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Perfusion operation mode is currently under fast expansion in mammalian cell based manufacturing of biopharmaceuticals, not only for labile drug protein but also for stable proteins such as monoclonal antibodies (mAbs). Perfusion mode can advantageously offer a stable cell environment, long-term production with high productivity and consistent product quality. Intensified high cell density culture (HCDC) is certainly one of the most attractive features of a perfusion process due to the high volumetric productivity in a small footprint that it can provide. Advancements in single-use technology have alleviated the intrinsic complexity of perfusion processes while the maturing in cell retention devices has improved process robustness. The knowledge for perfusion process has been gradually built and the “continuous” concept is getting more and more acceptance in the field. This thesis presents the development of robust perfusion process at very high cell densities in various culture systems. Four HCDC perfusion systems were developed with industrial collaborators with three different mAb producing Chinese Hamster Ovary (CHO) cell lines: 1-2) WAVE Bioreactor™ Cellbag prototype equipped with cell separation by hollow fiber filter utilizing Alternating Tangential Flow (ATF) and Tangential Flow Filtration (TFF) techniques; 3) Fiber matrix based CellTank™ prototype; 4) Glass stirred tank bioreactor equipped with ATF. In all the systems, extremely high viable cell densities above 130 million viable cells per milliliter (MVC/mL) up to 214 MVC/mL were achieved. Steady states were maintained and studied at 20-30 MVC/mL and 100-130 MVC/mL for process development. Perfusion rate selection based on cell specific perfusion rate (CSPR) was systematically investigated and exometabolome study was performed to explore the metabolic footprint of HCDC perfusion process. / <p>QC 20170523</p>

A ce jour, le contexte énergétique mondial est dominé par une utilisation massive des énergies fossiles non-renouvelables et épuisables par nature. La production de biohydrogène de 2ème génération issu de déchets organiques par le procédé de fermentation sombre constitue donc une solution attractive pour diversifier le mix énergétique actuel. Dans ce cadre, l’objectif de ce travail est d’étudier l’influence de la qualité du mélange sur l’efficacité de la voie fermentaire sombre. En effet, les conditions d’agitation mécanique (type d’agitateur, vitesse d’agitation) et la viscosité du digestat (fonction des intrants en cours de culture), comptent parmi les paramètres abiotiques les moins étudiés à ce jour dans ce procédé. Or, l’agitation joue un rôle clé puisqu’elle doit permettre non seulement d’homogénéiser la phase liquide riche en bactéries, en substrats organiques, en métabolites et en biogaz soluble, mais aussi de favoriser les échanges de matière liquide-bactéries et liquide-gaz. Cependant, pour atteindre la qualité de mélange requise, il faut faire face à deux contraintes : d’une part il faut maintenir un niveau acceptable de stress mécanique pour les bactéries du consortium ; d’autre part, la puissance mécanique consommée par l’agitation doit rester limitée pour assurer la viabilité économique du procédé. Dans ce travail, les effets combinés de la viscosité du digestat et de la vitesse d’agitation des mobiles sur la production de biohydrogène dans un bioréacteur ont été étudiés dans un premier temps. Les résultats ont montré une influence significative de ces deux facteurs sur la productivité en biohydrogène qui a pu être reliée au nombre adimensionnel de Reynolds et au régime d’écoulement du digestat. Un maximum de productivité a été observé lors de la transition laminaire-turbulent. Dans un deuxième temps, des méthodes de détermination du temps de mélange (conductimétrie, décoloration chimique, Fluorescence Induite par Nappe Laser) et du transfert de matière liquide-gaz (désoxygénation/oxygénation) ont été mises en oeuvre dans les mêmes conditions de viscosité et d’agitation afin de rechercher les étapes limitantes pouvant expliquer les évolutions observées lors des essais de fermentation. Les résultats ont montré que transfert interfacial et mélange ne sont limitants qu’en régime laminaire, alors que les faibles productivités en régime turbulent résultent vraisemblablement d’une interaction entre la turbulence et les agrégats bactériens. Ensuite, l’écoulement dans le bioréacteur a été modélisé par une approche de type Mécanique des Fluides Numérique (CFD) et analysé par une méthode de Vélocimétrie par Images de Particules (PIV) afin de déterminer les échelles spatiales locales de la turbulence et de pouvoir les comparer à la dimension caractéristique des agrégats bactériens. Les mesures locales confirment les hypothèses émises à partir des valeurs moyennes observées. Finalement, un modèle de type ADM1 (Anaerobic Digestion Model N°1) standard a été modifié en prenant en compte les ions lactate et un modèle hydrodynamique de type « cascade de cellules » dans le but de simuler la production de biohydrogène en systèmes batch et continu. Les simulations sont en bon accord avec les résultats expérimentaux dans les deux modes de culture en supposant un réacteur parfaitement mélangé. En conclusion, l’ensemble de ce travail confirme que la viscosité du digestat et les conditions de mélange sont effectivement des paramètres essentiels à prendre en compte pour l’optimisation et l’extrapolation du procédé de fermentation sombre. / The global energy trends are currently dominated by a massive use of fossil