Low-cost microbioreactor for high-throughput bioprocessing

Kinetic analysis of a trehalase-overexpressing strain grown on trehalose: a new tool for respiro-fermentative transition studies in Saccharomyces cerevisiae

AIMS

The aim was to demonstrate the use of a trehalase-overexpressing Saccharomyces cerevisiae strain grown on trehalose as a valuable tool in the studies of respiro-fermentative transition at a reduced scale.

METHODS AND RESULTS

A trehalase-overexpressing strain was cultivated in synthetic medium on trehalose under aerobic conditions. This strain grew at a maximum specific growth rate of 0.16 h(-1) and showed a pure oxidative metabolism. Glucose pulse experiments were carried out in this system in order to quantify the short-term Crabtree effect. These data were then compared with glucose pulse experiments carried out in the conventional way with the wild-type strain in glucose-limited chemostats. Glucose-pulse experiments in aerobic batch cultures grown on trehalose led to a metabolic respiro-fermentative transition similar to the one observed in glucose-limited chemostats.

CONCLUSIONS

This cultivation system allowed us to quantitatively mimic at the flask scale the Crabtree effect observed in conventional chemostat studies.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study is of primary interest in S. cerevisiae studies in which: (i) the implementation of oxidative growth is required (as with studies of the Crabtree effect and heterologous protein production); (ii) small-scale culture systems are required (e.g. high-throughput mutant screening and isotopic labelling experiments).

Application of a Novel Oscillatory Flow Micro-bioreactor to the Production of γ-decalactone in a Two Immiscible Liquid Phase Medium

A novel micro-bioreactor based on the oscillatory flow technology was applied to the scale-down of the biotechnological production of gamma-decalactone. A decrease up to 50% of the time required to obtain the maximum concentration of the compound was observed, when compared with other scaled-down platforms (stirred tank bioreactor or shake flask). A three-fold increase in gamma-decalactone productivity was obtained by increasing oscillatory mixing intensity from Re(o) approximately 482 to Re(o) approximately 1447. This was presumably related to the effective contribution of the reactor geometry to enhanced mass transfer rates between the two immiscible liquid phases involved in the process by increasing the interfacial area.

Validation of an optical sensor-based high-throughput bioreactor system for mammalian cell culture

Cell culture optimization is a labor-intensive process requiring a large number of experiments to be conducted under varying conditions. Here we describe a high-throughput bioreactor system that allows 12 mini stirred-tank bioreactors to be operated simultaneously. All bioreactors are monitored by low-cost minimally invasive optical sensors for pH and dissolved oxygen. The sensors consist of single-use patches affixed inside the bioreactors and monitored optically from the outside. Experimental results show that different sensing patches with the same composition respond consistently. The discrepancy between different pH sensors is less than 0.1 pH units over most of their responsive range. The discrepancy between different dissolved oxygen sensors is less than 10% over the whole range from 0% to 100% dissolved oxygen. The consistency of the sensing system ensures that only an initial one-time calibration is required for the sensing patches. After that, a calibration code is generated and sensing patches of the same composition can be used directly. This greatly reduces the time and cost required for monitored multi-bioreactor operations. We used SP2/0 myeloma/mouse hybridoma cell cultures to demonstrate reactor performance consistency. Transcriptional profiling, HPLC analysis, viable cell count, and viability inspection show that the presence of sensing patches and the use of optical monitoring have no apparent effect on the metabolism of the cells.

A new wireless system for decentralised measurement of physiological parameters from shake flasks

Background

Shake flasks are widely used because of their low price and simple handling. Many researcher are, however, not aware of the physiological consequences of oxygen limitation and substrate overflow metabolism that occur in shake flasks. Availability of a wireless measuring system brings the possibilities for quality control and design of cultivation conditions.

