Monte Carlo simulations of metasomatic enrichment in the lithosphere and implications for the source of alkaline basalts

One hypothesis for the origin of alkaline lavas erupted on oceanic islands and in intracontinental settings is that they represent the melts of amphibole-rich veins in the lithosphere (or melts of their dehydrated equivalents if metasomatized lithosphere is recycled into the convecting mantle). Amphibole-rich veins are interpreted as cumulates produced by crystallization of low-degree melts of the underlying asthenosphere as they ascend through the lithosphere. We present the results of trace-element modelling of the formation and melting of veins formed in this way with the goal of testing this hypothesis and for predicting how variability in the formation and subsequent melting of such cumulates (and adjacent cryptically and modally metasomatized lithospheric peridotite) would be manifested in magmas generated by such a process. Because the high-pressure phase equilibria of hydrous near-solidus melts of garnet lherzolite are poorly constrained and given the likely high variability of the hypothesized accumulation and remelting processes, we used Monte Carlo techniques to estimate how uncertainties in the model parameters (e.g. the compositions of the asthenospheric sources, their trace-element contents, and their degree of melting; the modal proportions of crystallizing phases, including accessory phases, as the asthenospheric partial melts ascend and crystallize in the lithosphere; the amount of metasomatism of the peridotitic country rock; the degree of melting of the cumulates and the amount of melt derived from the metasomatized country rock) propagate through the process and manifest themselves as variability in the trace-element contents and radiogenic isotopic ratios of model vein compositions and erupted alkaline magma compositions. We then compare the results of the models with amphibole observed in lithospheric veins and with oceanic and continental alkaline magmas. While the trace-element patterns of the near-solidus peridotite melts, the initial anhydrous cumulate assemblage (clinopyroxene +/- garnet +/- olivine +/- orthopyroxene), and the modelled coexisting liquids do not match the patterns observed in alkaline lavas, our calculations show that with further crystallization and the appearance of amphibole (and accessory minerals such as rutile, ilmenite, apatite, etc.) the calculated cumulate assemblages have trace-element patterns that closely match those observed in the veins and lavas. These calculated hydrous cumulate assemblages are highly enriched in incompatible trace elements and share many similarities with the trace-element patterns of alkaline basalts observed in oceanic or continental setting such as positive Nb/La, negative Ce/Pb, and similiar slopes of the rare earth elements. By varying the proportions of trapped liquid and thus simulating the cryptic and modal metasomatism observed in peridotite that surrounds these veins, we can model the variations in Ba/Nb, Ce/Pb, and Nb/U ratios that are observed in alkaline basalts. If the isotopic compositions of the initial low-degree peridotite melts are similar to the range observed in mid-ocean ridge basalt, our model calculations produce cumulates that would have isotopic compositions similar to those observed in most alkaline ocean island basalt (OIB) and continental magmas after similar to 0 center dot 15 Gyr. However, to produce alkaline basalts with HIMU isotopic compositions requires much longer residence times (i.e. 1-2 Gyr), consistent with subduction and recycling of metasomatized lithosphere through the mantle. such as a heterogeneous asthenosphere. These modelling results support the interpretation proposed by various researchers that amphibole-bearing veins represent cumulates formed during the differentiation of a volatile-bearing low-degree peridotite melt and that these cumulates are significant components of the sources of alkaline OIB and continental magmas. The results of the forward models provide the potential for detailed tests of this class of hypotheses for the origin of alkaline magmas worldwide and for interpreting major and minor aspects of the geochemical variability of these magmas.

Extent of hypoattenuation on CT angiography source images in basilar artery occlusion: prognostic value in the Basilar Artery International Cooperation Study.

