Thesis (Ph. D.)--University of Hong Kong, 2009. / Includes bibliographical references (leave 218-230). Also available in print.

Aspartate transcarbamoylase (ATCase) of Pseudomonas putida consists of two different polypeptides, PyrB and PyrC' (Schurr et al, 1995). The role of the PyrC' and the assembly of PyrB and PyrC' have been studied. The ATCase made in vitro of P.putida PyrB with P.putida PyrC', and of E.coli PyrB with P.putida PyrC ' were generated under two different conditions, denaturation and renaturation, and untreated. It was found that PyrC' plays a role in the enzymatic regulation by ATP, CTP and UTP. In addition to playing a role in substrate binding, the PyrB polypeptide is also involved in effector binding (Kumar et al., manuscript in preparation). The most energetically preferred form of the P.putida WT is a dodecamer with a molecular mass of 480 kDa. The ratio between the PyrB and the PyrC' is 1:1. In studies of nucleotide binding, it was discovered that the P.putida PyrB was phosphorylated by a protein kinase in the cell extract. In the presence of 20 mM EDTA, this phosphorylation was inhibited and the inhibition could be overcome by the addition of divalent cations such as Zn2+ and Mg2+. This result suggested that the phosphorylation reaction required divalent cations. In the CAD complex of eukaryotes, phosphorylations of the CPSase and the linker region between ATCase and DHOase did not occur in the presence of UTP and it was hypothesized (Carrey, 1993) that UTP and phosphorylation(s) regulated the conformational change in the enzyme complex. Therefore, the same idea was approached with P.putida ATCase, where it was found that 1.0 mM UTP inhibited the phosphorylation of PyrB by more than 50%. These results suggested that the regulation of the conformational change of the P.putida ATCase might be similar to that of CAD. Furthermore, peptide mapping for phosphorylation sites was performed on P.putida ATCase WT, WT --11 amino acids and WT --34 amino acids from the N-terminus of the PyrB polypeptide. The results showed that the phosphorylation sites were located on the fragment that contained amino acid number-35 to amino acid number-112 from the N-terminus of the PyrB polypeptide.

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Les peptides pénétrateurs de cellule (CPP) sont des oligopeptides cationiques faisant parti des vecteurs les plus étudiés dans le cadre du développement du transport ciblé de médicament à l’intérieur de l’organisme. Les applications principales sont par exemple le traitement des cancers ou la thérapie génique. Néanmoins, certaines caractéristiques des CPPs rendent leur utilisation médicale compliquée, tels que leur manque de spécificité à l’égard des cellules cibles ou la perte de leurs propriétés pénétrantes lorsqu’un cargo moléculaire leur est greffé. L’une des solutions envisagées pour résoudre ces problèmes est le greffage sur des polypeptides di-blocs auto-assemblés basés sur de l’élastine (ELPBC), des systèmes développés par l’équipe d’Ashutosh Chilkoti à l’Université de Duke (USA). Des travaux précédents ont montré que ces macromolécules, que l’on appelle CPP-ELPBC, retrouvaient les propriétés pénétrantes du CPP même en présence d’un cargo et permettaient également d’induire une spécificité à l’encontre des cellules cancéreuses. En revanche, le mécanisme de pénétration de ces systèmes restait inconnu.Dans cette thèse, je me suis concentré sur l’étude du mécanisme de pénétration des CPP et des CPP-ELPBC au travers de membranes lipidiques modèles, et en particulier sur l’adsorption de ces molécules à la surface de vésicules unilamellaires géantes (GUV). Le développement d’une nouvelle méthode de quantification de la fluorescence en microscopie confocale m’a permis de réaliser des mesures simples de comptage de peptides à la surface des vésicules, ce qui m’a permis par la suite de procéder à des mesures thermodynamiques de l’adsorption des peptides. / Cell-penetrating peptides (CPP) are cationic oligopeptides currently investigated as potential vectors for targeted drug delivery design, for applications in cancer treatment and/or gene therapy. Nevertheless, some drawbacks make the CPP complex for medical applications, such as their lack of specificity toward target cells or the loss of their penetrating properties once they have been grafted with a molecular cargo. One of the solutions studied to overcome these issues is the binding of the CPP unit on a self-assembling elastin-like diblock polypeptide (ELPBC), a macromolecular system designed by the team of Ashutosh Chilkoti from Duke University (USA). While it has already been proven that these molecules, named CPP-ELPBC, recover the penetrating properties of the CPP despite the presence of a cargo and also induce a selectivity toward tumorous cells, the exact mechanism of translocation is still under debate.In this PhD thesis, I focused on the investigation of the translocation mechanism of the CPP and CPP-ELPBC using model lipid membranes, and specifically the adsorption of these molecules at the surface of giant unilamellar vesicles (GUV). The development of a new quantification method of fluorescence in confocal microscopy allowed me to directly count the peptides adsorbed on the surface of the GUVs, which I used to perform thermodynamic measurements on the peptide adsorption.

