Tracing of the Rhône River, wastewater, and mixing within Lake Geneva : stable isotope compositions of water and dissolved inorganic carbon

This study presents an evaluation of the stable isotopic composition of water (hydrogen and oxygen) and dissolved inorganic carbon (DIC) of Lake Geneva, a deep, peri-alpine lake situated at the border between Switzerland and France. The research goal is to apply vertical and seasonal variations of the isotope compositions to evaluate mixing processes of pollutants, nutrients and oxygen. Depth profiles were sampled at different locations throughout Lake Geneva on a monthly and seasonal basis over the course of three years (2009-2011). The results of the oxygen isotopic composition indicate a Rhône River interflow, which can be traced for about 55 km throughout the lake during summer. The Rhône River interflow is 7 to 15 m thick and the molar fraction of Rhône water is estimated to amount up to 37 %. Calculated density of the water and measured isotopic compositions demonstrate that the interflow depth changes in conjunction with the density gradient in the water column during fall. Partial pressure of CO2 indicates that the epilimnion is taking up CO2 from the atmosphere between spring and fall. The epilimnion is most enriched in 13CDIC in September and a progressive depletion of 13CDIC can be observed in the metalimnion from spring to late fall. This stratification is dependent on the local density stratification and the results demonstrate that parameters, which are indicating photosynthesis, are not necessarily linked to δ13CDIC values. In addition, the amount of primary production shows a strong discrepancy between summer 2009 and 2010, but δ13CDIC values of the epilimnion and metalimnion do not indicate variations. In the hypolimnion of the deep lake δ13CDIC values are constant and the progressive depletion allows tracing remineralization processes. The combination of stable carbon and oxygen isotopic compositions allows furthermore tracing Rhône River water fractions, as well as wastewater, stormwater and anthropogenic induced carbon in the water column of the shallow Bay of Vidy. In combination with the results of measured micropollutants, the study underlines that concentrations of certain substances may be related to the Rhône River interflow and/or remineralization of particulate organic carbon. Water quality monitoring and research should therefore be extended to the metalimnion as well as sediment water interface.

Separation mechanisms in nanofiltration and retention changes of organic compounds

Orgaanisten yhdisteiden negatiivinen retentio nanosuodatuksessa on ilmiö, jota eiole kovin paljon tutkittu. Negatiivisen retentioon vaikuttavat syyt tai tekijäteivät ole kovin hyvin tiedossa. Erotusmenetelmänä negatiivinen retentio voi olla käyttökelpoinen tietyissä sovelluksissa. Työn kirjallisuusosa käsittelee nanosuodatuksen erotusmekanismeja ja retentioon vaikuttavia tekijöitä. Myös joitakin malleja on esitetty. Nanosuodatus on monimutkainen prosessi, josta ei voida löytää vain yhtä erotusmekanismia tai retentioon vaikuttavaa tekijää. Prosessit ovat kokonaisuuksia, joissa erottumiseen vaikuttavat syöttöliuoksen, erotettavan komponentin ja kalvon ominaisuudet, ja niiden väliset vuorovaikutukset. Työn kokeellisessa osassa koottiin mahdollisimman paljon esimerkkejä, joissa monosakkaridien negatiivinen retentio ilmenee. Muita orgaanisia ja epäorgaanisia yhdisteitä käytettiin 'häiriöyhdisteinä' syöttöliuoksessa monosakkaridien kanssa. Kokeet suoritettiin kahdella laboratoriomittakaavan suodatuslaitteella käyttäen kahta kaupallista nanosuodatuskalvoa. Negatiivinen retentio ilmeni useissa tapauksissa. Permeaattivuon ja 'häiriöyhdisteiden' pitoisuuksien havaittiin vaikuttavan voimakkaasti negatiivisen retention ilmenemiseen.