BACKGROUND AND PURPOSE: The posterior circulation Acute Stroke Prognosis Early CT Score (pc-ASPECTS) quantifies the extent of early ischemic changes in the posterior circulation with a 10-point grading system. We hypothesized that pc-ASPECTS applied to CT angiography source images predicts functional outcome of patients in the Basilar Artery International Cooperation Study (BASICS). METHODS: BASICS was a prospective, observational registry of consecutive patients with acute symptomatic basilar artery occlusion. Functional outcome was assessed at 1 month. We applied pc-ASPECTS to CT angiography source images of patients with CT angiography for confirmation of basilar artery occlusion. We calculated unadjusted and adjusted risk ratios (RRs) of pc-ASPECTS dichotomized at ≥8 versus <8. Primary outcome measure was favorable outcome (modified Rankin Scale scores 0-3). Secondary outcome measures were mortality and functional independence (modified Rankin Scale scores 0-2). RESULTS: Of 158 patients included, 78 patients had a CT angiography source images pc-ASPECTS≥8. Patients with a pc-ASPECTS≥8 more often had a favorable outcome than patients with a pc-ASPECTS<8 (crude RR, 1.7; 95% CI, 0.98-3.0). After adjustment for age, baseline National Institutes of Health Stroke Scale score, and thrombolysis, pc-ASPECTS≥8 was not related to favorable outcome (RR, 1.3; 95% CI, 0.8-2.2), but it was related to reduced mortality (RR, 0.7; 95% CI, 0.5-0.98) and functional independence (RR, 2.0; 95% CI, 1.1-3.8). In post hoc analysis, pc-ASPECTS dichotomized at ≥6 versus <6 predicted a favorable outcome (adjusted RR, 3.1; 95% CI, 1.2-7.5). CONCLUSIONS: pc-ASPECTS on CT angiography source images independently predicted death and functional independence at 1 month in the CT angiography subgroup of patients in the BASICS registry.

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension.

The Eukaryotic Promoter Database (EPD) is an annotated non-redundant collection of eukaryotic POL II promoters, experimentally defined by a transcription start site (TSS). There may be multiple promoter entries for a single gene. The underlying experimental evidence comes from journal articles and, starting from release 73, from 5' ESTs of full-length cDNA clones used for so-called in silico primer extension. Access to promoter sequences is provided by pointers to TSS positions in nucleotide sequence entries. The annotation part of an EPD entry includes a description of the type and source of the initiation site mapping data, links to other biological databases and bibliographic references. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis. Web-based interfaces have been developed that enable the user to view EPD entries in different formats, to select and extract promoter sequences according to a variety of criteria and to navigate to related databases exploiting different cross-references. Tools for analysing sequence motifs around TSSs defined in EPD are provided by the signal search analysis server. EPD can be accessed at http://www.epd. isb-sib.ch.

Hypertension pulmonaire d'origine indéterminée chez un homme de 56 ans.. [Pulmonary hypertension of undertermined origine in a man aged 56...]

The case of a patient with severe pulmonary hypertension whose etiology has remained unknown until an autopsy was performed is discussed in a symposium of pathological anatomy. This case helped to address the diagnostic and therapeutic management of pulmonary hypertension. The broad differential diagnosis of this disease requires a diagnostic strategy to be developped. Clinical reasoning leading to a probable diagnosis based on clinical biological and radiological information is not only a difficult task for the speaker but also a rich source of learning opportunities for our medical community.

Uncertainty about the true source. A note on the likelihood ratio at the activity level.

This paper focuses on likelihood ratio based evaluations of fibre evidence in cases in which there is uncertainty about whether or not the reference item available for analysis - that is, an item typically taken from the suspect or seized at his home - is the item actually worn at the time of the offence. A likelihood ratio approach is proposed that, for situations in which certain categorical assumptions can be made about additionally introduced parameters, converges to formula described in existing literature. The properties of the proposed likelihood ratio approach are analysed through sensitivity analyses and discussed with respect to possible argumentative implications that arise in practice.

