[ES] La comprensión de los aspectos de la funcionalidad de las células que cuentan para los mecanismos de las enfermedades es el mayor reto de la medicina personalizada. A pesar de la disponibilidad creciente de los datos de genómica y transcriptómica, sigue existiendo una notable brecha entre la detección de las perturbaciones en la expresión de genes y la comprensión de su contribución en los mecanismos moleculares que últimamente tienen relación importante con el fenotipo estudiado. A lo largo de la última década, distintos modelos computacionales y matemáticos se han propuesto para el análisis de las rutas. Sin embargo, estos modelos no toman en cuenta los mecanismos dinámicos de las rutas como la estructura y las interacciones entre genes y proteínas. En esta tesis doctoral, presento dos modelos matemáticos ligeramente distintos, para integrar los datos transcriptómicos masivos de humano con un conocimiento previo de de las rutas de señalización y metabólicas para estimar las actividades mecánicas que están detrás de esas rutas (MPAs). Las MPAs son variables continuas con valores de nivel individual que pueden ser usadas con los modelos de aprendizaje de máquinas y métodos estadísticos para determinar los biomarcadores que podemos usar para los diagnósticos tempranos y la clasificación de subtipos de enfermedades, además de poder sugerir las dianas terapéuticas potenciales para las intervenciones individualizadas. El objetivo global es desarrollar nuevos y avanzados enfoques de la biología de sistemas para proponer unas hipótesis funcionales que nos ayuden a entender e interpretar los mecanismos complejos de las enfermedades. Estos mecanismos son cruciales para mejorar los tratamientos personalizados y predecir los resultados clínicos. En primer lugar, contribuí al desarrollo de un método que está diseñado para extraer las subrutas elementales desde la ruta de señalización con sus actividades estimadas. Posteriormente, este algoritmo se ha adaptado a los módulos metabólicos y se ha implementado como una herramienta web. Finalmente , el método ha revelado un panorama metabólico para una lista completa de diferentes tipos de cánceres. En este estudio, analicé el perfil metabólico de 25 tipos de cáncer distintos y se validó el método usando varios enfoques computacionales y experimentales. Cada método desarrollado en esta tesis ha sido enfrentado a otros métodos similares existentes, evaluados por sus sensibilidades y especificidades, experimentalmente validados cuando fue posible y usados para predecir resultados clínicos de varios tipos de cánceres. La investigación descrita en esta tesis y los resultados obtenidos fueron publicados en distintas revistas arbitradas que están relacionadas con el cáncer y biología de sistemas, y también en los periódicos nacionales. / [CA] La comprensió dels aspectes de la funcionalitat de les cèl·lules que compten per als mecanismes de les malalties és el major repte de la medicina personalitzada. Malgrat la disponibilitat creixent de les dades de genòmica i transcriptómica, continua existint una notable bretxa entre la detecció de les pertorbacions en l'expressió de gens i la comprensió de la seua contribució en els mecanismes moleculars que últimament tenen relació important amb el fenotip estudiat. Al llarg de l'última dècada, diferents models computacionals i matemàtics s'han proposat per a l'anàlisi de les rutes. No obstant això, aquests models no tenen en compte els mecanismes dinàmics de les rutes com l'estructura i les interaccions entre gens i proteïnes. En aquesta tesi doctoral, presente dos models matemàtics lleugerament diferents, per a integrar les dades transcriptómicos massius d'humà amb un coneixement previ de de les rutes de senyalització i metabòliques per a estimar les activitats mecàniques que estan darrere d'aqueixes rutes (MPAs). Les MPAs són variables contínues amb valors de nivell individual que poden ser usades amb els models d'aprenentatge de màquines i mètodes estadístics per a determinar els biomarcadores que podem usar per als diagnòstics primerencs i la classificació de subtipus de malalties, a més de poder suggerir les dianes terapèutiques potencials per a les intervencions individualitzades. L'objectiu global és desenvolupar nous i avançats enfocaments de la biologia de sistemes per a proposar unes hipòtesis funcionals que ens ajuden a entendre i interpretar els mecanismes complexos de les malalties. Aquests mecanismes són crucials per a millorar els tractaments personalitzats i predir els resultats clínics. En primer lloc, vaig contribuir al desenvolupament d'un mètode que està dissenyat per a extraure les subrutas elementals des de la ruta de senyalització amb les seues activitats estimades. Posteriorment, aquest algorisme s'ha adaptat als mòduls metabòlics i s'ha implementat com una eina web. Finalment, el mètode ha revelat un panorama metabòlic per a una llista completa de diferents tipus de càncers. En aquest estudi, vaig analitzar el perfil metabòlic de 25 tipus de càncer diferents i es va validar el mètode usant diversos enfocaments computacionals i experimentals. Cada mètode desenvolupat en aquesta tesi ha sigut enfrontat a altres mètodes similars existents, avaluats per les seues sensibilitats i especificitats, experimentalment validats quan va ser possible i usats per a predir resultats clínics de diversos tipus de càncers. La investigació descrita en aquesta tesi i els resultats obtinguts van ser publicats en diferents revistes arbitrades que estan relacionades amb el càncer i biologia de sistemes, i també en els periòdics nacionals. / [EN] Understanding the aspects of the cell functionality that account for disease or drug action mechanisms is the main challenge for precision medicine. In spite of the increasing availability of genomic and transcriptomic data, there is still a gap between the detection of perturbations in gene expression and the understanding of their contribution to the molecular mechanisms that ultimately account for the phenotype studied. Over the last decade, different computational and mathematical models have been proposed for pathway analysis. However, they are not taking into account the dynamic mechanisms contained by pathways as represented in their layout and the interactions between genes and proteins. In this thesis, I present two slightly different mathematical models to integrate human transcriptomic data with prior knowledge of signalling and metabolic pathways to estimate the Mechanistic Pathway Activities (MPAs). MPAs are continuous and individual level values that can be used with machine learning and statistical methods to determine biomarkers for the early diagnosis and subtype classification of the diseases, and also to suggest potential therapeutic targets for individualized therapeutic interventions. The overall objective is, developing new and advanced systems biology approaches to propose functional hypotheses that help us to understand and interpret the complex mechanism of the diseases. These mechanisms are crucial for robust personalized drug treatments and predict clinical outcomes. First, I contributed to the development of a method which is designed to extract elementary sub-pathways from a signalling pathway and to estimate their activity. Second, this algorithm adapted to metabolic modules and it is implemented as a webtool. Third, the method used to reveal a pan-cancer metabolic landscape. In this study, I analyzed the metabolic module profile of 25 different cancer types and the method is also validated using different computational and experimental approaches. Each method developed in this thesis was benchmarked against the existing similar methods, evaluated for their sensitivity and specificity, experimentally validated when it is possible and used to predict clinical outcomes of different cancer types. The research described in this thesis and the results obtained were published in different systems biology and cancer-related peer-reviewed journals and also in national newspapers. / Cubuk, C. (2020). Modeling Functional Modules Using Statistical and Machine Learning Methods [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/156175

