Studies on on-line bioreactor identification. IV. Utilization of pH measurements for product estimation

Bridging Offline Functional Model Carrying Aging-Specific Growth Rate Information and Recombinant Protein Expression: Entropic Extension of Akaike Information Criterion

This study presents a mathematical model of recombinant protein expression, including its development, selection, and fitting results based on seventy fed-batch cultivation experiments from two independent biopharmaceutical sites. To resolve the overfitting feature of the Akaike information criterion, we proposed an entropic extension, which behaves asymptotically like the classical criteria. Estimation of recombinant protein concentration was performed with pseudo-global optimization processes while processing offline recombinant protein concentration samples. We show that functional models including the average age of the cells and the specific growth at induction or the start of product biosynthesis are the best descriptors for datasets. We also proposed introducing a tuning coefficient that would force the modified Akaike information criterion to avoid overfitting when the designer requires fewer model parameters. We expect that a lower number of coefficients would allow the efficient maximization of target microbial products in the upstream section of contract development and manufacturing organization services in the future. Experimental model fitting was accomplished simultaneously for 46 experiments at the first site and 24 fed-batch experiments at the second site. Both locations contained 196 and 131 protein samples, thus giving a total of 327 target product concentration samples derived from the bioreactor medium.

Model-Based Monitoring of Biotechnological Processes—A Review

The monitoring of the main variables and parameters of biotechnological processes is of key importance for the research and control of the processes, especially in industrial installations, where there is a limited number of measurements. For this reason, many researchers are focusing their efforts on developing appropriate algorithms (software sensors (SS)) to provide reliable information on unmeasurable variables and parameters, based on the available on-line information. In the literature, a large number of developments related to this topic that concern data-based and model-based sensors are presented. Up-to-date reviews of data-driven SS for biotechnological processes have already been presented in the scientific literature. Hybrid software sensors as a combination between the abovementioned ones are under development. This gives a reason for the article to be focused on a review of model-based software sensors for biotechnological processes. The most applied model-based methods for monitoring the kinetics and state variables of these processes are analyzed and compared. The following software sensors are considered: Kalman filters, methods based on estimators and observers of a deterministic type, probability observers, high-gain observers, sliding mode observers, adaptive observers, etc. The comparison is made in terms of their stability and number of tuning parameters. Particular attention is paid to the approach of the general dynamic model. The main characteristics of the classic variant proposed by D. Dochain are summarized. Results related to the development of this approach are analyzed. A key point is the presentation of new formalizations of kinetics and the design of new algorithms for its estimation in cases of uncertainty. The efficiency and applicability of the considered software sensors are discussed.

On the use of the pH control reagent addition rate for fermentation monitoring

The linear relation between the pH control reagent addition rate, the net conversion rates of metabolites, the carbon dioxide mass transfer rate and the feed rates is developed and shown to have the same form for batch, fed-batch, and continuous reactors, regardless of the number of feeds. The magnitudes of various biological and solution chemistry effects on the pH control reagent addition rate are estimated to be negligible, facilitating the use of the pH control reagent addition rate as a straightforward indicator of primary metabolism. Finally, application of the linear relation, termed the abiotic proton balance, is discussed for a number of fermentation processes. (c) 1995 John Wiley & Sons, Inc.

Characterization of proton production and consumption associated with microbial metabolism

BACKGROUND

Production or consumption of protons in growth medium during microbial metabolism plays an important role in determining the pH of the environment. Such pH changes resulting from microbial metabolism may influence the geochemical speciation of many elements in subsurface environments. Protons produced or consumed during microbial growth were measured by determining the amount of acid or base added in a 5 L batch bioreactor equipped with pH control for different species including Escherichia coli, Geobacter sulfurreducens, and Geobacter metallireducens.

RESULTS

An in silico model was used to predict the proton secretion or consumption rates and the results were compared with the data. The data was found to confirm predictions of proton consumption during aerobic growth of E. coli with acetate as the carbon source. However, in contrast to proton consumption observed during aerobic growth of E. coli with acetate, proton secretion was observed during growth of Geobacter species with acetate as the donor and Fe(III) as the extracellular electron acceptor.

