Protein synthesis is a complex process performed by sophisticated cellular particles known as ribosomes. Although RNA constitutes the major structural and functional component, ribosomes from all kingdoms contain an extensive array of proteins with largely undefined functional roles. The work presented in this thesis addresses ribosomal complexity using mutants of Salmonella typhimurium to examine the physiological effects of ribosomal protein (r-protein) removal and orthologous replacement on bacterial fitness and ribosome function. The results of paper I demonstrate that removal of small subunit protein S20 conferred two independent translation initiation defects: (i) a significant reduction in the rate and extent of mRNA binding and (ii) a drastic decrease in the yield of 70S complexes caused by an impairment in subunit association. The topographical location of S20 in mature 30S subunits suggests that these perturbations are the result of improper orientation of helix 44 of the 16S rRNA when S20 is absent. In paper II we show that the major functional impairment associated with loss of large subunit protein L1 manifested as an increase in free ribosomal subunits at the expense of translationally active 70S particles. Furthermore, the formation of free ribosomal subunits was imbalanced suggesting that L1 is required to suppress degradation or promote formation of 30S subunits. Compensatory evolution revealed that mutations in other large subunit proteins mitigate the cost of L1 removal, in one case seemingly via an increase in 70S complex formation. As shown in paper III, the large fitness costs associated with complete removal of r-proteins is in contrast to the generally mild costs of orthologous protein replacement, even in the absence of a high degree of homology to the native protein. This clearly demonstrates the robustness and plasticity of the ribosome and protein synthesis in general and it also implies that functional constraints are highly conserved between these proteins. The findings of paper III also allowed us to examine the barriers that constrain horizontal gene transfer and we find that increased gene dosage of the sub-optimal heterologous protein may be an initial response to stabilize deleterious transfer events. Overall the results highlight the requirement of r-proteins for the maintenance of ribosomal structural integrity.

abstract: The energy required in a eukaryotic cell is provided by mitochondria. Mitochondrial electron transport chain (ETC) coupled with oxidative phosphorylation generates ATP. During electron transport, electron leakage from the ETC produces reactive oxygen species (ROS). In healthy cells, there are preventive and defense mechanisms in place to manage ROS. Maintaining a steady balance of ROS is very important because overproduction of ROS can lead to several pathological conditions. There are several strategies to prevent ROS production. Addition of external antioxidants is widely used among them. Discussed in the first part of Chapter 1 is the mitochondrial ETC, ROS production and antioxidant strategies. The second part of Chapter 1 is concerned with ribosomal protein synthesis in bacteria. Ribosome, the organelle that synthesizes proteins with exceptional fidelity, has a strong bias for α-L-amino acids. It has been demonstrated that reengineering of the peptidyltransferase center (PTC) of the ribosome could enable the incorporation of both α-D-amino acids and β-amino acids into full length protein. Oxidative stress is a common cause of various neurological disorders such as Alzheimer’s disease and Parkinson’s disease. Antioxidative strategies are used widely for the treatment of these disorders. Although several antioxidants demonstrated positive results in vitro as well as in in vivo models, none of them have been effective in clinical settings. Hence, there is an ongoing search for effective neuroprotective drugs. Described in Chapter 2 is the synthesis and biological evaluation of several methylene blue analogues as potentially effective antioxidants for the treatment of pathologies related to oxidative stress. In Chapter 3, the synthesis and ribosomal incorporation of several rationally designed dipeptidomimetic analogues are discussed. The dipeptidomimetic analogues are structurally similar to the GFP chromophore and, therefore, highly fluorescent. In addition, the backbone of the dipeptidomimetic analogues resemble the peptide backbone of a dipeptide, due to which they can be incorporated into protein by modified ribosomes selected for the incorporation of dipeptides. Discussed in Chapter 4 is the synthesis of the pdCpA derivatives of several β-amino acids. The pdCpA derivatives were ligated to tRNA-COH and were used as probes for studying the regio- and stereoselectivity of modified ribosomes. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2016