Environmental and biological controls on the geochemistry (δ18O, δ13C, Mg/Ca, and Sr/Ca) of living ostracods from Lake Geneva

ABSTRACT : Ostracods are benthic microcrustaceans enclosed in low-Mg calcite bivalves. Stable isotope compositions, Mg/Ca, and Sr/Ca ratios of ostracod fossil valves have proven useful to reconstruct past environmental conditions. Yet, several discrepancies persist and the influence of many factors remains unclear. It is the aim of this study to improve the use of ostracod valve geochemistry as palaeoenvironmental proxies by examining the extent of isotope fractionation and trace element partitioning during valve calcification. To achieve this, the environmental parameters (pH, temperature) and chemical composition of water (C-and O-isotope composition and calcium, magnesium, and strontium content) were measured at sites where living ostracods were sampled. The sampling was on a monthly basis over the course of one year at five different water depths (2, 5, 13, 33, and 70 m) in Lake Geneva, Switzerland. The one-year sampling enabled collection of environmental data for bottom and interstitial pore water. In littoral to sublittoral zones, C-isotope composition of DIC and the Mg/Ca and Sr/Ca ratios of water are found to vary concomitantly with water temperature. This is due to the precipitation of calcite, which is induced by higher photosynthetic activity as temperature and/or solar radiation intensify in summer. In deeper zones, environmental parameters remain largely constant throughout the year. Variations of pH, DIC concentrations and C-isotope compositions in interstitial water result from aerobic as well as anaerobic respiration, calcite dissolution and methanogenesis. Bathymetric distribution, life cycles, and habitats were derived for 15 ostracod species and are predominantly related to water temperature and sediment texture. O-isotope compositions of ostracod valves in Lake Geneva reflect that of water and temperature. However, offsets of up to 3 permil are observed in comparison with proposed inorganic calcite precipitation equilibrium composition. Deprotonation of HCO3- and/or salt effect at crystallisation sites may explain the disequilibrium observed for O-isotopic compositions. C-isotope compositions of ostracod valves are not as well constrained and appear to be controlled by a complex interaction between habitat preferences and seasonal as well as spatial variations of the DIC isotope composition. For infaunal forms, C-isotope compositions reflect mainly the variation of DIC isotope composition in interstitial pore waters. For epifaunal forms, C-isotope compositions reflect the seasonal variation of DIC isotope compositions. C-isotope compositions of ostracod valves is at equilibrium with DIC except for a small number of species (L. inopinata, L. sanctipatricii and possibly C. ophtalmica, and I. beauchampi). Trace element uptake differs considerably from species to species. For most epifaunal forms, trace element content follows the seasonal cycle, recording temperature increases and/or variations of Mg/Ca and Sr/Ca ratios of water. In contrast, infaunal forms are predominantly related to sediment pore water chemistry. RÉSUMÉ EN FRANÇAIS : Les ostracodes sont de petits crustacés benthiques qui possèdent une coquille faite de calcite à faible teneur en magnésium. La composition isotopique et les rapports Mg/Ca et Sr/Ca d'ostracodes fossiles ont été utilisés maintes fois avec succès pour effectuer des reconstructions paléoenvironnementales. Néanmoins, certains désaccords persistent sur l'interprétation de ces données. De plus, l'influence de certains facteurs pouvant biaiser le signal reste encore inconnue. Ainsi, le but de cette étude est de rendre plus performant l'emploi de la composition géochimique des ostracodes comme indicateur paléoenvironnemental. Pour réaliser cela, cinq sites situés dans le Léman à 2, 5, 13, 33 et 70 m de profondeur ont été choisis pour effectuer les échantillonnages. Chaque site a été visité une fois par mois durant une année. Les différents paramètres environnementaux (pH, température) ainsi que la composition géochimique de l'eau (composition isotopique de l'oxygène et du carbone ainsi que teneur en calcium, magnésium et strontium) ont été déterminés pour chaque campagne. Des ostracodes vivants ont été récoltés au cinq sites en même temps que les échantillons d'eau. Ce travail de terrain a permis de caractériser la géochimie de l'eau se trouvant juste au-dessus des sédiments ainsi que celle de l'eau se trouvant dans les interstices du sédiment. Dans les zones littorales à sublittorales, la composition isotopique du carbone inorganique dissout (CID) ainsi que les rapports Mg/Ca et Sr/Ca de l'eau varient linéairement avec la température. Ceci peut être expliqué par la précipitation de calcite qui est contrôlée par l'activité photosynthétique, variant elle même linéairement avec la température. Dans les zones plus profondes, les paramètres environnementaux restent relativement constants tout au long de l'année. Les variations du pH, de la concentration et de la composition isotopique du CID dans les sédiments résultent de la libération de carbone engendrée par la dégradation de la matière organique avec présence d'oxygène ou via réduction de nitrates et de sulfates, par la dissolution de carbonates, ainsi que par la méthanogenèse. La distribution bathymétrique, le cycle de vie ainsi que l'habitat de 15 espèces ont été déterminés. Ceux-ci sont principalement reliés à la température de l'eau et à la texture des sédiments. La composition isotopique de l'oxygène des valves d'ostracodes reflète celle de l'eau et la température qui régnait lors de la calcification. Néanmoins, des écarts pouvant aller jusqu'à 3 0/00 par rapport à l'équilibre théorique ont été obtenus. La déprotonation de HCO3 ou un 'effet de sel' pourrait être à l'origine du déséquilibre observé. La composition isotopique du carbone des valves d'ostracodes n'est