On-line measurement in biotechnology: Exploitation, objectives and benefits

Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology

Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.

Current good manufacturing practice in plant automation of biological production processes

The production of biologicals is subject to strict governmental regulations. These are drawn up in current good manufacturing practices (cGMP), a.o. by the U.S. Food and Drug Administration. To implement cGMP in a production facility, plant automation becomes an essential tool. For this purpose Manufacturing Execution Systems (MES) have been developed that control all operations inside a production facility. The introduction of these recipe-driven control systems that follow ISA S88 standards for batch processes has made it possible to implement cGMP regulations in the control strategy of biological production processes. Next to this, an MES offers additional features such as stock management, planning and routing tools, process-dependent control, implementation of software sensors and predictive models, application of historical data and on-line statistical techniques for trend analysis and detection of instrumentation failures. This paper focuses on the development of new production strategies in which cGMP guidelines are an essential part.

Time-structure of the yeast metabolism in vivo

All previous studies on the yeast metabolome have yielded a plethora of information on the components, function and organisation of low molecular mass and macromolecular components involved in the cellular metabolic network. Here we emphasise that an understanding of the global dynamics of the metabolome in vivo requires elucidation of the temporal dynamics of metabolic processes on many time-scales. We illustrate this using the 40 min oscillation in respiratory activity displayed in auto-synchronous continuously grown cultures of Saccharomyces cerevisiae, where respiration cycles between a phase of increased respiration (oxidative phase) and decreased respiration (reductive phase). Thereby an ultradian clock, i.e. a timekeeping device that runs through many cycles during one day, is involved in the co-ordination of the vast majority of events and processes in yeast. Through continuous online measurements, we first show that mitochondrial and redox physiology are intertwined to produce the temporal landscape on which cellular events occur. Next we look at the higher order processes of DNA duplication and mitochondrial structure to reveal that both events are choreographed during the respiratory cycles. Furthermore, spectral analysis using the discrete Fourier transformation of high-resolution (10 Hz) time-series of NAD(P)H confirms the existence of higher frequency components of biological origin and that these follow a scale-free architecture even in stable oscillating modes. A different signal-processing approach using discrete wavelet transformations (DWT) indicates that there is a significant contribution to the overall signal from ` ~5, ~ 10 and ~ 20-minutes cycles and the amplitudes of these cycles are phase-dependent. Further investigation (derivative of Gaussian continuous wavelet transformation) reveals that the observed 20-minutes cycles are actually confined to the reductive phase and consist of two ~15-minutes cycles. Moreover, the 5 and 10-minutes cycles are restricted to the oxidative phase of the cycle. The mitochondrial origin of these signals was confirmed by pulse-injection of the cytochrome c oxidase inhibitor H(2)S. We next discuss how these multi-oscillatory states can impinge on the apparently complex reactome (represented as a phase diagram of 1,650 chemical species that show oscillatory behaviour). We conclude that biological processes can be considerably more comprehensible when dynamic in vivo time-structure is taken into account.

Microbial biomass estimation

The development of a fully automated on-line monitoring and control system is very important in bioprocesses. One of the most important parameters in these processes is biomass. This review discusses different methods for biomass quantification. A general definition of biomass and biovolume are presented. Interesting concepts about active but not culturable cells considerations are included as well as concepts that must be taken into account when selecting biomass quantification technology. Chemical methods have had few applications in biomass measurement to date; however, bioluminescence can selectively enumerate viable cells. Photometric methods including fluorescence and scattered light measurements are presented. Reference methods including dry and wet weight, viable counts and direct counts are discussed, as well as the physical methods of flow cytometry, impedancimetric and dielectric techniques.

Instrumentation of biotechnological processes

Modern bioprocesses are monitored by on-line sensing devices mounted either in situ or externally. In addition to sensor probes, more and more analytical subsystems are being exploited to monitor the state of a bioprocess on-line and in real time. Some of these subsystems deliver signals that are useful for documentation only, other, less delayed systems generate signals useful for closed loop process control. Various conventional and non-conventional monitoring instruments are evaluated; their usefulness, benefits and associated pitfalls are discussed.

