Literature DB >> 25126893

PR-PR: cross-platform laboratory automation system.

Gregory Linshiz1, Nina Stawski, Garima Goyal, Changhao Bi, Sean Poust, Monica Sharma, Vivek Mutalik, Jay D Keasling, Nathan J Hillson.   

Abstract

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.

Entities:  

Mesh:

Year:  2014        PMID: 25126893     DOI: 10.1021/sb4001728

Source DB:  PubMed          Journal:  ACS Synth Biol        ISSN: 2161-5063            Impact factor:   5.110


  13 in total

Review 1.  Bricks and blueprints: methods and standards for DNA assembly.

Authors:  Arturo Casini; Marko Storch; Geoffrey S Baldwin; Tom Ellis
Journal:  Nat Rev Mol Cell Biol       Date:  2015-06-17       Impact factor: 94.444

Review 2.  Design Automation in Synthetic Biology.

Authors:  Evan Appleton; Curtis Madsen; Nicholas Roehner; Douglas Densmore
Journal:  Cold Spring Harb Perspect Biol       Date:  2017-04-03       Impact factor: 10.005

3.  Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.

Authors:  David I Walsh; Marilene Pavan; Luis Ortiz; Scott Wick; Johanna Bobrow; Nicholas J Guido; Sarah Leinicke; Dany Fu; Shreya Pandit; Lucy Qin; Peter A Carr; Douglas Densmore
Journal:  SLAS Technol       Date:  2019-02-15       Impact factor: 3.047

4.  DNA Assembly in 3D Printed Fluidics.

Authors:  William G Patrick; Alec A K Nielsen; Steven J Keating; Taylor J Levy; Che-Wei Wang; Jaime J Rivera; Octavio Mondragón-Palomino; Peter A Carr; Christopher A Voigt; Neri Oxman; David S Kong
Journal:  PLoS One       Date:  2015-12-30       Impact factor: 3.240

5.  Development of a fast and easy method for Escherichia coli genome editing with CRISPR/Cas9.

Authors:  Dongdong Zhao; Shenli Yuan; Bin Xiong; Hongnian Sun; Lijun Ye; Jing Li; Xueli Zhang; Changhao Bi
Journal:  Microb Cell Fact       Date:  2016-12-01       Impact factor: 5.328

6.  A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering.

Authors:  Zain Y Dossani; Amanda Reider Apel; Heather Szmidt-Middleton; Nathan J Hillson; Samuel Deutsch; Jay D Keasling; Aindrila Mukhopadhyay
Journal:  Yeast       Date:  2017-12-07       Impact factor: 3.239

Review 7.  Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae.

Authors:  Ya-Tang Yang; Chun Ying Wang
Journal:  Micromachines (Basel)       Date:  2016-10-11       Impact factor: 2.891

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

Authors:  Gregory Linshiz; Erik Jensen; Nina Stawski; Changhao Bi; Nick Elsbree; Hong Jiao; Jungkyu Kim; Richard Mathies; Jay D Keasling; Nathan J Hillson
Journal:  J Biol Eng       Date:  2016-02-02       Impact factor: 4.355

9.  GeneMill: A 21st century platform for innovation.

Authors:  James R Johnson; Rosalinda D'Amore; Simon C Thain; Thomas Craig; Hannah V McCue; Christiane Hertz-Fowler; Neil Hall; Anthony J W Hall
Journal:  Biochem Soc Trans       Date:  2016-06-15       Impact factor: 5.407

10.  Mechanically activated artificial cell by using microfluidics.

Authors:  Kenneth K Y Ho; Lap Man Lee; Allen P Liu
Journal:  Sci Rep       Date:  2016-09-09       Impact factor: 4.379

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