Nd-, O-, and H-isotopic evidence for complex, closed-system fluid evolution of the peralkaline Ilimaussaq intrusion, South Greenland

Relatively homogeneous oxygen isotope compositions of amphibole, clinopyroxene, and olivine separates (+5.2 to +5.7parts per thousand relative to VSMOW) and neodymium isotope compositions (epsilon(Nd(T)) = -0.9 to -1.8 for primary magmatic minerals and epsilon(Nd(T)) = -0.1 and -0.5 for mineral separates from late-stage pegmatites and hydrothermal veins) from the alkaline to agpaitic llimaussaq intrusion, South Greenland, indicate a closed system evolution of this igneous complex and support a mantle derivation of the magma. In contrast to the homogeneous oxygen and neodymium isotopic data, deltaD values for hand-picked amphibole separates vary between -92 and -232parts per thousand and are among the most deuterium-depleted values known from igneous amphiboles. The calculated fluid phase coexisting with these amphiboles has a homogeneous oxygen isotopic composition within the normal range of magmatic waters, but extremely heterogeneous and low D/H ratios, implying a decoupling of the oxygen- and hydrogen isotope systems. Of the several possibilities that can account for such unusually low deltaD values in amphiboles (e.g., late-stage hydrothermal exchange with meteoric water, extensive magmatic degassing, contamination with organic matter, and/or effects of Fe-content and pressure on amphibole-water fractionation) the most likely explanation for the range in deltaD values is that the amphiboles have been influenced by secondary interaction and reequilibration with D-depleted fluids obtained through late-magmatic oxidation of internally generated CH(4) and/or H(2). This interpretation is consistent with the known occurrence of abundant magmatic CH(4) in the Ilimaussaq rocks and with previous studies on the isotopic compositions of the rocks and fluids. Copyright (C) 2004 Elsevier Ltd.

A species delimitation approach in the Trochulus sericeus/hispidus complex reveals two cryptic species within a sharp contact zone.

BACKGROUND: Mitochondrial DNA sequencing increasingly results in the recognition of genetically divergent, but morphologically cryptic lineages. Species delimitation approaches that rely on multiple lines of evidence in areas of co-occurrence are particularly powerful to infer their specific status. We investigated the species boundaries of two cryptic lineages of the land snail genus Trochulus in a contact zone, using mitochondrial and nuclear DNA marker as well as shell morphometrics. RESULTS: Both mitochondrial lineages have a distinct geographical distribution with a small zone of co-occurrence. In the same area, we detected two nuclear genotype clusters, each being highly significantly associated to one mitochondrial lineage. This association however had exceptions: a small number of individuals in the contact zone showed intermediate genotypes (4%) or cytonuclear disequilibrium (12%). Both mitochondrial lineage and nuclear cluster were statistically significant predictors for the shell shape indicating morphological divergence. Nevertheless, the lineage morphospaces largely overlapped (low posterior classification success rate of 69% and 78%, respectively): the two lineages are truly cryptic. CONCLUSION: The integrative approach using multiple lines of evidence supported the hypothesis that the investigated Trochulus lineages are reproductively isolated species. In the small contact area, however, the lineages hybridise to a limited extent. This detection of a hybrid zone adds an instance to the rare reported cases of hybridisation in land snails.

PPARgamma but not PPARalpha ligands are potent repressors of major histocompatibility complex class II induction in atheroma-associated cells.

Peroxisome proliferator-activated receptors (PPARs) are essential in glucose and lipid metabolism and are implicated in metabolic disorders predisposing to atherosclerosis, such as diabetes and dyslipidemia. Conversely, antidiabetic glitazones and hypolipidemic fibrate drugs, known as PPARgamma and PPARalpha ligands, respectively, reduce the process of atherosclerotic lesion formation, which involves chronic immunoinflammatory processes. Major histocompatibility complex class II (MHC-II) molecules, expressed on the surface of specialized cells, are directly involved in the activation of T lymphocytes and in the control of the immune response. Interestingly, expression of MHC-II has recently been observed in atherosclerotic plaques, and it can be induced by the proinflammatory cytokine interferon-gamma (IFN-gamma) in vascular cells. To explore a possible role for PPAR ligands in the regulation of the immune response, we investigated whether PPAR activation affects MHC-II expression in atheroma-associated cells. In the present study, we demonstrate that PPARgamma but not PPARalpha ligands act as inhibitors of IFN-gamma-induced MHC-II expression and thus as repressors of MHC-II-mediated T-cell activation. All different types of PPARgamma ligands tested inhibit MHC-II. This effect of PPARgamma ligands is due to a specific inhibition of promoter IV of CIITA and does not concern constitutive expression of MHC-II. Thus, the beneficial effects of antidiabetic PPARgamma activators on atherosclerotic plaque development may be partly explained by their repression of MHC-II expression and subsequent inhibition of T-lymphocyte activation.

