Reinventing shake flask fermentation: The breathable flask.

Cultivating cells in shake flasks is a routine operation that is largely unchanged since its inception. A glass or plastic Erlenmeyer vessel with the primary gas exchange taking place across various porous plugs is used with media volumes typically ranging from 100 mL to 2 L. Oxygen limitation and carbon dioxide accumulation in the vessel is a major concern for studies involving shake flask cultures. In this study, we enhance mass transfer in a conventional shake flask by replacing the body wall with a permeable membrane. Naturally occurring concentration gradient across the permeable membrane walls facilitates the movement of oxygen and carbon dioxide between the flask and the external environment. The modified flask called the breathable flask, has shown a 40% improvement in mass transfer coefficient (kLa) determined using the static diffusion method. The prokaryotic cell culture studies performed with Escherichia coli showed an improvement of 28%-66% in biomass and 41%-56% in recombinant product yield. The eukaryotic cell culture study performed with Pichia pastoris expressing proinsulin exhibited a 40% improvement in biomass and 115% improvement in protein yield. The study demonstrates a novel approach to addressing the mass transfer limitations in conventional shake flask cultures. The proposed flask amplifies its value by providing a membrane-diffusion-based sensing platform for the integration of low-cost, noninvasive sensing capabilities for real-time monitoring of critical cell culture parameters like dissolved oxygen and dissolved carbon dioxide.

Completely noninvasive multi-analyte monitoring system for cell culture processes.

Although online monitoring of dissolved O2, pH, and dissolved CO2 is critical in bioprocesses, nearly all existing technologies require some level of direct contact with the cell culture environment, posing risks of contamination. This study addresses the need for an accurate, and completely noninvasive technique for simultaneous measurement of these analytes. A "non-contact" technique for simultaneous monitoring of dissolved O2, pH, and dissolved CO2 was developed. Instead of direct contact with the culture media, the measurements were made through permeable membranes via either a sampling port in the culture vessel wall or a flow cell. The efficacy of the "non-contact" technique was validated in Escherichia coli (E.coli), Chinese hamster ovary (CHO) culture processes, and dynamic environments created by sparging gases in cell culture medium. The measurements obtained through the developed techniques were comparable to those obtained through control methods. The noninvasive monitoring system can offer accurate, and contamination-minimized monitoring of critical process parameters including dissolved O2, pH, and dissolved CO2. These advancements will enhance the control and optimization of cell culture processes, promising improved cell culture performance.

Air-permeable redox mediated transcutaneous CO2 sensor.

Standard clinical care of neonates and the ventilation status of human patients affected with coronavirus disease involves continuous CO2 monitoring. However, existing noninvasive methods are inadequate owing to the rigidity of hard-wired devices, insubstantial gas permeability and high operating temperature. Here, we report a cost-effective transcutaneous CO2 sensing device comprising elastomeric sponges impregnated with oxidized single-walled carbon nanotubes (oxSWCNTs)-based composites. The proposed device features a highly selective CO2 sensing response (detection limit 155 ± 15 ppb), excellent permeability and reliability under a large deformation. A follow-up prospective study not only offers measurement equivalency to existing clinical standards of CO2 monitoring but also provides important additional features. This new modality allowed for skin-to-skin care in neonates and room-temperature CO2 monitoring as compared with clinical standard monitoring system operating at high temperature to substantially enhance the quality for futuristic applications.

Rapid Ultrasensitive and High-Throughput Bioburden Detection: Microfluidics and Instrumentation.

Contamination detection often requires lengthy culturing steps to detect low-level bioburden. To increase the rate of detection and decrease the limit of detection (LOD), a system featuring microfluidics and a multichannel fluorometer has been developed. The eight-channel fluorometer enables parallel testing of multiple samples with the LOD as low as <1 cfu/mL. This low-cost system utilizes the slope of fluorescence intensity that serves as the criterion for bioburden detection. The redox indicator dye resazurin is used to monitor the presence of viable cells in this study and is reduced to resorufin with a high quantum yield at 585 nm. The sample under investigation is spiked with resazurin and loaded in a special-design microfluidic cassette, and the rate of change is observed via the fluorometer. The method was validated using primary Escherichia coli culture in comparison with a spectrophotometer which served as the gold standard. An optimized assay based on Luria-Bertani medium was developed. The impact on the assay sensitivity based on incubation and filtration steps was also explored. The assay is shown to pick up inadvertent contamination from test tubes and pipette tips showing its applicability in real-world settings. The data analysis demonstrated a comparable performance of the multichannel fluorometer vis-a-vis the conventional plate reader. The multichannel system is shown to detect bioburden presence in as low as 20 s for bacterial concentrations ≥5 cfu/mL after 6 h of incubation. Considering its portability, low cost, simplicity of operation, and relevant assay sensitivity, the system is well positioned to detect low-level bioburden in the laboratory, pharmaceutical, and field settings.