Effect of Tocopherol Extract, Staphylococcus carnosus Culture, and Celery Concentrate Addition on Quality Parameters of Organic and Conventional Dry-Cured Sausages

The effects of the addition to sausage mix of tocopherols (200 mg/kg), a conventional starter culture with or without Staphylococcus carnosus, celery concentrate (CP) (0.23% and 0.46%), and two doses of nitrate (70 and 140 mg/kg expressed as NaNO(3)) on residual nitrate and nitrite amounts, instrumental CIE Lab color, tocol content, oxidative stability, and overall acceptability were studied in fermented dry-cured sausages after ripening and after storage. Nitrate doses were provided by nitrate-rich CP or a chemical grade source. The lower dose complies with the EU requirements governing the maximum for ingoing amounts in organic meat products. Tocopherol addition protected against oxidation, whereas the nitrate dose, nitrate source, or starter culture had little influence on secondary oxidation values. The residual nitrate and nitrite amounts found in the sausages with the lower nitrate dose were within EU-permitted limits for organic meat products and residual nitrate can be further reduced by the presence of the S. carnosus culture. Color measurements were not affected by the CP dose. Product consumer acceptability was not affected negatively by any of the factors studied. As the two nitrate sources behaved similarly for the parameters studied, CP is a useful alternative to chemical ingredients for organic dry-cured sausage production.

Organic geochemistry across the Permian-Triassic transition at the Idrijca Valley, Western Slovenia

Bulk and molecular stable C isotopic compositions and biomarker distributions provide evidence for a diverse community of algal and bacterial organisms in the sedimentary organic matter of a carbonate section throughout the Permian-Triassic (P/Tr) transition at the Idrijca Valley, Western Slovenia. The input of algae and bacteria in all the Upper Permian and Lower Scythian samples is represented by the predominance of C-15-C-22 n-alkanes, odd C-number alkylcyclohexanes, C-27 steranes and substantial contents Of C-21-C-30 acyclic isoprenoids. The occurrence of odd long-chain n-alkanes (C-22-C-30) and C29 steranes in all the samples indicate a contribution of continental material. The decrease of C-org and C-carb contents, increase of Rock-Eval oxygen indices, and C-13-enrichment of the kerogen suggest a decrease in anoxia of the uppermost Permian bottom water. The predominance of odd C-number alkylcycloalkanes, C-27 steranes, and C-17 n-alkanes with delta(13)C values similar to-30parts per thousand, and C-13-enrichment of the kerogens in the lowermost Scythian samples are evidence of greater algal productivity. This increased productivity was probably sustained by a high nutrient availability and changes of dissolved CO2 speciation associated to the earliest Triassic transgression. A decrease Of Corg content in the uppermost Scythian samples, associated to a C-13-depletetion in the carbonates (up to 4parts per thousand) and individual n-alkanes (up to 3.4parts per thousand) compared to the Upper Permian samples, indicate lowering of the primary productivity (algae, cyanobacteria) and/or higher degradation of the organic matter. (C) 2003 Elsevier Ltd. All rights reserved.

Are R&D collaborative agreements persistent at the firm level? Empirical evidence for the Spanish case

We provide evidence on the dynamics in firms’ R&D cooperation behaviour. Our main objective is to analyse if R&D collaborative agreements are persistent at the firm level, and in such a case, to study what are the main drivers of this phenomenon. R&D cooperation activities at the firm level can be persistent due to true state dependence, this implying that cooperating in a given period enhances the probability of doing it in the subsequent period and it can also be a consequence of firms’ individual heterogeneity, so that certain firms have certain characteristics that make them more likely to carry out technological alliances.

Are R&D collaborative agreements persistent at the firm level? Empirical evidence for the Spanish case

We provide evidence on the dynamics in firms’ R&D cooperation behaviour. Our main objective is to analyse if R&D collaborative agreements are persistent at the firm level, and in such a case, to study what are the main drivers of this phenomenon. R&D cooperation activities at the firm level can be persistent due to true state dependence, this implying that cooperating in a given period enhances the probability of doing it in the subsequent period and it can also be a consequence of firms’ individual heterogeneity, so that certain firms have certain characteristics that make them more likely to carry out technological alliances.

Strategies and tools for preventing neurotoxicity: to test, to predict and how to do it

