Editorial: Bioprocess Development in the era of digitalization

Neubauer, Peter; Glauche, Florian; Bournazou, Mariano Nicolás Cruz

doi:10.1002/elsc.201770113

Cited by 15 publications

(19 citation statements)

References 10 publications

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“…The system was tested in an automated robotic facility, so it can be directly included in a broader process development framework reaching up to scale-down experiments at mL scale [ 45 , 46 ]. In order to increase a liquid handling facility towards an automated bioprocess development platform by [ 47 , 48 ], this method can be further connected to automated image analysis, colony counting, and clone picking.…”

Section: Discussionmentioning

confidence: 99%

Automated Cell Treatment for Competence and Transformation of Escherichia coli in a High-Throughput Quasi-Turbidostat Using Microtiter Plates

et al. 2018

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Metabolic engineering and genome editing strategies often lead to large strain libraries of a bacterial host. Nevertheless, the generation of competent cells is the basis for transformation and subsequent screening of these strains. While preparation of competent cells is a standard procedure in flask cultivations, parallelization becomes a challenging task when working with larger libraries and liquid handling stations as transformation efficiency depends on a distinct physiological state of the cells. We present a robust method for the preparation of competent cells and their transformation. The strength of the method is that all cells on the plate can be maintained at a high growth rate until all cultures have reached a defined cell density regardless of growth rate and lag phase variabilities. This allows sufficient transformation in automated high throughput facilities and solves important scheduling issues in wet-lab library screenings. We address the problem of different growth rates, lag phases, and initial cell densities inspired by the characteristics of continuous cultures. The method functions on a fully automated liquid handling platform including all steps from the inoculation of the liquid cultures to plating and incubation on agar plates. The key advantage of the developed method is that it enables cell harvest in 96 well plates at a predefined time by keeping fast growing cells in the exponential phase as in turbidostat cultivations. This is done by a periodic monitoring of cell growth and a controlled dilution specific for each well. With the described methodology, we were able to transform different strains in parallel. The transformants produced can be picked and used in further automated screening experiments. This method offers the possibility to transform any combination of strain- and plasmid library in an automated high-throughput system, overcoming an important bottleneck in the high-throughput screening and the overall chain of bioprocess development.

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Section: Discussionmentioning

confidence: 99%

Automated Cell Treatment for Competence and Transformation of Escherichia coli in a High-Throughput Quasi-Turbidostat Using Microtiter Plates

et al. 2018

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“…The development of effective bioprocesses requires screening of many microbial strains under various cultivation conditions. State-of-the-art bioprocess development is known to be time consuming, laborious, and for having a low success rate [1]. Process parameters, such as microbial host, vector size and copy-number, feeding strategy, and media composition have a significant impact on the profitability, reliability, and sustainability of the final manufacturing process.…”

Section: Introductionmentioning

confidence: 99%

Monitoring Parallel Robotic Cultivations with Online Multivariate Analysis

et al. 2020

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In conditional microbial screening, a limited number of candidate strains are tested at different conditions searching for the optimal operation strategy in production (e.g., temperature and pH shifts, media composition as well as feeding and induction strategies). To achieve this, cultivation volumes of >10 mL and advanced control schemes are required to allow appropriate sampling and analyses. Operations become even more complex when the analytical methods are integrated into the robot facility. Among other multivariate data analysis methods, principal component analysis (PCA) techniques have especially gained popularity in high throughput screening. However, an important issue specific to high throughput bioprocess development is the lack of so-called golden batches that could be used as a basis for multivariate analysis. In this study, we establish and present a program to monitor dynamic parallel cultivations in a high throughput facility. PCA was used for process monitoring and automated fault detection of 24 parallel running experiments using recombinant E. coli cells expressing three different fluorescence proteins as the model organism. This approach allowed for capturing events like stirrer failures and blockage of the aeration system and provided a good signal to noise ratio. The developed application can be easily integrated in existing data- and device-infrastructures, allowing automated and remote monitoring of parallel bioreactor systems.

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“…These factors are known to affect the underlying nonlinear dynamics of the bioprocess and are par t of the very complex time-dependent interaction between the bioreactor environment and the cell factory. This highly nonlinear behavior makes it difficult to predict the effect of changes in the cultivating conditions and is responsible for the high failure rate in scale-up [13,14]. In order to overcome these challenges, experiments in conditional screening require highly advanced experimental setups able to: (i) operate as similar as possible to the industrial strategy (e.g.…”

Section: Introductionmentioning

confidence: 99%

Automated Conditional Screening of Escherichia Coli Knockout Mutants in Parallel Adaptive Fed-Batch Cultivations

Hans¹,

Haby²,

Krausch³

et al. 2020

Preprint

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In bioprocess development, the host and the genetic construct for a new biomanufacturing process are selected in the early developmental stages. This decision, made at the screening scale with very limited information about the performance of the selected cell factory in larger reactors, has a major influence on the performance of the final process. To overcome this, scaledown approaches are essential to run screenings that show the real cell factory performance at industrial like conditions. We present a fully automated robotic facility with 24 parallel mini-bioreactors that is operated by a model based adaptive input design framework for the characterization of clone libraries under scale-down conditions. The cultivation operation strategies are computed and continuously refined based on a macro-kinetic growth model that is continuously re-fitted to the available experimental data. The added value of the approach is demonstrated with 24 parallel fed-batch cultivations in a mini-bioreactor system with eight different Escherichia coli strains in triplicate. The 24 fed-batches ran under the desired conditions generating sufficient information to define the fastest growing strain in an environment with varying glucose concentrations similar to industrial scale bioreactors.

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Editorial: Bioprocess Development in the era of digitalization

Cited by 15 publications

References 10 publications

Automated Cell Treatment for Competence and Transformation of Escherichia coli in a High-Throughput Quasi-Turbidostat Using Microtiter Plates

Automated Cell Treatment for Competence and Transformation of Escherichia coli in a High-Throughput Quasi-Turbidostat Using Microtiter Plates

Monitoring Parallel Robotic Cultivations with Online Multivariate Analysis

Automated Conditional Screening of Escherichia Coli Knockout Mutants in Parallel Adaptive Fed-Batch Cultivations

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