Results

Here we present a new wireless solution for the measurement of pH and oxygen from shake flasks with standard sensors, which allows data transmission over a distance of more than 100 metres in laboratory environments. This new system was applied to monitoring of cultivation conditions in shake flasks. The at-time monitoring of the growth conditions became possible by simple means. Here we demonstrate that with typical protocols E. coli shake flask cultures run into severe oxygen limitation and the medium is strongly acidified. Additionally the strength of the new system is demonstrated by continuous monitoring of the oxygen level in methanol-fed Pichia pastoris shake flask cultures, which allows the optimisation of substrate feeding for preventing starvation or methanol overfeed. 40 % higher cell density was obtained by preventing starvation phases which occur in standard shake flask protocols by adding methanol when the respiration activity decreased in the cultures.

Conclusion

The here introduced wireless system can read parallel sensor data over long distances from shake flasks that are under vigorous shaking in cultivation rooms or closed incubators. The presented technology allows centralised monitoring of decentralised targets. It is useful for the monitoring of pH and dissolved oxygen in shake flask cultures. It is not limited to standard sensors, but can be easily adopted to new types of sensors and measurement places (e.g., new sensor points in large-scale bioreactors).

Design and performance of a 24-station high throughput microbioreactor

Two prototype 24-unit microbioreactors are presented and reviewed for their relative merits. The first used a standard 24-well plate as the template, while the second consisted of 24-discrete units. Both systems used non-invasive optical sensors to monitor pH and dissolved oxygen. The systems were used to cultivate Escherichia coli. Both designs had their merits and the results obtained are presented. In addition, dissolved oxygen control was demonstrated at the milliliter scale and 24 simultaneously monitored fermentations were successfully carried out. These results demonstrated high quality high throughput bioprocessing and provide important insights into operational parameters at small scale.

Evaluation of the effects of various culture conditions on Cr(VI) reduction byShewanella oneidensis MR-1 in a novel high-throughput mini-bioreactor

The growth and Cr(VI) reduction by Shewanella oneidensis MR-1 was examined using a mini-bioreactor system that independently monitors and controls pH, dissolved oxygen (DO), and temperature for each of its 24, 10-mL reactors. Independent monitoring and control of each reactor in the cassette allows the exploration of a matrix of environmental conditions known to influence S. oneidensis chromium reduction. S. oneidensis MR-1 grew in minimal medium without amino acid or vitamin supplementation under aerobic conditions but required serine and glycine supplementation under anaerobic conditions. Growth was inhibited by DO concentrations >80%. Lactate transformation to acetate was enhanced by low concentration of DO during the logarithmic growth phase. Between 11 and 35 degrees C, the growth rate obeyed the Arrhenius reaction rate-temperature relationship, with a maximum growth rate occurring at 35 degrees C. S. oneidensis MR-1 was able to grow over a wide range of pH (6-9). At neutral pH and temperatures ranging from 30 to 35 degrees C, S. oneidensis MR-1 reduced 100 microM Cr(VI) to Cr(III) within 20 min in the exponential growth phase, and the growth rate was not affected by the addition of chromate; it reduced chromate even faster at temperatures between 35 and 39 degrees C. At low temperatures (<25 degrees C), acidic (pH < 6.5), or alkaline (pH > 8.5) conditions, 100 microM Cr(VI) strongly inhibited growth and chromate reduction. The mini-bioreactor system enabled the rapid determination of these parameters reproducibly and easily by performing very few experiments. Besides its use for examining parameters of interest to environmental remediation, the device will also allow one to quickly assess parameters for optimal production of recombinant proteins or secondary metabolites.

Optical analysis of liquid mixing in a minibioreactor

A novel optical sensor was used to study mixing and mean circulation time in a model minibioreactor (12.5 mL stirred vessel, equipped with a paddle impeller). Rotational rates in the range of 10-1,000 rpm corresponding to Reynolds number between 14 and 1,350 were studied. Results suggest that depending on the impeller rotational speed, mixing times up to 214 +/- 87 s can be reproducibly achieved. The minibioreactor was operated in the transitional regime, and it was determined that the non-dimensional form for mixing time, NTheta(M) was linearly dependent on Reynolds number. A linear correlation between mean circulation time and the inverse of rotational speed was also determined. The mean circulation time dependence on rotational speed in the 12.5 mL stirred vessel is similar to those found in large-scale stirred vessels. These results suggest that mixing and circulation times found in large-scale reactors can be replicated in minibioreactors.

