by Wai Ching Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 154-159). / Abstracts in English and Chinese. / Statement --- p.ii / Acknowledgements --- p.iii / Abstract --- p.v / 摘要 --- p.vii / List of Abbreviations --- p.viii / Table of contents --- p.x / List of Tables --- p.xiv / List of Figures --- p.xv / Chapter Chapter 1 --- Introduction --- p.1 / Chapter Chapter 2 --- Literature review --- p.4 / Chapter 2.1 --- Plant lectins --- p.4 / Chapter 2.1.1 --- Introduction --- p.4 / Chapter 2.1.2 --- Definition and subdivision of plant lectins --- p.4 / Chapter 2.2 --- Monocot mannose-binding lectins --- p.6 / Chapter 2.2.1 --- Occurrence and carbohydrate binding specificity --- p.6 / Chapter 2.2.2 --- Molecular structure and amino acid sequence --- p.7 / Chapter 2.2.3 --- "Molecular cloning, biosynthesis and post-translational modification" --- p.10 / Chapter 2.2.4 --- Mannose-binding lectins of Family Liliaceae --- p.11 / Chapter 2.2.4.1 --- Tulipa gesneriana lectins (TGL) --- p.12 / Chapter 2.2.4.2 --- Aloe arborescens lectins (AAL) --- p.13 / Chapter 2.2.4.3 --- Polygonatum multiflorum agglutinin (PMA) and lectin-related protein --- p.14 / Chapter 2.3 --- Polygonatum odoratum lectins (POL) --- p.15 / Chapter 2.3.1 --- Isolation and purification of POL from Yu Chu --- p.15 / Chapter 2.3.2 --- Agglutinating activity and anti-viral activities of POL --- p.17 / Chapter 2.3.3 --- Bacterial expression of POL in Escherichia coli --- p.18 / Chapter 2.4 --- Plant-based production of recombinant proteins --- p.20 / Chapter 2.4.1 --- Advantages of using plants as expression system --- p.20 / Chapter 2.4.2 --- Plant-derived recombinant proteins --- p.22 / Chapter 2.5 --- Expression of heterologous proteins in rice --- p.24 / Chapter 2.5.1 --- The facts of rice --- p.24 / Chapter 2.5.2 --- Rice storage proteins --- p.25 / Chapter 2.5.2 --- Expression of lysine-rich protein (LRP)/glutelin fusion proteinin rice seeds --- p.28 / Chapter 2.5.3 --- Expression of Galanthus nivalis agglutinin in rice --- p.29 / Chapter 2.6 --- Protein trafficking in plants --- p.30 / Chapter 2.6.1 --- Golgi-dependent pathways --- p.30 / Chapter 2.6.2 --- Golgi-independent pathway --- p.32 / Chapter 2.6.3 --- Expression of protein targeting determinants in tobacco plants and suspension cells --- p.33 / Chapter Chapter 3 --- Materials and Methods --- p.35 / Chapter 3.1 --- Introduction --- p.35 / Chapter 3.2 --- Chemcials --- p.35 / Chapter 3.3 --- Bacterial strains --- p.35 / Chapter 3.4 --- Cloning of POL cDNA --- p.36 / Chapter 3.4.1 --- Plant materials --- p.36 / Chapter 3.4.2 --- RNA extraction --- p.36 / Chapter 3.4.3 --- RT-PCR amplification of POL cDNA --- p.36 / Chapter 3.4.4 --- 5'RACE and 3'RACE --- p.38 / Chapter 3.4.5 --- Sequencing of POL cDNA --- p.39 / Chapter 3.5 --- Analysis of POL protein --- p.40 / Chapter 3.5.1 --- Protein extraction and Tricine-SDS PAGE --- p.40 / Chapter 3.5.2 --- Western blot analysis --- p.41 / Chapter 3.6 --- Chimeric gene construction --- p.42 / Chapter 3.6.1 --- Construction of the Cauliflower mosaic virus (CaMV)35S promoter/POL constructs --- p.44 / Chapter 3.6.2 --- Construction of the glutelin-1 promoter/POL constructs --- p.48 / Chapter 3.6.3 --- Sequence fidelity of chimeric genes --- p.55 / Chapter 3.7 --- Expression of transgenes in rice --- p.55 / Chapter 3.7.1 --- Plant materials --- p.55 / Chapter 3.7.2 --- Agrobacterium transformation --- p.55 / Chapter 3.7.3 --- Callus induction --- p.56 / Chapter 3.7.4 --- Agrobacterium culture and rice transformation --- p.56 / Chapter 3.7.5 --- Selection and regeneration of rice callus --- p.56 / Chapter 3.7.6 --- Isolation of genomic DNA --- p.58 / Chapter 3.7.7 --- Southern blot analysis --- p.58 / Chapter 3.7.8 --- Extraction of leaf total RNA --- p.59 / Chapter 3.7.9 --- Extraction of seed total RNA --- p.59 / Chapter 3.7.10 --- Northern blot analysis --- p.60 / Chapter 3.7.11 --- Protein extraction and Tricine SDS-PAGE --- p.60 / Chapter 3.7.12 --- Western blot analysis --- p.61 / Chapter 3.8 --- Cytopathic effect (CPE) reduction assay --- p.61 / Chapter 3.8.1 --- Protein extraction --- p.61 / Chapter 3.8.2 --- CPE reduction assay --- p.62 / Chapter 3.9 --- Confocal immunofluorescence --- p.63 / Chapter 3.9.1 --- Preparation of sections --- p.63 / Chapter 3.9.2 --- Labelling of fluorescence probes --- p.63 / Chapter 3.9.3 --- Image collection --- p.64 / Chapter Chapter 4 --- Results --- p.65 / Chapter 4.1 --- Cloning of POL cDNA from Yu Chu --- p.65 / Chapter 4.1.1 --- RNA extraction and partial POL cDNA amplification --- p.65 / Chapter 4.1.2 --- 5'RACE and 3'RACE --- p.67 / Chapter 4.1.3 --- Sequencing of POL cDNA --- p.68 / Chapter 4.1.4 --- Sequences comparison of POL and Liliaceae lectins --- p.75 / Chapter 4.2 --- Occurence of POL protein in Yu Chu plant --- p.77 / Chapter 4.3 --- Constitutional expression of POL in rice --- p.79 / Chapter 4.3.1 --- Construction of Cauliflower mosaic virus 35S promoter constructs --- p.80 / Chapter 4.3.2 --- Southern blot analysis --- p.82 / Chapter 4.3.3 --- Northern blot analysis --- p.84 / Chapter 4.3.4 --- Western blot analysis --- p.85 / Chapter 4.3.5 --- Western blot analysis of 35S/POL T1 plant --- p.87 / Chapter 4.4 --- Seed-specific expression of POL in rice --- p.88 / Chapter 4.4.1 --- Construction of the glutelin-1 promoter constructs --- p.89 / Chapter 4.4.2 --- Southern blot analysis --- p.92 / Chapter 4.4.3 --- Northern blot analysis --- p.96 / Chapter 4.4.4 --- Western blot analysis --- p.101 / Chapter 4.4.5 --- Western blot analysis of POL-BP-8O and POL-α-TIP T1 transgenic plants --- p.117 / Chapter 4.5 --- Cytopathic effect (CPE) reduction assay --- p.122 / Chapter 4.6 --- Confocal immunofluorescence studies --- p.125 / Chapter Chapter 5 --- Discussion --- p.134 / Chapter 5.1 --- Cloning of POL cDNA --- p.134 / Chapter 5.2 --- Analysis of constitutional expression of POL in rice --- p.136 / Chapter 5.3 --- Analysis of seed-specific expression of POL in rice --- p.138 / Chapter 5.4 --- Localization of POL in POL-BP-8O and POL-α-TIP transgenic rice seeds --- p.146 / Chapter 5.5 --- Cytopathic effect (CPE) reduction assay --- p.148 / Chapter 5.6 --- Future prospects --- p.151 / Chapter Chapter 6 --- Conclusion --- p.153

Ce travail étudie l'intérêt de l'ajout d'hydrolysats de levure dans un procédé de culture de cellules CHO productrices d'anticorps en vue, d'une part, de déterminer leur condition d'utilisation et leur rôle, et, d'autre part, de caractériser les composés actifs. Pour répondre à ces objectifs, une démarche intégrant des études cinétiques, des stratégies de fractionnement et l'analyse biochimique des hydrolysats et de leurs fractions a été développée. En premier lieu, il a été montré que les hydrolysats de levure présentent des effets significatifs sur les cultures selon leur composition et les conditions d'ajout. De même, des effets synergiques ont été mis en évidence par le mélange d'hydrolysats générés à partir de différents procédés. D'autre part, des études cinétiques ont permis de corréler l'influence positive des hydrolysats sur la croissance cellulaire à l'amélioration du métabolisme énergétique. Dans un deuxième temps, la nature biochimique et le rôle des composés actifs ont été étudiés par la mise en oeuvre d'un procédé de nanofiltration membranaire et la reconstitution de mélanges de molécules contenues dans un extrait de levure (EXL). Ces résultats ont mis en évidence l'intérêt des di- et tri-peptides pour approvisionner le métabolisme énergétique et de molécules non nutritives, de poids moléculaire supérieur à 500 Da, pour stimuler la vitesse spécifique de croissance des cellules. Finalement, le rétentat issu de la nanofiltration de l'EXL a été fractionné à l'aide de divers procédés chromatographiques, unitaires ou associés, pour caractériser les propriétés physico-chimiques des composés actifs. L'effet des fractions sur la culture de cellules a alors souligné l'intérêt des molécules chargées positivement, et plus particulièrement, des peptides hydrophiles et cationiques pour stimuler la croissance des cellules. Ainsi, nos travaux permettent de mieux appréhender les mécanismes d'action des hydrolysats de levure sur les cellules CHO productrices d'anticorps et proposent des voies d'optimisation pour la simplification d'additifs complexes dans les milieux de culture dédiés à la culture de cellules animales / This work studies the interest of the addition of yeast hydrolysates in culture medium of CHO cell producing antibody, to determine the operating conditions and their role, but also to improve the characterization of active compounds. In this way, an integrated approach including kinetic studies, fractionation strategies and biochemical analysis of hydrolysates and of their fractions was developed. First, we showed that yeast hydrolysates exhibited