pas aussi bien cernée. Celle-ci semble être principalement contrôlée par une interaction complexe entre l'habitat des ostracodes et les variations saisonnières et spatiales de la composition isotopique du CID. Pour les espèces endofaunes, la composition isotopique du carbone reflète principalement la variation de la composition isotopique du CID à l'intérieur des sédiments. Pour les formes épifaunes, c'est la variation saisonnière de la composition du CID qui contrôle celle de la coquille des ostracodes. En général, la composition isotopique du carbone des valves d'ostracodes est en équilibre avec celle de CID, hormis pour quelques rares espèces (L. inopinata, L. sanctipatricii et peut-être C. ophtalmica et I. beauchampi). L'incorporation des éléments traces diffère passablement d'une espèce à l'autre. Pour la plupart des espèces épifaunes, la teneur en éléments traces des coquilles reflète les variations saisonnières. Ces espèces semblent enregistrer les variations soit de la température soit des rapports Mg/Ca et Sr/Ca de l'eau. La teneur en élément traces des formes infaunales, au contraire, est principalement reliée à la chimie de l'eau interstitielle. RÉSUMÉ GRAND-PUBLIC : La connaissance de l'évolution du climat dans le futur est primordiale pour notre société, car elle permet de développer différentes stratégies pour faire face aux problèmes engendrés pas le changement climatique : stratégies environnementale, humanitaire, ou encore économique. Cette problématique est actuellement, à juste titre, sujet d'une vive préoccupation. La géologie peut-elle contribuer à l'effort communautaire entrepris? Naturellement, ce sont les climatologues qui sont sur le devant de la scène. Il n'empêche que ces derniers, pour pouvoir prédire l'avenir, doivent s'appuyer sur le passé. La géologie est alors d'un grand intérêt car c'est effectivement la seule science qui permette d'estimer les variations climatiques à grande échelle sur de longues périodes. Ainsi, voulant moi-même contribuer aux recherches menées dans ce domaine, je me suis tourné à la fin de mes études vers la paléoclimatologie, science qui a pour but de reconstruire le climat des temps anciens. Nous nous sommes rendu compte que l'évolution climatique de la région où nous habitons n'avait pas encore fait le sujet d'études approfondies. Il est pourtant important de connaître la variation locale des changements climatiques pour obtenir des modèles climatiques fiables. En conséquence, un vaste projet a vu le jour : reconstruire, à l'aide des sédiments du lac Léman, les variations paléoclimatiques et paléo-environnementales depuis le retrait du Glacier de Rhône, il y a environ 15'000 ans, jusqu'à nos jours. Pour ce genre de travail, la géochimie, qui est une forme de chimie, utilisée en science de la terre regroupant la chimie classique et la chimie isotopique, est une alliée particulièrement efficace. Elle permet en effet, via différentes mesures faites sur des archives géologiques (par exemple des fossiles ou des sédiments) d'obtenir des informations, souvent quantitatives, sur les conditions (le climat, la flore ou encore la bio productivité, etc...) qui régnaient il y a fort longtemps. Les coquilles d'ostracodes, qui sont de petits animaux vivant au fond des lacs, sont une des archives les plus prometteuses. Ces animaux sont des petits crustacés s'entourant d'une coquille calcaire qu'ils sécrètent eux-mêmes. A la mort de l'animal, la coquille est intégrée dans les sédiments et reste intacte à travers les âges. Des études ont montré qu'en analysant la géochimie de ces coquilles fossiles, il est possible de reconstruire les conditions environnementales qui régnaient à l'époque de vie de ces fossiles. Cette démarche nécessite qu'une condition bien précise soit remplie: la composition géochimique de la coquille doit enregistrer de manière fidèle la chimie de l'eau et/ou la température de l'eau présentes au moment de la sécrétion de la coquille. Le but spécifique de notre recherche a précisément été d'étudier la façon dont la chimie de l'eau ainsi que sa température sont enregistrées dans la coquillé des ostracodes. Une fois les relations entre ces divers paramètres dans l'étant actuel du système établies, il sera alors possible de les utiliser pour interpréter des données issues de coquilles fossiles. Pour ce faire, nous avons mesuré la température de l'eau de manière continue et récolté mensuellement des échantillons d'eau et des ostracodes vivants pendant une année. Cinq sites situés à 2, 5, 13, 33 et 70 mètres de profondeur ont été choisis pour effectuer ces échantillonnages dans le Léman. Le travail de terrain nous a amené à étudier la biologie de 15 espèces. Nous avons pu établir la profondeur à laquelle vivent ces animaux, leur période de développement ainsi que leur habitat respectifs. Ces résultats ont permis de mieux cerner la relation qu'il existe entre la chimie de l'eau, sa température et la composition géochimique des coquilles d'ostracodes. Nous avons ainsi pu confirmer que les coquilles d'ostracodes enregistrent de manière fidèle la composition chimique et isotopique de l'eau. De même, nous avons pu établir de manière plus précise l'effet de la température sur la géochimie des coquilles. Néanmoins, les relations trouvées entre ces trois éléments sont plus complexes pour certaines espèces, cette complexité étant souvent liée à un caractère spécifique de leur écologie. Nous avons mis en lumière certains effets qui biaisent les résultats et défini précisément les conditions dans lesquelles on peut s'attendre à avoir des difficultés dans leur interprétation. Maintenant que nous avons établi les relations entre le climat actuel et la composition géochimique des coquilles d'ostracodes actuels, nous pouvons, sur la base de ce modèle, reconstruire le climat depuis le retrait du Glacier du Rhône jusqu'à nos jours à l'aide d'ostracodes fossiles. Mais cela est une autre histoire et fera, je l'espère, le sujet de nos futures recherches.

