On-line bioprocess monitoring – an academic discipline or an industrial tool?

Quantitative Flow Cytometry to Understand Population Heterogeneity in Response to Changes in Substrate Availability in Escherichia coli and Saccharomyces cerevisiae Chemostats

Microbial cells in bioprocesses are usually described with averaged parameters. But in fact, single cells within populations vary greatly in characteristics such as stress resistance, especially in response to carbon source gradients. Our aim was to introduce tools to quantify population heterogeneity in bioprocesses using a combination of reporter strains, flow cytometry, and easily comprehensible parameters. We calculated mean, mode, peak width, and coefficient of variance to describe distribution characteristics and temporal shifts in fluorescence intensity. The skewness and the slope of cumulative distribution function plots illustrated differences in distribution shape. These parameters are person-independent and precise. We demonstrated this by quantifying growth-related population heterogeneity of Saccharomyces cerevisiae and Escherichia coli reporter strains in steady-state of aerobic glucose-limited chemostat cultures at different dilution rates and in response to glucose pulses. Generally, slow-growing cells showed stronger responses to glucose excess than fast-growing cells. Cell robustness, measured as membrane integrity after exposure to freeze-thaw treatment, of fast-growing cells was strongly affected in subpopulations of low membrane robustness. Glucose pulses protected subpopulations of fast-growing but not slower-growing yeast cells against membrane damage. Our parameters could successfully describe population heterogeneity, thereby revealing physiological characteristics that might have been overlooked during traditional averaged analysis.

The effect of acetate on population heterogeneity in different cellular characteristics of Escherichia coli in aerobic batch cultures

Acetate as the major by-product in industrial-scale bioprocesses with Escherichia coli is found to decrease process efficiency as well as to be toxic to cells, which has several effects like a significant induction of cellular stress responses. However, the underlying phenomena are poorly explored. Therefore, we studied time-resolved population heterogeneity of the E. coli growth reporter strain MG1655/pGS20PrrnBGFPAAV expressing destabilized green fluorescent protein during batch growth on acetate and glucose as sole carbon sources. Additionally, we applied five fluorescent stains targeting different cellular properties (viability as well as metabolic and respiratory activity). Quantitative analysis of flow cytometry data verified that bacterial populations in the bioreactor are more heterogeneous in growth as well as stronger metabolically challenged during growth on acetate as sole carbon source, compared to growth on glucose or acetate after diauxic shift. Interestingly, with acetate as sole carbon source, significant subpopulations were found with some cells that seem to be more robust than the rest of the population. In conclusion, following batch cultures population heterogeneity was evident in all measured parameters. Our approach enabled a deeper study of heterogeneity during growth on the favored substrate glucose as well as on the toxic by-product acetate. Using a combination of activity fluorescent dyes proved to be an accurate and fast alternative as well as a supplement to the use of a reporter strain. However, the choice of combination of stains should be well considered depending on which population traits to aim for.

On-line identification of fermentation processes for ethanol production

A strategy for monitoring fermentation processes, specifically, simultaneous saccharification and fermentation (SSF) of corn mash, was developed. The strategy covered the development and use of first principles, semimechanistic and unstructured process model based on major kinetic phenomena, along with mass and energy balances. The model was then used as a reference model within an identification procedure capable of running on-line. The on-line identification procedure consists on updating the reference model through the estimation of corrective parameters for certain reaction rates using the most recent process measurements. The strategy makes use of standard laboratory measurements for sugars quantification and in situ temperature and liquid level data. The model, along with the on-line identification procedure, has been tested against real industrial data and have been able to accurately predict the main variables of operational interest, i.e., state variables and its dynamics, and key process indicators. The results demonstrate that the strategy is capable of monitoring, in real time, this complex industrial biomass fermentation. This new tool provides a great support for decision-making and opens a new range of opportunities for industrial optimization.