various properties depending on their composition and the operating conditions. In addition, synergistic effects were observed with different hydrolysate mixtures. Besides, kinetic studies underlined that the positive influence of hydrolysates on cell growth is correlated with energetic metabolism improvement. Then, the biochemical nature and the role of active compounds were studied by the implementation of a nanofiltration process and the reconstitution of mixtures of molecules contained in a yeast extract (YE). The results highlighted the interest of di- and tri-peptides to supply energetic metabolism, and of non-nutritive molecules, exhibiting a molecular weight greater than 500 Da, to stimulate the specific cell growth rate. Finally, the retentate fraction of nanofiltrated YE was fractionated by various chromatographic processes to characterize the physico-chemical properties of active compounds. The effect of fractions on cell culture emphasized the positive effect of positively charged molecules, especially hydrophilic and cationic peptides, to stimulate the cell growth. Thus, our work provides important insights in yeast hydrolysate mechanisms on CHO cells and suggests procedures to simplify such a complex additive of media dedicated to mammalian cell culture

Células de mamíferos são os hospedeiros mais frequentemente utilizados para a fabricação de proteínas biofarmacêuticas e para a produção de vacinas virais, A qualidade é um elemento-chave para o estabelecimento de um processo de bioconversão eficiente. No presente trabalho utilizamos a linhagem de células BHK- 21C13(Baby Hamster Kidney) adaptadas para cultivo em suspensão. O uso de Soro Fetal Bovino (SFB) é tradicionalmente utilizado, sendo considerado um suplemento universal, pois permite o crescimento em várias linhagens de células de mamíferos; porém, uso de SFB apresenta risco de infecção por prions, variabilidade entre lotes e aumento no custo em etapa de purificação (Downstream processing). O objetivo do presente trabalho foi comparar o cultivo de células BHK-21 C13 entre dois meios suplementados com SFB e sem SFB, através do estudo cinético para cultivo em suspensão estático e agitado com frascoT, frasco spinner e biorreator, respectivamente. Os parâmetros; Xmáx e µmáx, não foram significativamente influenciados pelo meio de cultura em cultivo estático, em cultivo com agitação em frasco spinner e também no cultivo em biorreator. O tempo de duplicação ficou próximo para todas as condições testadas. A produtividade alcançada foi: 0,032x106 cel/mL.h-1 para o meio com SFB e 0,031 X106 cel/mL.h-1 para o meio sem SFB. Ao final do processo foi possível obter uma concentração celular em torno de 4,7x106 cel/mL, tanto para o cultivo com SFB quanto para o cultivo sem SFB. Dessa forma, o uso de meio de cultivo sem SFB não alterou os principais parâmetros cinéticos, não apresentando as desvantagens do uso do SFB. / Mammalian cells are the most frequently used hosts for the production of biopharmaceutical proteins and viral vaccines. Quality is a key element for the establishment of an efficient bioconversion process. In this work, we used the cell line Baby Hamster Kidney C13 (BHK-21 C13) adapted to suspension culture was used. Fetal Bovine Serum (FBS) is traditionally used and it is considered a universal insert due to its power to increase cell growth in this kind of animal cells. However, the utilization of FBS introduces risks of infection from prions, variability between batches and increase in cost associated to purification stages (downstream processing). This work aimed to compare the kinetic behaviors of BHK-21 C13 cells in two media supplemented with FBS and without FBS using both one static and two suspension systems, T-flask, spinner flask and bioreactor respectively. The parameters; Xmax and µmax were not significantly influenced by the culture medium in T- flask culture static, in spinner flask cultivation and were neither significantly influenced by growing in culture media stirred bioreactor. The doubling time was close to all conditions tested. At the end of the growth phase it was possible to obtain a nearby cell concentration of 4.7 x 106 cells / ml, both for cultivation with FBS as for FBS without cultivation. Thus, the use of culture medium without FBS did not affect the main kinetic parameters. Besides, it does not show the disadvantages of culture media using FBS.

