Respiration activity monitoring system for any individual well of a 48-well microtiter plate

Background

Small-scale micro-bioreactors have become the cultivation vessel of choice during the first steps of bioprocess development. They combine high cultivation throughput with enhanced cost efficiency per cultivation. To gain the most possible information in the early phases of process development, online monitoring of important process parameters is highly advantageous. One of these important process parameters is the oxygen transfer rate (OTR). Measurement of the OTR, however, is only available for small-scale fermentations in shake flasks via the established RAMOS technology until now. A microtiter plate-based (MTP) μRAMOS device would enable significantly increased cultivation throughput and reduced resource consumption. Still, the requirements of miniaturization for valve and sensor solutions have prevented this transfer so far. This study reports the successful transfer of the established RAMOS technology from shake flasks to 48-well microtiter plates. The introduced μRAMOS device was validated by means of one bacterial, one plant cell suspension culture and two yeast cultures.

Results

A technical solution for the required miniaturized valve and sensor implementation for an MTP-based μRAMOS device is presented. A microfluidic cover contains in total 96 pneumatic valves and 48 optical fibers, providing two valves and one optical fiber for each well. To reduce costs, an optical multiplexer for eight oxygen measuring instruments and 48 optical fibers is introduced. This configuration still provides a reasonable number of measurements per time and well. The well-to-well deviation is investigated by 48 identical Escherichia coli cultivations showing standard deviations comparable to those of the shake flask RAMOS system. The yeast Hansenula polymorpha and parsley suspension culture were also investigated.

Conclusions

The introduced MTP-based μRAMOS device enables a sound and well resolved OTR monitoring for fast- and slow-growing organisms. It offers a quality similar to standard RAMOS in OTR determination combined with an easier handling. The experimental throughput is increased 6-fold and the media consumption per cultivation is decreased roughly 12.5-fold compared to the established eight shake flask RAMOS device.

     

Kinetic characterization and fed-batch fermentation for maximal simultaneous production of esterase and protease from Lysinibacillus fusiformis AU01

The simultaneous production of intracellular esterase and extracellular protease from the strain Lysinibacillus fusiformis AU01 was studied in detail. The production was performed both under batch and fed-batch modes. The maximum yield of intracellular esterase and protease was obtained under full oxygen saturation at the beginning of the fermentation. The data were fitted to the Luedeking–Piret model and it was shown that the enzyme (both esterase and protease) production was growth associated. A decrease in intracellular esterase and increase in the extracellular esterase were observed during late stationary phase. The appearance of intracellular proteins in extracellular media and decrease in viable cell count and biomass during late stationary phase confirmed that the presence of extracellular esterase is due to cell lysis. Even though the fed-batch fermentation with different feeding strategies showed improved productivity, feeding yeast extract under DO-stat fermentation conditions showed highest intracellular esterase and protease production. Under DO-stat fed-batch cultivation, maximum intracellular esterase activity of 820?×?10³ U/L and extracellular protease activity of 172?×?10³ U/L were obtained at the 16th?hr. Intracellular esterase and extracellular protease production were increased fivefold and fourfold, respectively, when compared to batch fermentation performed under shake flask conditions.     

