Design-Build-Test Cycle
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SynBio’s Pathbreaking New Tools: Accelerating the Design-Build-Test Cycle

Anyone who has done serious work in a synthetic biology laboratory knows the challenge of managing thousands of stock bioparts and performing countless liquid handling processes that, while well-established, are often wasteful. These long-standing challenges have acted as a drag on the design-build-test cycle, slowing the pace of innovation and increasing the costs of research and production.

TTP Labtech now offers automated storage solutions that enable synthetic biologists to focus on the science and not waste valuable time and effort on the management of their biopart stocks, says product manager Paul Lomax. He’s one of six researchers who, at the big SynBioBeta SF 2016 meeting that convenes October 4-6 at the South San Francisco conference Center, will participate in a “Tools and Technology” session focused on synbio’s pathbreaking new tools.

Reducing reaction volume in such processes as assembly, colony PCR, and NGS library prep “can yield up to a 25 percent reduction in cost and massively increase a laboratory’s output capabilities while staying within budget,” says Lomax. TTP Labtech has provided automated low temperature storage devices and low volume liquid handling systems (down to nanolitre volumes) to the University of Liverpool GeneMill, one of the first open access synthetic biology laboratories to be established in the UK.

“Working with the team at the GeneMill, we have established and proven low-volume liquid handling protocols for assembly and colony PCR and integrated storage protocols, resulting in significant savings in cost and time,” he says. “Further developments will push reaction volumes even lower to further drive down costs.”

A Web-based Information System

Storage is also a concern for Richard Kitney, a professor of biomedical systems engineering at Imperial College London who serves additionally as chair of the Institute of Systems and Synthetic Biology and co-director of Imperial’s EPSRC National Centre for Synthetic Biology and Innovation and its UK National Industrial Translation Centre for Synthetic Biology.

At SynBioBeta, Kitney will discuss the development of a web-based information system that’s capable of capturing all of the detail of characterization experiments, including the data, metadata, and anecdotal notes. In relation to that work, Kitney also will discuss DICOM-SB, a new data acquisition standard for synthetic biology that’s based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine.

Designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments, the DICOM-SB model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. Based on the engineering principles of modularity, standardization, and characterization, the new standard – which has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London — also includes services orientated toward the automatic exchange of data and information between modalities and repositories using the Design-Build-Test-Learn design cycle paradigm.

“The problems which we are currently solving relate to the systematic design of biological devices,” says Kitney, who is also chair of Visbion, a successful biomedical data integration, storage, and display company that is now moving into synthetic biology. “We are now working hard on the development of standard operating procedures for our foundry and developing specific process management software for this purpose. One key aspect of the work is the ability to improve the reproducibility of synthetic biology components. We’re undertaking a joint study in this regard with colleagues in Singapore.”

A New Pipeline Technology

Another approach to cost-savings can be found in Sphere Fluidics’ new pipeline technology, ESI-Mine™, for which there is now a proof-of-concept focused on the “test” phase of the design-build-test-learn pathway. Sphere Fluidics has extensively patented both ESI-Mine™ and Cyto-Mine®, a related platform that’s currently in alpha and scheduled for release in 2017, says Xin Li, group leader of the firm’s chemistry group.

“We have spotted the potential of adapting our platform to automated CRISPR genome editing at the single cell level,” says Li, who joined Sphere Fluidics at its very early stage, and developed and launched the company’s specialist chemicals products, such as Pico-Surf™ and Pico-Glide™, and microfluidic device products, e.g. Pico-Gen™ and Pico-Sorter™.

“This would have the advantage of reducing costs by as much as 50-fold due to miniaturization and precision engineering at the single cell level by adding a specific number of cargoes, such as one per cell. Genome editing of a bulk cell population tends to give significant differences in the number of cargoes delivered to each cell, with some cells receiving no cargo or too much cargo, thereby increasing the chance of off-target mutations. We could also include phenotypic analysis of engineering cells prior to their sorting and subsequent dispensing and retrieval.”

“The ESI-Mine™ platform has generated a lot of excitement with synbio people around the world,” and Li says this it will be the main focus of his talk. “I’ll describe some recent work on different cell libraries and new advances in our biochip design, software, and system prototype development. We operate high-throughput, miniaturized tests at the single cell and molecule level, so there’s an ideal fit for our platforms with user needs in the test domain of the synbio space.”

A Toolset for CRISPR/Cas9 Workflows

For Breton Hornblower, Product Marketing Manager for New England Biolabs, a leading supplier of recombinant enzymes for molecular biology applications, the session will be an opportunity to discuss the firm’s recently launched EnGen product line as a toolset for CRISPR/Cas9 workflows.

“Cas9 is an RNA-directed DNA endonuclease that allows for the highly specific cleavage of DNA at almost any site in vitro or in vivo,” says Hornblower, who at both the University of California, Santa Cruz and the Rowland Institute at Harvard, he worked on developing nucleic acid analysis techniques using nanopores. “Our EnGen product line includes reagents for rapid generation of RNPs and sgRNA as well as analysis of editing. Online sgRNA synthesis protocols can require PCR steps for template assembly and transcription in a single reaction with transcription reactions. The EnGen sgRNA Synthesis Kit combines assembly and transcription in a single reaction with a total workflow under an hour. The only thing the user has to supply is an inexpensive 55mer oligonucleotide.”

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Dan Forbush

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