Modeling of the TCR-MHC-peptide complex.

The methodology for generating a homology model of the T1 TCR-PbCS-K(d) class I major histocompatibility complex (MHC) class I complex is presented. The resulting model provides a qualitative explanation of the effect of over 50 different mutations in the region of the complementarity determining region (CDR) loops of the T cell receptor (TCR), the peptide and the MHC's alpha(1)/alpha(2) helices. The peptide is modified by an azido benzoic acid photoreactive group, which is part of the epitope recognized by the TCR. The construction of the model makes use of closely related homologs (the A6 TCR-Tax-HLA A2 complex, the 2C TCR, the 14.3.d TCR Vbeta chain, the 1934.4 TCR Valpha chain, and the H-2 K(b)-ovalbumine peptide), ab initio sampling of CDR loops conformations and experimental data to select from the set of possibilities. The model shows a complex arrangement of the CDR3alpha, CDR1beta, CDR2beta and CDR3beta loops that leads to the highly specific recognition of the photoreactive group. The protocol can be applied systematically to a series of related sequences, permitting the analysis at the structural level of the large TCR repertoire specific for a given peptide-MHC complex.

Hybridization and Population Structure of the Culex Pipiens Complex in the Islands of Macaronesia

The Culex pipiens complex includes two widespread mosquito vector species, Cx. pipiens and Cx. quinquefasciatus. The distribution of these species varies in latitude, with the former being present in temperate regions and the latter in tropical and subtropical regions. However, their distribution range overlaps in certain areas and interspecific hybridization has been documented. Genetic introgression between these species may have epidemiological repercussions for West Nile virus (WNV) transmission. Bayesian clustering analysis based on multilocus genotypes of 12 microsatellites was used to determine levels of hybridization between these two species in Macaronesian islands, the only contact zone described in West Africa. The distribution of the two species reflects both the islands’ biogeography and historical aspects of human colonization. Madeira Island displayed a homogenous population of Cx. pipiens, whereas Cape Verde showed a more intriguing scenario with extensive hybridization. In the islands of Brava and Santiago, only Cx. quinquefasciatus was found, while in Fogo and Maio high hybrid rates (~40%) between the two species were detected. Within the admixed populations, second-generation hybrids (~50%) were identified suggesting a lack of isolation mechanisms. The observed levels of hybridization may locally potentiate the transmission to humans of zoonotic arboviruses such as WNV.

Identification of naturally processed hepatitis C virus-derived major histocompatibility complex class I ligands.

Fine mapping of human cytotoxic T lymphocyte (CTL) responses against hepatitis C virus (HCV) is based on external loading of target cells with synthetic peptides which are either derived from prediction algorithms or from overlapping peptide libraries. These strategies do not address putative host and viral mechanisms which may alter processing as well as presentation of CTL epitopes. Therefore, the aim of this proof-of-concept study was to identify naturally processed HCV-derived major histocompatibility complex (MHC) class I ligands. To this end, continuous human cell lines were engineered to inducibly express HCV proteins and to constitutively express high levels of functional HLA-A2. These cell lines were recognized in an HLA-A2-restricted manner by HCV-specific CTLs. Ligands eluted from HLA-A2 molecules isolated from large-scale cultures of these cell lines were separated by high performance liquid chromatography and further analyzed by electrospray ionization quadrupole time of flight mass spectrometry (MS)/tandem MS. These analyses allowed the identification of two HLA-A2-restricted epitopes derived from HCV nonstructural proteins (NS) 3 and 5B (NS3₁₄₀₆₋₁₄₁₅ and NS5B₂₅₉₄₋₂₆₀₂). In conclusion, we describe a general strategy that may be useful to investigate HCV pathogenesis and may contribute to the development of preventive and therapeutic vaccines in the future.

