A detailed model and Monte Carlo simulation for predicting DIP genome length distribution in baculovirus infection of insect cells.

Baculoviruses have enormous potential for use as biopesticides to control insect pest populations without the adverse environmental effects posed by the widespread use of chemical pesticides. However, continuous baculovirus production is susceptible to DNA mutation and the subsequent production of defective interfering particles (DIPs). The amount of DIPs produced and their genome length distribution are of great interest not only for baculoviruses but for many other DNA and RNA viruses. In this study, we elucidate this aspect of virus replication using baculovirus as an example system and both experimental and modeling studies. The existing mathematical models for the virus replication process consider DIPs as a lumped quantity and do not consider the genome length distribution of the DIPs. In this study, a detailed population balance model for the cell-virus culture is presented, which predicts the genome length distribution of the DIP population along with their relative proportion. The model is simulated using the kinetic Monte Carlo algorithm, and the results agree well with the experimental results. Using this model, a practical strategy to maintain the DIP fraction to near to its maximum and minimum limits has been demonstrated.

Statistical modeling of cell-to-cell variability in viral infection during passaging in suspension cell culture: Application in Monte-Carlo simulation.

Packaging during the passaging of viruses in cell cultures yields various phenotypes and is regulated by viral protein expression in infected cells. Although such a packaging mechanism has a profound effect in controlling the virus yield, little is known about the underlying statistical models followed by virus packaging and protein expression among cells infected with the virus. A predictive framework combining identification of the probability density function (PDF) based on log-likelihood and using the PDF for Monte-Carlo simulations is developed. The Birnbaum-Saunders distribution was found to be consistent with all three-virus packaging levels, including nucleocapsids/occlusion-derived virus (ODV), ODVs/polyhedra, and polyhedra/cell for both wild-type and genetically modified AcMNPV. Next, it was demonstrated that PDF fitting could be used to compare two viruses having distinctly different genetic configurations. Finally, the identified PDF can be incorporated in RNA synthesis parameters for baculovirus infection to predict the cell-to-cell variability in protein expression using Monte-Carlo simulations. The proposed tool can be used for the estimation of uncertainty in the kinetic parameter and prediction of cell-to-cell variability for other biological systems.

A structured review of baculovirus infection process: integration of mathematical models and biomolecular information on cell-virus interaction.

The baculovirus expression vector system (BEVS) is an emerging tool for the production of recombinant proteins, vaccines and bio-pesticides. However, a system-level understanding of the complex infection process is important in realizing large-scale production at a lower cost. The entire baculovirus infection process is summarized as a combination of various modules and the existing mathematical models are discussed in light of these modules. This covers a systematic review of the present understanding of virus internalization, viral DNA replication, protein expression, budded virus (BV) and occlusion-derived virus (ODV) formation, few polyhedral (FP) and defective interfering particle (DIP) mutant formation, cell cycle modification and apoptosis during the viral infection process. The corresponding theoretical models are also included. Current knowledge regarding the molecular biology of the baculovirus/insect cell system is integrated with population balance and mass action kinetics models. Furthermore, the key steps for simulating cell and virus densities and their underlying features are discussed. This review may facilitate the further development and refinement of mathematical models, thereby providing the basis for enhanced control and optimization of bioreactor operation.

Useful Tips, Widely Used Techniques, and Quantifying Cell Metabolic Behavior.

The insect cell culture/baculovirus system has three primary applications: (1) recombinant protein synthesis, (2) biopesticide synthesis, and (3) as a model system (e.g., for studying apoptosis). The fundamental techniques involved in these applications are described throughout this book. In this chapter the most widely used techniques are summarized and the reader is directed to detailed information found elsewhere in this book. Furthermore, many useful tips and my personal preferences that are rarely published are discussed in this chapter along with quantitative methods to characterize cell growth, baculovirus infection, and metabolism.

Effect of CO2 on uninfected Sf-9 cell growth and metabolism.

