Affinity molecules can serve as precision tools for selective recognition and measurement of specific biomolecules in the fields of therapeutic drug monitoring and quality control in recombinant protein production. In therapeutic drug monitoring, affinity molecules can enable the accurate quantification of drug concentrations within physiological fluids, enhancing both the safety and efficacy of clinical treatments. In the realm of recombinant protein production, these molecules can allow precise isolation and measurement of desired recombinant proteins from complex mixtures by selectively targeting specific protein tags or domains, ensuring the consistency and purity of protein products. Currently, antibodies are most commonly used affinity reagents in these fields but are limited by production complexity, batch variability, high cost, and low stability. Aptamers, known as ‘chemical antibodies’ but composed of nucleotides, are considered potential next-generation affinity reagents. Aptamers are obtained via a synthetic process, termed SELEX, of iterative affinity selection and polymerase chain reaction (PCR) amplification of target-binding members from a randomized oligonucleotide library. This process is traditionally labor and resource-intensive and time-consuming. In this thesis, microfluidic technology is employed to enable time-efficient and cost-effective generation of aptamers for monoclonal antibodies and recombinant proteins toward applications in therapeutic drug monitoring and quality control of recombinant protein production. This thesis starts with a comparative study of three SELEX strategies for aptamer isolation, including those using conventional agarose bead-based partitioning, microfluidic affinity selection (called “chip-selection SELEX”), and fully integrated microfluidic affinity selection and PCR amplification (termed “full-chip SELEX”). The comparison results indicate that chip-selection SELEX offers the lowest cost and highest efficiency in aptamer isolation. We then use chip-selection SELEX to streamline the process of isolating anti-idiotype aptamers targeting human monoclonal antibodies against spike protein of SARS-CoV-2 virus. The process is completed within only 5 rounds of SELEX within two days, which represented a significant improvement when compared to conventional methods whose completion generally requires more than 10 SELEX rounds in up to a month. These anti-idiotype aptamers are combined with a graphene-based affinity nanosensor to enable rapid antibody concentration measurements to inform therapeutic decisions in a timely manner. In addition, a microfluidic dual-aptamer sandwich assay with highly efficient isolation of aptamers is developed to enable rapid and cost-effective detection of tag-fused recombinant proteins. This approach addresses both the limitations of current dual-aptamer assays and commonly encountered difficulties in the lack of aptamers available for such assays, by first using chip-selection SELEX to generate aptamers and then employing these aptamers to implement a microfluidic dual-aptamer assay for quality control during recombinant protein production. Despite the high efficiency in aptamer isolation using chip-selection SELEX, the full-chip SELEX platform is still desired for minimal manual operation and reagent consumption. The current full-chip SELEX platform has low isolation efficiency and could not offer information of affinity selection process. Herein, by introducing asymmetric PCR into the full-chip SELEX process, we improve the efficiency in aptamer isolation and can successfully monitor the selection progress. This real-time monitoring capability allows us to identify the optimal point to terminate the SELEX process, preventing the potential loss of aptamer candidates and reducing the overall consumption of time and reagents. In addition, introducing solution phase-based asymmetric PCR addresses a notable technical challenge of on-chip PCR bead replenishment, toward complete automation of the full-chip SELEX platform. Furthermore, a holder equipped with connection pins is designed to enable the reversible connection between gold electrodes and electrical wires. This design promotes the reusability of gold electrode-deposited glass substrates, resulting in a substantial reduction in chip fabrication costs. In addition to the SELEX protocol development effort, we also present efficient and cost-effective microfluidic approaches for post-SELEX aptamer characterization, including aptamer identification and kinetic aptamer-target binding measurements. To mitigate the expensive and time-consuming nature of aptamer identification from SELEX-generated target-binding sequence pools, we present an approach that is based on a cost-effective and efficient procedure to generate modified single-stranded DNA copies of the aptamer candidates and then assess the affinity of the resulting modified ssDNA strands to target molecules. The approach is applied to identify aptamers from 12 candidates with consistent results, but at a cost three times lower than that of established methods. We also present a microfluidic fluorescence assay, which exploits a synergistic combination of microfluidic technology and fluorescence microscopy, to realize cost-effective and multiplexed measurement of kinetics of aptamer-target analyte binding without requiring special-purpose equipment.

