Metabolic engineering with multi-objective optimization of kinetic models

Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility.

Estratégias de Produção in vitro de Bioinseticida Viral: influências do Isolado, da Cinética e do Modo de operação

Societal concerns about environmental sustainability has lead to the development of ecologically-friendly alternatives to chemical insecticides for crop protection. One such alternative is biological pest control. In particular, baculoviruses are well suited as insect biopesticides due to their narrow host specificity and relative ease of propagation. In Brazil, the baculovirus Anticarsia gemmatalis nucleopolyhedrovirus (AgMNPV) is the main biological control agent employed for the soybean pest, Anticarsia gemmatalis. This baculovirus biopesticide is currently produced using caterpillars, but increasing market demand for the product has encouraged the development of an in vitro manufacturing process, which can be scaled up to much higher virus productivities. In this study, three wild-type AgMNPV isolates (AgMNPV-2D, AgMNPV-MP2 and AgMNPV-MP5) and a recombinant form (vAgEGT-LacZ) were characterised in terms of occlusion body (OB) production and infection kinetics, to enable future optimisation of the in vitro production process. These viruses were propagated using a Spodoptera frugiperda (IPLB-SF21) insect cell line grown in shaker-flask batch cultures. Among the virus isolates tested, AgMNPV-MP5 was found to be the best producer, yielding (5.3±0.85)x108 OB/mL after 8 days post infection. The characterisation of vAgEGT-LacZ propagation in suspension cell cultures has not been previously reported in the literature; hence it became the main focus for this thesis. In particular, it was carried out a study on the effect of the multiplicity of infection (MOI) on OB production. Five successive batches were performed getting a final production (8.9±1.42)x1014 occlusion bodies, considering that production is related for a bioreactor with final volume of 10m3. A low MOI associated with a fed-batch process for vAgEGT-LacZ production was found to support a 3-fold higher OB yield when compared to the default batch process (1.8x107 and 5.3x107 OB/mL, respectively). This yield is competitive with regards to the production process.

CURRENT ASPECTS OF FUEL ETHANOL-PRODUCTION IN BRAZIL

Brazil has become a great producer of bioethanol using sugarcane as the basic raw material. Fed-batch process and continuous process are used. Biogas generation from vinasse, production of dry yeast, and autolyzed bagasse for animal feed are making the ethanol production less polluting and more profitable. Bagasse surplus has also been converted into electrical energy. Another alternative use for bioethanol is its conversion to petrochemical derivatives. Up to the present, however, this conversion has been carried out on only a small scale by the industry.

Arthrospira (Spirulina) platensis cultivation in tubular photobioreactor: Use of no-cost CO2 from ethanol fermentation

The present study aimed at evaluating the production of Arthrospira platensis in tubular photobioreactor using CO2 from ethanol fermentation. The results of these cultivations were compared to those obtained using CO2 from cylinder at different protocols of simultaneous ammonium sulfate and sodium nitrate feeding. Maximum cell concentration (X-m), cell productivity (P-x), nitrogen-to-cell conversion factor (Y-X/N), and biomass composition (total lipids and proteins) were selected as responses and evaluated by analysis of variance. The source of CO2 did not exert any significant statistical influence on these responses, which means that the flue gas from ethanol fermentation could successfully be used as a carbon source as well as to control the medium pH, thus contributing to reduce the greenhouse effect. The results taken as a whole demonstrated that the best combination of responses mean values (X-m = 4.543 g L-1; P-x = 0.460 g L-1 d(-1); Y-X/N = 15.6 g g(-1); total lipids = 8.39%; total proteins = 18.7%) was obtained using as nitrogen source a mixture of 25% NaNO3 and 75% (NH4)(2)SO4, both expressed as nitrogen. (C) 2011 Elsevier Ltd. All rights reserved.