Submitted by LUCAS ROCHA REBELO (lucas-rebelo@hotmail.com) on 2017-07-07T17:01:11Z No. of bitstreams: 1 Lucas R. Rebelo, 2017 (Dissertação V. Definitiva).pdf: 2280665 bytes, checksum: b29a6bac1e5b9d5f3d59ba95d2fa0e55 (MD5) / Approved for entry into archive by Monique Sasaki (sayumi_sasaki@hotmail.com) on 2017-07-13T17:51:27Z (GMT) No. of bitstreams: 1 Lucas R. Rebelo, 2017 (Dissertação V. Definitiva).pdf: 2280665 bytes, checksum: b29a6bac1e5b9d5f3d59ba95d2fa0e55 (MD5) / Made available in DSpace on 2017-07-13T17:51:27Z (GMT). No. of bitstreams: 1 Lucas R. Rebelo, 2017 (Dissertação V. Definitiva).pdf: 2280665 bytes, checksum: b29a6bac1e5b9d5f3d59ba95d2fa0e55 (MD5) Previous issue date: 2017-06-19 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Este estudo objetivou avaliar o efeito da substituição da fonte de proteína verdadeira e da ureia por nitrato encapsulado (En) e enxofre (S) elementar sobre consumo, digestibilidade, parâmetros ruminais, eficiência de síntese de proteína microbiana e emissão de CH4 em bovinos Nelore. Foram utilizados cinco novilhos Nelore (352.7 ± 38.4 kg PV) canulados no rumen, e distribuídos em um delineamento em quadrado latino 5 × 5 (5 tratamentos e 5 períodos, 21 dias cada). O volumoso utilizado foi feno de Tifton 85 e o concentrado basal foi composto por milho, farelo de soja, e suplemento mineral comercial. Ureia, En e S foram adicionados para compor demais dietas. Os tratamentos foram: farelo de soja (SBM) como tratamento controle; ureia (U); U mais S elementar (US); nitrato encapsulado (EN); e EN mais S elementar (ENS). O En foi incluído nos tratamentos EN e ENS em 2% da MS (1,42% de NO3 - ânion), enquanto que a inclusão de ureia nos tratamentos U e US foi de 0,8% na MS da dieta. A inclusão de S nos tratamentos U e EN foi em 0,24% da MS, e a relação N:S foi reduzida de 8:1 para 4:1 com a adição de S. O En foi incluído gradualmente de 0,5% até 2% da MS da dieta. Os contrastes ortogonais para avaliar os efeitos de tratamento foram: SBM vs. EN + ENS; U + US vs. EN + ENS; U vs. US; e EN vs. ENS. Os novilhos apresentaram baixos níveis de MetHb (média de 1,1%) a medida em que a quantidade de En foi aumentada. O consumo de OM e NDF foram menores (P ≤ 0,01) para os animais alimentados com En comparado à SBM. A digestibilidade da DM, OM, e GE foram maiores (P ≤ 0,01) quanto fornecido En comparado à ureia. O pH ruminal foi maior (P = 0,01) e N-NH3 foi menor (P = 0,01) para animais recebendo En na dieta comparado à ureia. Comparado à ureia, o fornecimento de En causou redução (P = 0,01) na proporção de propionato, assim como aumento (P ≤ 0,03) na proporção de acetato e na relação acetato:propionato. O consumo de N foi menor (P ≤ 0,07) em animais alimentados com En comparado à SBM e ureia. O N retido (g N/d) foi menor (P = 0,01) com dietas com En comparado à SBM e ureia. Nitrogênio microbiano (MN; g MN/d) tendeu a aumentar (P = 0,06) com a inclusão de En comparado à SBM, e foi aumentado (P ≤ 0,04) pela adição de S elementar à dietas com NNP. O fornecimento de dietas com En aumentou (P ≤ 0,01) MN quando em proporção à ingestão de PB (CPI; g MN/kg CPI) e aumentou (P = 0,02) a eficiência de síntese de MN com base na ingestão de OM digestível (DOMI; g MN/kg DOMI) comparado à SBM, assim como tendeu a aumentar (P = 0,09) g MN/kg DOMI comparado à ureia. A adição de S elementar às dietas com NNP tendeu a aumentar (P ≥ 0,05) g MN/kg CPI, e aumentou (P = 0,04) g MN/kg DOMI quando incluído na dieta EN. Animais alimentados com En tiveram redução (P = 0,02) na emissão de CH4 em cerca de 31,2 g CH4/d, e tenderam a reduzir (P = 0,06) a emissão de CH4 em g CH4/kg DMI e como % da GEI, quando comparados à SBM. Portanto, En mais S elementar em substituição parcial à proteina verdadeira da ração ou substituindo totalmente a ureia pode otimizar a eficiência de síntese de proteína microbiana e concomitantemente reduzir a emissão de CH4 por bovinos Nelore. / The objective of this study was to investigate the replacement of true protein source as well as the conventional NPN source (urea) by encapsulated NO3 - (En) plus elemental sulfur (S) on microbial protein synthesis efficiency, and CH4 emission in Nellore beef cattle. Five ruminally-cannulated Nellore steers (352.7 ± 38.4 kg BW) were used in a 5 × 5 Latin square design with 5 periods of 21 d each. Tifton 85 hay was used as forage and the basal concentrate consisted of corn, soybean meal, and commercial mineral supplement (50:50 wt/wt, forage:concentrate). Urea, En and S were added to compose the other diets. The treatments were: true protein from soybean meal as control (SBM); urea (U); U plus elemental S (US); encapsulated NO3 - (EN); and EN plus elemental S (ENS). En was included in 2% on dietary DM (1.42% NO3 - anion), while the inclusion of urea in U and US diets was 0.8% on dietary DM. The inclusion of S for U and EN diets was 0.24% on dietary DM, and the N:S ratio was reduced from 8:1 to 4:1 with the addition of S. En was gradually included from 0.5 to 2% on dietary DM by 