Antibiotics are routinely used in modern livestock production systems to treat and prevent disease as well as to enhance livestock production and/or outputs. This widespread use of antibiotics has led to a growing worldwide interest in antibioticfree animal production. The addition of feed supplements such as nucleotides to improve intestinal health as well as the early development of the immune system needs to be investigated as an environmentally-friendly nutritional management activity. In this study four (4) groups of newborn Holstein calves (n=24) were evaluated after being treated as follows: Group 1 (Negative control), Group 2 (Investigational Veterinary Product (IVP) 1 – Oral supplement containing nucleotides, vitamins, essential fatty acids, essential amino acids, pre-biotics and trace-minerals), Group 3 (IVP 2 – Oral supplement containing nucleotides only at concentration and dosage equal to IVP1) and Group 4 (IVP 3 - Parenteral glucocorticoids). Results of the study indicated that: Pre-colostral Serum IgG titres – After titration of the serum the anti-BVDV results showed no difference between the study groups. All calves recorded a SP ratio of zero value (0.00 ± 0.2) indicating that they had not been nursed by their mothers prior to the start of the study. This was an entrance requirement for the calves to be enrolled into the study. Apparent Efficiency of Absorption % (AEA%) – Literature shows that an AEA% result of between 20%-30% is good and 35% is excellent. The AEA% recorded for this study fell within this range although there was no statistically significant difference shown between the groups. In spite of a strictly controlled study protocol, 7 of the 24 calves (29%) still suffered from FPT in this study. The result falls within the range of 19% - 37% reported on United States of America (USA) farms by Doepel and Bartier in 2014. Serum cortisol - When compared to the control group, there were no statistical significant difference evident for group 2 and group 3. However, the difference between the Glucocorticoid – Group 4 and the control and other groups was statistically significant (P = 0.0001; table 12) at the various time intervals. It was also evident that the inclusion of parenteral glucocorticoids (group 4) may have assisted in prolonging the natural “gut closure”. Gut closure – a positive 2 point linear regression forecast line indicated an increasing trend in IgG absorption post-24 hours for group number 4 whilst groups 1, 2 and 3 each had a negative 2 point linear regression forecast line (figure 23). Weight / ADG (D42) - Group 2 showed a statistically significant increase in mean D42 weight (P = 0.0042) of 59.167 kg ± 3.545 kg when compared to the other study groups and compared to the control group (P = 0.0227). A comparison of the relative increase in mass of groups indicated that Group 2 efficiently achieved this result with a statistically significant ADG of 0.536 kg (P = 0.014) compared to the other study groups and compared to the control group (P = 0.022). In addition, weight / FCR – FCR was calculated for all groups as follows: G1 – 4.000 kg, G2 - 2.593 kg, G3 – 2.703 kg and G4 - 3.012 kg feed required for the production of 1 kg meat. The results indicated that the group 2 feed input was the most economical followed by groups 3, 4 and control respectively. In conclusion, it is evident that a nutritional supplement containing nucleotides, vitamins, trace- minerals, essential fatty acids, essential amino acids and pre-biotics may contribute significantly to important economic indicators such as weight gain, ADG and FCR on a commercial dairy farm. / Environmental Sciences / Ph. D. (Environmental Science)

Cationic polymers have shown potential as gene delivery vectors due to their ability to condense DNA and protect it from cellular and restriction nucleases. Dendrimers are hyperbranched macromolecules with precisely defined molecular weights and highly symmetric branches stemming from a central core. The nanosize, tunable surface chemistries and ease of surface functionalization has made dendrimers an attractive alternative to conventional linear polymers for DNA delivery applications. The commercially available, cationic dendrimer poly(amidoamine) or PAMAM is the most widely studied dendrimer for use as a gene delivery vector. The aim of this dissertation is to provide an increased understanding of the packaging and forces within PAMAM–DNA complexes. In Chapter 4, we will discuss the effect of molecular chain architecture on DNA-DNA intermolecular forces by examining DNA condensed by low generation (G0 & G1) PAMAM and comparing them to comparably charged linear arginine peptides. Using osmotic stress coupled with X-ray scattering, we are able to determine the structure and forces within dendrimer-DNA complexes, or dendriplexes. We show that