Piu Wong. / Thesis submitted in: July 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 126-146). / Abstracts in English and Chinese. / Thesis committee --- p.i / Statement --- p.ii / Abstract --- p.iii / Acknowledgement --- p.viii / General abbreviations --- p.xi / Abbreviations of chemicals --- p.xiii / List of figures --- p.xv / List of Tables --- p.xvii / Table of contents --- p.xviii / Chapter 1 --- Literature review / Chapter 1.1 --- Overviews --- p.1 / Chapter 1.1.1 --- Nutritional and economical significance of aspartate family amino acidsin human and animal nutrition --- p.1 / Chapter 1.1.2 --- Synthesis of aspartate family amino acids in plants --- p.2 / Chapter 1.2 --- Regulation of aspartate family amino acids between sink and source organs --- p.6 / Chapter 1.2.1 --- Co-ordination of genes/enzymes involved in amide amino acid metabolism to channel aspartate for aspartate family amino acid synthesis --- p.6 / Chapter 1.2.2 --- Sink-source regulation as a general mechanism in plants --- p.9 / Chapter 1.3 --- Source regulation at free amino acid level --- p.11 / Chapter 1.3.1 --- Regulation of free methionine synthesis --- p.11 / Chapter 1.3.1.1 --- Competition for OPHS between TS and CGS --- p.11 / Chapter 1.3.1.2 --- Turnover of CGS mRNA --- p.12 / Chapter 1.3.1.3 --- Post-translational regulation of CGS enzyme --- p.13 / Chapter 1.3.2 --- Regulation of lysine synthesis and catabolism --- p.15 / Chapter 1.3.2.1 --- Feedback regulation loop --- p.15 / Chapter 1.3.2.2 --- Possible intracellular compartmentalization of enzymes and metabolitesin regulating lysine level --- p.21 / Chapter 1.3.2.3 --- Co-ordination of gene/enzyme in aspartate kinase pathway in regulating flux to Lys --- p.21 / Chapter 1.3.3 --- Significance of lysine catabolism in mammals and plants --- p.24 / Chapter 1.3.3.1 --- Complex developmental regulation and stress response of LKR/SDH gene expression --- p.28 / Chapter 1.3.3.2 --- Regulation through a novel composite locus LKR-SDH --- p.28 / Chapter 1.3.3.3 --- Post-translational control of LKR-SDH activity --- p.31 / Chapter 1.3.3.4 --- Implication of two metabolic flux in Lys catabolism --- p.34 / Chapter 1.4 --- Source (free lysine) enhancement in transgenic plants --- p.36 / Chapter 1.4.1 --- Expression of feedback insensitive enzyme in transgenic plants to enhance free lysine supply in transgenic plant --- p.36 / Chapter 1.4.2 --- Reducing or eliminating lysine catabolism to enhance free lysine poolin transgenic plants --- p.40 / Chapter 1.5 --- Sink regulation --- p.41 / Chapter 1.5.1 --- Engineering transgenic plants through expression of seed storage protein (sink) --- p.41 / Chapter 1.5.2 --- "Dynamic relationship between sink protein, nitrogen metabolism and sulphur metabolism" --- p.45 / Chapter 1.6 --- Transgenic plants with improved source or enhanced sinks related to aspartate family amino acids available for our research --- p.47 / Chapter 1.6.1 --- Enhanced source: ASN1 over-expressers --- p.47 / Chapter 1.6.2 --- Enhanced source: metL transgenic plants --- p.47 / Chapter 1.6.3 --- Altered source: RNAi line --- p.47 / Chapter 1.6.4 --- Effective sink: LRP transgenic plants --- p.48 / Chapter 1.7 --- Overall concept of this study --- p.48 / Chapter 2 --- Materials and methods --- p.50 / Chapter 2.1 --- Materials and growth conditions --- p.50 / Chapter 2.1.1 --- "Plants, bacterial strains and vectors" --- p.50 / Chapter 2.1.2 --- Chemicals and reagents used --- p.53 / Chapter 2.1.3 --- Solutions used --- p.53 / Chapter 2.1.4 --- Commercial kits used --- p.53 / Chapter 2.1.5 --- Equipment and facilities used --- p.53 / Chapter 2.1.6 --- Growth condition --- p.53 / Chapter 2.1.7 --- Tagging of A. thaliana siliques of different developmental stage --- p.54 / Chapter 2.2 --- Methods --- p.55 / Chapter 2.2.1 --- Expression pattern analysis --- p.55 / Chapter 2.2.1.1 --- RNA extraction --- p.55 / Chapter 2.2.1.2 --- Generation of single-stranded DIG-labelled ASN1 DNA probes --- p.55 / Chapter 2.2.1.3 --- Testing the concentration of DIG-labelled probes --- p.56 / Chapter 2.2.1.4 --- Northern blot --- p.57 / Chapter 2.2.1.5 --- Hybridization --- p.58 / Chapter 2.2.1.6 --- Stringency washes --- p.58 / Chapter 2.2.1.7 --- Chemiluminescent detection --- p.58 / Chapter 2.2.2 --- Amino acid analysis and nitrogen determination --- p.60 / Chapter 2.2.2.1 --- Free amino acids in A. thaliana --- p.60 / Chapter 2.2.2.2 --- Phloem exudates collection from A. thaliana --- p.60 / Chapter 2.2.2.3 --- Soluble Protein quantitation --- p.61 / Chapter 2.2.2.4 --- Extraction of salt and water soluble protein from A. thaliana seeds --- p.61 / Chapter 2.2.2.5 --- Purification and amino acid analysis of protein extracts from A. thaliana seeds --- p.62 / Chapter 2.2.2.6 --- Total amino acid determination in mature dry seeds --- p.63 / Chapter 2.2.3 --- Generation of crossing progenies --- p.64 / Chapter 2.2.3.1 --- Artificial crossing of A. thaliana --- p.64 / Chapter 2.2.3.2 --- CTAB extraction of genomic DNA --- p.64 / Chapter 2.2.3.3 --- PCR screening for successful crossing --- p.65 / Chapter 2.2.4 --- Generation of transgenic plants --- p.67 / Chapter 2.2.4.1 --- Cloning of E.coli dapA gene --- p.67 / Chapter 2.2.4.2 --- Preparation of recombinant plasmid --- p.68 / Chapter 2.2.4.3 --- Gene sequencing --- p.68 / Chapter 2.2.4.4 --- Homology search of differentially expressed genes --- p.69 / Chapter 2.2.4.5 --- Construction of chimeric dapA genes (TP-Phas-dapA) --- p.69 / Chapter 2.2.4.6 --- Transformation of electro-competent Agrobacterium cell --- p.73 / Chapter 2.2.4.7 --- Transformation of A. thaliana through vacuum infiltration --- p.73 / Chapter 2.2.4.8 --- Selection of hemizygous and homozygous transgenic plants --- p.74 / Chapter 2.2.4.9 --- Expression analysis of homozygous LRP/dapA transgenic plants --- p.75 / Chapter 3 --- Results --- p.77 / Chapter 3.1 --- Characterization of ASN1 over-expressers --- p.77 / Chapter 3.1.1 --- Overexpression of the ASN1 gene enhances the sink-source relationship of asparagine transport under regular daylight cycle --- p.88 / Chapter 3.1.2 --- Spatial distribution of total free amino acids under normal daylight cycle --- p.88 / Chapter 3.1.3 --- Over-expression of the ASN1 gene affects free amino acid level quantitatively under normal daylight cycle --- p.89 / Chapter 3.1.4 --- Over-expression of the ASN1 gene affects composition of total amino acid under normal daylight cycle --- p.89 / Chapter 3.2 --- Construction of dapA transgenic Arabidopsis --- p.91 / Chapter 3.2.1 --- Construction of chimeric gene for expression of the dapA gene --- p.91 / Chapter 3.2.2 --- Transformation of p1300/Phas-dapA into Arabidopsis and selection of homozygous progenies --- p.91 / Chapter 3.3 --- Generation of transgenic plants with altered sink-source relationship through crossing and in-planta transformation --- p.96 / Chapter 3.3.1 --- Rationale in methods for generating transgenic plants with different combination of sources and sinks --- p.96 / Chapter 3.3.2 --- Screening for double homozygous progenies through crossing --- p.98 / Chapter 3.3.3 --- Screening for F1 progenies of successful crossing --- p.100 / Chapter 3.3.4 --- Selection of homozygous crossing progenies --- p.102 / Chapter 3.3.5 --- Screening for homozygous dapA/LRP transgenic plants --- p.104 / Chapter 3.4 --- Amino acid composition analysis --- p.109 / Chapter 3.4.1 --- The change of aspartate family amino acids in mature seeds of transgenic plants with altered sources --- p.113 / Chapter 3.4.2 --- The change of aspartate family amino acids in mature seeds of transgenic plants with improved sink --- p.114 / Chapter 3.4.3 --- The change of aspartate family amino acids in mature seeds of transgenic plants with improved sink --- p.115 / Chapter 4. --- Discussion / Chapter 4.1 --- Characterization of ASN1 over-expressers --- p.116 / Chapter 4.1.1 --- Possible regulation of ASN1 mRNA stability through level of asparagine --- p.117 / Chapter 4.1.2 --- Over-expression of ASN1 gene may improve nitrogen remobilisation from source to sink tissues --- p.118 / Chapter 4.1.3 --- Over-expression of ASN1 gene has modified the composition of amino acidsin sink organs --- p.119 / Chapter 4.2 --- ASN1 RNAi transgenic plants increases the relative contents of lysine in the seeds --- p.122 / Chapter 4.2.1 --- Role of ASN1 in supplying or competing aspartate in developing seeds --- p.122 / Chapter 4.2.2 --- Possible role of glutamate receptor --- p.123 / Chapter 4.3 --- Lysine catabolism may strictly control the level of lysine --- p.123 / Chapter 4.3.1 --- Possible role of lysine-tRNA in protein synthesis --- p.124 / Chapter 5. --- Conclusion and prospective --- p.125 / References --- p.126 / Appendix --- p.147