WGS permet d'analyser et de déchiffrer l'étude de résistances de bactéries multirésistantes(MDR), en comprenant les différents mécanismes de résistance, les annuaires génétiques. Au cours de ma thèse de doctorat, j'ai réalisé: 1 revue de la littérature sur l'utilisation de nouveaux outils de diagnostic contemporains et les capacités dans la détection des foyers dans les maladies infectieuses causées par MDR. L'identification et l'analyse de résistances de bactéries multirésistantes Comme étant des Shewanellalgae, normalement de l'environnement marin, dans notre cas une souche clinique isolée du lavage bronchoalvéolaire d'un patient hospitalis avec pneumonie et Chryseobacteriumin dologenes, isolé d'une fibrose kystique du patient. Dans cette analyse, nous pouvons montrer que les bactéries environnementales telles que les S.algae peuvent être un réservoir de gènes de résistance aux antibiotiques. L'analyse exhaustive de ces bactéries a montré leur capacité à s'adapter à leurs écosystèmes, y compris l'acquisition de nouveaux éléments génétiques par transfert latéral de gènes. La détection des gènes impliqués dans la synthèse de peptides synthetasenon ribosomale et de polycétide synthétase peut avoir un rôle dans leur capacité à survivre dans des environnements hostiles tels que le tractus respiratoire des patients atteints de fibrose kystique ou leur présence chez des patients ayant subi plusieurs antibiotiques. Nous avons réalisé une analyse standardisée «insilico» afin de déterminer la résistance de ces bactéries et la présence de métabolites secondaires associés aux bactériocines et aux NRPS/PKS. L'application du NTS pour le séquençage du génome bactérien de nouvelles espèces bactériennes isolées dans le microbiome humain nous a permis de développer une plateforme capable d'analyser ces nouvelles espèces dans les 48heures. Ce travail permet de mieux comprendre la biodiversité des bactéries isolées dans le microbiome humain. / Theuse of WG Sallows to analyze and to decipherthe study of resistome of Multi Drug Resistant bacteria (MDR), understanding the different resistance mechanisms, genetic directories and their dissemination mechanisms at global level. During them y thesis I have achieved: 1. A literature review on the use of new contemporary diagnostic tools and capabilities in detecting out breaksin infectious diseases caused by MDR. 2: The identification and the analysis of resistome of multidrug resistant bacteria from clinical isolates suchasShewanellaalgae, normally marine environmental, in our case clinical strain isolated from the broncho alveolar lavage of a hospitalized patient with pneumonia and Chryseobacteriumin dologenes, isolated from a patient cysticfibrosis. In this analysis, we can show that environment albacteria suchas S.algae can be a reservoir of antibiotic resistance genes. The exhaustive analysis of these bacteria showed their ability to a dapttotheirecosystemsincludingtheacquisitionofnewgeneticelementsbylateralgenetransfer. The detection of genes in volved in the synthesis of nonribosomal peptide synthetase and polyketide synthases may have a role in their ability to survive in hostile environments suchas therespiratorytractofCFpatients or their presence inpatients having suffered multipleofantibiotic. 3:In this work,through theuse of the NTS onnew bacterial species isolated from human microbiome,we have a chieveda standardized analysis"insilico"to determine there sistome of these bacteria and the presence of secondary metabolites associated bacteriocins and the NRPS/PKS. The application of the NTS for sequenc in go bacterial genome of new bacterial species isolated in the human microbiome, allowe dus to develop a platform capable of analyzing the senew species within 48

