Disentangling the effects of key innovations on the diversification of Bromelioideae (bromeliaceae).

The evolution of key innovations, novel traits that promote diversification, is often seen as major driver for the unequal distribution of species richness within the tree of life. In this study, we aim to determine the factors underlying the extraordinary radiation of the subfamily Bromelioideae, one of the most diverse clades among the neotropical plant family Bromeliaceae. Based on an extended molecular phylogenetic data set, we examine the effect of two putative key innovations, that is, the Crassulacean acid metabolism (CAM) and the water-impounding tank, on speciation and extinction rates. To this aim, we develop a novel Bayesian implementation of the phylogenetic comparative method, binary state speciation and extinction, which enables hypotheses testing by Bayes factors and accommodates the uncertainty on model selection by Bayesian model averaging. Both CAM and tank habit were found to correlate with increased net diversification, thus fulfilling the criteria for key innovations. Our analyses further revealed that CAM photosynthesis is correlated with a twofold increase in speciation rate, whereas the evolution of the tank had primarily an effect on extinction rates that were found five times lower in tank-forming lineages compared to tank-less clades. These differences are discussed in the light of biogeography, ecology, and past climate change.

Arenavirus Nucleoprotein Targets Interferon Regulatory Factor-Activating Kinase IKKε.

Arenaviruses perturb innate antiviral defense by blocking induction of type I interferon (IFN) production. Accordingly, the arenavirus nucleoprotein (NP) was shown to block activation and nuclear translocation of interferon regulatory factor 3 (IRF3) in response to virus infection. Here, we sought to identify cellular factors involved in innate antiviral signaling targeted by arenavirus NP. Consistent with previous studies, infection with the prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) prevented phosphorylation of IRF3 in response to infection with Sendai virus, a strong inducer of the retinoic acid-inducible gene I (RIG-I)/mitochondrial antiviral signaling (MAVS) pathway of innate antiviral signaling. Using a combination of coimmunoprecipitation and confocal microscopy, we found that LCMV NP associates with the IκB kinase (IKK)-related kinase IKKε but that, rather unexpectedly, LCMV NP did not bind to the closely related TANK-binding kinase 1 (TBK-1). The NP-IKKε interaction was highly conserved among arenaviruses from different clades. In LCMV-infected cells, IKKε colocalized with NP but not with MAVS located on the outer membrane of mitochondria. LCMV NP bound the kinase domain (KD) of IKKε (IKBKE) and blocked its autocatalytic activity and its ability to phosphorylate IRF3, without undergoing phosphorylation. Together, our data identify IKKε as a novel target of arenavirus NP. Engagement of NP seems to sequester IKKε in an inactive complex. Considering the important functions of IKKε in innate antiviral immunity and other cellular processes, the NP-IKKε interaction likely plays a crucial role in arenavirus-host interaction.

Evaluation of exposure biomarkers in offshore workers exposed to low benzene and toluene concentrations.

Characterize ethylbenzene and xylene air concentrations, and explore the biological exposure markers (urinary t,t-muconic acid (t,t-MA) and unmetabolized toluene) among petroleum workers offshore. Offshore workers have increased health risks due to simultaneous exposures to several hydrocarbons present in crude oil. We discuss the pooled benzene exposure results from our previous and current studies and possible co-exposure interactions. BTEX air concentrations were measured during three consecutive 12-h work shifts among 10 tank workers, 15 process operators, and 18 controls. Biological samples were collected pre-shift on the first day of study and post-shift on the third day of the study. The geometric mean exposure over the three work shifts were 0.02 ppm benzene, 0.05 ppm toluene, 0.03 ppm ethylbenzene, and 0.06 ppm xylene. Benzene in air was significantly correlated with unmetabolized benzene in blood (r = 0.69, p < 0.001) and urine (r = 0.64, p < 0.001), but not with urinary t,t-MA (r = 0.27, p = 0.20). Toluene in air was highly correlated with the internal dose of toluene in both blood (r = 0.70, p < 0.001) and urine (r = 0.73, p < 0.001). Co-exposures were present; however, an interaction of metabolism was not likely at these low benzene and toluene exposures. Urinary benzene, but not t,t-MA, was a reliable biomarker for benzene at low exposure levels. Urinary toluene was a useful biomarker for toluene exposure. Xylene and ethylbenzene air levels were low. Dermal exposure assessment needs to be performed in future studies among these workers.