Purification and ligand binding of a soluble class I major histocompatibility complex molecule consisting of the first three domains of H-2Kd fused to beta 2-microglobulin expressed in the baculovirus-insect cell system.

A recombinant baculovirus encoding a single-chain murine major histocompatibility complex class I molecule in which the first three domains of H-2Kd are fused to beta 2-microglobulin (beta 2-m) via a 15-amino acid linker has been isolated and used to infect lepidopteran cells. A soluble, 391-amino acid single-chain H-2Kd (SC-Kd) molecule of 48 kDa was synthesized and glycosylated in insect cells and could be purified in the absence of detergents by affinity chromatography using the anti-H-2Kd monoclonal antibody SF1.1.1.1. We tested the ability of SC-Kd to bind antigenic peptides using a direct binding assay based on photoaffinity labeling. The photoreactive derivative was prepared from the H-2Kd-restricted Plasmodium berghei circumsporozoite protein (P.b. CS) peptide 253-260 (YIPSAEKI), a probe that we had previously shown to be unable to bind to the H-2Kd heavy chain in infected cells in the absence of co-expressed beta 2-microglobulin. SC-Kd expressed in insect cells did not require additional mouse beta 2-m to bind the photoprobe, indicating that the covalently attached beta 2-m could substitute for the free molecule. Similarly, binding of the P.b. CS photoaffinity probe to the purified SC-Kd molecule was unaffected by the addition of exogenous beta 2-m. This is in contrast to H-2KdQ10, a soluble H-2Kd molecule in which beta 2-m is noncovalently bound to the soluble heavy chain, whose ability to bind the photoaffinity probe is greatly enhanced in the presence of an excess of exogenous beta 2-m. The binding of the probe to SC-Kd was allele-specific, since labeling was selectively inhibited only by antigenic peptides known to be presented by the H-2Kd molecule.