A change in paradigm is needed in the prevention of toxic effects on the nervous system, moving from its present reliance solely on data from animal testing to a prediction model mostly based on in vitro toxicity testing and in silico modeling. According to the report published by the National Research Council (NRC) of the US National Academies of Science, high-throughput in vitro tests will provide evidence for alterations in"toxicity pathways" as the best possible method of large scale toxicity prediction. The challenges to implement this proposal are enormous, and provide much room for debate. While many efforts address the technical aspects of implementing the vision, many questions around it need also to be addressed. Is the overall strategy the only one to be pursued? How can we move from current to future paradigms? Will we ever be able to reliably model for chronic and developmental neurotoxicity in vitro? This paper summarizes four presentations from a symposium held at the International Neurotoxicology Conference held in Xi"an, China, in June 2011. A. Li reviewed the current guidelines for neurotoxicity and developmental neurotoxicity testing, and discussed the major challenges existing to realize the NCR vision for toxicity testing. J. Llorens reviewed the biology of mammalian toxic avoidance in view of present knowledge on the physiology and molecular biology of the chemical senses, taste and smell. This background information supports the hypothesis that relating in vivo toxicity to chemical epitope descriptors that mimic the chemical encoding performed by the olfactory system may provide a way to the long term future of complete in silico toxicity prediction. S. Ceccatelli reviewed the implementation of rodent and human neural stem cells (NSCs) as models for in vitro toxicity testing that measures parameters such as cell proliferation, differentiation and migration. These appear to be sensitive endpoints that can identify substances with developmental neurotoxic potential. C. Sun ol reviewed the use of primary neuronal cultures in testing for neurotoxicity of environmental pollutants, including the study of the effects of persistent exposures and/or in differentiating cells, which allow recording of effects that can be extrapolated to human developmental neurotoxicity.

Persistent Candida albicans colonization and molecular mechanisms of azole resistance in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) patients.

Objectives: Patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED, APS-I) suffer from chronic candidosis caused mainly by Candida albicans, and repeated courses of azole antifungals have led to the development of resistance in the APECED patient population in Finland. The aim of our study was to address whether the patients are persistently colonized with the same or genetically closely related strains, whether epidemic strains are present and which molecular mechanisms account for azole resistance. Methods: Sets of C. albicans (n?=?19) isolates from nine APECED patients reported with decreased susceptibility to fluconazole isolated up to 9 years apart were included. The strains were typed by multilocus sequence typing. CDR1/2, MDR1 and ERG11 mRNA expression was analysed by northern blotting and Cdr1, Cdr2 and Mdr1 protein expression by western blotting, and TAC1 and ERG11 genes were sequenced. Results: All seven patients with multiple C. albicans isolates analysed were persistently colonized with the same or a genetically closely related strain for a mean of 5 years. All patients were colonized with different strains and no epidemic strains were found. The major molecular mechanisms behind the azole resistance were mutations in TAC1 contributing to overexpression of CDR1 and CDR2. Six new TAC1 mutations were found, one of which (N740S) is likely to be a gain-of-function mutation. Most isolates were found to have gained multiple TAC1 and ERG11 point mutations. Conclusions: Despite clinically successful treatment leading to relief of symptoms, colonization by C. albicans strains is persistent within APECED patients. Microevolution and point mutations occur within strains, leading to the development of azole-resistant isolates.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

A Monte Carlo approach to the inverse problem of diffuse pollution risk in agricultural catchments

The hydrological and biogeochemical processes that operate in catchments influence the ecological quality of freshwater systems through delivery of fine sediment, nutrients and organic matter. Most models that seek to characterise the delivery of diffuse pollutants from land to water are reductionist. The multitude of processes that are parameterised in such models to ensure generic applicability make them complex and difficult to test on available data. Here, we outline an alternative - data-driven - inverse approach. We apply SCIMAP, a parsimonious risk based model that has an explicit treatment of hydrological connectivity. we take a Bayesian approach to the inverse problem of determining the risk that must be assigned to different land uses in a catchment in order to explain the spatial patterns of measured in-stream nutrient concentrations. We apply the model to identify the key sources of nitrogen (N) and phosphorus (P) diffuse pollution risk in eleven UK catchments covering a range of landscapes. The model results show that: 1) some land use generates a consistently high or low risk of diffuse nutrient pollution; but 2) the risks associated with different land uses vary both between catchments and between nutrients; and 3) that the dominant sources of P and N risk in the catchment are often a function of the spatial configuration of land uses. Taken on a case-by-case basis, this type of inverse approach may be used to help prioritise the focus of interventions to reduce diffuse pollution risk for freshwater ecosystems. (C) 2012 Elsevier B.V. All rights reserved.

