Metabolic flux analysis of CHO cells in perfusion culture by metabolite balancing and 2D [13C, 1H] COSY NMR spectroscopy

The physiological state of CHO cells in perfusion culture was quantified by determining fluxes through the bioreaction network using ¹³C glucose and 2D-NMR spectroscopy. CHO cells were cultivated in a 2.5 L perfusion bioreactor with glucose and glutamine as the primary carbon and energy sources. The reactor was inoculated at a cell density of 8×10⁶ cells/mL and operated at ～10×10⁶ cells/mL using unlabeled glucose for the first 13 days. The second phase lasted 12 days and the medium consisted of 10% [U-¹³C]glucose, 40% labeled [1-¹³C]glucose with the balance unlabeled. After the culture attained isotopic steady state, biomass samples from the last 3 days of cultivation were considered representative and used for flux estimation. They were hydrolyzed and analyzed by 2D [¹³C, ¹H] COSY measurements using the heteronuclear single quantum correlation sequence with gradients for artifacts suppression. Metabolic fluxes were determined using the 13C-Flux software package by minimizing the residuals between the experimental and the simulated NMR data. Normalized residuals exhibited a Gaussian distribution indicating good model fit to experimental data. The glucose consumption rate was 5-fold higher than that of glutamine with 41% of glucose channeled through the pentose phosphate pathway. The fluxes at the pyruvate branch point were almost equally distributed between lactate and the TCA cycle (55% and 45%, respectively). The anaplerotic conversion of pyruvate to oxaloacetate by pyruvate carboxylase accounted for 10% of the pyruvate flux with the remaining 90% entering the TCA cycle through acetyl-CoA. The conversion of malate to pyruvate catalyzed by the malic enzyme was 70% higher than that for the anaplerotic reaction catalyzed by pyruvate carboxylase. Most amino acid catabolic and biosynthetic fluxes were significantly lower than the glycolytic and TCA cycle fluxes. Metabolic flux data from NMR analysis validated a simplified model where metabolite balancing was used for flux estimation. In this reduced flux space, estimates from these two methods were in good agreement. This simplified model can routinely be used in bioprocess development experiments to estimate metabolic fluxes with much reduced analytical investment. The high resolution flux information from 2D-NMR spectroscopy coupled with the capability to validate a simplified metabolite balancing based model for routine use make ¹³C-isotopomer analysis an attractive bioprocess development tool for mammalian cell cultures.     

Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set

Stem cell differentiation involves critical changes in gene expression. Identification of these should provide endpoints useful for optimizing stem cell propagation as well as potential clues about mechanisms governing stem cell maintenance. Here we describe the results of a new meta-analysis methodology applied to multiple gene expression datasets from three mouse embryonic stem cell (ESC) lines obtained at specific time points during the course of their differentiation into various lineages. We developed methods to identify genes with expression changes that correlated with the altered frequency of functionally defined, undifferentiated ESC in culture. In each dataset, we computed a novel statistical confidence measure for every gene which captured the certainty that a particular gene exhibited an expression pattern of interest within that dataset. This permitted a joint analysis of the datasets, despite the different experimental designs. Using a ranking scheme that favored genes exhibiting patterns of interest, we focused on the top 88 genes whose expression was consistently changed when ESC were induced to differentiate. Seven of these (103728_at, 8430410A17Rik, Klf2, Nr0b1, Sox2, Tcl1, and Zfp42) showed a rapid decrease in expression concurrent with a decrease in frequency of undifferentiated cells and remained predictive when evaluated in additional maintenance and differentiating protocols. Through a novel meta-analysis, this study identifies a small set of genes whose expression is useful for identifying changes in stem cell frequencies in cultures of mouse ESC. The methods and findings have broader applicability to understanding the regulation of self-renewal of other stem cell types.     

Controlled shear affinity filtration (CSAF): a new technology for integration of cell separation and protein isolation from mammalian cell cultures

Up-flow anaerobic sludge blanket (UASB) reactors are being used with increasing regularity all over the world, especially in India, for a variety of wastewater treatment operations. Consequently, there is a need to develop methodologies enabling one to determine UASB reactor performance, not only for designing more efficient UASB reactors but also for predicting the performance of existing reactors under various conditions of influent wastewater flows and characteristics. This work explores the feasibility of application of an artificial neural network-based model for simulating the performance of an existing UASB reactor. Accordingly, a neural network model was designed and trained to predict the steady-state performance of a UASB reactor treating high-strength (unrefined sugar based) wastewater. The model inputs were organic loading rate, hydraulic retention time, and influent bicarbonate alkalinity. The output variables were one or more of the following, effluent substrate concentration (Se), reactor bicarbonate alkalinity, reactor pH, reactor volatile fatty acid concentration, average gas production rate, and percent methane content of the gas. Training of the neural network model was achieved using a large amount of experimentally obtained reactor performance data from the reactor mentioned above as the training set. Training was followed by validation using independent sets of performance data obtained from the same UASB reactor. Subsequently, simulations were performed using the validated neural network model to determine the impact of changes in parameters like influent chemical oxygen demand (COD) concentration and hydraulic retention time on the reactor performance. Simulation results thus obtained were carefully analyzed based on qualitative understanding of UASB process and were found to provide important insights into key variables that were responsible for influencing the working of the UASB reactor under varying input conditions.     