Simultaneous use of urea and potassium nitrate for Arthrospira (Spirulina) platensis cultivation

Urea has been considered as a promising alternative nitrogen source for the cultivation of Arthrospira platensis if it is possible to avoid ammonia toxicity; however, this procedure can lead to periods of nitrogen shortage. This study shows that the addition of potassium nitrate, which acts as a nitrogen reservoir, to cultivations carried out with urea in a fed-batch process can increase the maximum cell concentration (Xm) and also cell productivity (PX). Using response surface methodology, the model indicates that the estimated optimum Xm can be achieved with 17.3 mM potassium nitrate and 8.9 mM urea. Under this condition an Xm of 6077 +/- 199 mg/L and a PX of 341.5 +/- 19.1 mg L1day1 were obtained.

Avaliação do crescimento de Ankistrodesmus braunii em reator tubular empregando diferentes concentrações de nitrato em diferentes condições de cultivo

Microalgas são organismos unicelulares, eucariontes, fotossintetizantes e eficientes fixadores de gás carbônico que apresentam grande potencial para produção de ácidos graxos além de pigmentos, como os carotenóides e a clorofila, de interesse nas indústrias de alimentos, química, farmacêutica e de cosméticos. Dentre as microalgas, o microrganismo Ankistrodesmus braunii vem sendo citado como capaz de produzir grandes quantidades de lipídios, podendo corresponder a até 73% de sua massa seca, com produção de ácidos graxos insaturados, como o ácido linolênico. Esse microrganismo se destaca do ponto de vista industrial por poder ser conduzido em reatores e em meios de cultivo complexos. As fontes de nitrogênio, as concentrações empregadas destes nutrientes, bem como o tipo de processo de cultivo interferem na composição de biomassas fotossintetizantes. O uso de reatores tubulares tem sido estudado e tem se apresentado interessante por permitir a obtenção de altas concentrações celulares. Nesse sentido, este trabalho teve a finalidade de estudar o crescimento de Ankistrodesmus braunii em reator tubular com uso de diferentes quantidades de nitrato de sódio por processos descontínuo, descontínuo alimentado e semi-contínuo. Nos cultivos descontínuos, a máxima concentração celular (Xm) encontrada foi de 1588 ± 11 mg.L-1 com uso de 20 mM de NaNO3. O uso do processo descontínuo alimentado, o qual teve adição de 20 mM de NaNO3 feito num intervalo a cada 48 horas sendo iniciada a adição no primeiro dia, permitiu a obtenção de Xm = 2753 ± 7 mg.L-1; porém não foi possível eliminar a fase lag do cultivo, levando a uma produtividade em células (Px) de 351 ± 1 mg.L-1.dia-1. O processo semi-contínuo foi eficiente para eliminar a fase lag do cultivo, permitindo a obtenção de Xm = 2399 ± 5 mg.L-1 e um aumento de até 50% em Px, que chegou a valores de 525 ± 1 mg.L-1.dia-1 em cultivos com uso de 20 mM de NaNO3. Nesta condição os teores de proteínas e lipídios nas biomassas foram de 34,8 ± 0,2% e 38,6 ± 0,2%, respectivamente. Foi observado que, independentemente do tipo de processo empregado, há um decréscimo do valor do fator de conversão de nitrogênio em células (YX/N) com o aumento da adição de NaNO3. O maior valor de YX/N foi obtido no experimento com processo semi-contínuo e uso de 2 mM de NaNO3 no meio de cultivo, com valor médio de 29,1 ± 0,1 mg mg-1 ao final do segundo ciclo. Porém, nesta condição, o teor de proteínas da biomassa foi de 17,3 ± 0,4%. Já os maiores valores de YX/N encontrados nos processos descontínuo e descontínuo alimentado foram, respectivamente, de 22,5 ± 1,6 e 7,1 ± 0,1 mg mg-1. Os resultados obtidos neste trabalho evidenciam o potencial de Ankistrodesmus braunii como fonte de proteínas e lipídios para uso industrial.