by Sze Kwok Fung Calvin. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1996. / Includes bibliographical references (leaves 118-130). / Acknowledgement --- p.i / Abstract --- p.ii / Content --- p.iv / Chapter 1. --- Introduction --- p.1 / Chapter 1.1 --- Literature review --- p.1 / Chapter 1.1.1 --- Heavy metals in the environment --- p.1 / Chapter 1.1.2 --- Heavy metal pollution in Hong Kong --- p.2 / Chapter 1.1.3 --- Electroplating industry in Hong Kong --- p.6 / Chapter 1.1.4 --- Chemistry and toxicity of copper in the environment --- p.7 / Chapter 1.1.5 --- Methods of removal of heavy metal from industrial effluent --- p.9 / Chapter A. --- Physico-chemical methods --- p.9 / Chapter B. --- Biological methods --- p.9 / Chapter 1.1.6 --- Methods of recovery of heavy metal from metal-loaded biosorbent --- p.17 / Chapter 1.1.7 --- The physico-chemical properties of magnetites --- p.18 / Chapter 1.1.8 --- Magnetites for water and wastewater treatment --- p.19 / Chapter 1.1.9 --- Immobilized cell technology --- p.24 / Chapter 1.1.10 --- Stirrer-tank bioreactor --- p.26 / Chapter 1.2 --- Objectives of the present study --- p.28 / Chapter 2. --- Materials and Methods --- p.30 / Chapter 2.1 --- Selection of copper-resistant bacteria --- p.30 / Chapter 2.2 --- Culture media and chemicals --- p.30 / Chapter 2.3 --- Growth of the bacterial cells --- p.32 / Chapter 2.4 --- Immobilization of the bacterial cells on magnetites --- p.32 / Chapter 2.4.1 --- Effects of physical and chemical factors on the immobilization of the bacterial cells on magnetites --- p.34 / Chapter 2.4.2 --- Effects of pH on the desorption of bacterial cells from magnetites --- p.34 / Chapter 2.5 --- Copper ion uptake experiments --- p.35 / Chapter 2.6 --- Effects of physico-chemical and operational factors on the Cu2+ removal capacity of the magnetite-immobilized bacterial cells --- p.35 / Chapter 2.7 --- Transmission electron micrograph and scanning electron micrograph of Pseudomonas putida 5-X loaded with Cu2+ --- p.36 / Chapter 2.7.1 --- Transmission electron micrograph --- p.36 / Chapter 2.7.2 --- Scanning electron micrograph --- p.37 / Chapter 2.8 --- Copper ion adsorption isotherm of the magnetite-immobilized cells of Pseudomonas putida 5-X --- p.37 / Chapter 2.9 --- Recovery of adsorbed Cu2+ from the magnetite-immobilized cells of Pseudomonas putida 5-X --- p.38 / Chapter 2.9.1 --- Effects of eluents on the Cu2+ removal and recovery capacity of the magnetite-immobilized cells --- p.38 / Chapter 2.9.2 --- Batch type multiple adsorption-desorption cycles of Cu2+ using ethylenediaminetetra-acetic acid (EDTA) --- p.39 / Chapter 2.10 --- Removal and recovery of Cu2+ from the electroplating effluent by a bioreactor --- p.39 / Chapter 2.10.1 --- Batch type multiple adsorption-desorption cycles using the copper solution and electroplating effluent --- p.39 / Chapter 2.10.2 --- Continuous type bioreactor to remove and recover Cu2+ from copper solution and electroplating effluent --- p.40 / Chapter 2.11 --- Statistical analysis of data --- p.43 / Chapter 3. --- Results --- p.44 / Chapter 3.1 --- Effects of physical and chemical factors on the immobilization of the bacterial cells on magnetites --- p.44 / Chapter 3.1.1 --- Effects of cells to magnetites ratio --- p.44 / Chapter 3.1.2 --- Effects of pH --- p.44 / Chapter 3.1.3 --- Effects of temperature --- p.44 / Chapter 3.2 --- Effects of pH on the desorption of bacterial cells from magnetites --- p.49 / Chapter 3.3 --- Copper ion uptake experiments --- p.49 / Chapter 3.4 --- Effects of physico-chemical and operational factors on the Cu2+ removal capacity of the magnetite-immobilized bacterial cells --- p.49 / Chapter 3.4.1 --- Effects of pH --- p.49 / Chapter 3.4.2 --- Effects of temperature --- p.53 / Chapter 3.4.3 --- Effects of retention time --- p.53 / Chapter 3.4.4 --- Effects of cations --- p.53 / Chapter 3.4.5 --- Effects of anions --- p.57 / Chapter 3.5 --- Transmission electron micrograph of Pseudomonas putida 5-X loaded with Cu2+ --- p.62 / Chapter 3.6 --- Scanning electron micrograph of Pseudomonas putida 5-X loaded with Cu2+ --- p.62 / Chapter 3.7 --- Copper ion adsorption isotherm