Dans ce travail, nous avons développé des nanostructures théranostics à base de polypeptides fonctionnalisées avec un photosensibilisateur (PTS) dans le but d’être utilisées en thérapie photodynamique (PDT). La génération d'oxygène singulet et les propriétés de fluorescence du PTS peuvent ainsi à la fois diagnostiquer et traiter une tumeur. Un dérivé asymétrique et multifonctionnel de l'aza-dipyrrométhènes difluorure de bore chélate (aza-BODIPY) fluorogène a été synthétisé pour être utilisé comme photosensibilisateur en raison de ses propriétés non toxiques, son insensibilité à l'environnement biologique externe, sa production d'oxygène singulet élevée et son important rendement quantique de fluorescence. Pour permettre au photosensibilisant d’atteindre la tumeur, quatre copolymères à blocs amphiphiles différents en termes de localisation du PTS et de la longueur de la chaîne PEG ont été synthétisés. Les blocs amphiphiles sont constitués de segments poly(ɤ-benzyl-L-glutamate) (PBLG, DP ~ 50) et poly(éthylène glycol) (PEG, DP = 45 et 113). Ces copolymères sont en outre capables de s’auto-assembler en micelles et en vésicules. Nous avons développé une stratégie de synthèse permettant la liaison covalente du PTS pour les copolymères à blocs amphiphiles, empêchant ainsi une fuite du PTS avant que le nanoparticules atteignent le site de la tumeur. En outre, nous avons étudié l'activité du PTS en fonction de la concentration, de la morphologie des nanoparticules et de la localisation du PTS dans les nanoparticules. Enfin, l'efficacité des nanoparticules a été évaluée in vitro sur des cellules HeLa et B16F1. / In this work, we developed photosensitizer (PTS) functionalized polypeptide-based theranostic nano-assemblies to be used in photodynamic therapy (PDT). The singlet oxygen generation and fluorescence properties of the PTS provide simultaneous diagnosis and therapy of the tumor.An asymmetric and multifunctional derivative of the aza-dipyrromethene boron difluoride chelate (aza-BODIPY) fluorophore was synthesized to be used as a photosensitizer due to its nontoxic properties, insensitivity to external biological environment, high singlet oxygen generation and fluorescent quantum yield. To carry the photosensitizer to the tumor, four different (in terms of PTS localization and PEG chain length) amphiphilic block copolymers consisting of poly(ɤ-benzyl-L-glutamate) (PBLG, DP~50) and poly(ethylene glycol) (PEG, DP=45 and 113) chains, able to self-assembled into micelles and vesicles, were synthesized. We developed a synthetic strategy allowing covalent linkage of PTS to the amphiphilic block copolymers, thus preventing PTS leakage before the nano-assembly reaches the tumor site. Moreover, we investigated PTS activity as a function of concentration, morphology of the nano-assemblies and PTS localization in the nano-assemblies. Finally, the efficacy of the nano-assemblies has been evaluated in vitro on HeLa and B16F1 cells.