Nitrogen removal in a sequencing batch biofilm reactor with liquid circulation: Effect of feed strategy and carbon source in the denitrifying step

Ammonium nitrogen removal from a synthetic wastewater by nitrification and denitrification processes were performed in a sequencing batch biofilm reactor containing immobilized biomass on polyurethane foam with circulation of the liquid-phase. It was analyzed the effect of four external carbon sources (ethanol, acetate, carbon synthetic medium and methanol) acting as electron donors in the denitrifying process. The experiments were conducted with intermittent aeration and operated at 30+/-1 degrees C in 8-h cycles. The synthetic wastewater (100 mgCOD/L and 50 mgNH(4)(+)-N/L) was added batch-wise, while the external carbon sources were added fed-batch-wise during the periods where aeration was suspended. Ammonium nitrogen removal efficiencies obtained were 95.7, 94.3 and 97.5% for ethanol, acetate and carbon synthetic medium, respectively. As to nitrite, nitrate and ammonium nitrogen effluent concentrations, the results obtained were, respectively: 0.1, 5.7 and 1.4 mg/L for ethanol; 0.2, 4.1 and 1.8 mg/L for acetate and 0.2, 6.7 and 0.8 for carbon synthetic medium. On the other hand using methanol, even at low concentrations (50% of the stoichiometric value calculated for complete denitrification), resulted in increasing accumulation of nitrate and ammonium nitrogen in the effluent over time.

Biogas production and valorization by means of a two-step biological process

The scope of this research work was to investigate biogas production and purification by a two-step bench-scale biological system, consisting of fed-batch pulse-feeding anaerobic digestion of mixed sludge, followed by methane enrichment of biogas by the use of the cyanobacterium Arthrospira platensis. The composition of biogas was nearly constant, and methane and carbon dioxide percentages ranged between 70.5-76.0% and 13.2-19.5%, respectively. Biogas yield reached a maximum value (about 0.4 m(biogas)(3)/kgCOD(i)) at 50 days-retention time and then gradually decreased with a decrease in the retention time. Biogas CO(2) was then used as a carbon source for A. platensis cultivation either under batch or fed-batch conditions. The mean cell productivity of fed-batch cultivation was about 15% higher than that observed during the last batch phase (0.035 +/- 0.006 g(DM)/L/d), likely due to the occurrence of some shading effect under batch growth conditions. The data of carbon dioxide removal from biogas revealed the existence of a linear relationship between the rates of A. platensis growth and carbon dioxide removal from biogas and allowed calculating carbon utilization efficiency for biomass production of almost 95%. (C) 2009 Elsevier Ltd. All rights reserved.

Influence of carbon source and the fermentation process on levan production by Zymomonas mobilis analyzed by the surface response method

The aim of this study is to assess sugar cane juice and sucrose as substrates, the batch and fed batch processes and their interaction in the levan production using a complete factorial design. Zymomonas mobilis was cultivated in different sugar cane juice and sucrose concentrations in two fermentation processes at 25 °C for 20 h. A complete factorial design (2³) was used to analyze the effects of the type and concentration of the substrate, as well as the batch and fed batch processes. A complete second factorial design (2²) was used to observe the importance of sugar cane juice. The results indicated that the batch process improved the levan production reaching 40.14 g/L. The addition of sugar cane juice was not statistically significant for levan formation, however sugar cane juice stimulated biomass, sorbitol and ethanol production. The best medium for levan production was 150 g/L sucrose in batch.

Arthrospira platensis biomass with high protein content cultivated in continuous process using urea as nitrogen source