Immunology of viral disease, how to curb persistent infection

1. 1. Summaries 1.1. Preamble and extended abstract The present thesis dissertation addresses the question of antiviral immunity from the particular standpoint of the adaptive T cell-mediated immune response. The experimental work is presented in the form of three published articles (two experimental articles and one review article, see sections 4.1, 4.2 and 4.3 on pages 73, 81 and 91, respectively), describing advances both in our understanding of viral control by CD8 T lymphocytes, and in vaccine development against the Human Immunodeficiency Virus Type 1 (HIV-1). Because the articles focus on rather specialized areas of antiviral immunity, the article sections are preceded by a general introduction (section 3) on the immune system in general, and on four viruses that were addressed in the experimental work, namely HIV-1, Cytomegalovirus (CMV), Epstein Barr Virus (EBV) and Influenzavirus (Flu). This introduction section is aimed at providing a glimpse on viral molecular biology and immunity, to help the hypothetical non-expert reader proceeding into the experimental part. For this reason, each section is presented as individual entity and can be consulted separately. The four viruses described are of peculiar relevance to immunity because they induce an array of opposite host responses. Flu causes a self limiting disease after which the virus is eradicated. CMV and EBV cause pauci-symptomatic or asymptomatic diseases after which the viruses establish lifelong latency in the host cells, but are kept in check by immunity. Eventually, HIV-1 establishes both latency - by inserting its genome into the host cell chromosome - and proceeds in destroying the immune system in a poorly controlled fashion. Hence, understanding the fundamental differences between these kinds of viral host interactions might help develop new strategies to curb progressive diseases caused by viruses such as HIV-1. Publication #1: The first article (section 4.1, page 73) represents the main frame of my laboratory work. It analyses the ability of CD8 T lymphocytes recovered from viral-infected patients to secrete interferon γ (IFN-γ) alone or in conjunction with interleukin 2 (IL-2) when exposed in vitro to their cognate viral antigens. CD8 T cells are instrumental in controlling viral infection. They can identify infected cells by detecting viral antigens presented at the surface of the infected cells, and eliminate both the cell and its infecting virus by triggering apoptosis and/or lysis of the infected cell. Recognition of these antigens triggers the cognate CD8 cells to produce cytokines, including IFN-γ and IL-2, which in turn attract and activate other pro-inflammatory cells. IFN-γ triggers both intrinsic antiviral activity of the infected cells and distant activation of pro-inflammatory cells, which are important for the eradication of infection. IL-2 is essential for clonal expansion of the antigen (Ag)-specific CD8 T cell. Hence the existence of Ag-specific CD8 cells secreting both IFN-γand IL-2 should be beneficial for controlling infection. In this first work we determined the percentage of IFN-y/IL-2 double positive and single IFN-γsecreting CD8 T cells against antigens HIV-1, CMV, EBV and Flu in three groups of subjects: (i) HIV-1 infected patients progressing to disease (progressors), (ii) HIV-1-infected subjects not progressing to disease (long-term non progressors or LTNP), and (iii) HIV negative blood donors. The results disclosed a specific IFN-y/IL-2 double positive CD8 response in all subjects able to control infection. In other words, IFN-y/IL-2 double positive CD8 cells were present in virus-specific CD8 T cells against Flu, CMV and EBV as well against HIV-1 in LTNP. In contrast, progressors only had single IFN-γsecreting CD8 T cells. Hence, the ability to develop an IFN-y/IL-2 double positive response might be critical to control infection, independently of the nature of the virus. Additional experiments helped identify the developmental stage of the missing cells (using different markers such as CD45RA and CCR7) and showed a correlation between the absence of IL-2 secreting CD8 T cells and a failure in the proliferation capacity of virus-specific CD8 T cells. Addition of exogenous IL-2 could restore clonal expansion of HIV-1 specific CD8 T cells, at least in vitro. It could further been shown, that IL-2 secreting CD8 T cells are sufficient to support proliferation even in absence of CD4 help. However, the reason for the missing IFN-y/IL-2 double positive CD8 T cell response in HIV-1 progessors has yet to be determined. Publication #2: The second article (section 4.2, page 81) explores new strategies to trigger CD8 T cell immunity against specific HIV-1 proteins believed to be processed and exposed as "infection signal" at the surface of infected cells. Such signals consist of peptide fragments (8- 13 amino acids) originating from viral proteins and presented to CD8 T cells in the frame of particular cell surface molecules of the major histocompatibility complex class I* (MHC I). To mimic "natural" viral infection, the HIV-1 polyprotein Gagpolnef was inserted and expressed in either of two attenuated viruses i.e. vaccinia virus (MVA) or poxvirus (NYVAC). Mice were infected with these recombinant viruses and specific CD8 T cell response to Gagpolnef peptides was sought. Mice could indeed mount a CD8 T cell response against the HIV-1 antigens, indicating that the system worked, at least in this animal model. To further test whether peptides from Gagpolnef could also be presented in the frame of the human MHC class I proteins, a second round of experiments was performed in "humanized" transgenic mice expressing