Biological embedding of early life exposures and disease risk in humans: a role for DNA methylation.

BACKGROUND: Following wider acceptance of "the thrifty phenotype" hypothesis and the convincing evidence that early life exposures can influence adult health even decades after the exposure, much interest has been placed on the mechanisms through which early life exposures become biologically embedded. METHODS: In this review, we summarize the current literature regarding biological embedding of early life experiences. To this end we conducted a literature search to identify studies investigating early life exposures in relation to DNA methylation changes. In addition, we summarize the challenges faced in investigations of epigenetic effects, stemming from the peculiarities of this emergent and complex field. A proper systematic review and meta-analyses were not feasible given the nature of the evidence. RESULTS: We identified 7 studies on early life socioeconomic circumstances, 10 studies on childhood obesity, and 6 studies on early life nutrition all relating to DNA methylation changes that met the stipulated inclusion criteria. The pool of evidence gathered, albeit small, favours a role of epigenetics and DNA methylation in biological embedding, but replication of findings, multiple comparison corrections, publication bias, and causality are concerns remaining to be addressed in future investigations. CONCLUSIONS: Based on these results, we hypothesize that epigenetics, in particular DNA methylation, is a plausible mechanism through which early life exposures are biologically embedded. This review describes the current status of the field and acts as a stepping stone for future, better designed investigations on how early life exposures might become biologically embedded through epigenetic effects. This article is protected by copyright. All rights reserved.

