The 2-methylbranched chain acyl-CoA dehydrogenase (BCAD) is a mitochondrial enzyme that catalyzes the third reaction in isoleucine and valine metabolism, the oxidation of 2-methylbutyryl-CoA and isobutyryl-CoA, respectively. BCAD deficiency would result in the accumulation of branched chain acyl-CoAs or their derivatives. Three patients with a putative defect in BCAD have been reported. This study consists of a molecular examination of one such patient as well as the characterization of the BCAD gene. In Northern blot analysis of human fibroblast RNA, the BCAD cDNA hybridized to two RNA species of 2.7 and 6.5 kb. The 2.7 kb band corresponds to the size of the BCAD cDNA, which consists of the entire coding region of 1.3 kb and a 3$ sp prime$ untranslated region of 1.4 kb. The coding regions of the BCAD gene span approximately 21 kb and consist of 12 exons and 11 introns. The exons range in size from 39 to 108 bp. In the analysis of the putative BCAD-deficient patient, no significant difference was observed at the level of DNA (Southern), RNA (Northern) or protein (Western) when compared to controls, suggesting that the BCAD gene in this patient did not contain any large insertions or deletions, or a frameshift mutation. The single strand conformation polymorphism (SSCP) technique and sequencing of the entire coding region did not reveal any disease-causing mutations but two polymorphisms were identified: one in exon 6 and the other in exon 10.

Thesis (M. Phil.)--University of Hong Kong, 2000. / Includes bibliographical references (leaves 136-166).

Made available in DSpace on 2014-06-11T19:22:55Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-02-09Bitstream added on 2014-06-13T20:27:26Z : No. of bitstreams: 1 alho_mjo_me_botfm.pdf: 749891 bytes, checksum: 3d5f6a497d3423875e704bf6e56656f7 (MD5) / Ministério da Saúde / Fundação para o Desenvolvimento Médico e Hospitalar (Famesp) / Secretaria do Estado da Saúde de São Paulo / Em 1997 o Departamento de DST/AIS e Hepatites Virais estruturou em todo Brasil uma rede de laboratórios para realizar o exame de Carga Viral Plasmática do HIV (CV) denominada Rede Nacional de Carga Viral. O exame quantifica o RNA do HIV no plasma do paciente infectado utilizando a metodologia do branched-DNA, um ensaio de amplificação do sinal luminescente, o qual utiliza uma plataforma de detecção. Atualmente, esta rede é reconhecida internacionalmente e realiza 520.000 exames/ano. No entanto, vários fatores podem influenciar o resultado do exame como integridade do RNA, volume de amostra disponível, método e plataforma utilizados. Assim, o Departamento de DST/AIDS e Hepatites Virais implantou um protocolo pré-analítico para ser utilizado em todo o território nacional. Entretanto, as regiões brasileiras são muito diferentes e alguns laboratórios não conseguem seguir este protocolo. O objetivo deste estudo foi (a) avaliar as diferentes condições de transporte e armazenamento das amostras utilizadas no teste de CV, (b) validar a utilização de volumes iniciais de plasma inferiores ao preconizado, (c) comparar plataformas de detecção e (d) metodologias disponíveis para a execução do exame. Os resultados mostraram que as amostras podem ser processadas em até 8 h sem perda ou degradação do RNA, volumes iniciais inferiores ao preconizado podem ser utilizado com perda de sensibilidade e, as duas plataformas disponíveis no Brasil são equivalentes para a execução do teste. Apesar de existirem outras metodologias para a realização do teste, os resultados podem ser diferentes mostrando a necessidade da utilização da mesma metodologia em todo Brasil / The Department of the DST/AIDS and Viral Hepatitis implemented since 1997 a laboratory network in all Brazil to perform the HIV plasma viral load (PVL) test named Viral Load National Network as part of the attendance to infected patient. This exam quantify the HIV plasma RNA in infected patient using Branched-DNA methodology, a signal amplification nucleic acid probe assay, which use a detection platform. Nowadays this network has international appreciation and to execute 520.000 tests/year. However, several factors can alter the result of the test as RNA integrity, available sample volume, used method and detection platform. Then an optimized pre-analytic protocol was implanted by Department of the DST/Aids to be used in all national territory. However the Brazil regions are many different and some laboratories don’t get lead this protocol. The goal of this study was (a) to evaluate the different transport and storage conditions of the samples used to the PVL test, (b) to valid the use of the lower plasma initial input in the exam, (c) to compare the detection platforms and (d) methods available to execution of the test. The results showed blood sample can be process in until 8h after collection without RNA loss or degradation, lower initial input can be used with loss of sensibility and the two detection platforms available in Brazil are equivalent. In spite of others methods are available to execution of test, the results can be distinct showing the importance of the all laboratories in Brazil used the same method

No description available.