Células animais são alvo de pesquisas visando sua utilização como plataforma para a expressão de proteínas recombinantes, desde vacinas veterinárias até fatores de coagulação para hemofílicos. Exemplos incluem células de inseto Drosophila melanogaster S2 e células de mamífero BHK-21, que vêm sendo estudadas visando a sua utilização para a produção da glicoproteína do vírus da raiva. Independentemente da estratégia de cultivo utilizada, altas concentrações celulares são em geral associadas a uma maior produção da proteína de interesse. O objetivo deste trabalho foi o de investigar estratégias que possibilitariam o cultivo de células animais em altas concentrações celulares. Células de inseto Drosophila melanogaster S2 produtoras da glicoproteína do vírus da raiva foram cultivadas em frascos agitados a 100 rpm e 28, em meio livre de soro SF 900 II suplementado com os aminoácidos asparagina, cisteína, prolina e serina. A adição dos quatro aminoácidos no meio de cultura refletiu em um aumento da concentração celular máxima (XV MÁX) em 16%. Cisteína, quando adicionada isoladamente no meio de cultura, refletiu em uma velocidade específica máxima de crescimento celular (MÁX) 56% maior. Nessa condição, o fator de conversão glicose a célula (YX/GLC) foi 47% maior, indicando um metabolismo de glicose mais eficiente na geração de células. Esses resultados indicam que cisteína é provavelmente substrato limitante do cultivo de células S2AcGPV em meio SF 900 II. Já células de mamífero BHK-21 (C13), adaptadas ao crescimento em suspensão, foram cultivadas em processo de perfusão, processo contínuo em que há retenção celular, o que permite alcançar concentrações celulares mais altas que processos em batelada ou em modo contínuo sem retenção celular. Foi utilizado um biorreator do tipo tanque agitado com 1,5 L de volume de trabalho e spin-filter interno, com poro de diâmetro igual a 10 m, acoplado ao eixo do impelidor. Durante o cultivo, o pH foi controlado em 7,2, a agitação em 80 rpm, a temperatura em 37 e o oxigênio dissolvido em 50% da saturação com o ar. A concentração celular máxima alcançou 15,7 x 106 céls mL-1, muito superior à do cultivo em batelada (aproximadamente 5 x 106 céls mL-1). A viabilidade celular foi superior a 90% durante os 48 dias de cultivo. Na fase batelada do cultivo em perfusão, as velocidades de consumo de glicose (qGLC) e de glutamina (qGLN) foram 84% e 32% maiores, respectivamente, em relação às velocidades observadas no cultivo em batelada. Analogamente, as velocidades de produção de lactato (qLAC) e de amônio (qNH4) foram 78% e 102% maiores, respectivamente. Ainda, o coeficiente de manutenção celular não foi desprezível, e o consumo de glicose associado à manutenção celular foi de 83%. Esses dados indicam que a presença do spin-filter interno pode estar associada a estresse celular. Na perfusão, a concentração celular foi cerca de 3 vezes maior do que no cultivo contínuo sem reciclo de células. Provou-se que é possível cultivar células BHK-21 adaptadas a crescimento em suspensão em altas concentrações celulares em escala laboratorial, utilizando biorreator de bancada e spin-filter interno como sistema de retenção celular. / Animal cells have been under research as a platform for the expression of recombinant proteins, ranging from veterinary vaccines to blood coagulation factors for treating hemophilia. Examples include insect Drosophila melanogaster S2 and hamster BHK-21 cells, currently being studied for the production of rabies virus glycoprotein. Regardless of the cultivation strategy, high cell concentrations are usually associated to a higher protein production. Thus, the aim of this research was to investigate animal cell cultivation strategies that would allow higher cell concentrations than those previously reported. Cells of Drosophila melanogaster S2 expressing the rabies virus glycoprotein (S2AcGPV) were cultivated in shake flasks at 100 rpm and 28 , in SF 900 II serum-free medium supplemented with the following amino acids: asparagine, cysteine, proline, and serine. The addition of the four amino acids to the medium increased the maximum cell concentration (XV MAX) in 16%. When only cysteine was added to the medium, the maximum specific growth rate (ÊMAX) was 56% higher. In this condition, the cell yield on glucose (YX/GLC) was 47% higher, indicating a more efficient glucose metabolism. These results show that cysteine is likely a limiting substrate of S2AcGPV cells growing in SF 900 II medium. In turn, baby hamster kidney cells (BHK-21/C13), adapted to growth in suspension culture, were cultivated in perfusion, a continuous process with cell retention that allows higher cell concentration than batch or continuous cultures without cell retention. A stirred tank bioreactor with a working volume of 1.5 L was used, with an internal spin-filter with 10 µm diameter pores attached to the impeller shaft. Temperature was controlled at 37 , pH at 7.2, agitation at 80 rpm and dissolved oxygen at 50% of air saturation. The maximum cell concentration reached 15.7 x 106 cells mL-1, much higher than the cell concentration achieved in a standard batch cultivation (5 x 106 cells mL-1). Cell viability was above 90% during the 48-day cultivation period. During the batch phase of the perfusion cultivation, specific rates of glucose (qGLC) and glutamine (qGLN) consumption were 84% and 32% higher, respectively, when compared to the batch cultivation. Similarly, the specific rates of lactate (qLAC) and ammonium (qNH4) formation were 78% and 102% higher, respectively. During perfusion, the cell maintenance coefficient was not negligible and represented 83% of total glucose consumption. These data indicate that the presence of an internal spin-filter may be associated to cell stress. In perfusion, cell concentration was about 3 times higher than that in continuous culture without cell recycle. In conclusion, it was proved that suspension-adapted BHK-21 cells can be cultivated in a laboratory-scale bioreactor with an internal spin-filter, in order to achieve high cell concentrations.