Os argilominerais são empregados na área farmacêutica e cosmética tanto como excipientes quanto ingredientes ativos. Esses compostos inorgânicos são inertes quimicamente, apresentam estruturas definidas e alta estabilidade térmica, o que contribui para o uso nessas áreas. Atualmente a indústria farmacêutica busca modificações no sistema de entrega de drogas (melhorias no tempo, local e taxa de liberação), objetivando um aumento na estabilidade das drogas e a prevenção e diminuição de efeitos colaterais. Nesse sentido, surge a necessidade de desenvolver novas formulações farmacêuticas, novos métodos de preparação e novos materiais. Considerando o fato dos argilominerais incorporarem espécies diversas entre suas lamelas, é interessante explorar a possibilidade de uso dessas matrizes inorgânicas como carregadores de espécies bioativas. O principal objetivo do presente trabalho foi preparar e caracterizar argilas de uso farmacêutico e/ou cosmético intercaladas com espécies que apresentam potencial terapêutico. Para tanto, usou-se duas argilas esmectitas naturais do tipo montmorilonita (Cloisita Sódica e Veegum HS) e uma esmectita sintética do tipo hectorita (Laponita RD). Os aminoácidos L-lisina, L-arginina e L-ornitina, e o dipeptídeo L-carnosina foram imobilizados em argilas catiônicas, por meio de reação de troca iônica. Na preparação dos materiais híbridos, alguns parâmetros experimentais foram avaliados: concentração hidrogeniônica (pH) da suspensão de reação, proporção argila/aminoácido e tempo de reação. As argilas precursoras e os materiais híbridos obtidos foram caracterizados por difratometria de raios X, espectroscopia vibracional na região do infravermelho e Raman, análise termogravimétrica acoplada à espectrometria de massas e análise química de carbono. Os valores de distância interlamelar (d(001)) dos materiais sugerem que a cadeia carbônica das espécies orgânicas se orienta paralelamente em relação às lamelas de baixa densidade de carga dos argilominerais. Nos espectros vibracionais na região do infravermelho há predominância das bandas características da estrutura inorgânica, mas as bandas entre 1800 e 1400 cm-1 relativas aos grupos funcionais do aminoácido permitem inferir sobre o seu grau de protonação no material híbrido. A acidez de Brönsted gerada pela polarização das moléculas de água associadas à argila foi observada para as montmorilonitas empregadas neste estudo. Amostras preparadas em suspensões nas quais o valor do pH era maior que o valor da primeira constante ácida (pKa1) dos aminoácidos apresentam bandas atribuídas ao estiramento C=O de grupo carboxilato protonado. Os espectros Raman foram obtidos apenas para a argila sintética, uma vez que as naturais apresentam luminescência. O espectro Raman da L-carnosina imobilizada em Laponita indica a presença preponderante da espécie zwitteriônica; o deslocamento das bandas atribuídas aos grupos amida e carboxílico do dipeptídeo para região de menor energia sugere a formação de ligações de hidrogênio com os grupos silanol da Laponita. Os resultados de análise termogravimétrica acoplada à espectrometria de massas dos materiais híbridos são distintos daqueles observados para os aminoácidos livres. A temperatura de início de decomposição das espécies orgânicas não é praticamente modificada após imobilização nas argilas, mas os processos térmicos se estendem até regiões de maior temperatura, evidenciando a influência da estrutura inorgânica sobre a decomposição térmica dos aminoácidos. Através dos dados de quantidade de carbono e de água nas amostras, calculou-se a concentração de aminoácidos nos materiais híbridos (massa de aminoácido / 100 gramas de material). As maiores concentrações de aminoácido (entre seis e oito por cento) foram observadas para as amostras de