human MHC molecules. The transgenic mice were also able to load Gagpolnef peptides on their human MHC molecule, and these cells could be detected and destroyed by Ag-specific CD8 T cells isolated from HIV-1-infected patients. Therefore, expressing Gagpolnef on attenuated recombinant viruses might represent a valid strategy for anti-HIV-1 immunization in human. Publication #3: This is a review paper (section 4.3, page 91) describing the immune response to CMV and newly developed methods to detect this cellular immune response. Some of it focuses on the detection of T cells by using in vitro manufactured tetramers. These consist of four MHC class I molecules linked together and loaded with the appropriate antigenic peptide. The tetramer can be labeled with a fluorochrome and analyzed with a fluorescence-activated cell sorter. Taken together, the work presented indicates that (i) an appropriate CD8 T cell response consisting of IFN-y/IL-2 double positive effectors, can potentially control viral infection, including HIV-1 infection, (ii) such a response might be triggered by recombinant viral vaccines, and (iii) CD8 T cell response can be monitored by a variety of techniques, including recently-developed MHC class I tetramers. 1. 2. Préambule et résumé élargi Le présent travail de thèse s'intéresse à l'immunité antivirale du point de vue particulier de la réponse adaptative des cellules T. Le travail expérimental est présenté sous la forme de trois articles publiés (2 articles expérimentaux et 1 article de revue, voir sections 4.1, 4.2 et 4.3, pages 58, 66 et 77, respectivement), décrivant des progrès dans la compréhension du contrôle de l'infection virale par les lymphocytes T CD8, ainsi que dans le développement de nouveaux vaccins contre le Virus d'Immunodéficience de Humaine de type 1 (VIH-1). En raison du caractère spécialisé de l'immunité antivirale de type cellulaire, les articles sont précédés par une introduction générale (section 3), dont le but est de pourvoir le lecteur non avisé avec des bases nécessaire à une meilleure appréhension du travail expérimental. Cette introduction présente les grandes lignes du système immunitaire, et décrit de façon générale les 4 virus utilisés dans le travail expérimental: à savoir le virus VIH-1, le Cytomégalovirus (CMV), le virus Epstein Barr (EBV) et le virus Influenza A (Flu). Toutes les sections sont présentées de façon individuelle et peuvent être consultées séparément. La description des 4 virus a une pertinence particulière quant à leur interaction avec le système immun. En effet, ils induisent une panoplie de réponses immunitaires s'étendant aux extrêmes de la réaction de l'hôte. Influenza A est à l'origine d'une maladie cytopathique aiguë, au décours de laquelle le virus est éradiqué par l'hôte. CMV et EBV sont classiquement à l'origine d'infections pauci-symptomatiques, voire asymptomatiques, après lesquelles les virus persistent de façon latente dans la cellule hôte. Cependant, ils restent sous le contrôle du système immun, qui peut prévenir une éventuelle réactivation. Enfin, VIH-1 s'établit à la fois en infection latente - par l'insertion de son génome dans le chromosome des cellules hôtes - et en infection productive et cytopathique, échappant au contrôle immunitaire et détruisant ses cellules cibles. La compréhension des différences fondamentales entre ces différents types d'interactions virus-hôte devraient faciliter le développement de nouvelles stratégies antivirales. Article 1: Le premier article (section 4.1 Page 58) représente l'objet principal de mon travail de laboratoire. Il analyse la capacité des lymphocytes T CD8 spécifiques de différent virus à sécréter de l'interféron gamma (IFN-y) et/ou de l'interleukine 2 (IL-2) après stimulation par leur antigène spécifique. Les cellules T CD8 jouent un rôle crucial dans le contrôle des infections virales. Elles identifient les cellules infectées en détectant des antigènes viraux présentés à la surface de ces mêmes cellules, et éliminent à la fois les cellules infectées et les virus qu'elles contiennent en induisant l'apoptose et/ou la lyse des cellules cibles. Parallèlement, l'identification de l'antigène par la cellule T CD8 la stimule à sécréter des cytokines. L'IFN-γen est un exemple. L'IFN-γ stimule les cellules infectées à développer une activé antivirale intrinsèque. De plus, il attire sur place d'autres cellules de l'inflammation, et active leur fonction d'éradication des pathogènes. L'IL-2 est un autre exemple. L'IL-2 est essentielle à l'expansion clonale des cellules T CD8 spécifiques à un virus donné. Elle est donc essentielle à augmenter le pool de lymphocytes antiviraux. En conséquence, la double capacité de sécréter de l'IFN-γ et de IL-2 pourrait être un avantage pour le contrôle antiviral par les cellules T CD8. Dans ce travail nous avons comparé les proportions de lymphocytes T CD8 doubles positifs (IFN-γ/IL-2) et simples positifs (IFN-γ) chez trois groupes de sujets: (i) des patients infectés par VIH-1 qui ne contrôlent pas l'infection (progresseurs), (ii) des patients infectés par VIH-1, mais contrôlant l'infection malgré l'absence de traitement ("long term non progressors" [LTNP]) et (iii) des donneurs de sang négatifs pour l'infection à VIH-1. Les résultats ont montré que les individus capables de contrôler une infection possédaient des cellules T CD8 doubles positifs (IFN-γ/IL-2), alors que les patients ne contrôlant pas l'infection procédaient prioritairement des CD8 simples positifs (IFN-γ). Spécifiquement, les lymphocytes T spécifiques pour Flu, CMV, EBV, et VII-1-1 chez les LTNP étaient tous IFN-γ/IL-2 doubles positifs. Au contraire, les lymphocytes T CD8 spécifique à VIH-1 étaient IFN-γ simples positifs chez les progresseurs. La