This paper proposes a high-throughput, function-based screening approach of a metagenomic library for isolating novel microbial enzymes by droplet-based microfluidics. We used gel microdroplets (GMDs) dispersed in oil as picoliter-volume reaction vessels for lipolytic enzyme by encapsulating cells in individual GMDs. Using this approach, we monitored the growth of individual cells encapsulated in GMDs and assessed the enzyme reaction activities at the level of an individual GMD. We then applied this method to screen lipolytic enzyme genes from the metagenomic library constructed from soil collected from a quercus serrate forest of Mount Tsukuba, Ibaraki, Japan. In the workflow presented in this study, metagenomic library clones were encapsulated in 100-pL GMDs with a fluorogenic reporter substrate. A total of 67,000 metagenomic library clones can be screened in only 24 h with reduced consumption of reagents (i.e., <10 μL). As a result, we identified a novel lipolytic enzyme, EstT1, belonging to the EstD2 family of esterases and containing a putative signal peptide, which facilitates enzyme export and catalyzation of substrates in the periplasm. Our study demonstrates the potential of microfluidic GMDs as an efficient tool for metagenomic library screening of industrially relevant enzymes with the potential of significantly reducing the cost and time factors involved in successful practical application of microbial enzymes.

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A gradient elution system for pressure-driven liquid chromatography (LC) on a chip was developed for carrying out faster and more efficient chemical analyses. Through computational fluid dynamics simulations and an experimental study, we found that the use of a cross-Tesla structure with a 3 mm mixing length was effective for mixing two liquids. A gradient elution system using a cross-Tesla mixer was fabricated on a 20 mm × 20 mm silicon chip with a separation channel of pillar array columns and a sample injection channel. A mixed solution of water and fluorescein in methanol was delivered to the separation channel 7 s after the gradient program had been started. Then, the fluorescence intensity increased gradually with the increasing ratio of fluorescein, which showed that the gradient elution worked well. Under the gradient elution condition, the retention times of two coumarin dyes decreased with the gradient time. When the gradient time was 30 s, the analysis could be completed in 30 s, which was only half the time required compared to that required for an isocratic elution. Fluorescent derivatives of aliphatic amines were successfully separated within 110 s. The results show that the proposed system is promising for the analyses of complex biological samples.

In synthetic biology, the control of gene expression requires a multistep processing of biological signals. The key steps are sensing the environment, computing information and outputting products. To achieve such functions, the laborious, combinational networking of enzymes and substrate-genes is required, and to resolve problems, sophisticated design automation tools have been introduced. However, the complexity of genetic circuits remains low because it is difficult to completely avoid crosstalk between the circuits. Here, we have made an orthogonal self-contained device by integrating an actuator and sensors onto a DNA origami-based nanochip that contains an enzyme, T7 RNA polymerase (RNAP) and multiple target-gene substrates. This gene nanochip orthogonally transcribes its own genes, and the nano-layout ability of DNA origami allows us to rationally design gene expression levels by controlling the intermolecular distances between the enzyme and the target genes. We further integrated reprogrammable logic gates so that the nanochip responds to water-in-oil droplets and computes their small RNA (miRNA) profiles, which demonstrates that the nanochip can function as a gene logic-chip. Our approach to component integration on a nanochip may provide a basis for large-scale, integrated genetic circuits.

Environmental microbes are a great source of industrially valuable enzymes with potent and unique catalytic activities. Unfortunately, the majority of microbes remain unculturable and thus are not accessible by culture-based methods. Recently, culture-independent metagenomic approaches have been successfully applied, opening access to untapped genetic resources. Here we present a methodological approach for the identification of genes that encode metabolically active enzymes in environmental microbes in a culture-independent manner. Our method is based on activity-based single-cell sequencing, which focuses on microbial cells showing specific enzymatic activities. First, at the single-cell level, environmental microbes were encapsulated in water-in-oil microdroplets with a fluorogenic substrate for the target enzyme to screen for microdroplets that contain microbially active cells. Second, the microbial cells were recovered and subjected to whole genome amplification. Finally, the amplified genomes were sequenced to identify the genes encoding target enzymes. Employing this method, we successfully identified 14 novel β-glucosidase genes from uncultured bacterial cells in marine samples. Our method contributes to the screening and identification of genes encoding industrially valuable enzymes.

A hydrodynamic droplet pass filter for droplet-phase sample sorting was developed in this study.

This paper describes a microdroplet merging device that can actively control the merging of various droplets under a wide range of flow conditions, using a simple structure. The microdroplets were trapped and merged in a wide chamber divided by pillars, and their behavior was controlled by two horizontal pneumatic microactuators. Hydrodynamic flow control by the actuation was evaluated numerically, and the trapping and merging of droplets were achieved experimentally and controlled via pressure applied to the microactuators. Furthermore, two independently generated droplets were merged under four different modes, ranging from no merging to four-droplet merging, with different ratios and volumes. The pneumatic actuators allowed not only the control of the number of merged droplets, but also a wide range of applied droplet volumes. The device was fabricated simply using a single-layer PDMS (polydimethylsiloxane) structure, and the continuous merging performance operated using only hydrodynamic flow control without any surfactant. Finally, chemical synthesis of a metal complex was performed by the droplet merging method. Crystallization of the complex was visualized in real time, and the synthesis was verified by ultraviolet-visible spectroscopy.

In this study, a fast and quantitative determination method for branched-chain amino acids (BCAAs), namely leucine, isoleucine, and valine, was developed using a pillar array column. A pillar array column with low-dispersion turns was fabricated on a 20 × 20-mm(2) microchip using multistep ultraviolet photolithography and deep reactive ion etching. The BCAAs were fluorescently labeled with 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F), followed by reversed-phase separation on the pillar array column. The NBD derivatives of the three BCAAs and an internal standard (6-aminocaproic acid) were separated in 100 s. The calibration curves for the NBD-BCAAs had good linearity in the range of 0.4-20 μM, using an internal standard. The intra- and interday precisions were found to be in the ranges of 1.42-3.80 and 2.74-6.97%, respectively. The accuracies for the NBD-BCAA were from 90.2 to 99.1%. The method was used for the analysis of sports drink and human plasma samples. The concentrations of BCAAs determined by the developed method showed good agreements with those determined using a conventional high-performance liquid chromatography system. As BCAAs are important biomarkers of some diseases, these results showed that the developed method could be a potential diagnostic tool in clinical research.