Incorporating RNA-Seq transcriptomics into glycosylation-integrating metabolic network modelling kinetics: Multiomic Chinese hamster ovary (CHO) cell bioreactors.

In this work, the kinetic model based on the previously developed metabolic and glycan reaction networks of the ovarian cells of the Chinese hamster ovary (CHO) cell line was improved by the inclusion of transcriptomic data that took into account the values of the RPKM gene (Reads per Kilobase of Exon per Million Reads Mapped). The transcriptomic (RNASeq) data were obtained together with metabolic and glycan data from the literature, and the concentrations with RPKM values were collected at several points in time from two fed-batch processes. First, the fluxes were determined by regression analysis of the metabolic data, then these fluxes were corrected by using the fold change in gene expression as a measure of enzyme concentrations. Next, the corrected fluxes in the kinetic model were used to calculate the concentration profiles of the metabolites, and literature data were used to evaluate the predicted results of the model. Compared to other studies where the concentration profiles of CHO cell metabolites were described using a kinetic model without consideration of RNA-Seq data to correct the fluxes, this model is unique. The additional integration of transcriptomic data led to better predictions of metabolic concentrations in the fed-batch process, which is a significant improvement of the modelling technique used.

Dynamic multiscale metabolic network modeling of Chinese hamster ovary cell metabolism integrating N-linked glycosylation in industrial biopharmaceutical manufacturing.

Experimental and modeling work, described in this article, is focused on the metabolic pathway of Chinese hamster ovary (CHO) cells, which are the preferred expression system for monoclonal antibody protein production. CHO cells are one of the primary hosts for monoclonal antibodies production, which have extensive applications in multiple fields like biochemistry, biology and medicine. Here, an approach to explain cellular metabolism with in silico modeling of a microkinetic reaction network is presented and validated with unique experimental results. Experimental data of 25 different fed-batch bioprocesses included the variation of multiple process parameters, such as pH, agitation speed, oxygen and CO2 content, and dissolved oxygen. A total of 151 metabolites were involved in our proposed metabolic network, which consisted of 132 chemical reactions that describe the reaction pathways, and include 25 reactions describing N-glycosylation and additional reactions for the accumulation of the produced glycoforms. Additional eight reactions are considered for accumulation of the N-glycosylation products in the extracellular environment and one reaction to correlate cell degradation. The following pathways were considered: glycolysis, pentose phosphate pathway, nucleotide synthesis, tricarboxylic acid cycle, lipid synthesis, protein synthesis, biomass production, anaplerotic reactions, and membrane transport. With the applied modeling procedure, different operational scenarios and fed-batch techniques can be tested.

Protein A affinity chromatography of Chinese hamster ovary (CHO) cell culture broths containing biopharmaceutical monoclonal antibody (mAb): Experiments and mechanistic transport, binding and equilibrium modeling.

Protein A-based affinity chromatography is a highly-efficient separation method to capture, purify and isolate biosimilar monoclonal antibodies (mAb) - an important medical product of biopharmaceutical industrial manufacturing. It is considered the most expensive step in purification downstream operations; therefore, its performance optimization offers a great cost saving in the overall production expenditure. The biochemical mixture-separating specific interaction experiments with Chinese hamster ovary (CHO) cell culture harvest, containing glycosylated extracellular immunoglobulins (Ig), were made using five different state-of-the-art commercial resins. Packing breakthrough curves were recorded at an array of prolonged residence times. A mathematical simulation model was developed, applied and validated in combination with non-linear regression algorithms on bed effluent concentrations to determine the previously-unknown binding properties of stationary phase materials. Apart from the columns' differential partitioning, the whole external system was also integrated. It was confirmed that internal pore diffusion is the global rate-limiting resistance of the compound retention process. Immobilizing substrate characteristics, obtained in this engineering study, are indispensable for the scale-up of the periodic counter-current control with mechanistic load, elution and wash reduction. Furthermore, unit's volumetric flow screening measurements revealed dynamic effect correlation to eluate quality parameters, like the presence of aggregates, the host cell-related impurities at supernatant's extended feeding, and titre. Numerical sensitivity outputs demonstrated the impacts of fluidics (e.g. axial dispersion coefficient), thermodynamics (Langmuir adsorption) and mass transfer fluxes.

Multiple kinetic Langmuir modeling to predict the environmental behaviour of As(v) in soils.