0.5% every 4 d. The orthogonal contrasts for specific partitioning of treatment effects were: SBM vs. EN + ENS; U + US vs. EN + ENS; U vs. US; and EN vs. ENS. Steers displayed adequate MetHb levels as dietary En content increased. Organic matter and aNDF intake were smaller (P ≤ 0.01) for animals fed En diets compared to SBM. Digestibility of DM, OM, and GE were greater (P ≤ 0.01) when fed En diets compared to urea. Ruminal pH was greater (P = 0.01) and ruminal NH3-N was smaller (P = 0.01) for animals fed En diets compared to urea. Compared to urea, En supply resulted in lower propionate proportion (P = 0.01), but increased (P ≤ 0.03) acetate proportion and acetate:propionate ratio. Nitrogen intake was smaller (P ≤ 0.07) with En supply compared to SBM and urea. Retained N (g N/d) for animals fed En diets was smaller (P = 0.01) compared to SBM and urea. Microbial N (MN; g MN/d) tended to increase (P = 0.06) with En inclusion compared to SBM, and was increased (P ≤ 0.04) by the addition of elemental S to NPN diets. Encapsulated NO3 - diets supply increased (P ≤ 0.01) MN as a proportion of CPI (g MN/kg CPI), increased (P = 0.02) MN efficiency based on digestible OM intake (DOMI; g MN/kg DOMI) compared to SBM, and as well tended to increase (P = 0.09) g MN/kg DOMI compared to urea. The addition of elemental S to NPN diets tended to increase (P ≥ 0.05) g MN/kg CPI, and increased (P = 0.04) g MN/kg DOMI when included in EN. Animals fed En diets decreased (P = 0.02) CH4 emission by 31.2 (g CH4/d), and tended to decrease (P = 0.06) CH4 emission (g CH4/kg DMI, and CH4 as % of GEI) when compared to SBM. Thus, En plus elemental S as a dietary additive replacing part of true protein of the ration or totally urea can optimize microbial protein synthesis efficiency and concomitantly decrease CH4 emission by Nellore beef cattle. / FAPESP: 2016/01562-0

Esse trabalho compreendeu a avaliação do impacto do jogo Sintetizando Proteínas sobre o processo de ensino-aprendizagem de alunos do ensino médio e sua compreensão conceitual a respeito do tema proteínas, fundamentados na teoria sócio-interacionista de Vygotsky. Os conceitos formulados pelos alunos foram coletados em três etapas diferentes: a primeira, anterior à aplicação do jogo, por meio de um questionário diagnóstico e uma pré-entrevista; a segunda, durante o jogo, por meio de gravações áudio-visuais; a terceira, posterior à aplicação do jogo, por meio de uma pós-entrevista. Os dados levantados pelo questionário diagnóstico permitiram detectar algumas tendências do pensar dos alunos com relação ao conceito de proteína: a) tendência em definir genericamente o papel das proteínas; b) tendência dos alunos em associar proteínas aos alimentos de origem animal; c) tendência em entenderem as proteínas apenas como construtoras de tecidos, portanto uma função prioritariamente estrutural. A análise e interpretação dos dados referentes às pré e pós-entrevistas e das transcrições das gravações áudio-visuais nos mostraram que as interações ocorridas durante o jogo tiveram um importante papel na evolução de alguns conceitos antes incompreendidos pelos alunos. Dessa forma o jogo, enquanto um modelo que simula o processo de síntese protéica dentro da célula, proporcionou aos alunos experiências que os permitiram vivenciar esse processo, estabelecendo uma ponte entre o abstrato e o concreto, possibilitando aos mesmos o alcance de níveis de desenvolvimento mais elevados e a evolução de conceitos antes incompreendidos. / The main goal of this study was evaluating the impact of the game Synthesizing Proteins on the teaching-learning process of high school students and their conceptual understanding on the subject proteins, based on Vygotskys sociointeractionist theory. The concepts of the students were collected in three different stages: before the application of the game, using a diagnostic questionnaire and a pre-interview; during the game, by means of audio-visual recordings; after the application of the game, by a post-interview. The data raised from the diagnostic questionnaire had allowed to detect some trends of students thinking with regard to the protein concept: a) the trend in generically defining the role of proteins to the organism (human) b) students trend in only associating proteins to foods of animal origin c) trend in only understanding proteins as tissue constructors, so a function primarily structural. The analysis and interpretation of data collected by pre- and post-interviews and the transcripts of the audio-visual recordings showed that the interactions occurred during the game had an important role in the evolution of some concepts that were previously misunderstood by students. Thus, the game as a model that simulates the process of protein synthesis inside the cell, allowed the students experience this process, establishing a bridge between the abstract and concrete and allowing them to achieve high levels of development.