GENETIC AND BIOCHEMICAL ANALYSIS OF THE TESTIS-SPECIFIC ZINC FINGER PROTEIN CTCFL/BORIS

Abstract en FrançaisCTCFL a d'abord été identifié comme un paralogue de la protéine ubiquitaire CTCF en raison de sa forte homologie entre leurs onze « zinc fingers », un domaine de liaison à l'ADN. Parmi ses nombreux rôles, la liaison des zinc fingers de CTCF à la région de contrôle de l'empreinte (ICR) maternelle non-méthylée Igf2/H19, contrôle l'expression empreinte (monoallélique) de H19 et IGF2 dans les cellules somatiques. La méthylation de l'ICR Igf2/H19 paternelle est nécessaire à l'expression empreinte de ces deux gènes. Bien que le mécanisme par lequel l'ICR est méthylé soit mal compris, il est connu que l'établissement de la méthylation se produit pendant le développement des cellules germinales mâles et que les ADN méthyltransférases de novo DNMT3A et DNMT3L sont essentiels. Par conséquent, CTCFL fournit un bon candidat pour un rôle dans la méthylation de l'ICR paternelle Igf2/H19 en raison de son expression restreinte à certains types de cellules où la méthylation de l'ICR a lieu (spermatogonies et spermatocytes) ainsi qu'en raison sa capacité à lier les ICR lgf2/HÎ9 dans ces cellules. Les premiers travaux expérimentaux de cette thèse portent sur le rôle possible des mutations de CTCFL chez les patients atteints du syndrome de Silver-Russell (SRS), où une diminution de la méthylation de l'ICR IGF2/H19 a été observée chez 60% d'entre eux. Admettant que CTCFL pourrait être muté chez ces patients, j'ai examiné les mutations possibles de CTCFL chez 35 d'entre eux par séquençage de l'ADN et analyse du nombre de copies d'exons. N'ayant trouvé aucune mutation chez ces patients, cela suggère que les mutations de CTCFL ne sont pas associées au SRS. Les travaux expérimentaux suivants ont porté sur les modifications post-traductionnelles de CTCFL par la protéine SU MO « small ubiquitin-like modifier » (SUMO). La modification de protéines par SU MO change les interactions avec d'autres molécules (ADN ou protéines). Comme CTCFL régule sans doute l'expression d'un certain nombre de gènes dans le cancer et que plusieurs facteurs de transcription sont régulés par SUMO, j'ai mené des expériences pour déterminer si CTCFL est sumoylé. En effet, j'ai observé que CTCFL est sumoylated in vitro et in vivo et j'ai déterminé les deux résidus d'attachement de SUMO aux lysines 181 et 645. Utilisant les mutants de CTCFL K181R et K645R ne pouvant pas être sumoylated, j'ai évalué les conséquences fonctionnelles de la modification par SUMO. Je n'ai trouvé aucun changement significatif dans la localisation subcellulaire, la demi-vie ou la liaison à l'ADN, mais ai constaté que la sumoylation module à la fois {'activation CTCFL-dépendante et la répression de l'expression génique. Il s'agit de la première modification post-traductionnelle décrite pour CTCFL et les conséquences possibles de cette modification sont discutées pour le cancer et les testicules normaux. Avec cette thèse, j'espère avoir ajouté des résultats importants à l'étude de CTCFL et donné quelques idées pour de futures recherches.AbstractJeremiah Bernier-Latmani, Institute of Pathology, University of Lausanne, CHUVCTCFL was first identified as a paralog of the ubiquitous protein CTCF because of high homology between their respective eleven zinc fingers, a DNA binding domain. Among its many roles, CTCF zinc finger-mediated binding to the unmethylated maternal Igf2/H19 imprinting control region (ICR), controls the imprinted (monoallelic) expression of Igf2 and H19 in somatic cells. Methylation of the paternal Igf2/H19 ICR is necessary for the imprinted expression of the two genes. Although the mechanism by which the ICR is methylated is incompletely understood, it is known that establishment of methylation occurs during male germ cell development and the de novo DNA methyltransferases DNMT3A and DNMT3L are essential. Therefore, CTCFL provided a good candidate to play a role in methylation of the paternal Igf2/H19 ICR because of its restricted expression to cell types where ICR methylation takes place (spermatogonia and spermatocytes) and its ability to bind the Igf2/H19 ICR in these cells. The first experimental work of this thesis investigated the possible role of CTCFL mutations in Silver-Russell syndrome (SRS) patients, where it has been observed that 60% of the patients have reduced methylation of the IGF2/HÎ9 ICR. Reasoning that CTCFL could be mutated in these patients, I screened 35 patients for mutations in CTCFL by DNA sequencing and exon copy number analysis, I did not find any mutations in these patients suggesting that mutations of CTCFL are not associated with SRS. The next experimental work of my thesis focused on posttranslational modification of CTCFL by small ubiquitin-like modifier (SUMO) protein. SUMO modification of proteins changes the interactions with other molecules (DNA or protein). As CTCFL arguably regulates the expression of a number of genes in cancer and many transcription factors are regulated by SUMO, I conducted experiments to assess whether CTCFL is sumoylated. I found that CTCFL is sumoylated in vitro and in vivo and determined the two residues of SUMO attachment to be lysines 181 and 645. Using K181R, K645R mutated CTCFL- which cannot be detected to be sumoylated-1 assessed the functional consequences of SUMO modification. I found no significant changes in subcellular localization, half-life or DNA binding, but found that sumoylation modulates both CTCFL-dependent activation and repression of gene expression. This is the first posttranslational modification described for CTCFL and possible consequences of this modification are discussed in both cancer and normal testis. With this thesis, I hope I have added important findings to the study of CTCFL and provide some ideas for future research.

Current approaches and challenges for the metabolite profiling of complex natural extracts.

