Teaching mathematical modelling: a research based approach

A collaborative, research based laboratory experiment in mathematical modelling was included in a bioprocess engineering laboratory module, taught as part of an interdisciplinary program in biotechnology. The class was divided into six groups of three students and given the task of investigating a novel diafiltration process that is currently the focus of international research. Different aspects of the problem were assigned to each group and inter-group communication via email was required to ensure that there was a coherent set of objectives for each group and for the class as a whole. The software package, Berkeley Madonna, was used for all calculations. As well as giving the students an introduction to mathematical modelling and computer programming, this approach helped to illustrate the importance of research in bioprocess engineering. In general, the experiment was well received by the students and the fact that they were discovering new knowledge generated a degree of enthusiasm. However, many students were consumed by the technical demands of computer programming, especially the attention to detail required. Thus, they did not think too deeply about the physical aspects of the system they were modelling. In future years, therefore, consideration will be given to giving the student prior instruction in the use of the software

Rational development of bioprocess engineering strategies for recombinant protein production in Pichia pastoris (Komagataella phaffii) using the methanol-free GAP promoter. Where do we stand?

The increasing demand for recombinant proteins for a wide range of applications, from biopharmaceutical protein complexes to industrial enzymes, is leading to important growth in this market. Among the different efficient host organism alternatives commonly used for protein production, the yeast Pichia pastoris (Komagataella phaffii) is currently considered to be one of the most effective and versatile expression platforms. The promising features of this cell factory are giving rise to interesting studies covering the different aspects that contribute to improving the bioprocess efficiency, from strain engineering to bioprocess engineering. The numerous drawbacks of using methanol in industrial processes are driving interest towards methanol-free alternatives, among which the GAP promoter-based systems stand out. The aim of this work is to present the most promising innovative developments in operational strategies based on rational approaches through bioprocess engineering tools. This rational design should be based on physiological characterization of the producing strains under bioprocess conditions and its interrelation with specific rates. This review focuses on understanding the key factors that can enhance recombinant protein production in Pichia pastoris; they are the basis for a further discussion on future industrial applications with the aim of developing scalable alternative strategies that maximize yields and productivity

ECUT (Energy Conversion and Utilization Technologies) program: Biocatalysis Project

Fiscal year 1987 research activities and accomplishments for the Biocatalysis Project of the U.S. Department of Energy, Energy Conversion and Utilization Technologies (ECUT) Division are presented. The project's technical activities were organized into three work elements. The Molecular Modeling and Applied Genetics work element includes modeling and simulation studies to verify a dynamic model of the enzyme carboxypeptidase; plasmid stabilization by chromosomal integration; growth and stability characteristics of plasmid-containing cells; and determination of optional production parameters for hyper-production of polyphenol oxidase. The Bioprocess Engineering work element supports efforts in novel bioreactor concepts that are likely to lead to substantially higher levels of reactor productivity, product yields, and lower separation energetics. The Bioprocess Design and Assessment work element attempts to develop procedures (via user-friendly computer software) for assessing the economics and energetics of a given biocatalyst process

Bioprocess Forces and Their Impact on Cell Behavior: Implications for Bone Regeneration Therapy

Bioprocess forces such as shear stress experienced during routine cell culture are considered to be harmful to cells. However, the impact of physical forces on cell behavior is an area of growing interest within the tissue engineering community, and it is widely acknowledged that mechanical stimulation including shear stress can enhance osteogenic differentiation. This paper considers the effects of bioprocess shear stress on cell responses such as survival and proliferation in several contexts, including suspension-adapted cells used for recombinant protein and monoclonal antibody manufacture, adherent cells for therapy in suspension, and adherent cells attached to their growth substrates. The enhanced osteogenic differentiation that fluid flow shear stress is widely found to induce is discussed, along with the tissue engineering of mineralized tissue using perfusion bioreactors. Recent evidence that bioprocess forces produced during capillary transfer or pipetting of cell suspensions can enhance osteogenic responses is also discussed

Using peer review to enhance the quality of engineering laboratory reports

Peer review of third year bioprocess engineering laboratory reports was introduced in an attempt to improve the standard of report writing in the BSc in Biotechnology degree programme at DCU. Preliminary results suggest that the review process leads to improved report writing skills. The student response to the initiative was very positive but it was strongly felt that the process should be anonymous. On average, marks awarded by students were higher than those awarded by the lecturer but there was a slight tendency to award more extreme marks

Predictive engineering of CHO cells using systems biology models

Decades of bioprocess optimization have resulted in substantial improvements in recombinant protein production. However, some proteins remain difficult to express, and there is an increasing awareness of the need for improved control of critical quality attributes of recombinant protein drugs. To enable cell engineering efforts to enhance protein production and control product quality, we have enumerated the CHO cell parts through genome sequencing efforts,1,2 and are now providing context to these parts by reconstructing genome-scale networks of the secretory pathway, glycosylation, and metabolism CHO (Figure 1). Using these models, which account for the activities of more than 2000 genes, we have approached questions relevant to bioprocessing and guided cell engineering efforts. First, several bioprocess treatments have increased CHO cell specific productivity, but the yields still pale in comparison to professional secretory cells. Have these bioprocess treatments maximized specific productivity? To answer this question, transcriptomic, proteomic and metabolomic data were used build cell-line specific models. Through simulations we found that common treatments, such as NaBu and decreased temperature increase the yield inefficiently, as opposed to cell engineering efforts. Second, cell engineering efforts aim to match product quality attributes relevant to product activity. To aid in this, we developed a simple but powerful computational modeling platform to predict glycosylation and study how metabolism impacts glycans on products. Using this platform and an initial glycoprofile of a product under development, we can successfully predict the effects of genetic manipulations and media, thereby providing insights into which treatments are most likely to yield the desired glycoforms. In summary, these genome-scale models serve as valuable platforms for data analysis and simulation, thereby providing insights into the molecular basis of various bioprocess phenotypes and for guiding cell engineering efforts