CONCLUSIONS

In this study, we have also shown that the final pH of the medium can be either acidic or basic depending on the choice of the electron acceptor for the same electron donor. In all cases, the in silico model could predict qualitatively the proton production/consumption rates obtained from the experimental data. Therefore, measurements of pH equivalents generated or consumed during growth can help characterize the microbial physiology further and can be valuable for optimizing practical applications such as microbial fuel cells, where growth associated pH changes can limit current generation rates.

Software sensors for fermentation processes

Four software sensors based on standard on-line data from fermentation processes and simple mathematical models were used to monitor a number of state variables in Escherichia coli fed-batch processes: the biomass concentration, the specific growth rate, the oxygen transfer capacity of the bioreactor, and the new R(O/S) sensor which is the ratio between oxygen and energy substrate consumption. The R(O/S) variable grows continuously in a fed-batch culture with constant glucose feed, which reflects the increasing maintenance demand at declining specific growth rate. The R(O/S) sensor also responded to rapid pH shift-downs reflecting the increasing demand for maintenance energy. It is suggested that this sensor may be used to monitor the extent of physiological stress that demands energy for survival.

Modeling aerobic carbon source degradation processes using titrimetric data and combined respirometric-titrimetric data: experimental data and model structure

Experimental data are presented that resulted from aerobic batch degradation experiments in activated sludge with simple carbon sources (acetate and dextrose) as substrates. Data collection was done using combined respirometric-titrimetric measurements. The respirometer consists of an open aerated vessel and a closed non-aerated respiration chamber for monitoring the oxygen uptake rate related to substrate degradation. The respirometer is combined with a titrimetric unit that keeps the pH of the activated sludge sample at a constant value by addition of acid and/or base. The experimental data clearly showed that the activated sludge bacteria react with consumption or production of protons during aerobic degradation of the two carbon sources under study. Thus, the cumulative amount of added acid and/or base could serve as a complementary information source on the degradation processes. For acetate, protons were consumed during aerobic degradation, whereas for dextrose protons were produced. For both carbon sources, a linear relationship was found between the amount of carbon source added and the amount of protons consumed (in case of acetate: 0.38 meq/mmol) or produced (in case of dextrose: 1.33 meq/mmol) during substrate degradation. A model taking into account substrate uptake, CO(2) production, and NH(3) uptake for biomass growth is proposed to describe the aerobic degradation of a C(x)H(y)O(z)-type carbon source. Theoretical evaluation of this model for reference parameters showed that the proton effect due to aerobic substrate degradation is a function of the pH of the liquid phase. The proposed model could describe the experimental observations with both carbon sources.

Automatic inducer addition and harvesting of recombinant Escherichia coli cultures based on indirect on-line estimation of biomass concentration and specific growth rate

This article describes a novel bioreactor configuration for production optimization of recombinant proteins in Escherichia coli. Inducer addition and harvesting are controlled on-line based on indirect estimation of biomass concentration and specific growth rate from addition of NaOH to maintain constant pH. When either a predetermined biomass concentration is reached or the cultures have obtained, a constant specific growth rate inducer is introduced automatically. The induction period is ended by automatic harvesting of the cultures either at a predetermined biomass concentration or when substrate (in this study glucose) is depleted, detected as an increase of pH, or dissolved oxygen tension. During harvesting, metabolic activities are quenched within 3 min by cooling of the cell suspension. The system has been used to optimize expression of glutathione S-transferase (GST) fusion protein of the ligand binding domain of mouse peroxisome proliferator-activated receptor, GST-PPARalpha LBD. Total yield of GST-PPARalpha LBD was independent of the time of inducer addition as long as the length of induction period corresponded to at least 0.25 cell divisions while the yield of soluble GST-PPARalpha LBD, the only active form, increased with the length of induction period. Highest yields were obtained when the inducer was added at low cell concentration as soon as constant specific growth rate was detected, resulting in induction periods corresponding to 3.4 +/- 0.4 cell divisions. The specific growth rate remained almost constant for one cell division after inducer addition, whereafter it decreased. No decrease of specific growth rate was observed when inducer was added in the lag-phase, and no soluble protein was produced. These results suggest that solely soluble GST-PPARalpha LBD acts as a growth inhibitor and that GST-PPARalpha LBD is expressed predominantly as inclusion bodies immediately after inducer addition whereas the proportion expressed as soluble protein is increased after 1 h of induction. Compared to the procedures, which are generally used for protein expression in the laboratory, this system is less labor intensive, it automatically provides recording of biomass concentration and specific growth rate, and it allows direct comparisons between expression of different proteins and performance of different constructs since the induction period is linked to growth.