Rapid and low-cost sampling for detection of airborne SARS-CoV-2 in dehumidifier condensate.

Airborne spread of coronavirus disease 2019 (COVID-19) by infectious aerosol is all but certain. However, easily implemented approaches to assess the actual environmental threat are currently unavailable. We present a simple approach with the potential to rapidly provide information about the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the atmosphere at any location. We used a portable dehumidifier as a readily available and affordable tool to collect airborne virus in the condensate. The dehumidifiers were deployed in selected locations of a hospital ward with patients reporting flu-like symptoms which could possibly be due to COVID-19 over three separate periods of one week. Samples were analyzed frequently for both virus envelope protein and SARS-CoV-2 RNA. In several samples across separate deployments, condensate from dehumidifiers tested positive for the presence of SARS-CoV-2 antigens as confirmed using two independent assays. RNA was detected, but not attributable to SARS-CoV-2. We verified the ability of the dehumidifier to rapidly collect aerosolized sodium chloride. Our results point to a facile pool testing method to sample air in any location in the world and assess the presence and concentration of an infectious agent to obtain quantitative risk assessment of exposure, designate zones as "hot spots" and minimize the need for individual testing which may often be time consuming, expensive, and laborious.

Real-time dissolved carbon dioxide monitoring II: Surface aeration intensification for efficient CO2 removal in shake flasks and mini-bioreactors leads to superior growth and recombinant protein yields.

Mass transfer is known to play a critical role in bioprocess performance and henceforth monitoring dissolved O2 (DO) and dissolved CO2 (dCO2 ) is of paramount importance. At bioreactor level these parameters can be monitored online and can be controlled by sparging air/oxygen or stirrer speed. However, traditional small-scale systems such as shake flasks lack real time monitoring and also employ only surface aeration with additional diffusion limitations imposed by the culture plug. Here we present implementation of intensifying surface aeration by sparging air in the headspace of the reaction vessel and real-time monitoring of DO and dCO2 in the bioprocesses to evaluate the impact of intensified surface aeration. We observed that sparging air in the headspace allowed us to keep dCO2 at low level, which significantly improved not only biomass growth but also protein yield. We expect that implementing such controlled smart shake flasks can minimize the process development gap which currently exists in shake flask level and bioreactor level results.

Real-time dissolved carbon dioxide monitoring I: Application of a novel in situ sensor for CO2 monitoring and control.

Dissolved carbon dioxide (dCO2 ) is a well-known critical parameter in bioprocesses due to its significant impact on cell metabolism and on product quality attributes. Processes run at small-scale faces many challenges due to limited options for modular sensors for online monitoring and control. Traditional sensors are bulky, costly, and invasive in nature and do not fit in small-scale systems. In this study, we present the implementation of a novel, rate-based technique for real-time monitoring of dCO2 in bioprocesses. A silicone sampling probe that allows the diffusion of CO2 through its wall was inserted inside a shake flask/bioreactor and then flushed with air to remove the CO2 that had diffused into the probe from the culture broth (sensor was calibrated using air as zero-point calibration). The gas inside the probe was then allowed to recirculate through gas-impermeable tubing to a CO2 monitor. We have shown that by measuring the initial diffusion rate of CO2 into the sampling probe we were able to determine the partial pressure of the dCO2 in the culture. This technique can be readily automated, and measurements can be made in minutes. Demonstration experiments conducted with baker's yeast and Yarrowia lipolytica yeast cells in both shake flasks and mini bioreactors showed that it can monitor dCO2 in real-time. Using the proposed sensor, we successfully implemented a dCO2 -based control scheme, which resulted in significant improvement in process performance.

