Early Cretaceous life, climate and anoxia

Early Cretaceous life and the environment were strongly influenced by the accelerated break up of Pangaea, which was associated with the formation of a multitude of rift basins, intensified spreading, and important volcanic activity on land and in the sea. These processes likely interacted with greenhouse conditions, and Early Cretaceous climate oscillated between "normal" greenhouse, predominantly arid conditions, and intensified greenhouse, predominantly humid conditions. Arid conditions were important during the latest Jurassic and early Berriasian, the late Barremian, and partly also during the late Aptian. Humid conditions were particularly intense and widespread during shorter episodes of environmental change (EECs): the Valanginian Weissert, the latest Hauterivian Faraoni, the latest Barremian earliest Aptian Taxy, the early Aptian Selli, the early late Aptian Fallot and the late Aptian-early Albian Paquier episodes. Arid conditions were associated with evaporation, low biogeochemical weathering rates, low nutrient fluxes, and partly stratified oceans, leading to oxygen depletion and enhanced preservation of laminated, organic-rich mud (LOM). Humid conditions enabled elevated biogeochemical weathering rates and nutrient fluxes, important runoff and the buildup of freshwater lids in proximal basins, intensified oceanic and atmospheric circulation, widespread upwelling and phosphogenesis, important primary productivity and enhanced preservation of LOM in expanded oxygen-minimum zones. The transition of arid to humid climates may have been associated with the net transfer of water to the continent owing to the infill of dried-out groundwater reservoirs in internally drained inland basins. This resulted in shorter-term sea-level fall, which was followed by sea-level rise. These sea-level changes and the influx of freshwater into the ocean may have influenced oxygen-isotope signatures. Climate change preceding and during the Early Cretaceous EECs may have been rapid, but in general, the EECs had a "pre"-history, during which the stage was set for environmental change. Negative feedback on the climate through increased marine LOM preservation was unlikely, because of the low overall organic-carbon accumulation rates during these episodes. Life and climate co-evolved during the Early Cretaceous. Arid conditions may have affected continental life, such as across the Tithonian/Berriasian boundary. Humid conditions and the corresponding tendency to develop dys- to anaerobic conditions in deeper ocean waters led to phases of accelerated extinction in oceans, but may have led to more luxuriant vegetation cover on continents, such as during the Valanginian, to the benefit of herbivores. During Early Cretaceous EECs, reef systems and carbonate platforms in general were particularly vulnerable. They were the first to disappear and the last to recover, often only after several million years. (C) 2011 Elsevier Ltd. All rights reserved.

Functional and molecular evolutionary analysis of the "Brevix Radix" gene family in mono-and dicotyledonous plants