On-line metabolic pathway analysis based on metabolic signal flow diagram

In this work, an integrated modeling approach based on a metabolic signal flow diagram and cellular energetics was used to model the metabolic pathway analysis for the cultivation of yeast on glucose. This approach enables us to make a clear analysis of the flow direction of the carbon fluxes in the metabolic pathways as well as of the degree of activation of a particular pathway for the synthesis of biomaterials for cell growth. The analyses demonstrate that the main metabolic pathways of Saccharomyces cerevisiae change significantly during batch culture. Carbon flow direction is toward glycolysis to satisfy the increase of requirement for precursors and energy. The enzymatic activation of TCA cycle seems to always be at normal level, which may result in the overflow of ethanol due to its limited capacity. The advantage of this approach is that it adopts both virtues of the metabolic signal flow diagram and the simple network analysis method, focusing on the investigation of the flow directions of carbon fluxes and the degree of activation of a particular pathway or reaction loop. All of the variables used in the model equations were determined on-line; the information obtained from the calculated metabolic coefficients may result in a better understanding of cell physiology and help to evaluate the state of the cell culture process.

Rapid and quantitative analysis of recombinant protein expression using pyrolysis mass spectrometry and artificial neural networks: application to mammalian cytochrome b5 in Escherichia coli

Recombinant Escherichia coli clones encoding between 0 and 6 copies of the mammalian cytochrome b5 gene were subjected to pyrolysis mass spectrometry (PyMS). To deconvolute the pyrolysis mass spectra so as to obtain quantitative information on the amount of cytochrome b5 produced fully-interconnected feedforward artificial neural networks (ANNs) were studied. It was found that the combination of PyMS and ANNs could be used to predict the amount of cytochrome b5 expressed in E. coli. PyMS is a novel, convenient and rapid method for the screening and analysis of microbial and other cultures producing recombinant proteins.

A visual programming environment for bioprocess control

The paper introduces the use of a visual programming environment (LabVIEW) to program custom control functions for bioprocess research. The time taken for a bioprocess scientist to program new functions compared well with typical times expected for experienced programmers using conventional languages. Experienced LabVIEW programmers will develop applications significantly faster. The package described was flexible, easy to use and was ideally suited to developing new applications for control of bioprocesses. It was demonstrated with the development of a system to control specific growth rate in a fed-batch culture.

Fermentation monitoring and process control

During the past year, several papers describing the potential of new sensor devices for application in real bioprocesses have been published. Biosensors, optical sensors, and immunosensors are all gaining in importance. At present, the development of correct/adequate interfacing of biosensors to bioprocesses is the major limitation on progress. On the basis of new analytical data, a more precise modeling and control of fermentations can now be performed. Recent research efforts attest to the increasing importance of this area in biotechnology.

Evaluation of biomass

Evaluation of biomass concentration is an important problem encountered in many microbial and other bioprocesses. It determines the catalytic activity of the microbial cell in a given time. Various direct and indirect methods for the estimation of biomass have been developed using physical and biochemical techniques. Despite many promising classical methods available, the evaluation of microbial growth in bioprocesses may sometimes become laborious, impracticable and give erroneous values. Various methods for enumeration of organisms and determination of biomass, including recent developments in monitoring biomass concentration for the control of biotechnological processes, are discussed taking into the consideration their practical importance, usefulness and constraints in application.

Automatic bioprocess control. 4. A prototype batch of Saccharomyces cerevisiae

The recent investigations in our high performance bioreactors have shown that living cells can be extremely sensitive to physical-chemical environmental conditions and their changes. Consequently, the relationship bioreactor-living cell must thoroughly be investigated in order to discuss both: whether bioreactor characteristics are limiting/dominating during cultivation and to what extent controlled changes of the cellular environment can lead the cells to a desired physiological state. For these investigations, a generally accepted biological test organism would be helpful, of which the requirements and reactions under certain conditions are well known. Saccharomyces cerevisiae is a well known, very robust but nevertheless sensitive organism, eligible for this purpose. In this article a typical batch cultivation on glucose is presented, collected from approx. 300 experiments. Regarding metabolite production and consumption, seven different phases are distinguished on the basis of approx. 20 sensor signals and their metabolic background is discussed. Prerequisite, however, was an exhaustive knowledge upon extracellular conditions, a task which could successfully be fulfilled with the highly automated equipment introduced in the preceding articles of this series.

On-line measurement in biotechnology: Techniques

Bioprocesses are generally ill controlled. This is due to the fact that the measurement of relevant variables is difficult. Therefore, fundamental knowledge of metabolic interrelations is, at least in vivo, limited. In this article, some of the most important measurement techniques are reviewed in order to provide an evaluation of their current state. Emphasis is given to the underlying principles and on-line capability which allow to judge their importance and potential for exploitation resulting in well (maybe entirely) controlled bioprocesses in the future.