Fed-batch mode in shake flasks by slow-release technique

Most industrial production processes are performed in fed-batch operational mode. In contrast, the screenings for microbial production strains are run in batch mode which results in completely different physiological conditions than relevant for production conditions. This may lead to wrong selections of strains. Silicone elastomer discs containing glucose crystals were developed to realize fed-batch fermentation in shake flasks. No other device for feeding was required. Glucose was fed in this way to Hansenula polymorpha cultures controlled by diffusion. Two strains of H. polymorpha were investigated in shake flasks: the wild-type strain (DSM 70277) and a recombinant strain pC10-FMD (P(FMD)-GFP). The oxygen transfer rate (OTR) and respiratory quotient (RQ) of the cultures were monitored online in shake flasks with a Respiration Activity Monitoring System (RAMOS). Formation of biomass and green fluorescent protein (GFP), pH-drift and the metabolite dynamics of glucose, ethanol and acetic acid were measured offline. With the slow-release technique overflow metabolism could be reduced leading to an increase of 85% in biomass yield. To date, 23.4 g/L cell dry weight of H. polymorpha could be achieved in shake flask. Biomass yields of 0.38-0.47 were obtained which are in the same magnitude of laboratory scale fermentors equipped with a substrate feed pump. GFP yield could be increased by a factor of 35 in Syn6-MES mineral medium. In fed-batch mode 88 mg/L GFP was synthesized with 35.9 g/L fed glucose. In contrast, only 2.5 mg/L with 40 g/L metabolized glucose was revealed in batch mode. In YNB mineral medium over 420-fold improvement in fed-batch mode was achieved with 421 mg/L GFP at 41.3 g/L fed glucose in comparison to less than 1 mg/L in batch mode with 40 g/L glucose.     

Development of a modified Respiration Activity Monitoring System for accurate and highly resolved measurement of respiration activity in shake flask fermentations

ABSTRACT: BACKGROUND: The Respiration Activity Monitoring System (RAMOS) is an established device to measure on-line the oxygen transfer rate (OTR), thereby, yielding relevant information about metabolic activities of microorganisms and cells during shake flask fermentations. For very fast-growing microbes, however, the RAMOS technique provides too few data points for the OTR. Thus, this current study presents a new model based evaluation method for generating much more data points to enhance the information content and the precision of OTR measurements. RESULTS: In cultivations with E.coli BL21 pRSET eYFP-IL6, short diauxic and even triauxic metabolic activities were detected with much more detail compared to the conventional evaluation method. The decline of the OTR during the stop phases during oxygen limitations, which occur when the inlet and outlet valves of the RAMOS flask were closed for calibrating the oxygen sensor, were also detected. These declines reflected a reduced oxygen transfer due to the stop phases. In contrast to the conventional calculation method the new method was almost independent from the number of stop phases chosen in the experiments. CONCLUSIONS: This new model based evaluation method unveils new peaks of metabolic activity which otherwise would not have been resolved by the conventional RAMOS evaluation method. The new method yields substantially more OTR data points, thereby, enhancing the information content and the precision of the OTR measurements. Furthermore, oxygen limitations can be detected by a decrease of the OTR during the stop phases.     

Protease production by Bacillus subtilis in oxygen-controlled,glucose fed-batch fermentations

Summary An open-loop, on-off control system using the dissolved oxygen level to control a glucose feed was used in a study of growth and production of protease by Bacillus subtilis CNIB 8054. With this system, both glucose and oxygen were controlled at low concentrations. In batch fermentations, protease activity in the fermentation broth was maximum when growth had stopped. During oxygen-controlled, glucose fed-batch fermentations, growth and the production of protease activity continued during glucose feeding. Oxygen-controlled, glucose fed-batch fermentations produced more protease activity than batch fermentations, depending upon the set point for dissolved oxygen. These results indicate that control of glucose and oxygen concentrations can result in improvements in protease production.     

Establishing a Fed‐Batch Process for Protease Expression with Bacillus licheniformis in Polymer‐Based Controlled‐Release Microtiter Plates

Introducing fed‐batch mode in early stages of development projects is crucial for establishing comparable conditions to industrial fed‐batch fermentation processes. Therefore, cost efficient and easy to use small‐scale fed‐batch systems that can be integrated into existing laboratory equipment and workflows are required. Recently, a novel polymer‐based controlled‐release fed‐batch microtiter plate is described. In this work, the polymer‐based controlled‐release fed‐batch microtiter plate is used to investigate fed‐batch cultivations of a protease producing Bacillus licheniformis culture. Therefore, the oxygen transfer rate (OTR) is online‐monitored within each well of the polymer‐based controlled‐release fed‐batch microtiter plate using a µRAMOS device. Cultivations in five individual polymer‐based controlled‐release fed‐batch microtiter plates of two production lots show good reproducibility with a mean coefficient of variation of 9.2%. Decreasing initial biomass concentrations prolongs batch phase while simultaneously postponing the fed‐batch phase. The initial liquid filling volume affects the volumetric release rate, which is directly translated in different OTR levels of the fed‐batch phase. An increasing initial osmotic pressure within the mineral medium decreases both glucose release and protease yield. With the volumetric glucose release rate as scale‐up criterion, microtiter plate‐ and shake flask‐based fed‐batch cultivations are highly comparable. On basis of the small‐scale fed‐batch cultivations, a mechanistic model is established and validated. Model‐based simulations coincide well with the experimentally acquired data.     