A atividade contrátil no músculo esquelético é um estímulo potente na indução de alterações no metabolismo de glicose e ácidos graxos. Por sua vez, a contração muscular também aumenta a produção de espécies reativas de oxigênio (EROs). O objetivo do presente trabalho foi avaliar o efeito da remoção de EROs, induzida pelo tratamento com o antioxidante N-Acetilcisteína, na captação de glicose, atividades de enzimas glicolíticas e do ciclo de Krebs, produção de lactato, oxidação mitocondrial de ácidos graxos, expressão dos genes do transportador de glicose 4 (GLUT-4), hexoquinase II (HKII), fosfofrutoquinase 1 (PFK-1), carnitina palmitoil transferase 1 (CPT-1) e citrato sintase (CS) em células musculares esqueléticas durante contrações induzidas por eletroestimulação in vitro. Com esse estudo, demonstrou-se que as EROs atuam como sinalizadores das respostas metabólicas mediadas pela atividade contrátil e que a sinalização redox regula o metabolismo de glicose e ácidos graxos em células musculares esqueléticas. / Contractile activity is a potent stimulus for induce changes in glucose and fatty acid metabolism in skeletal muscle. During muscle contraction, the production of reactive oxygen species (ROS) is increased. The purpose of this study was evaluate the effect of removal of ROS, induced by treatment with the antioxidant N-Acetylcysteine, on glucose uptake, activities of glycolytic and TCA cycle enzymes, lactate production, mitochondrial fatty acid oxidation, gene expression of glucose transporter 4 (GLUT-4), hexokinase II (HKII), phosphofructokinase 1 (PFK-1), carnitine palmitoyl transferase 1 (CPT-1) and citrate synthase (CS) mediated by moderate contractions induced by electrical stimulation in vitro. In this study we demonstrated that ROS act as signaling molecules on contraction-mediated metabolic responses and that redox signaling regulates glucose and fatty acid metabolism in skeletal muscle cells.

Made available in DSpace on 2015-03-04T18:51:14Z (GMT). No. of bitstreams: 1 Tese Completa.pdf: 5651353 bytes, checksum: 51c96a7210d03ea18a0c2bf0251eec36 (MD5) Previous issue date: 2009-06-01 / As leucemias são desordens proliferativa nas células tronco hematopoiéticas pluripotentes caracterizada por mutações que comprometem seus precursores mielóides ou linfóides levando ao desenvolvimento de leucemias similares quanto ao fenótipo (Mielóide ou Linfóide) e forma (Crônica ou Aguda). Descrito em 1960, o cromossomo philadelphia (Ph) foi a primeira anomalia cromossômica associada a uma neoplasia, a Leucemia Mielóide Crônica (LMC). Em 1973, foi demonstrado que o cromossomo Ph resulta da translocação recíproca entre os braços longos do cromossomo 9 e 22 [t(9;22)(q34;q11)], produzindo um gene quimérico BCR-ABL, encontrado em 95% dos casos de LMC. A proteína quimérica codificada, BCR-ABL, com atividade tirosina quinase descontrolada, é o fator causal da LMC. Durante os anos 1990, uma série de moléculas sintéticas foram desenvolvidas e testadas para inibir especificamente a atividade tirosina quinase da proteína BCR-ABL, o Imatinib (STI-571 ou Gleevec) foi a primeira dessas drogas aprovadas e usadas como agente terapêutico contra a LMC, demonstrando redução do número de células leucêmicas em quase todos pacientes. No entanto muitos pacientes com resistências primárias ou secundárias foram frequentemente relatados. Os mecanismos de resistência são provavelmente heterogêneos, e no mínimo dois mecanismos envolvendo o gene BCR-ABL foram descritos em estudos realizados in vivo: amplificação do gene e ocorrência de mutações que resultam em substituições de aminoácidos associadas com o fenótipo de resistência. Diferentes níveis de resistência são frequentemente associadas a mutações pontuais recorrentes encontradas no domínio quinase da proteína c-ABL em regiões como: sítio catalítico, alça de ativação (A-loop) e alça de fosforilação (P-loop). Os primeiros estudos computacionais foram realizados com o mutante Thr334Ile e mutações na região do P-loop, e ajudaram a entender num nível molecular, os mecanismos de resistência ao Imatinib. Neste trabalho, realizamos um estudo estrutural e termodinâmico das interações entre os ligantes Imatinib e Nilotinib no sítio ativo da proteína c-ABL selvagem e em 12 proteínas com mutações específicas, além de determinar a importância do solvente (com particular interesse na molécula de água denominada Cw - que medeia a interação fármaco-proteína) no processo de resistência aos fármacos. No presente trabalho, utilizamos o método semi-empírico de energia de interação linear (LIE) de maneira alternativa: analisando as interações entre diferentes mutantes da proteína c-ABL e um inibidor (Imatinib ou Nilotinib). Os coeficientes de LIE obtidos foram os seguintes: com Cw fixa (restrição de Cw na posição inicial) = 0,2169; = 0,0654; = 1,4159; e Cw livre (sem restrição de Cw na posição inicial) = 0,0394; = 0,0077; = -2,0503. O melhor ajuste dos coeficientes de LIE foram obtidos nas simulações sem restrição da posição inicial de uma molécula de água conservada (Cw), essa escolha foi baseada no valor de energia livre absoluta da proteína c-ABL selvagem ( ) ser sempre um número mais negativo quando comparado com o valor da energia livre absoluta de cada proteína c-ABL mutada. O uso do método LIE (Linear Interaction Energy) com essa estratégia foi eficiente para analisar o efeito da interação entre diferentes proteínas c-ABL mutantes e um ligante (Imatinib ou Nilotinib). Até o momento não existem simulações de dinâmica molecular na presença de outros domínios da proteína BCR-ABL: SH2 e SH3.