non-renewable energy sources which are progressively depleting. In this way, the production of second-generation biohydrogen production from organic wastes by the dark fermentation process offers, therefore, an attractive solution to diversify the present energy mix. Within this framework, the aim of this work is to investigate the effect of the efficiency of the mixing process on dark fermentation. The conditions of mechanical agitation (mixer type, mixing speed) and the viscosity of the digestate (which depends on the variability of influent substrate concentration) are, indeed, among the abiotic factors that have been the most disregards up to now in this bioprocess. For example, mixing plays a key role because agitation conditions must ensure on the one hand the homogenization of the liquid phase enriched in bacteria, in organic substrate, in soluble metabolites, and in soluble biogas, and in the other hand promote liquid-to-bacteria and liquid-to-gas mass transfer. However, to reach the desired degree of mixing, two constraints must be faced: firstly, an acceptable level of mechanical stress must be maintained on the microbial consortium, and secondly, mechanical power input due to mixing must comply with the economic sustainability of the process. In this work, the combined effects of digestate viscosity and agitation conditions on the fermentative biohydrogen production in the bioreactor were studied first. Experimental results highlighted a significant effect of these factors on biohydrogen productivity which could be expressed as function of the purely hydrodynamic dimensionless Reynolds number and of the prevailing flow regime. Hydrogen production was maximized in the transition region between laminar and turbulent flow conditions. Secondly, experimental measuring methods of mixing time (conductimetric, chemical decolorization and Planar Laser Induced Fluorescence techniques) and mass transfer (dynamic deaeration/aeration) were implemented in the same conditions of viscosity and agitation conditions so as to investigate the possible limiting steps that could explain the trends observed in the mixed cultures. The results proved that mixing and liquid-gas transfer was slower than hydrogen production rate only in the laminar flow regime, while low production rate under turbulent flow conditions might stem from an interaction between turbulent eddies and bacterial aggregates. Then, the flow field in the bioreactor was simulated using a CFD (Computational Fluid Dynamics) methodology and analyzed experimentally using PIV (Particle Image Velocimetry) to determine the characteristic turbulent length scales and to compare them to the characteristic size of the bacterial aggregates. Local measurements confirmed the assumptions made from average values derived from power input data. Finally, a modified ADM1 model (Anaerobic Digestion Model N°1) was developed to simulate the biohydrogen production, accounting for lactate ions and non-ideal mixing, under batch and continuous culture conditions. Simulations fairly agree with experimental data in both modes of cultures assuming perfect mixing condition. As a conclusion, the present work as a whole confirms that digestate viscosity and mixing conditions constitute key parameters that must be considered for process optimization and for the scale-up of dark fermentation.

Stale bread contributes to the biggest volume of food waste in Sweden. Current method on recovering bread waste is by producing biogas or bioethanol. Despite advantages in the energy sector, the bread which still has relatively high quality could be recovered into new products with higher value, such as food for human consumption. Development of a product, termed ‘fungal cake’ by solid state fermentation on bread waste using Neurospora intermedia in small scale petri dishes have previously been successfully conducted. This study aims to scale up the production of fungal cake into bench scale production. Two systems using different bioreactors were used in this study. The first system operated in batch mode using a tray bioreactor, in which the effect of particle size, mixing, and bread loading were evaluated. The fermentation was conducted during 5 days. Bread crumb with a larger particle size of 2 mm resulted in similar outcomes as bread crumb with a smaller particle size of 0.5 mm in terms of CO2 evolution rate, cumulative CO2 production, starch, and protein content of the final product. However, larger particle size resulted in a more homogeneous growth of the fungus throughout the product, which is preferred. The presence of daily mixing had no significant effect compared to static condition for all measured variables. Thus, mixing could be introduced to promote product homogeneity. Likewise, bread loading had no significant effect on the measured variables, which implies that a higher productivity can be achieved using a higher bread loading. The second system operated in continuous mode using a newly developed continuous tubular bioreactor with product recycle. Two experiments, in which the residence time (48h and 24h) and recycle ratio (10/65 and 20/55) were conducted. Both experiments yielded product with stable starch and protein content, indicated by a stable CO2 evolution rate over time. The performance using continuous tubular bioreactor was compared to batch fermentation in tray bioreactor using the same ratio of inoculum and both system yielded product with the same starch and protein content. Successful operation in continuous bioreactor certainly improved the productivity of fungal cake production.