ABSTRACTIn contrast to animals, plants cannot move from their place of birth and, therefore, need to adapt to their particular habitat in order to survive. Thus, plant development is remarkably plastic, making plants an ideal system for the isolation of genes that account for intraspecific natural variation and possibly environmental adaptation. However, to date, this approach mostly identified null alleles and missed mutations with subtle effects. For instance, BREVIS RADIX (BRX) has been isolated as a key regulator of root growth through a naturally occurring loss-of-function allele in the Arabidopsis thaliana accession Uk-1 and is the founding member of a highly-conserved plant-specific gene family.In this work, we show that a strong selective pressure is acting on the BRX gene family and dates back before the monocot-dicot divergence. However, functional diversification is observed mainly in dicotyledon BRX family genes and is correlated with acceleration in the evolutionary rates in the N-terminal regions. Population genetic data revealed that BRX is highly conserved across Arabidopsis accessions and presents signatures of adaptation. Interestingly, a seven amino acid deletion polymorphism in BRX sequence was found in a few accessions, which seems to be responsible for their enhanced primary root growth. Nevertheless, BRX might not only be active in the root, as suggested by its expression in the shoot. Indeed, leaves and cotyledons of brx mutants are significantly smaller than wild- type. This phenotype is a direct consequence of the absence of BRX function in the shoot rather than an indirect effect of an altered root system growth. Interestingly, cotyledons of brx plants reflect the same physiological defects as the root. Moreover, phenotypes in BRX gain-of-function plants, such as epinastic leaves and increased epidermal cell size, could be associated with an increase in leaf brassinosteroid content.Collectively, these results indicate that BRX contributes to local adaptation by ubiquitously regulating plant growth, probably through the modulation of brassinosteroid biosynthesis.RÉSUMÉContrairement à la plupart des animaux, les plantes ne peuvent se mouvoir et doivent ainsi s'adapter à leur environnement pour survivre. Pour cette raison, elles représentent un système idéal pour l'identification de gènes contribuant à la variation naturelle intra- spécifique, ainsi qu'à l'adaptation. Cependant, cette approche a, jusqu'à présent, surtout permis d'isoler des allèles nuls et non des mutations conférant des effets plus subtiles. C'est le cas du gène Β REVIS RADIX (BRX), un régulateur clé de la croissance racinaire, qui a été identifié grâce à un allèle non-fonctionnel présent dans l'accession naturelle d'Arabidopsis thaliana Uk-1. BRX et ses homologues des plantes mono- et dicotylédones forment une famille très conservée et spécifique aux plantes.Dans ce travail, nous démontrons que la famille de gènes BRX est soumise à une forte pression de sélection qui remonte avant la divergence entre mono- et dicotylédones. Cependant, une diversification fonctionnelle a été observée chez les gènes des dicotylédones et corrèle avec une accélération de la vitesse d'évolution dans leur région N- terminale. Une analyse génétique de différentes accessions naturelles d'Arabidopsis a révélé que BRX est hautement conservé et présente des signatures d'adaptation. Remarquablement, un polymorphisme de délétion de sept acides aminés a été détecté dans quelques accessions et a pour conséquence une plus forte croissance de la racine primaire. Néanmoins, il semble que le rôle de BRX ne se limite pas qu'à la racine, comme indiqué par son expression dans les parties aériennes de la plante. En effet, les mutants brx présentent des cotylédons et des feuilles significativement plus petits que le type sauvage, une conséquence directe de l'absence d'activité de BRX dans ces organes. Nous avons aussi noté que les cotylédons des mutants brx, à l'instar des racines, ont une perception altérée de l'auxine et peuvent être complémentés par l'application exogène de brassinostéroïdes. De plus, dans des plantes présentant un gain de fonction BRX, les feuilles sont épinastiques et les cellules de leur épiderme plus grandes. Ces phénotypes sont accompagnés d'une augmentation de la concentration de brassinostéroïdes dans les feuilles. Conjointement, ces résultats démontrent que BRX contribue à une adaptation locale de la plante par la régulation générale de sa croissance, probablement en modulant la biosynthèse des brassinostéroïdes.

Cryptic diversity among Western Palearctic tree frogs: postglacial range expansion, range limits, and secondary contacts of three European tree frog lineages (Hyla arborea group).

We characterize divergence times, intraspecific diversity and distributions for recently recognized lineages within the Hyla arborea species group, based on mitochondrial and nuclear sequences from 160 localities spanning its whole distribution. Lineages of H. arborea, H. orientalis, H. molleri have at least Pliocene age, supporting species level divergence. The genetically uniform Iberian H. molleri, although largely isolated by the Pyrenees, is parapatric to H. arborea, with evidence for successful hybridization in a small Aquitanian corridor (southwestern France), where the distribution also overlaps with H. meridionalis. The genetically uniform H. arborea, spread from Crete to Brittany, exhibits molecular signatures of a postglacial range expansion. It meets different mtDNA clades of H. orientalis in NE-Greece, along the Carpathians, and in Poland along the Vistula River (there including hybridization). The East-European H. orientalis is strongly structured genetically. Five geographic mitochondrial clades are recognized, with a molecular signature of postglacial range expansions for the clade that reached the most northern latitudes. Hybridization with H. savignyi is suggested in southwestern Turkey. Thus, cryptic diversity in these Pliocene Hyla lineages covers three extremes: a genetically poor, quasi-Iberian endemic (H. molleri), a more uniform species distributed from the Balkans to Western Europe (H. arborea), and a well-structured Asia Minor-Eastern European species (H. orientalis).