Cloisita e Veegum HS, isoladas em condições nas quais predomina a interação eletrostática entre as lamelas e os aminoácidos com carga positiva. Nas condições experimentais empregadas neste trabalho não foi observada a saturação das argilas com os aminoácidos, ou seja, as cargas das lamelas não foram totalmente neutralizadas pelos íons orgânicos. / Clay minerals are used as excipients or active ingredients in the pharmaceutical and cosmetic fields. These inorganic compounds are chemically inert, have defined structures and high thermal stability, which make them useful for these areas. Currently the pharmaceutical industry seeks modifications in the drug delivery systems (improvements in the time, place and rate of release), aiming an increase in the stability of the drugs and also the prevention and reduction of side effects. In this way, it is a need to develop new pharmaceutical formulations, new preparation methods and new materials. Considering the fact that clay minerals incorporate various species between their layers, it is interesting to explore the possibility of using these inorganic matrices as carriers of bioactive species. The main aim of this work was to prepare and characterize clays of pharmaceutical and/or cosmetic usage intercalated with species of therapeutic potential. Two natural smectite clays of montmorillonite type (Sodium Cloisite and Veegum HS) and one synthetic smectite of hectorite type (Laponita RD) were employed. The amino acids L-lysine, L-arginine and L-ornithine, and the L-carnosine dipeptide were immobilized on cationic clays by ion exchange reaction. Some experimental parameters were evaluated in the preparation of hybrid materials: hydrogen ion concentration (pH) of reaction suspension, clay/amino acid proportion and reaction time. Pristine clays and hybrid materials were characterized by X-ray diffraction, infrared and Raman vibrational spectroscopies, thermogravimetric analyses coupled to mass spectrometry and chemical analysis of carbon. The materials values of interlayer distance (d(001)) suggest that the carbon chain of the organic species is oriented parallel to the layers of clay minerals. The infrared vibrational spectra are dominated by the inorganic structure bands; however the bands between 1800 and 1400 cm-1 related to the functional groups of the amino acid allow to infer about the protonation degree in the hybrid material. The Brönsted acidity generated by the polarization of water molecules associated with the clay was observed for montmorillonite samples used in this study. Materials prepared in suspensions in which the pH value was greater than the value of the first acid constant (pKa1) show bands assigned to the C=O stretching of protonated carboxylate group. Raman spectra were obtained only for the synthetic clay, since the natural ones luminesce. Raman spectrum of L-carnosine immobilized on Laponita indicates the presence of mostly zwitterionic species; the displacement of bands assigned to amide and carboxylic groups of the dipeptide to the lower energy region suggests the formation of hydrogen bonds with the Laponita silanol groups. The results of thermogravimetric analyses coupled to mass spectrometry of hybrid materials are different from those observed for the free amino acids. The onset temperature of the organic species decomposition is practically unmodified after the immobilization on clays, but thermal processes are postponed up to higher temperature, revealing the inorganic structure influence on the amino acids thermal decomposition. Data on the carbon and water amounts in the samples were used to calculate the concentration of amino acids in the hybrid materials (mass of amino acid / 100 grams of material). The highest concentrations of amino acid (between six and eight percent) was observed for Cloisite and Veegum HS samples, isolated under conditions in which the electrostatic interaction between the layers and the positively charged amino acids are predominant. Under the experimental conditions employed in this study no saturation of clay with amino acids was observed, i.e. the layer charges were not completely neutralized by the organic ions.