A arginina é um aminoácido condicionalmente essencial que participa de inúmeras reações metabólicas no organismo como, por exemplo, o ciclo da uréia, a síntese de creatina e a geração de óxido nítrico (NO). Além dessas funções a arginina é associada, com a sensibilidade à insulina, a secreção de GH e mais recentemente com a síntese protéica muscular. O objetivo deste trabalho foi investigar o efeito da suplementação via oral crônica de L-arginina sobre a síntese protéica muscular, pela via da mTOR, a fim de contribuir com as novas discussões científicas acerca deste aminoácido de ampla atuação. Métodos: Foram utilizados ratos wistar machos adultos com cerca de 200g de peso corporal divididos em quatro grupos de quatorze animais denominados na seguinte forma: Arginina Treinado (AT), Arginina Sedentário (AS), Dieta-Controle Treinado (CT) e Dieta-Controle Sedentário (CS). Ambas as dietas foram elaboradas com base das recomendações da AIN-93, sendo que a dieta enriquecida com arginina recebeu acréscimo de 2% deste aminoácido e a dieta controle recebeu um mix de aminoácidos não essenciais para garantir que ambas fossem isonitrogenadas e isocalóricas e as proporções de aminoácidos presente nas rações foi conferida por aminograma. O treinamento dos animais consistiu em exercício anaeróbio com sessões que eram compostas de 4 séries de 10 saltos com um minuto de descanso entre estas em tanque de água. Os saltos eram desempenhados com carga de 50% do peso corporal acoplado ao tórax dos animais na freqüência de 5 dias por semana por 6 semanas. A evolução da massa corporal dos animais bem como o consumo de ração foram avaliadas três vezes por semana e estimada uma média semanal. Foram realizados testes de tolerância oral à glicose (OGTT) e tolerância à insulina (ITT) no início e ao final do experimento em todos os animais para avaliar alterações na sensibilidade à insulina. Após 72hs da última sessão de treinamento os animais foram anestesiados para infusão de insulina, coleta dos músculos gastrocnêmio e plantar, fígado, sangue e eutanasiados conforme protocolo aprovado pelo CEA-USP. As análises bioquímicas foram determinações séricas de insulina, GH, IGF-1 e a proteína transportadora de IGF-1 (IGFBP-3), glicose plasmática, uréia e creatinina séricas, IGF-1 muscular e hepático por kits comerciais de tecnologia multiplex Luminex e aminograma sérico por cromatografia. As análises moleculares foram realizadas para as proteínas chaves envolvidas na via de síntese protéica muscular em sua forma total e fosforilada, sendo estas: IRS-1, Akt, mTOR, 4E-BP1 e p70S6K determinadas por método de western blotting. Resultados: Não foram encontradas diferenças estatisticamente significativas nos parâmetros avaliados com exceção da creatinina que se mostrou mais elevada nos grupos suplementados com arginina. A suplementação de arginina, nas concentrações administradas, bem como o exercício de alta intensidade pelo período determinado não foram capazes de alterar a expressão das proteínas envolvidas na regulação de síntese protéica muscular de ratos nem a sensibilidade celular à insulina. Conclusão: não houve aumento da síntese protéica muscular com a suplementação de arginina, nestas condições experimentais. / The arginine is an amino acid conditionally essential that participates in innumerous metabolic reactions in the body like, for instance, the urea cycle, the synthesis of creatine and production of nitric oxide (NO). Besides those functions the arginine is associated, with the insulin sensitivity, GH secretion and most recently with muscle protein synthesis. The aim of this work was to investigate the effect of L-arginine chronic oral supplementation on the muscle protein synthesis, through mTOR pathway, in order to contribute with new scientific discussions about this broad action amino acid. Methods: Wistar male adult rats were used with about 200g body weight distribute into four groups of fourteen animals named this way: Trained Arginine (TA), sedentary Arginine (SA), Trained Diet-Control (TC) and Sedentary Diet-control (SC). Both diets were elaborated based on the AIN-93 recommendations, considering that the enriched diet with arginine was added 2% of this amino acid and the control diet received a mix of non-essential amino acid in order to ensure that both were isonitrogenous and isocaloric and the proportions of present amino acids in the rations have been checked through aminogram. The animals training consisted of anaerobic exercise with sections composed by four jump series, with one minute rest among these in a PVC cube water. The jumps were performed with a load of 50% of their body weight attached in the animal\'s trunk, five days a week over six weeks. The animals\' body weight evolution as well as the food intake were evaluated three times a week in order to figure a weekly average. Oral glucose test tolerance (OGTT) and insulin test tolerance (ITT) have been done in the beginning and in the end of the experiment in all animals to evaluate insulin sensitive changes. The animals were anesthetized to insulin infusion, gastrocnemic and plantaris muscles, liver and blood collects 72 hrs after the last training section and afterwards sacrificed according to CEA-USP approved protocol. The biochemical analysis were blood determination of insulin, GH, IGF-1 and its binding protein 3 (IGFBP-3), glucose, urea and creatinine, and muscle and liver IGF-1 through commercial kits of multiplex Luminex technology and seric aminogram through chromatography. The molecular analysis were performed for the key proteins of the muscle protein synthesis pathway in its total and phosphorylated form: IRS-1, Akt-1, mTOR, 4E-BP1 and p70S6K determined by western blotting method. Results: Significant statistical differences were not found to all evaluated biomarkers in this experiment except for creatinine which was more elevated in groups supplemented with arginine. The arginine supplementation, in these given doses, as well as the high-intense exercise, failed in stimulate both the expression of the proteins involved in the muscle protein synthesis regulation and the insulin sensitivity in the rats in this condition. Conclusion: There hasn\'t been any increase in the muscle protein synthesis with arginine supplementation, in these experimental conditions.