A problem in the mass production of recombinant proteins and biopesticides using insect cell culture is CO2 accumulation. This research investigated the effect of elevated CO2 concentration on insect cell growth and metabolism. Spodoptera frugiperda Sf-9 insect cells were grown at 20% air saturation, 27(°) C, and a pH of 6.2. The cells were exposed to a constant CO2 concentration by purging the medium with CO2 and the headspace with air. The population doubling time (PDT) of Sf-9 cells increased with increasing CO2 concentration. Specifically, the PDT for 0-37, 73, 147, 183, and 220 mm Hg CO2 concentrations were 23.2 ± 6.7, 32.4 ± 7.2, 38.1 ± 13.3, 42.9 ± 5.4, and 69.3 ± 35.9 h (n = 3 or 4, 95% confidence level), respectively. The viability of cells in all experiments was above 90%, i.e., while increased CO2 concentrations inhibited cell growth, it did not affect cell viability. The osmolality for all bioreactor experiments was observed to be 300-360 mOsm/kg, a range that is known to have a negligible effect on insect cell culture. Elevated CO2 concentration did not significantly alter the cell specific glucose consumption rate (2.5-3.2 × 10(-17) mol/cell s), but slightly increased the specific lactate production rate from -3.0 × 10(-19) to 10.2 × 10(-19) mol/cell s. Oxidative stress did not contribute to CO2 inhibition in uninfected Sf-9 cells as no significant increase in the levels of lipid hydroperoxide and protein carbonyl concentrations was discovered at elevated CO2 concentration. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:465-469, 2016.

On-line near infrared bioreactor monitoring of cell density and concentrations of glucose and lactate during insect cell cultivation.

Near infrared spectroscopy is demonstrated as a suitable method for monitoring real time cell density and concentrations of glucose and lactate during insect cell cultivation. The utility of this approach is illustrated during the cultivation of Trichoplusia ni BTI-Tn-5B1-4 insect cells in a stirred-tank bioreactor. On-line near infrared measurements are made by passing unaltered culture medium through an autoclavable near infrared flow-through sample cell during the cultivation process. Single-beam near infrared spectra were collected over the combination spectral range (5000-4000cm(-1)) through a 1.5mm path length sample. Cell density calibration model was established by uni-variable linear regressions with measured mean absorbance values of on-line spectra collected during a cultivation run. Calibration models are generated for glucose and lactate by regression analysis of both off line and on line spectra collected during a series of pre-measurement cultivation runs. Analyte-specific calibration models are generated by using a combination of spectra from both natural, unaltered samples and samples spiked with known levels of glucose and lactate. Spiked samples are used to destroy concentration correlations between solutes, thereby enhancing the selectivity of the calibration models. Absorbance spectra are used to build partial least squares calibration models for glucose and lactate. The calibration model for cell density corresponds to a univariate linear regression calibration model based on the mean absorbance between 4750 and 4250cm(-1). The standard errors of prediction are 1.54mM, 0.83mM, and 0.38×10(6)cells/mL for the glucose, lactate, and cell density models, respectively.

Production of baculovirus defective interfering particles during serial passage is delayed by removing transposon target sites in fp25k.

Accumulation of baculovirus defective interfering particle (DIP) and few polyhedra (FP) mutants is a major limitation to continuous large-scale baculovirus production in insect-cell culture. Although overcoming these mutations would result in a cheaper platform for producing baculovirus biopesticides, little is known regarding the mechanism of FP and DIP formation. This issue was addressed by comparing DIP production of wild-type (WT) Autographa californica multiple nucleopolyhedrovirus (AcMNPV) with that of a recombinant AcMNPV (denoted Ac-FPm) containing a modified fp25k gene with altered transposon insertion sites that prevented transposon-mediated production of the FP phenotype. In addition to a reduction in the incidence of the FP phenotype, DIP formation was delayed on passaging of Ac-FPm compared with WT AcMNPV. Specifically, the yield of DIP DNA in Ac-FPm was significantly lower than in WT AcMNPV up to passage 16, thereby demonstrating that modifying the transposon insertion sites increases the genomic stability of AcMNPV. A critical component of this investigation was the optimization of a systematic method based on the use of pulsed-field gel electrophoresis (PFGE) to characterize extracellular virus DNA. Specifically, PFGE was used to detect defective genomes, determine defective genome sizes and quantify the amount of defective genome within a heterogeneous genome population of passaged virus.

