Distribution of events of positive selection and population differentiation in a metabolic pathway: the case of asparagine N-glycosylation

Background: Asparagine N-Glycosylation is one of the most important forms of protein post-translational modification in eukaryotes. This metabolic pathway can be subdivided into two parts: an upstream sub-pathway required for achieving proper folding for most of the proteins synthesized in the secretory pathway, and a downstream sub-pathway required to give variability to trans-membrane proteins, and involved in adaptation to the environment andinnate immunity. Here we analyze the nucleotide variability of the genes of this pathway in human populations, identifying which genes show greater population differentiation and which genes show signatures of recent positive selection. We also compare how these signals are distributed between the upstream and the downstream parts of the pathway, with the aim of exploring how forces of population differentiation and positive selection vary among genes involved in the same metabolic pathway but subject to different functional constraints. Results:Our results show that genes in the downstream part of the pathway are more likely to show a signature of population differentiation, while events of positive selection are equally distributed among the two parts of the pathway. Moreover, events of positive selection arefrequent on genes that are known to be at bifurcation points, and that are identified as beingin key position by a network-level analysis such as MGAT3 and GCS1.Conclusions: These findings indicate that the upstream part of the Asparagine N-Glycosylation pathway has lower diversity among populations, while the downstream part is freer to tolerate diversity among populations. Moreover, the distribution of signatures of population differentiation and positive selection can change between parts of a pathway, especially between parts that are exposed to different functional constraints. Our results support the hypothesis that genes involved in constitutive processes can be expected to show lower population differentiation, while genes involved in traits related to the environment should show higher variability. Taken together, this work broadens our knowledge on how events of population differentiation and of positive selection are distributed among different parts of a metabolic pathway.

Evolutionary analysis of genes of two pathways involved in placental malaria infection

Placental malaria is a special form of malaria that causes up to 200,000 maternal and infant deaths every year. Previous studies show that two receptor molecules, hyaluronic acid and chondroitin sulphate A, are mediating the adhesion of parasite-infected erythrocytes in the placenta of patients, which is believed to be a key step in the pathogenesis of the disease. In this study, we aimed at identifying sites of malaria-induced adaptation by scanning for signatures of natural selection in 24 genes in the complete biosynthesis pathway of these two receptor molecules. We analyzed a total of 24 Mb of publicly available polymorphism data from the International HapMap project for three human populations with European, Asian and African ancestry, with the African population from a region of presently and historically high malaria prevalence. Using the methods based on allele frequency distributions, genetic differentiation between populations, and on long-range haplotype structure, we found only limited evidence for malaria-induced genetic adaptation in this set of genes in the African population; however, we identified one candidate gene with clear evidence of selection in the Asian population. Although historical exposure to malaria in this population cannot be ruled out, we speculate that it might be caused by other pathogens, as there is growing evidence that these molecules are important receptors in a variety of host-pathogen interactions. We propose to use the present methods in a systematic way to help identify candidate regions under positive selection as a consequence of malaria.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Constraints on palaeodrainage evolution induced by uplift and exhumation on the southern flank of the Zagros-Iranian Plateau

Foreland sedimentary rocks from the northern Fars region of Iran contain a record of deformation associated with the Cenozoic collision between Arabia and Eurasia that resulted in formation of the Zagros orogen. The timing of the deformation associated with this event is poorly known. To address this we conducted a study of Miocene foreland sedimentary rocks (19.7-14.8 Ma) of the Chahar-Makan syncline using clast composition, clay mineralogy and low-temperature fission-track dating. The results showed that most of the sedimentary rocks were sourced from ophiolitic rocks. Detrital apatite fission-track (AFT) age signatures of Miocene sedimentary rocks record exhumation in the hanging wall of the Main Zagros Thrust and confirm that the change from underthrusting of the stretched Arabian margin to widespread crustal thickening and deformation in the Zagros region is no younger than 19.7 Ma. A transition from Late Oligocene to Mesozoic-Eocene AFT detrital age signatures between 19.7-16.6 Ma and 16.6-13.8 Ma is interpreted to reflect a possible rearrangement of palaeodrainage distribution that resulted from folding and expansion-uplift of the Zagros-Iranian Plateau region.

Deleterious mutation accumulation in asexual Timema stick insects.