Orientador: Elenice Aparecida de Moraes Ferrari / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T21:27:10Z (GMT). No. of bitstreams: 1 Sperandeo_MariaLuizaAntunes_D.pdf: 3058745 bytes, checksum: 13c43e27d3d229473548efb9ae77c620 (MD5) Previous issue date: 2013 / Resumo: O estudo do condicionamento clássico aversivo contribuiu para caracterizar as fases da formação da memória (aquisição, consolidação, reconsolidação, persistência e extinção) e os mecanismos de plasticidade neuronal subjacentes. Entre estes, a ativação de receptores glutamatérgicos NMDA, de transcrição gênica e síntese proteica parecem fundamentais. O fator neurotrófico derivado de cérebro (BDNF) e o gene de expressão imediata (IEG) zenk são ativados no hipocampo de mamíferos durante a reconsolidação e a extinção. Este estudo investigou os efeitos da inibição da síntese proteica e do bloqueio dos receptores NMDA no hipocampo de pombos na reconsolidação e extinção da memória de medo contextual. No Experimento 1, pombos foram condicionados, testados ao contexto (reativação), submetidos à infusão intra-hipocampo de salina (SAL-PR), de anisomicina (ANI-PR) ou de MK-801 (MK-PR) após o teste (pós-reativação; PR), e retestados 2 dias depois (Rt 2d). No Experimento 2, três grupos tiveram um segundo reteste, 9 dias após a infusão (Rt 9d), enquanto que outros três grupos não passaram pelo teste (sem reativação- SR). O treino (20 min) teve três pareamentos som-choque. No teste e no Rt 2d houve exposição ao contexto do condicionamento por 5 min e no reteste Rt 9d, por 30 min. Nos dois experimentos, todos os grupos apresentaram alta ocorrência de congelamento (CONG) nas sessões de treino e de teste, mas no Rt 2d os grupos ANI-PR e MK-PR mostraram uma redução significativa de CONG (p < 0,05). Os grupos SR exibiram alta ocorrência de CONG tanto no Rt 2d, quanto no início do Rt 9d (p > 0,05). No Rt 9d o grupo MK-PR não teve recuperação espontânea de CONG, sugerindo prejuízo irreversível provocado pelo MK-801 na memória de medo contextual. Os grupos, SAL-PR, SAL-SR, ANI-PR, ANI-SR e MK-SR mostraram diminuição gradual de CONG durante a sessão de Rt 9d, evidenciando a extinção. Análises com Western blotting após o Rt 9d indicaram que o conteúdo de BDNF-maduro no hipocampo dos pombos SAL-PR foi significativamente maior em comparação aos demais grupos (p < 0,05), mas não foram observadas diferenças entre os grupos para o Zenk (p > 0,05). Isso sugere a participação do BDNF hipocampal na reconsolidação e na extinção da memória de medo contextual em pombos. Assim, a inibição da síntese proteica e o bloqueio dos receptores NMDA no hipocampo de pombos, após o teste ao contexto, prejudicaram a reconsolidação da memória de medo condicionado ao contexto. Além disso, os prejuízos observados foram dependentes da reativação da memória durante o teste / Abstract: The study of classical aversive conditioning has contributed to the characterization of different phases in memory formation (acquisition, consolidation, reconsolidation, extinction and persistence) and the underlying mechanisms of neuronal plasticity. Among these, the activation of NMDA glutamate receptors, gene transcription and protein synthesis are pointed as essentials. The brain-derived neurotrophic factor (BDNF) and immediate expression gene (IEG) zenk are activated in the hippocampus of mammals during reconsolidation and extinction. This study investigated the effects of protein synthesis inhibition and blockade of NMDA receptors in the hippocampus of pigeons on reconsolidation and extinction of contextual fear memory. In Experiment 1, pigeons were conditioned, tested in the context (reactivation), received intra-hippocampus infusion of saline (SAL-PR), anisomycin (ANI-PR) or MK-801 (MK-PR) after the test (post-reactivation, PR), and had a retest two days later (Rt 2d). Experiment 2, had a retest 9 days after intra-hippocampus infusion (Rt 9d) for three PR groups, and other three groups that were not tested 24h after training served as control for reactivation (no reactivation-NR). Three tone-shock pairings were presented during training (20 min). Pigeons were exposed to the context during 5 min in the test and Rt 2d sessions and during 30 min in Rt 9d. In both experiments, the occurrence of freezing (FRZ) was high in training and testing sessions for all the groups, but ANI-PR and MK-PR pigeons showed a significant decrease in FRZ during the Rt 2d (p < 0.05). The NR groups exhibited high occurrence of FRZ both in the Rt 2d and in the beginning of Rt 9d (p > 0.05). MK-PR pigeons had no spontaneous recovery of FRZ, suggesting irreversible impairment caused by MK-801 in contextual fear memory. The groups, SAL-PR, SAL-NR, ANI-PR, ANI-NR and MK-NR showed a gradual decrease in FRZ during the Rt 9d session, evidencing extinction. Western Blotting analysis indicated that the content of mature BDNF in the hippocampus of SAL-PR group after Rt 9d session was higher than that seen for the other groups (p < 0.05), but no between-group differences for Zenk were observed (p > 0.05). This suggests the involvement of hippocampal BDNF in reconsolidation and extinction of contextual fear memory in pigeons. The present data show that inhibition of protein synthesis and blockade of NMDA receptors in the hippocampus of pigeons, after the testing session to context, impaired reconsolidation of contextual fear conditioning memory and affected the process of extinction. Furthermore, the impairments were dependent on the reactivation of fear memory during the test / Doutorado / Fisiologia / Doutor em Biologia Funcional e Molecular

