Ph.D. Biochemistry
The University of Calgary
Calgary, Alberta, Canada
B.Sc. Biochemistry
East China University of Science and Technology
Shanghai, China
RESEARCH, TEACHING, or OTHER INTERESTS
Biochemistry, Biotechnology, Bioengineering, Filtration and Separation
26
Scopus Publications
Scopus Publications
Hands-free from inoculation to harvest: Microbial fermentation with multivariate model to automate induction of recombinant protein expression Jennifer Reid, Andrew Szto, Airong Chen, Patricia Gomes, Craig Kearse, et al. Biotechnology Progress, 2025 Industrial fermentation continually improves biological process control for a wide range of microorganisms used in multi‐billion‐dollar industries including industrial enzymes, pharmaceuticals, foods, beverages, commodity chemicals, and bioenergy. In the case of recombinant protein production, batch and fed‐batch phases of fermentation are usually followed by an induction phase, where chemical or thermal induction initiates the expression of a target protein. Fed‐batch processes are usually automated, whereas “out‐of‐the‐box” distributed control systems (DCS) are often unable to define the threshold for induction and respond accordingly. The present study demonstrates the integration of optical density (OD) process analytical technology (PAT) and Lucullus®, a process information management system (PIMS), to enable end‐to‐end automated fermentation at bench and pilot scale. Data aggregated from tens of fermenter runs and hundreds of offline training measurements enabled the development of an accurate multivariate model to predict OD in real‐time. This eliminated the requirement to generate offline correlation models for each OD probe, allowed for model transfer, and incorporated additional predictor terms such as antifoam usage. Automating the induction phase enabled end‐to‐end fermentation, reducing labor and operational costs while increasing yield through higher reactor utilization within the same time period.
Exploration of alternative microfiltration modalities for the harvest and clarification of diverse recombinant proteins from high-density E. coli culture and lysate using hollow fibre, flat sheet cassette, and vibro membrane filtration technologies Jennifer Reid, Joyce Ni, Airong Chen, Patricia Gomes, Andrew Szto, et al. Journal of Industrial Microbiology and Biotechnology, 2025 Industrial bioprocess optimization has significantly increased the productivity of biomass and biologics in upstream production. Such process improvement in fermentation often translates to challenges in recovering intracellularly expressed recombinant proteins due to increased matrix complexity, resulting in a higher performance burden in midstream. Tangential flow filtration (TFF) is a popular industry standard for buffer exchange and protein separation from cellular debris. However, due to variations in the physicochemical properties of recombinant proteins, solutions for E. coli-based protein clarification remain challenging and often necessitate extensive exploration and process optimization. With growing options in filtration-based technologies, the identification of a near-universal clarification platform is desirable to accelerate bioprocess development overall. In this study, three TFF modalities, hollow fibre (HF), flat-sheet cassette (CAS), and vibro membrane filtration (VMF), were assessed in parallel to evaluate their clarification performance for three E. coli recombinant proteins with different biochemical properties. Reverse phase liquid chromatography data showed target protein recovery was uniformly higher for VMF than HF at equivalent loading. Cell density and lysate protein load were comparable for HF and VMF, and lower for CAS. These results support the choice of VMF and HF as easily optimized and operated TFF modalities for clarification of recombinant protein from complex crude bacterial matrix, where either can be efficiently performed with ease and minimum supervision. Both TFF applications were successfully demonstrated in primary cell harvest, cell wash and cell lysate clarification, for E. coli-based recombinant proteins. One-Sentence Summary High-density E. coli microfiltration and lysate clarification were tested for three diverse recombinant proteins, where hollow fibre and vibro membrane filtration outperformed flat sheet cassette in terms of process time, suspended solid loading, and target protein recovery.