Glucose-containing polymer rings enable fed-batch operation in microtiter plates with parallel online measurement of scattered light,fluorescence, dissolved oxygen tension,and pH

Bioprocesses operated in batch mode can induce adverse effects like overflow metabolism, substrate inhibition, osmotic inhibition, oxygen limitation, and catabolite repression. To avoid these adverse effects, fed-batch is the predominant operation mode in industrial production. Nevertheless, screening for optimal production strains is usually performed in microtiter plates and shake flasks operated in batch mode without any online monitoring. Recently, a polymer-based controlled-release fed-batch microtiter plate with stable glucose release characteristics was described. In this study, a glucose-containing polymer matrix was used to manufacture polymer rings that were placed at the bottom of a 48-well microtiter plate. Thereby, the liquid content of the well became accessible for optical measurement by the BioLector device. Reflections caused by the polymer ring were minimized by adjusting the scattered-light measurement position. Influences on the measurement of the dissolved oxygen tension and pH could be avoided by choosing appropriate polymer-ring geometries. These adjustments enabled parallel online measurement of scattered light, fluorescence, dissolved oxygen tension, and pH of Escherichia coli BL21 (DE3) fed-batch cultivations. The online monitoring and fed-batch operation capabilities of the fed-batch microtiter plate presented in this study finds optimal application in screenings and initial process development.     

Process-induced cell cycle oscillations in CHO cultures: Online monitoring and model-based investigation

The influence of process strategies on the dynamics of cell population heterogeneities in mammalian cell culture is still not well understood. We recently found that the progression of cells through the cell cycle causes metabolic regulations with variable productivities in antibody-producing Chimese hamster ovary (CHO) cells. On the other hand, it is so far unknown how bulk cultivation conditions, for example, variable nutrient concentrations depending on process strategies, can influence cell cycle-derived population dynamics. In this study, process-induced cell cycle synchronization was assessed in repeated-batch and fed-batch cultures. An automated flow cytometry set-up was developed to measure the cell cycle distribution online, using antibody-producing CHO DP-12 cells transduced with the cell cycle-specific fluorescent ubiquitination-based cell cycle indicator (FUCCI) system. On the basis of the population-resolved model, feeding-induced partial self-synchronization was predicted and the results were evaluated experimentally. In the repeated-batch culture, stable cell cycle oscillations were confirmed with an oscillating G1 phase distribution between 41% and 72%. Furthermore, oscillations of the cell cycle distribution were simulated and determined in a (bolus) fed-batch process with up to cells/ml. The cell cycle synchronization arose with pulse feeding only and ceased with continuous feeding. Both simulated and observed oscillations occurred at higher frequencies than those observable based on regular (e.g., daily) sample analysis, thus demonstrating the need for high-frequency online cell cycle analysis. In summary, we showed how experimental methods combined with simulations enable the improved assessment of the effects of process strategies on the dynamics of cell cycle-dependent population heterogeneities. This provides a novel approach to understand cell cycle regulations, control cell population dynamics, avoid inadvertently induced oscillations of cell cycle distributions and thus to improve process stability and efficiency.     