La perte de masse et de force musculaires liée à l’âge, ou sarcopénie, pourrait être partiellementexpliquée par un défaut de récupération de masse musculaire après des épisodes générateursd’atrophie musculaire. Ainsi, les périodes d’immobilisation qui augmentent avec l’âge (alitement,convalescence, fracture) pourraient être suivies d’une absence de récupération musculaire etcontribuer à la fonte musculaire au cours du vieillissement. Les causes de ce défaut de récupérationimpliquent notamment un déséquilibre du taux de renouvellement protéique et du taux derenouvellement cellulaire. L’objectif de cette thèse a donc été de mettre en évidence les mécanismesresponsables de l’atrophie musculaire chez le rat âgé au cours de l’immobilisation et ceux quiseraient défaillants afin de déceler les mécanismes à cibler pour favoriser la récupérationmusculaire.Des rats âgés ont été immobilisés pendant 8 jours par plâtrage unilatéral de la patte arrière, puislaissés en récupération pendant 40 jours après le déplâtrage. Nous avons montré que chez cesanimaux nourris avec un régime contenant 13% de caséine, l’immobilisation entraîne une atrophiedes muscles immobilisés mais, contrairement au rat adulte, le rat âgé ne récupère jamais la massemusculaire perdue. L’atrophie des muscles immobilisés peut être expliquée par 1/ une augmentationde l’apoptose et de la protéolyse ubiquitine-protéasome-dépendante musculaires, 2/ une diminutionde la régénération des cellules musculaires et 3/ une diminution de la protéosynthèse musculaire àl’état nourri. Tous ces phénomènes pourraient résulter de la présence d’un fort stress oxydant etd’une importante inflammation intramusculaire. Tous ces paramètres sont normalisés dès 10 jours derécupération, ce qui permet de stopper l’atrophie mais ne permet pas d’initier la phase derécupération musculaire. Nous avons donc testé l’effet de différentes supplémentationsnutritionnelles au cours de la période de récupération afin de favoriser un gain de masse musculairepost immobilisation. Des supplémentations en leucine (acide aminé bien connu pour stimuler laprotéosynthèse et inhiber la protéolyse) ont ainsi été réalisées. Chez les rats supplémentés, uneamélioration de la synthèse protéique et une normalisation plus précoce des activités protéolytiquesdu protéasome ont été observées. Cependant cette amélioration du métabolisme protéique ne s’estpas traduite par un gain de masse musculaire. Par contre, la modulation qualitative et quantitative desapports en protéines a pu permettre d’obtenir une récupération significative de masse musculaire :ainsi des régimes contenant 13% de lactosérum et des régimes hyper-protéinés ont permis de gagner50% de la masse perdue et ce, dès 20 jours de récupération.Nos résultats montrent que l’immobilisation chez le rat âgé aggrave la sarcopénie. Une fortealtération du métabolisme protéique permet d’expliquer la perte de muscle et la seule normalisationde la protéolyse et de la protéosynthèse permet d’expliquer l’absence de récupération musculaire.Nous avons montré que la modulation des apports en protéines au cours de la phase de récupérationpouvait permettre un gain de protéines. / Sarcopenia, the age-related muscle mass loss, might be partially explained by an impairedmuscle mass recovery of skeletal muscle mass after a catabolic state. Thus, immobilization periodswhich increase with aging could induce a muscle atrophy followed by a lack of muscle massrecovery. An imbalance of protein and cellular metabolisms are certainly involved in this absenceof recovery. The aim on this Ph.D thesis was to explore the mechanisms involved in muscle massatrophy during immobilization and their possible alteration during the recovery period in old rats.Old rats were immobilized for 8 days by unilateral hind limb casting and then allowed torecover for 40 days. Our results showed that animals fed a 13% casein diet wasted muscle mass inimmobilized muscles but, contrarily to adult animals, they never recovered the muscle mass loss.Muscle atrophy was due to 1/ an increase of apoptotic and ubiquitine-proteasome-dependentproteolytic pathways, 2/ a decrease of muscle regeneration processes and 3/ a decrease of muscleprotein synthesis at the fed state. These changes paralleled an increase of intracellular inflammationand oxidative stress. As these parameters were only normalized during the recovery period, theresultant nitrogen balance was then not enough positive as required for the muscle protein gain,hence contributing to the age-related incomplete muscle mass recovery. We tested free leucinesupplementation (an amino acid known for its stimulatory effect on protein metabolism) during therecovery period to improve muscle mass gain. This supplementation induced a greater muscleprotein synthesis in supplemented animals, but without any muscle mass gain. However, wedemonstrated here for the first time that muscle protein accretion after immobilization-inducedatrophy could be achieved with whey protein or high protein diets.In conclusion, we demonstrated that immobilization in old rats induced a muscle mass atrophyfollowed by an incomplete recovery, hence contributing to the development of sarcopenia. We alsodemonstrated that this lack of recovery cannot be overcome by a dietary free leucinesupplementation, despite a positive effect on protein metabolism, contrarily to high protein andwhey protein diets.