Wood Microfluidics.

As nonbiodegradable plastics continue to pollute our land and oceans, countries are starting to ban the use of single-use plastics. In this paper, we demonstrated the fabrication of wood-based microfluidic devices and their adaptability for single-use, point-of-care (POC) applications. These devices are made from easily sourced renewable materials for fabrication while exhibiting all the advantages of plastic devices without the problem of nonbiodegradable waste and cost. To build these wood devices, we utilized laser engraving and traditional mechanical methods and have adapted specific surface coatings to counter the wicking effect of wood. To demonstrate their versatility, wood microfluidic devices were adapted for (i) surface plasmon coupled enhancement (SPCE) of fluorescence for detection of proteins, (ii) T-/Y-geometry microfluidic channel mixers, and (iii) devices for rapid detection of microbial contamination. These provide proof of concept for the use of wooden platforms for POC applications. In this study, we measured the fluorescence intensities of recombinant green fluorescent protein (GFP) standards (ranging from 1.5-25 ng/µL) and 6XHis-G-CSF (ranging from 0.1-100 ng/µL) expressed in cell-free translation systems. All tested devices perform as well as or better than their plastic counterparts.

Improving the recombinant human erythropoietin glycosylation using microsome supplementation in CHO cell-free system.

Cell-Free Protein Synthesis (CFPS) offers many advantages for the production of recombinant therapeutic proteins using the CHO cell-free system. However, many complex proteins are still difficult to express using this method. To investigate the current bottlenecks in cell-free glycoprotein production, we chose erythropoietin (40% glycosylated), an essential endogenous hormone which stimulates the development of red blood cells. Here, we report the production of recombinant erythropoietin (EPO) using CHO cell-free system. Using this method, EPO was expressed and purified with a twofold increase in yield when the cell-free reaction was supplemented with CHO microsomes. The protein was purified to near homogeneity using an ion-metal affinity column. We were able to analyze the expressed and purified products (glycosylated cell-free EPO runs at 25-28 kDa, and unglycosylated protein runs at 20 kDa on an SDS-PAGE), identifying the presence of glycan moieties by PNGase shift assay. The purified protein was predicted to have ∼2,300 IU in vitro activity. Additionally, we tested the presence and absence of sugars on the cell-free EPO using a lectin-based assay system. The results obtained in this study indicate that microsomes augmented in vitro production of the glycoprotein is useful for the rapid production of single doses of a therapeutic glycoprotein drug and to rapidly screen glycoprotein constructs in the development of these types of drugs. CFPS is useful for implementing a lectin-based method for rapid screening and detection of glycan moieties, which is a critical quality attribute in the industrial production of therapeutic glycoproteins.

Minimally invasive technique for measuring transdermal glucose with a fluorescent biosensor.

There is a need for blood glucose monitoring techniques that eliminate the painful and invasive nature of current methods, while maintaining the reliability and accuracy of established medical technology. This research aims to ultimately address these shortcomings in critically ill pediatric patients. Presented in this work is an alternative, minimally invasive technique that uses microneedles (MN) for the collection of transdermal glucose (TG). Due to their comparable skin properties, diffusion studies were performed on full thickness Yucatan miniature pig skin mounted to an in-line diffusion flow cell and on different skin sites of human subjects. Collected TG samples were measured with a L255C mutant of the E. coli glucose-binding protein (GBP) with an attached fluorescent probe. The binding constant (Kd = 0.67 µM) revealed the micromolar sensitivity and high selectivity of the his-tagged GBP biosensor for glucose, making it suitable for TG measurements. In both the animal and human models, skin permeability and TG diffusion across the skin increased with MN application. For intact and MN-treated human skin, a significant positive linear correlation (r > 0.95, p < 0.01) existed between TG and BG. The micromolar sensitivity of GBP minimized the volume required for interstitial fluid glucose analysis allowing MN application time (30 s) to be shortened compared to other studies. This time reduction can help in eliminating skin irritation issues and improving practical use of the technique by caregivers in the hospital. In addition, the his-tagged optical biosensor used in this work can be immobilized and used with a portable sensing fluorometer device at the point of care (POC) making this minimally invasive technology more ideal for use in the pediatric intensive care unit. Graphical abstract ᅟ.