A chemometric-assisted method for the simultaneous determination of malachite green and crystal violet in water based on absorbance-pH data generated by a homemade pH gradient apparatus

An attractive method of generating second-order data was developed by a dropping technique to generate pH gradient simultaneously coupled with diode-array spectrophotometer scanning. A homemade apparatus designed for the pH gradient. The method and the homemade apparatus were used to simultaneously determine malachite green (MG) and crystal violet (CV) in water samples. The absorbance-pH second-order data of MG or CV were obtained from the spectra of MG or CV in a series of pH values of HCl-KCl solution. The second-order data of mixtures containing MG and CV that coexisted with interferents were analyzed using multidimensional partial least-squares with residual bilinearization. The method and homemade apparatus were used to simultaneously determine MG and CV in fish farming water samples and in river ones with satisfactory results. The presented method and the homemade apparatus could serve as an alternative tool to handle some analysis problems.

Comprehensive, quantitative bioprocess productivity monitoring using fluorescence EEM spectroscopy and chemometrics

Using fluorescence excitation-emission matrix spectroscopy and chemometric methods we demonstrate an effective and rapid method for quantitative monitoring of a mammalian cell culture based manufacturing process.

Development and evaluation of methods to infer biosynthesis and substrate consumption in cultures of cellulolytic microorganisms

Concentrations of biosynthate (microbial biomass plus extracellular proteins) and residual substrate were inferred using elemental analysis for batch cultures of Clostridium thermocellum. Inferring residual substrate based on elemental analysis for a cellulose (Avicel)-grown culture shows similar results to residual substrate determined by quantitative saccharification using acid hydrolysis. Inference based on elemental analysis is also compared to different on-line measurements: base addition, CO2 production, and Near Infra Red optical density (OD850 ). Of these three on-line techniques, NIR OD850 has the best correlation with residual substrate concentration and is the most practical to use. Both biosynthate and residual substrate concentration demonstrate typical sigmoidal trends that can easily be fitted with a five-parameter Richards curve. The sigmoidal character of the inferred concentrations and on-line data, especially the CO2 production rate, suggest that there is a maximum in cell-specific rates of growth and substrate utilization during batch fermentations of crystalline cellulose, which is not observed during grown on cellobiose. Using a sigmoidal fit curve, the instantaneous specific growth rate was determined. While soluble substrate grown cultures show a constant growth rate, cultures grown on solid substrate do not. Features of various approaches are compared, with some more appropriate for rapid general indication of metabolic activity and some more appropriate for quantitative physiological studies.

Acoustofluidics 21: ultrasound-enhanced immunoassays and particle sensors

In part 21 of the tutorial series "Acoustofluidics--exploiting ultrasonic standing wave forces and acoustic streaming in microfluidic systems for cell and particle manipulation", we review applications of ultrasonic standing waves used for enhancing immunoassays and particle sensors. The paper covers ultrasonic enhancement of bead-based immuno-agglutination assays, bead-based immuno-fluorescence assays, vibrational spectroscopy sensors and cell deposition on a sensor surface.

Automated high-throughput Vibrio fischeri assay for (eco)toxicity screening: application to ionic liquids

An automated high-throughput Vibrio fischeri assay was developed and further applied to the evaluation of ionic liquids (ILs) (eco)toxicity. The assay was based on the reduction of bacterial bioluminescence in the presence of test compounds and the results were presented as EC(50). The assays were performed with eight commercially available ILs with distinct cationic head groups, alkyl side chains and anions. EC(50) values between 6.5 and 691.9 mmol L(-1) were obtained for the tested ILs, being hmim [Cl] the most toxic and bmim [Cl] the less toxic ones, confirming the influence of the different structural elements. Moreover, all the tested ILs exhibited a (eco)toxicity lower than Cu(II), used as a positive control during the optimization and analysis steps. The automated assay assured the precise control of the contact time between V. fischeri and test compound by means of a simple protocol that guaranteed adequate aspiration and handling of the solutions as well as the precise implementation of a computer controlled stop period. Furthermore, a significant reduction of the assay costs was achieved through automation mainly by a drastic reduction of the volume of bacterial suspension and test compound. The methodology was validated by comparison with a microplate assay; it was stated that the results, obtained after a 3min contact time, changed proportionally relatively to Cu(II) in both assays. This confirmed the applicability of the methodology as an (eco)toxicity screening assay, with reduction of time and increase of robustness and repeatability (n=10; rsd<1.1%). It is expected that due to its simplicity and reduced cost the developed assay can be integrated in the early stage of development of new compounds as a rapid screening test.