Pancreatic cell immobilization in alginate beads produced by emulsion and internal gelation

Alginate has been used to protect transplanted pancreatic islets from immune rejection and as a matrix to increase the insulin content of islet progenitor cells. The throughput of alginate bead generation by the standard extrusion and external gelation method is limited by the rate of droplet formation from nozzles. Alginate bead generation by emulsion and internal gelation is a scaleable alternative that has been used with biological molecules and microbial cells, but not mammalian cells. We describe the novel adaptation of this process to mammalian cell immobilization. After optimization, the emulsion process yielded 90 ± 2% mouse insulinoma 6 (MIN6) cell survival, similar to the extrusion process. The MIN6 cells expanded at the same rate in both bead types to form pseudo‐islets with increased glucose stimulation index compared to cells in suspension. The emulsion process was suitable for primary pancreatic exocrine cell immobilization, leading to 67 ± 32 fold increased insulin expression after 10 days of immobilized culture. Due to the scaleability and broad availability of stirred mixers, the emulsion process represents an attractive option for laboratories that are not equipped with extrusion‐based cell encapsulators, as well as for the production of immobilized or encapsulated cellular therapeutics on a clinical scale. Biotechnol. Bioeng. 2011;108: 424–434. © 2010 Wiley Periodicals, Inc.     

Thermoreversible gel formulation containing sodium lauryl sulfate as a potential contraceptive device

The contraceptive properties of a gel formulation containing sodium lauryl sulfate were investigated in both in vitro and in vivo models. Results showed that sodium lauryl sulfate inhibited, in a concentration-dependent manner, the activity of sheep testicular hyaluronidase. Sodium lauryl sulfate also completely inhibited human sperm motility as evaluated by the 30-sec Sander-Cramer test. The acid-buffering capacity of gel formulations containing sodium lauryl sulfate increased with the molarity of the citrate buffers used for their preparations. Furthermore, experiments in which semen was mixed with undiluted gel formulations in different proportions confirmed their physiologically relevant buffering capacity. Intravaginal application of the gel formulation containing sodium lauryl sulfate to rabbits before their artificial insemination with freshly ejaculated semen completely prevented egg fertilization. The gel formulation containing sodium lauryl sulfate was fully compatible with nonlubricated latex condoms. Taken together, these results suggest that the gel formulation containing sodium lauryl sulfate could represent a potential candidate for use as a topical vaginal spermicidal formulation to provide fertility control in women.     

A kinetic study of the lactic acid fermentation. Batch process at controlled pH. Reprinted from Journal of Biochemical and Microbiological Technology Engineering Vol. I, No. 4. Pages 393-412 (1959)

Kinetic data are needed to develop basic understanding of fermentation processes and to permit rational design of continuous fermentation processes. The kinetics of the fermentation of glucose to lactic acid have been studied at six constant pH levels between 4. 5 and 6.0 by measuring the instantaneous rates of bacterial growth and of lactic acid formation throughout each fermentation. It was found that the instantaneous rate of acid formation dP/dt, should be related to the instantaneous rate of bacterial growth dN/dt, and to the bacterial density N, throughout a fermentation at a given pH, by the expression when the constants alpha and beta are determined by the pH of the fermentation.     

Sex‐allocation conflict and sexual selection throughout the lifespan of eusocial colonies

Models of sex‐allocation conflict are central to evolutionary biology but have mostly assumed static decisions, where resource allocation strategies are constant over colony lifespan. Here, we develop a model to study how the evolution of dynamic resource allocation strategies is affected by the queen‐worker conflict in annual eusocial insects. We demonstrate that the time of dispersal of sexuals affects the sex‐allocation ratio through sexual selection on males. Furthermore, our model provides three predictions that depart from established results of classic static allocation models. First, we find that the queen wins the sex‐allocation conflict, while the workers determine the maximum colony size and colony productivity. Second, male‐biased sex allocation and protandry evolve if sexuals disperse directly after eclosion. Third, when workers are more related to new queens, then the proportional investment into queens is expected to be lower, which results from the interacting effect of sexual selection (selecting for protandry) and sex‐allocation conflict (selecting for earlier switch to producing sexuals). Overall, we find that colony ontogeny crucially affects the outcome of sex‐allocation conflict because of the evolution of distinct colony growth phases, which decouples how queens and workers affect allocation decisions and can result in asymmetric control.     

Estimating cell specific oxygen uptake and carbon dioxide production rates for mammalian cells in perfusion culture

We present robust methods for online estimation of cell specific oxygen uptake and carbon dioxide production rates (q(O2) and q(CO2), respectively) during perfusion cultivation of mammalian cells. Perfusion system gas and liquid phase mass balance expressions for oxygen and carbon dioxide were used to estimate q(O2), q(CO2) and the respiratory quotient (RQ) for Chinese hamster ovary (CHO) cells in perfusion culture over 12 steady states with varying dissolved oxygen (DO), pH, and temperature set points. Under standard conditions (DO = 50%, pH = 6.8, T = 36.5°C), q(O2) and q(CO2) ranges were 5.14-5.77 and 5.31-6.36 pmol/cell day, respectively, resulting in RQ values of 0.98-1.14. Changes to DO had a slight reducing effect on respiration rates with q(O2) and q(CO2) values of 4.64 and 5.47, respectively, at DO = 20% and 4.57 and 5.12 at DO = 100%. Respiration rates were lower at low pH with q(O2) and q(CO2) values of 4.07 and 4.15 pmol/cell day at pH = 6.6 and 4.98 and 5.36 pmol/cell day at pH = 7. Temperature also impacted respiration rates with respective q(O2) and q(CO2) values of 3.97 and 4.02 pmol/cell day at 30.5°C and 5.53 and 6.25 pmol/cell day at 37.5°C. Despite these changes in q(O2) and q(CO2) values, the RQ values in this study ranged from 0.98 to 1.23 suggesting that RQ was close to unity. Real-time q(O2) and q(CO2) estimates obtained using the approach presented in this study provide additional quantitative information on cell physiology both during bioprocess development and commercial biotherapeutic manufacturing.