of the magnetite-immobilized cells of Pseudomonas putida 5-X --- p.68 / Chapter 3.8 --- Recovery of adsorbed Cu2+ from the magnetite-immobilized cells of Pseudomonas putida 5-X --- p.68 / Chapter 3.8.1 --- Effects of eluents on the Cu2+ removal and recovery capacity of the magnetite-immobilized cells --- p.68 / Chapter 3.8.2 --- Batch type multiple adsorption-desorption cycles of Cu2+ using ethylenediaminetetra-acetic acid (EDTA) --- p.74 / Chapter 3.9 --- Removal and recovery of Cu2+ from the electroplating effluent by a bioreactor --- p.74 / Chapter 3.9.1 --- Batch type multiple adsorption-desorption cycles using the copper solution and electroplating effluent --- p.74 / Chapter 3.9.2 --- Continuous type bioreactor to remove and recover Cu2+ from copper solution and electroplating effluent --- p.81 / Chapter 4. --- Discussion --- p.89 / Chapter 4.1 --- Selection of copper-resistant bacteria --- p.89 / Chapter 4.2 --- Effects of physical and chemical factors on the immobilization of the bacterial cells on magnetites --- p.89 / Chapter 4.2.1 --- Effects of cells to magnetites ratio --- p.89 / Chapter 4.2.2 --- Effects of pH --- p.90 / Chapter 4.2.3 --- Effects of temperature --- p.91 / Chapter 4.2.4 --- Effects of pH on the desorption of bacterial cells from magnetites --- p.92 / Chapter 4.3 --- Copper ion uptake experiments --- p.93 / Chapter 4.4 --- Effects of physico-chemical and operational factors on the Cu2+ removal capacity of the magnetite-immobilized bacterial cells --- p.94 / Chapter 4.4.1 --- Effects of pH --- p.95 / Chapter 4.4.2 --- Effects of temperature --- p.96 / Chapter 4.4.3 --- Effects of retention time --- p.97 / Chapter 4.4.4 --- Effects of cations --- p.98 / Chapter 4.4.5 --- Effects of anions --- p.101 / Chapter 4.5 --- Transmission electron micrograph of Pseudomonas putida 5-X loaded with Cu2+ --- p.101 / Chapter 4.6 --- Scanning electron micrograph of Pseudomonas putida 5-X loaded with Cu2+ --- p.102 / Chapter 4.7 --- Copper ion adsorption isotherm of the magnetite-immobilized cells of Pseudomonas putida 5-X --- p.103 / Chapter 4.8 --- Recovery of adsorbed Cu2+ from the magnetite-immobilized cells of Pseudomonas putida 5-X --- p.104 / Chapter 4.8.1 --- Effects of eluents on the Cu2+ removal and recovery capacity of the magnetite-immobilized cells --- p.104 / Chapter 4.8.2 --- Batch type multiple adsorption-desorption cycles of Cu2+ using ethylenediaminetetra-acetic acid (EDTA) --- p.105 / Chapter 4.9 --- Removal and recovery of Cu2+ from the electroplating effluent by a bioreactor --- p.107 / Chapter 4.9.1 --- Batch type multiple adsorption-desorption cycles using the copper solution and electroplating effluent --- p.107 / Chapter 4.9.2 --- Continuous type bioreactor to remove and recover Cu2+ from copper solution and electroplating effluent --- p.108 / Chapter 5. --- Conclusion --- p.110 / Chapter 6. --- Summary --- p.112 / Chapter 7. --- References --- p.115

Células de mamíferos são os hospedeiros mais frequentemente utilizados para a fabricação de proteínas biofarmacêuticas e para a produção de vacinas virais, A qualidade é um elemento-chave para o estabelecimento de um processo de bioconversão eficiente. No presente trabalho utilizamos a linhagem de células BHK- 21C13(Baby Hamster Kidney) adaptadas para cultivo em suspensão. O uso de Soro Fetal Bovino (SFB) é tradicionalmente utilizado, sendo considerado um suplemento universal, pois permite o crescimento em várias linhagens de células de mamíferos; porém, uso de SFB apresenta risco de infecção por prions, variabilidade entre lotes e aumento no custo em etapa de purificação (Downstream processing). O objetivo do presente trabalho foi comparar o cultivo de células BHK-21 C13 entre dois meios suplementados com SFB e sem SFB, através do estudo cinético para cultivo em suspensão estático e agitado com frascoT, frasco spinner e biorreator, respectivamente. Os parâmetros; Xmáx e µmáx, não foram significativamente influenciados pelo meio de cultura em cultivo estático, em cultivo com agitação em frasco spinner e também no cultivo em biorreator. O tempo de duplicação ficou próximo para todas as condições testadas. A produtividade