End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

DNAConstructor scripts.zip. Zip file containing files gfp_DNAConstructor.txt and rfp_DNAConstructor.txt, input script files for DNA Constructor. (ZIP 1.7 kb

Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water.

We report an all-in-one platform - ScanDrop - for the rapid and specific capture, detection, and identification of bacteria in drinking water. The ScanDrop platform integrates droplet microfluidics, a portable imaging system, and cloud-based control software and data storage. The cloud-based control software and data storage enables robotic image acquisition, remote image processing, and rapid data sharing. These features form a "cloud" network for water quality monitoring. We have demonstrated the capability of ScanDrop to perform water quality monitoring via the detection of an indicator coliform bacterium, Escherichia coli, in drinking water contaminated with feces. Magnetic beads conjugated with antibodies to E. coli antigen were used to selectively capture and isolate specific bacteria from water samples. The bead-captured bacteria were co-encapsulated in pico-liter droplets with fluorescently-labeled anti-E. coli antibodies, and imaged with an automated custom designed fluorescence microscope. The entire water quality diagnostic process required 8 hours from sample collection to online-accessible results compared with 2-4 days for other currently available standard detection methods

End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis.

BackgroundSynthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening.ResultsHerein, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform's capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, and proteogenic and metabolic output analysis.ConclusionsTaken together, we demonstrate the microfluidic platform's potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis

PaR-PaR Laboratory Automation Platform

Labor-intensive multistep biological tasks, such as the construction and cloning of DNA molecules, are prime candidates for laboratory automation. Flexible and biology-friendly operation of robotic equipment is key to its successful integration in biological laboratories, and the efforts required to operate a robot must be much smaller than the alternative manual lab work. To achieve these goals, a simple high-level biology-friendly robot programming language is needed. We have developed and experimentally validated such a language: Programming a Robot (PaR-PaR). The syntax and compiler for the language are based on computer science principles and a deep understanding of biological workflows. PaR-PaR allows researchers to use liquid-handling robots effectively, enabling experiments that would not have been considered previously. After minimal training, a biologist can independently write complicated protocols for a robot within an hour. Adoption of PaR-PaR as a standard cross-platform language would enable hand-written or software-generated robotic protocols to be shared across laboratories

Editorial Special Issue Introduction Algorithmic Game Theory

n We briefly survey the rise of game theory as a topic of study in artificial intelligence an

PR-PR: Cross-Platform Laboratory Automation System

To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms

Schematic overview of a ScanDrop cloud-based water quality assessment system.

<p>The ScanDrop detector network is enabled by PR-PR and cloud-based data storage. Users send requests for water quality assessment at different locations in the distribution system. ScanDrop detectors perform the tests, the results are stored in the cloud, and the collected data is shared between users and applications.</p

Bacteria capturing and detection assay.

<p>Magnetic bead capture of <i>E. coli</i> from enriched water samples, and downstream chip encapsulation for fluorescent labeling and detection. 1L of water is passed through a 0.22 µm filter, which is then incubated for 6 hr in LB media. Dynabeads® MAX anti-<i>E. coli</i> O157 are added to the resulting cell culture (“sample”), incubated for 20 min, and concentrated via magnet. The beads (potentially conjugated with bacteria) are then co-encapsulated with secondary fluorescently labeled anti-<i>E. coli</i> antibodies in the chip and incubated up to 1 hour before imaging.</p

Portable fluorescence microscope system.

<p><b>A</b>) Microscope design scheme. <b>B</b>) Robotic stage and two cameras (arrows) for chip observation and data acquisition. <b>C</b>) ScanDrop system set up, including 2 pressure pumps to create droplets, a microscope imaging system, internet access, and a monitor for local data viewing.</p