Optimizing cell-free protein expression in CHO: Assessing small molecule mass transfer effects in various reactor configurations.

Cell-free protein synthesis (CFPS) is an ideal platform for rapid and convenient protein production. However, bioreactor design remains a critical consideration in optimizing protein expression. Using turbo green fluorescent protein (tGFP) as a model, we tracked small molecule components in a Chinese Hamster Ovary (CHO) CFPS system to optimize protein production. Here, three bioreactors in continuous-exchange cell-free (CECF) format were characterized. A GFP optical sensor was built to monitor the product in real-time. Mass transfer of important substrate and by-product components such as nucleoside triphosphates (NTPs), creatine, and inorganic phosphate (Pi) across a 10-kDa MWCO cellulose membrane was calculated. The highest efficiency measured by tGFP yields were found in a microdialysis device configuration; while a negative effect on yield was observed due to limited mass transfer of NTPs in a dialysis cup configuration. In 24-well plate high-throughput CECF format, addition of up to 40 mM creatine phosphate in the system increased yields by up to ∼60% relative to controls. Direct ATP addition, as opposed to creatine phosphate addition, negatively affected the expression. Pi addition of up to 30 mM to the expression significantly reduced yields by over ∼40% relative to controls. Overall, data presented in this report serves as a valuable reference to optimize the CHO CFPS system for next-generation bioprocessing. Biotechnol. Bioeng. 2017;114: 1478-1486. © 2017 Wiley Periodicals, Inc.

Measuring transdermal glucose levels in neonates by passive diffusion: an in vitro porcine skin model.

Current glucose monitoring techniques for neonates rely heavily on blood glucose monitors which require intermittent blood collection through skin-penetrating pricks on the heel or fingers. This procedure is painful and often not clinically conducive, which presents a need for a noninvasive method for monitoring glucose in neonates. Our motivation for this study was to develop an in vitro method for measuring passive diffusion of glucose in premature neonatal skin using a porcine skin model. Such a model will allow us to initially test new devices for noninvasive glucose monitoring without having to do in vivo testing of newborns. The in vitro model is demonstrated by comparing uncompromised and tape-stripped skin in an in-line flow-through diffusion apparatus with glucose concentrations that mimic the hypo-, normo-, and hyper-glycemic conditions in the neonate (2.0, 5.0, and 20 mM, respectively). Transepidermal water loss (TEWL) of the tape-stripped skin was approximately 20 g m-2 h-1, which closely mimics TEWL for neonatal skin at about 190 days post-conceptional age. The tape-stripped skin showed a >15-fold increase in glucose diffusion compared to the uncompromised skin. The very small concentrations of collected glucose were measured with a highly selective and highly sensitive fluorescent glucose biosensor based on the glucose binding protein (GBP). The demonstrated method of glucose determination is noninvasive and painless, which makes it especially desirable for glucose testing in neonates and children. This study is an important step towards an in vitro model for noninvasive real-time glucose monitoring that may be easily transferred to the clinic for glucose monitoring in neonates. Graphical Abstract Glucose diffusion through model skin was measured using an in-line flow-through diffusion apparatus with glucose solutions mimicking hypo-, normo- and hyperglycemia in the neonate. Phosphate buffered saline was added to the top chamber and the glucose that diffused through the model skin into the buffer was measured using a fluorescent glucose binding protein biosensor.

A unique noninvasive approach to monitoring dissolved O2 and CO2 in cell culture.

Although online monitoring of dissolved oxygen (DO) and carbon dioxide (DCO2 ) is highly desirable in bioprocesses, small-scale bioreactors are usually not monitored due to the lack of suitable sensors. Traditional electrochemical sensors are usually not used because they are bulky and invasive. Disposable optical sensors are small and only partially invasive, but there are concerns regarding the toxicity of the patch and the phototoxicity of the illuminating light. Here we present a novel, noninvasive, rate-based technique for monitoring DO and DCO2 in cell cultures. A silicone sampling loop which allowed the diffusion of O2 and CO2 through its wall was inserted inside a bioreactor, and then flushed with N2 until the CO2 and O2 inside the loop were completely removed. The gas inside the loop was then allowed to recirculate through gas impermeable tubing to the O2 and CO2 sensors. We have shown that by measuring the initial diffusion rate we were able to determine the partial pressures of the two gases in the culture. The technique could be readily automated and measurements could be made in minutes. It was tested in demonstration experiments by growing murine hybridoma cells in a T-flask and a spinner-flask at 37°C. The results were comparable to those measured with commercially available fluorescence-based patch sensors. These results show that the rate-based method is an effective way to monitor small-scale cell cultures. This measurement mechanism can be easily built into disposable cell culture vessels for facile use.