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.

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.

Fermentation reactor coupled with capillary electrophoresis for on-line bioprocess monitoring

In this paper, a filter probe integrated into a computerized pneumatic sampler for capillary electroseparations was developed for an on-line monitoring of bioprocesses. The optimization of the performance of the coupled system was done by using a response surface modeling and three-level two-factor design. The resolution was found to be the most important parameter influencing the performance of an on-line analysis of the microbial metabolism. For the on-line analysis the migration time and detection limit were also found to be important parameters. Different parameters were combined by using an overall desirability function to find optimum conditions for all parameters. The equipment with an optimized separation protocol was used to monitor the bioaccumulation of Cu, Zn, Co and Cd (with detection limits 0.46, 0.37, 1.2, 0.84 mM correspondingly) by the Rhodococcus sp. bacteria isolated from the highly polluted technogenic soil of northeastern Estonia during a 2-week experiment.

Determination of cell mass and polymyxin using multi-wavelength fluorescence

Multi-wavelength fluorescence was applied for on-line monitoring of cell mass and the antibiotic polymyxin B in Bacillus polymyxa cultivations. By varying the phosphate and nitrogen content of the medium different polymyxin-cell mass ratios could be obtained. Using this strategy, it was possible to investigate if multi-wavelength fluorescence is able to give independent prediction of the two parameters. Partial least square (PLS) regression was applied to establish mathematical relationships between off-line determined cell mass and polymyxin concentrations and on-line collected fluorescence data. For polymyxin one universal PLS model, with a correlation of 0.95 and a root mean square error of cross validation (RMSECV) of 35 mgl(-1), could be constructed. However, correlation between fluorescence and cell mass dry weight could not be established including data from all three types of cultivations. For data from each type of cultivation, separate models with high correlation and low RMSECV values were built. A large variation in cellular composition as a result of the different levels of nitrogen and phosphorus in the cultivations was the probable reason to the necessity of building three models. The results of the present investigation indicate that production of polymyxin is concomitantly regulated by phosphate and nitrogen as the highest polymyxin yield on cell mass, 0.17+/-0.01 gg(-1), was reached in the cultivations where both nitrogen and phosphate concentrations were kept low.

Application of sequential injection analysis to pharmaceutical analysis

Sequential injection analysis is a well established tool for automation of pharmaceutical analysis. A short historical background of this technique is given as well as a brief discussion on the basic principles and potentials. The current applications of SIA in the pharmaceutical analysis are also described and discussed. The manifolds developed offer good analytical characteristics and are suitable for analysis of drug formulations, process analysis, drug-dissolution, drug-release testing and functional assays for screening potential drugs. The results obtained are in good agreement with those furnished by the application of the reference methods presented in the pharmacopoeias.

Online LC-MS-MS process monitoring for optimization of biological treatment of wastewater containing azo dye concentrates

A biological high-performance treatment process comprising two 40-L reactor compartments has been developed for purification and decoloration of concentrated textile wastewater containing up to 15 g L(-1) reactive dyestuff. The decoloration rate of 95% meets the requirements of German legislation for textile wastewater treatment. Successful process development and optimization was achieved by use of high-performance liquid chromatography, with diode-array and electrospray tandem mass spectrometric (LC-ESI-MS-MS) detection, coupled with inline microfiltration membrane-sampling devices, applied online to bioreactors as a process analytical tool for the first time. The optimum process performance was found by correlation of dye and decoloration product-specific concentrations with summary properties such as redox potential and dissolved oxygen content. Details of the degradation and decoloration mechanism for the azo dye reactive black 5 was revealed by using mass spectrometry for structure elucidation.

