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Vanillin (4-hydroxy-3methoxybenzaldehyde) is one of the most employed aromatic and flavoring additives in food and cosmetic industry. The industrial interest in vanillin could also apply to its biodegradation products. The microbial transformation of vanillin can open the possibility of new products with new areas of application for products related to vanillin. For example, vanillyl alcohol, vanillic acid and ferulic acid are currently used in the pharmaceutical or food industry. Some species reported to biodegrade vanillin into the related products vanillyl alcohol and vanillic acid, are: Brettanomyces anomalus and Saccharomyces cerevisiae. Moreover, certain microorganisms possess the ability to accumulate lipids when cultivated on different carbon sources, opening the possibility of microbial lipid production as another industrial application. The present investigation focuses on the optimization of extraction methods for vanillin biodegradation products, as well as identifying the isolates of a collection of microorganisms originating from the Faroe Islands that are amenable to being cultivated on a lignin-based media. Finally, the potential for microbial lipid accumulation was also studied. Two analytical methods, Thin-Layer Chromatography (TLC) and Gas Chromatography (GC) were employed for characterizing the biodegradation products obtained after 24 hours and 72 hours of culture in growth medium supplemented with 1 mM of vanillin. The results showed that after 24 hours of incubation, the model microorganism, strain FMYD002, had consumed some of the vanillin and transformed it into biodegradation products. TLC retention factors and GC chromatograms revealed that the main biodegradation product after 24 hours - when compared to a standard – is likely to be to vanillyl alcohol. Furthermore, vanillin and its biodegradation products were relatively temperature-stable based on a temperature test of supernatant from a 24-hour culture, however, when the 72-hour culture had been subjected to the highest temperature (60 °C) some spontaneous decomposition occurred. The biodegradation pattern of the 72-hour culture evidenced by TLC revealed two additional biodegradation products, one of which migrates in a similar fashion to vanillic acid. After 72 hours of incubation, the biodegradation product presumed to be vanillyl alcohol was no longer observed. Acidification tests showed that the best route for extraction of the product believed to be vanillyl alcohol is to adjust the extracted sample to a pH of 9. The cultivation test of the isolates in media prepared from different lignin-based residual products showed that 26 out of 60 initial strains grew regardless of the concentration of lignosulfonates and vanillin. Moreover, 17 strains grew in nitrogen-limited medium. Eight of the strains accumulated lipids. A preliminary categorization of isolates based on their colony morphology and capacity of growth on different substrates showed that to some extent, their morphology can predict the ability to grow on lignin- and vanillin-based media. This could help future scientists to easily screen for and select isolates with interesting activity for the ligno-cellulose industry.

L’objectif de cette thèse était d’explorer les bases cognitives et cérébrales des processus de compréhension du langage figuré via l’utilisation d’outils de neuroimagerie (EEG et IRMf). Nous nous sommes particulièrement intéressés aux processus inférentiels sémantiques et pragmatiques. Afin de mieux les cerner, nous avons étudié la compréhension de la métaphore verbale nouvelle (« catapulter ses paroles ») et de l’ironie verbale (« Il est détesté de tous. Cet homme est très populaire. »). Ce choix repose sur l’hypothèse selon laquelle chacune de ces figures sollicite spécifiquement un type de processus inférentiel ; de nature sémantique pour la métaphore et pragmatique pour l’ironie. Conformément à cette hypothèse, nos résultats indiquent que la compréhension des métaphores verbales nouvelles se fonde sur des processus de recherche et d’intégration d’informations sémantiques, supportant l’hypothèse d’un traitement séquentiel. L’examen des bases cérébrales du traitement de ces expressions précédées d’un contexte a mis en évidence des régions cérébrales postérieures, suggérant la mise en œuvre d’un processus de manipulation conceptuelle. Concernant le traitement de l’ironie, nous avons observé un