A well-mixed, polymer-based microbioreactor with integrated optical measurements

We describe a 150 microL microbioreactor fabricated in poly(methylmethacrylate) (PMMA) and poly(dimethylsiloxane) (PDMS) to cultivate microbial cell cultures. Mixing is achieved by a small magnetic stir bar and fluorescent sensors are integrated for on-line measurement of pH and dissolved oxygen. Optical transmission measurements are used for cell density. The body of the reactor is poly(methylmethacrylate) with a thin layer of poly (dimethylsiloxane) for aeration, oxygen diffuses through this gas-permeable membrane into the microbioreactor to support metabolism of bacterial cells. Mixing in the reactor is characterized by observation of mixing of dyes and computational fluid dynamics simulations. The oxygenation is described in terms of measured K(L)a values for microbioreactor, 20-75/h corresponding to increasing stirring speed 200-800 rpm. Escherichia coli cell growth in the microbioreactor is demonstrated and the growth behavior is benchmarked with conventional bench-scale bioreactors, flasks and tubes. Batch culture experiments with Saccharomyces cerevisiae further demonstrate the reproducibility and flexibility of the microbioreactor system.

Development of a multiplexed microbioreactor system for high-throughput bioprocessing

A multiplexed microbioreactor system for parallel operation of multiple microbial fermentation is described. The system includes miniature motors for magnetic stirring of the microbioreactors and optics to monitor the fermentation parameters optical density (OD), dissolved oxygen (DO), and pH, in-situ and in real time. The microbioreactors are fabricated out of poly(methylmethacrylate)(PMMA) and poly(dimethylsiloxane)(PDMS), and have a working volume of 150 microl. Oxygenation of the cells occurs through a thin PDMS membrane at the top of the reactor chamber. Stirring is achieved with a magnetic spin bar in the reactor chamber. Parallel microbial fermentations with Escherichia coli are carried out in four stirred microbioreactors and demonstrate the reproducible performance of the multiplexed system. The profiles for OD, DO, and pH compare favourably to fermentations performed in bioreactor systems with multiple bench-scale reactors. Finally, the multiplexed system is used to compare two different reactor designs, demonstrating that the reproducibility of the system permits the quantification of microbioreactor performance.

Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat

Using an active approach to preventing biofilm formation, we implemented a microfluidic bioreactor that enables long-term culture and monitoring of extremely small populations of bacteria with single-cell resolution. We used this device to observe the dynamics of Escherichia coli carrying a synthetic "population control" circuit that regulates cell density through a feedback mechanism based on quorum sensing. The microfluidic bioreactor enabled long-term monitoring of unnatural behavior programmed by the synthetic circuit, which included sustained oscillations in cell density and associated morphological changes, over hundreds of hours.

Development of a small-scale bioreactor: application to in vivo NMR measurement

A perfused bioreactor allowing in vivo NMR measurement was developed and validated for Eschscholtzia californica cells. The bioreactor was made of a 10-mm NMR tube. NMR measurement of the signal-to-noise ratio was optimized using a sedimented compact bed of cells that were retained in the bioreactor by a supporting filter. Liquid medium flow through the cell bed was characterized from a mass balance on oxygen and a dispersive hydrodynamic model. Cell bed oxygen demand for 4 h perfusion required a minimal medium flow rate of 0.8 mL/min. Residence time distribution assays at 0.8-2.6 mL/min suggest that the cells are subjected to a uniform nutrient environment along the cell bed. Cell integrity was maintained for all culture conditions since the release of intracellular esterases was not significant even after 4 h of perfusion. In vivo NMR was performed for (31)P NMR and the spectrum can be recorded after only 10 min of spectral accumulation (500 scans) with peaks identified as G-6P, F-6P, cytoplasmic Pi, vacuolar Pi, ATP(gamma) and ADP(beta), ATP(alpha) and ADP(alpha), NADP and NDPG, NDPG and ATP(beta). Cell viability was shown to be maintained as (31)P chemical shifts were constant with time for all the identified nuclei, thus suggesting constant intracellular pH.

