Development of a large-scale biocalorimeter to monitor and control bioprocesses

Novel Strategy for the Calorimetry-Based Control of Fed-Batch Cultivations of Saccharomyces cerevisiae

Typical controllers for fed-batch cultivations are based on the estimation and control of the specific growth rate in real time. Biocalorimetry allows one to measure a heat signal proportional to the substrate consumed by cells. The derivative of this heat signal is usually used to evaluate the specific growth rate, introducing noise to the resulting estimate. To avoid this, this study investigated a novel controller based directly on the heat signal. Time trajectories of the heat signal setpoint were modelled for different specific growth rates, and the controller was set to follow this dynamic setpoint. The developed controller successfully followed the setpoint during aerobic cultivations of Saccharomyces cerevisiae, preventing the Crabtree effect by maintaining low glucose concentrations. With this new method, fed-batch cultivations of S. cerevisiae could be reliably controlled at specific growth rates between 0.075 h−1 and 0.20 h−1, with average root mean square errors of 15 ± 3%.

Control of Specific Growth Rate in Fed-Batch Bioprocesses: Novel Controller Design for Improved Noise Management

Accurate control of the specific growth rate (µ) of microorganisms is dependent on the ability to quantify the evolution of biomass reliably in real time. Biomass concentration can be monitored online using various tools and methods, but the obtained signal is often very noisy and unstable, leading to inaccuracies in the estimation of μ. Furthermore, controlling the growth rate is challenging as the process evolves nonlinearly and is subject to unpredictable disturbances originating from the culture’s metabolism. In this work, a novel feedforward-feedback controller logic is presented to counter the problem of noise and oscillations in the control variable and to address the exponential growth dynamics more effectively. The controller was tested on fed-batch cultures of Kluyveromyces marxianus, during which μ was estimated in real time from online biomass concentration measurements obtained with dielectric spectroscopy. It is shown that the specific growth rate can be maintained at different setpoint values with an average root mean square control error of 23 ± 6%.

Application of heat compensation calorimetry to an E. coli fed-batch process

The application of biocalorimetry to fermentation processes offers advantageous insights, while being less complex compared to other, sophisticated PAT solutions. Although the general concept is established, calorimetric methods vary in detail. In this work, a special approach, called heat compensation calorimetry, was applied to an E. coli fed-batch process. Much work has been done for batch processes, proving the validity and accuracy of this calorimetric mode. However, the adaption of this strategy to fed-batch processes has some implications. In the first section of this work, batch fermentations were performed, comparing heat capacity calorimetry to the compensation mode. Both processes showed very good agreement by means of growth behavior. The heat related differences, e.g. temperature profiles, were obvious. In addition, the impact of the chosen mode on the calculation of in-process heat transfer coefficients was shown. Finally, a fed-batch fermentation was performed. The compensation mode was kept sufficiently, up to the point where the metabolic heat production accelerated strongly. Controller tuning was a neuralgic point, which would have needed further optimization under these conditions. Nevertheless, in the present work it was possible to realize a working compensation process while demonstrating critical aspects that must be considered when establishing such approach.

Measurement of heat transfer coefficients in stirred single-use bioreactors by the decay of hydrogen peroxide

Single-use bioreactors are barely described by means of their heat transfer characteristics, although some of their properties might affect this process. Steady-state methods that use external heat sources enable precise investigations. One option, commonly present in stirred, stainless steel tanks, is to use adjustable electrical heaters. An alternative are exothermic chemical reactions that offer a higher flexibility and scalability. Here, the catalytic decay of hydrogen peroxide was considered a possible reaction, because of the high reaction enthalpy of -98.2 kJ/mole and its uncritical reaction products. To establish the reaction, a proper catalyst needed to be determined upfront. Three candidates were screened: catalase, iron(III)-nitrate and manganese(IV)-oxide. Whilst catalase showed strong inactivation kinetic and general instability and iron(III)-nitrate solution has a pH of 2, it was decided to use manganese(IV)-oxide for the bioreactor studies. First, a comparison between electrical and chemical power input in a benchtop glass bioreactor of 3.5 L showed good agreement. Afterwards the method was transferred to a 50 L stirred single-use bioreactor. The deviation in the final results was acceptable. The heat transfer coefficient for the electrical method was 242 W/m²/K, while the value achieved with the chemical differed by less than 5%. Finally, experiments were carried out in a 200 L single-use bioreactor proving the applicability of the chemical power input at technical relevant scales.