Effect of bioreactor configuration on substrate uptake by cell suspension cultures of the plant Eschscholtzia californica

Summary The uptake of carbohydrates and oxygen by cell suspension cultures of the plant Eschscholtzia californica (California poppy) was studied in relation to biomass production in shake flasks, a 1-1 stirred-tank bioreactor and a 1-1 pneumatically agitated bioreactor. The sequence of carbohydrate uptake was similar in all cases, with sucrose hydrolysis occurring followed by the preferential uptake of glucose. The uptake of fructose was found to be affected by the oxygen supply rate. Carbohydrate utilization occurred at a slower rate in the bioreactors. Apparent biomass yields, Y _X/S, ranged from 0.42 to 0.50 g biomass/g carbohydrate, while true biomass yields, Y _X/S, were about 0.69 g/g. The maintenance coefficient for carbohydrate, m _S, ranged between 0.002 and 0.008 g/dry weight (DW) per hour. The maximum measured specific oxygen uptake rate was 0.56 mmol O₂/g DW per hour and occurred early in the growth stage. The decline in specific uptake rate coincided with a decline in cell viability. The oxygen uptake rate was faster in shake flasks, corresponding to the higher growth rate obtained. The true growth yield on oxygen, YX/O₂, was calculated to range from 0.83 to 1.23 g biomass/g O₂, while the maintenance coefficient, mO₂, ranged from 0.15 to 0.25 mmol O₂/g DW per hour. The growth yields for oxygen determined from the stoichiometry of an elemental balance were within 10% of those calculated from experimental data. Offprint requests to: Raymond L. Legge     

Characterization of photosynthetically active duckweed (<Emphasis Type="Italic">Wolffia australiana</Emphasis>) in vitro culture by Respiration Activity Monitoring System (RAMOS)

The feasibility of oxygen transfer rate (OTR) measurement to non-destructively monitor plant propagation and vitality of photosynthetically active plant in vitro culture of duckweed (Wolffia australiana, Lemnaceae) was tested using Respiration Activity Monitoring System (RAMOS). As a result, OTR proofed to be a sensitive indicator for plant vitality. The culture characterization under day/night light conditions, however, revealed a complex interaction between oxygen production and consumption, rendering OTR measurement an unsuitable tool to track plant propagation. However, RAMOS was found to be a useful tool in preliminary studies for process development of photosynthetically active plant in vitro cultures.     

A mechanistic model for gas–liquid mass transfer prediction in a rocking disposable bioreactor

Rocking disposable bioreactors are a newer approach to smaller-scale cell growth that use a cyclic rocking motion to induce mixing and oxygen transfer from the headspace gas into the liquid. Compared with traditional stirred-tank and pneumatic bioreactors, rocking bioreactors operate in a very different physical mode and in this study the oxygen transfer pathways are reassessed to develop a fundamental mass transfer (k_La) model that is compared with experimental data. The model combines two mechanisms, namely surface aeration and oxygenation via a breaking wave with air entrainment, borrowing concepts from ocean wave models. Experimental data for across the range of possible operating conditions (rocking speed, angle, and liquid volume) confirms the validity of the modeling approach, with most predictions falling within ±20% of the experimental values. At low speeds (up to 20 rpm) the surface aeration mechanism is shown to be dominant with a of around 3.5 hr⁻¹, while at high speeds (40 rpm) and angles the breaking wave mechanism contributes up to 91% of the overall (65 hr⁻¹). This model provides an improved fundamental basis for understanding gas–liquid mass transfer for the operation, scale-up, and potential design improvements for rocking bioreactors.     

Automated feeding strategies for high-cell-density fed-batch cultivation of Pseudomonas putida KT2440