Removal of transposon target sites from the Autographa californica multiple nucleopolyhedrovirus fp25k gene delays, but does not prevent, accumulation of the few polyhedra phenotype.

Low-cost, large-scale production of the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) using continuous insect cell culture is seriously hindered by the accumulation of AcMNPV mutants. Specifically, few-polyhedra (FP) mutants, with a reduced yield of occluded virus (polyhedra) and decreased infectivity, usually accumulate upon passaging in cell culture. FP mutations result from transposon insertions in the baculovirus fp25k gene, leading to significantly reduced levels of FP25K protein synthesis. This study evaluated the effects of removing the transposon insertion sites from the wild-type baculovirus fp25k gene; the mutated virus was denoted Ac-FPm. Specifically, this study involved a detailed comparison of wild-type (WT) AcMNPV and Ac-FPm with regard to the proportion of cells having polyhedra, number of polyhedra per cell, the fraction of empty polyhedra, number of occlusion-derived viruses per polyhedron, number of nucleocapsids in the nuclei, FP25K protein synthesis and genetic analysis of the fp25k gene. Removal of TTAA transposon insertion sites from the fp25k gene stabilized FP25K protein synthesis and delayed the appearance of the FP phenotype from passage 5 to passage 10. Electron micrographs revealed that more virus particles were found inside the nuclei of cells infected with Ac-FPm than in the nuclei of cells infected with WT AcMNPV (at passage 10). Abnormalities, however, were observed in envelopment of nucleocapsids and virus particle occlusion within Ac-FPm polyhedra. Thus, the FP phenotype appeared in spite of continued FP25K protein synthesis, suggesting that mechanisms other than fp25k gene disruption can lead to the FP phenotype.

Useful tips, widely used techniques, and quantifying cell metabolic behavior.

The insect cell culture/baculovirus system has three primary applications: (1) recombinant protein synthesis, (2) biopesticide synthesis, and (3) as a model system (e.g., for studying apoptosis). The fundamental techniques involved in these applications are described throughout this book. In this chapter, the most widely techniques are summarized and the reader is directed to detailed information found elsewhere in this book. Furthermore, many useful tips and the author's personal preferences that are rarely published are discussed in this chapter along with quantitative methods to characterize cell growth, baculovirus infection, and metabolism.

Metabolic alteration of the N-glycan structure of a protein from patients with a heterozygous protein deficiency.

Glycosylation, an important post-translation modification, could alter biological activity or influence the clearance rates of glycoproteins. We report here the first example of a heterozygous protein deficiency leading to metabolic alteration of N-glycan structures in residual secreted protein. Analysis of C1 esterase inhibitor (C1INH) glycans from normal individuals and patients with hereditary deficiency of C1INH demonstrated identical O-glycan structures but the N-glycans of patients with a heterozygous genetic deficiency were small, highly charged and lacked sialidase releasable N-acetylneuraminic acid. Structural studies indicate that the charge character of these aberrant N-glycan structures may result from the presence of mannose-6-phosphate residues. These residues might facilitate secretion of C1INH through an alternate lysosomal pathway, possibly serving as a compensatory mechanism to enhance plasma levels of C1INH in these deficient patients.

Effect of expression of manganese superoxide dismutase in baculovirus-infected insect cells.

