Design automation of microfluidic droplet sorting platforms

Both basic research and biological design require high throughput screening to parse through the massive amounts of variants generated in experiments. However, the cost and expertise needed for use of such technology limit accessibility. Simple and reproducible designs of a sorting platform would reduce the barrier for implementation of affordable bench-top screening platforms. Droplet microfluidics present a promising approach for automating biology, reducing reaction volumes to picoliter droplets and allowing for deterministic manipulation of samples. Droplet microfluidics have been used extensively for high throughput screening and directed evolution, yet limitations in fabrication have prevented the characterization needed for a design tool and subsequent widespread adoption. Here, we present a finite element analysis (FEA) model-based design framework for dielectrophoretic droplet microfluidic sorters and its preliminary experimental validation. This framework extends previous work from our group creating microfluidic designs tools, increasing their usability in the lab

Repository-based plasmid design

There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs.Accepted manuscrip

Automating functional enzyme screening & characterization

This work has been presented in the 10th IWBDA workshop.Microfluidics continue to gain traction as an inexpensive alternative to standard multi-well plate-based, and flow cytometry- based, assay platforms. These devices are especially useful for the types of ultra-high throughput screens needed for enzyme discovery applications where large numbers (>106) of unique samples must be screened rapidly1. Coupled with cell-free protein synthesis2, microfluidics are being used to identify novel enzymes useful for a variety of applications with unprecedented speed. However, these devices are typically produced using PDMS, and require considerable infrastructure and artisanal skill to fabricate, limiting their accessibility. Likewise, enzyme hits obtained from a screen are often validated manually and would benefit from automation of downstream validation processes. To address these limitations, we propose a workflow which leverages software tools to automate the rapid design and fabrication of low-cost polycarbonate microfluidic devices for use as high-throughput screening platforms for enzyme discovery, as well as an automated DNA assembly tool to streamline validation of screening candidates. Using this workflow, we aim to identify novel oxidoreductase enzymes from environmental metagenomic DNA libraries, for use in electrochemical biosensors

A reverse predictive model towards design automation of microfluidic droplet generators

This work has been presented in the 10th IWBDA workshop.Droplet-based microfluidic devices in comparison to test tubes can reduce reaction volumes 10^9 times and more due to the encapsulation of reactions in micro-scale droplets [4]. This volume reduction, alongside higher accuracy, higher sensitivity and faster reaction time made droplet microfluidics a superior platform particularly in biology, biomedical, and chemical engineering. However, a high barrier of entry prevents most of life science laboratories to exploit the advantages of microfluidics. There are two main obstacles to the widespread adoption of microfluidics, high fabrication costs, and lack of design automation tools. Recently, low-cost fabrication methods have reduced the cost of fabrication significantly [7]. Still, even with a low-cost fabrication method, due to lack of automation tools, life science research groups are still reliant on a microfluidic expert to develop any new microfluidic device [3, 5]. In this work, we report a framework to develop reverse predictive models that can accurately automate the design process of microfluidic droplet generators. This model takes prescribed performance metrics of droplet generators as the input and provides the geometry of the microfluidic device and the fluid and flow settings that result in the desired performance. We hope this automation tool makes droplet-based microfluidics more accessible, by reducing the time, cost, and knowledge needed for developing a microfluidic droplet generator that meets certain performance requirement

Microstrip Yagi array for MSAT vehicle antenna application

A microstrip Yagi array was developed for the MSAT system as a low-cost mechanically steered medium-gain vehicle antenna. Because its parasitic reflector and director patches are not connected to any of the RF power distributing circuit, while still contributing to achieve the MSAT required directional beam, the antenna becomes a very efficient radiating system. With the complete monopulse beamforming circuit etched on a thin stripline board, the planar microstrip Yagi array is capable of achieving a very low profile. A theoretical model using the Method of Moments was developed to facilitate the ease of design and understanding of this antenna

Design automation based on fluid dynamics

This article was accepted and presented at the 9th International Workshop on Bio-Design Automation, Pittsburgh, Pennsylvania (2017).Microfluidic devices provide researchers with numerous advantages such as high throughput, increased sensitivity and accuracy, lower cost, and reduced reaction time. However, design, fabrication, and running a microfluidic device are still heavily reliant on expertise. Recent studies suggest micro-milling can be a semi-automatic, inexpensive, and simple alternative to common fabrication methods. Micro-milling does not require a clean-room, mask aligner, spin-coater, and Plasma bonder, thus cutting down the cost and time of fabrication significantly. Moreover, through this protocol researchers can easily fabricate microfluidic devices in an automated fashion eschewing levels of expertise required for typical fabrication methods, such as photolithography, soft-lithography, and etching. However, designing a microfluidic chip that meets a certain set of requirements is still heavily dependent on a microfluidic expert, several days of simulation, and numerous experiments to reach the required performance. To address this, studies have reported random automated design of microfluidic devices based on numerical simulations for micro-mixing. However, random design generation is heavily reliant on time-consuming simulations carried out beforehand, and is prone to error due to the accuracy limitations of the numerical method. On the other hand, by using micro-milling for ultra-fast and inexpensive fabrication of microfluidic devices and Taguchi design of experiments for state-space exploration of all of the geometric parameters, we are able to generate a database of geometries, flow rates, and flow properties required for a single primitive to carry out a specified microfluidic task

From the Hicksites to the Progressive Friends: The Rural Roots of Perfectionism and Social Reform among North American Friends

In the 1840s and 1850s, North American Friends endured a series of localized separations. This paper examines the Progressive Friends separations in Genesee Yearly Meeting in 1848, centered in the \u27burned-over district\u27 of New York State, and in Western Quarterly Meeting of Philadelphia Yearly Meeting (Hicksite) in 1852-53. Both separations had roots in the controversy among Friends over appropriate anti-slavery activities and both challenged the existing structures of the Religious Society of Friends. These separations were both radical and rural, and mark a distinct change from the earlier deference of Friends towards the leadership of London and Philadelphia Yearly Meetings

Automated robotic liquid handling assembly of modular DNA devices

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available "design space" represented by "devices" created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophistication and scale of synthetic biology research necessitates an efficient, reproducible way to accommodate large-scale, complex, and high throughput device construction. Here, a DNA assembly protocol using the Type-IIS restriction endonuclease based Modular Cloning (MoClo) technique is automated on two liquid-handling robotic platforms. Automated liquid-handling robots require careful, often times tedious optimization of pipetting parameters for liquids of different viscosities (e.g. enzymes, DNA, water, buffers), as well as explicit programming to ensure correct aspiration and dispensing of DNA parts and reagents. This makes manual script writing for complex assemblies just as problematic as manual DNA assembly, and necessitates a software tool that can automate script generation. To this end, we have developed a web-based software tool, http://mocloassembly.com, for generating combinatorial DNA device libraries from basic DNA parts uploaded as Genbank files. We provide access to the tool, and an export file from our liquid handler software which includes optimized liquid classes, labware parameters, and deck layout. All DNA parts used are available through Addgene, and their digital maps can be accessed via the Boston University BDC ICE Registry. Together, these elements provide a foundation for other organizations to automate modular cloning experiments and similar protocols. The automated DNA assembly workflow presented here enables the repeatable, automated, high-throughput production of DNA devices, and reduces the risk of human error arising from repetitive manual pipetting. Sequencing data show the automated DNA assembly reactions generated from this workflow are ~95% correct and require as little as 4% as much hands-on time, compared to manual reaction preparation