Os cereais representam importantes fontes de proteína para alimentação humana e animal. Entretanto, são caracterizados pela baixa qualidade nutricional de suas proteínas devido à composição desbalanceada de aminoácidos, causada pelo excesso dos aminoácidos prolina e glutamina e deficiência de lisina, treonina e triptofano. As proteínas de reserva prolaminas constituem 50% do conteúdo total de proteínas no endosperma e são as principais responsáveis por tais características nos cereais. As informações sobre o metabolismo de lisina e o acúmulo de proteínas de reserva no endosperma vêm sendo utilizadas para desenvolver e aplicar estratégias em programas de melhoramento de plantas que visam suprir a deficiência de lisina encontrada nos cereais. Lange e colaboradores (2007) relataram a produção de linhagens transgênicas de cevada com padrão de proteínas de reserva alterado e que apresentaram incremento no teor de lisina e outros aminoácidos essenciais. O presente trabalho teve como objetivo identificar os mecanismos responsáveis pelas alterações observadas. Para tanto, avaliou-se a atividade das enzimas envolvidas na síntese e degradação de lisina, além da caracterização das proteínas de reserva e sua composição de aminoácidos. Observou-se redução na fração protéica das prolaminas (5,91 a 18,34%) e incrementos compensatórios na fração protéica das glutelinas (2,16 a 6,52%). As demais frações apresentaram respostas variáveis dependendo do evento avaliado. Além disso, a composição de aminoácidos foi alterada nas diferentes frações protéicas. As prolaminas exibiram incrementos nos teores de lisina (1,79 a 49,13%), treonina (5,04 a 22,60%) e metionina (13,57 a 45,38%), enquanto que as globulinas aumentaram principalmente o conteúdo de metionina (32,30 a 142,56%). Para os aminoácidos solúveis, foram observados incrementos na ordem de duas a três vezes de histidina, lisina, fenilalanina e metionina. A análise das enzimas envolvidas no metabolismo de lisina revelou que ocorreram alterações nas três principais enzimas da via do ácido aspártico. A enzima aspartato quinase (AK) apresentou aumentos na atividade (4,44 a 47,27%), entretanto, foi mais sensível a inibição causada por lisina. A enzima dihidrodipicolinato sintase (DHDPS) também apresentou incremento na atividade (1,50 a 66,32%), mas diferente da AK, foi menos sensível à inibição causada por lisina. A enzima homoserina desidrogenase (HSDH), a qual compete o substrato ASA com a enzima DHDPS, exibiu redução na atividade (3,36% a 28,80%) (exceto um evento de transformação) e foi menos sensível a inibição causada por treonina. Embora as enzimas envolvidas na degradação de lisina também foram alteradas, os resultados foram variáveis para os diferentes eventos. Para aqueles que foram observados redução na atividade da enzima lisina cetoglutarato redutase (LOR), foi também verificado para enzima sacaropina desidrogenase (SDH), mas na ordem de duas vezes, sendo válido para aqueles que apresentaram incremento. Este trabalho mostrou que a alteração no padrão de proteínas de reserva ocasionou mudanças no metabolismo de aminoácidos, neste caso a lisina, para suprir a demanda necessária para incorporação em proteínas de reserva / Cereals represent an important source of protein to human food and animal feed. However, they are characterized by low nutritional quality of proteins due to the unbalanced composition of amino acids, caused by the excess of the amino acids proline and glutamine and deficiency of lysine, threonine and tryptophan. The prolamin storage proteins constitute 50% of the total protein content in the endosperm and is primarily responsible for these characteristics in cereals. Information on the metabolism of lysine and accumulation of storage proteins in endosperm have been used to develop and implement strategies in plant breeding programs that aim to address the deficiencies found in cereals. Lange and coworkers (2007) reported the production of transgenic lines of barley with a pattern of storage proteins that showed altered and increase in the levels of lysine and other amino acids. This study aimed to identify what were the mechanisms responsible for observed changes. For this, we evaluated the activity of enzymes involved in synthesis and degradation of lysine, besides the characterization of storage proteins and their amino acid composition. There was a reduction in the prolamin protein fraction (5.91 to 18.34%) and compensatory increases in the glutelin fractions (2.16 to 6.52%). The other fractions had variable responses depending on the event evaluated. Moreover, the amino acid composition was changed in the different protein fractions. Prolamins exhibited increases in levels of lysine (1.79 to 49.13%), threonine (5.04 to 22.60%) and methionine (13.57 to 45.38%), whereas increases were mainly globulins content of methionine (32.30 to 142.56%). With respect to soluble amino acids, increases were observed in the order of 2-3 fold of histidine, lysine, phenylalanine and methionine. Analysis of enzymes involved in