Emerging platforms for high-throughput enzymatic bioassays

Acoustic levitation and manipulation of columns of droplets with integrated optical detection for parallelisation of reactions

The most common methodology for performing multiple chemical and biological reactions in parallel is to use microtitre plates with either manual or robotic dispensing of reactants and wash solutions. We envision a paradigm shift where acoustically levitated droplets serve as wells of microtitre plates and are acoustically manipulated to perform chemical and biological reactions in a non-contact fashion. This in turn requires that lines of droplets can be levitated and manipulated simultaneously so that the same operations (merge, mix, and detect) can be performed on them in parallel. However, this has not been demonstrated until this work. Because of the nature of acoustic standing waves, a single focus has more than one trap, and can allow levitation of columns of droplets at the focal point and at half a wavelength above and below that point. Using this approach, we increased the number of acoustically levitated and merged droplets to 6 compared to 2 in the state-of-the-art. We showed that droplets in a column can be moved and merged with droplets in another column simultaneously and in a controlled manner to perform repeats and/or parallelisation of chemical and biological reactions. To demonstrate our approach experimentally, we built an acoustic levitator with top and bottom surfaces made of a 16 × 16 grid of 40 kHz phased array transducers and integrated optical detection system, studied two acoustic trap generation and movement algorithms, and performed an exemplar enzyme assay. This work has made significant steps towards acoustic levitation and manipulation of large numbers of droplets to eventually significantly reduce the use of the current state-of-the-art tools, microtitre plates and robots, for performing parallelised chemical and biological reactions.

Affinity-Controlled Partitioning of Biomolecules at Aqueous Interfaces and Their Bioanalytic Applications

All-aqueous phase separation systems play essential roles in bioanalytical and biochemical applications. Compared to conventional oil and organic solvent-based systems, these systems are characterized by their rich bulk and interfacial properties, offering superior biocompatibility. In particular, phase separation in all-aqueous systems facilitates the creation of compartments with specific physicochemical properties, and therefore largely enhances the accessibility of the systems. In addition, the all-aqueous compartments have diverse affinities, with an important property known as partitioning, which can concentrate (bio)molecules toward distinct immiscible phases. This partitioning affinity imparts all-aqueous interfaces with selective permeability, enabling the controlled enrichment of target (bio)molecules. This review introduces the basic principles and applications of partitioning-induced interfacial phenomena in a typical all-aqueous system, namely aqueous two-phase systems (ATPSs); these applications include interfacial chemical reactions, bioprinting, and assembly, as well as bio-sensing and detection. The primary challenges associated with designing all-aqueous phase separation systems and several future directions are also discussed, such as the stabilization of aqueous interfaces, the handling of low-volume samples, and exploration of suitable ATPSs compositions with the efficient protocol.

Automated and miniaturized screening of antibiotic combinations via robotic-printed combinatorial droplet platform

Antimicrobial resistance (AMR) has become a global health crisis in need of novel solutions. To this end, antibiotic combination therapies, which combine multiple antibiotics for treatment, have attracted significant attention as a potential approach for combating AMR. To facilitate advances in antibiotic combination therapies, most notably in investigating antibiotic interactions and identifying synergistic antibiotic combinations however, there remains a need for automated high-throughput platforms that can create and examine antibiotic combinations on-demand, at scale, and with minimal reagent consumption. To address these challenges, we have developed a Robotic-Printed Combinatorial Droplet (RoboDrop) platform by integrating a programmable droplet microfluidic device that generates antibiotic combinations in nanoliter droplets in automation, a robotic arm that arranges the droplets in an array, and a camera that images the array of thousands of droplets in parallel. We further implement a resazurin-based bacterial viability assay to accelerate our antibiotic combination testing. As a demonstration, we use RoboDrop to corroborate two pairs of antibiotics with known interactions and subsequently identify a new synergistic combination of cefsulodin, penicillin, and oxacillin against a model E. coli strain. We therefore envision RoboDrop becoming a useful tool to efficiently identify new synergistic antibiotic combinations toward combating AMR.

Core-Shell Droplet-Based Microfluidic Screening System for Filamentous Fungi

Filamentous fungi are competitive hosts for the production of drugs, proteins, and chemicals. However, their utility is limited by screening methods and low throughput. In this work, a universal high-throughput system for optimizing protein production in filamentous fungi was described. Droplet microfluidics was used to encapsulate large mutant strain pools in biocompatible core-shell microdroplets designed to avoid mycelial punctures and thus sustain prolonged culture. The self-assembled split GFP was then used to characterize the secretory capacity of the strains and isolate strains with superior production titers according to the fluorescence signals. The platform was applied to optimize the α-amylase secretion of Aspergillus niger, resulting in the isolation of a strain with 2.02-fold higher secretion capacity. The system allows the analysis of >105 single cells per h and will facilitate ultrahigh-throughput screening experiments of filamentous fungi. This method could help identify improved hosts for the large-scale production of biotechnology-relevant proteins. This is a broadly applicable system that can be equally used in other hosts.

FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride

Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.