Aims: Arthrospira platensis has been studied for single-cell protein production because of its biomass composition and its ability of growing in alternative media. This work evaluated the effects of different dilution rates (D) and urea concentrations (N0) on A.similar to platensis continuous culture, in terms of growth, kinetic parameters, biomass composition and nitrogen removal. Methods and results: Arthrospira platensis was continuously cultivated in a glass-made vertical column photobioreactor agitated with Rushton turbines. There were used different dilution rates (0.040.44 day-1) and urea concentrations (0.5 and 5 mmol l-1). With N0 = 5 mmol l-1, the maximum steady-state biomass concentration was1415 mg l-1, achieved with D = 0.04 day-1, but the highest protein content (71.9%) was obtained by applying D = 0.12 day-1, attaining a protein productivity of 106.41 mg l-1 day-1. Nitrogen removal reached 99% on steady-state conditions. Conclusions: The best results were achieved by applying N0 = 5 mmol l-1; however, urea led to inhibitory conditions at D = 0.16 day-1, inducing the system wash-out. The agitation afforded satisfactory mixture and did not harm the trichomes structure. Significance and Impact of the Study: These results can enhance the basis for the continuous removal of nitrogenous wastewater pollutants using cyanobacteria, with an easily assembled photobioreactor.

Chemical kinetic investigation of a commercial batch reactor process

The aim of this investigation was to study the chemical reactions occurring during the batchwise production of a butylated melamine-formaldehyde resin, in order to optimise the efficiency and economics of the batch processes. The batch process models are largely empirical in nature as the reaction mechanism is unknown. The process chemistry and the commercial manufacturing method are described. A small scale system was established in glass and the ability to produce laboratory resins with the required quality was demonstrated, simulating the full scale plant. During further experiments the chemical reactions of methylolation, condensation and butylation were studied. The important process stages were identified and studied separately. The effects of variation of certain process parameters on the chemical reactions were also studied. A published model of methylolation was modified and used to simulate the methylolation stage. A major result of this project was the development of an indirect method for studying the condensation and butylation reactions occurring during the dehydration and acid reaction stages, as direct quantitative methods were not available. A mass balance method was devised for this purpose and used to collect experimental data. The reaction scheme was verified using this data. The reactions stages were simulated using an empirical model. This has revealed new information regarding the mechanism and kinetics of the reactions. Laboratory results were shown to be comparable with plant scale results. This work has improved the understanding of the batch process, which can be used to improve product consistency. Future work has been identified and recommended to produce an optimum process and plant design to reduce the batch time.

Bioreaction and separation in preparative batch chromatographic columns : the hydrology of lactose to yield glucose,galactose and oligosaccharides

The initial aim of this project was to improve the performance of a chromatographic bioreactor-separator (CBRS). In such a system, a dilute enzyme solution is pumped continuously through a preparative chromatographic column, while pulses of substrate are periodically injected on to the column. Enzymic reaction and separation are therefore performed in a single unit operation. The chromatographic columns used were jacketed glass columns ranging from 1 to 2 metres long with an internal diameter of 1.5 cm. Linking these columns allowed 1, 2, 3 and 4 metre long CBRS systems to be constructed. The hydrolysis of lactose in the presence of β~galactosidase was the reaction of study. From previous work at Aston University, there appeared to be no difficulties in achieving complete lactose hydrolysis in a CBRS. There did, however, appear to be scope for improving the separative performance, so this was adopted as an initial goal. Reducing the particle size of the stationary phase was identified as a way of achieving this improvement. A cation exchange resin was selected which had an average particle size of around half that previously used when studying this reaction. A CBRS system was developed which overcame the operational problems (such as high pressure drop development) associated with use of such a particle size. A significant improvement in separative power was achieved. This was shown by an increase in the number of theoretical plates (N) from about 500 to about 3000 for a 2 metre long CBRS, coupled with higher resolution. A simple experiment with the 1 metre column showed that combined bioreaction and separation was achievable in this system. Having improved the separative performance of the system, the factors affecting enzymic reaction in a CBRS were investigated; including pulse volume and the degree of mixing between enzyme and substrate. The progress of reaction in a CBRS was then studied. This information was related to the interaction of reaction and separation over the reaction zone. The effect of injecting a pulse over a length of time as in CBRS operation was simulated by fed batch experiments. These experiments were performed in parallel with normal batch experiments where the substrate is mixed almost instantly with the enzyme. The batch experiments enabled samples to be taken every minute and revealed that reaction is very rapid. The hydrodynamic characteristics of the two injector configurations used in CBRS construction were studied using Magnetic Resonance Imaging, combined with hydrodynamic calculations. During the optimisation studies, galactooligosaccharides (GOS) were detected as intermediates in the hydrolysis process. GOS are valuable products with potential and existing applications in food manufacture (as nutraceuticals), medicine and drug targeting. The focus of the research was therefore turned to GOS production. A means of controlling reaction to arrest break down of GOS was required. Raising temperature was identified as a possible means of achieving this within a CBRS. Studies were undertaken to optimise the yield of oligosaccharides, culminating in the design, construction and evaluation of a Dithermal Chromatographic Bioreactor-separator.