Activated sludge monitoring with combined respirometric-titrimetric measurements

A short review of different respirometric methods is presented, and advantages and disadvantages of different principles are discussed. In this study a combined respirometric-titrimetric set-up was applied to monitor the degradation processes during batch experiments with activated sludge. The respirometer consists of an open aerated vessel and a closed non-aerated respiration chamber. It is operated with two oxygen probes resulting in two sources of information on the oxygen uptake rate; both collected at a high frequency. The respirometer is combined with a titrimetric unit that keeps the pH of the activated sludge sample at a constant value through the addition of acid and/or base. The cumulative amount of added acid and base serves as a complementary information source on the degradation processes. Interpretation of respirometric data resulting from validation experiments (additions of acetate and urea as ammonium source) showed that the set-up provided reliable data. Data interpretation was approached in two ways: (1) via a basic calculation procedure, in which the oxygen uptake rates were obtained by an oxygen mass balance over the respiration chamber, and (2) via a model-based procedure in which substrate transport was included for a more accurate data interpretation. Simulation examples showed that the presence of substrate transport in the model may be crucial for a correct data interpretation, since experimental conditions (e.g. low flow rate) and/or the biodegradation kinetic parameters (e.g. high Ks) may otherwise lead to data interpretation errors. Earlier studies already pointed out that titrimetric data can be related to nitrification, and this was also confirmed in this study. However, in addition, it was shown here for experiments with acetate that the amount of acid dosed was clearly related to the amount of acetate degraded. This indicates that the titrimetric data can be used to study the carbon source degradation. For the titrimetric data in this study, a model-based analysis was however only applied for the nitrification process. For an experiment with ammonium, it was illustrated that the estimation of biodegradation kinetics on a combined respirometric-titrimetric data set significantly improves confidence intervals of the parameters compared to the parameter estimation based on respirometric or titrimetric data separately.

Development of bioreaction engineering

In addition to summarizing the early investigations in bioreaction engineering, the present short review covers the development of the field in the last 50 years. A brief overview of the progress of the fundamentals is presented in the first part of this article and the key issues of bioreaction engineering are advanced in its second part.

Proton production and consumption pathways in yeast metabolism. A chemostat culture analysis

In this investigation, a method for the accurate quantitative determination of net proton production or consumption in biological cultures has been devised. Cells are cultured under constant pH conditions. The specific rate of proton production or consumption by the culture (qH+, mmol h-1 per g biomass) is proportional to the mmol of base or acid required to maintain constant pH per unit time, and this equivalence is independent of the buffering capacity of the culture medium. The above method has been applied to chemostat cultures of Candida utilis growing on glucose or glycerol as carbon source, and different nitrogen sources. The results indicate that the nitrogen assimilation pathway alone determines the value of qH+, and a fixed stoichiometric relationship between nitrogen uptake rate qN (meq h-1 per g biomass) and qH+ has been found for each nitrogen source employed. Thus, qH+/qN values of +1, 0 and -1 were found for ammonium ions, urea and nitrate respectively. Under oxidative metabolism, the contribution of carbon catabolism to the value of qH+ was undetectable. Sine qN may be related to growth and production of type 1 compounds in fermentation processes, the parameter qH+ was incorporated into a model of growth and energy metabolism in chemostat culture (Castrillo and Ugalde, Yeast 10, 185 - 197, 1994), resulting in adequate simulations of experimentally observed culture performance. Thus, it is suggested that qH+ may be employed as a simple and effective control parameter for biotechnological processes involving biomass-related products.

Uptake of ammonia by Saccharomyces cerevisiae carrying the plasmid pCYG4 related with ammonia assimilation

Batch culture experiments involving ammonia uptake in Saccharomyces cerevisiae BC55 pCYG4 have been carried out. This strain carries the plasmid pCYG4 that directs substantial overproduction of NADP-GDH, conferring an 11-fold increase in activity. The wild type cells had a specific growth rate greater than BC55 pCYG4. The ammonia uptake was practically the same until 15 h of growth. However, the amount of ammonia hydroxide added during growth (60 h) was two and half times greater in the BC55 pCYG4 than wild type cells. The results suggest that the presence of the plasmid pCYG4 can increase the amount of ammonia taken by the cells, but not the amount of biomass.