TRADD protein is an essential component of the RIG-like helicase antiviral pathway

Upon detection of viral RNA, the helicases RIG-I and/or MDA5 trigger, via their adaptor Cardif (also known as IPS-1, MAVS, or VISA), the activation of the transcription factors NF-kappaB and IRF3, which collaborate to induce an antiviral type I interferon (IFN) response. FADD and RIP1, known as mediators of death-receptor signaling, are implicated in this antiviral pathway; however, the link between death-receptor and antiviral signaling is not known. Here we showed that TRADD, a crucial adaptor of tumor necrosis factor receptor (TNFRI), was important in RIG-like helicase (RLH)-mediated signal transduction. TRADD is recruited to Cardif and orchestrated complex formation with the E3 ubiquitin ligase TRAF3 and TANK and with FADD and RIP1, leading to the activation of IRF3 and NF-kappaB. Loss of TRADD prevented Cardif-dependent activation of IFN-beta, reduced the production of IFN-beta in response to RNA viruses, and enhanced vesicular stomatitis virus replication. Thus, TRADD is not only an essential component of proinflammatory TNFRI signaling, but is also required for RLH-Cardif-dependent antiviral immune responses

Beyond Prejudice : conservation in the City : a case study from Switzerland

Conservation in the city is challenging because of a continued view that the urban realm is antithetical to nature. This was clearly the case when the first Swiss National Park was established at the beginning of the 20th century. New Swiss legislation brought new approaches to the establishment of natural parks, in particular by including human activities as a logical component in their development. In 2010, a Federal think tank discussed opportunities for launching a new kind of park: the Urban Natural Park. This paper reports an analysis of this discussion, together with the study of the literature dealing with conservation in the city and natural parks. It shows that a clear antagonism between city and nature still remains present, reflected in an implicit hierarchy hidden in the designation of natural parks: wild nature is nominated as the best nature; if not wild, the best nature is identified as rural; if neither wild nor rural, nature is thought not to be the concern of natural park policy. The Swiss Biodiversity Strategy implemented in 2012 is a recent recognition of the importance of urban nature for biodiversity conservation. This recognition, however, condemns urban nature to a special status, situated outside the usual framework of conservation management. I conclude by arguing that anti-urban bias must be addressed because it inhibits effective conservation strategy, prevents the identification of existing environmental qualities of cities and, eventually, has negative impacts on biological conservation outside the city because it fosters urban spreading.

Variability of a peripheral dose among various linac geometries for second cancer risk assessment.

Second cancer risk assessment for radiotherapy is controversial due to the large uncertainties of the dose-response relationship. This could be improved by a better assessment of the peripheral doses to healthy organs in future epidemiological studies. In this framework, we developed a simple Monte Carlo (MC) model of the Siemens Primus 6 MV linac for both open and wedged fields that we then validated with dose profiles measured in a water tank up to 30 cm from the central axis. The differences between the measured and calculated doses were comparable to other more complex MC models and never exceeded 50%. We then compared our simple MC model with the peripheral dose profiles of five different linacs with different collimation systems. We found that the peripheral dose between two linacs could differ up to a factor of 9 for small fields (5 × 5 cm(2)) and up to a factor of 10 for wedged fields. Considering that an uncertainty of 50% in dose estimation could be acceptable in the context of risk assessment, the MC model can be used as a generic model for large open fields (≥10 × 10 cm(2)) only. The uncertainties in peripheral doses should be considered in future epidemiological studies when designing the width of the dose bins to stratify the risk as a function of the dose.

DAI/ZBP1 recruits RIP1 and RIP3 through RIP homotypic interaction motifs to activate NF-kappaB.