The work discussed in this thesis deals with the significance of initiator tRNA gene copy number in Escherichia coli. A summary of the relevant literature discussing the process of protein synthesis, initiator tRNA selection and gene redundancy is presented in Chapter 1. Chapter 2 describes the ‘Materials and Methods’ used in the experimental work carried out in this thesis. The next three chapters address the significance of initiator tRNA gene copy number in E. coli at three levels; at the level of the molecule (Chapter 3), at the level of the cell (Chapter 4) and at the level of the population (Chapter 5). At the end of the thesis are appended three publications, which include two papers where I have contributed to work not discussed in this thesis and one review article. A brief summary of chapters 3 to 5 is provided below: (i) Chapter 3: Can E. coli remain viable without the 3 G-C base pairs in initiator tRNA? Initiator tRNAs are distinguished from elongator tRNAs by several features key among which are the three consecutive and near universally conserved G-C base pairs found in the anticodon stem of initiator tRNAs. These bases have long been believed to be essential for the functioning of a living cell, both from in vitro and in vivo analysis. In this study, using targeted mutagenesis and an in vivo genetics based approach, we have shown that the 3 G-C base pairs can be dispensed with in E. coli, and the cell can be sustained on unconventional initiator tRNAs lacking the intact 3 G-C base pairs. Our study uncovered the importance of considering the relative amounts of molecules in a living cell, and their role in maintaining the fidelity of protein synthesis. (ii) Chapter 4: Can elongator tRNAs initiate protein synthesis? There are two types of tRNAs; initiator tRNA, of which there is one representative in the cell, and elongator tRNAs of which there are several representatives. In this study, we have uncovered initiation of protein synthesis by elongator tRNAs by depleting the initiator tRNA content in the cell. This raises the possibility that competition between initiator and elongator tRNAs at the P site of the ribosome occurs routinely in the living cell, and provides a basis for initiation at several 'start' sites in the genome that may not be currently annotated as such. We speculate that such a phenomenon could be exploited by the cell to generate phenotypic diversity without compromising genomic integrity. (iii) Chapter 5: How many initiator tRNA genes does E. coli need? E. coli has four genes that encode initiator tRNA, these are the metZWV genes that occur at 63.5 min in the genome, and the metY gene that occurs at 71.5 min in the genome. Earlier studies indicated that the absence of metY had no apparent impact on cell growth. In view of the importance of initiator tRNA gene copy number in maintaining the rate and fidelity of protein synthesis, we examined the fitness of strains carrying different numbers of initiator tRNA genes by competing them against each other in both rich and limited nutrient environments. Our results indicate a link between caloric restriction and protein synthesis mediated by the initiator tRNA gene copy number.

O aumento mundial na incidência da obesidade está associado com um aumento significante com os custos com a saúde. Somente nos Estados Unidos, os gastos com os tratamentos associados a obesidade superam 9% dos custos anuais com a saúde, em torno de $147 bilhões de dólares por ano. Os efeitos da obesidade no músculo esquelético estão relacionados com o desenvolvimento da resistência à insulin (IR), diabetes e piora da qualidade de vida. Trabalhos rescentes tem demonstrado que a dieta hiperlipídica (DHL) diminui a capacidade do músculo esquelético responder a sinais de crescimento. Este efeito negativo relacionado a diminuição na ativação da via Akt/mTOR e aumento nd estresse de retículo endoplasmático (ERE) é denominado de resistência anabólica. Por outro lado, estudos têm demonstrado um possível efeito benéfico da suplementaçãoo com o ácido graxo polinsaturado ômega 3 (Ag-w3) e do treinamento físico aeróbico em diversos parâmetros como, melhora da capacidade oxidativa, sistema imunológico, síntese proteica e degradação em saudáveis ou com alguma patologia associada. Dessa maneira, o presente trabalho demonstra que 8 semanas de DHL contribuíram para o desenvolvimento da obseidade. Por outro lado, o protocolo de TA promoveu um efeito protetor ao ganho de peso nos animais obesos. A suplementação com o AG-w3 foi capaz de prevenir alguns parametros analisados e a associação do óleo de peixe não foi capaz de potencializar os efeitos benéficos encontrados com o TA. / There is a worldwide increase in the incidence of obesity that is associated with significant increases in medical costs. In the United States alone, treatment of obesity related health problems accounts for up to 9% of the total annual cost of healthcare, an estimated $147 billion per year. The effects of obesity on skeletal muscle are correlated with insulin resistance (IR), diabetes and decreased of quality of life. Recent work has demonstrated that a high fat diet (HFD) decreases the ability of skeletal muscle to hypertrophy in a model of increased mechanical load. This negative effect on muscle growth is correlated with a decrease in activation of the Akt/mTOR signaling pathway and an increase in endoplasmic reticulum stress.