Using mixed-culture fermentation, the carboxylate platform produces carboxylic acids, which are chemically converted into chemicals and fuels. To optimize the mixed-acid fermentation, different bioreactor configurations and operating modes were investigated. Intermittent air exposure did not affect fermentation performance and bacterial profiles, but reduced the high-molecular-weight carboxylic acids. The microbial flora contained strict and facultative microbes, suggesting the presence of a facultative anaerobic community existing in a biofilm. Compared to countercurrent trains, propagated fixed-bed fermentations have similar selectivity and acid distribution, but lower yield, conversion, productivity, and acid concentration. One- to six-stage countercurrent fermentations were operated with similar conditions. Fewer stages increased conversion, whereas more stages increased acid concentration and selectivity. One to four stages achieved similar yield, and four to six stages achieved similar maximum acid concentration. Maximum conversion was achieved with a single stage. Recycling residual biomass retained microorganisms and nutrients and increased yield and productivity. Relative to lower biomass reflux, higher reflux increased conversion, decreased selectivity, and did not affect yield. The recommended carbon-nitrogen ratio is ~24 g carbon/g nitrogen. In four-stage fermentations, recycle to the second fermentor and in parallel to the first three fermentors was optimal. Fermentations with excess or insufficient nitrogen had higher selectivity, but decreased yield and conversion. The glucose-utilization assay is a rapid and repeatable method for determining the amount of microbial activity in a sample. This method determined ~25% efficiency of a new cell separation method. In continuous fermentation, compared to no cell recycle, recycling cellular biomass increased selectivity and yield, but decreased conversion. Compared to lower cell reflux, higher reflux increased productivity, yield, and conversion, but decreased selectivity. Compared to residual biomass recycle, cell recycle had increased selectivity and yield, but decreased conversion. A new method to screen and rank inoculum sources from natural environments was successfully developed and tested.

Made available in DSpace on 2016-06-02T19:56:57Z (GMT). No. of bitstreams: 1 6615.pdf: 4694610 bytes, checksum: 288df2441cd04d5e5e4c36da49c66cb9 (MD5) Previous issue date: 2015-03-05 / Financiadora de Estudos e Projetos / Mesenchymal stromal cells (MSCs) are required by the scientific community in the development and enhancement of therapeutic techniques in different fields of medicine. The MSCs are present in small concentrations in tissues, which makes necessary the expansion in vitro for enable studies and therapeutic applicability. These are cells with high sensitivity to environmental conditions of cultivation. So, for increase productivity in vitro is used the technology of bioreactors in the development of processes in order to produce high cell densities in less time, with reduce use of resources and maintaining a safe operation. The new concepts of "disposable bioreactors", as the wave-induced motion bioreactor or Wave bioreactor, with possibility operating in a closed system, controlled and automated, reduced investment cost and operation, less risk of contamination, higher level biosecurity, added to the fact of being a underexplored technology and already approved by the FDA (Food and Drugs Administration) becomes a highly attractive alternative bioprocessing for cultivation of animal cells in large scale. In this context, the present work aims to develop a protocol for cultivation of MSCs in the Wave Bioreactor System 2/10. Experiments were performed to characterize the CEMs's culture behavior in the Wave bioreactor to obtain high cell productivity while maintaining the therapeutic potential of the CEMs. The experiments were carried out with 2 L Cellbag and Cultispher-S microcarrier with 300 ml of &#945;-MEM medium culture supplemented with glucose, glutamine, and arginine and 15% v/v fetal bovine serum at 37 ° C and pH between 6,9-7,4. In the preliminary experiments it was verified that most of the inoculated cells did not adhere to the microcarriers. It was shown that such behavior is due to low relation between adhesion area (AMC = total projected area of the microcarriers) and wet surface area of Cellbag (ASMCellbag), which in the normal condition of operation results an adhesion between 25,7 and 61,7% of the inoculated cells. To solve the problem were performed experiments reducing ACellbag which enabled improvements in cell adhesion by up to 100%. It was also found low performance of the cell expansion phase, presumably linked to operational problems like: microcarriers segregation in certain regions of the bioreactor causing depletion of nutrients, formation of aggregates of MCs colonized with cells and adhesion of MCs to Cellbag. In addition, it was observed that reducing CEM/MC ratio at the start of the culture, the cell expansion factor could be increased to values equal to or greater than 10. These results show that the Wave bioreactor has good potential for expansion of MSCs and that the same can be improved. / As células estromais