Jeno M. Scharer

Metabolic pathways of clostridia for producing butanol

Worldwide demand for energy has been the impetus for research to produce alcohol biofuels from renewable resources. This review focuses on the biosynthesis of butanol, which is regarded to be superior to ethanol as a fuel. Although acetone/butanol fermentation is one of the oldest large-scale fermentation processes, butanol yield by anaerobic fermentation remains sub-optimal. Metabolic engineering provides a means for fermentation improvements. Consequently, a comprehensive assessment of the intermediary enzymes involved in butanol formation from carbohydrates by the saccharolytic bacterium, Clostridium acetobutylicum and other closely allied clostridia was performed to provide guidelines for potentially enhancing butanol productivity. The activity of the enzymes, their regulation and contribution to the metabolic pathways was reviewed. Published kinetic data for each important enzymatic reaction were assessed. For most enzymatic reactions, the systematic investigation of the kinetic data and the properties of the enzymes led to the development of rate equations that were able to describe activity as the function of the substrates, products, and allosteric effectors.

Application of statistical design for the optimization of amino acid separation by reverse-phase HPLC

Modified resolution and overall separation factors used to quantify the separation of complex chromatography systems are described. These factors were proven to be applicable to the optimization of amino acid resolution in reverse-phase (RP) HPLC chromatograms. To optimize precolumn derivatization with phenylisothiocyanate, a 2(5-1) fractional factorial design in triplicate was employed. The five independent variables for optimizing the overall separation factor were triethylamine content of the aqueous buffer, pH of the aqueous buffer, separation temperature, methanol/acetonitrile concentration ratio in the organic eluant, and mobile phase flow rate. Of these, triethylamine concentration and methanol/acetonitrile concentration ratio were the most important. The methodology captured the interaction between variables. Temperature appeared in the interaction terms; consequently, it was included in the hierarchic model. The preliminary model based on the factorial experiments was not able to explain the response curvature in the design space; therefore, a central composite design was used to provide a quadratic model. Constrained nonlinear programming was used for optimization purposes. The quadratic model predicted the optimal levels of the variables. In this study, the best levels of the five independent variables that provide the maximum modified resolution for each pair of consecutive amino acids appearing in the chromatograph were determined. These results are of utmost importance for accurate analysis of a subset of amino acids.

An arsenate effect on ferrihydrite dissolution kinetics under acidic oxic conditions

The dissolution behaviour of ferrihydrite and ferrihydrite incorporating arsenate at different levels was investigated under low pH, oxic conditions. The dissolution of pure ferrihydrite was found to be well described by the cube root law for mineral dissolution. The rate of dissolution of ferrihydrite precipitated in the presence of selected levels of arsenate was strongly retarded by the presence of the arsenate. The surface coordinative chemical model of mineral dissolution was applied to interpret and quantify proton dissolution rates of ferrihydrite and the inhibitory effect of arsenate. The inhibitory effect of the arsenate appears to be related to its complexation with the ferrihydrite surface and the consequent involvement of the surface iron centres in competitive equilibria between protons and the surface-complexed arsenate. From the iron:arsenic ratios obtained during dissolution, it has been concluded that arsenic is incorporated into these precipitates by sorption onto existing surfaces of the ferrihydrite during precipitation, rather than by the formation of a solid solution or by co-deposition.

Descriptive parameter evaluation in mammalian cell culture.

Several methods exist for assessing population growth and protein productivity in mammalian cell culture. These methods were critically examined here, based on experiments with two hybridoma cell lines. It is shown that mammalian cell culture parameters must be evaluated on the same basis. In batch culture mode most data is obtained on a cumulative basis (protein product titre, substrate concentration, metabolic byproduct concentration). A simple numerical integration technique can be employed to convert cell concentration data to a cumulative basis (cell-hours). The hybridoma lines used in this study included a nutritionally non-fastidious line producing low levels of MAb and a nutritionally fastidious hybridoma with high productivity. In both cases the cell-hour approach was the most appropriate means of expressing the relationship between protein productivity and cell population dynamics. The cell-hour approach could be used as the basis for all metabolic population parameter evaluations. This method has the potential to be used successfully for both prediction and optimization purposes.

Metabolic flux-based modeling of mAb production during batch and fed-batch operations.

