Mixing at the microscale: Power input in shaken microtiter plates

Synthesis and Characterization of Lignin-Silver Nanoparticles

Metal nanoparticle synthesis via environmentally friendly methods is gaining interest for their potential advantages over conventional physico-chemical approaches. Herein, we propose a robust green synthesis route for lignin-modified silver nanoparticles, utilizing the recovery of lignin as a renewable raw material and exploring its application in valuable areas. Through a systematic approach combining UV-Vis spectroscopy with AAS and DLS, we identified repeatable and scalable reaction conditions in an aqueous solution at pH 11 for homogeneous silver nanoparticles with high uniformity. The TEM median sizes ranged from 12 to 15 nm with circularity between 0.985 and 0.993. The silver nanoparticles yield exceeded 0.010 mol L-1, comparable with traditional physico-chemical methods, with a minimal loss of silver precursor ranging between 0.5 and 3.9%. Characterization by XRD and XPS revealed the presence of Ag-O bonding involving lignin functional groups on the pure face-centered cubic structure of metallic silver. Moreover, the lignin-modified silver nanoparticles generated a localized thermal effect upon near-infrared laser irradiation (808 nm), potentially allowing for targeted applications in the biomedical field. Our study showcases the potential of lignin as a renewable reducing and capping agent for silver nanoparticle synthesis, addressing some shortcomings of green synthesis approaches and contributing to the development of suitable nanomaterials.

A microtiter peg lid with ziggurat geometry for medium-throughput antibiotic testing and in situ imaging of biofilms

Bacteria biofilm responses to disinfectants and antibiotics are quantified and observed using multiple methods, though microscopy, particularly confocal laser scanning microscopy (CLSM) is preferred due to speed, a reduction in user error, and in situ analysis. CLSM can resolve biological and spatial heterogeneity of biofilms in 3D with limited throughput. The microplate peg-lid-based assay, described in ASTM E2799-22, is a medium-throughput method for testing biofilms but does not permit in situ imaging. Breaking off the peg, as recommended by the manufacturer, risks sample damage, and is limited to easily accessible pegs. Here we report modifications to the peg optimized for in situ visualization and visualization of all pegs. We report similar antibiotic challenge recovery via colony formation following the ASTM E2799-22 protocol and in situ imaging. We report novel quantifiable effects of antibiotics on biofilm morphologies, specifically biofilm streamers. The new design bridges the MBEC® assays design that selects for biofilm phenotypes with in situ imaging needs.

Development of a novel microplate for high-throughput screening and optimization of DHA producing strains based on CFD technology

Microtiter plates are suitable for screening and process development of most microorganisms. They are currently the container of choice for high-throughput and small-scale microbial culture, but require optimization for specific work. In this research, a novel type of microtiter plate was developed using computational fluid dynamics (CFD) technology. The new plate provided high oxygen supply and optimal mixing effects for the fermentation culture of docosahexaenoic acid (DHA) producing strains, surpassing the conventional method of strain screening with shake flasks, which was insufficient. The shape of the microtiter plate was modified, and baffles were introduced to improve mass transfer and oxygen supply effects in the vibrating bioreactor. CFD technology was used to model the new plate's characteristics, establishing the superiority of hexagonal microtiter plates with six baffles. Parameters in the incubation process, such as vibration frequency and liquid load, were optimized, and the final result achieved an oxygen transfer coefficient (KL a) of 0.61 s-1 and a volume power input of 2364 w m-3 , which was four to five times better than the original 96-well plate. The culture results optimized by the model were also verified. Therefore, this new microtiter plate provides a powerful tool for future high-throughput screening of strains.

Characterization of hydrodynamics and volumetric power input in microtiter plates for the scale-up of downstream operations

Parameter estimation for scale-up of downstream operations from microtiter plates (MTPs) is mostly done empirically because engineering correlations between microplates and stirred tank reactors (STRs) are not yet available. It is challenging to change the operation mode from shaken MTPs to large-scale STRs. For the scale-up of STRs, volumetric power input is well-established although it is unclear whether this parameter can be used to transfer the operations from MTPs. We determine the volumetric power input in MTPs via the temperature increase caused by the motion of the liquid. The hydrodynamics in MTPs are studied with computational fluid dynamics (CFD). Mixing is investigated in 96-, 24-, and 6-well MTPs to cover different geometries, filling volumes, shaking diameters, and shaking frequencies. All CFD simulations are validated by experimental results, which now allows prediction of the volumetric power input and hydrodynamics at various conditions in MTPs without the need for further experiments. We provide a map of the power input achievable in MTPs. Based on this map, from knowing about large-scale conditions, adequate microscale conditions can be adjusted for process development. This enables the direct scale-up of downstream unit operations from MTPs to STRs.