alcançada foi: 0,032x106 cel/mL.h-1 para o meio com SFB e 0,031 X106 cel/mL.h-1 para o meio sem SFB. Ao final do processo foi possível obter uma concentração celular em torno de 4,7x106 cel/mL, tanto para o cultivo com SFB quanto para o cultivo sem SFB. Dessa forma, o uso de meio de cultivo sem SFB não alterou os principais parâmetros cinéticos, não apresentando as desvantagens do uso do SFB. / Mammalian cells are the most frequently used hosts for the production of biopharmaceutical proteins and viral vaccines. Quality is a key element for the establishment of an efficient bioconversion process. In this work, we used the cell line Baby Hamster Kidney C13 (BHK-21 C13) adapted to suspension culture was used. Fetal Bovine Serum (FBS) is traditionally used and it is considered a universal insert due to its power to increase cell growth in this kind of animal cells. However, the utilization of FBS introduces risks of infection from prions, variability between batches and increase in cost associated to purification stages (downstream processing). This work aimed to compare the kinetic behaviors of BHK-21 C13 cells in two media supplemented with FBS and without FBS using both one static and two suspension systems, T-flask, spinner flask and bioreactor respectively. The parameters; Xmax and µmax were not significantly influenced by the culture medium in T- flask culture static, in spinner flask cultivation and were neither significantly influenced by growing in culture media stirred bioreactor. The doubling time was close to all conditions tested. At the end of the growth phase it was possible to obtain a nearby cell concentration of 4.7 x 106 cells / ml, both for cultivation with FBS as for FBS without cultivation. Thus, the use of culture medium without FBS did not affect the main kinetic parameters. Besides, it does not show the disadvantages of culture media using FBS.

A stable mixed culture, deposited as ATCC 55644, previously shown to degrade petroleum hydrocarbons at relatively high concentrations was used as the source of inoculum. This culture was grown in Stanier’s minimal media, either in the presence of different concentrations of naphthalene, nitrobenzene and toluene (NNT) or naphthalene and toluene (NT) as the sole source of C and/or N. Results showed that the majority of the strains isolated from the mixed culture were able to grow in the presence of NNT or NT. A total of 20 different isolates were isolated from the mixed culture. Individual isolates were grown in Stanier’s minimal medium containing a single hydrocarbon as the source of carbon or carbon and nitrogen. Only one strain was found to grow solely in the presence of nitrobenzene as the source of C and N. Most of the other isolates were able to grow in the presence of naphthalene, toluene, acenaphthene, anthracene, fluoranthene and phenanthrene, n-dodecane, hexadecane, n-pentadecane, n-tetradecane, and n-octadecane. Planktonic and immobilized cells of the controlled mixed culture (ATCC 55644) were grown in separate Sequential Batch Reactors (SBR) using Stanier's media, to which naphthalene, nitrobenzene and toluene were added as the sole source of C and/or N. Biodegradation was determined by measuring the residual hydrocarbon in the SBR and the amount of trapped volatile organic carbon (VOC) and the evolved CO2. Gas chromatography data showed that immobilized cells were able to degrade NNT faster than the planktonic cells. This observation was confirmed by CO2 evolution. Over time the loading of hydrocarbon was significantly increased from a starting level of 400 ppm (Naphthalene), 100 ppm (Nitrobenzene), and 500 ppm (toluene), to a final level of 3000 ppm (Naphthalene), 400 ppm (Nitrobenzene), and 1600 ppm (toluene). While increasing nutrient loading, the frequency of re-feeding with hydrocarbons was changed from an initial re-feeding every 60 hrs to a final re-feeding frequency of 18 hrs. The experiments clearly showed that the attached, mixed microbial community was able to effectively and rapidly degrade high concentrations of hydrocarbons. This demonstrated the practical advantages of employing attached, mixed microbial cultures in a SBR.