capacité de développer une réponse IFN-γ/IL-2 pourraient être primordiale pour le contrôle de l'infection, indépendamment de la nature du virus. En effet, il a été montré que l'absence de sécrétion d'IL2 par les lymphocytes T CD8 corrélait avec leur incapacité de proliférer. Dans nos mains, cette prolifération a pu être restaurée in vitro par l'adjonction exogène d'IL-2. Toutefois, la faisabilité de ce type de complémentation in vivo n'est pas claire. Des expériences additionnelles ont permis de préciser de stade de développement des lymphocytes doubles positifs et simples positifs par le biais des marqueurs CD45RA et CCR7. Il reste maintenant à comprendre pourquoi certains lymphocytes T CD8 spécifiques sont incapables à sécréter de l'IL-2. Article 2: Le deuxième article explore des nouvelles stratégies pour induire une immunité T CD8 spécifique aux protéines du VIH-1, qui sont édités et exposés à la surface des cellules infectées. Ces signaux consistent en fragments de peptide de 8-13 acide aminés provenant de protéines virales, et exposées à la surface des cellules infectées dans le cadre des molécules spécialisées d'histocompatibilité de classe I (en anglais "major histocompatibility class I" ou MHC I). Pour mimer une infection virale, la polyprotéine Gagpolnef du VIH-1 a été insérée et exprimée dans deux vecteurs viraux atténués, soit MVA (provenant de vaccinia virus) ou NYVAC (provenant d'un poxvirus). Ensuite des souris ont été infectées avec ces virus recombinants et la réponse T CD8 aux peptides issus de Gagpolnef a été étudiée. Les souris ont été capables de développer une réponse de type CD8 T contre ces antigènes du VIH-1. Pour tester si ces antigènes pouvaient aussi être présentés par dans le cadre de molécules MHC humaines, des expériences supplémentaires ont été faites avec des souris exprimant un MHC humain. Les résultats de ces manipulations ont montré que des cellules T CD8 spécifique aux protéines du VIH pouvaient être détectées. Ce travail ouvre de nouvelles options quant à l'utilisation des virus recombinants exprimant Gagpolnef comme stratégie vaccinale contre le virus VIH-I chez l'homme. Article 3: Ces revues décrivent la réponse immunitaire à CMV ainsi que des nouvelles méthodes pouvant servir à sa détection. Une partie du manuscrit décrit la détection de cellule T à l'aide de tétramères. Il s'agit de protéines chimériques composées de 4 quatre molécules MHC liées entre elles. Elles sont ensuite "chargées" avec le peptide antigénique approprié, et utilisée pour détecter les cellules T CD8 spécifiques à ce montage. Elles sont aussi marquées par un fluorochrome, qui permet une analyse avec un cytomètre de flux, et l'isolement ultime des CD8 d'intérêt. En résumé, le travail présenté dans cette thèse indique que (i) une réponse T CD8 appropriée - définie par la présence des cellules effectrices doublement positives pour l'IFN-γ et l'IL-2 - semble indispensable pour le contrôle des infections virales, y compris par le VIH-1, (ii) une telle réponse peut être induite par des vaccin viral recombinant, et (iii) la réponse T CD8 peut être analysée et suivie grâce à plusieurs techniques, incluant celle des tétramères de MHC class I. 1.3. Résumé pour un large public Le système immunitaire humain est composé de différents éléments (cellules, tissus et organes) qui participent aux défenses de l'organisme contre les pathogènes (bactéries, virus). Parmi ces cellules, les lymphocytes T CD8, également appelés cellules tueuses, jouent un rôle important dans la réponse immunitaire et le contrôle des infections virales. Les cellules T CD8 reconnaissent de manière spécifique des fragments de protéines virales qui sont exposés à la surface des cellules infectées par le virus. Suite à cette reconnaissance, les cellules T CD8 sont capables de détruire et d'éliminer ces cellules infectées, ainsi que les virus qu'elles contiennent. Dans le contexte d'une infection par le virus de l'immunodéficience humaine (VIH), le virus responsable du SIDA, il a pu être montré que la présence des cellules T CD8 est primordiale. En effet, en l'absence de ces cellules, les individus infectés par le VIH progressent plus rapidement vers le SIDA. Au cours de la vie, l'Homme est exposé à plusieurs virus. Mais à l'opposé du VIH, certains d'entre eux ne causent pas des maladies graves : par exemple le virus de la grippe (Influenza), le cytomégalovirus ou encore le virus d'Epstein-Barr. Certains de ces virus peuvent être contrôlés et éliminés de l'organisme (p. ex. le virus de la grippe), alors que d'autres ne sont que contrôlés par notre système immunitaire et restent présents en petite quantité dans le corps sans avoir d'effet sur notre santé. Le sujet de mon travail de thèse porte sur la compréhension du mécanisme de contrôle des infections virales par le système immunitaire : pourquoi certains virus peuvent être contrôlés ou même éliminés de l'organisme alors que d'autres, et notamment le VIH, ne le sont pas. Ce travail a permis de démontrer que les cellules T CD8 spécifiques du VIH ne sécrètent pas les mêmes substances, nécessaires au développement d'une réponse antivirale efficace, que les cellules T CD8 spécifiques des virus contrôlés (le virus de la grippe, le cytomégalovirus et le virus d'Epstein-Barr). Parallèlement nous avons également observé que les lymphocytes T CD8 spécifiques du VIH ne possèdent pas la capacité de se diviser. Ils sont ainsi incapables d'être présents en quantité suffisante pour assurer un combat efficace contre le virus du SIDA. La (les) différence(s) entre les cellules T CD8 spécifiques aux virus contrôlés (grippe, cytomégalovirus et Epstein-Barr) et au VIH pourront peut-être nous amener à comprendre comment restaurer une immunité efficace contre ce dernier.