Sexual reproduction is extremely widespread in spite of its presumed costs relative to asexual reproduction, indicating that it must provide significant advantages. One postulated benefit of sex and recombination is that they facilitate the purging of mildly deleterious mutations, which would accumulate in asexual lineages and contribute to their short evolutionary life span. To test this prediction, we estimated the accumulation rate of coding (nonsynonymous) mutations, which are expected to be deleterious, in parts of one mitochondrial (COI) and two nuclear (Actin and Hsp70) genes in six independently derived asexual lineages and related sexual species of Timema stick insects. We found signatures of increased coding mutation accumulation in all six asexual Timema and for each of the three analyzed genes, with 3.6- to 13.4-fold higher rates in the asexuals as compared with the sexuals. In addition, because coding mutations in the asexuals often resulted in considerable hydrophobicity changes at the concerned amino acid positions, coding mutations in the asexuals are likely associated with more strongly deleterious effects than in the sexuals. Our results demonstrate that deleterious mutation accumulation can differentially affect sexual and asexual lineages and support the idea that deleterious mutation accumulation plays an important role in limiting the long-term persistence of all-female lineages.

The Exotic Palaeo-Thethys Terrane in Central Iran: New geological data from Anarak, Jandaq and Posht-e-Badam areas

Résumé Le « terrane » d'Anarak-Jandak occupe une position géologique clé au nord-ouest du Microcontinent Centre-East Iranien (CE1M), connecté avec le Bloc du Grand Kavir et la ceinture métamorphique de Sanandaj-Sirjan. Nous discutons ici l'origine de ces différentes unités, reliées jusqu'à présent à des épisodes orogéniques d'âge Précambrien à Paléozoïque inférieur, pour conclure finalement de leur affinité paléotéthysienne. Leur histoire commence par un épisode de rifting d'âge Ordovicien supérieur-Dévonien inférieur, pour se terminer au Trias par la collision des blocs Cimmériens dérivé du Gondwana avec le Bloc du Turan d'affinité asiatique (événement Eocimmérien). La plus importante unité métamorphique affleurant au sud-ouest de la région de Jandak-Anarak-Kaboudan est une épaisse séquence silicoclastique à grains fins contenant des blocs ophiolitiques (marginal-sea-type), et des associations basalte-gabbro à signatures géochimiques de type supra-subduction. Dans la région de Nakhlak, nous avons daté ces gabbros par la méthode U-Pb à 387f0.11 Ma ; les roches métamorphiques pélitiques ont donné des âges de refroidissement Ar-Ar pour la muscovite de 320 à 333 Ma. Ce complexe d'accrétion "varisque" a été métamorphisé dans le faciès schiste vert-amphibolite au cours de l'accrétion de la ceinture granitique d'Airekan, d'âge Cambrien inférieur (549±15 Ma par la méthode U/Pb), qui affleure aujourd'hui à l'extrémité nord-ouest du terrane d'Anarak-Jandak . La subduction vers le nord de l'océan Paléotéthys depuis le Paléazoïque supérieur jusqu'au Trias, a permis l'accumulation de grandes quantités de matériel océanique dans la zone de subduction. Par exemple, une succession de guyots (Anarak, Kaboudan, et Meraji Seamounts) et de hauts sous-marins, entrés en collision oblique avec le prisme d'accrétion, est à l'origine d'un léger métamorphisme de type HP qui affecte ces séries {âges Ar-Ar de 280 à 230 Ma). De plus, le magmatisme bimodal de Chah Gorbeh est caractérisé d'une part par des roches de type trondjémite-gabbros (262 Ma), d'autre part par des laves en coussin de type basaltes alcalins-rhyolites; ces roches magmatiques ont recoupé l'ophiolite d'Anarak lors de la mise en place de cette dernière dans la fosse interne de subduction. Quant au prisme d'accrétion de Doshakh, d'âge essentiellement Permien supérieur, i1 a été accrété le long de la marge continentale et métamorphisé dans le faciès schiste vert. La fermeture de la Paléotéthys s'enregistre finalement par la sédimentation dans le bassin d'avant pays du flysch de Bayazeh, d'âge probable Triasique. Le matériel issu de l'arc magmatique de la Paléotéthys est très bien préservé dans les dépôts infra-arc Dévonien supérieur-Carbonifère de Godar-e-Siah, ainsi que dans la succession d'avant-arc de Nakhlak. Pendant l'intervalle Paléozoïque supérieur-Trias, la région de Jandak a été soumise à un régime extensif de type bassin d'arrière-arc, dont un témoin pourrait être la ceinture ophiolitique d'Arusan, elle-même comparable aux écailles ophiolitiques