Monitoring of innate and adaptive immune responses in the context of human immunotherapy

Summary1 SummaryCancer patients have a better clinical outcome when their tumours display marked infiltration by memory Τ cells. Moreover, the overrepresentation of Th1 gene signatures in primary tumours correlates with favourable prognosis. Thus, vaccination to induce Τ cells capable of infiltrating and eradicating the tumour seems a promising strategy for the treatment of cancer. Here, I monitored CD4 Τ cell responses in melanoma patients vaccinated with the long synthetic peptides Melan- A16-35(A27L) and NY-ESO-179.108. Most of the patients developed strong and diverse peptide antigen specific CD4 Τ cell responses. Analysis of the fine specificity of CD4 Τ cell antigen recognition led to the identification of two new epitopes. The peptide Melan-A16_35(A27L) was delivered by virus-like particles (VLPs) derived from bacteriophage Οβ, which themselves displayed strong immunogenicity. I show evidence for induction of Οβ- and Melan-A specific CD4 Τ cell responses that developed a Th1 functional profile after repeated vaccination cycles. They also specifically released the chemokines CCL-3 and CCL-4, which play important roles in attracting CD8 Τ cells to the APC surface for priming and formation of Τ cell memory. We further found induction of robust humoral IgG responses upon VLP vaccination, and the lgG1-lgG4 isotype composition depended on the adjuvant used. Since heavy chain class switching largely dépends on the presence of CD4 Τ cell help, this result suggests that the adjuvant can influence the differentiation of elicited CD4 Τ cells, thereby contributing to the quality and function of both Β cells and CD8 Τ cells. The nature of the inflammatory processes in the tumour microenvironment can modulate CD8 Τ cell function. A collaboration was established for the investigation regulation of inflammasome activation in human primary monocytes. We identified IL- 4 and TGF-β as strong inhibitors of IL-1 β secretion, Indicating some level of regulation from effector Th2 and Treg responses. We further found a potent inhibition of inflammasome activation by type I interferon, and demonstrated in vivo inhibition of IL-1 β responses in monocytes from active multiple sclerosis patients under IFN-β therapy. This finding further offers a possible explanation for its success, which mechanism of action is still largely unclear. Interestingly, type I interferon is also being used as adjuvant treatment for tumour free metastatic cutaneous melanoma patients. While its clinical benefit has remained controversial, recent data suggest that the subset of patients with ulcerated primary melanoma lesions can benefit from this therapy. Future investigations will shed light on the implication of the inflammasome in this context, and may offer new strategies for improved adjuvant treatments of melanoma.2 RésuméLes patients atteints de cancer ont une meilleure chance de survie si leurs tumeurs s'avèrent être largement infiltrées par des cellules Τ mémoires. De plus, la surreprésentation d'une signature génique Th1 est en corrélation avec un pronostic favorable. Ainsi, la vaccination visant à induire