Modeling of exo-inulinase biosynthesis by Kluyveromyces marxianus in fed-batch mode: correlating production kinetics and metabolic heat fluxes

A metabolic heat-based model was used for estimating the growth of Kluyveromyces marxianus, and the modified Luedeking-Piret kinetic model was used for describing the inulinase production kinetics. For the first time, a relationship was developed to relate inulinase production kinetics directly to metabolic heat generated, which corroborated well with the experimental data (with R ² values of above 0.9). It also demonstrated the predominantly growth-associated nature of the inulinase production with Luedeking-Piret parameters α and β, having values of 0.75 and 0.033, respectively, in the exponential feeding experiment. MATLAB was used for simulating the inulinase production kinetics which demonstrated the model's utility in performing real-time prediction of inulinase concentration with metabolic heat data as input. To validate the model predictions, a biocalorimetric (Bio RC1e) experiment for inulinase production by K. marxianus was performed. The inulinase concentration (IU/mL) values acquired from the model in were validated with the experimental values and the metabolic heat data. This modeling approach enabled the optimization, monitoring, and control of inulinase production process using the real-time biocalorimetric (Bio RC1e) data. Gas chromatography and mass spectrometry analysis were carried out to study the overflow metabolism taking place in K. marxianus inulinase production.

A soft sensor for bioprocess control based on sequential filtering of metabolic heat signals

Soft sensors are the combination of robust on-line sensor signals with mathematical models for deriving additional process information. Here, we apply this principle to a microbial recombinant protein production process in a bioreactor by exploiting bio-calorimetric methodology. Temperature sensor signals from the cooling system of the bioreactor were used for estimating the metabolic heat of the microbial culture and from that the specific growth rate and active biomass concentration were derived. By applying sequential digital signal filtering, the soft sensor was made more robust for industrial practice with cultures generating low metabolic heat in environments with high noise level. The estimated specific growth rate signal obtained from the three stage sequential filter allowed controlled feeding of substrate during the fed-batch phase of the production process. The biomass and growth rate estimates from the soft sensor were also compared with an alternative sensor probe and a capacitance on-line sensor, for the same variables. The comparison showed similar or better sensitivity and lower variability for the metabolic heat soft sensor suggesting that using permanent temperature sensors of a bioreactor is a realistic and inexpensive alternative for monitoring and control. However, both alternatives are easy to implement in a soft sensor, alone or in parallel.

Choline-based ionic liquids-enhanced biodegradation of azo dyes

Industrial wastewaters such as tannery and textile processing effluents are often characterized by a high content of dissolved organic dyes, resulting in large values of chemical and biological oxygen demand (COD and BOD) in the aquatic systems into which they are discharged. Such wastewater streams are of rapidly growing concern as a major environmental issue in developing countries. Hence there is a need to mitigate this challenge by effective approaches to degrade dye-contaminated wastewater. In this study, several choline-based salts originally developed for use as biocompatible hydrated ionic liquids (i.e., choline sacchrinate (CS), choline dihydrogen phosphate (CDP), choline lactate (CL), and choline tartarate (CT)) have been successfully employed as the cosubstrate with S. lentus in the biodegradation of an azo dye in aqueous solution. We also demonstrate that the azo dye has been degraded to less toxic components coupled with low biomass formation.