d'Aghdarband au nord-est de l'Iran. Cet ensemble métamorphique est recoupé par des granites d'arc à collisionnel datés à 215±15 Ma. Dans la région de Yazd, témoin de la marge passive Cimmérienne, la sédimentation syn-rift Silurienne à Dévonienne inférieure a été interrompue pendant l'intervalle Trias moyen-Trias supérieur; il en a été de même pour les dépôts de plate-forme Paléozoïque supérieur. L'érosion, qui dans ce dernier cas a atteint le Permien, pourrait être liée au bombement flexural de la marge passive. La collision finale n'a pas induit de déformations trop importantes, et se caractérise par la mise en place de nappes sur la marge passive. Cet événement est scellé par des dépôts molassique du Lias. D'un point de vue régional, la zone s'étendant actuellement de la Mer Noire au Pamir a été soumise à six épisodes d'extension-compression du Jurassique inférieur (début du l'ouverture en position arrière-arc de la Néotéthys) à l'Eocène moyen. Par exemple, le terrane d'AnarakJandak, probablement situé entre le Kopeh Dagh et la plate-forme nord Afghane, s'est complètement détaché de sa patrie d'origine au début du Crétacé supérieur. Des preuves de cet événement se retrouvent dans les séries de plate-forme de Khur (préservation de séries syn-rift puis de marge passive). Les ophiolites de Nain et de Sabzevar sont de plus interprétée comme un témoin de l'existence de ce bassin d'arrière-arc. Dans l'intervalle Eocène-Oligocène, l'indentation par la plaque indienne de l'Eurasie a été contemporaine de la rotation horaire de fragments de l'ancien microcontinent Iranien et de la formation du CEIM. Cette rotation est responsable du transport du terrane d'Anarak-Jandak vers sa position actuelle en Iran Central, et de la dislocation de Terranes de moindre importance, comme le bloc de Posht-e Badam. Depuis le Miocène supérieur, et à la suite de la collision entre l'Arabie et l'Iran, le ternane d'Anarak-Jandak a subi des déformations liées à l'activité d'une zone de cisaillement dextre parallèle à la suture du Zagros, à l'arrière de l'arc magmatique d'Uromieh-Dokhtar. Résumé large public Le Microcontinent Centre-Est Iranien occupe une position géologique clé au centre de l'Iran. Les différentes unités qui le composent, reliées jusqu'à présent à des épisodes orogéniques d'âge Précambrien à Paléozoïque inférieur, sont maintenant rajeunies et liés à la fermeture de l'océean Paléotéthys. Leur histoire commence par un épisode de rifting d'âge Ordovicien supérieur à Dévonien inférieur, pour se terminer au Trias par la collision des- blocs Cimmériens, dérivés du Gondwana, avec le Bloc du Turan d'affinité asiatique. Dans la marge active asiatique de la Paléotéthys, nous avons daté les restes d'un océan marginal à 387±0.11 Ma. Ce complexe d'accrétion a été métamorphisé au cours de la réaccrétion de la ceinture granitique d'Airekan, d'âge Cambrien inférieur (549±15 Ma), qui affleure aujourd'hui à l'extrémité nord-ouest du « terrane » d'Anarak-Jandak correspondant à la plus grande partie de la région étudiée. Le matériel issu de l'arc magmatique de la Paléotéthys est très bien préservé et daté du Dévonien supérieur-Carbonifère. Pendant l'intervalle Paléozoïque supérieur-Trias, la région a été soumise à un régime extensif de type bassin d'arrière-arc, dont un témoin pourrait être la ceinture ophiolitique d'Arusan, comparable aux écailles ophiolitiques d'Aghdarband au nord-est de l'Iran. Cet ensemble métamorphique est recoupé par des granites datés à 215±15 Ma. La subduction vers le nord de l'océan Paléotéthys depuis le Paléozoïque supérieur jusqu'au Trias, a permis l'accumulation de grandes quantités de matériel océanique dans la zone de subduction. Par exemple, une succession de volcans sous-marins, entrés en collision avec le prisme d'accrétion, est à l'origine d'un léger métamorphisme de type HP qui affecte ces séries (280 à 230 Ma). Quant au prisme d'accrétion de Doshakh, d'âge essentiellement Permien supérieur, il a été mis en place le long de la marge continentale et métamorphisé dans le faciès schiste vert. La fermeture de la Paléotéthys s'enregistre finalement par la sédimentation dans le bassin d'avant pays du flysch de Bayazeh, d'âge Triasique. Dans la région de Yazd, on trouve les témoins de la marge passive Cimmérienne, la sédimentation syn-rift Silurienne à Dévonienne inférieure a été interrompue pendant l'intervalle Trias moyen-Trias supérieur, marqué par la flexuration de la marge passive lorsqu'elle rentra en collision avec la marge active asiatique. Cet événement est scellé par des dépôts molassique à charbon du Lias. Le «terrane» d'Anarak-Jandak, probablement situé à l'origine entre le Kopeh Dagh et la plate-forme nord Afghane, s'est complètement détaché de cette région au début du Crétacé supérieur lors de l'ouverture d'un bassin d'arrière-arc, engendré, cette fois, par la subduction de l'océan Néotéthys situé au sud des blocs cimmériens. Des preuves de cet événement se retrouvent dans les séries syn-rift, puis de marge passive de Khour. Les ophiolites de Nain et de Sabzevar sont interprétées comme un témoin de l'existence de ce bassin d'arrière-arc. Dans l'intervalle Eocène-Oligocène, l'indentation de l'Eurasie par la plaque indienne a été contemporaine de la rotation horaire de fragments de l'ancien microcontinent centre-Iranien. Cette rotation de près de 90° est responsable du transport du « terrane » d'Anarak-Jandak vers sa position actuelle. Abstract The Anarak-Jandaq terrane occupies a strategic geological situation at the north-western part of the Central-East Iranian Microcontinent (CEIM) and in connection with the Great Kavir Block and Sanandaj-Sirjan metamorphic belt. Our recent findings redefine the origin of these mentioned areas so far attributed to the Precambrian-Early Palaeozoic orogenic episodes, to be now directly related to the tectonic evolution of the Palaeo-Tethys Ocean, commenced by Late Ordovician-Early Devonian rifting events and terminated in the Triassic by the Eocimmerian tectonic event due to the collision of the Cimmerian blocks with the Asiatic Turan block. The most distributed metamorphic unit that is exposed from the south-west of Jandaq to the Anarak and Kaboudan areas is a thick and fine grain siliciclastic sequence accompanied by marginal-sea-basin ophiolitic blocks including basalt-gabbro association with supra-subduction-geochemical signature. These gabbros in the Nakhlak area were dated by U/Pb method at 387.6 ± 0.11 Ma and the metamorphic pelitic rocks yielded a range of 320 to 333 Ma muscovite-cooling ages based on 40Ar/39 Ar method. This "Variscan" accretionary complex was metamorphosed in greenschist-amphibolite facies during accretion to the Lower Cambrian Airekan granitic belt (549 ± 15 Ma by U/Pb method) that crops out at the northwestern edge of the Anarak-Jandaq terrane. Continued northward subduction of the Palaeo-Tethys Ocean during the entire Late Palaeozoic-Middle Triassic brought huge amount of oceanic material to the subduction zone. One chain of Carboniferous-Triassic oceanic rises and seamounts (the Anarak, Kaboudan, and Meraji Seamounts) obliquely collided with the accretionary wedge and created a mild HP metamorphic event (280-230 Ma based on 40Ar/39Ar results). Bimodal magmatism of the Chah Gorbeh area is characterized by a 262 Ma trondjemite-gabbro as well as pillow alkalibasalts-rhyolites which intruded the Anarak ophiolite when it was being emplaced within the inner-wall trench. The mainly Late Permian-Triassic Doshakh wedge was accreted along the continent and metamorphosed under lower greenschist facies and the probable Triassic Bayazeh flysch filled the foreland basin during the final closure. The Palaeo-Tethys magmatic arc products have been well preserved in the Late Devonian-Carboniferous Godar-e-Siah intra-arc deposits and the Triassic Nakhlak fore-arc succession. During the Late Palaeozoic-Triassic times, the Jandaq area has been affected by back-arc extension and probably the Arusan ophiolitic belt is the remnant of this narrow basin comparable to the Aqdarband ophiolitic remnant in north-east Iran. This metamorphic belt was intruded by 215 ± 15 Ma arc to collisional granites. In the passive margin of the Cimmerian block, on the Yazd region, the Silurian-Early Devonian syn-rift succession as well as the nearly continuous Upper Palaeozoic platform-type deposition was interrupted during the Middle to Late Triassic time, local erosion down to Devonian levels may be related to flexural bulge erosion. The collision event was not so strong to generate intensive deformation but was accompanied by some nappe thrusting onto the passive margin. It is finally unconformably covered by Liassic continental molassic deposits. Related to the onset of Neo-Tethyan back-arc opening in Early Jurassic to Mid-Eocene times, six periods of extensional-compressional events have differently influenced an elongated area, extending from the West Black Sea to Pamir. The Anarak-Jandaq terrane which was situated somewhere in this affected area, probably between the Kopeh Dagh and North Afghan platform, was completely detached from its source at the beginning of the Late Cretaceous