Reliability of the density functional approximation to describe the charge transfer and electrostatic complexes involved in the modeling of organic conducting polymers

Both the intermolecular interaction energies and the geometries for M ̄ thiophene, M ̄ pyrrole, M n+ ̄ thiophene, and M n+ ̄ pyrrole ͑with M = Li, Na, K, Ca, and Mg; and M n+ = Li+ , Na+ , K+ , Ca2+, and Mg2+͒ have been estimated using four commonly used density functional theory ͑DFT͒ methods: B3LYP, B3PW91, PBE, and MPW1PW91. Results have been compared to those provided by HF, MP2, and MP4 conventional ab initio methods. The PBE and MPW1PW91 are the only DFT methods able to provide a reasonable description of the M ̄ complexes. Regarding M n+ ̄ ␲ complexes, the four DFT methods have been proven to be adequate in the prediction of these electrostatically stabilized systems, even though they tend to overestimate the interaction energies.

Surface functionalization of alumina ceramic foams with organic ligands.

Different anchoring groups have been studied with the aim of covalently binding organic linkers to the surface of alumina ceramic foams. The results suggested that a higher degree of functionalization was achieved with a pyrogallol derivative - as compared to its catechol analogue - based on the XPS analysis of the ceramic surface. The conjugation of organic ligands to the surface of these alumina materials was corroborated by DNP-MAS NMR measurements.