PAMAM–DNA assemblies display significantly different physical behavior than linear cation–DNA assemblies. In Chapter 5, we examine the role of pH on condensation in these same low generation PAMAM-DNA complexes. PAMAM dendrimers have both terminal primary amines and internal tertiary amines with different pKas of approximately 9 and 6, respectively. We show changes in the pH at condensation greatly influence the resulting packaging as well as the resulting phase behavior for PAMAM dendriplexes. In Chapter 6, we examine the packaging of DNA by G4 PAMAM as a function of the percent zwitterionic modification. Many cationic polymers, including PAMAM, have shown high transfection efficiency in cell culture and potential for in vitro and in vivo applications, but its development is hindered by cytotoxicity in many cell lines and tissues. We hypothesize that zwitterionic PAMAM (zPAMAM) represent a new means to tune polymer-DNA interactions through PAMAM surface charge potentially enhancing intracellular unpackaging while reducing cellular toxicity. These zPAMAM complexes are currently under investigation for their potential as safer and more efficient materials for DNA delivery.

RNA nanotechnology is an emerging field that holds great promise for advancing drug delivery and materials science. Recently, RNA nanoparticles have seen increased use as an in vivo delivery system. RNA was once thought to have little potential for in vivo use due to biological and thermodynamic stability issues. However, these issues have been solved by: (1) Finding of a thermodynamically stable three-way junction (3WJ) motif; (2) Chemical modifications to RNA confer enzymatic stability in vivo; and (3) the finding that RNA nanoparticles exhibit low immunogenicity in vivo. In vivo biodistribution and pharmacokinetics are affected by the physicochemical properties, such as size, shape, stability, and surface chemistry/properties, of the nanoparticles being delivered. RNA has an inherent advantage for nanoparticle construction as each of these properties can be finely tuned. The focus of this study is as follows: (1) Construction of diverse size and shape RNA nanoparticles with tunable physicochemical properties; (2) Investigation of the effect that size, shape, and nanoparticle properties have on in vivo biodistribution; (3) Development of drug encapsulation and release mechanism utilizing RNA nanotechnology; and (4) Establishment of large-scale synthesis and purification methods of RNA nanoparticles. In (1), RNA triangle, square, and pentagon shaped nanoparticles were constructed using the phi29 pRNA-3WJ as a core motif. Square nanoparticles were constructed with sizes of 5, 10, and 20 nanometers. The RNA polygons were characterized by AFM to demonstrate formation of their predicted geometry per molecular models. Furthermore, the properties of RNA polygons were tuned both thermodynamically and chemically by substitution of nucleic acid type used during nanoparticle assembly. In (2), the biodistribution of RNA nanosquares of diverse sizes and RNA polygons of diverse shapes were investigated using tumor models in nude mice. It was found that increasing the size of the nanosquares led to prolonged circulation time in vivo and higher apparent accumulation in the tumor. However, it was observed that changing of shape had little effect on biodistribution. Furthermore, the effect of the hydrophobicity on RNA nanoparticles biodistribution was examined in mouse models. It was found that incorporation of hydrophobic ligands into RNA nanoparticles causes non-specific accumulation in healthy organs, while incorporation of hydrophilic ligands does not. Lower accumulation in vital organs of hydrophobic chemicals was observed after conjugation to RNA nanoparticles, suggesting RNA has the property to solubilize hydrophobic chemicals and reduce accumulation and toxicity in vital organs. In (3), a 3D RNA nanoprism was constructed to encapsulate a small molecule fluorophore acting as a model drug. The fluorophore was held inside the nanoprism by binding to an RNA aptamer. The ability of the stable frame of the nanoprism to protect the fragile aptamer inside was evidenced by a doubling of the fluorescent half-life in a degrading environment. In (4), a method for large-scale in vitro synthesis and purification of RNA nanoparticles was devised using rolling circle transcription (RCT). A novel method for preparing circular double stranded DNA was developed, overcoming current challenges in the RCT procedure. RCT produced more than 5 times more RNA nanoparticles than traditional run-off transcription, as monitored by gel electrophoresis and fluorescence monitoring. Finally, large-scale purification methods using rate-zonal and equilibrium density gradient ultracentrifugation, as well as gel electrophoresis column, were developed.