Recognition in ants: social origin matters.

The ability of group members to discriminate against foreigners is a keystone in the evolution of sociality. In social insects, colony social structure (number of queens) is generally thought to influence abilities of resident workers to discriminate between nestmates and non-nestmates. However, whether social origin of introduced individuals has an effect on their acceptance in conspecific colonies remains poorly explored. Using egg-acceptance bioassays, we tested the influence of social origin of queen-laid eggs on their acceptance by foreign workers in the ant Formica selysi. We showed that workers from both single- and multiple-queen colonies discriminated against foreign eggs from single-queen colonies, whereas they surprisingly accepted foreign eggs from multiple-queen colonies. Chemical analyses then demonstrated that social origins of eggs and workers could be discriminated on the basis of their chemical profiles, a signal generally involved in nestmate discrimination. These findings provide the first evidence in social insects that social origins of eggs interfere with nestmate discrimination and are encoded by chemical signatures.

Analysis of malaria associated genetic traits in Cabo Verde, a melting pot of European and sub Saharan settlers

Malaria has occurred in the Cabo Verde archipelago with epidemic characteristics since its colonization. Nowadays, it occurs in Santiago Island alone and though prophylaxis is not recommended by the World Health Organization, studies have highlight the prospect of malaria becoming a serious public health problem as a result of the presence of antimalarial drug resistance associated with mutations in the parasite populations and underscore the need for tighter surveillance. Despite the presumptive weak immune status of the population, severe symptoms of malaria are not observed and many people present a subclinical course of the disease. No data on the prevalence of sicklecell trait and red cell glucose-6-phosphate dehydrogenase deficiency (two classical genetic factors associated with resistance to severe malaria) were available for the Cabo Verde archipelago and, therefore, we studied the low morbidity from malaria in relation to the particular genetic characteristics of the human host population. We also included the analysis of the pyruvate kinase deficiency associated gene, reported as putatively associated with resistance to the disease. Allelic frequencies of the polymorphisms examined are closer to European than to African populations and no malaria selection signatures were found. No association was found between the analyzed human factors and infection but one result is of high interest: a linkage disequilibrium test revealed an association of distant loci in the PKLR gene and adjacent regions, only in non-infected individuals. This could mean a more conserved gene region selected in association to protection against the infection and/or the disease.

The InterPro protein families database: the classification resource after 15 years.

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.

Characterization of modern and fossil mineral dust transported to high altitude in the Western Alps: Saharan sources and transport patterns

Mineral dust aerosols recently collected at the high-altitude Jungfraujoch research station (46 degrees 33'51 `' N, 7 degrees 59'06 `' E; 3580 m a.s.l.) were compared to mineral dust deposited at the Colle Gnifetti glacier (45 degrees 52'50 `' N, 7 degrees 52'33 `' E; 4455 m a.s.l.) over the last millennium. Radiogenic isotope signatures and backward trajectories analyses indicate that major dust sources are situated in the north-central to north-western part of the Saharan desert. Less radiogenic Sr isotopic compositions of PM10 aerosols and of mineral particles deposited during periods of low dust transfer likely result from the enhancement of the background chemically-weathered Saharan source. Saharan dust mobilization and transport were relatively reduced during the second part of the Little Ice Age (ca. 1690-1870) except within the greatest Saharan dust event deposited around 1770. After ca. 1870, sustained dust deposition suggests that increased mineral dust transport over the Alps during the last century could be due to stronger spring/summer North Atlantic southwesterlies and drier winters in North Africa. On the other hand, increasing carbonaceous particle emissions from fossil fuel combustion combined to a higher lead enrichment factor point to concomitant anthropogenic sources of particulate pollutants reaching high-altitude European glaciers during the last century.