des cellules Τ capables d'infiltrer et de détruire la tumeur parait être une stratégie prometteuse pour le traitement du cancer. Dans ce travail, j'ai procédé au monitoring de la réponse des cellules Τ CD4 dans des patients atteints de mélanome vaccinés avec les longs peptides synthétiques Melan-A16_35(A27L) et NY-ESO-179_108. Ces peptides représentent des antigènes tumoraux reconnus par des lymphocytes T. La majorité des patients a développé une réponse forte et diversifiée des cellules Τ CD4 spécifiques contre les peptides. L'analyse de la spécificité fine de la reconnaissance antigénique des cellules Τ CD4 nous a conduits à l'identification de deux nouveaux épitopes. Le peptide Melan-Aie. 35(A27L) a été délivré par des particules de type viral (VLPs) dérivés de bactériophages Qβ, qui ont eux-mêmes démontré une forte immunogénicité. Mon travail montre les preuves d'une induction de réponses spécifiques des cellules Τ CD4 contre les Qβ et Melan-A développant un profil fonctionnel Th1 après plusieurs cycles de vaccination. Elles secrètent aussi spécifiquement les chimiokines CCL-3 et CCL-4, qui jouent un rôle important dans l'attraction des cellules Τ CD8 à la surface des cellules présentatrices d'antigènes et contribuent ainsi à induire et former la mémoire cellulaire Τ CD8. Nous avons également remarqué une induction de fortes réponses humorales IgG après vaccination avec les VLPs, et que la composition des isotypes lgG1-lgG4 dépendait de l'adjuvant utilisé. Etant donné qu'une commutation de classe de la chaîne lourde dépend largement ùie l'aide des cellules Τ CD4, ce résultat suggère que l'adjuvant puisse influencer la différeritiation de cellules Τ CD4 en différent types, contribuant ainsi à la qualité et à la fonction des cellules Β et des cellules Τ CD8.La nature des processus d'inflammation dans le microenvironnement tumoral peut moduler la fonction des cellules Τ CD8. Une collaboration a été établie pour investiguer la régulation de l'activation de l'inflammasome dans des monocytes primaires humains. Nous avons identifié l'IL-4 et le TGF-β comme étant de puissants inhibiteurs de la sécrétion de IL-Ιβ, indiquant une certaine régulation de la réponse inflammatoire induite par les cellules Th2 et Τ régulatrices. Nous avons également trouvé une forte inhibition de l'activation de l'inflammasome par l'interféron type I, et nous avons démontré une inhibition in vivo de la réponse IL-1 β dans des monocytes de patients atteints d'une sclérose en plaque active sous traitement IFN-β. Ce résultat nous offre une possible explication du succès de cette thérapie, dont le mécanisme reste à ce jour encore largement obscur. Il est intéressant de noter que l'interféron de type I est également utilisé pour le traitement de patients atteints de mélanome cutané métastasique sans tumeurs. Bien que le bénéfice clinique de ce traitement reste controversé, des études récentes montrent qu'une partie des patients atteints de mélanome primaire ulcéré peut tirer bénéfice de cette thérapie. De futures investigations pourront mieux nous renseigner sur l'implication de l'inflammasome dans ce contexte et offrir de nouvelles stratégies pour améliorer les traitements adjuvants du mélanome.

