomonas spp. The gacA gene of Pseudomonas aeruginosa PAO1 was isolated and its role in cell-density-dependent gene expression was characterized. Mutational inactivation of gacA resulted in delayed and reduced formation of the cell-density signal N-butyryl-L-homoserine lactone (BHL), of the cognate transcriptional activator RhIR (VsmR), and of the transcriptional activator LasR, which is known to positively regulate RhIR expression. Amplification of gacA on a multicopy plasmid caused precocious and enhanced production of BHL, RhIR and LasR. In parallel, the gacA gene dosage markedly influenced the BHL/RhIR-dependent formation of the cytotoxic compounds pyocyanin and cyanide and the exoenzyme lipase. However, the concentrations of another known cell-density signal of P. aeruginosa, N-oxododecanoyl-L-homoserine lactone, did not always match BHL concentrations. A model accounting for these observations places GacA function upstream of LasR and RhIR in the complex, cell-density-dependent signal-transduction pathway regulating several exoproducts and virulence factors of P. aeruginosa via BHL.

La pertinence de la Global Health pour la Suisse

L'une des premières activités du groupe spécialisé "Global Health", créé au sein de la société de discipline médicale Santé Publique Suisse, a été de formuler une définition appropriée au contexte helvétique du terme de "Global Health" (santé globale). La "Global Health est un espace destiné à la recherche, à la pratique et aux règles y afférents, qui met la priorité sur l'amélioration de la santé, en général, et sur un accès équitable à la santé pour tous, en particulier. La Global Health répond aux questions de santé transnationales et s'intéresse aux déterminants et aux possibilités de solution. Elle implique beaucoup de disciplines, tant du secteur médical que d'autres domaines, promouvant ainsi la collaboration interdisciplinaire; elle encourage la bonne gouvernance pour anticiper et s'adapter à un environnement qui change rapidement ". A l'avenir, une plateforme sera créée dans le but d'offrir un accès aux expériences internationales et de les fructifier en Suisse mais aussi de partager les expériences acquises ici localement, avec des partenaires internationaux tels que les associations européenne et mondiale de santé publique. Last but not least, le groupe spécialisé susmentionné va plaider pour une compréhension large et commune de la Global Health.