The research presented in this thesis was carried out as part of a collaboration between the groups of Dr Tanja van Mourik at the School of Chemistry, University of St Andrews and Professor Jonathan Tennyson at the Department of Physics and Astronomy at University College London. This thesis presents State-Averaged Complete Active Space Self Consistent Field (SA-CASSCF) calculations on nucleic acid bases, deoxyribose and phosphoric acid H₃PO₄). In the case of uracil, for comparison, Multireference Configuration Interaction calculations were also performed. The SA-CASSCF orbitals were subsequently used in R-matrix electron scattering calculations using the close-coupling model. Of major importance for obtaining accurate SA-CASSCF results is the choice of the active space and the number of calculated states. Properties such as the electronic energy, number of configurations, excitation energy and dipole moment were considered in the choice of active space. Electron-collision calculations were performed on two of the most stable isomers of phosphoric acid, a weakly dipolar form with all OH groups pointing up and a strongly dipolar form where one OH group points down. A broad shape resonance at about 7 eV was found for both isomers. Ten-state close-coupling calculations suggest the presence of narrow, Feshbach resonances in a similar energy region. Elastic and electronically inelastic cross sections were calculated for both isomers. The R-matrix calculations on uracil were done by the group from UCL. R-matrix calculations are currently being done on guanine. Scattering calculations on the other DNA bases will be performed in the near future.

A PEGlação é uma bem sucedida estratégia nano-biotecnológica que envolve a ligação covalente do polietilenoglicol (PEG) a uma droga para melhorar sua farmacocinética, farmacodinâmica e perfil imunológico, e portanto, aumentar seu efeito terapêutico. Atualmente, a PEGlação é usada para modificar proteínas, peptídeos, oligonucleotídeos e fragmentos de anticorpos. A Uricase (EC 1.7.3.3, UC) é uma enzima pertencente à classe das oxidorredutases, responsável pela oxidação do ácido úrico, produzindo alantoína. Essa enzima é encontrada em muitos organismos vivos como: bactérias, leveduras, fungos, vegetais e animais. Entretanto, durante a evolução das espécies o gene da UC tornou-se inativo, por isso, em humanos a UC é inativa. Nesse sentido, a UC adquiriu destaque como um potencial fármaco uricolítico, devido à necessidade do desenvolvimento de novos agentes terapêuticos no tratamento de hiperuricemia e gota. Neste estudo, a uricase recombinante purificada de Candida sp (UC-r) e a de rim bovino (UC-b) foram modificadas por PEGlação com mPEG-p-nitrofenil carbonato (mPEG-pNP) e 2-O-mPEG-4,6-dicloro-s-triazina (mPEG-CN), produzindo conjugados com considerável atividade enzimática residual UC-r-mPEG-pNP (87%), UC-r-mPEG-CN (75%) e UC-b-mPEG-pNP (75%), UC-b-mPEG-CN (50%).Além disso, os conjugados obtidos com a UC-r e UC-b apresentaram valores de KM menores do que as enzimas nativas, indicando que a PEGlação conferiu uma interessante propriedade aos conjugados, que permitiu um aumento da afinidade da UC-r e UC-b pelo ácido úrico. O efeito do pH e da temperatura sobre a UC-r e UC-b modificadas indicou que os conjugados obtidos foram mais ativos em pH próximo ao fisiológico e mais estáveis do que a respectiva enzima nativa. As formas PEGladas da UC-r e UC-b foram mais resistentes à ação de diferentes proteases e mantiveram-se estáveis em soro humano, indicando que a PEGlação favoreceu a resistência a degradação proteolítica. Análises espectroscópicas de dicroísmo circular (CD) e infravermelho (FTIR) não apresentaram