Automated measurement and monitoring of bioprocesses: key elements of the M(3)C strategy

The state-of-routine monitoring items established in the bioprocess industry as well as some important state-of-the-art methods are briefly described and the potential pitfalls discussed. Among those are physical and chemical variables such as temperature, pressure, weight, volume, mass and volumetric flow rates, pH, redox potential, gas partial pressures in the liquid and molar fractions in the gas phase, infrared spectral analysis of the liquid phase, and calorimetry over an entire reactor. Classical as well as new optical versions are addressed. Biomass and bio-activity monitoring (as opposed to "measurement") via turbidity, permittivity, in situ microscopy, and fluorescence are critically analyzed. Some new(er) instrumental analytical tools, interfaced to bioprocesses, are explained. Among those are chromatographic methods, mass spectrometry, flow and sequential injection analyses, field flow fractionation, capillary electrophoresis, and flow cytometry. This chapter surveys the principles of monitoring rather than compiling instruments.

Potentials and limitations of miniaturized calorimeters for bioprocess monitoring

In theory, heat production rates are very well suited for analysing and controlling bioprocesses on different scales from a few nanolitres up to many cubic metres. Any bioconversion is accompanied by a production (exothermic) or consumption (endothermic) of heat. The heat is tightly connected with the stoichiometry of the bioprocess via the law of Hess, and its rate is connected to the kinetics of the process. Heat signals provide real-time information of bioprocesses. The combination of heat measurements with respirometry is theoretically suited for the quantification of the coupling between catabolic and anabolic reactions. Heat measurements have also practical advantages. Unlike most other biochemical sensors, thermal transducers can be mounted in a protected way that prevents fouling, thereby minimizing response drifts. Finally, calorimetry works in optically opaque solutions and does not require labelling or reactants. It is surprising to see that despite all these advantages, calorimetry has rarely been applied to monitor and control bioprocesses with intact cells in the laboratory, industrial bioreactors or ecosystems. This review article analyses the reasons for this omission, discusses the additional information calorimetry can provide in comparison with respirometry and presents miniaturization as a potential way to overcome some inherent weaknesses of conventional calorimetry. It will be discussed for which sample types and scientific question miniaturized calorimeter can be advantageously applied. A few examples from different fields of microbiological and biotechnological research will illustrate the potentials and limitations of chip calorimetry. Finally, the future of chip calorimetry is addressed in an outlook.

Calorimetric control for high cell density cultivation of a recombinant Escherichia coli strain

In order to achieve maximum productivity of recombinant proteins in Escherichia coli high cell density cultivation (HCDC) strategies have been the subject of many studies. The aim of this work was the application of calorimetric methods to HCDC. The specific growth rate of a recombinant E. coli strain producing green fluorescent protein (GFP) was controlled during fed-batch cultivations by estimating the specific growth rate from the measured heat flow produced by the cells. For the cultivation a standard 30 l laboratory bioreactor was used, which was extended in such a way that heat balancing is possible. The feed rate was adjusted by an adaptive controller such that the specific growth rate was kept on the desired set point value. On the basis of experimental investigations with a recombinant E. coli strain using glucose as limiting C-source it was demonstrated that the specific growth rate can be kept on a given set point value and biomass concentrations of up to 120 g l(-1) can be obtained, reproducibly.

What heat is telling us about microbial conversions in nature and technology: from chip- to megacalorimetry

The exploitation of microorganisms in natural or technological systems calls for monitoring tools that reflect their metabolic activity in real time and, if necessary, are flexible enough for field application. The Gibbs energy dissipation of assimilated substrates or photons often in the form of heat is a general feature of life processes and thus, in principle, available to monitor and control microbial dynamics. Furthermore, the combination of measured heat fluxes with material fluxes allows the application of Hess' law to either prove expected growth stoichiometries and kinetics or identify and estimate unexpected side reactions. The combination of calorimetry with respirometry is theoretically suited for the quantification of the degree of coupling between catabolic and anabolic reactions. New calorimeter developments overcome the weaknesses of conventional devices, which hitherto limited the full exploitation of this powerful analytical tool. Calorimetric systems can be integrated easily into natural and technological systems of interest. They are potentially suited for high‐throughput measurements and are robust enough for field deployment. This review explains what information calorimetric analyses provide; it introduces newly emerging calorimetric techniques and it exemplifies the application of calorimetry in different fields of microbial research.