processus tardif d’intégration d’informations plus important pour les énoncés ironiques comparés aux énoncés littéraux, suggérant un traitement pragmatique plus difficile. Enfin, nous avons mis en évidence un réseau fronto-temporal bilatéral lors du traitement de l’ironie, dont une part serait sensible au contraste entre le contexte et l’énoncé et à l’humour des énoncés. Nos résultats sont confrontés aux théories psycholinguistiques et cognitives du traitement du langage figuré. / Our main aim was to assess the cognitive and neural basis of the figurative language processing using neuroimaging tools (EEG and fMRI). We were especially interested in semantic and pragmatic inferential processes. In order to better grasp these processes, we have studies the comprehension of novel verbal metaphor (“to catapult his/her words”) and verbal irony (“Everybody thinks he is foul. He is a very popular man.”). This choice was based upon the hypothesis that each of these figurative expressions specifically engages one of the two inferential processes: semantic for metaphors and pragmatic for irony. Following this hypothesis, our results point out that the comprehension of novel metaphoric expression is built on the research and the integration of a semantic congruent information, supporting a sequential processing hypothesis. The assessment of the cerebral basis of the processing of such expressions embedded in a context has revealed regions in posterior areas, suggesting a conceptual manipulation process. Concerning the irony processing, we observed a greater late integration processing for ironic sentences than literal ones, suggestion a more effortful pragmatic processing. Finally, we observed a fronto-temporal network specific to irony processing. Some part of this network could be involved in both the contrast between the utterance and the context and the humor processing of the sentences. Our results are confronted with psycholinguistic and cognitive theories about figurative language processing.

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Magister Scientiae - MSc / In this study SBA-15 mesoporous silica template was synthesized and used as a sacrificial template in the preparation of ordered mesoporous carbon material. A chemical vapour deposition (CVD) technique using LPG or alternatively sucrose, pyrolyzed upon a mesoporous Si matrix were used to produce nanostructured ordered mesoporous carbon (OMC) with graphitic character after removing the Si template. The sucrose method was found to be a suitable route for preparing OMC. The OMC was used as a conductive three dimensional porous support for depositing catalytic nanophase Pt metal. Deposition of Pt nanoparticles on OMC was accomplished using a CVD method with Pt(acac)2 as a precursor. The synthesized nano-composite materials were characterized by several techniques such as, HRTEM, HRSEM, EDS, XRD, BET, TGA, FT-IR and CV. / South Africa

Recombination Activating Genes (RAGs) orchestrate the process called V (D) J recombination, which enables the vertebrate adaptive immune system to specifically recognize millions of antigens. During this recombination process, V (variable), D (diversity) and J (joining) gene segments of antibody (B cell receptor) and TCR (T cell receptor) join by different possible combinations to generate antigen receptor diversity. This unique site specific recombination process is actuated by lymphoid specific proteins called RAG1 and RAG2 (RAGs or RAG complex). RAGs recognize a conserved sequence motif flanking the above subexons called Recombination Signal Sequence (RSS). There are two types of RSS known as 12-RSS and 23-RSS, where a conserved heptamer sequence and nonameric sequence is separated by 12 or 23 bp, respectively. RAGs specifically bind to RSS by RAG1 Nonamer Binding Domain (NBD) and generate nicks which are converted to DSBs via a hairpin intermediate and finally repaired by Non-Homologous DNA End Joining (NHEJ), a major DSB repair pathway in eukaryotes. Thus, RAGs act as a sequence specific endonuclease, and is unique to higher eukaryotes. Therefore, reduced or loss of RAG activity could result in immune deficiency syndromes like Omenn Syndrome (OS) and Severe Combined Immunodeficiency (SCID). Apart from acting as a sequence specific nuclease, RAGs have been shown to cleave on altered DNA structures like mismatches (bubbles), hairpins, flaps, gaps, triplexes and 3’ overhangs. This structure specific nuclease activity