Gene expression profiling of human glioblastomas for the identification of predictive factors and characterisation of molecular mechanism implicated in response to therapy and outcome

ABSTRACT Poor outcome for glioblastoma patients is largely due to resistance to chemoradiation therapy. While epigenetic inactivation of MGMT mediated DNA repair is highly predictive for benefit from the alkylating agent therapy Temozolomide, additional mechanisms for resistance associated with molecular alterations exist. Furthermore, new concepts in cancer suggest that resistance to treatment may be linked to cancer stem cells that escape therapy and act as source for tumour recurrence. We determined gene expression signatures associated with outcome in glioblastoma patients enrolled in a phase II and phase III clinical trial establishing the new combination therapy of radiation plus concomitant and adjuvant Temozolomide. Correlating stable gene clusters emerging from unsupervised analysis with survival of 42 treated patients identified a number of biological processes associated with outcome. Most prominent, a gene cluster dominated by HOX genes and comprising PROM1, was associated with resistance. PROM1 encodes CD133, a marker for a subpopulation of tumour cells enriched for glioblastoma stem- like cells. The core of this correlated HOX cluster was comprised in the top genes of a "self-renewal signature" defined in a mouse model for MLL-AF9 initiated leukaemia. The association of the HOX gene cluster with tumour resistance was confirmed in two external data sets of 146 malignant glioma As additional resistance factors we identified over-expression of the epidermal growth factor receptor gene, EGFR, while increased gene expression related to biological features of tumour host interaction, including markers for tumour vascular and cell adhesion, and innate immune response, were associated with better outcome. The "self-renewal" signature associated with resistance to the new combination chemoradiation therapy provides first clinical evidence that glioma stem like cells may implicated in resistance in a uniformly treated cohort of glioblastoma patients. This study underlines the need to target the tumour stem cell compartment, and provides some testable hypothesis for biological mechanisms relevant for malignant behaviour of glioblastoma that may be targeted in new treatment approaches. Résumé Le glioblastome, tumeur cérébrale primaire maligne la plus fréquente, est connue pour son mauvais pronostique. Des avancées chimiothérapeutiques récentes avec des agents alkylants comme le témozolomide (TMZ), ont permis une amélioration notable dans la survie de certains patients. Les bénéficiaires ont la caractéristique commune de présenter une particularité génétique, la methylation du MGMT (methylguanine methyltransferase). Néanmoins, d'autres mécanismes de résistance en fonction des aberrations moléculaires existent. Nous avons établi les profils d'expressions génétiques des patients traités par irradiation et TMZ dans des études cliniques de phase II et III. En combinant des méthodes non-supervisées et supervisées, de l'étude de la cohorte des patients traités nous avons découvert des groupes de gènes associés à la survie. Un ensemble de gènes contenant les gènes Hox semble lié au mécanisme de résistance au traitement. Récemment, les gènes Hox ont été décrits comme faisant partie d"une signature d'autorenouvellement (self-renewal) des cellules souches cancéreuses de la leucémie. L'autorenouvellement est un processus grâce auquel les cellules souches se maintiennent tout au long de la vie. Cette association à la résistance est confirmée dans deux autres études indépendantes. Un autre facteur de résistance au traitement est la surexpression du gène EGFR. D'autre part, deux groupes de gènes associés à la relation entre hôte-tumeur tels que les marqueurs des vaisseaux tumoraux et de la réponse immunitaire innée s'avèrent avoir un effet positif sur la survie des patients traités. La découverte de la signature d'autorenouvellement comme facteur de résistance à la nouvelle chimio-radiothérapie offre une preuve clinique que les cellules souches cancéreuses sont impliquées dans la résistance au traitement. If est donc logique de penser que le traitement ciblé contre des cellules souches cancéreuses va dans l'avenir permettre des thérapies anticancéreuses plus performantes.

