High-Content Screening of Plankton Alkaline Phosphatase Activity in Microfluidics

Fluorescent assay for alkaline phosphatase by integrating strand displacement amplification with DNAzyme-catalytic recycling cleavage of molecular beacons

A fluorescence sensing method for the quantification of alkaline phosphatase (ALP) was developed by integrating the strand displacement amplification with DNAzyme-catalytic recycling cleavage of molecular beacons. ALP can hydrolyze a 3'-phosphoralated primer into a 3'-hydroxy primer which can initiate the strand displacement amplification to produce the Mg2+-dependent DNAzyme. The DNAzyme can then catalyze the cleavage of the DNA molecular beacon labeled with FAM fluorophore at its 5'-end and BHQ1 quencher at its 3'-end, turning on the fluorescence of FAM fluorophore. The content of ALP in a sample can be deduced from the measured fluorescence intensity. Due to the cascading nature of its amplification strategy, the proposed method achieved sensitive and specific ALP detection in human serum samples. Its results were in good consistent with the corresponding values obtained by a commercial ALP detection kit. The limit of detection of the proposed method for ALP is about 0.015 U/L, lower than some methods recently reported in literature, demonstrating its potential for ALP detection in biomedical research and clinical diagnosis.

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.

Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments

Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >10⁷-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >10⁷ variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.

Fast and sensitive near-infrared ratiometric fluorescent probe with a self-immolative spacer for imaging of endogenous alkaline phosphatase activity in cells and in vivo

Alkaline phosphatase (ALP), a vital hydrolase widely distributed in organisms, is regarded as a critical biomarker strongly associated with many physiological and pathological processes. Therefore, fast and efficient detection of ALP activity in vivo is of great value for clinical diagnosis. Herein, a novel near-infrared (NIR) ratiometric fluorescent probe (HP) was designed based on ESIPT for trapping ALP activity in cells and in vivo. Notably, incorporating a self-immolative spacer dramatically reduces the response time (8.5 min) of HP. Moreover, the probe exhibits excellent water solubility, large Stokes shift (147 nm), the ratiometric determination of ALP at 570 nm and 689 nm, low detection limit (3.98 U L^-1). More importantly, the probe was also successfully applied to detect and monitor variations in endogenous ALP activity in zebrafish due to the drug (APAP) induced organ damages.

Enzyme-triggered click chemistry combined with surface-enhanced Raman spectroscopy for the simple and sensitive detection of alkaline phosphatase activity from complex biological samples

Schematic of the enzyme-triggered click chemistry combined with the SERS technique for ALP detection.

Versatile Microfluidic Platform for Automated Live-Cell Hyperspectral Imaging Applied to Cold Climate Cyanobacterial Biofilms

Microfluidic bioanalytical platforms are driving discoveries from synthetic biology to the health sciences. In this work, we present a platform for in vivo live-cell imaging and automated species detection in mixed cyanobacterial biofilms from cold climate environments. Using a multimodal microscope with custom optics applied to a chip with six parallel growth channels, we monitored biofilm dynamics via continuous imaging at natural irradiance levels. Machine learning algorithms were applied to the collected hyperspectral images for automatic segmentation of mixed-species biofilms into individual species of cyanobacteria with similar filamentous morphology. The coupling of microfluidic technology with modern multimodal imaging and computer vision systems provides a versatile platform for the study of cause-and-effect scenarios of cyanobacterial biofilms, which are important elements of many ecosystems, including lakes and rivers of the polar regions.

A novel aggregation-induced dual emission probe for in situ light-up detection of endogenous alkaline phosphatase

Abnormal level of alkaline phosphatase (ALP) activity has been linked to many diseases in human. The development of fluorescent molecular probes that can report the expression and activity of ALP in various biological systems will be extremely valuable. However, the in vivo monitoring for ALP in living cells and more complex biological systems remains a great challenge. The excited-state intramolecular proton transfer (ESIPT) probe with proportional fluorescence has low background noise, while the aggregation induced emission (AIE) probe has the advantages of signal amplification and good light stability. Herein, an "AIE + ESIPT" fluorescent probe 2-(benzo[d]thiazol-2-yl)-4-(1,4,5-triphenyl-1H-imidazole-2-yl)phenyl dihydrogen phosphate (THP) was constructed for the highly selective and sensitive detection of ALP. By introducing a phosphate ester at the hydroxyl position of the solid fluorophore 2-(benzo[d]thiazol-2-yl)-4-(1,4,5-triphenyl-1H-imidazole-2-yl)phenol, ESIPT was hindered and the probe present a faint blue fluorescence in DMSO solution. While ALP was introduced, causing the phosphate in THP hydrolyzed, and the ESIPT process was restored to yield a yellow fluorescence at 550 nm, thereby achieving proportionality detection. THP exhibited high selectivity and sensitively to ALP with low limit of detection (1.21228 U/L), and the reaction completed within 20 min. In addition, with its outstanding advantages of low biological toxicity and enzyme conversion characteristics, THP has been successfully applied to ALP imaging in living cells (Hela cells, A549 cells and Hek293 cells), and can provide in situ information on the reaction site. Therefore, THP has the potential for detecting ALP activity in biomedical application.