It has previously been demonstrated that baculovirus infection of the Spodoptera frugiperda Sf-9 (Sf-9) and Trichoplusia ni BTI-Tn-5B1-4 (Tn-5B1-4) insect cell lines leads to oxidative stress as measured by protein and membrane lipid oxidation and that this oxidative damage contributes to cell death. As a result of these findings, it was hypothesized that baculovirus infection stimulates superoxide radical (O(2)(.-)) synthesis in the mitochondria and that the resulting O(2)(.-) accumulation overwhelms the cells' antioxidant defenses. We investigated the ability of manganese superoxide dismutase (MnSOD) expression (which reduces O(2)(.-) to H(2)O(2) to overcome the oxidative damage caused by baculovirus infection. It was found that MnSOD expression significantly reduced oxidative damage in baculovirus-infected Tn-5B1-4 cells but had no significant effect on oxidative damage in baculovirus-infected Sf-9 cells. The results are consistent with the hypothesis that O(2)(.-) accumulation in the mitochondria is at least partially responsible for the oxidative damage resulting from the baculovirus infection of insect cells.

Pure component selectivity analysis of multivariate calibration models from near-infrared spectra.

A novel procedure is proposed as a method to characterize the chemical basis of selectivity for multivariate calibration models. This procedure involves submitting pure component spectra of both the target analyte and suspected interferences to the calibration model in question. The resulting model output is analyzed and interpreted in terms of the relative contribution of each component to the predicted analyte concentration. The utility of this method is illustrated by an analysis of calibration models for glucose, sucrose, and maltose. Near-infrared spectra are collected over the 5000-4000-cm(-)(1) spectral range for a set of ternary mixtures of these sugars. Partial least-squares (PLS) calibration models are generated for each component, and these models provide selective responses for the targeted analytes with standard errors of prediction ranging from 0.2 to 0.7 mM over the concentration range of 0.5-50 mM. The concept of the proposed pure component selectivity analysis is illustrated with these models. Results indicate that the net analyte signal is solely responsible for the selectivity of each individual model. Despite strong spectral overlap for these simple carbohydrates, calibration models based on the PLS algorithm provide sufficient selectivity to distinguish these commonly used sugars. The proposed procedure demonstrates conclusively that no component of the sucrose or maltose spectrum contributes to the selective measurement of glucose. Analogous conclusions are possible for the sucrose and maltose calibration models.

On-line monitoring of human prostate cancer cells in a perfusion rotating wall vessel by near-infrared spectroscopy.

PC-3 human prostate cancer cells have been cultivated in a rotating wall vessel in which glucose, lactate, and glutamine profiles were monitored noninvasively and in real time by near-infrared (NIR) spectroscopy. The calibration models were based on off-line spectra from tissue culture experiments described previously (Rhiel et al., Biotechnol Bioeng 77:73-82). Monitoring performance was improved by Fourier filtering of the spectra and initial off-set adjustment. The resulting standard errors of predictions were 0.95, 0.74, and 0.39 mM for glucose, lactate, and glutamine, respectively. The concentration of ammonia could not be accurately measured from the same spectra. In addition, metabolite uptake and production rates were determined for PC-3 prostate cancer cells during exponential growth in batch-mode cultivation. Cells grew with a doubling time of 21 h and consumed glucose and glutamine at rates of 6.8 and 1.8 x 10(-17) mol/cell.s, respectively. This resulted in lactate and ammonia production rates of 11.9 and 1.3 x 10(-17) mol/cell.s, respectively. Compared with other monitoring technologies, this technology has many advantages for spaceflights and stand-alone units; for instance, calibration can be performed at one time and then applied in a reagentless, low-maintenance way at a later time. The resulting concentration information can be incorporated into closed-loop control schemes, thereby leading to better in vitro models of in vivo behavior.

Monitoring and controlling the dissolved oxygen (DO) concentration within the high aspect ratio vessel (HARV).