Detection of viral nucleic acids is central to antiviral immunity. Recently, DAI/ZBP1 (DNA-dependent activator of IRFs/Z-DNA binding protein 1) was identified as a cytoplasmic DNA sensor and shown to activate the interferon regulatory factor (IRF) and nuclear factor-kappa B (NF-kappaB) transcription factors, leading to type-I interferon production. DAI-induced IRF activation depends on TANK-binding kinase 1 (TBK1), whereas signalling pathways and molecular components involved in NF-kappaB activation remain elusive. Here, we report the identification of two receptor-interacting protein (RIP) homotypic interaction motifs (RHIMs) in the DAI protein sequence, and show that these domains relay DAI-induced NF-kappaB signals through the recruitment of the RHIM-containing kinases RIP1 and RIP3. We show that knockdown of not only RIP1, but also RIP3 affects DAI-induced NF-kappaB activation. Importantly, RIP recruitment to DAI is inhibited by the RHIM-containing murine cytomegalovirus (MCMV) protein M45. These findings delineate the DAI signalling pathway to NF-kappaB and suggest a possible new immune modulation strategy of the MCMV.

Evaluation des pratiques d'irrigation, de fertilisation et d'application de pesticides dans l'agriculture périurbaine de Dakar, Sénégal

RESUMEL'agriculture urbaine et périurbalne - nommée ci-après AU - est un thème fort de recherche transversale, au vu des nombreux enjeux économiques, sociaux et environnementaux. L'objectif de cette recherche était de contribuer à une meilleure connaissance des processus de transfert de polluants et du cycle des nutriments à l'échelle locale, afin de déterminer sous quelles conditions l'AU de Dakar peut être pratiquée sans porter atteinte à la santé et à l'environnement.Une approche basée sur l'étude des processus géochimiques dans ie sol jusqu'à la nappe a été choisie, à l'échelle de la parcelle cultivée et à une échelle un peu plus large de la zone périurbaine de Dakar pour déterminer les influences du type d'occupation du sol.L'évaluation des impacts de l'irrigation avec des eaux usées brutes et des eaux de nappe saumâtres sur la qualité des sols (chapitre 2) a montré que l'alcalinité et les teneurs en calcium élevées des eaux saumâtres induisent la précipitation de CaC03 dans l'horizon superficiel du sol. Na remplace consécutivement Ca sur le complexe argilo-humique du sol et les bicarbonates diminuent dans la solution du sol. Le carbone organique dissout (COD) augmente significativement dans la solution du sol et dans la nappe sous-jacente. Malgré l'alcalinité et les teneurs très élevées en calcium des eaux usées, il y a peu de précipitation de CaC03 dans l'horizon superficiel du sol et une faible augmentation du sodium échangeable ESP. La nitrification de l'ammonium des eaux usées (moy 190mg/L à Pikine) produit des protons, qui ne sont plus tamponnés par les bicarbonates exportés hors du profil. Il y a alors une nette baisse de pH des sols irrigués par des eaux usées non traitées. Les sols irrigués par des eaux usées et saumâtres stockent moins de C et Ν que les sols de référence.L'évaluation de l'influence de l'occupation des sols en zone périurbaine sur à la nappe phréatique peu profonde (chapitre 3) a permis de déterminer les traceurs représentatifs de l'occupation du sol, à savoir Br/CI, NO3/CI et δ180-Ν03 pour l'irrigation par des eaux usées, pH et δ15Ν-Ν03 pour l'irrigation par des eaux de nappe, et Rb+Cr et Κ pour les lixiviats de fosses septiques. Ce chapitre a mis en évidence des points importants de la dynamique de l'azote en zone périurbaine sous deux occupations du sol : (1) la dénitrification est un processus important dans l'agrosystème périurbain de Dakar en bas de dune, dans les gleysols où l'on trouve des conditions temporairement réduites et un substrat organique favorables aux microorganismes de la dénitrification. Les teneurs en nitrates sont presque nulles avec irrigation d'eau de nappe. (2) en bas de pente, mais avec irrigation quotidienne par les eaux usées, l'apport continu d'ammonium inhibe probablement la dénitrification, mais favorise la volatilisation. (3) la nitrification de l'ammonium dans la nappe lors de la lixiviation des fosses septiques se distingue de la nitrification de l'ammonium dans la zone non saturée dans la zone d'agriculture périurbaine par la composition isotopique de l'oxygène de l'eau. Une comparaison des flux d'azote entre l'agrosystème et les quartiers périurbains de Dakar (chapitre 4) ont révélé que ces derniers étaient du même ordre de grandeur par unité de surface, à savoir 2-4 tonnes Ν /ha/an.L'évaluation des flux de pesticides dans l'agrosystème et des risques induits pour les eaux souterraines (chapitre 5) a révélé un fiux total de pesticides de 60kg/ha/an, totalisant 15 matières actives. Seules deux de ces matières actives sont autorisées par le comité des pesticides sahélien. Les pesticides les plus utilisés par les producteurs sont l'organochloré dicofol, les organophosphorés methamidophos, dimethoate et fenithrotion ainsi que le cabamate