Proposed doctoral thesis deals with microbial production of biopolymers (polysaccharides and polyesters) using renewableble inexpensive resources as carbon and nitrogen source. At first, production of extracellular metabolites, mainly pullulan and poly-L-malic acid, by polymorphic microorganism Aureobasisium pullulans was studied. Further part of thesis was focused on production of bacterial biopolyesters polyhydroxyalkanoates (PHA). PHA are produced in the form of intracellular granules by various bacteria species. During the study of PHA production, sythesis of poly(3-hydroxybutyrate) and technologically significant copolymer poly(3-hydroxybutyrate-co-3-hydroxyvalerate) was investigated as well with regard to waste substrate utilization in biorafinery concept. Spent coffee ground seemed to be applicable waste in biorefinery proces. One of the coffee wastes used for PHA production was spent coffee ground hydrolysate which was converted to PHA by Burkholderia cepacia. Moreover, copolymer of 3HB and 3HV was accumulated when SCGH was used as a sole carbon source, no precursor had to be added. Another coffee waste, which was utillized by Cupriavidus necator H16, is represented by oil extracted from spent coffee grounds. Hydrolysis proces of waste substrates had to be optimized, to reach the highest possible saccharide concentration. Due to the hydrolysis process several toxic compounds can be formed, hence, influence of hydrolysis procesings on polyphenols content in hydrolysates was monitored. Waste substrates were also tested as potentional complex nitrogen source for PHA production. Hydrolysates of cheese whey and chicken feather were used as inexpensive complex nitrogen source for PHA production by C. necator, when waste frying oil was used as a carbon substrate. The finnal part of the thesis is dealing with possibilities how the PHA can be processed into atractive aplication forms. Liposomes with partial content of PHB had been prepared, moreover, for improving of antioxidant activity and antimicrobial effect the waste coffee oil was added. Micro-fibrous PHB materials were prepared for the purposes of water filtration. Higher filtration effectivity was observed when composite PHB fibrous material containing active charcoal or metal oxides was used. Important part of thesis is represented by study of degradation processes of prepared PHA-based aplication forms. Various microorganisms were tested on PHA depolymerases production. Biodegradability of PHA materials was tested in of composting conditions by standard composting test IS/ISO 20200. Changes in mechanical properties of polyurethan, where polyol was partialy replaced by PHB, were tested depending on the exposure of composting condition.

Semiflexible Polymere erfüllen als Hauptbausteine intrazellulärer Gerüste und extrazellulärer Matrizen eine zentrale Rolle in biologischen Systemen. In der vorgelegten Arbeit wird der Einfluss kollektiver Effekte auf die physikalischen Eigenschaften semiflexibler Polymerstrukturen untersucht. Mikrorheologische Messungen sowohl an verwickelten als auch an quervernetzten Aktinfilamentnetzweken enthüllen, dass Aktingele drastisch durch die Belichtung fluoreszierender Kügelchen mit der entsprechenden Anregungswellenlänge erweicht werden. Dies beeinflusst die Resultate bei der Untersuchung von Aktinnetzwerken mit Mikrorheologie und kann zu großen Unterschieden zwischen mikro- und makrorheologischen Messungen führen. Messungen an mehrfaserigen Aktinbündlen mit Hilfe optischer Pinzetten enthüllen kontraktile Kräfte mit einem harmonischen Potential beim Auseinanderziehen und Kontrahieren der Bündel. Die beobachteten Dynamiken werden durch ein analytisches Modell als emergentes, kollektives Phänomen erklärt welches durch additive, paarweise Interaktionen der Filamente im Bündel verursacht wird. Auf der Netzwerkebene wird gezeigt, dass Kompositnetzwerke aus rekonstituierten Aktin- und Vimentinproteinen als Superposition zweier nichtinteragierender Gerüste beschrieben werden können. Hierbei entstehende Effekte werden durch die Verbindung von Einzelfilamentdynamiken mit makrorheologischen Netzwerkeigenschaften dargestellt und innerhalb eines inelasitschen Glassy Wormlike Chain Modells erfasst. Dies bereitet den Weg um die mechanischen Eigenschaften des Zytoskeletts auf der Basis der Eigenschaften der Einzelkomponenten vorherzusagen. Weitere Untersuchungen an Netzwerken bestehend aus Aktinfilamenten, Intermediärfilamenten und synthetischen DNS Nanoröhren zeigen, dass Mengeneigenschaften durch diverse Interfilamentinterkationen beeinflusst werden. Es wird vorgeschlagen, dass diese Interaktionen in einen einzelnen Parameter im Rahmen des Glassy Wormlike Chain Modells zusammengefasst werden können. Die Interpretation dieses Parameters als polymerspezifische 'Stickiness' ist sowohl für makrorheologische Beobachtungen als auch im Reptationsverhalten konsistent. Diese Erkenntnisse zeigen, dass Stickiness im Allgemeinen nicht in semiflexiblen Polymermodellen ignoriert werden sollte. / Semiflexible polymers play a central role in biological systems as major building blocks of intracellular scaffolds and extracellular matrices. The presented thesis investigates the influence of collective effects on the physical properties of semiflexible polymer structures. Microrheological measurements on both entangled and cross-linked actin filament networks reveal that illumination of fluorescent beads with their appropriate excitation wavelength leads to a drastic softening of actin gels. This impairs results when studying the microrheology of actin networks and can cause large discrepancies between micro and macro-rheological measurements. Optical tweezers measurements on multifilament actin bundles reveal contractile forces with a harmonic potential upon bundle extension and contraction. The observed dynamics are explained as an emergent, collective phenomenon stemming from the additive, pairwise interactions of filaments within a bundle through an analytical model. On the network level, it is shown that composite networks reconstituted from actin and vimentin can be described by a superposition of two non-interacting scaffolds. Arising effects are demonstrated in a scale-spanning frame connecting single filament dynamics to macro-rheological network properties and are captured within an inelastic glassy wormlike chain model. This paves the way to predict the mechanics of the cytoskeleton based on the properties of its single structural components. Further investigations on networks assembled from filamentous actin, intermediate filaments and synthetic DNA nanotubes show bulk properties are affected by various inter-filament interactions. It is proposed that these interactions can be merged into a single parameter in the frame of the glassy wormlike chain model. The interpretation of this parameter as a polymer specific stickiness is consistent with observations from macro-rheological measurements and reptation behavior. These findings demonstrate that stickiness should generally not be ignored in semiflexible polymer models.