A probe-type oxygen sensor was developed utilizing a radioluminescent (RL)-based light source and a ruthenium-based sensing chemistry for monitoring the dissolved oxygen (DO) concentration in a modified version of the NASA-designed high aspect ratio vessel (HARV), a batch rotating wall vessel. This sensor provided the means to monitor the DO concentration in the HARV without influencing the flow pattern, thereby retaining the low shear HARV environment conducive to the formation of 3-dimensional cell aggregates. This sensor lost significant signal as a result of exposure to the first three autoclave cycles, but only minimal change in signal was observed following exposure to subsequent autoclave cycles. A new calibration model requiring only one fitted parameter was developed that accurately fit data over the entire range from 0% to 100% oxygen saturation. The ability for DO concentration control within the vessel was demonstrated by using this sensor to monitor the DO concentration inside the HARV.

Evaluating prostate cancer cell culturing methods: a comparison of cell morphologies and metabolic activity.

LNCaP prostate cancer cells were grown under four unique cultivation conditions. Two types of bioreactor systems were used to observe the influence of low-shear culture conditions allowing for three-dimensional growth: a) a perfusion rotating wall vessel (RWV) bioreactor; and b) a high aspect ratio vessel (HARV) RWV bioreactor, with periodic medium exchanges (fed-batch). In addition, two growth methods utilized tissue culture flasks (TCFs): a) unaltered or conventional TCFs; and b) poly(2-hydroxyethyl methacrylate) [poly(HEMA)] coated TCFs, to inhibit cell attachment. Comparisons were drawn based on qualitative observation of cell morphology and quantitative metabolic data. Similar cellular metabolism was demonstrated for cells grown under each condition. The degree of aggregation, however, varies considerably. Spherical shaped aggregates with diameters of 1 to 3 mm were produced when cells were grown within the perfusion-RWV bioreactor. All other growth conditions produced irregular shaped aggregates of various sizes. Quantitative results demonstrated the expected glucose utilization concomitant with lactate accumulation. Immunohistochemical evaluations were unremarkable for all four cultivation conditions. Results demonstrate that use of the perfusion-RWV bioreactor is advantageous in obtaining spherical aggregates, while grown in a controlled environment.

The response of virally infected insect cells to dissolved oxygen concentration: recombinant protein production and oxidative damage.

The effects of dissolved oxygen (DO) concentration on virally infected insect cells were investigated in 3-L bioreactor culture. Specifically, cultures of Spodoptera frugiperda Sf-9 (Sf-9) and Trichoplusia ni BTI-Tn-5B1-4 (Tn-5B1-4) were infected with Autographa californica multiple nucleopolyhedrovirus expressing secreted alkaline phosphatase (SEAP). Following infection at a DO concentration of 50% air saturation, the DO concentration was adjusted to a final value of either 190%, 50%, or 10% air saturation. Recombinant SEAP production, cell viability, protein carbonyl content, and thiobarbituric acid reactive substances (TBARS) content were monitored. The increases in protein carbonyl and TBARS contents are taken to be indicators of protein oxidation and lipid oxidation, respectively. DO concentration was found to have no noticeable effect on SEAP production or cell viability decline in the Sf-9 cell line. In the Tn-5B1-4 cell line, cells displayed an increased peak SEAP production rate for 190% air saturation and displayed an increased rate of viability decline at increased DO concentration. Protein carbonyl content showed no significant increase in the Sf-9 cell line by 72 h postinfection (pi) at any DO concentration but showed a twofold increase at 10% and 50% DO concentration and a threefold increase at 190% DO concentration by 72 h pi in Tn-5B1-4 cells. TBARS content was found to increase by approximately 50% in Sf-9 cells and by approximately twofold in Tn-5B1-4 cells by 72 h pi with no clear relationship to DO concentration. It is hypothesized that oxygen uptake changes due to the viral infection process may bear a relation to the observed increases in protein and lipid oxidation and that lipid oxidation may play an important role in the death of virally infected insect cells.