methomyl. Les flux les plus importants sont de 9 à 7 kg/ha/an (methomyl, methamidophos, ethoprophos et dicofol). Les pesticides qui présentent un risque élevé de contamination des eaux souterraines et qui devraient être prioritaires pour un suivi analytique sont : le carbofuran, le dimethoate, l'ethoprophos et le methomyl.En conclusion, une meilleure gestion de la fertilisation est nécessaire dans la zone d'AU de Dakar, afin de (1) réduire les pertes gazeuses qui contribuent à l'effet de serre, (2) de ralentir la minéralisation du carbone et de l'azote organiques pour créer un stock de C et Ν dans ces sols, (3) de limiter le lessivage dans la nappe et enfin, 4) d'augmenter l'efficacité d'utilisation de Ν par les plantes. Une optimisation de l'irrigation devrait limiter l'alcalinisation secondaire. Enfin, la mise en place d'une lutte intégrée ou biologique contre les ravageurs est indispensable afin de minimiser les risques pour les eaux souterraines et les mares permanentes.ABSTRACTUrban and periurban agriculture (UA) is an important issue in southern countries, because of its key role in their social and economical development and its environmental concern. The goal of this study was to contribute to a better understanding of pollutant transfer and nutrient cycling at the local scale, in order to implement the necessary improvements to guarantee the sustainability of this practice.An approach based on geochemical processes occurring in the vadose zone from the surface down to the groundwater level was chosen, at the scale of cultivated plots and at the regional scale of Dakar periurban areas, to determine the influence of land use.The assessment of irrigation with untreated domestic wastewater and brackish water on soil quality (chapter 2) showed: (1) that the high alkalinity and calcium contents of brackish water induce CaC03 precipitation in the top layer of the soil and therefore a replacement of Ca by Na on the clay- humic complexes, strongly marked during the dry season. Dissolved organic carbon (DOC) increased significantly in the soil solution and in the underlying groundwater. (2) in spite of the similarly high alkalinity and Ca contents of waste water, there is only little CaC03 precipitation and a low increase of the percentage of exchangeable sodium (ESP) in the soil top layer. The nitrification of the ammonium of wastewater (mean 190 mg/L in Pikine) produces protons, which are not any more buffered by bicarbonates exported out of the soil profile, which leads to a net decline of soil pH. Both soils irrigated with untreated wastewater and brackish water store less of C and Ν than soils irrigated with non saline groundwater.The assessment of the impact of land use on the shallow groundwater (chapter 3) allowed determining representative tracers of the land use. Low Br/CI ratio, high NO3/CI ratio and low δ1βΟ- nitrate indicated the influence of wastewater; high pH and high 515N-nitrates indicated the influence of brackish water together with high amendments of organic fertilizers; high Rb+Cr and Κ indicated the influence of poor sanitation facilities in periurban districts (septic tank leakage). This chapter also pointed out the following facts about the nitrogen dynamics : (1) denitrification is a key-process in the Dakar UA agrosystem in the gleysols irrigated with groundwater. The underlying groundwater is almost nitrate free. (2) in the Gleysols irrigated with waste water, ammonium inhibits denitrification but facilitate ammoniac volatilization. A comparison of nitrogen balance between the UA agrosystem and the periurban districts of Dakar (chapter 4) revealed similar flows per surface unit, namely 2-4 tons Ν / ha / year.The evaluation of pesticides use in the UA agrosystem and the risk assessment for the groundwater (chapter 5) revealed a total flow of pesticides of 60kg / ha / year, totalizing 15 active substances. Only two of these are authorized by the Sahelian Pesticides Committee. The most used pesticides are dicofol (organochlorinated), methamidophos, dimethoate and fenithrotion (organophosphate) as well as methomyl. (carbamate). The most important flows vary between 9 to 7 kg / ha / year. Pesticides with a high risk of groundwater contamination - according to SIRIS and EPRIP 2 indicators - are: carbofuran, dimethoate, ethoprophos and methomyl. These substances should be established as a priority for an analytical follow-up in the different environmental compartments.In conclusion, a better management of the fertilization is necessary in the Dakar UA, (1) to reduce the gaseous losses which contribute to greenhouse emissions (2) to slow down the mineralization of the organic carbon and the nitrogen, in order to enhance the C and Ν stock in these soils, (3) to limit the nitrate leaching in the groundwater and finally, 4) to increase the N-use efficiency of plants. An optimization of the irrigation scheme should limit the secondary sodisation if coupled with an increase the stable organic matter of the soil. An integrated or biologic