Investigation and evaluation of a 3D-printed optical modified cultivation vessel for improved scattered light measurement of biotechnologically relevant organisms.

In the field of bioprocess development miniaturization, parallelization and flexibility play a key role reducing costs and time. To precisely meet these requirements, additive manufacturing (3D-printing) is an ideal technology. 3D-printing enables rapid prototyping and cost-effective fabrication of individually designed devices with complex geometries on demand. For successful bioprocess development, monitoring of process-relevant parameters, such as pH, dissolved oxygen (DO), and biomass, is crucial. Online monitoring is preferred as offline sampling is time-consuming and leads to loss of information. In this study, 3D-printed cultivation vessels with optical prisms are evaluated for the use in upstream processes of different industrially relevant microorganisms and cell lines. It was shown, that the 3D-printed optically modified well (OMW) is of benefit for a wide range of biotechnologically relevant microorganisms and even for mammalian suspension cells. Evaluation tests with Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, and Chinese hamster ovary (CHO) cells were performed, providing highly reproducible results. Growth behavior of OMW cultures was comparable to behavior of shake flask (SF) cultivations and the signal to noise ratio in online biomass measurement was shown to be reduced up to 95.8% by using the OMW. Especially the cultivation phases with low turbidity respective optical densities below 1.0 rel.AU could be monitored accurately for the first time. Furthermore, it was demonstrated that the 3D-printed optics are transferable to different well geometries and sizes, enabling efficient biomass monitoring for individual requirements with tailor-made 3D-printed cultivation vessels in small scale.

Sensors and Techniques for On-Line Determination of Cell Viability in Bioprocess Monitoring.

In recent years, the bioprocessing industry has experienced significant growth and is increasingly emerging as an important economic sector. Here, efficient process management and constant control of cellular growth are essential. Good product quality and yield can only be guaranteed with high cell density and high viability. Whereas the on-line measurement of physical and chemical process parameters has been common practice for many years, the on-line determination of viability remains a challenge and few commercial on-line measurement methods have been developed to date for determining viability in industrial bioprocesses. Thus, numerous studies have recently been conducted to develop sensors for on-line viability estimation, especially in the field of optical spectroscopic sensors, which will be the focus of this review. Spectroscopic sensors are versatile, on-line and mostly non-invasive. Especially in combination with bioinformatic data analysis, they offer great potential for industrial application. Known as soft sensors, they usually enable simultaneous estimation of multiple biological variables besides viability to be obtained from the same set of measurement data. However, the majority of the presented sensors are still in the research stage, and only a few are already commercially available.

Improved Time Resolved KPI and Strain Characterization of Multiple Hosts in Shake Flasks Using Advanced Online Analytics and Data Science.

Shake flasks remain one of the most widely used cultivation systems in biotechnology, especially for process development (cell line and parameter screening). This can be justified by their ease of use as well as their low investment and running costs. A disadvantage, however, is that cultivations in shake flasks are black box processes with reduced possibilities for recording online data, resulting in a lack of control and time-consuming, manual data analysis. Although different measurement methods have been developed for shake flasks, they lack comparability, especially when changing production organisms. In this study, the use of online backscattered light, dissolved oxygen, and pH data for characterization of animal, plant, and microbial cell culture processes in shake flasks are evaluated and compared. The application of these different online measurement techniques allows key performance indicators (KPIs) to be determined based on online data. This paper evaluates a novel data science workflow to automatically determine KPIs using online data from early development stages without human bias. This enables standardized and cost-effective process-oriented cell line characterization of shake flask cultivations to be performed in accordance with the process analytical technology (PAT) initiative. The comparison showed very good agreement between KPIs determined using offline data, manual techniques, and automatic calculations based on multiple signals of varying strengths with respect to the selected measurement signal.

Predictive Monitoring of Shake Flask Cultures with Online Estimated Growth Models.