Four automatic substrate feeding strategies were developed and investigated in this study to obtain rapid, repeatable, and reliable high cell densities of Pseudomonas putida KT2440 from glucose. Growth yield data of the key nutrients, Y _X/Glucose, Y _X/NH4, Y _X/PO4, Y _X/Mg, and Y _CO2/Glucose, were determined to be 0.41, 5.44, 13.70, 236, and 0.65 g g⁻¹, respectively. Although standard exponential feeding strategy worked well when the predetermined μ was set at 0.25 h⁻¹, an exponential glucose feeding strategy with online μ _max estimation resulted in a higher average biomass productivity (3.4 vs 2.8 g l⁻¹ h⁻¹). A CO₂ production rate based pulse glucose feeding strategy also resulted in good overall productivity (3.0 g l⁻¹ h⁻¹) and can be used as an alternative to pH-stat or DO-stat feeding. A cumulative CO₂ production based continuous feed with real-time cumulative glucose consumption estimation resulted in much higher biomass productivity (4.3 g l⁻¹ h⁻¹) and appears to be an excellent and reliable approach to fully automating high-cell-density fed-batch cultivation of P. putida.     

Simulated oxygen and glucose gradients as a prerequisite for predicting industrial scale performance a priori

Transferring bioprocesses from lab to industrial scale without loss of performance is key for the successful implementation of novel production approaches. Because mixing and mass transfer is usually hampered in large scale, cells experience heterogeneities eventually causing deteriorated yields, that is, reduced titers, productivities, and sugar-to-product conversions. Accordingly, reliable and easy-to-implement tools for a priori prediction of large-scale performance based on dry and wet-lab tests are heavily needed. This study makes use of computational fluid dynamic simulations of a multiphase multi-impeller stirred tank in pilot scale. So-called lifelines, records of 120,000 Corynebacterium glutamicum cells experiencing fluctuating environmental conditions, were identified and used to properly design wet-lab scale-down (SD) devices. Physical parameters such as power input, gas hold up, , and mixing time showed good agreement with experimental measurements. Analyzing the late fed-batch cultivation revealed that the complex double gradient of glucose and oxygen can be translated into a wet-lab SD setup with only few compartments. Most remarkably, the comparison of different mesh sizes outlined that even the coarsest approach with a mesh density of was sufficient to properly predict physical and biological readouts. Accordingly, the approach offers the potential for the thorough analysis of realistic industrial case scenarios.     

Design of a microaerobically inducible replicon for high-yield plasmid DNA production

A pUC-derived replicon inducible by oxygen limitation was designed and tested in fed-batch cultures of Escherichia coli. It included the addition of a second inducible copy of rnaII, the positive replication control element. The rnaII gene was expressed from P_trc and cloned into pUC18 to test the hypothesis that the ratio of the positive control molecule RNAII to the negative control element, RNAI, was the determinant of plasmid copy number per chromosome (PCN). The construct was evaluated in several E. coli strains. Evaluations of the RNAII/RNAI ratio, PCN and plasmid yield normalized to biomass (Y_pDNA/X) were performed and the initial hypothesis was probed. Furthermore, in high cell-density cultures in shake flasks, an outstanding amount of 126 mg/L of plasmid was produced. The microaerobically inducible plasmid was obtained by cloning the rnaII gene under the control of the oxygen-responsive Vitreoscilla stercoraria hemoglobin promoter. For this plasmid, but not for pUC18, the RNAII/RNAI ratio, PCN and Y_pDNA/X efficiently increased after the shift to the microaerobic regime in fed-batch cultures in a 1 L bioreactor. The Y_pDNA/X of the inducible plasmid reached 12 mg/g at the end of the fed-batch but the original pUC18 only reached ca. 6 mg/g. The proposed plasmid is a valuable alternative for the operation and scale-up of plasmid DNA production processes in which mass transfer limitations will not represent an issue.     