Variable inter and intraspecies alkaline phosphatase activity within single cells of revived dinoflagellates

Adaptation of cell populations to environmental changes is mediated by phenotypic variability at the single-cell level. Enzyme activity is a key factor in cell phenotype and the expression of the alkaline phosphatase activity (APA) is a fundamental phytoplankton strategy for maintaining growth under phosphate-limited conditions. Our aim was to compare the APA among cells and species revived from sediments of the Bay of Brest (Brittany, France), corresponding to a pre-eutrophication period (1940's) and a beginning of a post-eutrophication period (1990's) during which phosphate concentrations have undergone substantial variations. Both toxic marine dinoflagellate Alexandrium minutum and the non-toxic dinoflagellate Scrippsiella acuminata were revived from ancient sediments. Using microfluidics, we measured the kinetics of APA at the single-cell level. Our results indicate that all S. acuminata strains had significantly higher APA than A. minutum strains. For both species, the APA in the 1990's decade was significantly lower than in the 1940's. For the first time, our results reveal both inter and intraspecific variabilities of dinoflagellate APA and suggest that, at a half-century timescale, two different species of dinoflagellate may have undergone similar adaptative evolution to face environmental changes and acquire ecological advantages.

Fluorescence assay based on the thioflavin T-induced conformation switch of G-quadruplexes for TET1 detection

A simple and label-free fluorescence method is developed for the highly sensitive detection of TET1 based on ThT/G-quadruplexes in combination with the specific design of oligonucleotides.

Droplet Microfluidics for Microbial Biotechnology

Droplet microfluidics has recently evolved as a prominent platform for high-throughput experimentation for various research fields including microbiology. Key features of droplet microfluidics, like compartmentalization, miniaturization, and parallelization, have enabled many possibilities for microbiology including cultivation of microorganisms at a single-cell level, study of microbial interactions in a community, detection and analysis of microbial products, and screening of extensive microbial libraries with ultrahigh-throughput and minimal reagent consumptions. In this book chapter, we present several aspects and applications of droplet microfluidics for its implementation in various fields of microbial biotechnology. Recent advances in the cultivation of microorganisms in droplets including methods for isolation and domestication of rare microbes are reviewed. Similarly, a comparison of different detection and analysis techniques for microbial activities is summarized. Finally, several microbial applications are discussed with a focus on exploring new antimicrobials and high-throughput enzyme activity screening. We aim to highlight the advantages, limitations, and current developments in droplet microfluidics for microbial biotechnology while envisioning its enormous potential applications in the future.

Ratiometric Fluorescent Strategy for Localizing Alkaline Phosphatase Activity in Mitochondria Based on the ESIPT Process

Fluorescent probes are powerful tools for detecting and mapping the species of interest in vitro and in vivo. Although the probes always show high selectivity and sensitivity, they are usually affected by some factors, such as detecting conditions and the probe concentrations. Ratiometric fluorescent strategies, possessing advantage of low background noise, would solve the problem effectively and lead to a higher sensing performance. Thus, an ESIPT-based ratiometric probe (HBTP-mito) was developed on the basis of a phosphorylated 2-(2'-hydroxyphenyl)-benzothiazole derivative for the determination of ALP activity. HBTP-mito is water soluble and emits green fluorescence in TBS buffer due to the blockage of ESIPT. Upon the introduction of ALP, the phosphate ester of HBTP-mito was hydrolyzed and the ESIPT process was restored. Accordingly, the fluorescence at 514 nm decreases, while emission at 650 nm shows a "turn-on" response. The ratio of intensity (I_514nm/I_650nm) decreases linearly with ALP activity increasing from 0 to 60 mU/mL, obtained an LOD of 0.072 mU/mL. The favorable performance of the probe enables its application not only in the detection of ALP activity in biological samples, but also in the localization of the ALP levels in living cells and in vivo.

Microfluidic technology for plankton research

Plankton produces numerous chemical compounds used in cosmetics and functional foods. They also play a key role in the carbon budget on the Earth. In a context of global change, it becomes important to understand the physiological response of these microorganisms to changing environmental conditions. Their adaptations and the response to specific environmental conditions are often restricted to a few active cells or individuals in large populations. Using analytical capabilities at the subnanoliter scale, microfluidic technology has also demonstrated a high potential in biological assays. Here, we review recent advances in microfluidic technologies to overcome the current challenges in high content analysis both at population and the single cell level.