Cellular defense and metabolism are important biological processes in living cells. In this study, these two biological processes were investigated in two selected disease models: diabetes mellitus (DM) and severe acute respiratory syndrome associated coronavirus (SARS-CoV) infection by two-dimensional gel electrophoresis (2DE) coupled with Matrix-Assisted Laser Desorption Ionisation Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)-based proteomic approaches. The major findings are summarized as follows: / Our results on DM investigation can help to better understand the pathophysiological changes in patients with DM and the pathogenesis of hyperglycemia-caused complications. Data obtained from SARS-CoV studies provided novel insights into the molecular basis of the host cell response upon viral infection. / Protein profile of streptozotocin (STZ)-induced diabetic animal tissues, including mice liver, kidney and eye, and rats sera, indicated that DM has an impaired cellular defense system. These include the impairment in reactive oxygen species scavenging and the impairment in activation of complement system and innate immunity, and the enhancement in blood coagulation reaction. Our results also demonstrated that glycolysis and gluconeogenesis did not alter significantly in the liver of STZ-diabetic mice, while fatty acid oxidation and TCA cycle were attenuated under the same conditions. Moreover, we also detected other abnormal metabolism in aldehyde and amino acid, especially glutamate metabolism and the urea cycle. Abnormalities were also detected in lipid transport and metabolism. Besides, protein profile of mouse liver c37 cells indicated that high glucose may induce apoptosis in these cells, and this apoptotic effect may be mediated via the mitochondrial pathway. Furthermore, the proteomic results from the in vivo and in vitro diabetic models have prompted us to look for glucose responsive element on the promoters of these up-regulated hepatic genes. We found that the mouse aldolase 2 gene has glucose responsiveness in c37 cells treated with high glucose by semi-quantitative RT-PCR and promoter transfection assay. Finally, protein profile of Vero E6 cells strongly implicated that SARS-CoV can induce anti-apoptosis. This effect may be mediated via the mitochondrial pathway. Our data also suggested that the anti-apoptotic activity may be required for viral replication at the early stage of infection. While under the condition of long-term infection, this may be needed for viral survival. / Zhong Mingqi. / "October 2005." / Advisers: Sai Ming Ngai; Hon Ki Cheng. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6217. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (p. 223-248). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Vitamin B₁₂ deficiency has been difficult to diagnose, mainly due to the vitamin's lack of biological significance in serum in which it is usually assayed. This research has investigated the marker of vitamin B₁₂/cobalt (Co) deficiency in sheep, methylmalonic acid (MMA), in comparison with serum and liver vitamin B₁₂ concentrations in farm situations where vitamin B₁₂ deficiency is expected in order to establish more accurate reference ranges for serum and liver vitamin B₁₂, and MMA. In addition, an attempt was made to ascertain the vitamin B₁₂ requirements of preruminant (PR) lambs, and to determine whether metabolic demand for vitamin B₁₂ influences tissue concentrations. Furthermore, since the vitamin is active in biological tissues in form of its coenzymes, 5’ -deoxyadenosylcobalamin and methylcobalamin, a preliminary assessment of variation in the distribution of these coenzymes in liver in different situations has been sought. The first trial was set up to find out if the addition of propionate to the PR lamb's diet stimulated the uptake and/or storage of vitamin B₁₂ in the liver as a reflection of the need to deal with the incoming propionate. Sixteen ten day old lambs (Dorset Down/Coopworth cross-bred) were housed indoors soon after birth and fed on milk replacer. For half of the lambs 7.5 % (w:w) of the milk powder was replaced by propionate. Within each group, four lambs were treated with 250 µg vitamin B₁₂ twice weekly. Supplementation with vitamin B₁₂ increased liver concentrations from ~250 to ~900 nmol/kg fresh tissue, but there was no effect of propionate. Propionate addition did, however, result in increased plasma vitamin B₁₂ concentrations in vitamin B₁₂ supplemented groups, values being 3323 and 2355 pmol/l in propionate supplemented and control groups, respectively. This suggested that diet could influence plasma vitamin B₁₂ concentrations. An attempt was made to quantify the PR lamb's ability to absorb vitamin B₁₂ from the alimentary tract by comparing the ability of intra-muscular (IM) and oral vitamin B₁₂ to raise plasma and liver vitamin B₁₂ concentrations. Twenty-seven three to four day old lambs from a farm with marginal Co status were housed indoors and fed on milk replacer. They were divided into three groups: control (n=3), IM treatment (n=12) and oral treatment (n=12). The two treatment groups were further subdivided into five sub-groups. These received, respectively, 0.2 (n=3), 0.4 (n=2), 0.8 (n=2), 1.6 (n=2) and 3.2 µg OH-cbl/d (n=3). The oral groups received tenfold the amount of the comparable IM groups, on the assumption that if oral absorption of the vitamin is about 10 % both groups would show similar increases in plasma and liver vitamin B₁₂ concentration. None of the IM groups showed any significant change in plasma or liver vitamin B₁₂. In the oral groups only the group on the highest dose of vitamin B₁₂, viz 32 µg/d, showed increases in plasma and liver concentrations. It was concluded that either absorption of vitamin B₁₂ was greater than 10 % or that the vitamin was retained better when administered orally. The amount retained in the livers of the lambs in the highest oral group was calculated to represent ~ 7.5 % of the dose. In a follow-up 24 h trial, 14 of the above lambs were divided into three groups: Control (n=3), oral (n=6) and IM (n=5) treatment. The IM group received 3.2 µg OH-cbl and the oral group tenfold the amount as single doses at 0800 h. Blood samples were taken at regular intervals throughout the 24 h period and assayed for vitamin B₁₂, Vitamin B₁₂ concentrations in the IM group rose steeply within the first hour after injection to a concentration that was calculated to reflect 100 % uptake of the vitamin. It rose more slowly over about 8 h in the oral group. From the area under the curve absorption of the oral dose was estimated to be ~ 7 %. The next experiment involved a