No description available.

Groundwater contaminants such as chlorinated ethenes, chlorinated ethanes and nitroaromatic explosive compounds (e.g. 2,4,6-Trinitrotoluene (TNT)) degrade in the subsurface primarily by microbially catalyzed reductive transformation reactions. From a regulatory point of view, the capability to simulate the kinetics of these reductive transformation reactions coupled with other attenuation processes in the subsurface (e.g., sorption, advection, and dispersion) is required for site-specific solute transport models. A kinetic model based on Michaelis-Menten type equations (Widdowson 2004) has been successfully validated for the linear reductive dechlorination pathway of chlorinated ethenes, and implemented in solute transport codes such as SEAM3D (Waddill and Widdowson 2000). However, TNT degrades through more complex branched pathways, and kinetic models are lacking in the current literature. This research study was undertaken with the objective of extending the kinetic model developed for the linear reductive pathway of chlorinated ethenes to branched pathways. The proposed extended kinetic model was validated with experimental concentration-time data of TNT and its metabolites from two prior published laboratory studies (Daun et al. 2000; Hwang et al. 2000), both in the presence and absence of sorption. The model-predicted concentrations with time of TNT and its degradation intermediates and end-products correlated well with the experimental data. The model is further compatible with and can be easily incorporated into solute transport codes (e.g., SEAM3D), and used to evaluate the fate and transport of TNT and other similar contaminants in the subsurface. / Master of Science

Yes / For the first time a series of functional hydrogels based on semi-interpenetrating networks with both branched and crosslinked polymer components have been prepared and we show the successful use of these materials as substrates for cell culture. The materials consist of highly branched poly(N-isopropyl acrylamide)s with peptide functionalised end groups in a continuous phase of crosslinked poly(vinyl pyrrolidone). Functionalisation of the end groups of the branched polymer component with the GRGDS peptide produces a hydrogel that supports cell adhesion and proliferation. The materials provide a new synthetic functional biomaterial that has many of the features of extracellular matrix, and as such can be used to support tissue regeneration and cell culture. This class of high water content hydrogel material has important advantages over other functional hydrogels in its synthesis and does not require post-processing modifications nor are functional-monomers, which change the polymerisation process, required. Thus, the systems are amenable to large scale and bespoke manufacturing using conventional moulding or additive manufacturing techniques. Processing using additive manufacturing is exemplified by producing tubes using microstereolithography. / EPSRC

The research presented focused on the synthesis and the characterization of graft polymers, of interest either as model systems or for large-scale applications. The materials selected as substrates for grafting reactions were carbosilane dendrimers, linear and branched polystyrenes, and cross-linked polystyrene latex particles. The synthesis of dendrimer-arborescent polymer hybrids was thus achieved by derivatization of the carbosilane dendrimers with dichlorosilane moieties and coupling with 1,4-polybutadiene side chains with Mn ≈ 1000. A second derivatization and coupling reaction with Mn ≈ 1500, 5000, or 30000 side chains yielded hybrid polymers with narrow molecular weight distributions (Mw/Mn ≤ 1.16). In the second part of the thesis, a procedure for the large-scale (100-g) synthesis of arborescent styrene homopolymers and copolymers incorporating poly(2-vinylpyridine) segments is presented. End-capping of the polystyryllithium chains with 1,1-diphenylethylene in the presence of LiCl, followed by the addition of 3 – 6 equivalents of 2-vinylpyridine per side chain, eliminated side reactions and led to grafting yields of up to 95 %. A systematic investigation of the solution properties of polyelectrolytes obtained by protonation of the poly(2-vinylpyridine) arborescent copolymers with a strong acid (trifluoroacetic acid) is also presented. The relative importance of the electrostatic repulsion and the elastic deformation forces on molecular expansion was investigated by examining the solution properties of the copolymers as a function of structure, protonation level, and the presence of salts in polar solvents (methanol, DMF, H2O). The viscosity of the arborescent copolymer solutions was also found to be much lower than for linear P2VP samples under the same conditions. In the last part of the thesis, the synthesis of model filler particles was achieved by grafting polyisoprene chains onto cross-linked polystyrene latex particles derivatized with acetyl coupling sites. These substrates, which can be viewed as an extreme case of a dense (hard-sphere) arborescent polymer structure, were used to investigate the influence of filler-matrix polymer interactions on the rheological behavior of filled polyisoprene samples. The influence of the filler structure on the rheological behavior of the blends was examined by dynamic mechanical analysis in terms of frequency-dependent complex viscosity, storage modulus, and damping factor. All the blends exhibited enhanced complex viscosity, storage modulus, and decreased damping factor values relative to the matrix polymer.