Development of automated metabolite control using mid-infrared probe for bioprocesses and vaccine manufacturing Jennifer Reid, Manjit Haer, Airong Chen, Calvin Adams, Yu Chen Lin, et al. Journal of Industrial Microbiology and Biotechnology, 2024 Automation of metabolite control in fermenters is fundamental to develop vaccine manufacturing processes more quickly and robustly. We created an end-to-end process analytical technology and quality by design-focused process by replacing manual control of metabolites during the development of fed-batch bioprocesses with a system that is highly adaptable and automation-enabled. Mid-infrared spectroscopy with an attenuated total reflectance probe in-line, and simple linear regression using the Beer-Lambert Law, were developed to quantitate key metabolites (glucose and glutamate) from spectral data that measured complex media during fermentation. This data was digitally connected to a process information management system, to enable continuous control of feed pumps with proportional-integral-derivative controllers that maintained nutrient levels throughout fed-batch stirred-tank fermenter processes. Continuous metabolite data from mid-infrared spectra of cultures in stirred-tank reactors enabled feedback loops and control of the feed pumps in pharmaceutical development laboratories. This improved process control of nutrient levels by 20-fold and the drug substance yield by an order of magnitude. Furthermore, the method is adaptable to other systems and enables soft sensing, such as the consumption rate of metabolites. The ability to develop quantitative metabolite templates quickly and simply for changing bioprocesses was instrumental for project acceleration and heightened process control and automation. One-Sentence Summary Intelligent digital control systems using continuous in-line metabolite data enabled end-to-end automation of fed-batch processes in stirred-tank reactors.
Investigation into the misincorporation of norleucine into a recombinant protein vaccine candidate Joyce Ni, Meg Gao, Andrew James, Jiansheng Yao, Tao Yuan, et al. Journal of Industrial Microbiology and Biotechnology, 2015 A high level of norleucine misincorporation was detected in a recombinant methionine-rich protein vaccine candidate expressed in E. coli K12. An investigation was conducted to evaluate a simple remediation strategy to reduce norleucine misincorporation and to determine if the phenomenon was either (a) due to the depletion of methionine during fermentation, (b) a result of the cultivation environment, or (c) a strain-specific effect. While supplementation with exogenous methionine improved product quality, the undesirable biosynthesis of non-standard amino acids such as norleucine and norvaline persisted. In contrast, non-standard amino acid biosynthesis was quickly minimized upon selection of an appropriate fed-batch process control strategy, fermentation medium, and nutrient feed. By expressing the same protein in E. coli BL21(DE3), it was determined that the biosynthesis of norleucine and norvaline, and the misincorporation of norleucine into the protein were primarily attributed to the use of E. coli K12 as the host for protein expression.
Mapping the interface between calmodulin and MARCKS-related protein by fluorescence spectroscopy Andreas Ulrich, Arndt A. P. Schmitz, Thomas Braun, Tao Yuan, Hans J. Vogel, et al. Proceedings of the National Academy of Sciences of the United States of America, 2000 MARCKS-related protein (MRP) is a myristoylated protein kinase C substrate that binds calmodulin (CaM) with nanomolar affinity. To obtain structural information on this protein, we have engineered 10 tryptophan residues between positions 89 and 104 in the effector domain, a 24-residue-long amphipathic segment that mediates binding of MRP to CaM. We show that the effector domain is in a polar environment in free MRP, suggesting exposure to water, in agreement with a rod-shaped structure of the protein. The effector domain participates in the binding of MRP to CaM, as judged by the dramatic changes observed in the fluorescent properties of the mutants on complex formation. Intermolecular quenching of the fluorescence emission of the tryptophan residues in MRP by selenomethionine residues engineered in CaM reveals that the N-terminal side of the effector domain contacts the C-terminal domain of CaM, whereas the C-terminal side of the effector domain contacts the N-terminal domain of CaM. Finally, a comparison of the fluorescent properties of the myristoylated and unmyristoylated forms of a construct in which a tryptophan residue was introduced at position 4 close to the myristoylated N terminus of MRP suggests that the lipid moiety is also involved in the interaction of MRP with CaM.
Calmodulin target database Kyoko L. Yap, Justin Kim, Kevin Truong, Marc Sherman, Tao Yuan, et al. Journal of Structural and Functional Genomics, 2000
Interaction of calmodulin with its binding domain of rat cerebellar nitric oxide synthase: A multinuclear NMR study Journal of Biological Chemistry, 1995