Genetics of cadmium hyperaccumulation variance in Thlaspi caerulescens natural populations from Switzerland

SUMMARY Heavy metal presence in the environment is a serious concern since some of them can be toxic to plants, animals and humans once accumulated along the food chain. Cadmium (Cd) is one of the most toxic heavy metal. It is naturally present in soils at various levels and its concentration can be increased by human activities. Several plants however have naturally developed strategies allowing them to grow on heavy metal enriched soils. One of them consists in the accumulation and sequestration of heavy metals in the above-ground biomass. Some plants present in addition an extreme strategy by which they accumulate a limited number of heavy metals in their shoots in amounts 100 times superior to those expected for a non-accumulating plant in the same conditions. Understanding the genetic basis of the hyperaccumulation trait - particularly for Cd - remains an important challenge which may lead to biotechnological applications in the soil phytoremediation. In this thesis, Thlaspi caerulescens J. & C. Presl (Brassicaceae) was used as a model plant to study the Cd hyperaccumulation trait, owing to its physiological and genetic characteristics. Twenty-four wild populations were sampled in different regions of Switzerland. They were characterized for environmental and soil parameters as well as intrinsic characteristics of plants (i.e. metal concentrations in shoots). They were as well genetically characterized by AFLPs, plastid DNA polymorphism and genes markers (CAPS and microsatellites) mainly developed in this thesis. Some of the investigated genes were putatively linked to the Cd hyperaccumulation trait. Since the study of the Cd hyperaccumulation in the field is important as it allows the identification of patterns of selection, the present work offered a methodology to define the Cd hyperaccumulation capacity of populations from different habitats permitting thus their comparison in the field. We showed that Cd, Zn, Fe and Cu accumulations were linked and that populations with higher Cd hyperaccumulation capacity had higher shoot and reproductive fitness. Using our genetic data, statistical methods (Beaumont & Nichols's procedure, partial Mantel tests) were applied to identify genomic signatures of natural selection related to the Cd hyperaccumulation capacity. A significant genetic difference between populations related to their Cd hyperaccumulation capacity was revealed based on somè specific markers (AFLP and candidate genes). Polymorphism at the gene encoding IRTl (Iron-transporter also participating to the transport of Zn) was suggested as explaining part of the variation in Cd hyperaccumulation capacity of populations supporting previous physiological investigations. RÉSUMÉ La présence de métaux lourds dans l'environnement est un phénomène préoccupant. En effet, certains métaux lourds - comme le cadmium (Cd) -sont toxiques pour les plantes, les animaux et enfin, accumulés le long de la chaîne alimentaire, pour les hommes. Le Cd est naturellement présent dans le sol et sa concentration peut être accrue par différentes activités humaines. Certaines plantes ont cependant développé des stratégies leur permettant de pousser sur des sols contaminés en métaux lourds. Parmi elles, certaines accumulent et séquestrent les métaux lourds dans leurs parties aériennes. D`autres présentent une stratégie encore plus extrême. Elles accumulent un nombre limité de métaux lourds en quantités 100 fois supérieures à celles attendues pour des espèces non-accumulatrices sous de mêmes conditions. La compréhension des bases génétiques de l'hyperaccumulation -particulièrement celle du Cd - représente un défi important avec des applications concrètes en biotechnologies, tout particulièrement dans le but appliqué de la phytoremediation des sols contaminés. Dans cette thèse, Thlaspi caerulescens J. & C. Presl (Brassicaceae) a été utilisé comme modèle pour l'étude de l'hyperaccumulation du Cd de par ses caractéristiques physiologiques et génétiques. Vingt-quatre populations naturelles ont été échantillonnées en Suisse et pour chacune d'elles les paramètres environnementaux, pédologique et les caractéristiques intrinsèques aux plantes (concentrations en métaux lourds) ont été déterminés. Les populations ont été caractérisées génétiquement par des AFLP, des marqueurs chloroplastiques et des marqueurs de gènes spécifiques, particulièrement ceux potentiellement liés à l'hyperaccumulation du Cd (CAPS et microsatellites). La plupart ont été développés au cours de cette thèse. L'étude de l'hyperaccumulation du Cd en conditions naturelles est importante car elle permet d'identifier la marque, éventuelle de sélection naturelle. Ce travail offre ainsi une méthodologie pour définir et comparer la capacité des populations à hyperaccumuler le Cd dans différents habitats. Nous avons montré que les accumulations du Cd, Zn, Fe et Cu sont liées et que les populations ayant une grande capacité d'hyperaccumuler le Cd ont également une meilleure fitness végétative et reproductive. Des méthodes statistiques (l'approche de Beaumont & Nichols, tests de Martel partiels) ont été utilisées sur les données génétiques pour identifier la signature génomique de la sélection naturelle liée à la capacité d'hyperaccumuler le Cd. Une différenciation génétique des populations liée à leur capacité d'hyperaccumuler le Cd a été mise en évidence sur certains marqueurs spécifiques. En accord avec les études physiologiques connues, le polymorphisme au gène codant IRT1 (un transporteur de Fe impliqué dans le transport du Zn) pourrait expliquer une partie de la variance de la capacité des populations à hyperaccumuler le Cd.