Strategies for continuous on-line high performance liquid chromatography coupled with diode array detection and electrospray tandem mass spectrometry for process monitoring of sulphonated azo dyes and their intermediates in anaerobic–aerobic bioreactors

On-line HPLC with diode array detection (DAD) coupled to electrospray tandem mass spectrometry (ESI-MS/MS) is presented as an integrated quality control and process integrated optimisation tool for the continuous monitoring of sulphonated azo dyes (SADs) and their intermediates in anaerobic and aerobic bioprocesses. Ion-pair RP-HPLC is found out to be more suitable for simultaneous monitoring of aromatic amines (AAs), sulphonated aromatic amines (SAAs) and sulphonated azo dyes in comparison to RP-HPLC with polar embedded phases. Monitoring of the anaerobic degradation of the diazo Reactive Black 5 displays the dependency of a two stage azo group reduction mechanism on the redox potential of the bioreactor. An autoxidation sensitive intermediate released from the anaerobic reduction is characterised by ESI-MS/MS for the first time. The functionality of the method is demonstrated by the control and evaluation of selective adaptation of bacteria to certain pollutants and the identification of unknown intermediates causing re-gaining colour released from azo dye treatment.

Process monitoring of anaerobic azo dye degradation by high-performance liquid chromatography-diode array detection continuously coupled to membrane filtration sampling modules

Process integrated microfiltration and ultrafiltration based membrane sampling modules were compared by means of HPLC with diode array detection based monitoring of an anaerobic azodye biodegradation process. The sampling matrix consisted of anaerobic sludge from a municipal wastewater treatment plant. The hydrolysed azo dye Reactive Black 5 (RB5-H) and three products (ionic and nonionic) released from reductive cleavage under anaerobic conditions were continuously monitored by simultaneously separation by ion-pair chromatography. Microfiltration membrane-based sampling showed no retention for any compound observed. Sampling by ultrafiltration significantly retained the observed ionic compounds between 58 and 83% whereas a nonionic compound was not retained. On-line monitoring of an oxygen-sensitive compound was possible whereas off-line detection failed. Robust long time monitoring could be performed for up to 1 week without cleaning the membrane.

Assessment of near-infrared spectral information for rapid monitoring of bioprocess quality

Access to real-time process information is desirable for consistent and efficient operation of bioprocesses. Near-infrared spectroscopy (NIRS) is known to have potential for providing real-time information on the quantitative levels of important bioprocess variables. However, given the fact that a typical NIR spectrum encompasses information regarding almost all the constituents of the sample matrix, there are few case studies that have investigated the spectral details for applications in bioprocess quality assessment or qualitative bioprocess monitoring. Such information would be invaluable in providing operator-level assistance on the progress of a bioprocess in industrial-scale productions. We investigated this aspect and report the results of our investigation. Near-infrared spectral information derived from scanning unprocessed culture fluid (broth) samples from a complex antibiotic production process was assessed for a data set that incorporated bioprocess variations. Principal component analysis was applied to the spectral data and the loadings and scores of the principal components studied. Changes in the spectral information that corresponded to variations in the bioprocess could be deciphered. Despite the complexity of the matrix, near-infrared spectra of the culture broth are shown to have valuable information that can be deconvoluted with the help of factor analysis techniques such as principal component analysis (PCA). Although complex to interpret, the loadings and score plots are shown to offer potential in process diagnosis that could be of value in the rapid assessment of process quality, and in data assessment prior to quantitative model development.

On-line bioprocess monitoring with a multi-wavelength fluorescence sensor using multivariate calibration

Cultivations of Pseudomonas fluorescens were monitored with a multi-wavelength on-line fluorescence sensor. The multi-wavelength fluorometer used excitation light from 270 to 550 nm with 20 nm steps and measured fluorescence emission from 310 to 590 nm. The fluorescence, on-line exhaust gas measurements and off-line analysis of nitrate, succinate, optical density and protein were compared chemometrically by multivariate calibration, i.e. computing partial least square (PLS) regression models. Based on the multivariate regression models, it was possible to determine CO2 and O2 composition in the exhaust gas (the correlation coefficients, R2 between the predicted values by the PLS model and the measured values was 0.97 for CO(2) and 0.97 for O2, respectively). Also to make quantitative determinations of succinate (R(2) = 0.97), protein (R(2) = 0.94), optical density (R(2) = 1.0) and nitrate (R(2) = 0.98) in the medium based on the fluorescence spectra. Only a limited data set was available but the results indicated that the sensor could indirectly determine non-fluorescent compounds, i.e. nitrate and succinate, which probably is due to the stoichiometric relationship between fluorescent cellular components and non-fluorescent compounds. Consequently multi-wavelength fluorescence is an interesting technique for a wide range of applications.