farm where Co deficiency had been reported previously. In the first year, 50 pregnant two-tooth Half-bred ewes were divided randomly into two groups of 25. One group received a Co bullet plus 1000 µg OH-cb1 IM, the other group remained unsupplemented. In the following year the trial was repeated. Ewes from the previous year's trial (by then four-tooths) were augmented by a new cohort of pregnant two-tooths to make up numbers to 75. After lambing the lambs were divided into four groups: first by their dams' vitamin B₁₂ treatment, then half of each group received injections of vitamin B₁₂ at approximately three weekly intervals while the other half remained untreated. The trials lasted about five months, from mid-pregnancy until weaning. Pasture Co was at its lowest at lambing in both years, 0.09 and 0.10µg/g DM, respectively. In the first year, vitamin B₁₂ concentrations in the untreated ewes rose from 340 to 950 pmol/l in plasma and decreased in liver from 330 to 170 nmol/kg fresh tissue. In the Co treated group, vitamin B₁₂ concentrations in plasma rose from 500 to 1550 pmol/l and in liver from 310 to 560 nmol/kg fresh tissue. In the second year, vitamin B₁₂ concentrations in serum in the unsupplemented groups fell from 500 to 260 pmol/l around lambing before rising again to starting values at weaning, and liver vitamin B₁₂ concentrations fell from 450 at the start to 230 nmol/kg fresh tissue at the end of the trial. Serum vitamin B₁₂ concentrations in the two-tooth supplemented group rose from < 500 to > 3000 pmol/l whereas in the four-tooth supplemented group serum vitamin B₁₂ levels started at ~2800 and rose to nearly 5000 pmol/l. The supplemented four-tooths maintained higher liver vitamin B₁₂ concentrations throughout compared to the supplemented two-tooths, viz 680 compared to below 400 at the start and 900 versus 650 nmol/kg fresh tissue at weaning, respectively. MMA in the untreated groups rose to 15 and to 8 µmol/l during early lactation in the first and second years, respectively, whereas MMA in the treated groups stayed below 3 µmol/l in the first season and below 1.5 µmol/l in the second season. There was a live weight response to treatment in the ewes as the unsupplemented groups showed a significantly lower weight gain during the trials than the supplemented groups, viz 10.0 versus 13.6 kg in the first year, and 10.6 versus 13.3 kg in the four-tooths and 9.9 versus 12.1 kg in the two-tooths in the second year. There was also a significant difference in faecal egg count (FEC) in the first year. FEC in the untreated group was higher during lactation than in the treated group, viz 590 versus 170 eggs per gram wet faeces (epg), respectively. In the second year, the two-tooths had a higher FEC than the four-tooths, viz 120 versus 40 epg during the same time span, respectively. While there was a trend for treatment having an effect on FEC similar to that in the first year it was not significant. Supplementation of ewes in the first year increased mean milk vitamin B₁₂ concentrations at lambing from 800 to 1400 pmol/l and at weaning from 1750 to 4000 pmol/l. In the second year, Co bullet treatment increased milk vitamin B₁₂ concentrations in the four-tooths and two-tooths from 1500 and 2300 to 4000 and 2900 pmol/l at lambing, and from 1800 and 1400 to 6200 and 4500 pmol/l at weaning, respectively. Treatment of ewes increased vitamin B₁₂ concentrations in the lambs which were not themselves supplemented. Plasma values in the first year increased from 160 to 325 pmol/l soon after birth and from 650 to 900 pmol/l at weaning, and liver values from 75 to 140 nmol/kg fresh tissue soon after birth and from 150 to 240 nmol/kg fresh tissue at weaning. In the second year, plasma vitamin B₁₂ concentrations increased from 160 to 380 pmol/l soon after birth and from 500 to 700 pmol/l at weaning, and in liver from 130 to 260 nmol/kg fresh tissue soon after birth and from 220 to 340 nmol/kg fresh tissue at weaning. There was also a significant effect of ewe supplementation on lamb MMA in 1997/1998 when values decreased from 19 to 8 µmol/l around the time of rumen development. MMA in the second year stayed below 3 µmol/l throughout in all groups of lambs. There was no difference in LWG between any groups of lambs. FEC was lowest in the group where both ewes and lambs were supplemented and highest in the group where neither ewes nor lambs were treated. Further investigations were conducted on farms in Southland with lambs post-weaning in order to compare changes in serum and liver vitamin B₁₂ with serum MMA and LWG to determine the critical time and level of deficiency. In the first year, three farms with 50 lambs each participated. Lambs from each farm were allocated to five groups of 10 animals each. The first group received a Co bullet at weaning, and each month another group was treated with a Co bullet. The lambs were weighed monthly, and blood and liver samples were taken prior to treatment and each subsequent month from five lambs of the first supplemented group. The trial lasted about four months. Serum vitamin B₁₂ concentrations in lambs at weaning were between 500 and 1000 pmol/l. Although supplementation increased serum levels for the first month this was followed by a drop to near or below starting concentrations. An exception was Farm 3 where serum vitamin B₁₂ concentrations rose again at the end of the trial. Liver vitamin B₁₂ concentrations also showed an overall decline from starting levels (200 to 300 nmol/kg fresh tissue) to the end of the trial (100 to 200 nmol/kg fresh tissue). MMA started around 2 µmol/l and reached between 6 and 7 µmol/l in the untreated lambs on Farms 1 and 3 two months after weaning before decreasing to around 3 µmol/l at the end of the trial, whereas the treated lambs maintained MMA concentrations around 2 µmol/l. On Farm 2 MMA started just below 5 µmol/l, decreased to around 1 µmol/l for treated and untreated lambs one month later and rose again to between 2.5 and 4 µmol/l, respectively, at the end of the trial. LWG was below average for all lambs (between 0.20 and 0.04 kg/d except for Farm I in the first month after weaning) but no significant differences were noted between treated and untreated lambs on any of the farms. Another trial was conducted on one of these farms in the following year. One hundred lambs were divided into two groups of 50 each at weaning and sampled monthly for about six months. One group was treated with two Co bullets, the other group remained untreated. Pasture Co was between 0.04 and 0.07 µg/g DM, yet serum levels for the untreated group stayed ~500 pmol/l throughout the trial. Serum vitamin B₁₂ concentrations for