Browsing by Subject "biotechnology"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Item
    Advancing Cell Culture Engineering Through Mechanistic Model Optimization
    (2020-04) O'Brien, Conor
    Over the past few decades, the emergence of new classes of treatments, including protein therapeutics, gene therapies, and cell therapies, has ushered in a new era of medicine. Unlike small molecule therapeutics, these treatments are produced in or consist of cells, typically mammalian in origin. Processes have been developed to produce many of these drugs at large scale, often in stirred tank bioreactors. Significant effort has driven staggering increases in the productivity of these processes, enabling economical manufacturing, and the potential to drive down costs and make drugs more widely available. However, the bioreactor is not a natural environment for cells isolated from a multicellular mammalian organism. Many biological regulations are carried over from the cells’ origin and can result in numerous undesirable behaviors manifesting in the dense, highly productive reactor environment. In certain culture stages, or in the case of excess nutrient supply, cells will secrete undesirable metabolites including lactate, ammonia, and many byproducts of amino acid metabolism. These compounds can retard cell growth, or otherwise alter the potency or productivity of the cultures. Traditional biologics process development employs the use of statistical design of experiments, often encompassing several reactors run in parallel for multiple rounds of experiments over a few months. There is thus substantial room for improvement for both the outcome of the development process, such as an increase in titer, and the time it takes to complete the development stage. Given that cell culture processes share intrinsic similarities in their underlying mechanistic behavior, there exists significant opportunity to reduce the overall number of experiments needed for process development, scaling, and diagnostics using models rather than treating cell culture processes as a black box. In this thesis, we present the case for the use of mathematical optimization of mechanistic models to accurately describe cell culture processes and augment their behavior. We first outline recent advances in understanding of metabolic regulation and homeostasis. Cell signaling and metabolic networks interact over multiple time-scales and through multiple means, resulting in cell metabolism with nonlinear behavior that is consequently context-dependent. In the following sections of this work, we then develop an optimization framework which can efficiently be used for the design of experiments to rewire cellular metabolism through metabolic engineering, or to otherwise understand the biological requirements of different metabolic phenomena. This framework is first applied to the Warburg effect, a century-old unsolved problem of rapid lactate production in proliferating cells to identify which enzymes may be altered to mitigate the lactate production. This framework in then applied to the problem of hepatic gluconeogenesis to study metabolic disease. As the expression of the enzymes specific to gluconeogenesis is not sufficient for glucose production, we explore what other requirements exist for the synthesis of glucose from different substrates. The next portion discusses the construction and optimization of a bioprocess model which includes metabolism, signaling, cell growth, and the reactor environment. This model is fit to a manufacturing-scale dataset to explore the origins of process variability and potential mitigation strategies. In the final segment of this thesis, we explore another aspect of protein therapeutics: product quality. A model of N-glycosylation is optimized in conjunction with successive rounds of experimentation with the goal of improving the galactose content on an antibody. This work highlights the benefits of feeding back experimental data to refine model parameters for better design and prediction of subsequent experiments.
  • Thumbnail Image
    Item
    Physical and Biochemical Strategies for Improving the Yield and Material Properties of Polyhydroxyalkanoate Biopolymers
    (2014-10) Barrett, John
    Polyhydroxyalkanoates (PHAs) are a diverse class of microbially synthesized biopolymers that are valued for their synthesis from renewable feedstocks and rapid biodegradation. As such, the commercial development of PHA plastics has potential to reduce the environmental impact of many, current polymers, which are non-biodegradable and rely on the use of unsustainable petroleum feedstocks. But despite the desirable traits of PHAs, the proliferation of these materials into commercial markets remains slow. Part of this is due to the greater cost of the renewable substrates used for PHA production versus the artificially low cost of petroleum-derived feedstocks. The other part of the challenge of promoting PHA utilization owes to the relatively limited diversity of physical and mechanical properties of PHAs that are currently available. As such, additional work is needed to develop new PHAs, which can satisfy the performance characteristics of many polymers already in use. Motivated by these two main challenges, 1.) to lower the production cost of PHAs and 2.) to broaden the range of unique PHAs materials available, the thesis presented herein details the development of new technologies to increase the substrate-to-product yield of PHA production and to expand the range of physical and mechanical properties of PHA-based materials. Chapter1 gives a broad introduction to polyhydroxyalkanoates and discuss various aspects of their production and application. Chapter 2 highlights the value of block-copolymers as a rich source for scientific discovery and technological development of PHAs. Methods are detailed in Chapter 3. The experimental results are presented in Chapters 4, 5, and 6, which focus generally upon: 4.) production of PHA copolymers in recombinant E. coli , 5.) fabrication and testing of PHA-graphene nanocomposites and 6.) production of PHA copolymers and block-copolymers directly from CO2 using Ralstonia eutropha. Finally, conclusions and prospects for future PHA research and development are given in Chapter 7. Taken all together, this thesis provides a solid foundation in theory and practice, for several technological approaches, which have great potential
  • Thumbnail Image
    Item
    Safety First: Making It a Reality for Biotechnology Products
    (Institute for Social, Economic and Ecological Sustainability, 2002-04-22) Institute for Social, Economic & Ecological Sustainability
    The Initiative is proposing a model for pro-active, industry-wide biosafety standards. This pro-active approach uses science and representative public deliberation to: anticipate and resolve biosafety issues as far upstream of commercialization as possible before developers seek regulatory approval of a product; stress public-private partnerships beyond government regulation; and produce biosafety policies that are financially and administratively feasible. Towards this end, the Initiative proposes moving forward to establish the standards and framework for an industry-wide safety program for genetic engineering (and other biotechnology) products, using a process that utilizes the principles of safety engineering that have been successful in other industries.