Alteration of mammalian cell metabolism by dynamic nutrient feeding

The metabolism of hybridoma cells was controlled to reduce metabolic formation in fed-batch cultures by dynamically feeding a salt-free nutrient concentrate. For this purpose, on-line oxygen uptake rate (OUR) measurement was used to estimate the metabolic demand of hybridoma cells and to determine the feeding rate of a concentrated solution of salt-free DMEM/F12 medium supplemented with other medium components. The ratios among glucose, glutamine and other medium components in the feeding nutrient concentrate were adjusted stoichiometrically to provide balanced nutrient conditions for cell growth. Through on-line control of the feeding rate of the nutrient concentrate, both glucose and glutamine concentrations were maintained at low levels of 0.5 and 0.2 mM respectively during the growth stage. The concentrations of the other essential amino acids were also maintained without large fluctuations. The cell metabolism was altered from that observed in batch cultures resulting in a significant reduction of lactate, ammonia and alanine production. Compared to a previously reported fed-batch culture in which only glucose was maintained at a low level and only a reduced lactate production was observed, this culture has also reduced the production of other metabolites, such as ammonium and alanine. As a result, a high viable cell concentration of more than 1.0 × 10⁷ cells/mL was achieved and sustained over an extended period. The results demonstrate an efficient nutrient feeding strategy for controlling cell metabolism to achieve and sustain a high viable cell concentration in fed-batch mammalian cell cultures in order to enhance the productivity. This revised version was published online in July 2006 with corrections to the Cover Date.     

Regulation and optimization of xylanase production inClostridium thermolacticum

Summary In substrate-limited continuous or fed-batch cultures,Clostridium thermolacticum excreted high yield of xylanases even when readily metabolizable compounds such as glucose were used as substrate. These results demonstrated that theC. thermolacticum xylanases were constitutive and were catabolite repressed. Optimization of culture conditions showed that the highest yields were obtained in fed-batch culture.     

Production of Alkaline Protease with <Emphasis Type="Italic">Teredinobacter turnirae</Emphasis> in Controlled Fed-batch Fermentation

By using our previously optimized media and a fed-batch operation controlled by LabVIEW Software, the key parameter for a high production of alkaline protease using the marine bacterium, Teredinobacter turnirae, was to maintain a low concentration of C and N-sources ( < 2 g sucrose l⁻¹ and < 0.2 g NH₄C l l⁻¹) using an appropriate fed-batch culture system. A maximum protease activity of 8250 U ml⁻¹ was thus achieved.     

Production of recombinant β-galactosidase in bioreactors by fed-batch culture using DO-stat and linear control

β-Galactosidase enzymes continue to play an important role in food and pharmaceutical industries. These enzymes hydrolyze lactose in its constituent monosaccharides, glucose and galactose. The industrial use of enzymes presents an increase in process costs reflecting in higher final product value. An alternative to enhance processes’ productivity and yield would be the use of recombinant enzymes and their large-scale fed-batch production. The overexpression of recombinant β-galactosidase from Kluyveromyces sp. was carried out in 2-L bioreactors using Escherichia coli strain BL21 (DE3) as host. Effect of induction time on recombinant enzyme expression was studied by adding 1?mM isopropyl thiogalactoside (IPTG) at 12?h, 18?h and 24?h of cultivation. Glucose feeding strategies were compared employing feedback-controlled DO-stat and ascendant linear pump feeding in bioreactor fed-batch cultivations. Linear feeding strategy with IPTG addition at 18?h of cultivation resulted in approximately 20?g/L and 17,745?U/L of biomass and β-galactosidase activity, respectively. On the other hand, although the feedback-controlled DO-stat feeding strategy induced at 12?h of cultivation led to lower final biomass of 18?g/L, it presented an approximately 2.5 increase in enzymatic activity, resulting in 42,367?U/L, and most importantly it led to the most prominent specific enzymatic activity of approximately 40?U/mg_protein. Comparing to previous results, these results suggest that the DO-stat feeding is a promising strategy for recombinant β-galactosidase enzyme production.     

Production of alkaline protease with Bacillus licheniformis in a controlled fed-batch process

Summary A production method for alkaline serine protease with Bacillus licheniformis in a synthetic medium was developed. Employing closed-loop control of oxygen, nitrogen and carbon source the pO₂ was held at 5%, the ammonium concentration kept below 1 mM and the glycerol concentration was maintained between 20 and 100 mM. Protease production was monitored by flow injection analysis. Thus, in a fed-batch procedure production could be increased 4.6-fold in comparison to an uncontrolled batch process. Offprint requests to: G. Bierbaum