crop pest strategy is urgently needed to minimize risks with respect to ground and surface water (ponds used for fishing).RESUME LARGE PUBLICL'agriculture mondiale connaît actuellement une crise majeure, affectée par les changements climatiques, la sécurité alimentaire et les dégradations de l'environnement. Elle n'a plus le rôle unique de produire, mais devient un élément essentiel de la protection des ressources naturelles et du paysage. Les politiques agricoles basées sur les marchés mondiaux devront se réorienter vers une agriculture locale basée sur le développement durable.La production alimentaire située dans l'enceinte des villes, nommée agriculture urbaine ou périurbaine (AU ci-après) joue un rôle important dans le contexte actuel d'accroissement de la population et de la pauvreté urbaines. L'AU concerne en effet la majorité des mégapoies du monde, fait vivre plus de 200 millions de personnes dans les pays du Sud, fournit jusqu'à 80% de la demande urbaine en certains produits frais, fait barrière à l'extension urbaine et permet un recyclage de certains déchets urbains. L'AU a pour particularité d'être à cheval entre des politiques rurales et urbaines, d'où un délaissement ce cette activité au secteur informel. Ce qui a développé de nombreuses stratégies à risques, comme à Dakar, où les petits producteurs périurbains irriguent quotidiennement avec des eaux usées domestiques par manque d'accès à une eau de bonne qualité et pour raccourcir les cycles de production. L'extrême précarité foncière des acteurs de l'AU de Dakar les empêchent d'investir à long terme et induit des pratiques inadéquates d'irrigation, d'usage de pesticides et de fertilisation de ces sols sableux.L'objectif de cette recherche était de contribuer à une meilleure connaissance des processus de transfert de polluants et du cycle des nutriments à l'échelle des parcelles cultivées par des eaux usées et des eaux saumâtres, afin de déterminer sous quelles conditions l'AU de Dakar peut être pratiquée et surtout maintenue sans porter atteinte à la santé et à l'environnement. Pour cela, une approche basée sur l'étude des processus géochimiques dans le sol jusqu'à la nappe a été choisie, à l'échelle de la parcelle cultivée et à une échelle un peu plus large de la zone périurbaine de Dakar pour déterminer les influences du type d'occupation du sol.Les résultats principaux de cette étude ont montré que (1) il y a un processus de salinisation anthropique des sols (sodisation) lors d'irrigation avec des eaux de nappe saumâtres, un processus accentué en saison sèche et lors d'années à pluviométrie déficitaire. Bien que les eaux usées soient aussi salines que les eaux de nappe, la salinisation des sols irrigués' par des eaux usées est limitée par l'ammonium présent dans les eaux usées (moy 190mg NH4/L à Pikine) qui produit de l'acidité lors de la transformation en nitrates dans le sol (nitrification). (2) les sols irrigués par des eaux usées (EU) stockent moins de C et Ν que les sois de référence, ce qui montrent bien que l'azote des eaux usées n'est pas disponible pour les plantes, mais est lessivé dans la nappe (100 à 450 mg/L N03 sous irrigation par EU, alors que la limite de OMS est de 50mg/L). (3) l'utilisation des isotopes stables des nitrates et des éléments traces, notamment le bore et le brome, ont permis de distinguer l'influence de l'irrigation par des eaux usées, de l'irrigation par des eaux de nappe et des lixiviats de fosses septiques sur les propriétés de la nappe. (4) Le processus de la dénitrification (atténuation naturelle des concentrations en nitrates de la nappe par biotransformation en azote gazeux) est important dans les zones basses de l'agrosystème périurbain de Dakar, sous irrigation par eaux naturelles (ΝΟ3 < 50mg/L). Tandis que sous habitat sans assainissement adéquat, les nitrates atteignent 300 à 700 mg/L. (5) Le flux total de pesticides dans l'AU est énorme (60kg/ha/an) totalisant 15 pesticides, dont deux seulement sont autorisés. Les pesticides les plus utilisés sont des insecticides organophosphorés et organochlorés classés extrêmement dangereux à dangereux par l'OMS, appliqués à des doses de 2 à 9 kg/ha/an. Les pesticides qui ont montré un risque élevé de contamination des eaux souterraines avec les indicateurs SIRIS et EPRIP2 sont : le carbofuran, le dimethoate, l'ethoprophos et le methomyl.En conclusion, nous recommandons la reconstitution d'un horizon superficiel des sols riche en matière organique stable et structuré par production locale de compost. Cette mesure réduira les pertes gazeuses contribuant à l'effet de serre, augmentera le stock de Ν dans ces sols, alors utilisable par les plantes et permettra de diminuer l'irrigation car la capacité de rétention de l'eau dans le sol sera accru, ce qui limitera le lessivage des nitrates dans la nappe et l'alcalinisation secondaire. Enfin, la mise en place d'une lutte intégrée ou biologique contre les ravageurs est indispensable afin de minimiser les risques pour les eaux souterraines et lesmares permanentes.