Simplicity renders shake flasks ideal for strain selection and substrate optimization in biotechnology. Uncertainty during initial experiments may, however, cause adverse growth conditions and mislead conclusions. Using growth models for online predictions of future biomass (BM) and the arrival of critical events like low dissolved oxygen (DO) levels or when to harvest is hence important to optimize protocols. Established knowledge that unfavorable metabolites of growing microorganisms interfere with the substrate suggests that growth dynamics and, as a consequence, the growth model parameters may vary in the course of an experiment. Predictive monitoring of shake flask cultures will therefore benefit from estimating growth model parameters in an online and adaptive manner. This paper evaluates a newly developed particle filter (PF) which is specifically tailored to the requirements of biotechnological shake flask experiments. By combining stationary accuracy with fast adaptation to change the proposed PF estimates time-varying growth model parameters from iteratively measured BM and DO sensor signals in an optimal manner. Such proposition of inferring time varying parameters of Gompertz and Logistic growth models is to our best knowledge novel and here for the first time assessed for predictive monitoring of Escherichia coli (E. coli) shake flask experiments. Assessments that mimic real-time predictions of BM and DO levels under previously untested growth conditions demonstrate the efficacy of the approach. After allowing for an initialization phase where the PF learns appropriate model parameters, we obtain accurate predictions of future BM and DO levels and important temporal characteristics like when to harvest. Statically parameterized growth models that represent the dynamics of a specific setting will in general provide poor characterizations of the dynamics when we change strain or substrate. The proposed approach is thus an important innovation for scientists working on strain characterization and substrate optimization as providing accurate forecasts will improve reproducibility and efficiency in early-stage bioprocess development.

A Portable Biosensor for 2,4-Dinitrotoluene Vapors.

Buried explosive material, e.g., landmines, represent a severe issue for human safety all over the world. Most explosives consist of environmentally hazardous chemicals like 2,4,6-trinitrotoluene (TNT), carcinogenic 2,4-dinitrotoluene (2,4-DNT) and related compounds. Vapors leaking from buried landmines offer a detection marker for landmines, presenting an option to detect landmines without relying on metal detection. 2,4-Dinitrotoluene (DNT), an impurity and byproduct of common TNT synthesis, is a feasible detection marker since it is extremely volatile. We report on the construction of a wireless, handy and cost effective 2,4-dinitrotoluene biosensor combining recombinant bioluminescent bacterial cells and a compact, portable optical detection device. This biosensor could serve as a potential alternative to the current detection technique. The influence of temperature, oxygen and different immobilization procedures on bioluminescence were tested. Oxygen penetration depth in agarose gels was investigated, and showed that aeration with molecular oxygen is necessary to maintain bioluminescence activity at higher cell densities. Bioluminescence was low even at high cell densities and 2,4-DNT concentrations, hence optimization of different prototypes was carried out regarding radiation surface of the gels used for immobilization. These findings were applied to sensor construction, and 50 ppb gaseous 2,4-DNT was successfully detected.

Toward Microbioreactor Arrays: A Slow-Responding Oxygen Sensor for Monitoring of Microbial Cultures in Standard 96-Well Plates.

In this study, a slow-responding chemo-optical sensor for dissolved oxygen (DO) integrated into a 96-well plate was developed. The slow response time ensures that the measured oxygen value does not change much during plate transport to the microplate reader. The sensor therefore permits at-line DO measurement of microbial cultures. Moreover, it eliminates the necessity of individual optical measurement systems for each culture plate, as many plates can be measured successively. Combined with the 96-well format, this increases the experimental throughput enormously. The novel sensor plate (Slow OxoPlate) consists of fluorophores suspended in a polymer matrix that were placed into u-bottom 96-well plates. Response time was measured using sodium sulfite, and a t90 value of 9.7 min was recorded. For application, DO values were then measured in Escherichia coli and Saccharomyces cerevisiae cultures grown under fed-batch-like conditions. Depending on the DO sensor's response time, different information on the oxygenation state of the culture plate was obtained: a fast sensor variant detects disturbance through sampling, whereas the slow sensor indicates oxygen limitation during incubation. A combination of the commercially available OxoPlate and the Slow OxoPlate enables operators of screening facilities to validate their cultivation procedures with regard to oxygen availability.

Application of an online-biomass sensor in an optical multisensory platform prototype for growth monitoring of biotechnical relevant microorganism and cell lines in single-use shake flasks.

In the context of this work we evaluated a multisensory, noninvasive prototype platform for shake flask cultivations by monitoring three basic parameters (pH, pO2 and biomass). The focus lies on the evaluation of the biomass sensor based on backward light scattering. The application spectrum was expanded to four new organisms in addition to E. coli K12 and S. cerevisiae [1]. It could be shown that the sensor is appropriate for a wide range of standard microorganisms, e.g., L. zeae, K. pastoris, A. niger and CHO-K1. The biomass sensor signal could successfully be correlated and calibrated with well-known measurement methods like OD600, cell dry weight (CDW) and cell concentration. Logarithmic and Bleasdale-Nelder derived functions were adequate for data fitting. Measurements at low cell concentrations proved to be critical in terms of a high signal to noise ratio, but the integration of a custom made light shade in the shake flask improved these measurements significantly. This sensor based measurement method has a high potential to initiate a new generation of online bioprocess monitoring. Metabolic studies will particularly benefit from the multisensory data acquisition. The sensor is already used in labscale experiments for shake flask cultivations.