The abilities of fungi and bacteria to degrade simple and complex carbon compounds derived from different sources, such as root exudates, litter, soil organic matter or fungal mycelium were studied in this dissertation. Knowledge of functional traits, especially degradation abilities of fungi and bacteria, are important for deciphering the black box of microbial functioning in topsoil and thus aiding in modeling and predicting future directions of microbial communities development in face of global changes. Among fungal cultures form culture collection representing strains with different taxonomy and ecophysiology, the ecophysiology of fungi was more important in manifestation of functional traits than taxonomy. Among bacterial isolates from the litter and soil of spruce forest, Acidobacteria were confirmed to express multiple decomposition enzymes in high rates in vitro and were also abundant and active degraders in acidic spruce forest soil. The expression of degradation capacities of both bacteria and fungi were further studied in situ in spruce forest topsoil, that represents an important environment due to the ubiquity of coniferous forests on the Northern hemisphere. There is an obvious gap of knowledge, when comes to our understanding of seasonal effect on microbial functioning, and this is...

Methicillin-resistant Staphylococcus Aureus (MRSA) is now the most challenging bacterial pathogen affecting patients in hospitals and in care centers, and has brought on the need to develop new drugs for MRSA. This thesis centers on studies of N-thiolated β-lactams, a new family of potent antibacterial compounds that selectively inhibit the growth of methicillin-resistant Staphylococcus aureus (MRSA). Chapter 1 describes MRSA in more detail. Chapter 2 outlines experiments on the effect of a fatty ester group (CO2R) on the C4-phenyl ring of N-methylthio β-lactams, expecting that attachment of long chain ester moieties might increase the hydrophobicity, and thus enhance the drugs ability to penetrate through the cell membrane. However, the results indicate that antibacterial activity drops off rapidly when more than seven carbon atoms are in the chain. These results led to the idea about examining a β-lactam conjugated polymer as a possible pro-drug delivery method, which is the focus of Chapter 3. To synthesize the initial drug-polymer candidate, microemulsion polymerization of an acrylate-substituted lactam was done in aqueous solution to form hydrophilic polymeric nanoparticles containing the highly water-insoluble solid antibiotic, N-methylthio fO-lactam. This method has advantages over the conventional emulsion polymerization methods because a solid co-monomer (β-lactam drug) can be utilized. SEM studies show that these polymeric nanoparticles have a microspherical morphology with nano-sizes of 40-150 nm. The N-thiolated fO-lactam containing nanoparticles display potent anti-MRSA activity at much lower drug amounts compared with free lactam drug, penicillin G or vancomycin. Although at this time the relationship between particle size and activity is not clear and the mode of action is unknown, the Nthiolated β-lactam containing nanoparticles dramatically enhance bioactivity, possibly due to increased bioavailability of the antibiotic via endocytosis. In chapter 4, Fluorescence-active emulsified nanoparticles containing naphthyl or anthracenyl side chains were also successfully prepared by microemulsion polymerization for possible use in fluorescence studies to determine if the drug enters the cell of MRSA through endocytosis, and where possible bioaccumulation site are located.