the treated group started at ~500 pmol/l, rose to ~2500 pmol/l before falling back to ~2000 pmol/l. Liver vitamin B₁₂ concentrations for the untreated and treated groups were 529 and 427 nmol/kg fresh tissue at weaning, respectively. This decreased for both groups to ~350 nmol/kg fresh tissue one month after weaning. In the untreated lambs liver values decreased further to ~290 nmol/kg fresh tissue whereas they increased to ~450 nmol/kg fresh tissue for the treated group at the end of the trial. MMA concentrations started between 2 and 3 µmol/l for both groups and increased to 4.5 µmol/l for the untreated group one month later before falling back to 3.2 µmol/l. In the treated group MMA decreased to ~1µmol/l and stayed at that level throughout the trial. There was no difference in weight gain. In order to obtain an understanding of the distribution of corrinoids in biological tissues a High Performance Liquid Chromatography method was developed. The sensitivity of the analytical method meant that it was only practical to assay mainly liver samples because of the higher vitamin B₁₂ concentrations than in other tissues. The general finding was that the coenzyme 5’ –deoxyadenosylcobalamin (ado-cbl) constituted the highest proportion of corrinoids in liver (45 %), followed by analogues (28 %), OH-cbl (24 %) and lastly methy1cobalamin (3 %). Ado-cbl did tend to be proportionately higher in supplemented than in unsupplemented animals (56 and 42 %, respectively), whereas biologically non-active analogues tended to be higher in untreated than in treated sheep (29 and 21 %, respectively). It was concluded that in the farm trials Co deficiency was only mild or not present although deficiency would have been predicted from the low vitamin B₁₂ concentrations in serum and liver and from raised MMA values. Therefore, currently used thresholds in New Zealand appear to be too high for vitamin B₁₂, and overseas values for MMA do not seem to be appropriate. Revised marginal ranges of 100 to 200 pmol/l for serum, 100 to 200 nmol/kg fresh tissue for liver and 10 to 20 µmol/l for MMA are suggested. Further, this work shows that Co bullets were effective in elevating blood and liver vitamin B₁₂concentrations for longer than one year. In the trials with preruminant lambs it was found that maintenance requirements were met by the vitamin B₁₂ content of milk replacer. There is evidence from indoor and farm trials that vitamin B₁₂ from milk was much more readily absorbed than vitamin B₁₂ from supplements. It was estimated that suckling lambs probably require between 1200 and 4000 pmol vitamin B₁₂/d, depending on age.

Thesis (Ph. D.)--University of Missouri--Columbia, 2004. / Typescript. Vita. Includes bibliographical references (leaves 166-179). Also issued on the Internet.

Les thérapies anti-tumorales se sont considérablement améliorées au cours de la dernière décennie. Toutefois, les traitements utilisés actuellement rencontrent d'importantes limitations, notamment dans le cas de cancers métastatiques, révélant l'urgence de développer de nouvelles approches. Ainsi, l'immunothérapie par transfert adoptif de cellules T représente une approche innovante particulièrement prometteuse. Son principe s'appuie sur l'injection de cellules T autologues spécifiques d'antigènes tumoraux, préalablement manipulées et amplifiées ex vivo, chez des patients rendus lymphopéniques par chimiothérapie et/ou radiothérapie. Toutefois, même si l'état lymphopénique est induit par ces 2 protocoles de conditionnements, leurs effets sur l'environnement de l'hôte ainsi que sur le devenir des cellules T greffées étaient, jusqu'à nos travaux, mal connus. Par le biais de modèles murins, nous avons pu démontrer que le devenir des cellules T diffère après transfert dans des souris irradiées ou traitées par chimiothérapie (Bu/Cy). Ainsi, après transfert dans des animaux irradiés, on observe une prolifération préférentielle des cellules T CD8, dépendante de l'IL-7, est observée alors qu'un transfert chez des souris traitées Bu/Cy se traduit par une prolifération rapide, indépendante de l'IL-7, des cellules T CD4. De plus, ces comportements sont associés à d'importantes modifications de l'environnement généré chez l'hôte. Plus spécifiquement, nous avons démontré, dans les organes lymphoïdes secondaires, que la localisation et la représentation des différentes sous-populations de cellules dendritiques présentes étaient différentiellement modulées par le type de conditionnement utilisé. Par ailleurs, l'élimination spécifique des cellules CD11c+ chez des souris traitées Bu/Cy était accompagnée d'une inhibition importante de la prolifération rapide des cellules T CD4 greffées. L'ensemble de nos travaux montrent que les traitements lymphopéniques génèrent des environnements distincts capables de moduler le devenir des cellules T greffées.Durant ma thèse, nous avons également abordé de façon originale un aspect novateur de l'environnement en étudiant le rôle potentiel des nutriments comme régulateurs métaboliques des fonctions effectrices des cellules T. La glutamine est l'acide aminé le plus abondant du plasma, pouvant contribuer aux besoins bionénergétiques et biosynthétiques des cellules T en prolifération. Nous avons démontré dans nos travaux qu'une carence en glutamine lors de l'activation de cellules T CD4 par leur TCR entrainait un délai dans l'activation de la voie mTOR, une réduction de la production intracellulaire d'ATP aux temps précoces et se traduisait par une diminution de la prolifération. De plus, ces conditions étaient associées à une augmentation de la conversion de cellules CD4 T naïves, via TGFβ, en cellules régulatrices Foxp3+ , y compris en condition de polarization Th1. Par contre, la carence en glutamine n'a pas inhibé la différenciation Th2. Les cellules T Foxp3+ ainsi générées en condition limitante de glutamine présentaient in vivo des fonctions suppressives aussi efficaces que celles des cellules régulatrices nTregs. En effet, elles ont la capacité de bloquer l'induction de la colite provoquée par la greffe de cellules T effectrices dans des souris Rag2-/- . Nos travaux démontrent ainsi que l'environnement métabolique peut être un régulateur clé de la différenciation des cellules T CD4. L'ensemble de mes travaux de thèse ont mis en évidence de nouveaux paramètres capables de potentiellement modifier la survie et la réactivité des cellules T greffées. / Anti-tumor therapies have improved significantly over the decade. However, the currently used treatments have important limitations, notably for metastatic cancers, and the development of new approaches is therefore a high priority. Adoptive T cell therapy (ACT) represents an innovative strategy that has shown much promise. This therapy is based on the infusion of tumor-specific T cells, which have been manipulated and expanded ex vivo, into patients who have been rendered lymphopenic by chemotherapy and/or irradiation. It is interesting to note that while lymphodepletion is attained by the vast majority of conditioning regimens, the effects of these protocols on the host environment and potentially, on the destiny of adoptively-transferred T cells had not been elucidated prior to the studies which we initiated. Using a murine model, we found that the fate of adoptively-transferred T cells differs markedly in mice rendered lymphopenic by sub-lethal irradiation as compared to a busulfan/cyclophosphamide (Bu/Cy) chemotherapy regimen. Irradiation-mediated lymphopenia resulted in a skewed IL-7-dependent proliferation of donor CD8+ T cells, whereas Bu/Cy treatment led to an increased IL-7-independent, rapid CD4+ T cell proliferation. These alterations in T cell proliferation were associated with striking changes in the host microenvironment. More specifically, we demonstrated that the proportion and localization of different dendritic cell (DC) subsets in lymphoid organs were differentially affected by the type of conditioning. Furthermore, we found that these DC controlled the rapid donor CD4+ T cell division detected in Bu/Cy-treated mice as depletion of CD11c+ DC inhibited this proliferation. Altogether, our studies demonstrate that lymphopenic regimens generate distinct host environments which modulate the fate of adoptively-transferred T cells. Durind my PhD, we also investigated an original and novel aspect of the microenvironement by studying the potential role of nutrients as metabolic regulators of T cell effector function. Glutamine is the most abundant amino acid in the plasma and contributes to the bioenergetic and biosynthetic requirements of proliferating T cells. Here, we demonstrated that activation of CD4+ T cells under glutamine-deprived conditions results in a delayed mTOR activation with reduced early ATP production and decreased proliferation. Moreover, these conditions resulted in the conversion of naïve CD4+ T cells into Foxp3+ regulatory T cells (Tregs). This de novo Treg differentiation occurred even under Th1-polarizing conditions and was TGFβ-dependent. Interestingly, glutamine deprivation did not inhibit Th2 differentiation. Importantly, these converted Foxp3+ T cells showed enhanced in vivo persistence and were highly suppressive, completely protecting Rag-deficient mice from the development of autoimmune inflammatory bowel disease as efficiently as natural-occuring Tregs. Thus, our data reveal the external metabolic environment to be a key regulator of a CD4 T lymphocyte's differentiation. Altogether, the data generated during my PhD provide new insights into the identification of parameters that can potentially alter the survival and reactivity of adoptively-transferred T cells.

RNA modifications and processing events are important modulators of global gene expression. Genomic mutations in the RNA methylase NSun2 and the alternative splicing factor Srsf2 are linked to neurological disorders and cancer in humans, respectively. NSun2 methylates cytosine-5 in most tRNAs and, to a lesser extent, other ncRNAs and mRNAs. Srsf2 is a critical component of the spliceosome and interacts with abundant ncRNAs that are methylated by NSun2. However, how precisely these processes effect homeostasis is largely unexplored. Therefore, the main aims of my PhD were (1) to dissect the molecular mechanisms of NSun2-mediated RNA methylation pathways that regulate cell survival under normal conditions and in response to oxidative stress, and (2) to investigate the importance of Srsf2 in stem cells using skin as a model system. In the context of RNA modifications, firstly I described how NSun2-expressing cells enrich for transcripts related to enhanced cell survival. Subsequently, by metabolically profiling wildtype and patient-derived dermal fibroblasts carrying loss-of-function mutations in the NSUN2 gene, I showed that the absence of NSun2 is synonymous to an energy-saving, low-translating and stressed cellular state. I further confirmed that lack of NSun2 was sufficient to instigate a cellular stress response, by monitoring BIRC5, a member of the inhibitor of apoptosis family. To further answer whether lack of NSun2 enhanced the susceptibility of patient cells to external stress stimuli, I next exposed them to oxidative stress and measured transcriptional and translational changes. I discovered that NSun2 is required to adapt global protein synthesis to the stress response, while NSun2-depleted cells failed to do so. This was concurrent with NSun2-depleted cells enriching for transcripts related to mRNA degradation and negative regulators of protein translation in response to stress. Generally, since loss of NSun2-driven methylation in tRNAs triggers their cleavage into small ncRNA fragments by angiogenin, I asked how angiogenin or tRNA-derived ncRNAs affect translation levels. In the presence of NSun2, angiogenin alone did not reduce global protein synthesis, yet tRNA fragmentation was required to modulate translation levels. Finally, to uncover how the lack of NSun2 influenced tRNA cleavage and methylation patterns in response to stress, I exposed wildtype and patient cells to sodium arsenite and measured the abundance of tRNA-derived fragments and occurrence of methylation events. With this I discovered unique tRNA fragmentation patterns and global RNA methylation profiles for wildtype and NSun2-depleted cells, that can account for the underlying molecular and phenotypical differences in response to stress. In the context of alternative splicing, and since the cellular functions of Srsf2 are largely unknown, I explored its role in cellular survival and differentiation. By conditionally deleting SRSF2 in two different stem cell populations of the mouse epidermis, I observed significant thickening of the epidermis, altered expression of cell proliferation and stem cell differentiation markers, and distorted hair follicle structures. Moreover, I demonstrated that lack of Srsf2 promotes skin regeneration following injury, thus strongly indicating that Srsf2 is required for normal skin development and regeneration after injury. In summary, my research suggests that NSun2-mediated RNA methylation pathways orchestrate transcriptional and translational programmes in response to external stress stimuli, and my studies are the first to show that the alternative splicing factor Srsf2 is required for stem cell differentiation in skin.