Simultaneous co-expression of memory- and effector-related genes by individual human CD8 T cells depends on antigen specificity and differentiation

Purpose/Objective: Phenotypic and functional T cell properties are usually analyzed at the level of defined cell populations. However, large differences between individual T cells may have important functional consequences. To answer this issue, we performed highly sensitive single-cell gene expression profiling, which allows the direct ex vivo characterization of individual virus- and tumor-specific T cells from healthy donors and melanoma patients. Materials and methods: HLA-A*0201-positive patients with stage III/ IV metastatic melanoma were included in a phase I clinical trial (LUD- 00-018). Patients received monthly low-dose of the Melan-AMART- 1 26_35 unmodified natural (EAAGIGILTV) or the analog A27L (ELAGIGILTV) peptides, mixed CPG and IFA. Individual effector memory CD28+ (EM28+) and EM28- tetramer-specific CD8pos T cells were sorted by flow cytometer. Following direct cell lysis and reverse transcription, the resulting cDNA was precipitated and globally amplified. Semi-quantitative PCR was used for gene expression and TCR BV repertoire analyses. Results: We have previously shown that vaccination with the natural Melan-A peptide induced T cells with superior effector functions as compared to the analog peptide optimized for enhanced HLA binding. Here we found that natural peptide vaccination induced EM28+ T cells with frequent co-expression of both memory/homing-associated genes (CD27, IL7R, EOMES, CXCR3 and CCR5) and effector-related genes (IFNG, KLRD1, PRF1 and GZMB), comparable to protective EBV- and CMV-specific T cells. In contrast, memory/homing- and effectorassociated genes were less frequently co-expressed after vaccination with the analog peptide. Conclusions: These findings reveal a previously unknown level of gene expression diversity among vaccine- and virus-specific T cells with the simultaneous co-expression of multiple memory/homing- and effector- related genes by the same cell. Such broad functional gene expression signatures within antigen-specific T cells may be critical for mounting efficient responses to pathogens or tumors. In summary, direct ex vivo high-resolution molecular characterization of individual T cells provides key insights into the processes shaping the functional properties of tumor- and virus-specific T cells.

Mobile or fixed bearing for total knee arthroplasty? Ambulatory gait analysis results

Background: Mobile-bearing knee replacements have some theoretical advantages over fixed-bearing devices. However, very few randomized controlled clinical trials have been published to date, and studies showed little clinical and subjective advantages for the mobile-bearing using traditional systems of scoring. The choice of the ideal outcome measure to assess total joint replacement remains a complex issue. However, gait analysis provides objective and quantifying evidences of treatment evaluation. Significant methodological advances are currently made in gait analysis laboratories and ambulatory gait devices are now available. The goal of this study was to provide gait parameters as a new objective method to assess total knee arthroplasty outcome between patients with fixed- and mobile-bearing, using an ambulatory device with minimal sensor configuration. This randomized controlled double-blind study included to date 14 patients: the gait signatures of four patients with mobile-bearing were compared to the gait signatures of nine patients with fixed-bearing pre-operatively and post-operatively at 6 weeks, 3 months and 6 months. Each participant was asked to perform two walking trials of 30m long at his/her preferred speed and to complete a EQ-5D questionnaire, a WOMAC and Knee Society Score (KSS). Lower limbs rotations were measured by four miniature angular rate sensors mounted respectively, on each shank and thigh. A new method for a portable system for gait analysis has been developed with very encouraging results regarding the objective outcome of total knee arthroplasty using mobile- and fixed-bearings.

Lymphodepletion by short-term chemotherapy does not alter the highly stable and persistent EBV specific CD8 T cell repertoire