lysine metabolism showed that changes in three key enzymes of the pathway of aspartic acid. The enzyme aspartate kinase (AK) showed increase in activity (4.44 to 47.27%), however, was more sensitive to inhibition by lysine. The enzyme dihydrodipicolinate synthase (DHDPS) also showed increased activity (from 1.50 to 66.32%), but unlike the AK, was less sensitive to inhibition by lysine. The enzyme homoserine dehydrogenase (HSDH) that competes for the substrate ASA with the DHDPS, exhibited reduced activity (3.36% to 28.80%) (an exception one transgenic line) and was less sensitive to inhibition by threonine. The enzymes involved in degradation of lysine were also changed, though the results varied for different events. Those who observed decreased activity of the enzyme lysine ketoglutarate reductase (LOR) was also found for enzyme saccharopine dehydrogenase (SDH), but the order of twice, which was valid for those who had increased. This study showed that the change in the pattern of storage proteins produced changes in amino acid metabolism, in this case lysine, to supply the demand needed for incorporation into storage proteins.

Thesis (M.Sc) (Agriculture)--University of Limpopo,2007. / Two experiments were carried out to evaluate the effects of feed restriction during the starter stage and lysine supplementation during realimentation on productivity and carcass characteristics of Ross 308 broiler chickens. In the first experiment, the effects of level and period of feed restriction during the starter period on subsequent productivity were evaluated. A 2 (male and female chickens) x 3 (feeding levels, ad libitum and 75% and 50% of ad libitum) x 3 (restriction periods of 5, 7 and 9 days), factorial arrangement in a Completely Randomized Design was used. The effects interactions were not included in the results because earlier analyses including all the interactions showed that they were not important. Level and period of feed restriction during the starter stage had an effect (P<0.05) on live weight of the chickens at 21 days of age. However, female and male chickens had similar live weights at 21 days of age. Chickens on 75% ad libitum feeding attained complete live weight compensation at the age of 42 days. However, chickens on 50% ad libitum feeding did not ‘catch-up’ with those on ad libitum feeding. Differences due to the period of feed restriction during the starter stage were maintained up to the age of 42 days. Male chickens had higher (P<0.05) live weights at 42 days of age. Abdominal fat pad was not affected (P>0.05) by level and period of feed restriction and sex of chickens at 42 days of age. The second experiment evaluated the effects of feed restriction during the starter stage (14 to 21 days) and levels of lysine supplementation during realimentation (21 to 42 days) on productivity and carcass characteristics of male and female chickens. Feed v restriction affected (P<0.05) live weight of chickens at the age of 21 days and males were heavier (P<0.05) than females at the same age. Chickens on 75% ad libitum feeding attained complete compensation in live weight while those on 50% ad libitum feeding did not. Lysine supplementation during realimentation had no effects (P>0.05) on live weight and carcass characteristics of the chickens at 42 days of age. Male chickens attained higher (P<0.05) live weights than female chickens at 42 days of age. / National Research Foundation

La thérapie génique de myopathies telles que la dystrophie musculaire de Duchenne nécessite une approche systémique afin de traiter l'ensemble de la musculature. Le vecteur AAV est actuellement le plus efficace pour transduire le muscle. Nous montrons que la biodistribution du vecteur AAV administré par voie veineuse peut être modifiée en utilisant diverses stratégies adjuvantes chez la souris saine. La pré-injection de polymères permet ainsi d'améliorer la transduction des muscles par le vecteur AAV, ou encore de baisser la réponse immune neutralisante induite par l'injection intraveineuse du vecteur. Nous abordons également l'impact de facteurs modulateurs exogènes ou endogènes – tels que la procédure d'administration ou certains facteurs sanguins – sur la transduction systémique de l'AAV. Dans une seconde approche, nous avons évalué le transfert de gènes dans le muscle dystrophique afin de sécréter dans la circulation sanguine une protéine transgénique fusionnant le récepteur soluble I du TNF-α avec le fragment constant d'une immunoglobuline (TNFR-Is/mIgG1). La comparaison des cinétiques de sécrétion obtenu après le transfert de gène dans le muscle de souris saines ou de souris dystrophiques mdx indique que le contexte inflammatoire du muscle dystrophique favorise une réponse immune contre le transgène. Nous montrons que l'expression et la sécrétion d'un variant murin peu immunogène du TNFR-Is/mIgG1 améliore la fonction musculaire de la souris mdx sans toutefois conférer un avantage sélectif aux fibres musculaires dystrophiques qui continuent leur cycle de nécrose et de régénération.