The thesis involves the development and implementation of a new and robust control system based on permeability trends but at the same time capable of reducing aeration proportionally to permeate flux. Permeability was made a key parameter for directly comparing temporary changes in membrane performance. Transmembrane pressure and flux were gathered every 10 seconds and permeability values were automatically calculated; different mathematical algorithms were applied for the signal filtering of on-line data. Short term and long term permeability trends were compared once a day, and a control action was applied proportionally to the short term/long term permeability ratio without exceeding the aeration flow recommended by the membrane suppliers. / El treball presentat a la tesi inclou el desenvolupament i la implementacio d’un nou sistema de control robust basat en les tendencies de la permeabilitat i, al mateix temps, capac de reduir l’aeracio de forma proporcional al flux de permeat. S’ha seleccionat la permeabilitat com el parametre clau per comparar directament els canvis temporals en el funcionament de les membranes. La pressio transmembrana i el flux es mesuren cada 10 segons i llavors la permeabilitat es calcula automaticament. El senyal de les dades recollides en linia es filtra adequadament mitjancant diversos algoritmes matematics. L’algoritme de control compara diariament una tendencia a curt termini de la permeabilitat amb una tendencia a llarg termini de la permeabilitat, i s’aplica una accio de control proporcional al quocient de les dues tendencies, sense excedir mai el cabal d’aeracio recomanat pels fabricants de membranes.

Polymer hydrolysis is the first (and rate limiting) step for biomethanation of heterogeneous biomass feedstock’s. Satisfactory hydrolysis has been difficult to achieve, understand and predict adequately, to run anaerobic bioreactors with such feedstock’s efficiently. The fraction of hot water soluble extracts (crude proteins and extractables, Fcpe), the nature and material of intercellular binding and the extent and complexity of lignin present have been considered as key parameters for hydrolysis and has been analyzed for a variety of biomass degradation data available at the Centre for Sustainable Technologies, Indian Institute of Science. Feedstocks were grouped into those bound with high levels of pectic/protein materials or lignin-bound types. The data on the initial (10-15d) as well as the overall rates of hydrolysis (0-50d) has been analyzed. The extent of hydrolysis achieved for pectin bound substrates were high (≥65%) and that of lignin bound substrate was low (≤30% VS, Acacia). The initial hydrolysis rates were strongly correlated to the content of extractables (=0.117Fcpe). Subsequently, the hydrolysis rates rise to reach maxima and then begin to fall. Most fresh feedstock had somewhat similar rates of the increase in hydrolysis rates but the time to reach maximum and its value varied among feed stocks. Many lignin bound feed stocks did not have such a pattern. With regards to the overall hydrolysis rate constant, it was found that these clustered into two groups that represented pectin bound (0.154/d) and lignin bound (0.045/d) types. Therefore from this study it was concluded that anaerobic decomposition of heterogeneous biomass could be predicted using two rate parameters and one intrinsic property of the biomass feedstock, namely, a. the initial rate of hydrolysis (based on the extent of extractables =0.117 Fcpe) b.the maximum rate achieved and the time when it is reached (an intrinsic property based on feed stock and but not determined in this study) c. the overall hydrolysis rate (choosing between 0.154 /d or 0.045 /d depending upon the nature of inter-cellular binding material, pectin or lignin, respectively). This research provides new insights into the prediction of hydrolysis rate a key limiting step for heterogeneous biomass biomethanation (hydrolysis) based on the level of extractables, the type of cellular cementing material and the maxima that can be achieved.

Living cells and their components play a key role within biotechnology industry. Cell cultures and their products of interest are used for the design of vaccines as well as in the agro-alimentary field. In order to ensure optimal working of such bioprocesses, the understanding of the complex mechanisms which rule them is fundamental. Mathematical models may be helpful to grasp the biological phenomena which intervene in a bioprocess. Moreover, they allow prediction of system behaviour and are frequently used within engineering tools to ensure, for instance, product quality and reproducibility.<p> <p>Mathematical models of cell cultures may come in various shapes and be phrased with varying degrees of mathematical formalism. Typically, three main model classes are available to describe the nonlinear dynamic behaviour of such biological systems. They consist of macroscopic models which only describe the main phenomena appearing in a culture. Indeed, a high model complexity may lead to long numerical computation time incompatible with engineering tools like software sensors or controllers. The first model class is composed of the first principles or white box models. They consist of the system of mass balances for the main species (biomass, substrates, and products of interest) involved in a reaction scheme, i.e. a set of irreversible reactions which represent the main biological phenomena occurring in the considered culture. Whereas transport phenomena inside and outside the cell culture are often well known, the reaction scheme and associated kinetics are usually a priori unknown, and require special care for their modelling and identification. The second kind of commonly used models belongs to black box modelling. Black boxes consider the system to be modelled in terms of its input and output characteristics. They consist of mathematical function combinations which do not allow any physical interpretation. They are usually used when no a priori information about the system is available. Finally, hybrid or grey box modelling combines the principles of white and black box models. Typically, a hybrid model uses the available prior knowledge while the reaction scheme and/or the kinetics are replaced by a black box, an Artificial Neural Network for instance.