Development, parallelization, and automation of a gas-inducing milliliter-scale bioreactor for high-throughput bioprocess design (HTBD)

A novel milliliter-scale bioreactor equipped with a gas-inducing impeller was developed with oxygen transfer coefficients as high as in laboratory and industrial stirred-tank bioreactors. The bioreactor reaches oxygen transfer coefficients of >0.4 s(-1). Oxygen transfer coefficients of >0.2 s(-1) can be maintained over a range of 8- to 12-mL reaction volume. A reaction block with integrated heat exchangers was developed for 48-mL-scale bioreactors. The block can be closed with a single gas cover spreading sterile process gas from a central inlet into the headspace of all bioreactors. The gas cover simultaneously acts as a sterile barrier, making the reaction block a stand-alone device that represents an alternative to 48 parallel-operated shake flasks on a much smaller footprint. Process control software was developed to control a liquid-handling system for automated sampling, titration of pH, substrate feeding, and a microtiter plate reader for automated atline pH and atline optical density analytics. The liquid-handling parameters for titration agent, feeding solution, and cell samples were optimized to increase data quality. A simple proportional pH-control algorithm and intermittent titration of pH enabled Escherichia coli growth to a dry cell weight of 20.5 g L(-1) in fed-batch cultivation with air aeration. Growth of E. coli at the milliliter scale (10 mL) was shown to be equivalent to laboratory scale (3 L) with regard to growth rate, mu, and biomass yield, Y(XS).

Continuous perfusion microfluidic cell culture array for high-throughput cell-based assays

We present for the first time a microfluidic cell culture array for long-term cellular monitoring. The 10 x 10 array could potentially assay 100 different cell-based experiments in parallel. The device was designed to integrate the processes used in typical cell culture experiments on a single self-contained microfluidic system. Major functions include repeated cell growth/passage cycles, reagent introduction, and real-time optical analysis. The single unit of the array consists of a circular microfluidic chamber, multiple narrow perfusion channels surrounding the main chamber, and four ports for fluidic access. Human carcinoma (HeLa) cells were cultured inside the device with continuous perfusion of medium at 37 degrees C. The observed doubling time was 1.4 +/- 0.1 days with a peak cell density of approximately 2.5*10(5) cells/cm(2). Cell assay was demonstrated by monitoring the fluorescence localization of calcein AM from 1 min to 10 days after reagent introduction. Confluent cell cultures were passaged within the microfluidic chambers using trypsin and successfully regrown, suggesting a stable culture environment suitable for continuous operation. The cell culture array could offer a platform for a wide range of assays with applications in drug screening, bioinformatics, and quantitative cell biology.

Gene expression analysis of Escherichia coli grown in miniaturized bioreactor platforms for high-throughput analysis of growth and genomic data

Combining high-throughput growth physiology and global gene expression data analysis is of significant value for integrating metabolism and genomics. We compared global gene expression using 500 ng of total RNA from Escherichia coli cultures grown in rich or defined minimal media in a miniaturized 50-microl bioreactor. The microbioreactor was fabricated out of poly(dimethylsiloxane) (PDMS) and glass and equipped to provide on-line, optical measurements. cDNA labeling for microarray hybridizations was performed with the GeniconRLS system. From these experiments, we found that the expression of 232 genes increased significantly in cells grown in minimum medium, including genes involved in amino acid biosynthesis and central metabolism. The expression of 275 genes was significantly elevated in cells grown in rich medium, including genes involved in the translational and motility apparatuses. In general, these changes in gene expression levels were similar to those observed in 1,000-fold larger cultures. The increasing rate at which complete genomic sequences of microorganisms are becoming available offers an unprecedented opportunity for investigating these organisms. Our results from microscale cultures using just 500 ng of total RNA indicate that high-throughput integration of growth physiology and genomics will be possible with novel biochemical platforms and improved detection technologies.