Equal mixing time enables scale-down and optimization of a CHO cell culture process using a shaken microbioreactor system

The advancement of microbioreactor technology in recent years has transformed early- and mid-stage process development. The monitoring and control capabilities of microbioreactors not only promote the quick accumulation of process knowledge but has also led to an increased scalability when compared to traditionally used systems such as shake flasks and microtitre plates. This study seeks to establish a framework for the micro-Matrix microbioreactor (Applikon-Biotechnology BV) as process development tool. Using the Dual Indicator System for Mixing Time, the system was initially characterized for mixing properties at varying operating conditions, which was found to yield mixing times between 0.9 and 41.8 s. A matched mixing time was proposed as scale-down criterion for an IgG4 producing GS-CHO fed-batch process between a 5 L stirred tank reactor (STR) and the micro-Matrix microbioreactor. Growth trends, maximum viable cell concentrations, final titre, and glycoprofiles were nearly identical at both scales. The scale-down model was then employed to optimize a bolus feeding regime using response surface methodology, which led to a 25.4% increase of the space-time yield and a 25% increase of the final titre. The optimized feeding strategy was validated at the small-scale and successfully scaled up to the 5 L STR. This work for the first time provides a framework of how the micro-Matrix microbioreactor can be implemented in a bioprocess development workflow and demonstrates scalability of growth and production kinetics as well as IgG4 glycosylation between the micro-Matrix and a benchtop-scale STR system.

Mixing Performance Analysis of Orbitally Shaken Bioreactors

This study investigated the efficacy of a novel correlation of power input, energy dissipation rate and mixing time as a potential route to identify the orbitally shaken bioreactor (OSB) system. The Buckingham’s π-theorem was used to designate and transform dimensionless Newton numbers with five relevant power input variables. These variables were empirically varied to evaluate the correlation among the dimensionless numbers. The Newton number decreases with the increased shaking frequency and filling volume. Previous work has focused on optimizing the mixing process by evaluating different shaking and agitation mixing methods. We establish a new mixing process and assessable measurement of the mixing time in the OSB. An innovative explanation of mixing time for the thermal method is proposed. The optimal mixing time is independent of the temperature of filled liquid. The dimensionless mixing number remained constant in the turbulent regime and increasing with the increased liquid viscosity and filling volume. Our findings revealed that the observed correlation is a practical tool to figure the power consumption and mixing efficiency as cell cultivation in all OSB scales and is fully validated when scaling–up system.

Semi-automation of process analytics reduces operator effect

The aim of this study was to semi-automate process analytics for the quantification of common impurities in downstream processing such as host cell DNA, host cell proteins and endotoxins using a commercial liquid handling station. By semi-automation, the work load to fully analyze the elution peak of a purification run was reduced by at least 2.41 h. The relative standard deviation of results among different operators over a time span of up to 6 months was at the best reduced by half, e.g. from 13.7 to 7.1% in dsDNA analysis. Automation did not improve the reproducibility of results produced by one operator but released time for data evaluation and interpretation or planning of experiments. Overall, semi-automation of process analytics reduced operator-specific influence on test results. Such robust and reproducible analytics is fundamental to establish process analytical technology and get downstream processing ready for Quality by Design approaches.

Reassessing the out-of-phase phenomenon in shake flasks by evaluating the angle-dependent liquid distribution relative to the direction of the centrifugal acceleration

Shake flasks are still the most relevant experimental tool in the development of viscous fermentation processes. The phase number, which defines the onset of the unfavorable out-of-phase (OP) phenomenon in shake flasks, was previously defined via specific power input measurements. In the OP state, the bulk liquid no longer follows the orbital movement of the imposed centrifugal force, which is for example, detrimental to oxygen transfer. In this study, an optical fluorescence technique was used to measure the three-dimensional liquid distribution in shake flasks. Four new optically derived evaluation criteria for the phase transition between the in-phase and OP condition were established: (a) thickness of the liquid film left on the glass wall by the rotating bulk liquid, (b) relative slope of the leading edge of bulk liquid (LB) lines, (c) trend of the angular position of LB, and (d) very high angular position of the leading edge. In contrast to the previously applied power input measurements, the new optical evaluation criteria describe the phase transition in greater detailed. Instead of Ph = 1.26, a less conservative value of Ph = 0.91 is now suggested for the phase transfer, which implies a broader operating window for shake flask cultivations with higher viscosities.