Modulation of genetic associations with serum urate levels by body-mass-index in humans.

We tested for interactions between body mass index (BMI) and common genetic variants affecting serum urate levels, genome-wide, in up to 42569 participants. Both stratified genome-wide association (GWAS) analyses, in lean, overweight and obese individuals, and regression-type analyses in a non BMI-stratified overall sample were performed. The former did not uncover any novel locus with a major main effect, but supported modulation of effects for some known and potentially new urate loci. The latter highlighted a SNP at RBFOX3 reaching genome-wide significant level (effect size 0.014, 95% CI 0.008-0.02, Pinter= 2.6 x 10-8). Two top loci in interaction term analyses, RBFOX3 and ERO1LB-EDARADD, also displayed suggestive differences in main effect size between the lean and obese strata. All top ranking loci for urate effect differences between BMI categories were novel and most had small magnitude but opposite direction effects between strata. They include the locus RBMS1-TANK (men, Pdifflean-overweight= 4.7 x 10-8), a region that has been associated with several obesity related traits, and TSPYL5 (men, Pdifflean-overweight= 9.1 x 10-8), regulating adipocytes-produced estradiol. The top-ranking known urate loci was ABCG2, the strongest known gout risk locus, with an effect halved in obese compared to lean men (Pdifflean-obese= 2 x 10-4). Finally, pathway analysis suggested a role for N-glycan biosynthesis as a prominent urate-associated pathway in the lean stratum. These results illustrate a potentially powerful way to monitor changes occurring in obesogenic environment.

Sanitary quality of edible bivalve mollusks in Southeastern Brazil using an UV based depuration system