mesenquimais (CEMs) estão sendo visadas pela comunidade científica no desenvolvimento e aprimoramento de técnicas terapêuticas em diferentes ramos da medicina. As CEMs estão presentes em pequenas concentrações nos tecidos, o que torna necessário a sua expansão in vitro para viabilizar pesquisas e a aplicabilidade terapêutica. Tratam-se de células com elevada sensibilidade em relação às condições do ambiente de cult ivo. Assim, para o aumento da produtividade in vitro utiliza-se a tecnologia de biorreatores no desenvolvimento de processos com objetivo de produzir altas densidades celulares em curto tempo, de forma econômica e respeitando as normas impostas pelos órgãos reguladores. O novo conceito de biorreator descartável, como o do biorreator com movimento induzido em forma de ondas, ou biorreator Wave, apresenta possibilidade de operação em sistema fechado segundo as boas práticas de fabricação (BPF), controlado e automatizado. O custo de investimento e operação reduzido, com menor risco de contaminação, maior nível de biossegurança, somado ao fato de utilizar uma tecnologia pouco explorada e já aprovada pelo FDA (Food and Drugs Administration) se transforma numa alternativa de bioprocessamento altamente atrativa para cultivo de células animais em larga escala. Nesse contexto, o presente trabalho tem por meta avaliar o desempenho do biorreator Wave 2/10 na expansão das CEMs. Para tal, foram realizados experimentos visando caracterizar o comportamento do cultivo nesse biorreator a fim de obter alta produtividade celular mantendo a potencialidade terapêutica das CEMs. Os experimentos foram realizados com saco plástico (doravante Cellbag) de 2 L e microcarregador (MC) Cultispher-S com 300 mL me io de cultivo &#945;-MEM suplementado com glicose, glutamina e arginina e 15% v/v de soro fetal bovino a 37°C e pH entre 6,9-7,4. Nos experimentos preliminares constatou-se que grande parte das células inoculadas não aderiam aos microcarregadores. Comprovou-se que tal comportamento se devia à baixa relação entre área de adesão (AMC = área total projetada dos microcarregadores) e área de superfície molhada da Cellbag (ASMCellbag) que na condição normal de operação resultava numa adesão entre 25,7 e 61,7% das células inoculadas. Para melhorar a adesão foram realizados experimentos reduzindo a ASMCellbag, o que possibilitou melhoria na adesão celular em até 100%. Na etapa de expansão celular verificou-se baixo desempenho, presumivelmente vinculado a problemas de operação como: segregação de microcarregadores em determinadas regiões do biorreator provocando o esgotamento de nutrientes, formação de agregados de MCs colonizados com células e adesão dos MCs à Cellbag. Em adição, notou-se que diminuindo a relação CEM/MC no início do cultivo a expansão celular podia ser aumentada para valores iguais ou maiores que 10. Ao todo, os resultados mostraram que o biorreator Wave possui bom potencial para a expansão de CEMs e que o mesmo ainda pode ser melhorado.

No description available.

The work presented in this thesis leads to the formulation of a dynamic mathematical model of an immersed membrane bioreactor (iMBR) for wastewater treatment. This thesis is organised into three parts, each one describing a different set of tasks associated with model development and simulation. In the first part, the Author qualitatively and quantitatively compares various published activated sludge models, i.e. models of biochemical processes associated with bacterial growth, decay, lysis and substrate utilisation in activated sludge systems. As the thesis is focused on modelling membrane bioreactors (MBRs) which are known to experience membrane fouling as a result of adsorption of biopolymers present in the bulk liquid onto and within the membrane, all activated sludge models considered in this thesis are able to predict, with various levels of accuracy, the concentrations of biopolymeric substances, namely soluble microbial products (SMP) and extracellular polymeric substances (EPS). Some of the published activated sludge models dedicated to modelling SMP and EPS kinetics in MBR systems were unable to predict the SMP and EPS concentrations with adequate levels of accuracy, without compromising the predictions of other sludge and wastewater constituents. In other cases, the model equations and the assumptions made by their authors were questionable. Hence, two new activated sludge models with SMP and EPS as additional components have been formulated, described, and simulated. The first model is based on the Activated Sludge Model No. 1 (ASM1) whereas the second model is based on the Activated Sludge Model No. 3 (ASM3). Both models are calibrated on two sets of data obtained from a laboratory-scale system and a full-scale system and prove to be in very good agreement with the measurements. The second part of this thesis explains the development of two membrane fouling models. These models are set to describe the loss of membrane permeability during filtration of various solutions and suspensions. The main emphasis is placed on filtration of activated sludge mixtures, however the models are designed to be as general as feasibly possible. As fouling is found to be caused by a large number of often very complex processes which occur at different