nenhuma diferença relevante entre a estrutura protéica da UC-r nativa e PEGlada. Estudos in vivo com coelho e camundongos Balb/c mostraram que a UC-r nativa induziu uma intensa resposta imune sendo altamente imunogênica. Por outro lado, a UC-r PEGlada quando injetada cronicamente em camundongos não induziu qualquer resposta detectável de anticorpos. Esses resultados indicam uma suficiente redução da imunogenicidade dessa enzima, devido à conjugação do mPEG-pNP ou mPEG-CN, tornando-a adequada para um possível uso terapêutico. Portanto, nesse trabalho, os resultados obtidos com a UC-r de Candida sp, mostram que dois conjugados apresentaram interessantes propriedades físico-química, biológicas e imunológicas, que permitiram um significativo avanço na transformação de uma enzima de origem fúngica em uma droga, com uma possível aplicação terapêutica no tratamento de hiperuricemia e gota. / PEGylation is a successful nanobiotechnology strategy that involves the covalent attachment of polyethylene glycol (PEG) to a drug to improve its pharmacokinetic, pharmacodynamic, and immunological profiles, and thus, enhance its therapeutic effect. Currently, PEGylation is used to modify proteins, peptides, oligonucleotides, antibody fragments, and small organic molecules. Uricase (EC 1.7.3.3, UC) is an enzyme belonging to the class of oxidorreductases responsible for the oxidation of uric acid, producing allantoin. This enzyme is found in many living organisms such as bacteria, yeasts, fungi, plants and animals. However, during the evolution of the species gene became inactive UC, therefore, in humans UC is inactive. Accordingly, UC has acquired prominence as a potential drug uricolytic due to the need of developing new therapeutic agents for the treatment of hyperuricemia and gout. In this study, purified recombinant uricase from Candida sp (UC-r) and ox kidney (UC-b) were modified by PEGylation with mPEG-p-nitrophenyl-carbonate (mPEG-pNP) and 2-O-mPEG-4,6-dichloro-s-triazine (mPEG-CN), producing conjugates with considerable residual enzyme activity UC-r-mPEG-pNP (87%), UC-r-mPEG-CN (75%) and UC-b-mPEG-pNP (75%),UC-b-mPEG-CN (50%). In addition, conjugates obtained with the UC-r and UC-b had lower KM values than native enzymes, indicating that the PEGylation gave an interesting property the conjugate that increased the affinity of UC-r and UC-b by uric acid. The effect of pH and temperature on the modified UC-r and UC-b indicated that the conjugates were more active at pH close to the physiological and more stable than its native enzyme. PEGylated forms of UC-r and UC-b were more resistant to the action of different proteases and remained stable in human serum, indicating that the PEGylation favored resistance to proteolytic degradation. Spectroscopic analysis of circular dichroism (CD) and infrared (FTIR) did not show any relevant difference in protein structure between native and PEGylated UC-r. In vivo studies with rabbit and Balb/c mice showed that UC-r native elicited an intense immune response being highly immunogenic. On the other hand, the PEGlated UC-r when chronically injected into mice did not induce any detectable response to antibodies. These results indicate a sufficient reduction of immunogenicity of this enzyme, due to conjugation of mPEG-pNP or mPEG-CN, making it suitable for possible therapeutic use. Therefore, the results obtained with the UC-r of Candida sp, showed that two conjugates have interesting physical-chemical, biological and immunological, which allowed a significant advance in the transformation of an enzyme of fungal origin in a drug with a possible application therapeutic in the treatment of hyperuricemia and gout.