Batch and continuous fermentation methods for the production of dextransucrase

The available literature concerning dextransucrase and dextran production and purification has been reviewed along with the reaction mechanisms of the enzyme. A discussion of basic fermentation theory is included, together with a brief description of bioreactor hydrodynamics and general biotechnology. The various fermenters used in this research work are described in detail, along with the various experimental techniques employed. The micro-organism Leuconostoc mesenteroides NRRL B512 (F) secretes dextransucrase in the presence of an inducer, sucrose, this being the only known inducer of the enzyme. Dextransucrase is a growth related product and a series of fed-batch fermentations have been carried out to extend the exponential growth phase of the organism. These experiments were carried out in a number of different sized vessels, ranging in size from 2.5 to 1,000 litres. Using a 16 litre vessel, dextransucrase activities in excess of 450 DSU/cm3 (21.67 U/cm3) have been obtained under non-aerated conditions. It has also been possible to achieve 442 DSU/cm3 (21.28 U/cm3) using the 1,000 litre vessel, although this has not been done consistently. A 1 litre and a 2.5 litre vessel were used for the continuous fermentations of dextransucrase. The 2.5 litre vessel was a very sophisticated MBR MiniBioreactor and was used for the majority of continuous fermentations carried out. An enzyme activity of approximately 108 DSU/cm3 (5.20 U/cm3) was achieved at a dilution rate of 0.50 h-1, which corresponds to the maximum growth rate of the cells under the process conditions. A number of continuous fermentations were operated for prolonged periods of time, with experimental run-times of up to 389 h being recorded without any incidence of contamination. The phenomenon of enzyme enhancement on hold-up of up to 100% was also noted during these fermentations, with dextransucrase of activity 89.7 DSU/cm3 (4.32 U/cm3) being boosted to 155.7 DSU/cm3 (7.50 U/cm3) following 24 hours of hold-up. These findings support the recommendation of a second reactor being placed in series with the existing vessel.

Improved production of industrially relevant recombinant proteins: application of multi-factorial design of experiments and scalable process modelling

The work described in this thesis focuses on the use of a design-of-experiments approach in a multi-well mini-bioreactor to enable the rapid establishments of high yielding production phase conditions in yeast, which is an increasingly popular host system in both academic and industrial laboratories. Using green fluorescent protein secreted from the yeast, Pichia pastoris, a scalable predictive model of protein yield per cell was derived from 13 sets of conditions each with three factors (temperature, pH and dissolved oxygen) at 3 levels and was directly transferable to a 7 L bioreactor. This was in clear contrast to the situation in shake flasks, where the process parameters cannot be tightly controlled. By further optimisating both the accumulation of cell density in batch and improving the fed-batch induction regime, additional yield improvement was found to be additive to the per cell yield of the model. A separate study also demonstrated that improving biomass improved product yield in a second yeast species, Saccharomyces cerevisiae. Investigations of cell wall hydrophobicity in high cell density P. pastoris cultures indicated that cell wall hydrophobin (protein) compositional changes with growth phase becoming more hydrophobic in log growth than in lag or stationary phases. This is possibly due to an increased occurrence of proteins associated with cell division. Finally, the modelling approach was validated in mammalian cells, showing its flexibility and robustness. In summary, the strategy presented in this thesis has the benefit of reducing process development time in recombinant protein production, directly from bench to bioreactor.