Embolic strokes of undetermined source in the athens stroke registry: a descriptive analysis.

BACKGROUND AND PURPOSE: A new clinical construct termed embolic stroke of undetermined source (ESUS) was recently introduced, but no such population has been described yet. Our aim is to provide a detailed descriptive analysis of an ESUS population derived from a large prospective ischemic stroke registry using the proposed diagnostic criteria. METHODS: The criteria proposed by the Cryptogenic Stroke/ESUS International Working Group were applied to the Athens Stroke Registry to identify all ESUS patients. ESUS was defined as a radiologically confirmed nonlacunar brain infarct in the absence of (a) extracranial or intracranial atherosclerosis causing ≥50% luminal stenosis in arteries supplying the ischemic area, (b) major-risk cardioembolic source, and (c) any other specific cause of stroke. RESULTS: Among 2735 patients admitted between 1992 and 2011, 275 (10.0%) were classified as ESUS. In the majority of ESUS (74.2%), symptoms were maximal at onset. ESUS were of moderate severity (median National Institute Health Stroke Scale score, 5). The most prevalent risk factor was arterial hypertension (64.7%), and 50.9% of patients were dyslipidemic. Among potential causes of the ESUS, covert atrial fibrillation (AF) was the most prevalent: in 30 (10.9%) patients, AF was diagnosed during hospitalization for stroke recurrence, whereas in 50 (18.2%) patients AF was detected after repeated ECG monitoring during follow-up. Also, covert AF was strongly suggested in 38 patients (13.8%) but never recorded. CONCLUSIONS: About 10% of patients with first-ever ischemic stroke met criteria for ESUS; covert paroxysmal AF seems to be a frequent cause of ESUS.

High-density electric source imaging (esi) in focal epilepsy: a prospective study of 150 operated patients

Purpose: EEG is mandatory in the diagnosis of the epilepsy syndrome. However, its potential as imaging tool is still under estimated. In the present study, we aim to determine the prerequisites of maximal benefit of electric source imaging (ESI) to localize the irritative zone in patients with focal epilepsy. Methods: One hundred fifty patients suffering from focal epilepsy and with minimum 1 year postoperative follow-up were studied prospectively and blinded to the underlying diagnosis. We evaluated the influence of two important factors on sensitivity and specificity of ESI: the number of electrodes (low resolution, LR-ESI: <30 versus high resolution, HR-ESI: 128-256 electrodes), and the use of individual MRI (i-MRI) versus template MRI (t-MRI) as the head model. Findings: ESI had a sensitivity of 85% and a specificity of 87% when HR-ESI with i-MRI was used. Using LR-ESI, sensitivity decreased to 68%, or even 57% when only t-MRI was available. The sensitivity of HR-ESI/i-MRI compared favorably with those of MRI (76%), PET (69%) and ictal/interictal SPECT (64%). Interpretation: This study on a large patient group shows excellent sensitivity and specificity of ESI if 128 EEG channels or more are used for ESI and if the results are coregistered to the patient's individual MRI. Localization precision is as high as or even higher than established brain imagery techniques. HR-ESI appears to be a valuable additional imaging tool, given that larger electrode arrays are easily and rapidly applied with modern EEG equipment and that structural MRI is nearly always available for these patients.

Defining the role of common variation in the genomic and biological architecture of adult human height.