Amino acid biosynthesis is an essential process in living organisms. Certain amino acids can be synthesized by some organisms but not by others. L-Lysine is one of the essential amino acids that bacteria can synthesize but humans cannot. This is somewhat inconvenient for humans as much of their L-lysine must come from their diet. However, the lack of the lysine biosynthetic pathway in humans makes the bacterial enzymes within the pathway attractive drug targets. Recently, a novel lysine biosynthetic pathway was discovered in plants, Chlamydiae and some archaea. It is called the diaminopimelate aminotransferase (DAP-AT) pathway. In this pathway, LL-DAP-AT plays a key role by directly converting L-tetrahydrodipicolinate to LL-DAP in a single step. This is a quite interesting characteristic of LL-DAP-AT as the above conversion takes three sequential enzymatic steps in the previously known lysine biosynthetic pathways. Due to its absence in humans, LL-DAP-AT would be an attractive target for the development of novel antibiotics. In order to understand the catalytic mechanism and substrate recognition of LL-DAP-AT, the structural characterization of LL-DAP-AT is of paramount importance. In this thesis, the overall architecture of LL-DAP-AT and its substrate recognition mechanism revealed by the crystal structures of LL-DAP-AT from Arabidopsis thaliana and Chlamydia trachomatis will be discussed. The crystal structure of the native LL-DAP-AT from A. thaliana (AtDAP-AT) presented in this thesis is the first structure of LL-DAP-AT to be determined. This structure revealed that LL-DAP-AT forms a functional homodimer and belongs to the type I fold family of PLP dependent aminotransferases. The subsequent determination of the substrate-bound AtDAP-AT structure showed how the two substrates, (LL-DAP and L-Glu) significantly different in size, are recognized by the same set of residues without significant conformational changes in the backbone structure. In addition, the LL-DAP-bound AtDAP-AT structure shows that the C-amino group of LL-DAP is recognized stereospecifically by the active site residues that are unique to the family of LL-DAP-AT enzymes. Lastly, the chlamydial LL-DAP-AT presented in this thesis shows a new open conformation for LL-DAP-AT. The implications of the conformational flexibility of CtDAP-AT on the differences in substrate specificities among LL-DAP-AT are discussed.

In Saccharomyces cerevisiae, Set1p-mediated deposition of trimethylation on lysine 4 of histone H3 is a histone modification often associated with active transcription. Recently, it was discovered that members of the Jumonji family of proteins have the enzymatic ability to remove methylation on histone lysine residues. Here, I describe the function of the yeast Jumonji protein Jhd2p, the only yeast Jumonji with known demethylase activity towards histone H3 lysine 4 methylation. I find that during the development program of yeast sporulation, Jhd2p is responsible for demethylating lysine 4 on a global scale. Further, ChIP analysis examining lysine 4 methylation levels reveals that genes whose expression is dependent on JHD2 during sporulation are subject to what appears to be Jhd2p-mediated demethylation. Additionally, synthetic dosage lethality screens performed to identify genetic interactors of Jhd2p revealed that Jhd2p is a likely component of mitochondrial retrograde signaling, working alongside the transcription factors Rtg1p/Rtg3p.

In Saccharomyces cerevisiae, Set1p-mediated deposition of trimethylation on lysine 4 of histone H3 is a histone modification often associated with active transcription. Recently, it was discovered that members of the Jumonji family of proteins have the enzymatic ability to remove methylation on histone lysine residues. Here, I describe the function of the yeast Jumonji protein Jhd2p, the only yeast Jumonji with known demethylase activity towards histone H3 lysine 4 methylation. I find that during the development program of yeast sporulation, Jhd2p is responsible for demethylating lysine 4 on a global scale. Further, ChIP analysis examining lysine 4 methylation levels reveals that genes whose expression is dependent on JHD2 during sporulation are subject to what appears to be Jhd2p-mediated demethylation. Additionally, synthetic dosage lethality screens performed to identify genetic interactors of Jhd2p revealed that Jhd2p is a likely component of mitochondrial retrograde signaling, working alongside the transcription factors Rtg1p/Rtg3p.

