https://escholarship.org/content/qt9pm0x5mh/qt9pm0x5mh.pdf?t=qv78lu

Machine learning for metabolic engineering: A review.

We report an approach for the online coupling of digital microfluidics (DMF) with mass spectrometry (MS) using a chip-integrated microspray hole (μSH). The technique uses an adapted electrostatic spray ionization (ESTASI) method to spray a portion of a sample droplet through a microhole in the cover plate, allowing its chemical content to be analyzed by MS. This eliminates the need for chip disassembly or the introduction of capillary emitters for MS analysis, as required by state-of-the-art. For the first time, this allows the essential advantage of a DMF device─free droplet movement─to be retained during MS analysis. The broad applicability of the developed seamless coupling of DMF and mass spectrometry was successfully applied to the study of various on-chip organic syntheses as well as protein and peptide analysis. In the case of a Hantzsch synthesis, we were able to show that the method is very well suited for monitoring even rapid chemical reactions that are completed in a few seconds. In addition, the strength of the low resource consumption in such on-chip microsyntheses was demonstrated by the example of enzymatic brominations, for which only a minute amount of a special haloperoxidase is required in the droplet. The unique selling point of this approach is that the analyzed droplet remains completely movable after the MS measurement and is available for subsequent on-DMF chip processes. This is illustrated here for the example of MS analysis of the starting materials in the corresponding droplets before they are combined to investigate the reaction progress by DMF-MS further. This technology enables the ongoing and almost unlimited tracking of multistep chemical processes in a DMF chip and offers exciting prospects for transforming digital microfluidics into automated synthesis platforms.

On-the-Fly Mass Spectrometry in Digital Microfluidics Enabled by a Microspray Hole: Toward Multidimensional Reaction Monitoring in Automated Synthesis Platforms.

/pdf/fast-biofoundries-coping-with-the-challenges-of-u7lfkqse.pdf

Fast biofoundries: coping with the challenges of biomanufacturing

Digital microfluidics (DMF) is a technology suitable for bioanalytical applications requiring miniaturized, automated, and multiplexed liquid handling. Its use in LC-MS-based proteomics, however, has so far been limited to qualitative proteome analyses. This is mainly due to the need for detergents that enable facile, reproducible droplet movement, which are compatible with organic solvents commonly used in targeted chemical modifications of peptides. Aiming to implement isobaric peptide labeling, a widely applied technique allowing multiplexed quantitative proteome studies, on DMF devices, we tested different commercially available detergents. We identified the maltoside-based detergent 3-dodecyloxypropyl-1-β-d-maltopyranoside (DDOPM) to enable facile droplet movement and show micelle formation even in the presence of organic solvent, which is necessary for isobaric tandem mass tag (TMT) labeling. The detergent is fully compatible with reversed phase LC-MS, not interfering with peptide identification. Tryptic digestion in the presence of DDOPM was more efficient than without detergent, resulting in more protein identifications. Using this detergent, we report the first on-DMF chip isobaric labeling strategy, with TMT-labeling efficiency comparable to conventional protocols. The newly developed labeling protocol was evaluated in the multiplexed analyses of a protein standard digest spiked into 25 cells. Finally, using only 75 cells per biological replicate, we were able to identify 39 proteins being differentially abundant after treatment of Jurkat T cells with the anticancer drug doxorubicin. In summary, we demonstrate an important step toward multiplexed quantitative proteomics on DMF, which, in combination with larger chip arrays and optimized hardware, could enable high throughput low cell number proteomics.

Isobaric Peptide Labeling on Digital Microfluidics for Quantitative Low Cell Number Proteomics

We report on a co-planar light-actuated digital microfluidics device that features a metal mesh grid integrated on the device surface to allow droplets to be exposed from above. We discuss a theoretical circuit model for our co-planar optoelectrowetting (OEW) design that allows for the optimization of droplet actuation while maintaining reliable droplet movement. Basic droplet manipulations such as merging and parallel actuation of droplets are achieved at speeds of up to 4.5  cm  /  s. The co-planar OEW device design benefits from having an open top design that allows for a wider range of system integration configurations than previous generations of OEW devices. A droplet-on-demand dispensing system from above is integrated with the co-planar OEW device to demonstrate the versatility of this optofluidic platform. The ability to inject, collect, and position individual droplets to form large-scale droplet arrays of up to 20  ×  20 is achieved.

https://www.spiedigitallibrary.org/journals/journal-of-optical-microsystems/volume-1/issue-3/034001/Co-planar-light-actuated-optoelectrowetting-microfluidic-device-for-droplet-manipulation/10.1117/1.JOM.1.3.034001.pdf

Co-planar light-actuated optoelectrowetting microfluidic device for droplet manipulation

Digital microfluidics (DMF) is a liquid handling technique that has been demonstrated to automate biological experimentation in a low-cost, rapid, and programmable manner This review discusses the role of DMF as a "digital bioconverter"-a tool to connect the digital aspects of the design-build-learn cycle with the physical execution of experiments Several applications are reviewed to demonstrate the utility of DMF as a digital bioconverter, namely, genetic engineering, sample preparation for sequencing and mass spectrometry, and enzyme-, immuno-, and cell-based screening assays These applications show that DMF has great potential in the role of a centralized execution platform in a fully integrated pipeline for the production of novel organisms and biomolecules In this paper, we discuss how the function of a DMF device within such a pipeline is highly dependent on integration with different sensing techniques and methodologies from machine learning and big data In addition to that, we examine how the capacity of DMF can in some cases be limited by known technical and operational challenges and how consolidated efforts in overcoming these challenges will be key to the development of DMF as a major enabling technology in the computer-aided biology framework

https://journals.sagepub.com/doi/pdf/10.1177/2472630320931794

Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable

A pre-culture stage is required to obtain robustly-dividing cells with high hydrogen (H2) production capabilities. However, a step-by-step process for biohydrogen production is scarcely reported, mainly from palm oil wastewater. Therefore, this study developed a guideline to find the best inoculum heat treatment conditions and implement the selected conditions for biohydrogen production using palm oil wastewater. This study used raw palm oil mill effluent (POME) and POME sludge as substrate and inoculum, respectively. Our findings reveal that 80 C and 30 min were the best conditions for inoculum heat treatment. When testing the conditions on POME sludge and inoculating with raw POME (28 g COD/L) at 37 C (reaction temperature), 24 h (reaction time), and pH 5.5, 34 mL H2/d was recorded. A slight increase (1.1-fold) was observed compared to 5 g COD/L POME co-digested with 5 g/L glucose (31 mL H2/d). This discovery indicates that raw POME is a potential source for biohydrogen production under anaerobic fermentation and can be directly used as substrate up to 30 g COD/L. The proposed guideline could also be implemented for different organic wastes for biohydrogen production study.

/pdf/preliminary-investigation-of-different-types-of-inoculums-825qfuxb.pdf

Sabrina Zaini

Papers

Role of Digital Microfluidics in Enabling Access to Laboratory Automation and Making Biology Programmable

Preliminary Investigation of Different Types of Inoculums and Substrate Preparation for Biohydrogen Production