Low-cost noninvasive optical CO2 sensing system for fermentation and cell culture

High-throughput bioprocessing is a very promising technique for bioprocess development and optimization because of its high efficiency. The key to its development has been the availability of simple and inexpensive sensors to monitor the bioprocesses conducted in its small-scale bioreactors. Here we report on a low-cost noninvasive CO2 sensing system suitable for any transparent vessel. The system was composed of a CO2 sensing patch, a coaster, an interface, and a computer. The sensing film was prepared using the ion-pair technique. The coaster was a small self-made device with necessary optics and electronics for ratiometric measurements with a component cost of less than dollar 100. Results show that the system was stable and reliable despite its simplicity and low cost. The sensitivity of the CO2 sensing system was not affected by pH, media type, or temperature. It was shown to be stable for at least 10 days, long enough for most bioprocesses.

The design and fabrication of three-chamber microscale cell culture analog devices with integrated dissolved oxygen sensors

Whole animal testing is an essential part in evaluating the toxicological and pharmacological profiles of chemicals and pharmaceuticals, but these experiments are expensive and cumbersome. A cell culture analog (CCA) system, when used in conjunction with a physiologically based pharmacokinetic (PBPK) model, provides an in vitro supplement to animal studies and the possibility of a human surrogate for predicting human response in clinical trials. A PBPK model mathematically simulates animal metabolism by modeling the absorption, distribution, metabolism, and elimination kinetics of a chemical in interconnected tissue compartments. A CCA uses mammalian cells cultured in interconnected chambers to physically represent the corresponding PBPK. These compartments are connected by recirculating tissue culture medium that acts as a blood surrogate. The purpose of this article is to describe the design and basic operation of the microscale manifestation of such a system. Microscale CCAs offer the potential for inexpensive, relatively high throughput evaluation of chemicals while minimizing demand for reagents and cells. Using microfabrication technology, a three-chamber ("lung"-"liver"-"other") microscale cell culture analog (microCCA) device was fabricated on a 1 in. (2.54 cm) square silicon chip. With a design flow rate of 1.76 microL/min, this microCCA device achieves approximate physiological liquid-to-cell ratio and hydrodynamic shear stress while replicating the liquid residence time parameters in the PBPK model. A dissolved oxygen sensor based on collision quenching of a fluorescent ruthenium complex by oxygen molecules was integrated into the system, demonstrating the potential to integrate real-time sensors into such devices.

Microbioreactor arrays with parametric control for high-throughput experimentation

A scalable array technology for parametric control of high-throughput cell cultivations is demonstrated. The technology makes use of commercial printed circuit board (PCB) technology, integrated circuit sensors, and an electrochemical gas generation system. We present results for an array of eight 250 microl microbioreactors. Each bioreactor contains an independently addressable suite that provides closed-loop temperature control, generates feed gas electrochemically, and continuously monitors optical density. The PCB technology allows for the assembly of additional off-the-shelf components into the microbioreactor array; we demonstrate the use of a commercial ISFET chip to continuously monitor culture pH. The electrochemical dosing system provides a powerful paradigm for reproducible gas delivery to high-density arrays of microreactors. Growth data are presented for Escherichia coli cultured in the array with varying microaerobic conditions using electrochemically generated oxygen. Additionally, we present data on carbon dioxide generation for pH dosing.