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ∼2,000, ∼3,700 and ∼9,500 SNPs explained ∼21%, ∼24% and ∼29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/β-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

Pathogenesis-related proteins and the jasmonate signaling pathway

Résumé Etant une importante source d'énergie, les plantes sont constamment attaquées par des pathogènes. Ne pouvant se mouvoir, elles ont développé des systèmes de défense sophistiqués afin de lutter contre ces prédateurs. Parmi ces systèmes, les voies de signalisation mettant en jeu des éliciteurs endog8nes tels que les jasmonates permettent d'induire la production de protéines de défense telles que les protéines dites "liées à la pathogénèse". Les gènes codant pour ces protéines appartiennent à des familles multigéniques. Le premier but de cette thèse est d'évaluer le nombre de ces gènes dans le génome d'Arabidopsis thaliana et d'estimer la part de ce système de défense, dépendant de la voie de signalisation des jasmonates. Nous avons défini un cluster de seulement 1S gènes sur 266, "liés à la pathogénèse", exclusivement régulés par les jasmonates. De multiples membres des familles des lectines de type jacaline et des inhibiteurs de trypsines semblent dépendre du jasmonate. Présente dans tous les systèmes immunitaires des eucaryotes, la famille des défensines est une famille très intéressante. Chez Arabidopsis thaliana, 317 protéines similaires aux défensines ont été définies, cependant seulement 15 défensines (PDF) sont bien annotées. Ces 15 défensines sont séparées en deux groupes dont un semble avoir évolué plus récemment. Le second but de cette thèse est d'étudier ce groupe de défensines à l'aide de la bioinformatique et des techniques de biologie moléculaire (gêne rapporteur, PCR en temps réel). Nous avons montré que ce groupe contenait une défensine acide intéressante, PDF1.5, qui semblait avoir subi une sélection positive. Cette protéine n'avait encore jamais été étudiée. Contrairement à ce que nous pensions, nous avons établi que cette protéine pouvait avoir une activité biologique liée à la défense. Ce travail de thèse a permis de préciser le nombre de gènes "liées à la pathogénèse" induits par la voie des jasmonates et d'apporter des éléments de réponse sur la question de la redondance des gènes de défense. En conclusion, même si de nombreuses familles de gènes intervenant dans la défense sont bien définies chez Arabidopsis, il reste encore de nombreuses études à faire sur chacun de ces membres. Abstract Being an important source of energy, plants are constantly attacked by herbivores and pathogens. As sessile organisms, they have developed sophisticated defense responses to cope with attack. Among these responses, signalling pathways, using endogenous elicitors including jasmonates (JA), allow the plant to induce the production of defense proteins such as pathogenesis-related (PR) proteins. The genes encoding these proteins belong to multigenic families. The first goal of this thesis was to evaluate the number of PR genes in the genome of Arabidopsis thaliana and estimate how much of this plant defense system was dependent on the jasmonate signaling pathway in leaves. Surprisingly a cluster of only 1S genes out of 2ó6 PR genes was exclusively regulated by JA. Multiple members of the jacalin lectin and trypsin inhibitor gene families were shown to be regulated by JA. Present in all eukaryotic immune systems, defensins are an attractive PR family to study. In Arabidopsis thaliana, 317 defensin-related proteins have been found but just 1S defensins (i.e. PDF family) are well annotated. These defensins are split into 2 groups. One of these groups may have appeared and diversified recently. The second goal of this thesis was to study this defensin gene group combining bioinformatic, reporter gene and quantitative PCR techniques. We have shown that this group contains an interesting acidic defensin, PDF1.S, which seems to have undergone positive selection. No information was known on this protein. We have established that this protein may have a biological activity in plant defense. This thesis allowed us to define the number of PR genes induced by the jasmonate pathway and gave initial leads to explain the redundancy of the PR genes in the genome of Arabidopsis. In conclusion, even if many defense gene families are already defined in the Arabidopsis genome, much work remains to be done on individual members.

A cell biological view of the siderophore pyochelin iron uptake pathway in Pseudomonas aeruginosa.