is implicated in causing genomic instability in B and T cells, particularly leading to generation of chromosomal translocations in certain lymphoid cancers. However, unlike the sequence- specific cleavage activity, this novel property of RAGs is poorly understood. Structure-specific nuclease activity of RAGs was characterized by using heteroduplex DNA substrate containing bubble region. RAG proteins were overexpressed and purified from human cell line and used for the assay. Results showed that RAGs cleave different bubble substrates with different efficiency. The role of DNA sequence at single-stranded region of heteroduplex DNA on RAG cleavage was investigated by synthesizing the substrate DNA having either adenineguanine/ thymine/ cytosine in the bubble sequence. Interestingly, efficient RAG cleavage was observed only when cytosines were present at single-stranded region, while thymine bubbles were cleaved with much lower efficiency. Adenine and guanine containing bubbles were not cleaved by RAGs. This was the first observation showing sequence specificity during structure-specific nuclease activity of RAGs. Besides, it was observed that RAG cleavage on bubbles with cytosines resulted in DSB formation, which is essential for generation of chromosomal translocations. Further, such specificity and cytosine preference was observed, even when RAGs acted on other altered DNA substrates like hairpin loops, 3’ overhangs and gaps. When the role of flanking duplex region on RAG cleavage was tested, only the 5’ duplex nucleotide was critical for RAG cleavage reaction and cytosine was the most preferred nucleotide. By systematic mutation of bubble region, it was observed that the two cytosines present at the double strand-single strand junction are critical for RAG cleavage. A single nucleotide bubble (mismatch) with cytosines was cleaved by RAGs with low but detectable efficiency. A bubble with at least 2 nt length possessing cytosine was cleaved with higher efficiency resulting in both single-stranded nicks and DSBs. Based on these studies, “C(d)C(s)C(s)” was proposed as a novel recognition motif for RAG cleavage, on altered DNA structures, where“d” and “s” represent double- and single-strand region, respectively. To be targeted by RAGs in vivo, the altered DNA substrates have to compete with RSS, the physiological substrate. It is not known whether such structures will be cleaved by RAGs, when present along with RSS. Besides, the regulation of the both structure and sequence specific nuclease activities are not studied. To address the above questions, RAG cleavage on bubble substrates was performed in presence of RSS either in cis or trans configuration. Results showed that both bubble substrates and RSS were cleaved with similar efficiency by RAGs. In fact, they can compete out each other in a concentration dependent manner. When kinetics of RSS and bubble cleavage were performed, RSS cleavage reaction was faster and saturated within 10-15 min, while bubbles cleavage started slow and went on increasing with time. This difference in kinetics persisted when both substrates were present together. This could be a regulatory mechanism for targeting RAGs to RSS sites and limiting bubble cleavage which can be deleterious to cells. HMGB1, a DNA binding protein which is shown to enhance RSS binding and synapsis, does not affect RAG action on bubble substrates. RAG postcleavage complex is formed during V(D)J recombination process where RAGs remain bound to cleaved RSS after cleavage, which limits further RAG action on other sites. Such cleavage complex was not detected on bubble substrates, which suggests that after cleavage RAGs were not associated to DSBs of bubble cleavage. Finally, the nonamer binding domain of RAG1 involved in RSS binding in V(D)J recombination, was found to be dispensable for the structure-specific nuclease activity and it appears that RAGs bind to bubble substrates using a different domain. In summary, in this study, the structure-specific nuclease activity of RAGs was characterized. A novel sequence motif that can regulate this activity of RAGs was identified. Though altered structures can be equally favored substrates as RSS, differences in reaction kinetics, cleavage complex formation and separate DNA binding domains regulate RAG cleavage, when it acts as a structure-specific nuclease. Thus, this study may help in the better understanding of RAG induced genomic instabilities in lymphoid tissues.