spatial as well as temporal scales, the two fouling models developed here have to consider a number of significant simplifications and assumptions. These simplifications are required to balance the model's accuracy, generality and completeness with its usability in terms of execution times, identifiability of parameters and ease of implementation in general purpose simulators. These requirements are necessary to ascertain that long term simulations as well as optimisation and sensitivity studies performed in this thesis either individually on fouling models or on the complete model of a MBR can be carried out within realistic time-scales. The first fouling model is based on an idea that fouling can be subdivided into just two processes: short-term reversible fouling and long-term irreversible fouling. These two processes are described with two first order ordinary differential equations (ODEs). Whilst the first model characterises the membrane filtration process from an observer's input-output point of view without any rigorous deterministic description of the underlying mechanisms of membrane fouling, the second model provides a more theoretical and in-depth description of membrane fouling by incorporating and combining three classical macroscopic mechanistic fouling equations within a single simulation framework. Both models are calibrated on a number of experimental data and show good levels of accuracy for their designated applications and within the intended ranges of operating conditions. In the third part, the first developed biological model (CES-ASM1) is combined with the behavioural fouling model and the links between these two models are formulated to allow complete simulation of a hollow fibre (HF) immersed membrane bioreactor (iMBR). It is assumed that biological processes affect the membrane through production of mixed liquor suspended solids (MLSS), SMP and EPS which cause pore blockage, cake formation, pore diameter constriction, and affect the specific cake resistance (SCR). The membrane, on the other hand, has a direct effect on the bulk liquid SMP concentration due to its SMP rejection properties. SMP are assumed to be solely responsible for irreversible fouling, MLSS is directly linked to the amount of cake depositing on the membrane surface, whereas EPS content in activated sludge affects the cake's SCR. Other links provided in the integrated MBR model include the effects of air scouring on the rate of particle back-transport from the membrane surface and the effects of MLSS concentration on oxygen mass transfer. Although backwashing is not described in great detail, its effects are represented in the model by resetting the initial condition in the cake deposition equation after each backwash period. The MBR model was implemented in Simulink® using the plant layout adopted in the MBR benchmark model of Maere et al. [160]. The model was then simulated with the inputs and operational parameters defined in [36, 160]. The results were compared against the MBR benchmark model of Maere et al. [160] which, contrary to this work, does not take into account the production of biopolymers, the membrane fouling, nor any interactions between the biological and the membrane parts of an MBR system.

Melanoma is an aggressive disease with few effective treatment options. Non-toxic, anti-tumor therapies and prophylactic approaches are currently being investigated to identify treatment options that will control and remove late-stage melanoma. The overall goal of this project was to establish an effective delivery method for a plasmid encoding human interleukin (phIL-15) into mouse melanoma cells (B16.F10) using the gene transfer technique electroporation (EP)1. The EP delivery phIL-15 was optimized using an in vitro 3D tumor model. The purpose was to translate these IL-15 delivery conditions into an in vivo mouse melanoma model to study IL-15 signal transduction and stimulate immune cells to destroy tumor antigens as well as promote an anti-tumor immune memory response. The in vitro 3D tumor model and the mouse model demonstrated similar expression patterns when delivering phIL-15 with different EP conditions. Intra-tumoral delivery using 500V/cm 20ms enhanced gene delivery and increased IL-15 protein expression compared to 1300V/cm 100μs. There was also a visible increase in transfection efficacy between tumor cells compared to skin cells when delivering pmIL-12 and phIL-15 plasmid constructs in vivo. The plasmid+EP groups 1300V/cm and 500V/cm stimulated increased expression of cytokines IL-1β, IL-6, INFγ, MIP-1β and TNFα. These EP groups also promoted tumor regression by up-regulating CD8+ T cells and CD4+ T cells which targeted melanoma. Regression and survival studies demonstrated that 73.3% of mice cleared B16.F10 cells when treated with phIL-xi15+1300V/cm and pVax+500V/cm. In addition, 53% of the mice responded to the phIL-15+500V/cm treatment group. Furthermore, 75% of the mice from group phIL-15+500V/cm survived secondary inoculation and tumor challenge. In conclusion, plasmid with encoding gene insert phIL-15 delivered by EP has the potential to act as an anti-tumor therapy because it promotes melanoma regression and enhances mouse survival through innate and adaptive cell-mediated immune responses.