O objetivo deste trabalho foi avaliar os nucleotídeos, como potenciais promotores do crescimento de leitões recém-desmamados, por meio de estudos da morfometria de órgãos, histologia do epitélio intestinal e desempenho dos animais. Foi realizado um experimento em blocos casualizados, com 33 dias de duração, para testar cinco tratamentos que consistiam em ração basal com níveis de 0, 2.000, 4.000, 6.000 e 8.000 ppm de nucleotídeos. Para o desempenho, foram utilizados 60 leitões com idade média de 21 dias e peso inicial de 5,50 ± 1,56 kg, quatro repetições por tratamento e três animais por unidade experimental. Ao final do período experimental, um animal de cada unidade experimental (totalizando 20 animais) foi abatido para avaliação da morfometria dos órgãos e histologia do epitélio intestinal. Não foi detectado qualquer efeito significativo (P>0,05) dos níveis de nucleotídeos sobre o ganho diário de peso e consumo diário de ração durante os períodos de 1 a 14 e 1 a 33 dias de experimentação. Contudo, é importante ressaltar que, em relação ao tratamento controle, o melhor nível (4.000 ppm) para conversão alimentar no período de 1 a 14 dias (melhora de 7%), foi o pior no período de 1 a 33 dias de experimentação, (piora de 12%), muito embora sem afetar negativamente o ganho de peso e o consumo de ração. Com relação à morfometria dos órgãos e a histologia do epitélio intestinal dos animais, os nucleotídeos proporcionaram redução linear no peso relativo do fígado e do colón. Assim, os nucleotídeos não evidenciaram o efeito promotor do crescimento de leitões na fase de creche, alimentados com dietas práticas complexas, baseadas em milho, milho prégelatinizado, glúten de milho, soro de leite em pó, farelo de soja, levedura seca, farinha de peixe, (suplementados com aminoácidos sintéticos, óxido de zinco e colistina) e alojados em adequadas condições de ambiente. / The purpose of this work was to evaluate the effect of nucleotides as potential growth promoters of weanling pigs, based on performance, organ morphometry and intestinal epithelium histology. A 33-d randomized complete block design experiment was carried out to test five treatments, consisting on basal diet with 0, 2,000, 4,000, 6,000 and 8,000 ppm of nucleotides. Sixty pigs (averaging 21 days of age and 5.50 ± 1.56 kg live weight), four replications per treatment, and three animals per experimental unit were used for performance data. At the end of experimental period, one animal per pen (a total of 20 animals) was slaughtered for organ morphometry and intestinal epithelium histology data. No significant effects of nucleotide levels (P>0.05), on daily weight gain and daily feed intake were observed, during the period of 1 to 14 and 1 to 33 days of experiment. However is important to emphasize that, compared to control treatment, the best level (4,000 ppm) for feed conversion for 1-14 d period (7 % improvement) was the worse level (P=0.003) for 1-33 d period (12 % worse), even though any effect was observed on daily gain and daily feed intake. Concerning to organ morphometry and intestinal epithelium histology, added nucleotides gave linear depressive effects on relative liver and colon weights. Thus, nucleotides did not show growth promoter effect on weaniling pigs fed practical complex diet, based on corn, pre-cooked corn, corn gluten meal, dried whey, soy bean, dried yeast, fish meal, (supplemented with amino acid, zinc oxide and colistin) and housed in a clean environment.