The amine oxidase family of enzymes has been the center of numerous mechanistic studies because of the medical relevance of the reactions they catalyze. This study describes transient and steady-state kinetic analyses of two flavin amine oxidases, mouse polyamine oxidase (PAO) and human lysine specific demethylase (LSD1), to determine the mechanisms of amine oxidation. PAO is a flavin adenine dinucleotide (FAD)-dependent enzyme that catalyzes the oxidation of N1-acetylated polyamines. The pH-dependence of the kcat/Kamine indicates that the monoprotonated form of the substrate is required for catalysis, with the N4 nitrogen next to the site of CH bond cleavage being unprotonated. Stopped-flow spectroscopy shows that the pH-dependence of the rate constant for flavin reduction, kred, displays a pKa of 7.3 with a decrease in activity at acidic pH. This is consistent with an uncharged nitrogen being required for catalysis. Mutating Lys315 to methionine has no effect on the kcat/Kamine-pH profile with the substrate spermine, and the kred value only shows a 1.5-fold decrease with respect to wild-type PAO. The mutation results in a 30- fold decrease in kcat/KO2. Solvent isotope effects and proton inventories are consistent with Lys315 accepting a proton from a water molecule hydrogen-bonded to the flavin N5 during flavin oxidation. Steady-state and transient kinetic studies of para-substituted N,N'-dibenzyl-1,4- diaminobutanes as substrates for PAO show that the kred values for each correlate with the van der Waals volume (VW) and the value. The coefficient for VW is the same at pH 8.6 and 6.6, whereas the p value increases from -0.59 at pH 8.6 to -0.09 at pH 6.6. These results are most consistent with a hydride transfer mechanism. The kinetics of oxidation of a peptide substrate by human lysine specific demethylase (LSD1) were also studied. The kcat/KM pH-profile is bell-shaped, indicating the need for one unprotonated nitrogen next to the site of CH bond cleavage and another protonated nitrogen. The kcat and kred values are equal, and identical isotope effects are observed on kred, kcat, and kcat/KM, indicating that CH bond cleavage is rate-limiting with this substrate.

In this study we fabricated free standing multilayer films of polyelectrolyte complexes for potential use in tissue engineering of corneal stroma by using the layer-by-layer (LbL) approach. In the formation of these LbL films negatively charged, photocrosslinkable (methacrylated) hyaluronic acid (MA-HA) was used along with polycations polyethyleneimine (PEI) and poly(L-lysine) (PLL). Type I collagen (Col) was blended in with PLL for improving the water absorption and cell attachment properties of the films. It was shown that the LbL films could be easily peeled off from glass substrates due to the photocrosslinking of one of the LbL components, the hyaluronic acid. Film growth and composition were monitored with FTIR-ATR. Heights of peaks at 3383 cm-1, and 2958 cm-1increased along with the bilayer number confirming the polymer build-up. Film integrity and thickness were investigated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). Films thicker than 5 bilayers (BLs) were found to be uniform in appearance and 10 BL (PEI/MeHA) films were calculated to be ca. 6 &mu / m thick. Atomic force microscopy (AFM) revealed that as the number of BLs increased, surface roughness decreased. Activity of methacrylated hyaluronic acid was shown by the increased resistance of photocrosslinked multilayer films against hydrolysis by hyaluronidase. Patterns could be created on the films by photocrosslinking further proving that the crosslinking step is successful. Since the ultimate goal was to construct a corneal stroma PEI/MA-HA films were tested with corneal stroma cells, keratocytes. Cell proliferation on PEI/MA-HA films was quite poor in comparison to TCPS. In order to improve the cell adhesion the tests were repeated with PLL/MA-HA. Collagen was added to decrease the hydrophilicity and introduce cell adhesion sequences (Arg-Gly-Asp, RGD) to improve cell proliferation on the films and thus PLL+Col/MA-HA films were also tested. Introduction of collagen to the PLL/MA-HA films was found to decrease water retention of the multilayer films and improve cell viability and proliferation. Col+PLL/MA-HA LbL thus appear to be a promising platform for tissue engineering, especially of corneal stroma.