Recently, efforts have been made for self-powering the batteries and portable electronic devices by piezoelectric nanogenerators. The piezoelectric nanogenerators can work as a power source for nano-systems and also as an active sensor. The piezoelectric nanogenerator is a device that converts random mechanical energy into electrical energy by utilizing the semiconducting and piezoelectric properties. Also, the mechanical energy is always available in and around us for powering these nano devices. The aim of the present thesis work is to explore 1D and 2D ZnO nanostructures (nanorods and nanosheets) on metal alloy substrates for the development of piezoelectric nanogenerators in energy harvesting and sensors applications. Hydrothermal synthesis method was adopted for the growth of ZnO nanostructures. The nanogenerators were fabricated by using the optimized synthesis parameters and subsequently studied their performance for power generation and as an active speed sensor. These 1D and 2D nanostructures based nanogenerators have opened up a new window for the energy harvesting applications and sensors development. The thesis is divided into following six chapters. Chapter 1: This chapter gives a general introduction about energy harvesting devices such as nanogenerators, available energy sources, mechanical energy harvesting, ZnO material and the details on hydrothermal synthesis process. A brief literature survey on different applications of piezoelectric nanogenerators is also included. Chapter 2: A novel flexible metal alloy (Phynox) and its properties along with its applications are discussed in this chapter. Details on the synthesis of 1D ZnO nanorods on Phynox alloy substrate by hydrothermal method are presented. Further, the optimization of parameters such as growth temperature, seed layer annealing and substrate temperature effects on the synthesis of ZnO nanorods are discussed in detail. As-synthesized ZnO nanorods have been characterized using XRD, FE-SEM, TEM and XPS. Chapter 3: It reports on the fabrication of piezoelectric nanogenerator on Phynox alloy substrate as power generating device by harvesting the mechanical energy. Initially, the performance of the nanogenerator for power generation due to finger tip impacts was studied and subsequently its switching polarity test was also carried out. Output voltage measurements were carried out using the in-house developed experimental setup. Stability test was also carried out to see the robustness of the nanogenerator. Finally, the output voltage response of the nanogenerator was studied for its use as an active speed sensor. Chapter 4: Synthesis of Al doped 2D ZnO nanorsheets on Aluminum alloy (AA-6061) substrate by hydrothermal method is reported in this chapter. The optimized parameters such as growth temperature and growth time effects on the synthesis of ZnO nanosheets are discussed. As-synthesized ZnO nanosheets were characterized using XRD, FE-SEM, TEM and XPS. The Al doping in ZnO is confirmed by EDXS and XPS analysis. Chapter 5: Cost effective fabrication of Al doped 2D ZnO nanosheets based nanogenerator for direct current (DC) power generation is reported in this chapter. The performance of the nanogenerator for DC power generation due to finger tip impacts was studied and subsequently its switching polarity test was also carried out. Output voltage measurements were carried out using the in-house developed experimental setup. Stability test was also carried out to see the robustness of the nanogenerator. Finally, the DC output voltage response of the nanogenerator was studied for its use as an active speed sensor. Chapter 6: The first section summarizes the significant features of the work presented in this thesis. In the second section the scope for carrying out the further work is given.

ABCG2 ou BCRP est une protéine membranaire de la famille des transporteurs ABC. Elle utilise l’énergie de l’hydrolyse de l’ATP pour exporter des composés endogènes et exogènes hors des cellules. Elle participe ainsi à la protection et la détoxication de l’organisme. En revanche, dans le cas des cellules cancéreuses, elle est surexprimée et participe donc au phénotype de résistance à de multiples médicaments (MDR : Multi Drug Resistance). En effet, lors de la surexpression de cette protéine, les agents anti-cancéreux sont exportés hors des cellules tumorales, ce qui diminue leurs concentrations intracellulaires sous leurs seuils de cytotoxicité et les rend inefficaces. De par l’importance d’ABCG2 dans la chimiorésistance, de nombreux efforts sont effectués pour concevoir des inhibiteurs afin de restaurer la sensibilité des cellules cancéreuses. Dans ce contexte, le projet de thèse vise à caractériser ABCG2 sur les