VARIABILITY OF PHENOTYPIC, PROTEOMIC AND TRANSCRIPTOMIC EXPRESSION OF STAPHYLOCOCCUS AUREUS SURFACE ADHESINS

Staphylococcus aureus is a highly successful pathogen responsible of a wide variety of diseases, from minor skin infection to life-threatening sepsis or infective endocarditis, as well as food poisoning and toxic shock syndrome. This heterogeneity of infections and the ability of S. aureus to develop antibiotic-resistance to virtually any available drugs reflect its extraordinary capacity to adapt and survive in a great variety of environments. The pathogenesis of S. aureus infection involves a wide range of cell wall-associated adhesins and extracellular toxins that promote host colonization and invasion. In addition, S. aureus is extremely well equipped with regulatory systems that sense environmental conditions and respond by fine tuning the expression of metabolic and virulence determinants. Surface adhesins referred to MSCRAMMs - for Microbial Surface Component Recognizing Adherence Matrix Molecules - mediate binding to the host extracellular matrix or serum components, including fibrinogen, fibronectin, collagen and elastin, and promote tissue colonization and invasion. Major MSCRAMMs include a family of surface-attached proteins covalently bound to the cell wall peptidoglycan via a conserved LPXTG motif. Genomic analyses indicate that S. aureus contain up to 22 LPXTG surface proteins, which could potentially act individually or in synergy to promote infection. In the first part of this study we determined the range of adherence phenotypes to fibrinogen and fibronectin among 30 carriage isolates of S. aureus and compared it to the adherence phenotypes of 30 infective endocarditis and 30 blood culture isolates. Overall there were great variations in in vitro adherence, but no differences were observed between carriage and infection strains. We further determined the relation between in vitro adherence and in vivo infectivity in a rat model of experimental endocarditis, using 4 isolates that displayed either extremely low or high adherence phenotypes. Unexpectedly, no differences were observed between the in vivo infectivity of isolates that were poorly and highly adherent in vitro. We concluded that the natural variability of in vitro adherence to fibrinogen and fibronectin did not correlate with in vivo infectivity, and thus that pathogenic differences between various strains might only be expressed in in vivo conditions, but not in vitro. Therefore, considering the importance of adhesins expression for infection, direct measurement of those adhesins present on the bacterial surface were made by proteomic approach. 5 In the second series of experiments we assessed the physical presence of the LPXTG species at the staphylococcal surface, as measured at various time points during growth in different culture media. S. aureus Newman was grown in either tryptic soy broth (TSB) or in Roswell Park Memorial Institute (RPMI) culture medium, and samples were removed from early exponential growth phase to late stationary phase. Experiments were performed with mutants in the global accessory-gene regulator (agr), surface protein A (Spa) and clumping factor A (ClfA). Peptides of surface proteins were recovered by "trypsin-shaving" of live bacteria, and semi-quantitative proteomic analysis was performed by tandem liquid-chromatography and mass-spectrometry (LC-MS). We also determined in parallel the mRNA expression by microarrays analysis, as well as the phenotypic adherence of the bacteria to fibrinogen in vitro. The surface proteome was highly complex and contained numerous proteins theoretically not belonging to the bacterial envelope, including ribosomal proteins and metabolic enzymes. Sixteen of the 21 known LPXTG species were detected, but were differentially expressed. As expected, 9 known agr-regulated proteins (e.g. including Spa, FnBPA, ClfA, IsdA, IsdB, SasH, SasD, SasG and FmtB) increased up to the late exponential growth phase, and were abrogated in agr-negative mutants. However, only Spa and SasH modified their proteomic and mRNA profiles in parallel in the parent and its agr negative mutant, while all other LPXTG proteins modified their proteomic profiles independently of their mRNA. Moreover, ClfA became highly transcribed and active in in vitro fibrinogen adherence tests during late growth (24h), whereas it remained poorly detected by proteomics. Differential expression was also detected in iron-rich TSB versus iron-poor RPMI. Proteins from the iron-regulated surface determinant (isd) system, including IsdA, IsdB and IsdH were barely expressed in iron-rich TSB, whereas they increased their expression by >10 time in iron-poor RPMI. We conclude that semi-quantitative proteomic analysis of specific protein species is feasible in S. aureus and that proteomic, transcriptomic and adherence phenotypes demonstrated differential profiles in S. aureus. Furthermore, peptide signatures released by trypsin shaving suggested differential protein domain exposures in various environments, which might be relevant for antiadhesins vaccines. A comprehensive understanding of the S. aureus physiology should integrate all these approaches.

Détermination de la séquence chronologique entre les impressions électrophotographiques (imprimantes laser et photocopieurs) et les traits de stylos à bille, sans croisement

Ce travail décrit une méthode optique pour établir l'ordre chronologique de la séquence entre les impressions électrophotographiques (imprimantes laser et photocopieurs) et les signatures apposées au stylo à bille, sans croisement. Les auteurs ont utilisé un microscope optique avec des grossissements allant de 100 à 500 fois qui permettent de distinguer l'apparence des microparticules de toner selon qu'elles se situent au-dessus ou au-dessous de l'encre de stylo à billes. Les tests à l'aveugle ont montré un taux de réussite de 100 % permettant ainsi de valider les résultats proposés par Aginsky (2002).