A soil with a relatively high Fe content (2.82% [w/w]) was loaded for up to one year with As(v) by equilibrating it with a solution containing 1000 mg l(-1) As(v) at a soil mass-to-solution ratio of 0.1 kg l(-1). The incorporation of As(v) into the soil and its distribution over the soil phases were monitored by sampling at strategic time intervals using an operationally defined five-step sequential extraction procedure (Wenzel et al., Anal. Chim. Acta, 2001, 436, 309) and subsequent As measurement. A multiple kinetic Langmuir model was developed to retrieve the dynamic parameters (adsorption and desorption rate constants, capacities and Langmuir equilibrium constants) for each of the soil phases by numerical fitting of the experimental adsorption data to the model. Under the equilibration conditions used the adsorption rate constants for all five operationally defined soil phases were very similar but the desorption rate constants decreased by a factor of ca. 150 from soil phase 1 (non-specifically sorbed As) to 5 (residual phases). This implies that As(v) incorporation "deeper" into the soil leads to stronger binding which is associated with the Langmuir equilibrium constants (adsorption rate constants/desorption rate constants). Equilibration of the soil with As(v) was complete in ca. 10 days with As(v) predominantly bound to soil phase 2 (specifically sorbed As) and soil phase 3 (amorphous and poorly crystalline hydrous oxides). X-Ray absorption spectroscopy techniques revealed that these binding characteristics may be related to adsorption of As(v) on Si- and/or Al-containing structures and natural hydrous iron oxide (HFO) surface sites, respectively. Since the model is independent of the initial As(v) concentration in the solution and the soil mass-to-solution ratio, the behaviour of the thus characterized soil-As(v) system can be predicted for a range of conditions. Simulations showed that in an accidental As(v) spill the soil studied would actively scavenge As(v) by instantaneous adsorption onto all soil phases followed by redistribution of As(v) from weaker binding sites to stronger ones over time.

Assessment of physical leaching processes of some elements in soil upon ingestion by continuous leaching and modeling.

The physical processes controlling the desorption of some elements (B, Cd, Co, Mn, Ni, and Sr) from soils in a continuous leaching system representing the human stomach are investigated here by fitting experimental leaching data to a mathematical particle diffusion model. Soil samples (50 mg) from Cornwall, UK, contained in a flow-through extraction chamber (ca. 6.5 mL) were intimately contacted with artificial gastric solution at various flow rates (0.42-1.42 mL min(-1)) for up to ca. 4 h, followed by analysis of the fractions collected with inductively coupled plasma mass spectrometry (ICP-MS). The leaching profiles of the various elements were fitted to a mathematical model incorporating two mass transfer processes (liquid film diffusion and apparent solid phase diffusion) to determine the effective external mass transfer coefficient (beta) and the apparent intraparticle soil diffusion coefficient (D(a)). A system of partial differential equations was solved numerically with a finite difference discretization of the computational domain allowing the rate limiting physical desorption process(es) for each element to be determined. The (thermodynamic) driving force of the leaching process is defined by the distribution coefficient (K(d0)) between soil and leachant. Although the K(d0) values investigated are very similar (ca. 6-15 L kg(-1)) for the elements studied with the exception of B (ca. 2.7 L kg(-1)), the leaching profiles are very different due to diffusion-limited processes. The elements may be classified as limited by beta (B, Sr, and Cd), by D(a) (Co, and Mn) or by beta and D(a) (Ni). This results in quantifiable parameters for the liability of elements in soil upon ingestion which may be implemented in future risk assessment protocols.

Lipase-catalyzed synthesis of isoamyl acetate in an ionic liquid/n-heptane two-phase system at the microreactor scale.

A continuously operated psi-shaped microreactor was used for lipase-catalyzed synthesis of isoamyl acetate in the 1-butyl-3-methylpyridinium dicyanamide/n-heptane two-phase system. The chosen solvent system with dissolved Candida antarctica lipase B, which was attached to the ionic liquid/n-heptane interfacial area due to its amphiphilic properties, was shown to be highly efficient and enabled simultaneous esterification and product removal. At preliminarily selected conditions regarding the type of acyl donor, its molar ratio to alcohol and enzyme concentration, 48.4 g m(-3) s(-1) of isoamyl acetate was produced, which was almost three-fold better as compared to the intensely mixed batch process. This was mainly a consequence of efficient reaction-diffusion dynamics in the microchannel system, where the developed flow pattern comprising of intense emulsification provided a large interfacial area for the reaction and simultaneous product extraction.