Metabolite profiling is critical in many aspects of the life sciences, particularly natural product research. Obtaining precise information on the chemical composition of complex natural extracts (metabolomes) that are primarily obtained from plants or microorganisms is a challenging task that requires sophisticated, advanced analytical methods. In this respect, significant advances in hyphenated chromatographic techniques (LC-MS, GC-MS and LC-NMR in particular), as well as data mining and processing methods, have occurred over the last decade. Together, these tools, in combination with bioassay profiling methods, serve an important role in metabolomics for the purposes of both peak annotation and dereplication in natural product research. In this review, a survey of the techniques that are used for generic and comprehensive profiling of secondary metabolites in natural extracts is provided. The various approaches (chromatographic methods: LC-MS, GC-MS, and LC-NMR and direct spectroscopic methods: NMR and DIMS) are discussed with respect to their resolution and sensitivity for extract profiling. In addition the structural information that can be generated through these techniques or in combination, is compared in relation to the identification of metabolites in complex mixtures. Analytical strategies with applications to natural extracts and novel methods that have strong potential, regardless of how often they are used, are discussed with respect to their potential applications and future trends.

ZNRD1 (zinc ribbon domain-containing 1) is a host cellular factor that influences HIV-1 replication and disease progression.

BACKGROUND: Human immunodeficiency virus (HIV) takes advantage of multiple host proteins to support its own replication. The gene ZNRD1 (zinc ribbon domain-containing 1) has been identified as encoding a potential host factor that influenced disease progression in HIV-positive individuals in a genomewide association study and also significantly affected HIV replication in a large-scale in vitro short interfering RNA (siRNA) screen. Genes and polymorphisms identified by large-scale analysis need to be followed up by means of functional assays and resequencing efforts to more precisely map causal genes. METHODS: Genotyping and ZNRD1 gene resequencing for 208 HIV-positive subjects (119 who experienced long-term nonprogression [LTNP] and 89 who experienced normal disease progression) was done by either TaqMan genotyping assays or direct sequencing. Genetic association analysis was performed with the SNPassoc package and Haploview software. siRNA and short hairpin RNA (shRNA) specifically targeting ZNRD1 were used to transiently or stably down-regulate ZNRD1 expression in both lymphoid and nonlymphoid cells. Cells were infected with X4 and R5 HIV strains, and efficiency of infection was assessed by reporter gene assay or p24 assay. RESULTS: Genetic association analysis found a strong statistically significant correlation with the LTNP phenotype (single-nucleotide polymorphism rs1048412; [Formula: see text]), independently of HLA-A10 influence. siRNA-based functional analysis showed that ZNRD1 down-regulation by siRNA or shRNA impaired HIV-1 replication at the transcription level in both lymphoid and nonlymphoid cells. CONCLUSION: Genetic association analysis unequivocally identified ZNRD1 as an independent marker of LTNP to AIDS. Moreover, in vitro experiments pointed to viral transcription as the inhibited step. Thus, our data strongly suggest that ZNRD1 is a host cellular factor that influences HIV-1 replication and disease progression in HIV-positive individuals.

Increased mobility of major histocompatibility complex I-peptide complexes decreases the sensitivity of antigen recognition.

CD8(+) cytotoxic T lymphocytes (CTL) can recognize and kill target cells expressing only a few cognate major histocompatibility complex (MHC) I-peptide complexes. This high sensitivity requires efficient scanning of a vast number of highly diverse MHC I-peptide complexes by the T cell receptor in the contact site of transient conjugates formed mainly by nonspecific interactions of ICAM-1 and LFA-1. Tracking of single H-2K(d) molecules loaded with fluorescent peptides on target cells and nascent conjugates with CTL showed dynamic transitions between states of free diffusion and immobility. The immobilizations were explained by association of MHC I-peptide complexes with ICAM-1 and strongly increased their local concentration in cell adhesion sites and hence their scanning by T cell receptor. In nascent immunological synapses cognate complexes became immobile, whereas noncognate ones diffused out again. Interfering with this mobility modulation-based concentration and sorting of MHC I-peptide complexes strongly impaired the sensitivity of antigen recognition by CTL, demonstrating that it constitutes a new basic aspect of antigen presentation by MHC I molecules.