Oxygen supply in disposable shake-flasks: prediction of oxygen transfer rate, oxygen saturation and maximum cell concentration during aerobic growth.

Dissolved oxygen plays an essential role in aerobic cultivation especially due to its low solubility. Under unfavorable conditions of mixing and vessel geometry it can become limiting. This, however, is difficult to predict and thus the right choice for an optimal experimental set-up is challenging. To overcome this, we developed a method which allows a robust prediction of the dissolved oxygen concentration during aerobic growth. This integrates newly established mathematical correlations for the determination of the volumetric gas-liquid mass transfer coefficient (kLa) in disposable shake-flasks from the filling volume, the vessel size and the agitation speed. Tested for the industrial production organism Corynebacterium glutamicum, this enabled a reliable design of culture conditions and allowed to predict the maximum possible cell concentration without oxygen limitation.

Optical device for parallel online measurement of dissolved oxygen and pH in shake flask cultures.

We describe a new device with parallel optical measurement of dissolved oxygen (DO) and pH in up to nine shake flasks applicable in any conventional shaking incubator. Measurement ranges are 0-500% of air saturation for oxygen and 5.5-8.5 for pH. It was used to characterize growth profiles of different L-lysine producing strains of Corynebacterium glutamicum, of Saccharomyces cerevisiae and of Escherichia coli. Cultures in unbaffled flasks were highly reproducible. Oxygen limitation was indicated online which is particularly important when cultivating fast growing cells as E. coli. C. glutamicum strains showed distinct characteristic patterns of DO and pH indicating biological events. During the cultivation of S. cerevisiae on glucose, fructose and galactose, oxygen uptake rate was determined using the predetermined value of k(L)a. pH measurement was used to determine the minimum buffer requirement for a culture of C. glutamicum.

Methods and milliliter scale devices for high-throughput bioprocess design.

Based on electromagnetic simulations as well as on computational fluid dynamics simulations gas-inducing impellers and their magnetic inductive drive were optimized for stirred-tank reactors on a 10 ml-scale arranged in a bioreaction block with 48 bioreactors. High impeller speeds of up to 4,000 rpm were achieved at very small electrical power inputs (63 W with 48 bioreactors). The maxima of local energy dissipation in the reaction medium were estimated to be up to 50 W L(-1) at 2,800 rpm. Total power input and local energy dissipation are thus well comparable to standard stirred-tank bioreactors. A prototype fluorescence reader for 8 bioreactors with immobilized fluorometric sensor spots was applied for online measurement of dissolved oxygen concentration making use of the phase detection method. A self-optimizing scheduling software was developed for parallel control of 48 bioreactors with a liquid-handling system for automation of titration and sampling. It was shown on the examples of simple parallel batch cultivations of Escherichia coli with different media compositions that high cell densities of up to 16.5 g L(-1) dry cell mass can be achieved without pH-control within 5 h with a high parallel reproducibility (standard deviation<3.5%, n=48) due to the high oxygen transfer capability of the gas-inducing stirred-tank bioreactors.

Microplates with integrated oxygen sensors for kinetic cell respiration measurement and cytotoxicity testing in primary and secondary cell lines.

This paper presents a cytotoxicity and cell respiration assay that is nondestructive and kinetic. It makes use of 96-well microplates integrated with oxygen sensors. The oxygen signal monitored on-line gives an indication of the cell viability. We show its application for suspension cell lines (Chinese hamster ovary and HL60 cells) as well as adherent (Caco2 cells) and primary (rat hepatocytes) cells using well-known cytotoxic compounds (sodium azide, diclofenac, clozapine, sodium dodecyl sulfate, 2-thiouracil, tamoxifen, and tranylcypromine). The 50% lethality concentration (LC50) obtained from the assay is compared with the standard 3-(4,5-dimethylthiazol-2- yl)-2,5-diphenyl-2H-tetrazolium bromide end-point assay. The cells can be grown directly in the plates, and the assay requires no further reagents or processing. The cells can be harvested for further analysis, if required. The on-line dynamic measurement allows the calculation of LC50 as a function of exposure time. LC50 was shown to decrease with time in HL60 cells. The dynamics of this process was considerably different for the three compounds sodium dodecyl sulfate, tamoxifen, and diclofenac, indicating a large potential of application of this method for cell death studies. The assay system can be applied to almost any cell-based systems with little adaptation. The assay is robust, flexible, and applicable for medium- to high-throughput systems requiring only minimal handling and no additional agent.