L'impact de la nutrition sur l'immunité intestinale de la truite arc-en-ciel est encore mal connu. C'est pourquoi cette thèse avait pour objectifs de mieux caractériser son système immunitaire intestinal et d'évaluer les possibilités de modulation de la réponse immune intestinale par l'ajout de nucléotides libres dans son alimentation. Nos résultats indiquent que les phagocytes intestinaux présentent une activité de phagocytose plus faible que ceux du rein antérieur. La cytotoxicité naturelle mesurée au niveau intestinal est deux fois plus élevée que celle du rein antérieur et cette observation est corrélée à une augmentation du transcrit codant NKEF (Natural Killer Enhancement Factor). Nous avons également montré que les lymphocytes intestinaux ne répondent pas à une stimulation mitogénique in vitro et que ceci n'est pas due à l'apoptose des cellules. Une forte expression des transcrits codant CD8a et CD3 a été détectée dans les leucocytes intestinaux, ce qui suggère une importante proportion de lymphocytes T exprimant la forme homodimérique aa de CD8 dans ce tissu. Enfin, nous avons montré que l'ajout de nucléotides libres à l'alimentation de truites saines stimule la prolifération spontanée ainsi que la phagocytose des leucocytes intestinaux in vitro. Par contre, aucune modulation de la cytotoxicité naturelle ou de l'expression des transcrits codant les marqueurs spécifiques des lymphocytes T et B et les cytokines inflammatoires n'a été observée. Il serait à présent intéressant de renouveler ces essais en utilisant des poissons infectés afin de pouvoir observer l'effet des nucléotides sur la réponse inflammatoire et sur la réponse spécifique / The impact of nutrition on rainbow trout intestinal immunity, a farmed fish with high economic value, remains unclear. Consequently, the objectives of this thesis were to better characterize the intestinal immune system of that fish and to determine if it is possible to modulate its intestinal immune response by dietary free nucleotides. Our results show that intestinal phagocytes are less activated by yeast cells but when they are activated they can ingest as many yeast cells as their head kidney (HK) counterparts. We noted that the natural cytotoxic activity of intestinal leukocytes is twice higher than the one of HK leukocytes. This natural cytotoxic activity is correlated with an increase of transcripts encoding the natural killer enhancement factor (NKEF). Intestinal leukocytes did not respond to an in vitro mitogenic stimulation. This lack of response is not due to apoptosis. We also observed a high expression of CD8a and CD3 transcripts in gut leukocytes, suggesting that the intestine could contain a high proportion of T cells expressing the aa homodimeric form of CD8. Finally, we observed that dietary free nucleotides stimulate the spontaneous proliferation and the phagocytic activity of intestinal leucocytes in vitro. However, they did not modulate natural cytotoxicity activity nor did they affect the amounts of transcripts encoding specific markers of T and B lymphocytes and inflammatory cytokines. In the future, it will be interesting to repeat these experiments using infected fish in order to study the effect of nucleotides on the inflammatory and specific immune responses

L’objectif de cette thèse était de caractériser le rôle des différentes familles de phosphodiestérases (PDEs), les enzymes de dégradation du 3'-5'- adénosine monophosphate cyclique (AMPc), dans la régulation de la signalisation de l’AMPc dans deux types de cellules musculaires lisses (CMLs), l’aorte de rat (CMLAR) et la vessie de rat néonatal (CMLVRN). Dans les CMLARs en culture, nous avons déterminé le profil d’expression et d’activité des PDE-AMPc. Nous avons alors montré, à l’aide de la technique de FRET basée sur une sonde sensible à l’AMPc pour mesurer l’AMPc en temps réel dans une cellule isolée, que l’inhibition de la PDE4 démasque un effet d’hydrolyse de l’AMPc cytosolique par la PDE1 et la PDE3, alors que les PDE3 et PDE4 agissent de façon synergistique dans le compartiment sous-membranaire. Les mécanismes de cette compartimentation subcellulaire des signaux restent à caractériser.Dans les CMLVRNs, les PDE3 et PDE4 régulent les contractions phasiques, par des mécanismes différents. L’inhibition de la PDE4 limite les contractions stimulées par le carbachol par un mécanisme dépendant de la protéine kinase A, impliquant une augmentation de la fréquence des sparks calciques, qui entrainent l’activation des canaux potassiques BK, assurant en final une diminution des transitoires calciques. Au contraire, l’effet de l’inhibition de la PDE3 implique la protéine kinase G mais par un mécanisme qui reste à définir.En conclusion, ce travail montre que dans les CMLs, les différents familles de PDE-AMPc sont douées de spécificité de fonction et/ou de mécanisme d’action, et participent ainsi à une compartimentation subcellulaire des voies de signalisation. / The aim of the present thesis was to characterize the role of the different families of phosphodiesterases (PDEs), the enzymes degrading 3'-5'-cyclic adenosine monophosphate (cAMP), in controlling the cAMP signalling in two distinct smooth muscle cells (SMCs), the rat aorta SMC (RASMCs) and the rat bladder SMC (RBSMCs).In cultured RASMCs, we firstly characterized the pattern of cAMP-PDE expression and activity. We then showed, by using a FRET-based cAMP sensor to explore cAMP signals in living cells, that PDE4 inhibition unmasks an effect of PDE1 and PDE3 on cytosolic cAMP hydrolyzis, whereas PDE3 and PDE4 act synergistically at the submembrane compartment. The mechanisms of this subcellular compartmentation need to be characterized. In neonatal RBSMCs, we showed that both PDE3 and PDE4 are involved in regulating the phasic contractions albeit through distinct mechanisms. PDE4 inhibition inhibits the carbachol-enhanced contractions through a protein kinase A-dependent pathway involving an increase in Ca2+ sparks frequency which activates BK channels to ultimately decrease Ca2+ transients, whereas PDE3 inhibition acts through a protein kinase G-dependent pathway through a still unknown mechanism.In conclusion, our work shows that in the SMC, the different cAMP-PDE families exhibit a specificity in their function and/or mechanism of action, thus participating to a subcellular signaling compartmentation.