published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

Small diameter synthetic vascular grafts have yet to be clinically successful due to luminal narrowing from thrombosis and intimal hyperplasia. Current attempts to address this issue include the development of materials that support endothelialisation and protein modification to the material surfaces that reduce thrombosis. The extracellular matrix protein elastin has been found to be one of the least thrombogenic components of blood vessels, and its purified and recombinant forms have shown reduced thrombogenicity in both in vitro and in vivo models. Biomaterial coatings of elastin-like polypeptides (ELPs) recombinantly produced in the Woodhouse laboratory showed reduced fibrinogen adsorption, platelet adhesion, and platelet activity. However, the reason for their relative non-thrombogenicity is still not fully understood. In this work, the leukocyte response to ELP-coated materials was investigated. In particular, ELP1 and ELP4, which differ in molecular weight and sequence length, were physically adsorbed to a polyethylene terephthalate surface (MylarTM), yielding 0.22 ± 0.13 μg/cm2 and 0.37 ± 0.19 μg/cm2 surface coverage, respectively, as determined by the colorimetric assay, FastinTM Elastin. These surfaces were exposed to flowing citrated whole blood for surface and bulk evaluation of leukocyte activity using scanning electron microscopy and flow cytometry, respectively. Little leukocyte activation was observed on the surface of the controls, low-density polyethylene and uncoated MylarTM. In the bulk, tissue factor (TF) expression (monocytes: ELP1 = 38.6 ± 16.3 %, ELP4 = 33.9 ± 18.1 %) and platelet-leukocyte aggregates determined by CD61 (monocytes: ELP1 = 63.1 ± 17.1 %, ELP4 = 61.8 ± 16.8 %; granulocytes: ELP1 = 62.7 ± 17.0 %, ELP4 = 60.5 ± 20.1 %) were both decreased compared to uncoated MylarTM, while CD11b upregulation (monocytes: ELP1 = 18.7 ± 2.2 %, ELP4 = 19.7 ± 2.7 %; granulocytes: ELP = 21.4 ± 3.7 %, ELP4 = 22.0 ± 3.2 %) was increased. The statistical dependence of TF expression and platelet-monocyte aggregates was tested; however, no correlation was found. Overall, platelet-leukocyte aggregate formation was reduced and there were conflicting results with regards to the reduction of leukocyte activation for the ELP coatings on MylarTM. / Thesis (Master, Chemical Engineering) -- Queen's University, 2013-10-10 15:34:51.802

The development of small-diameter artificial blood vessels that mimic the properties of natural blood vessels has proven to be a clinical challenge. While autologous vessels are the standard, they can be difficult to obtain and require invasive surgeries. Synthetic materials have been successful in large diameter applications, but they have been unsuccessful in small-caliber environments due to a number of factors including thrombus formation, intimal hyperplasia, and infection. Intimal hyperplasia, of particular interest in this study, involves the build up of smooth muscle cells (SMCs) in the intimal layer of the artery due to abnormal migration and proliferation. This work focuses on the development of a new polymer that has the potential to function as an intimal/medial component of a small-diameter blood vessel. Using recombinant elastin-like polypeptides (ELPs) developed by the Woodhouse laboratory, as well as chondroitin sulphate-specific binding sequences (CSBD1 and CSBD2) determined by the Panitch laboratory, a new elastin-like polypeptide-chondroitin sulphate binding domain (ELP-CSBD) block copolymer has been developed and characterized. The expression of the ELP1-CSBDs was accomplished using E. coli BL21 cells in a bioreactor or shaker flask systems. The polypeptides were purified using dialysis and ion exchange chromatography and expression and purity were characterized using mass spectrometry and amino acid analysis. Both ELP1-CSBDs were successfully expressed using these methods and ELP1-CSBD1 was produced to high purities. ELP1-CSBD1 was able to undergo coacervation in vitro, suggesting that ELP1-CSBD1 is able to self-assemble in a manner similar to native elastin. In the presence of the glycosaminoglycan chondroitin sulphate (CS), the temperature of coacervation of ELP1-CSBD1 is increased, the rate and extent of coacervation is decreased, and aggregates remain in solution even at higher temperatures. The influence of heparin was also explored as previous studies indicated that the CS binding domains were shown to also bind to heparin. Studies completed in the presence of heparin showed that there were no significant changes to the coacervation characteristics of ELP1-CSBD1. It is anticipated that when combined with CS, ELP1-CSBD1 will gel, forming a basis for an intimal/medial layer of a TEBV that will modulate SMC response and increase graft integrity. / Thesis (Master, Chemical Engineering) -- Queen's University, 2013-01-06 21:03:37.788