Le collagène est un élément majeur de l'architecture des organes chez les mammifères. Cette protéine s'organise en structures tridimensionnelles (3D) spécifiques à chaque tissu et responsables de leurs propriétés biophysiques et biomécaniques. La microscopie multiphoton permet de visualiser le collagène fibrillaire dans les tissus biologiques, sans aucun marquage, grâce aux signaux de génération de second harmonique (SHG). Cette thèse présente des mesures SHG résolues en polarisation (P-SHG), dans le but de caractériser la structure 3D du collagène dans divers tissus, de l'échelle moléculaire à l'échelle macroscopique.Nous avons d'abord étudié la sensibilité et la fiabilité des mesures P-SHG, afin de valider cette technique comme un outil quantitatif d'observation de la structure 3D du collagène dans des tissus intacts.En collaboration avec le Laboratoire de Chimie de la Matière Condensée de Paris, cette technique a ensuite été appliquée à l'étude de systèmes modèles de collagène présentant une organisation de type cristal liquide, afin de caractériser les conditions physico-chimiques menant à des phases proches de celles observées à l’état stabilisé dans la cornée.Enfin, nous présentons une imagerie SHG en différence circulaire (CD-SHG), permettant de déterminer la polarité des fibrilles de collagène par rapport au plan de l'image. Ces mesures sont complémentaires de l'information obtenue en P-SHG. Une première mise en place expérimentale de cette technique est présentée dans des coupes histologiques de cornée humaine. Nous présentons de plus les résultats préliminaires d'une imagerie corrélative CD-SHG/I-SHG, en collaboration avec l'INRS, donnant une information complète sur la polarité des fibrilles de collagène. / Collagen is a key element of organs architecture in mammals. This protein is organized in tridimensional (3D) structures specific to each tissue and responsible for its biophysical and biomechanical properties. Multiphoton microscopy allows the visualization of unstained fibrillar collagens in biological tissues, by use of their endogenous second harmonic generation (SHG) signals. This work focuses on polarization-resolved SHG measurements (P-SHG), in order to characterize the collagen 3D structure in tissues, from the molecular scale to the macroscopic scale.We first studied the sensitivity and the reliability of those P-SHG measurements, and validated this technique as a quantitative tool to probe collagen structure in intact tissues.In collaboration with the Laboratoire de Chimie de la Matière Condensée de Paris, this technique was then applied to the study of collagen model systems with a liquid crystal like organization, in order to find the physico-chemical conditions leading to organizations close to the one observed in cornea.Finally, we introduced SHG circular difference measurements (CD-SHG). This technique allowed us to probe the polarity of collagen fibrils with respect to the image plane. Those measurements complement P-SHG measurements. An experimental implementation of this technique is introduced, as well as preliminary measurements in cornea. We present also preliminary results from CD-SHG/I-SHG correlative imaging, in collaboration with INRS, giving full information about collagen polarity.

Filled hydrogel particles consisting of emulsified oil droplets encapsulated within a hydrogel matrix were fabricated based on the phase separation of proteins and polysaccharides through aggregative and segregative mechanisms. A 3% (wt/wt) pectin and 3% (wt/wt) caseinate mixture at pH 7 separated into an upper pectin-rich phase and a lower casein-rich phase. Casein-coated lipid droplets added to this mixture partitioned into the lower casein-rich phase. When shear was applied, an oil-in-water-in-water (O/W1/W2) emulsion consisting of oil droplets (O) contained within a casein-rich dispersed phase (W1) suspended in a pectin-rich continuous phase (W2) was formed. Acidification from pH 7 to 5 promoted adsorption of pectin onto casein-rich W1 droplets, forming filled hydrogel particles. Particles were then cross-linked using transglutaminase. Particles were assessed for stability to changes in pH, increasing levels of salts (sodium chloride and calcium chloride), and susceptibility to lipid oxidation. Both cross-linked and not cross-linked particles were stable at low pH (pH 2-5). At high pH, cross-linked particles maintained their integrity while not cross-linked particles disintegrated. Particles were stable to sodium chloride (0-500 mM). Calcium chloride levels above 4 mM resulted in system gelation. The rate of lipid oxidation for 1% (vol/vol) fish oil encapsulated within filled hydrogel particles was compared to that of oil-in-water emulsions stabilized by either Tween 20 or casein. Emulsions stabilized by Tween 20 oxidized faster than either filled hydrogel particles or casein stabilized emulsions, while filled hydrogel particles and casein stabilized emulsions showed similar oxidation rates. Using an in-vitro digestion model, the digestion of lipid encapsulated within filled hydrogel particles was compared to that of a casein stabilized oil-in-water emulsion. Results showed similar rates of digestion for both hydrogel and emulsion samples. Attempts to fabricate particles using free oil (rather than emulsified oil) were unsuccessful and resulted in the formation of large non-encapsulated oil droplets (d ~10 μm). By controlling particle concentrations of biopolymer, water, and oil, it was possible to fabricate particles that were highly resistant to gravitational separation which was attributed to the equivalent density of the continuous and particle phases. Results highlight the potential applications and versatility of this delivery system.