The magmatic to hydrothermal evolution of the intrusive Mont Saint-Hilaire Complex: Insights into the late-stage evolution of peralkaline rocks

The Cretaceous Mont Saint-Hilaire complex (Quebec, Canada) comprises three major rock units that were emplaced in the following sequence: (I) gabbros; (II) diorites; (III) diverse partly agpaitic foid syenites. The major element compositions of the rock-forming minerals, age-corrected Nd and oxygen isotope data for mineral separates and trace element data of Fe-Mg silicates from the various lithologies imply a common source for all units. The distribution of the rare earth elements in clinopyroxene from the gabbros indicates an ocean island basalt type composition for the parental magma. Gabbros record temperatures of 1200 to 800 degrees C, variable silica activities between 0 center dot 7 and 0 center dot 3, and f(O2) values between -0 center dot 5 and +0 center dot 7 (log delta FMQ, where FMQ is fayalite-magnetite-quartz). The diorites crystallized under uniform a(SiO2) (a(SiO2) = 0 center dot 4-0 center dot 5) and more reduced f(O2) conditions (log delta FMQ similar to-1) between similar to 1100 and similar to 800 degrees C. Phase equilibria in various foid syenites indicate that silica activities decrease from 0 center dot 6-0 center dot 3 at similar to 1000 degrees C to < 0 center dot 3 at similar to 550 degrees C. Release of an aqueous fluid during the transition to the hydrothermal stage caused a(SiO2) to drop to very low values, which results from reduced SiO(2) solubilities in aqueous fluids compared with silicate melts. During the hydrothermal stage, high water activities stabilized zeolite-group minerals. Fluid inclusions record a complex post-magmatic history, which includes trapping of an aqueous fluid that unmixed from the restitic foid syenitic magma. Cogenetic aqueous and carbonic fluid inclusions reflect heterogeneous trapping of coexisting immiscible external fluids in the latest evolutionary stage. The O and C isotope characteristics of fluid-inclusion hosted CO(2) and late-stage carbonates imply that the surrounding limestones were the source of the external fluids. The mineral-rich syenitic rocks at Mont Saint-Hilaire evolved as follows: first, alkalis, high field strength and large ion lithophile elements were pre-enriched in the (late) magmatic and subsequent hydrothermal stages; second, percolation of external fluids in equilibrium with the carbonate host-rocks and mixing processes with internal fluids as well as fluid-rock interaction governed dissolution of pre-existing minerals, element transport and precipitation of mineral assemblages determined by locally variable parameters. It is this hydrothermal interplay between internal and external fluids that is responsible for the mineral wealth found at Mont Saint-Hilaire.

Direct MR arthrography of the shoulder under axial traction: Feasibility study to evaluate the superior labrum-biceps tendon complex and articular cartilage.

PURPOSE: To assess the value of adding axial traction to direct MR arthrography of the shoulder, in terms of subacromial and glenohumeral joint space widths, and coverage of the superior labrum-biceps tendon complex and articular cartilage by contrast material. MATERIALS AND METHODS: Twenty-one patients investigated by direct MR arthrography of the shoulder were prospectively included. Studies were performed with a 3 Tesla (T) unit and included a three-dimensional isotropic fat-suppressed T1-weighted gradient-recalled echo sequence, without and with axial traction (4 kg). Two radiologists independently measured the width of the subacromial, superior, and inferior glenohumeral joint spaces. They subsequently rated the amount of contrast material around the superior labrum-biceps tendon complex and between glenohumeral cartilage surfaces, using a three-point scale: 0 = no, 1 = partial, 2 = full. RESULTS: Under traction, the subacromial (Δ = 2.0 mm, P = 0.0003), superior (Δ = 0.7 mm, P = 0.0001) and inferior (Δ = 1.4 mm, P = 0.0006) glenohumeral joint space widths were all significantly increased, and both readers noted significantly more contrast material around the superior labrum-biceps tendon complex (P = 0.014), and between the superior (P = 0.001) and inferior (P = 0.025) glenohumeral cartilage surfaces. CONCLUSION: Direct MR arthrography of the shoulder under axial traction increases subacromial and glenohumeral joint space widths, and prompts better coverage of the superior labrum-biceps tendon complex and articular cartilage by contrast material. J. Magn. Reson. Imaging 2013;37:1228-1233. © 2012 Wiley Periodicals, Inc.