Membrane-aerated microbioreactor for high-throughput bioprocessing

A microbioreactor with a volume of microliters is fabricated out of poly(dimethylsiloxane) (PDMS) and glass. Aeration of microbial cultures is through a gas-permeable PDMS membrane. Sensors are integrated for on-line measurement of optical density (OD), dissolved oxygen (DO), and pH. All three parameter measurements are based on optical methods. Optical density is monitored via transmittance measurements through the well of the microbioreactor while dissolved oxygen and pH are measured using fluorescence lifetime-based sensors incorporated into the body of the microbioreactor. Bacterial fermentations carried out in the microbioreactor under well-defined conditions are compared to results obtained in a 500-mL bench-scale bioreactor. It is shown that the behavior of the bacteria in the microbioreactor is similar to that in the larger bioreactor. This similarity includes growth kinetics, dissolved oxygen profile within the vessel over time, pH profile over time, final number of cells, and cell morphology. Results from off-line analysis of the medium to examine organic acid production and substrate utilization are presented. By changing the gaseous environmental conditions, it is demonstrated that oxygen levels within the microbioreactor can be manipulated. Furthermore, it is demonstrated that the sensitivity and reproducibility of the microbioreactor system are such that statistically significant differences in the time evolution of the OD, DO, and pH can be used to distinguish between different physiological states. Finally, modeling of the transient oxygen transfer within the microbioreactor based on observed and predicted growth kinetics is used to quantitatively characterize oxygen depletion in the system.

Optical sensor systems for bioprocess monitoring

Bioreactors are closed systems in which microorganisms can be cultivated under defined, controllable conditions that can be optimized with regard to viability, reproducibility, and product-oriented productivity. To drive the biochemical reaction network of the biological system through the desired reaction optimally, the complex interactions of the overall system must be understood and controlled. Optical sensors which encompass all analytical methods based on interactions of light with matter are efficient tools to obtain this information. Optical sensors generally offer the advantages of noninvasive, nondestructive, continuous, and simultaneous multianalyte monitoring. However, at this time, no general optical detection system has been developed. Since modern bioprocesses are extremely complex and differ from process to process (e.g., fungal antibiotic production versus mammalian cell cultivation), appropriate analytical systems must be set up from different basic modules, designed to meet the special demands of each particular process. In this minireview, some new applications in bioprocess monitoring of the following optical sensing principles will be discussed: UV spectroscopy, IR spectroscopy, Raman spectroscopy, fluorescence spectroscopy, pulsed terahertz spectroscopy (PTS), optical biosensors, in situ microscope, surface plasmon resonance (SPR), and reflectometric interference spectroscopy (RIF).

Accelerated design of bioconversion processes using automated microscale processing techniques

Microscale processing techniques are rapidly emerging as a means to increase the speed of bioprocess design and reduce material requirements. Automation of these techniques can reduce labour intensity and enable a wider range of process variables to be examined. This article examines recent research on various individual microscale unit operations including microbial fermentation, bioconversion and product recovery techniques. It also explores the potential of automated whole process sequences operated in microwell formats. The power of the whole process approach is illustrated by reference to a particular bioconversion, namely the Baeyer-Villiger oxidation of bicyclo[3.2.0]hept-2-en-6-one for the production of optically pure lactones.

High-throughput protein expression for the post-genomic era

In the past, protein expression has been perceived as the principle bottleneck in protein characterization and structure determination. The challenge now is to rapidly express large numbers of genes in the search for new drug targets and therapeutic proteins encoded by the human genome. In this competitive environment, several high-throughput expression strategies for protein production are being used to industrialize the process of protein expression.

Bioprocess monitoring

Electrochemical sensors for pH and dissolved oxygen remain the most commonly used in bioprocess monitoring, but continued research has resulted in improved optical sensors. Optical sensors for dissolved oxygen and dissolved carbon dioxide are now commercially available. Advances in optics and electronics are further driving down the costs of these sensors. In the near future, bioprocess optimization will change paradigms as massively parallel, fully instrumented bioreactors become available and high-throughput bioprocessing becomes a reality.