This paper proposes mathematical models that predict the physiology, growth behavior and productivity of hybridoma cells in both batch and fed-batch systems. Murine hybridoma 130-8F producing anti-F-glycoprotein monoclonal antibody was employed as a model system. A systematic approach based on metabolic flux analysis (MFA) was utilized to yield a dynamic model for predicting the concentration of significant metabolites over time. Correlation analysis was performed to formulate a Biomass Model for predicting cell concentration and viability as a function of the extracellular metabolite concentrations. The coefficients of the model equation were estimated by employing the Metropolis–Hastings algorithm. The Metabolites Model was combined with the Biomass Model to get an Integrated Model capable of predicting concentration values for substrates, extracellular metabolites, and viable and dead cell concentration by utilizing only starting concentrations as input. The prediction accuracy of the model was tested by using experimental data.

Dynamic metabolic modeling for a MAB bioprocess

Production of monoclonal antibodies (MAb) for diagnostic or therapeutic applications has become an important task in the pharmaceutical industry. The efficiency of high‐density reactor systems can be potentially increased by model‐based design and control strategies. Therefore, a reliable kinetic model for cell metabolism is required. A systematic procedure based on metabolic modeling is used to model nutrient uptake and key product formation in a MAb bioprocess during both the growth and post‐growth phases. The approach combines the key advantages of stoichiometric and kinetic models into a complete metabolic network while integrating the regulation and control of cellular activity. This modeling procedure can be easily applied to any cell line during both the cell growth and post‐growth phases. Quadratic programming (QP) has been identified as a suitable method to solve the underdetermined constrained problem related to model parameter identification. The approach is illustrated for the case of murine hybridoma cells cultivated in stirred spinners.

Effects of nutrient levels and average culture pH on the glycosylation pattern of camelid-humanized monoclonal antibody.

The impact of operating conditions on the glycosylation pattern of humanized camelid monoclonal antibody, EG2-hFc produced by Chinese hamster ovary (CHO) cells has been evaluated by a combination of experiments and modeling. Cells were cultivated under different levels of glucose and glutamine concentrations with the goal of investigating the effect of nutrient depletion levels and ammonia build up on the cell growth and the glycoprofiles of the monoclonal antibody (Mab). The effect of average pH reduction on glycosylation level during the entire culture time or during a specific time span was also investigated. The relative abundance of glycan structures was quantified by hydrophilic interaction liquid chromatography (HILIC) and the galactosylation index (GI) and the sialylation index (SI) were determined. Lower initial concentrations of glutamine resulted in lower glucose consumption and lower cell yield but increased GI and SI levels when compared to cultures started with higher initial glutamine levels. Similarly, reducing the average pH of culture resulted in lower growth but higher SI and GI levels. These findings indicate that there is a tradeoff between cell growth, resulting Mab productivity and the achievement of desirable higher glycosylation levels. A dynamic model, based on a metabolic flux analysis (MFA), is proposed to describe the metabolism of nutrients, cell growth and Mab productivity. Finally, existing software (GLYCOVIS) that describes the glycosylation pathways was used to illustrate the impact of extracellular species on the glycoprofiles.

Heterologous expression of lipase in Escherichia coli is limited by folding and disulfide bond formation

Functional expression of lipase B from Pseudozyma antarctica (PalB) in the cytoplasm of Escherichia coli BL21(DE3) and its mutant derivative Origami B(DE3) was explored. Coexpression of DsbA was found to be effective in enhancing PalB expression. The improvement was particularly pronounced with Origami B(DE3) as a host, suggesting that both folding and disulfide bond formation may be major factors limiting PalB expression. Fusion tag technique was also explored by constructing several PalB fusions for the evaluation of their expression performance. While the solubility was enhanced for most PalB fusions, only the DsbA tag was effective in boosting PalB activity, possibly by both enhanced solubility and correct disulfide bond formation. Our results suggest that PalB activity is closely associated with correct disulfide bond formation, and increased solubilization by PalB fusions does not necessarily result in activity enhancement.

Computer simulation for large scale bioprocess design

Abstract Two bioprocess simulators, Aspen BPS™ and SuperPro Designer®, were used to simulate and compare two flowsheets for production of tissue plasminogen activator (t-PA) from Chinese hamster ovary (CHO) cells. The flowsheets were designed to compare the economics of using serum and serum-free medium in the bioreactor. The base case flowsheet used a medium with 10% serum while the alternative flowsheet used a serum-free medium. Affinity chromatography was the major step in the downstream processing of the base case flowsheet. The alternate flowsheet was designed for two-step cell culture growth and production. Ion-exchange chromatography was considered sufficient for purification of the low protein medium for this case. At a price of US

The effect of phosphate on the transformation of ferrihydrite into crystalline products in alkaline media

25/l for serum-free medium, the alternate flowsheet was found to have an return on investment (ROI), of 115% compared to 65% for the base case flowsheet.