Miniature bioreactors for automated high-throughput bioprocess design (HTBD): reproducibility of parallel fed-batch cultivations with Escherichia coli.

To verify the reproducibility of cultivations of Escherichia coli in novel millilitre-scale bioreactors, fully automated fed-batch cultivation was performed in seven parallel-operated ml-scale bioreactors with an initial volume of 10 ml/reactor. The process was automatically controlled by a liquid-handling system responsible for glucose feeding, titration and sampling. Atline analysis (carried out externally of the reaction vessel with a short time delay) comprised automated pH and attenuance measurements. The partial pressure of oxygen (pO2) was measured online by a novel fluorimetric sensor block measuring the fluorescence lifetime of fluorophors immobilized inside the millilitre-scale bioreactors. Within a process time of 14.6 h, the parallel cultivation yielded a dry cell weight of 36.9+/-0.9 g.l(-1). Atline pH measurements were characterized by an S.D. of <1.1% throughout the process. Computational-fluid-dynamics simulation of single-phase flow yields a mean power input of 21.9 W.l(-1) at an impeller speed of 2800 rev./min corresponding to a power number (NP) of 3.7.

Gas sensing in microplates with optodes: influence of oxygen exchange between sample, air, and plate material.

Microplates with integrated optical oxygen sensors are a new tool to study metabolic rates and enzyme activities. Precise measurements are possible only if oxygen exchange between the sample and the environment is known. In this study we quantify gas exchange in plastic microplates. Dissolved oxygen was detected using either an oxygen-sensitive film fixed at the bottom of each well or a needle-type sensor. The diffusion of oxygen into wells sealed with different foils, paraffin oil, and paraffin wax, respectively, was quantified. Although foil covers showed the lowest oxygen permeability, they include an inevitable gas phase between sample and sealing and are difficult to manage. The use of oil was found to be critical due to the extensive shaking caused by movement of the plates during measurements in microplate readers. Thus, paraffin wax was the choice material because it avoids convection of the sample and is easy to handle. Furthermore, without shaking, significant gradients in pO2 levels within a single well of a polystyrene microplate covered with paraffin oil were detected with the needle-type sensor. Higher pO2 levels were obtained near the surface of the sample as well as near the wall of the well. A significant diffusion of oxygen through the plastic plate material was found using plates based on polystyrene. Thus, the location of a sensor element within the well has an effect on the measured pO2 level. Using a sensor film fixed on the bottom of a well or using a dissolved pO2-sensitive indicator results in pO2 offset and in apparently lower respiration rates or enzyme activities. Oxygen diffusion through a polystyrene microplate was simulated for measurements without convection--that is, for samples without oxygen diffusion through the cover and for unshaken measurements using permeable sealings. This mathematical model allows for calculation of the correct kinetic parameters.

Evaluation of OxoPlate for real-time assessment of antibacterial activities.

We have evaluated the OxoPlate OP96F for its usefulness in the characterization of antibacterial compounds. Each well of the plate carries two different fluorescent dyes, an oxygen-sensitive indicator dye and a reference dye. Fluorescence intensity is proportional to the amount of dissolved oxygen in the medium. Growth of bacterial cells is measured indirectly via the gradual depletion of oxygen. In this study, Bacillus subtilis was treated with 14 different antibacterials of various modes of action. The OxoPlate was not only useful to deduce MIC values directly from the oxygen-depletion curves, but was also able to discriminate bactericidal from bacteriostatic compounds. Oxygen levels of cultures treated with bactericidal compounds dropped initially and then increased after the cells had died. In contrast, oxygen levels remained low when cultures were treated with bacteriostatic compounds. The system described herein gives valuable insight into the kinetics of growth inhibition and killing, and we conclude that the OxoPlate is highly useful for the initial characterization of antibacterials.

PH-sensing 96-well microtitre plates for the characterization of acid production by dairy starter cultures.

A new method for characterization of acid production by dairy starter cultures is presented. Microplates with integrated optical pH sensors are developed. Two fluorophores, a pH-sensitive and a pH-insensitive one are immobilised at the bottom of a polystyrene 96-well microtitre plate. The pH-insensitive fluorophore serves as an internal reference and makes calibration unnecessary. The sensor measures pH accurately in optically well-defined media. Particles and fluorophores contained in the bulk medium disturbed the measurements. Despite these disturbances it was possible to clearly sense differences in inoculum type and in inoculum sizes of cultures of Lactococcus lactis and of Streptococcus thermophilus at 30 and 37 degrees C. Besides a pH-related signal there is information about other changes during milk fermentation. The cultivation results were compared with those from the established CINAC-method. From this comparison it can be concluded that the new method can be used reliably to characterize particularly a large number of strains for screening purposes but also for quality control.