The increase in seafood production, especially in mariculture worldwide, has brought out the need of continued monitoring of shellfish production areas in order to ensure safety to human consumption. The purpose of this research was to evaluate pathogenic protozoa, viruses and bacteria contamination in oysters before and after UV depuration procedure, in brackish waters at all stages of cultivation and treatment steps and to enumerate microbiological indicators of fecal contamination from production site up to depuration site in an oyster cooperative located at the Southeastern estuarine area of Brazil. Oysters and brackish water were collected monthly from September 2009 to November 2010. Four sampling sites were selected for enteropathogens analysis: site 1- oyster growth, site 2- catchment water (before UV depuration procedure), site 3 - filtration stage of water treatment (only for protozoa analysis) and site 4- oyster's depuration tank. Three microbiological indicators ! were examined at sites 1, 2 and 4. The following pathogenic microorganisms were searched: Giardia cysts, Cryptosporidium oocysts, Human Adenovirus (HAdV), Hepatitis A virus (HAV), Human Norovirus (HnoV) (genogroups I and II), JC strain Polyomavirus (JCPyV) and Salmonella sp. Analysis consisted of molecular detection (qPCR) for viruses (oysters and water samples); immunomagnetic separation followed by direct immunofluorescence assay for Cryptosporidium oocysts and Giardia cysts and also molecular detection (PCR) for the latter (oysters and water samples); commercial kit (Reveal-Neogee (R)) for Salmonella analysis (oysters). Giardia was the most prevalent pathogen in all sites where it was detected: 36.3%, 18.1%, 36.3% and 27.2% of water from sites 1, 2, 3 and 4 respectively; 36.3% of oysters from site 1 and 54.5% of depurated oysters were harboring Giardia cysts. The huge majority of contaminated samples were classified as Giardia duodenalis. HAdv was detected in water and o! ysters from growth site and HnoV GI in two batches of oysters ! (site 1) in huge concentrations (2.11 x 10(13), 3.10 x 10(12) gc/g). In depuration tank site, Salmonella sp., HAV (4.84 x 10(3)) and HnoV GII (7.97 x 10(14)) were detected once in different batches of oysters. Cryptosporidium spp. oocysts were present in 9.0% of water samples from site four. These results reflect the contamination of oysters even when UV depuration procedures are employed in this shellfish treatment plant. Moreover, the molecular comprehension of the sources of contamination is necessary to develop an efficient management strategy allied to shellfish treatment improvement to prevent foodborne illnesses. (C) 2011 Elsevier Ltd. All rights reserved.

High-density linkage maps fail to detect any genetic component to sex determination in a Rana temporaria family.

Sex chromosome differentiation in Rana temporaria varies strikingly among populations or families: whereas some males display well-differentiated Y haplotypes at microsatellite markers on linkage group 2 (LG2 ), others are genetically undistinguishable from females. We analysed with RADseq markers one family from a Swiss lowland population with no differentiated sex chromosomes, and where sibship analyses had failed to detect any association between the phenotypic sex of progeny and parental haplotypes. Offspring were reared in a common tank in outdoor conditions and sexed at the froglet stage. We could map a total of 2177 SNPs (1123 in the mother, 1054 in the father), recovering in both adults 13 linkage groups (= chromosome pairs) that were strongly syntenic to Xenopus tropicalis despite > 200 My divergence. Sexes differed strikingly in the localization of crossovers, which were uniformly distributed in the female but limited to chromosome ends in the male. None of the 2177 markers showed significant association with offspring sex. Considering the very high power of our analysis, we conclude that sex determination was not genetic in this family; which factors determined sex remain to be investigated.

Emergent geomorphic-vegetation interactions on a subalpine alluvial fan

Following perturbation, an ecosystem (flora, fauna, soil) should evolve as a function of time at a rate conditioned by external variables (relief, climate, geology). More recently, biogeomorphologists have focused upon the notion of co-development of geomorphic processes with ecosystems over very short through to very long (evolutionary) timescales. Alpine environments have been a particular focus of this co-development. However, work in this field has tended to adopt a simplified view of the relationship between perturbation and succession, including: how the landform and ecosystem itself conditions the impact of a perturbation to create a complex spatial response impact; and how perturbations are not simply ecosystem destroyers but can be a significant source of ecosystem resources. What this means is that at the within landform scale, there may well be a complex and dynamic topographic and sedimentological template that co-develops with soil, flora and fauna. Here, we present and test a conceptual model of this template for a subalpine alluvial fan. We combine detailed floristic inventory with soil inventory, determination of edaphic variables and analysis of historical aerial imagery. Spatial variation in the probability of perturbation of sites on the fan surface was associated with down fan variability in the across-fan distribution of fan ages, fan surface channel characteristics and fan surface sedimentology. Floristic survey confirmed that these edaphic factors distinguished site floristic richness and plant communities up until the point that the soil-vegetation system was sufficiently developed to sustain plant communities regardless of edaphic conditions. Thus, the primary explanatory variable was the estimated age of each site, which could be tied back into perturbation history and its spatial expression due to the geometry of the fan: distinct plant communities were emergent both across fan and down fan, a distribution maintained by the way in which the fan dissipates potentially perturbing events.