Células animais são alvo de pesquisas visando sua utilização como plataforma para a expressão de proteínas recombinantes, desde vacinas veterinárias até fatores de coagulação para hemofílicos. Exemplos incluem células de inseto Drosophila melanogaster S2 e células de mamífero BHK-21, que vêm sendo estudadas visando a sua utilização para a produção da glicoproteína do vírus da raiva. Independentemente da estratégia de cultivo utilizada, altas concentrações celulares são em geral associadas a uma maior produção da proteína de interesse. O objetivo deste trabalho foi o de investigar estratégias que possibilitariam o cultivo de células animais em altas concentrações celulares. Células de inseto Drosophila melanogaster S2 produtoras da glicoproteína do vírus da raiva foram cultivadas em frascos agitados a 100 rpm e 28, em meio livre de soro SF 900 II suplementado com os aminoácidos asparagina, cisteína, prolina e serina. A adição dos quatro aminoácidos no meio de cultura refletiu em um aumento da concentração celular máxima (XV MÁX) em 16%. Cisteína, quando adicionada isoladamente no meio de cultura, refletiu em uma velocidade específica máxima de crescimento celular (MÁX) 56% maior. Nessa condição, o fator de conversão glicose a célula (YX/GLC) foi 47% maior, indicando um metabolismo de glicose mais eficiente na geração de células. Esses resultados indicam que cisteína é provavelmente substrato limitante do cultivo de células S2AcGPV em meio SF 900 II. Já células de mamífero BHK-21 (C13), adaptadas ao crescimento em suspensão, foram cultivadas em processo de perfusão, processo contínuo em que há retenção celular, o que permite alcançar concentrações celulares mais altas que processos em batelada ou em modo contínuo sem retenção celular. Foi utilizado um biorreator do tipo tanque agitado com 1,5 L de volume de trabalho e spin-filter interno, com poro de diâmetro igual a 10 m, acoplado ao eixo do impelidor. Durante o cultivo, o pH foi controlado em 7,2, a agitação em 80 rpm, a temperatura em 37 e o oxigênio dissolvido em 50% da saturação com o ar. A concentração celular máxima alcançou 15,7 x 106 céls mL-1, muito superior à do cultivo em batelada (aproximadamente 5 x 106 céls mL-1). A viabilidade celular foi superior a 90% durante os 48 dias de cultivo. Na fase batelada do cultivo em perfusão, as velocidades de consumo de glicose (qGLC) e de glutamina (qGLN) foram 84% e 32% maiores, respectivamente, em relação às velocidades observadas no cultivo em batelada. Analogamente, as velocidades de produção de lactato (qLAC) e de amônio (qNH4) foram 78% e 102% maiores, respectivamente. Ainda, o coeficiente de manutenção celular não foi desprezível, e o consumo de glicose associado à manutenção celular foi de 83%. Esses dados indicam que a presença do spin-filter interno pode estar associada a estresse celular. Na perfusão, a concentração celular foi cerca de 3 vezes maior do que no cultivo contínuo sem reciclo de células. Provou-se que é possível cultivar células BHK-21 adaptadas a crescimento em suspensão em altas concentrações celulares em escala laboratorial, utilizando biorreator de bancada e spin-filter interno como sistema de retenção celular. / Animal cells have been under research as a platform for the expression of recombinant proteins, ranging from veterinary vaccines to blood coagulation factors for treating hemophilia. Examples include insect Drosophila melanogaster S2 and hamster BHK-21 cells, currently being studied for the production of rabies virus glycoprotein. Regardless of the cultivation strategy, high cell concentrations are usually associated to a higher protein production. Thus, the aim of this research was to investigate animal cell cultivation strategies that would allow higher cell concentrations than those previously reported. Cells of Drosophila melanogaster S2 expressing the rabies virus glycoprotein (S2AcGPV) were cultivated in shake flasks at 100 rpm and 28 , in SF 900 II serum-free medium supplemented with the following amino acids: asparagine, cysteine, proline, and serine. The addition of the four amino acids to the medium increased the maximum cell concentration (XV MAX) in 16%. When only cysteine was added to the medium, the maximum specific growth rate (ÊMAX) was 56% higher. In this condition, the cell yield on glucose (YX/GLC) was 47% higher, indicating a more efficient glucose metabolism. These results show that cysteine is likely a limiting substrate of S2AcGPV cells growing in SF 900 II medium. In turn, baby hamster kidney cells (BHK-21/C13), adapted to growth in suspension culture, were cultivated in perfusion, a continuous process with cell retention that allows higher cell concentration than batch or continuous cultures without cell retention. A stirred tank bioreactor with a working volume of 1.5 L was used, with an internal spin-filter with 10 µm diameter pores attached to the impeller shaft. Temperature was controlled at 37 , pH at 7.2, agitation at 80 rpm and dissolved oxygen at 50% of air saturation. The maximum cell concentration reached 15.7 x 106 cells mL-1, much higher than the cell concentration achieved in a standard batch cultivation (5 x 106 cells mL-1). Cell viability was above 90% during the 48-day cultivation period. During the batch phase of the perfusion cultivation, specific rates of glucose (qGLC) and glutamine (qGLN) consumption were 84% and 32% higher, respectively, when compared to the batch cultivation. Similarly, the specific rates of lactate (qLAC) and ammonium (qNH4) formation were 78% and 102% higher, respectively. During perfusion, the cell maintenance coefficient was not negligible and represented 83% of total glucose consumption. These data indicate that the presence of an internal spin-filter may be associated to cell stress. In perfusion, cell concentration was about 3 times higher than that in continuous culture without cell recycle. In conclusion, it was proved that suspension-adapted BHK-21 cells can be cultivated in a laboratory-scale bioreactor with an internal spin-filter, in order to achieve high cell concentrations.