Characterization and application of an optical sensor for quantification of dissolved O2 in shake-flasks.

On-line measurement of dissolved O2 in shake-flasks was realized via immobilized sensor spots containing a fluorophore with an O2-dependent luminescent decay time. An unaffected sensor signal during 80 autoclaving cycles suggests multi-usage of sensor equipped shake-flasks. The sensor had a response time of 6 s. Quantification of gas-liquid mass transfer revealed maximum kLa values of 150 h(-1), from which maximum O2 transfer capacity of 33 mM h(-1) was calculated. Liquid volume and shaking frequency have a strong influence on kLa. Exemplified by cultivations of Corynebacterium glutamicum the importance of shaking rate for O2 supply of bacterial cultures is shown. Sampling of microbial cultures with intermittent shaking of a few minutes can cause O2 limitation. Based on the results of this work a simple and straightforward tool is now available for accurate O2 sensing in shake-flasks, which are widely used in microbial cultivations.

Rapid evaluation of oxygen and water permeation through microplate sealing tapes.

Eight commercially available microplate sealing tapes and 10 other suitable materials (transparent wound dressings) are compared qualitatively in terms of their ability to minimize water evaporation from a multiwell plate while maintaining the oxygen supply as high as possible, which is necessary for applications like aerobic growth. The transparency and sterility of the products are considered as well. All evaluated commercially available sealing tapes fall into one of the following two classes: (1) O(2) transfer is comparable to that of an unsealed plate, but water vapor retention is relatively low, or (2) O(2) transfer via the sealing is slower, but the water retention capability is comparably high. All but one of the evaluated wound dressings fall under the second class. That dressing, however, constitutes a compromise by showing both moderate O(2) permeability and medium water retention. But the estimated mass transport in a microtiter plate sealed with this dressing is about 5 times slower than that of an unsealed 96 well plate. The aim of this publication is to enable the reader to choose a microtiter plate sealing from the materials evaluated within this work and to use the rapid methods described herein to easily perform tests of additional sealing materials.

Integrated optical sensing of dissolved oxygen in microtiter plates: a novel tool for microbial cultivation.

Microtiter plates with integrated optical sensing of dissolved oxygen were developed by immobilization of two fluorophores at the bottom of 96-well polystyrene microtiter plates. The oxygen-sensitive fluorophore responded to dissolved oxygen concentration, whereas the oxygen-insensitive one served as an internal reference. The sensor measured dissolved oxygen accurately in optically well-defined media. Oxygen transfer coefficients, k(L)a, were determined by a dynamic method in a commercial microtiter plate reader with an integrated shaker. For this purpose, the dissolved oxygen was initially depleted by the addition of sodium dithionite and, by oxygen transfer from air, it increased again after complete oxidation of dithionite. k(L)a values in one commercial reader were about 10 to 40 h(-1). k(L)a values were inversely proportional to the filling volume and increased with increasing shaking intensity. Dissolved oxygen was monitored during cultivation of Corynebacterium glutamicum in another reader that allowed much higher shaking intensity. Growth rates determined from optical density measurement were identical to those observed in shaking flasks and in a stirred fermentor. Oxygen uptake rates measured in the stirred fermentor and dissolved oxygen concentrations measured during cultivation in the microtiter plate were used to estimate k(L)a values in a 96-well microtiter plate. The resulting values were about 130 h(-1), which is in the lower range of typical stirred fermentors. The resulting maximum oxygen transfer rate was 26 mM h(-1). Simulations showed that the errors caused by the intermittent measurement method were insignificant under the prevailing conditions.

Modeling of mixing in 96-well microplates observed with fluorescence indicators.

Mixing in 96-well microplates was studied using soluble pH indicators and a fluorescence pH sensor. Small amounts of alkali were added with the aid of a multichannel pipet, a piston pump, and a piezoelectric actuator. Mixing patterns were observed visually using a video camera. Addition of drops each of about 1 nL with the piezoelectric actuator resulted in umbrella and double-disklike shapes. Convective mixing was mainly observed in the upper part of the well, whereas the lower part was only mixed quickly when using the multichannel pipet and the piston pump with an addition volume of 5 microL or larger. Estimated mixing times were between a few seconds and several minutes. Mixing by liquid dispensing was much more effective than by shaking. A mixing model consisting of 21 elements could describe mixing dynamics observed by the dissolved fluorescence dye and by the optical immobilized pH sensor. This model can be applied for designing pH control in microplates or for design of kinetic experiments with liquid addition.