<p><p>Among these numerous models, which one has to be used to obtain the best possible representation of a bioprocess? We attempt to answer this question in the first part of this work. On the basis of two simulated bioprocesses and a real experimental one, two model kinds are analysed. First principles models whose reaction scheme and kinetics can be determined thanks to systematic procedures are compared with hybrid model structures where neural networks are used to describe the kinetics or the whole reaction term (i.e. kinetics and reaction scheme). The most common artificial neural networks, the MultiLayer Perceptron and the Radial Basis Function network, are tested. In this work, pure black box modelling is however not considered. Indeed, numerous papers already compare different neural networks with hybrid models. The results of these previous studies converge to the same conclusion: hybrid models, which combine the available prior knowledge with the neural network nonlinear mapping capabilities, provide better results.<p><p>From this model comparison and the fact that a physical kinetic model structure may be viewed as a combination of basis functions such as a neural network, kinetic model structures allowing biological interpretation should be preferred. This is why the second part of this work is dedicated to the improvement of the general kinetic model structure used in the previous study. Indeed, in spite of its good performance (largely due to the associated systematic identification procedure), this kinetic model which represents activation and/or inhibition effects by every culture component suffers from some limitations: it does not explicitely address saturation by a culture component. The structure models this kind of behaviour by an inhibition which compensates a strong activation. Note that the generalization of this kinetic model is a challenging task as physical interpretation has to be improved while a systematic identification procedure has to be maintained.<p><p>The last part of this work is devoted to another kind of biological systems: proteins. Such macromolecules, which are essential parts of all living organisms and consist of combinations of only 20 different basis molecules called amino acids, are currently used in the industrial world. In order to allow their functioning in non-physiological conditions, industrials are open to modify protein amino acid sequence. However, substitutions of an amino acid by another involve thermodynamic stability changes which may lead to the loss of the biological protein functionality. Among several theoretical methods predicting stability changes caused by mutations, the PoPMuSiC (Prediction Of Proteins Mutations Stability Changes) program has been developed within the Genomic and Structural Bioinformatics Group of the Université Libre de Bruxelles. This software allows to predict, in silico, changes in thermodynamic stability of a given protein under all possible single-site mutations, either in the whole sequence or in a region specified by the user. However, PoPMuSiC suffers from limitations and should be improved thanks to recently developed techniques of protein stability evaluation like the statistical mean force potentials of Dehouck et al. (2006). Our work proposes to enhance the performances of PoPMuSiC by the combination of the new energy functions of Dehouck et al. (2006) and the well known artificial neural networks, MultiLayer Perceptron or Radial Basis Function network. This time, we attempt to obtain models physically interpretable thanks to an appropriate use of the neural networks.<p> / Doctorat en sciences appliquées / info:eu-repo/semantics/nonPublished

The following thesis presents a computational framework that can capture inherently non-linear and emergent biocomplex phenomena. The main motivation behind the investigations undertaken was the absence of a suitable platform that can simulate, both the continuous features as well as the discrete, interaction-based dynamics of a given biological system, or in short, dynamic reciprocity. In order to determine the most powerful approach to achieve this, the efficacy of two modelling paradigms, transport phenomena as well as agent-based, was evaluated and eventually combined. Computational Fluid Dynamics (CFD) was utilised to investigate optimal boundary conditions, in terms of meeting cellular glucose consumption requirements and exposure to physiologically relevant shear fields, that would support mesenchymal stem cell growth in a 3-dimensional culture maintained in a commercially available bioreactor. In addition to validating the default bioreactor configuration and operational parameter ranges as suitable towards sustaining stem cell growth, the investigation underscored the effectiveness of CFD as a design tool. However, due to the homogeneity assumption, an untenable assumption for most biological systems, CFD often encounters difficulties in simulating the interaction-reliant evolution of cellular systems. Therefore, the efficacy of the agent-based approach was evaluated by simulating a morphogenetic event: development of in vitro osteogenic nodule. The novel model replicated most aspects observed in vitro, which included: spatial arrangement of relevant players inside the nodule, interaction-based development of the osteogenic nodules, and the dependence of nodule growth on its size. The model was subsequently applied to interrogate the various competing hypotheses on this process and identify the one that best captures transformation of osteoblasts into osteocytes, a subject of great conjecture. The results from this investigation annulled one of the competing hypotheses, which purported the slow-down in the rate of matrix deposition by certain osteoblasts, and also suggested the acquisition of polarity to be a non-random event. The agent-based model, however, due to being inherently computationally expensive, cannot be recommended to model bulk phenomena. Therefore, the two approaches were integrated to create a modelling platform that was utilised to capture dynamic reciprocity in a bioreactor. As a part of this investigation, an amended definition of dynamic reciprocity and its computational analogue, dynamic assimilation, were proposed. The multi-paradigm platform was validated by conducting melanoma chemotaxis under foetal bovine serum gradient. Due to its CFD and agent-based modalities, the platform can be employed as both a design optimisation as well as hypothesis testing tool.