Geoquímica das rochas magmáticas da Ilha Brava:implicações para a origem e variabilidade espaço-temporal do ponto quente de Cabo Verde

A Ilha Brava (64 km2) localiza-se no extremo oeste do alinhamento meridional do arquipélago de Cabo Verde, sendo constituída por três unidades vulcanoestratigráficas que testemunham uma história vulcânica de cerca de 3 Ma. Foi escolhida como objecto de estudo na tentativa de contribuir para a melhor compreensão da origem e local de residência de alguns dos componentes mantélicos, das relações genéticas entre magmas silicatados e carbonatíticos, dos processos de desgaseificação de magmas carbonatíticos e da origem do carbono neles contido, da variabilidade geoquímica espaço-temporal do ponto quente de Cabo Verde, e da profundidade de enraizamento da sua pluma mantélica. A Brava contrasta com as outras ilhas do arquipélago por definir dois grupos geoquímicos distintos. As amostras do Complexo Basal, sendo menos radiogénicas Sr e He e mais em Nd e Pb que a unidade mais recente, são idênticas às ilhas do norte e explicáveis pela mistura de um componente do tipo HIMU (crosta oceânica reciclada com 1.3 Ga) e manto inferior (3He/4He até 12.85 Ra), carreados para a “superfície” pela pluma mantélica. Tal como é usual nas ilhas do sul, a Unidade Superior sugere, em adição, o envolvimento de um componente com afinidade EM-1, aqui considerado representativo de fragmentos de litosfera subcontinental dispersos na astenosfera. Os carbonatitos definem dois grupos com assinaturas isotópicas semelhantes às das rochas silicatadas contemporâneas. Os calciocarbonatitos resultaram de imiscibilidade líquida produzindo magmas nefeliníticos e carbonatíticos, enquanto os magnesiocarbonatitos representam líquidos residuais após a fraccionação de calcite a partir de um magma carbonatítico. As muito baixas razões 4He/40Ar* (≈ 0.25) que caracterizam a fonte dos carbonatitos do Complexo Basal indicam uma evolução a partir de razões K/U muito mais elevadas que o conjunto dos reservatórios silicatados da Terra. Sendo estes valores, também incompatíveis com a reciclagem de componentes crostais, foram aqui interpretados como podendo reflectir a contribuição do “missing Ar reservoir” para a fonte mantélica dos carbonatitos.

Differentiation of focal liver lesions: usefulness of parametric imaging with contrast-enhanced US.

Purpose: To evaluate whether parametric imaging with contrast material-enhanced ultrasonography (US) is superior to visual assessment for the differential diagnosis of focal liver lesions (FLLs). Materials and Methods: This study had institutional review board approval, and verbal patient informed consent was obtained. Between August 2005 and October 2008, 146 FLLs in 145 patients (63 women, 82 men; mean age, 62.5 years; age range, 22-89 years) were imaged with real-time low-mechanical-index contrast-enhanced US after a bolus injection of 2.4 mL of a second-generation contrast agent. Clips showing contrast agent uptake kinetics (including arterial, portal, and late phases) were recorded and subsequently analyzed off-line with dedicated image processing software. Analysis of the dynamic vascular patterns (DVPs) of lesions with respect to adjacent parenchyma allowed mapping DVP signatures on a single parametric image. Cine loops of contrast-enhanced US and results from parametric imaging of DVP were assessed separately by three independent off-site readers who classified each lesion as benign, malignant, or indeterminate. Sensitivity, specificity, accuracy, and positive and negative predictive values were calculated for both techniques. Interobserver agreement (κ statistics) was determined. Results: Sensitivities for visual interpretation of cine loops for the three readers were 85.0%, 77.9%, and 87.6%, which improved significantly to 96.5%, 97.3%, and 96.5% for parametric imaging, respectively (P < .05, McNemar test), while retaining high specificity (90.9% for all three readers). Accuracy scores of parametric imaging were higher than those of conventional contrast-enhanced US for all three readers (P < .001, McNemar test). Interobserver agreement increased with DVP parametric imaging compared with conventional contrast-enhanced US (change of κ from 0.54 to 0.99). Conclusion: Parametric imaging of DVP improves diagnostic performance of contrast-enhanced US in the differentiation between malignant and benign FLLs; it also provides excellent interobserver agreement.