Non-Invasive Optical Sensor Based Approaches for Monitoring Virus Culture to Minimize BSL3 Laboratory Entry.

High titers of infectious viruses for vaccine and diagnostic reference panel development are made by infecting susceptible mammalian cells. Laboratory procedures are strictly performed in a Bio-Safety Level-3 (BSL3) laboratory and each entry and exit involves the use of  disposable Personnel Protective Equipment (PPE) to observe cell culture conditions. Routine PPE use involves significant recurring costs. Alternative non-invasive optical sensor based approaches to remotely monitor cell culture may provide a promising and cost effective approach to monitor infectious virus cultures resulting in lower disruption and costs. We report here the monitoring of high titer cultures of Human Immunodeficiency Virus-1 (HIV-1) and Herpes Simplex Virus-2 (HSV-2) remotely with the use of optical oxygen sensors aseptically placed inside the cell culture vessel. The replacement of culture media for cell and virus propagation and virus load monitoring was effectively performed using this fluorescent sensor and resulted in half the number of visits to the BSL3 lab (five versus ten).

An automatic glucose monitoring system based on periplasmic binding proteins for online bioprocess monitoring.

Glucose is one of the most vital nutrients in all living organisms, so its monitoring is critical in healthcare and bioprocessing. Enzymatic sensors are more popular as a technology solution to meet the requirement. However, periplasmic binding proteins have been investigated extensively for their high sensitivity, enabling microdialysis sampling to replace existing complex and expensive glucose monitoring solutions based on enzymatic sensors. The binding proteins are used as optical biosensors by introducing an environment-sensitive fluorophore to the protein. The biosensor's construction, characterization, and potential application are well studied, but a complete glucose monitoring system based on it is yet to be reported. This work documents the development of the first glucose sensor prototype based on glucose binding protein (GBP) for automatic and continuous glucose measurements. The development includes immobilizing the protein into reusable chips and a low-cost solution for non-invasive glucose sampling in bioprocesses using microdialysis sampling technique. A program was written in LabVIEW to accompany the prototype for the complete automation of measurement. The sampling technique allowed glucose measurements of a few micromolar to 260 mM glucose levels. A thorough analysis of the sampling mode and the device's performance was conducted. The reported measurement accuracy was 81.78%, with an RSD of 1.83%. The prototype was also used in online glucose monitoring of E. coli cell culture. The mode of glucose sensing can be expanded to the measurement of other analytes by switching the binding proteins.

Bioburden detection on surface and water samples in a rapid, ultra-sensitive and high-throughput manner.

Bioburden detection is crucial for food, water, and biopharmaceutical applications as it can directly impact public health. The objective of this study is to develop and validate an assay and protocol for detecting bioburden on solid surfaces, as well as in water, with high sensitivity and accuracy in a rapid manner. Henceforth, a resazurin-based assay optimized for detecting bioburden has been integrated with a previously developed portable multichannel fluorometer. The microbes were isolated from solid surfaces in different laboratory settings by swabbing technique, and stream water was collected for contamination analysis. Based on the results, the assay and protocol can successfully detect bioburden as low as 20 CFU/cm2 and 10 CFU/mL present in both surface and water samples, respectively.

A novel, low-cost microfluidic device with an integrated filter for rapid, ultrasensitive, and high-throughput bioburden detection.