Detection of phase shifts in batch fermentation via statistical analysis of the online measurements: A case study with rifamycin B fermentation

Industrial production of antibiotics, biopharmaceuticals and enzymes is typically carried out via a batch or fed-batch fermentation process. These processes go through various phases based on sequential substrate uptake, growth and product formation, which require monitoring due to the potential batch-to-batch variability. The phase shifts can be identified directly by measuring the concentrations of substrates and products or by morphological examinations under microscope. However, such measurements are cumbersome to obtain. We present a method to identify phase transitions in batch fermentation using readily available online measurements. Our approach is based on Dynamic Principal Component Analysis (DPCA), a multivariate statistical approach that can model the dynamics of non-stationary processes. Phase-transitions in fermentation produce distinct patterns in the DPCA scores, which can be identified as singular points. We illustrate the application of the method to detect transitions such as the onset of exponential growth phase, substrate exhaustion and substrate switching for rifamycin B fermentation batches. Further, we analyze the loading vectors of DPCA model to illustrate the mechanism by which the statistical model accounts for process dynamics. The approach can be readily applied to other industrially important processes and may have implications in online monitoring of fermentation batches in a production facility.

Control of yeast fed-batch process through regulation of extracellular ethanol concentration

At high growth rates, the biomass yield of baker's yeast (Saccharomyces cerevisiae) decreases due to the production of ethanol. For this reason, it is standard industrial practice to use a fed-batch process whereby the specific growth rate, mu, is fixed at a level below the point of ethanol production, i.e., mucrit. Optimally, growth should be maintained at mucrit, but in practice, this is difficult because mucrit is dependent upon strain and culture conditions. In this work, growth was maintained at a point just above mucrit by regulating ethanol concentration in the bioreactor. The models used for control design are shown, as are the experimental results obtained when this strategy was implemented. This technique should be applicable to all microorganisms that exhibit an "overflow" type metabolism.

Bioreactor state estimation and control

Advanced control methods have been effectively employed for industrial chemical processing for decades. Only recently, however, have model-based strategies been implemented for biological processes. Some notable advances include the enhancement of metabolic flux models to describe the dynamic behavior observed in biochemical reactors. The combination of more than one type of model in a hybrid form was shown to perform well for bioprocess control applications.

Know-how and know-why in biochemical engineering

This contribution analyzes the position of biochemical engineering in general and bioprocess engineering particularly in the force fields between fundamental science and applications, and between academia and industry. By using culture technology as an example, it can be shown that bioprocess engineering has moved slowly but steadily from an empirical art concerned with mainly know-how to a science elucidating the know-why of culture behavior. Highly powerful monitoring tools enable biochemical engineers to understand and explain quantitatively the activity of cellular culture on a metabolic basis. Among these monitoring tools are not just semi-online analyses of culture broth by HPLC, GC and FIA, but, increasingly, also noninvasive methods such as midrange IR, Raman and capacitance spectroscopy, as well as online calorimetry. The detailed and quantitative insight into the metabolome and the fluxome that bioprocess engineers are establishing offers an unprecedented opportunity for building bridges between molecular biology and engineering biosciences. Thus, one of the major tasks of biochemical engineering sciences is not developing new know-how for industrial applications, but elucidating the know-why in biochemical engineering by conducting research on the underlying scientific fundamentals.

Back to basics: thermodynamics in biochemical engineering

Rational and efficient process development in chemical technology always makes heavy use of process analysis in terms of balances, kinetics, and thermodynamics. While the first two of these concepts have been extensively used in biotechnology, it appears that thermodynamics has received relatively little attention from biotechnologists. This state of affairs is one among several reasons why development and design of biotechnological processes is today mostly carried out in an essentially empirical fashion and why bioprocesses are often not as thoroughly optimized as many chemical processes. Since quite a large body of knowledge in the area of bio thermodynamics already existed in the early nineties, the Steering Committee of a European Science Foundation program on Process Integration in Biochemical Engineering identified a need to stimulate a more systematic use of thermodynamics in the area. To this effect, a bianual course for advanced graduate students and researchers was developed. The present contribution uses the course structure to provide an outline of the area and to characterize very briefly the achievements, the challenges, and the research needs in the various sub-topics.