Com o objetivo de estudar a espécie bubalina quanto ao desempenho de machos bubalinos do nascimento ao abate em regime de pastejo e as características de carcaça em dois pesos de abate, assim como o metabolismo ruminal de dietas com diferentes níveis de proteína e energia e a produção de gases in vitro, o presente trabalho apresenta-se avaliações feitas em quatro partes. A parte 1 foi realizada com búfalos em crescimento criados à pasto, do nascimento até atingirem dois pesos distintos de abate (517 e 568 kg). Avaliações do desempenho foram realizadas com medição do peso vivo, perímetro torácico, altura de cernelha e comprimento corporal e as avaliações das características da carcaça e carne com determinação do rendimento de carcaça quente e fria, perda no resfriamento, peso da gordura, peso do fígado, temperatura e pH da carcaça, área de olho de lombo, espessura de gordura subcutânea, marmorização, maciez e coloração. A segunda parte avaliou dietas com três níveis de proteína (9%, 12% e 15%) no metabolismo ruminal. Os Itens analisados foram: consumo de nutrientes, pH, amônia e ácidos graxos voláteis no rúmen e degradabilidade in situ. Na parte 3, foram avaliadas dietas com dois níveis de proteína (9 e 15%) e dois de energia (65 e 69% NDT) no metabolismo ruminal. Além dos Itens avaliados na parte 2 foram ainda analisados a digestibilidade com uso de marcador, taxa de passagem de liquido ruminal e volume do rúmen e síntese de proteína microbiana. Na última parte foi realizada avaliação de produção de gases in vitro com estudo da cinética da degradabilidade in vitro no tempo de 72 horas. Animais abatidos com diferentes pesos apresentaram desenvolvimento ponderal diferenciado desde o início do crescimento. Não houve diferença entre os dois grupos de animais nas características de carne e carcaça, mas os búfalos abatidos mais pesados (568 kg) apresentaram maior deposição de gordura interna. Níveis de proteína de 9%, 12% e 15% não influenciaram na degradabilidade in situ dos nutrientes e no pH ruminal. A concentração de amônia e AGV foram maiores com níveis de 15% de proteína na dieta. Os níveis de energia (alta ou baixa) combinados com teores de proteína (alto ou baixo) e as correlações entre os níveis de energia e proteína não promoveram efeitos significativos sobre o pH ruminal concentração de amônia, taxa de passagem de líquido e volume ruminal em búfalos, entretanto, dieta com teor de 15% de proteína bruta, independente dos níveis de energia na dieta apresentaram melhores degradabilidades efetivas dos nutrientes. Os níveis de energia não influenciaram significativamente na concentração amônia ruminal ao contrário dos níveis de proteína em que a maior quantidade de proteína na dieta produziu maior concentração de amônia. Não houve diferença significativa na taxa de passagem e volume ruminal entre as quatro dietas fornecidas aos animais. Dietas com diferentes níveis de energia e proteína não influenciaram na qualidade do inóculo para a produção de gases in vitro. / With the aim of studying the buffalo on the performance of males from birth to slaughter in buffalo grazing and carcass characteristics in two slaughter weights, as well as the metabolism of diets with different levels of protein and energy and the production of gases in vitro, this work presents evaluations conducted in four parts. Part 1 was performed with buffalo raised in pasture from birth until they reach two different slaughter weights (517 and 568 kg). Performance assessments were performed with measurement of body weight, chest girth, height and body length and evaluations of carcass characteristics and meat with determining the hot and cold carcass, the cooling loss, fat weight, liver weight, temperature and pH of the carcass, ribeye area, fat thickness, marbling, tenderness and color. The second part evaluated diets with three protein levels (9%, 12% and 15%) on rumen metabolism. Items discussed were the amount of nutrients, pH, ammonia and volatile fatty acids in the rumen and degradability in situ. In Part 3, were evaluated diets with two protein levels (9 and 15%) and two energy (65 and 69% of TDN) on rumen metabolism. Besides the items evaluated in Part 2, were also analyzed the digestibility, passage rate and ruminal volume and rumen microbial protein synthesis. In the last part was done evaluation of gas production in vitro with study of the kinetics of degradation in 72 hours. Animals slaughtered at different weights showed differential weight performance since the beginning of growth. There were no differences between the two groups of animals on meat and carcass characteristics, but the buffaloes slaughtered heavier (568 kg) had higher deposition of internal fat. Protein levels of 9%, 12% and 15% did not influence the in situ degradability of nutrients and rumen pH. The concentration of ammonia and VFA levels were higher with 15% protein diet. Energy levels (high or low) combined with protein levels (high or low) and the correlations between the levels of energy and protein did not cause significant effects on rumen pH, ammonia concentration, liquid passage rate and ruminal volume in buffalo, however, dietary content of 15% crude protein, independent of the energy levels in the diet showed better effective degradability of nutrients. Energy levels did not significantly modify the rumen ammonia concentration unlike the protein levels where in the higher protein diet resulted in higher ammonia concentration. There was no significant difference in passage rate and ruminal volume between the four diets fed to the animals. Diets with different levels of energy and protein did not influence the quality of inoculum for the gas production in vitro.