Protective T cell responses againstpersistent viruses like Epstein-Barrvirus in healthy individuals are characterizedby a remarkable stability ofthe T cell receptor (TCR) clonotypicrepertoire, with highly preservedclonotype selection and persistenceover time. Here, we extended recentwork to the study of EBV-specificCD8 T cell responses in melanomapatients treated by short-term chemotherapyfor transient lymphodepletion,followed by adoptive cell transfer(ACT) and immune reconstitutionfor cancer therapy. After this treatment,we observed increased proportionsof virus-specific T cells in 3/5patients, accompanied by a more differentiatedphenotype (EMRA/CD28neg), compared to specific cells ofhealthy individuals. Yet, similarly tohealthy donors, clonotype selectionand composition of virus-specific Tcells varied along the pathway of celldifferentiation, with some clonotypesthat were selected with late differentiation,while others were not. Aftertreatment, we did not observe noveldominant clonotypes, likely related toabsence of EBV reactivation measuredas viral load levels by quantitativePCR in PBMCs and antibody levelsin plasma samples. Furthermore,public TCR BV signatures were frequentlyfound within T cell clonotypesthat dominated the repertoiresof patients, in line with those observedin healthy individuals. Ourfindings indicate that even in situationswhere the immune system isstrongly challenged such as followinglymphodepletion and homeostatic repopulation,cytotoxic T cells specificfor EBV remain strikingly stable interms of clonotype selection and com-position along T cell differentiation.We are currently characterizing theclonotype selection and gene expressionprofiles of single EBV-specificCD8 T lymphocytes sorted ex-vivo inone patient who underwent two cyclesof lymphodepletion with escaladingdoses of chemotherapy overone-year interval. Observations madefrom this setting will provide additionalinsight into the degree of stabilityof virus specific T cells, and changesin the expression levels of genesimportant for cytolytic function andlong-term survival of T cells. Thiswork is supported by the Swiss NationalCenter of Competence in Research(NCCR) Molecular Oncology,and the Swiss National Science Foundation.

Rhinovirus Genome Variation during Chronic Upper and Lower Respiratory Tract Infections.

Routine screening of lung transplant recipients and hospital patients for respiratory virus infections allowed to identify human rhinovirus (HRV) in the upper and lower respiratory tracts, including immunocompromised hosts chronically infected with the same strain over weeks or months. Phylogenetic analysis of 144 HRV-positive samples showed no apparent correlation between a given viral genotype or species and their ability to invade the lower respiratory tract or lead to protracted infection. By contrast, protracted infections were found almost exclusively in immunocompromised patients, thus suggesting that host factors rather than the virus genotype modulate disease outcome, in particular the immune response. Complete genome sequencing of five chronic cases to study rhinovirus genome adaptation showed that the calculated mutation frequency was in the range observed during acute human infections. Analysis of mutation hot spot regions between specimens collected at different times or in different body sites revealed that non-synonymous changes were mostly concentrated in the viral capsid genes VP1, VP2 and VP3, independent of the HRV type. In an immunosuppressed lung transplant recipient infected with the same HRV strain for more than two years, both classical and ultra-deep sequencing of samples collected at different time points in the upper and lower respiratory tracts showed that these virus populations were phylogenetically indistinguishable over the course of infection, except for the last month. Specific signatures were found in the last two lower respiratory tract populations, including changes in the 5'UTR polypyrimidine tract and the VP2 immunogenic site 2. These results highlight for the first time the ability of a given rhinovirus to evolve in the course of a natural infection in immunocompromised patients and complement data obtained from previous experimental inoculation studies in immunocompetent volunteers.

The evolutionary history of the CD209 (DC-SIGN) family in humans and non-human primates

The CD209 gene family that encodes C-type lectins in primates includes CD209 (DC-SIGN), CD209L (L-SIGN) and CD209L2. Understanding the evolution of these genes can help understand the duplication events generating this family, the process leading to the repeated neck region and identify protein domains under selective pressure. We compiled sequences from 14 primates representing 40 million years of evolution and from three non-primate mammal species. Phylogenetic analyses used Bayesian inference, and nucleotide substitutional patterns were assessed by codon-based maximum likelihood. Analyses suggest that CD209 genes emerged from a first duplication event in the common ancestor of anthropoids, yielding CD209L2 and an ancestral CD209 gene, which, in turn, duplicated in the common Old World primate ancestor, giving rise to CD209L and CD209. K(A)/K(S) values averaged over the entire tree were 0.43 (CD209), 0.52 (CD209L) and 0.35 (CD209L2), consistent with overall signatures of purifying selection. We also assessed the Toll-like receptor (TLR) gene family, which shares with CD209 genes a common profile of evolutionary constraint. The general feature of purifying selection of CD209 genes, despite an apparent redundancy (gene absence and gene loss), may reflect the need to faithfully recognize a multiplicity of pathogen motifs, commensals and a number of self-antigens

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.