Espécies autopoliploides são extremamente importantes na agricultura. No entanto, a estrutura complexa de seus genomas não é bem compreendida. Apesar de todos os avanços no mapeamento genético de autotetraploides, a grande maioria dos modelos utilizados para a construção de mapas em espécies autopoliploides com elevado nível de ploidia, tais como a canade- açúcar, são aproximações daqueles usados para organismos diplóides. Assim, este trabalho teve como objetivo o desenvolvimento de um novo modelo para construção de mapas genéticos em espécies autopoliploides com qualquer nível de ploidia e incluindo marcadores com todas as dosagens possíveis. Para tanto foi utilizada a tecnologia dos modelos de Markov ocultos. O modelo aqui apresentado pode ser aplicado a dados de marcadores dominantes e codominantes, com comportamento bialélico ou multialélico. O método baseia-se no cálculo das probabilidades condicionais que compõem a matriz de transição seguido da redução de sua dimensão usando uma abordagem computacional. O uso do método foi ilustrado em uma população de mapeamento de cana-de-açúcar proveniente do cruzamento entre duas variedades pré-comerciais (IACSP 95-3018 × IACSP 93-3046) e genotipadas com três tipos de marcadores: SNPs, microssatélites e AFLPs. Os resultados indicam que o novo método é muito eficiente na obtenção de mapas genéticos, mesmo em situações com níveis de ploidia altos e marcadores com altas doses, particularmente quando estes marcadores têm comportamento codominante. Também foi possível estimar a verossimilhança, as frações de recombinação e as fases de ligação usando a abordagem multiponto, a qual leva em consideração todos os marcadores do grupo de ligação analisado simultaneamente. O novo modelo aqui proposto representa um importante passo para realizar futuramente a localização de regiões genômicas associadas à variação das características quantitativas, no entendimento da arquitetura genética de tais características e na montagem de genomas de espécies autopoliploides. / Autopolyploid species are extremely important in agriculture. However, the complex structure of their genomes is not well understood. Despite all advances in genetic mapping of autotetraploids, the vast majority of the models used for autopolyploid species with high ploidy level, such as sugarcane, are approximations of those used in diploid organisms. Thus, the aim of this work was to develop a new model to build genetic linkage maps in autopolyploid species with any ploidy level, including markers with all possible dosages. For doing so, hiddenMarkov model technology was used. The new model presented herein can be applied to dominant and codominantmarkers data, with biallelic or multiallelic behavior. The method is based on the calculation of conditional probabilities that comprise the transition matrix followed by a reduction of its dimension using a computer-based approach. An application of the method was illustrated with a sugarcane mapping population derived from a cross between two pre-commercial varieties (IACSP 95-3018 × IACSP 93-3046), scored with three types of markers: SNPs, microssatellite and AFLPs. The results indicate that the new method is very efficient in obtaining genetic maps, even for high ploidy levels and for markers with high dosages, particularly when these markers have codominant behavior. It was also possible to estimate the likelihood, the recombination fractions and the linkage phases between allmarkers using themultipoint approach, which takes into account all markers of the linkage group simultaneously. The new model proposed in this work represents a major step towards the location of genomic regions associated with variation in quantitative traits and its genetic architecture, and assembling autopoliploid genome sequences.