Inférence de source de traces d'essence retrouvées dans des débris d'incendie: Evaluation de la contribution de la chromatographie en phase gazeuse couplée à la spectrométrie de masse à rapport isotopique

Lorsque de l'essence est employée pour allumer et/ou propager un incendie, l'inférence de la source de l'essence peut permettre d'établir un lien entre le sinistre et une source potentielle. Cette inférence de la source constitue une alternative intéressante pour fournir des éléments de preuve dans ce type d'événements où les preuves matérielles laissées par l'auteur sont rares. Le but principal de cette recherche était le développement d'une méthode d'analyse de spécimens d'essence par GC-IRMS, méthode pas routinière et peu étudiée en science forensique, puis l'évaluation de son potentiel à inférer la source de traces d'essence en comparaison aux performances de la GC-MS. Un appareillage permettant d'analyser simultanément les échantillons par MS et par IRMS a été utilisé dans cette recherche. Une méthode d'analyse a été développée, optimisée et validée pour cet appareillage. Par la suite, des prélèvements d'essence provenant d'un échantillonnage conséquent et représentatif du marché de la région lausannoise ont été analysés. Finalement, les données obtenues ont été traitées et interprétées à l'aide de méthodes chimiométriques. Les analyses effectuées ont permis de montrer que la méthodologie mise en place, aussi bien pour la composante MS que pour l'IRMS, permet de différencier des échantillons d'essence non altérée provenant de différentes stations-service. Il a également pu être démontré qu'à chaque nouveau remplissage des cuves d'une station-service, la composition de l'essence distribuée par cette station est quasi unique. La GC-MS permet une meilleure différenciation d'échantillons prélevés dans différentes stations, alors que la GC-IRMS est plus performante lorsqu'il s'agit de comparer des échantillons collectés après chacun des remplissages d'une cuve. Ainsi, ces résultats indiquent que les deux composantes de la méthode peuvent être complémentaires pour l'analyse d'échantillons d'essence non altérée. Les résultats obtenus ont également permis de montrer que l'évaporation des échantillons d'essence ne compromet pas la possibilité de grouper des échantillons de même source par GC-MS. Il est toutefois nécessaire d'effectuer une sélection des variables afin d'éliminer celles qui sont influencées par le phénomène d'évaporation. Par contre, les analyses effectuées ont montré que l'évaporation des échantillons d'essence a une forte influence sur la composition isotopique des échantillons. Cette influence est telle qu'il n'est pas possible, même en effectuant une sélection des variables, de grouper correctement des échantillons évaporés par GC-IRMS. Par conséquent, seule la composante MS de la méthodologie mise en place permet d'inférer la source d'échantillons d'essence évaporée. _________________________________________________________________________________________________ When gasoline is used to start and / or propagate an arson, source inference of gasoline can allow to establish a link between the fire and a potential source. This source inference is an interesting alternative to provide evidence in this type of events where physical evidence left by the author are rare. The main purpose of this research was to develop a GC-IRMS method for the analysis of gasoline samples, a non-routine method and little investigated in forensic science, and to evaluate its potential to infer the source of gasoline traces compared to the GC-MS performances. An instrument allowing to analyze simultaneously samples by MS and IRMS was used in this research. An analytical method was developed, optimized and validated for this instrument. Thereafter, gasoline samples from a large sampling and representative of the Lausanne area market were analyzed. Finally, the obtained data were processed and interpreted using chemometric methods. The analyses have shown that the methodology, both for MS and for IRMS, allow to differentiate unweathered gasoline samples from different service stations. It has also been demonstrated that each new filling of the tanks of a station generates an almost unique composition of gasoline. GC-MS achieves a better differentiation of samples coming from different stations, while GC-IRMS is more efficient to distinguish samples collected after each filling of a tank. Thus, these results indicate that the two components of the method can be complementary to the analysis of unweathered gasoline samples. The results have also shown that the evaporation of gasoline samples does not compromise the possibility to group samples coming from the same source by GC-MS. It is however necessary to make a selection of variables in order to eliminate those which are influenced by the evaporation. On the other hand, the carried out analyses have shown that the evaporation of gasoline samples has such a strong influence on the isotopic composition of the samples that it is not possible, even by performing a selection of variables, to properly group evaporated samples by GC-IRMS. Therefore, only the MS allows to infer the source of evaporated gasoline samples.