Less Sacrifice, More Insight: Repeated Low-Volume Sampling of Microbioreactor Cultivations Enables Accelerated Deep Phenotyping of Microbial Strain Libraries

With modern genetic engineering tools, high number of potentially improved production strains can be created in a short time. This results in a bottleneck in the succeeding step of bioprocess development, which can be handled by accelerating quantitative microbial phenotyping. Miniaturization and automation are key technologies to achieve this goal. In this study, a novel workflow for repeated low-volume sampling of BioLector-based cultivation setups is presented. Six samples of 20 μL each can be taken automatically from shaken 48-well microtiter plates without disturbing cell population growth. The volume is sufficient for quantification of substrate and product concentrations by spectrophotometric-based enzyme assays. From transient concentration data and replicate cultures, valid performance indicators (titers, rates, yields) are determined through process modeling and random error propagation analysis. Practical relevance of the workflow is demonstrated with a set of five genome-reduced Corynebacterium glutamicum strains that are engineered for Sec-mediated heterologous cutinase secretion. Quantitative phenotyping of this strain library led to the identification of a strain with a 1.6-fold increase in cutinase yield. The prophage-free strain carries combinatorial deletions of three gene clusters (Δ3102-3111, Δ3263-3301, and Δ3324-3345) of which the last two likely contain novel target genes to foster rational engineering of heterologous cutinase secretion in C. glutamicum.

Microbioreactor Systems for Accelerated Bioprocess Development

In recent years, microbioreactor (MBR) systems have evolved towards versatile bioprocess engineering tools. They provide a unique solution to combine higher experimental throughput with extensive bioprocess monitoring and control, which is indispensable to develop economically and ecologically competitive bioproduction processes. MBR systems are based either on down-scaled stirred tank reactors or on advanced shaken microtiter plate cultivation devices. Importantly, MBR systems make use of optical measurements for non-invasive, online monitoring of important process variables like biomass concentration, dissolved oxygen, pH, and fluorescence. The application range of MBR systems can be further increased by integration into liquid handling robots, enabling automatization and, thus standardization, of various handling and operation procedures. Finally, the tight integration of quantitative strain phenotyping with bioprocess development under industrially relevant conditions greatly increases the probability of finding the right combination of producer strain and bioprocess control strategy. This review will discuss the current state of the art in the field of MBR systems and we can readily conclude that their importance for industrial biotechnology will further increase in the near future.

Bioprocess microfluidics: applying microfluidic devices for bioprocessing

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Microfluidic devices as novel bioprocess development tools.

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Processes with stem cells, microbes and enzymes are viable in microfluidic devices.

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Microfluidic devices with integrated sensors provide high quality data.

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Laminar flow enables spatial and temporal control over transport phenomena.

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Standardization of devices required for automation and industrial uptake.

Scale-down approaches have long been applied in bioprocessing to resolve scale-up problems. Miniaturized bioreactors have thrived as a tool to obtain process relevant data during early-stage process development. Microfluidic devices are an attractive alternative in bioprocessing development due to the high degree of control over process variables afforded by the laminar flow, and the possibility to reduce time and cost factors. Data quality obtained with these devices is high when integrated with sensing technology and is invaluable for scale-translation and to assess the economical viability of bioprocesses. Microfluidic devices as upstream process development tools have been developed in the area of small molecules, therapeutic proteins, and cellular therapies. More recently, they have also been applied to mimic downstream unit operations.

Editorial: ECAB focus issue: Engineered catalysts, robust, cost-effective and integrated bioprocesses and high-throughput screening

How can technology and industrial biotechnology contribute to a more bio-based economy? At the 3^rd European Congress of Applied Biotechnology (ECAB3) in Nice in 2015, relevant topics and technologies and their contribution to sustainability were presented and discussed. In this issue of Biotechnology Journal, five special articles are selected from this conference, highlighting processes and technologies envisaging the development of engineered catalysts, robust bioprocesses, as well as high-throughput screening methods for process development.