Rapid and accurate bioburden detection has become increasingly necessary for food, health, pharmaceutical and environmental applications. To detect bioburden accurately, and in a highly sensitive manner, we have fabricated a novel microfluidic device with an integrated filter to trap the cells. Bioburden is detected on the filter paper in situ using the redox reaction of fluorescent label resorufin and a portable multichannel fluorometer is used for fluorescence measurement. The microfluidic device was fabricated in a facile, low-cost, and rapid way with microwave-induced thermally assisted bonding. To characterize the bonding quality of the microfluidic cassettes, different tests were performed, and the filter paper material and size were optimized. Primary Bacillus subtilis culture bacterial samples were filtered through the device to validate and investigate the performance parameters. Our results show that a limit of detection (LOD) of 0.037 CFU/mL can be achieved through this microfluidic device whereas the LOD in a normal microfluidic cassette in the fluorometer and the golden standard spectrophotometer are 0.378 and 0.128 CFU/mL respectively. The results depict that three to ten times LOD improvement is possible through this microfluidic cassette and more sensitive detection is possible depending on the volume filtered within a rapid 3 min. This novel microfluidic device along with the fluorometer can be used as a rapid portable tool for highly sensitive, accurate and high-throughput bacterial detection for different applications.

A novel approach to noninvasive monitoring of dissolved carbon dioxide in small-scale cell culture processes.

Disposable small-scale vessels are commonly used in cell culture studies in academia as well as early stages of bioprocess development. These types of research are crucial for our understanding about cells and bioprocesses as they provide important information regarding different parameters affecting cells. Dissolved carbon dioxide (DCO2) is one main parameter affecting cell metabolism. It is also an indicator of cell culture well-being. Despite CO2 being a critical process parameter, there is a lack of appropriate monitoring system for CO2 in small-scale vessels. Here, we present a membrane-based noninvasive method for measuring DCO2 in cell culture medium. The idea was achieved by modifying a T-flask and replacing a small area of it with CO2 permeable silicone membrane. In the proposed method, the concentration of CO2 dissolved in the cell culture medium is determined by measuring the initial diffusion rate of CO2 through a silicone membrane attached to the bottom wall of the T-flask. The measurement method was validated previously, and the efficacy of the noninvasive method was evaluated by growing E.coli, Pichia pastoris, and CHO cells in the proposed prototype. The results obtained from this method were verified with other quantitative data obtained from the process such as optical density (OD), cell density, dissolved oxygen (DO) and pH. The results show that the proposed membrane-based method is an effective way for completely noninvasive monitoring of DCO2 in small-scale cell culture processes. Additional diffusing species such as oxygen could also be measured using the same approach.

Microwave induced thermally assisted solvent-based bonding of biodegradable thermoplastics: an eco-friendly rapid approach for fabrication of microfluidic devices and analyte detection.

There is an increasing interest in low-cost, facile and versatile thermoplastic bonding for microfluidic applications that can be easily transitioned from laboratory prototyping to industrial manufacturing. In addition, owing to the surge in the usage of thermoplastic microfluidics and its adverse effect on the environment, it is prudent to source alternative materials that are biodegradable, providing a sustainable, green approach. To address the problems, here we introduce an environment friendly, low-cost and safe welding technology used in the fabrication of microcassettes from biodegradable cellulose acetate (CA) thermoplastics. The thermally assisted solvent based bonding of the thermoplastics was accomplished in a domestic microwave oven with the aid of a polyether ether ketone (PEEK) vise. To characterize the quality of the bonding, our in-house technique was compared with a conventional thermally assisted solvent bonding configuration using a heat press machine and tested under different conditions. Our microwave induced bonding of CA presents three times reduced bonding time with higher bonding strength, good reliability and does not necessitate the use of cumbersome instrumentation. Finally, we demonstrate an electrophoresis application and vitamin C detection accomplished using this biodegradable microcassette presenting comparable results with traditional techniques, illustrating the potential of this fabrication technique in different microfluidic applications.

Transdermal sensing: in-situ non-invasive techniques for monitoring of human biochemical status.

Improving life expectancy necessitates prevention and early diagnosis of any disease state based on active self-monitoring of symptoms and longitudinal biochemical profiling. Non-invasive and continuous measurement of molecular biomarkers that reflect metabolism and health must however be established to realize this plan. Human samples non-invasively obtained via the skin are suitable in this context for in-situ biochemical monitoring. We present a brief classification of transdermal sampling in aqueous and gaseous phases and then introduce a new generation of transdermal monitoring devices for rapid and accurate assessment of important parameters. Finally, we have summarized the diversity of body-wide skin characteristics that have possible effects for transdermal sampling. Because of its passive nature, in-situ biochemical monitoring via transdermal sampling will potentially lead to a greater understanding of important biochemical markers and their temporal variation.