plans structural et fonctionnel afin de comprendre son mécanisme d’action. La protéine ABCG2 exprimée chez E. coli, a été purifiée, sous forme stable et homogène et le rendement est de 1,5 mg de protéine par litre de culture. La caractérisation fonctionnelle de celle-ci témoigne de son repliement correct. En effet, il a été démontré qu’elle est capable de fixer différents substrats (naturels et agents anti-cancéreux) avec des affinités différentes. Des essais préliminaires de cristallisation ainsi que des observations par microscopie électronique révèlent des résultats encourageants pour la suite de la caractérisation structurale / ABCG2 or BCRP is a membrane protein that belongs to the ABC transporter family. It uses the hydrolysis energy of ATP to export endogenous and exogenous compounds out of cells. It is thus involved in the protection and detoxification of the body. However, it is overexpressed by cancer cells and participates in the multidrug resistance phenotype (MDR); in fact, anti-cancer agents are exported out of the tumor cells, which reduce their concentration below their cytotoxicity threshold and renders them ineffective. Because of its importance in chemoresistance, many efforts are made to design inhibitors to restore the sensitivity of cancer cells. In this context, the PhD project aims to characterize ABCG2 at structural and functional levels in order to understand its mechanism of action. We have succeeded in purifying ABCG2 expressed in E. coli, the protein obtained is stable and homogeneous, with a yield of 1.5 mg of protein per liter of culture. The functional characterization of ABCG2 demonstrates its correct folding. In fact, we have demonstrated that it is able to bind different substrates (natural and anti-cancer agents) with different affinities. Preliminary crystallization assays and electron microscopy observations reveal encouraging results for subsequent structural characterization

Pro zpracování a nakládání s odpadními substráty lze použít řadu postupů a možností. Stále se rozšiřující spektrum metod a technologií umožňuje další využití materiálů a energie ve formě obnovitelných zdrojů. Jedním z řešení pro zpětné získávání některých odpadních materiálů je využití tzv. bílé (průmyslové) biotechnologie, která zahrnuje praktickou aplikaci metabolických aktivit celé řady různých mikroorganizmů včetně jejich specifických biologických drah k produkci látek s vysokou přidanou hodnotou. V předložené práci screeningového typu bylo pro zhodnocení odpadních surovin využito několik druhů mikroorganizmů kultivovaných za různých specifických podmínek včetně kultivace na odpadních materiálech získaných zejména ze zemědělství a potravinářství. Cílem bylo získání vybraných typů průmyslově cenných metabolitů, případně energie. Předložená studie byla zaměřena na srovnání růstu a produkčních vlastností několika kmenů karotenogenních kvasinek rodu Rhodotorula, Sporobolomyces a Cystofilobasidium, kultivovaných v médiích s obsahem glycerolu (technický a odpadní glycerol), dále v médiích obsahujících pšeničnou slámu, hydrolyzovanou slámu zpracovanou v hydrotermálním procesu při vysoké teplotě a zbytky po filtraci hydrolyzátu. Dalším testovaným odpadním substrátem byla syrovátka. Všechny testované kvasinky byly schopny využít glycerol jako jediný zdroj uhlíku. Produkce biomasy při kultivaci na technickém glycerolu se více či méně přibližovala kontrole (cca 7 - 10 gl-1), zatímco při kultivaci na odpadním glycerolu byla produkce vyšší (10.9 - 14.5 gl-1). Produkce karotenoidů a ergosterolu byla vyšší v glukózovém médiu než v médiu s obsahem glycerolu. Všechny testované kvasinky byly rovněž schopny produkovat neutrální lipidy, a to v rozmezí 11 - 15 %, s výjimkou C. capitatum, kde produkce dosahovala více než 22 % obsahu neutrálních lipidů. Pšeničná sláma a produkty z ní připravené se ukázaly být využitelnými substráty s vysokým potenciálem pro produkci biomasy i metabolitů, a to zejména u kmene S. roseus. Syrovátka, jako odpadní produkt mlékarenství, byla účinně využita jako substrát pro kokultivaci karotenogenních kvasinek a bakterií mléčného kvašení. Kokultivační proces může vyvolat nadprodukci pigmentů a ergosterolu, přičemž získaná biomasa díky obohacení o bakterie L. casei dosahovala vyšší kvality. Za účelem energetického využití mikrobiálního metabolismu formou mikrobiálních palivových článků, tzv. „Microbial Fuel Cell“ byla aplikována směsná kultura bakterií získaných z čistírny odpadních vod. Tyto mikroorganizmy hrají významnou roli při výrobě elektrické energie a současně také při čištění odpadních vod. Elektřina je generována přímo z organických látek přítomných v kultivačním médiu a lze ji použít pro provoz čistírny samotné a případně i pro další aplikace.