The research presented focused on the synthesis and the characterization of graft polymers, of interest either as model systems or for large-scale applications. The materials selected as substrates for grafting reactions were carbosilane dendrimers, linear and branched polystyrenes, and cross-linked polystyrene latex particles. The synthesis of dendrimer-arborescent polymer hybrids was thus achieved by derivatization of the carbosilane dendrimers with dichlorosilane moieties and coupling with 1,4-polybutadiene side chains with Mn ≈ 1000. A second derivatization and coupling reaction with Mn ≈ 1500, 5000, or 30000 side chains yielded hybrid polymers with narrow molecular weight distributions (Mw/Mn ≤ 1.16). In the second part of the thesis, a procedure for the large-scale (100-g) synthesis of arborescent styrene homopolymers and copolymers incorporating poly(2-vinylpyridine) segments is presented. End-capping of the polystyryllithium chains with 1,1-diphenylethylene in the presence of LiCl, followed by the addition of 3 – 6 equivalents of 2-vinylpyridine per side chain, eliminated side reactions and led to grafting yields of up to 95 %. A systematic investigation of the solution properties of polyelectrolytes obtained by protonation of the poly(2-vinylpyridine) arborescent copolymers with a strong acid (trifluoroacetic acid) is also presented. The relative importance of the electrostatic repulsion and the elastic deformation forces on molecular expansion was investigated by examining the solution properties of the copolymers as a function of structure, protonation level, and the presence of salts in polar solvents (methanol, DMF, H2O). The viscosity of the arborescent copolymer solutions was also found to be much lower than for linear P2VP samples under the same conditions. In the last part of the thesis, the synthesis of model filler particles was achieved by grafting polyisoprene chains onto cross-linked polystyrene latex particles derivatized with acetyl coupling sites. These substrates, which can be viewed as an extreme case of a dense (hard-sphere) arborescent polymer structure, were used to investigate the influence of filler-matrix polymer interactions on the rheological behavior of filled polyisoprene samples. The influence of the filler structure on the rheological behavior of the blends was examined by dynamic mechanical analysis in terms of frequency-dependent complex viscosity, storage modulus, and damping factor. All the blends exhibited enhanced complex viscosity, storage modulus, and decreased damping factor values relative to the matrix polymer.

RNAs have gained significant attention in recent years because they can fold into well-defined secondary or tertiary structures. These three dimensional architectures provide interfaces for specific RNA-RNA or RNA-protein interactions that are essential for biological processes in a living system. These discoveries greatly increased interest in RNA as a potential drug target for the treatment of diseases. Two of the most studied RNA based regulatory systems are HIV-1 trans-activating response element (TAR)/Tat replication pathway and Rev response element (RRE)/Rev export pathway. To efficiently target TAR and RRE RNA, we designed and synthesized three generations of branched peptide libraries that resulted in medium sized molecules. The first generation of BPs were discovered from screening a one-bead one-compound library (4,096 compounds) against HIV-1 TAR RNA. One peptide FL4 displayed a binding affinity of 600 nM to TAR RNA, which is tighter than its native protein counterpart, Tat. Biophysical characterization of these BP demonstrated that "branches" in BPs impart multivalency, and they are cell permeable and non-toxic. The second generation peptides were discovered from an on-bead high-throughput screening of a 3.3.4 branched peptide boronic acids (BPBAs) library that bind selectively to the tertiary structure of RRE IIB. The library comprised of 46,656 unique sequences. We demonstrate that our highest affinity BPBA (BPBA1) selectively binds RRE IIB in the presence of competitor tRNAs as well as against six RRE IIB structural variants. Further, we show that the boronic acid moieties afford a novel binding mode towards RNA that is tunable; their Lewis acidity has critical effects on binding affinity. In addition, biophysical characterizations provide evidence that "branching" in these peptides is a key structural motif for multivalent interactions with the target RNA. Finally, RNA footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB. BPBA1 is cell permeable and non-toxic. In the next generation of branched peptides, a 3.3.4 branched peptide library composed of 4,096 unique sequences that featured boronic acid and acridine moieties was designed. We chose acridine as the amino acid side chain due to its potential for π-stacking interaction that provides high binding affinity to RNA target. The library was screened against HIV-1 RRE IIB RNA. Fifteen peptides were sequenced and four contained acridine alone and/or in conjunction with boronic acid moieties displayed dissociation constants lower than 100 nM. The ribonuclease protection assays of A7, a sequence that contains both boronic acid and acridine residues, showed a similar protection pattern compared to previous peptide BPBA1, suggesting that the 3.3.4 branched peptides shared similar structural elements and contacted comparable regions of the RRE IIB RNA. The results from this research indicated that "branching" in peptides imparts multivalent interactions to the RNA, and that functional groups such as boronic acid and acridine are key structural features for efficient binding and selectivity for the folded RNA target. We demonstrated that the branched peptides are cell permeable and non-toxic. / Ph. D.