Elastin-like polypeptides (ELP) are artificially designed protein biopolymers that can be produced by living organisms. These proteins have the unique ability to undergo reversible inverse phase transition, in response to changes in temperature and/or addition of chaotropic salts. Below the transition temperature (T1) , ELP is soluble in water. Increasing the temperature above Ti, ELP coacervates into an aqeous ELP-rich phase. In this thesis, this unique feature of ELP was used in for recombinant protein purification and for the formation of aqueous multiple-phase systems. For protein purification, ELP was fused with an intein and a model protein (thioredoxin), to demonstrate a simple and inexpensive approach for recombinant protein purification. The ELP tags replace the chromatographic media and the intein replaces the use of the protease in conventional methods. Using ELP tags was found to be consistent with large -scale recombinant protein production/purification by purifying an ELP tagged protein using a stirred cell equipped with a microfiltration membrane. When the temperature and/or salt concer.tration is increased for mixtures containing free ELP and ELP tagged proteins, simultaneous phase transition takes place. This served as the basis for the development of a method suitable for selectively recovering molecules from complex mixtures with high specificity, full reversibility, and virtually unlimited affinity. The second parts of this thesis focus on the ability of ELP to form aqueous twophase systems (A TPS) in vitro and most importantly, in vivo- with the formation of aqueous microcompartments in living cells. These compartments exclude the protein making machinery of the cell, acting as depots for newly expressed protein. It is also shown (in vitro) that ELP bastd droplets exclude proteases, protecting proteins from degradation. These observations are important for high-level production of recombinant proteins. Also described, is the formation of protein based aqueous multiphasic systems, with tunable morphologies. / Thesis / Doctor of Philosophy (PhD)

No description available.

<p>Electrochemical methods show great promise in the deposition of biocompatible coatings for biomedical applications with advanced functionality. Consequently, methods of creating coatings of bioactive materials, such as halloysite nanotubes (HNT), hydroxyapatite (HA), chitosan, hyaluronic acid (HYH), poly-L-ornithine (PLO) and poly-L-lysine (PLL) and polyacrylic acid (PAA) have been developed through the use of electrophoretic deposition (EPD). The co-deposition of these materials are achieved at voltages ranging from 5 to 20 V on a 304 stainless steel substrate using suspensions of 0.5 and 1.0 gL^-1 biopolymer (chitosan, PAA, PLO, PLL) containing 0.3, 0.5 0.6, 1.0 and 2.0 gL^-1 bioceramic (HNT, HA). The resulting films were then investigated to further understand the kinetics and mechanics of deposition, determine their properties, and evaluate their suitability for physiological applications. The films were studied using X-Ray Diffraction (XRD), Differential Thermal Analysis and Thermogravimetric Analysis (DTA/TGA), Scanning Electron Microscopy (SEM), Quartz Crystal Microbalance (QCM) and Linear Polarisation. The results indicate that film thickness, composition and morphology can be controlled and modified at will, and that the deposition of composite films, multilayer laminates and functionally graded films are possible.</p> / Master of Applied Science (MASc)

The extracellular polymers produced by bacteria play an important role in bacterial aggregation or bacterial flocculation in secondary waste treatment. The mechanisms responsible for this floc formation are thought to be polymer induced adsorption and interparticle bridging among bacterial cells or between bacterial cells and inorganic colloids. The efficiency of the processes following flocculation in the treatment line such as sedimentation, sludge thickening, and sludge dewatering depends on the extent of this bacterial flocculation. In this research, sludge samples from under various substrate conditions were examined for type, molecular weight, physical characteristics„ and quantity of extracellular polymers so that the general characteristics of the various polymers could be established. An attempt was made to determine if a relationship exists between the state of bacterial aggregation and the polymer characteristics. This research also investigated the sludge physical properties. The effect of various parameters such as pH, divalent cation (mixture and concentration), and mixing (period and intensity) on dewatering properties were studied. A major goal of this study was to develop a flocculation model for activated sludge. This model could be used to determine if plants can increase the efficiency of waste treatment and sludge thickening and sludge dewatering processes. / Ph. D.