Enzyme kinetics and glycan structural characterization of secreted alkaline phosphatase prepared using the baculovirus expression vector system.

Secreted human alkaline phosphatase (SEAP, a model protein containing a single N-glycan chain) was expressed in Spodoptera frugiperda Sf-9 (Sf-9) and Trichoplusia ni BTI-Tn-5B1-4 (Tn-5B1-4) insect cell lines infected with recombinant Autographa californica multiple nuclear polyhedrovirus expressing SEAP under control of the polyhedrin promoter. SDS-PAGE showed that both systems expressed fairly pure rSEAP products. The rSEAP expression level was 7.0 U/mL in Tn-5B1-4, higher than the 4.1 U/mL produced by Sf-9. Kinetic analysis showed that Vmax and Km of human placental SEAP were approx 10-fold higher than that of rSEAP, whereas the Vmax and Km of rSEAP prepared using both insect cell lines were comparable. To characterize the recombinant SEAP (rSEAP) glycosylation, the purified rSEAP was digested with PNGase F to release the N-glycan chains. Glycan analysis showed the presence of oligomannose-type N-linked glycans (i.e., Man(2-8)GlcNAc2 and FucMan(3 or 4)GlcNAc2) in rSEAP from Sf9 and Tn-5B1-4 cell lines. The proportions of these oligosaccharide structures were different in the two cell lines. Man4GlcNAc2 and FucMan4GlcNAc2 were the major rSEAP N-glycans produced in Sf-9 cells, while Man2GlcNAc2 was the major rSEAP N-glycan produced in Tn-5B1-4 cells.

Nondestructive near-infrared spectroscopic measurement of multiple analytes in undiluted samples of serum-based cell culture media.

An adaptive calibration procedure is used to build selective multivariate calibration models for the measurement of glucose, lactate, glutamine, and ammonia in undiluted serum-based cell culture media. This adaptive procedure removes metabolism-induced covariance between these analytes in a series of calibration samples collected during the cultivation of PC-3 human prostate cancer cells. Partial least-squares calibration models are generated from single-beam near-infrared (NIR) spectra collected over the 4800- to 4200-cm(-1) combination spectral range. Calibration models were generated with both the full spectral range and optimized spectral ranges. In both cases, the number of model factors was optimized and model validity was determined by comparing analyte concentrations predicted from a series of independent and unaltered samples that were obtained during a subsequent cultivation of the PC-3 cells. Similar analytical performance was achieved with fewer model factors when the optimized spectral range was used. The lowest standard errors of prediction were 0.82, 0.94, 0.55, and 0.76 mM for glucose, lactate, glutamine, and ammonia, respectively. Different spectral ranges were optimal for each analyte and the optimized spectral range coincided with the distinguishing spectral features of the analyte. The results of this study demonstrate that NIR spectroscopy can be used effectively in the off-line measurement of important nutrients (glucose and glutamine) and byproducts (lactate and ammonia) in a serum-based animal cell culture medium.

The effect of dissolved oxygen (DO) concentration on the glycosylation of recombinant protein produced by the insect cell-baculovirus expression system.

The effect of dissolved oxygen concentration on human secreted alkaline phosphatase (SEAP) glycosylation by the insect cell-baculovirus expression system was investigated in a well-controlled bioreactor. Oligomannose-type N-linked glycans (i.e., Man2 to Man6 and Man3F) were present in SEAP produced by Spodoptera frusiperda Sf-9 (Sf-9) and Trichoplusia ni BTI-Tn-5B1-4 (Tn-5B1-4) insect cell lines. The relative amounts of the most highly processed glycans (i.e., Man3F and Man2 in the SEAP from Sf-9 and Tn-5B1-4 cells, respectively) were significantly higher at 50% of air saturation than at either 10% or 190% of air saturation. That is, glycan processing was inhibited at both low and high dissolved oxygen concentrations.