Les proliférations de microalgues peuvent être nocives. L'augmentation récente de la fréquence et de l’étendue géographique des efflorescences de dinoflagellés benthiques toxiques comme Ostreopsis cf. ovata peut poser de réels problèmes de santé publique. La côte méditerranéenne Nord-Occidentale (lieu de cette étude) est l'une des nombreuses régions méditerranéennes où les proliférations d'algues nuisibles représentent une menace pour l’économie touristique. Dans les années à venir, une attention particulière devra être portée à la gestion et la prévision des proliférations de ces microalgues nuisibles benthiques et c'est dans ce contexte que cette étude a été menée. Une étude bibliographique portant sur les proliférations d’Ostreopsis spp. indique un manque important de données en relation avec l'écologie d’O. cf. ovata, en particulier concernant les substrats biotiques, ainsi que les communautés les habitats benthiques et, par conséquent, les rôles éventuels que ceux-ci peuvent jouer en tant que stimulateurs majeurs des efflorescences d’Ostreopsis spp. Durant les étés 2015 et 2016, des expériences in situ de courte durée ont été menées sur les récifs côtiers et ont été complétées par des expériences en laboratoire. Les résultats obtenus ont permis d’établir que quatre communautés distinctes de macroalgues abritent des abondances différentes d’O. cf. ovata. En particulier, les abondances les plus élevées ont été enregistrées dans des sites dominés par des structures communautaires peu complexes ; Turf et Dictyotales, alors que les sites dominés par des communautés complexes de Cystoseira n’ont montré aucune prolifération significative de microalgues. Ces résultats impliquent que les régions côtières dominées par les communautés composées de Cystoseira spp. pourraient potentiellement réduire les proliférations de Ostreopsis spp. En outre, d’autres facteurs abiotiques, tels que les concentrations en nutriments et métaux traces, ne contribuent pas (ou peu) à expliquer la dynamique des populations de O. cf. ovata. Les multiples facteurs de stress d’origine anthropique continueront à influencer le fonctionnement de l’écosystème marin. La compréhension de ces impacts et la façon dont ils influencent la dynamique des dinoflagellés benthiques toxiques est impérative pour prévoir, gérer et éventuellement réduire ces proliférations, à l’échelle de l’océan mondial. / Algal blooms can be harmful. The global management and forecasting of benthic harmful algal blooms (BHABs) will be of increasing importance in the years ahead and that is what this study sets out to address. The increase over recent decades, in both frequency and geographical range, of the potentially harmful benthic dinoflagellate Ostreopsis cf. ovata can pose real problems for human health. The French Côte d’Azur, the location for this study, is just one of many Mediterranean areas where harmful algal blooms pose a potential economic threat to a tourist-based economy. A review of the existing literature on Ostreopsis spp. blooms shows a severe lack of information about the ecology of O. cf. ovata in relation to biotic substrates, communities and habitats and thus any possible roles these may play in fostering major Ostreopsis spp. blooms. Through a series of in situ experiments on temperate reefs on the Côte d’Azur over the summers of 2015 and 2016 with follow-up experiments in the laboratory, this study establishes that four distinct macroalgal communities harbour different O. cf. ovata abundances. The results indicated that higher abundances were recorded in sites which were dominated by less complex community structures; Turf and Dicyotales, while sites with Cystoseira spp. communities present did not harbour significant microalgal blooms. These results imply that coastal regions with a dominance of Cystoseira-composed-communities could potentially be less prone to blooms or even inhibit Ostreopsis spp. proliferation. Although, no clear relationship was found between inorganic nutrient concentrations and O. cf. ovata abundances, it was observed that in the bloom onset period, nitrogen compounds were higher than in the rest of the study period (both in 2015 and 2016). Multiple human stressors will continue to impact marine vegetation, understanding these impacts and how they then influence bloom dynamics is imperative for the global management and mitigation of BHABs.