Pyochelin (PCH) is a siderophore produced and secreted by Pseudomonas aeruginosa for iron capture. Using (55) Fe uptake and binding assays, we showed that PCH-Fe uptake in P. aeruginosa involves, in addition to the highly studied outer membrane transporter FptA, the inner membrane permease FptX, which recognizes PCH-(55) Fe with an affinity of 0.6 ± 0.2 nM and transports the ferri-siderophore complex from the periplasm into the cytoplasm: fptX deletion inhibited (55) Fe accumulation in the bacterial cytoplasm. Chromosomal replacement was used to generate P. aeruginosa strains producing fluorescent fusions with FptX, PchR (an AraC regulator), PchA (the first enzyme involved in the PCH biosynthesis) and PchE (a non-ribosomic peptide-synthetase involved in a further step). Fluorescence imaging and cellular fractionation showed a uniform repartition of FptX in the inner membrane. PchA and PchE were found in the cytoplasm, associated to the inner membrane all over the bacteria and also concentrated at the bacterial poles. PchE clustering at the bacterial poles was dependent on PchA expression, but on the opposite PchA clustering and membrane association was PchE-independent. PchA and PchE cellular organization suggests the existence of a siderosome for PCH biosynthesis as previously proposed for pyoverdine biosynthesis (another siderophore produced by P. aeruginosa).

In-vitro cell exposure studies for the assessment of nanoparticle toxicity in the lung: a dialog between aerosol science and biology

The introduction of engineered nanostructured materials into a rapidly increasing number of industrial and consumer products will result in enhanced exposure to engineered nanoparticles. Workplace exposure has been identified as the most likely source of uncontrolled inhalation of engineered aerosolized nanoparticles, but release of engineered nanoparticles may occur at any stage of the lifecycle of (consumer) products. The dynamic development of nanomaterials with possibly unknown toxicological effects poses a challenge for the assessment of nanoparticle induced toxicity and safety.In this consensus document from a workshop on in-vitro cell systems for nanoparticle toxicity testing11Workshop on 'In-Vitro Exposure Studies for Toxicity Testing of Engineered Nanoparticles' sponsored by the Association for Aerosol Research (GAeF), 5-6 September 2009, Karlsruhe, Germany. an overview is given of the main issues concerning exposure to airborne nanoparticles, lung physiology, biological mechanisms of (adverse) action, in-vitro cell exposure systems, realistic tissue doses, risk assessment and social aspects of nanotechnology. The workshop participants recognized the large potential of in-vitro cell exposure systems for reliable, high-throughput screening of nanoparticle toxicity. For the investigation of lung toxicity, a strong preference was expressed for air-liquid interface (ALI) cell exposure systems (rather than submerged cell exposure systems) as they more closely resemble in-vivo conditions in the lungs and they allow for unaltered and dosimetrically accurate delivery of aerosolized nanoparticles to the cells. An important aspect, which is frequently overlooked, is the comparison of typically used in-vitro dose levels with realistic in-vivo nanoparticle doses in the lung. If we consider average ambient urban exposure and occupational exposure at 5mg/m3 (maximum level allowed by Occupational Safety and Health Administration (OSHA)) as the boundaries of human exposure, the corresponding upper-limit range of nanoparticle flux delivered to the lung tissue is 3×10-5-5×10-3μg/h/cm2 of lung tissue and 2-300particles/h/(epithelial) cell. This range can be easily matched and even exceeded by almost all currently available cell exposure systems.The consensus statement includes a set of recommendations for conducting in-vitro cell exposure studies with pulmonary cell systems and identifies urgent needs for future development. As these issues are crucial for the introduction of safe nanomaterials into the marketplace and the living environment, they deserve more attention and more interaction between biologists and aerosol scientists. The members of the workshop believe that further advances in in-vitro cell exposure studies would be greatly facilitated by a more active role of the aerosol scientists. The technical know-how for developing and running ALI in-vitro exposure systems is available in the aerosol community and at the same time biologists/toxicologists are required for proper assessment of the biological impact of nanoparticles.

Robust regression in biological assay: application to the evaluation of alternative experimental techniques.

Robust Huber type regression and testing of linear hypotheses are adapted to statistical analysis of parallel line and slope ratio assays. They are applied in the evaluation of results of several experiments carried out in order to compare and validate alternatives to animal experimentation based on embryo and cell cultures. Computational procedures necessary for the application of robust methods of analysis used the conversational statistical package ROBSYS. Special commands for the analysis of parallel line and slope ratio assays have been added to ROBSYS.