Literature DB >> 28602523

Engineering biological systems using automated biofoundries.

Ran Chao1, Shekhar Mishra1, Tong Si2, Huimin Zhao3.   

Abstract

Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society. However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering. In recent years, biological foundries or biofoundries have been developed to automate design-build-test engineering cycles in an effort to accelerate these processes. This review summarizes the enabling technologies for such biofoundries as well as their early successes and remaining challenges.
Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

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Year:  2017        PMID: 28602523      PMCID: PMC5544601          DOI: 10.1016/j.ymben.2017.06.003

Source DB:  PubMed          Journal:  Metab Eng        ISSN: 1096-7176            Impact factor:   9.783


  123 in total

Review 1.  Partners and pathwaysrepairing a double-strand break.

Authors:  J E Haber
Journal:  Trends Genet       Date:  2000-06       Impact factor: 11.639

2.  The KEGG databases at GenomeNet.

Authors:  Minoru Kanehisa; Susumu Goto; Shuichi Kawashima; Akihiro Nakaya
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides.

Authors:  H M Ellis; D Yu; T DiTizio; D L Court
Journal:  Proc Natl Acad Sci U S A       Date:  2001-05-29       Impact factor: 11.205

Review 4.  Automation for genomics, part one: preparation for sequencing.

Authors:  D Meldrum
Journal:  Genome Res       Date:  2000-08       Impact factor: 9.043

Review 5.  DNA microarray technology: devices, systems, and applications.

Authors:  Michael J Heller
Journal:  Annu Rev Biomed Eng       Date:  2002-03-22       Impact factor: 9.590

6.  Lab automation and robotics: Automation on the move.

Authors:  Tim Chapman
Journal:  Nature       Date:  2003-02-06       Impact factor: 49.962

Review 7.  Single-cell electroporation.

Authors:  Jessica Olofsson; Kerstin Nolkrantz; Frida Ryttsén; Bradley A Lambie; Stephen G Weber; Owe Orwar
Journal:  Curr Opin Biotechnol       Date:  2003-02       Impact factor: 9.740

8.  DNA cloning by homologous recombination in Escherichia coli.

Authors:  Y Zhang; J P Muyrers; G Testa; A F Stewart
Journal:  Nat Biotechnol       Date:  2000-12       Impact factor: 54.908

9.  DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis.

Authors:  David M Hoover; Jacek Lubkowski
Journal:  Nucleic Acids Res       Date:  2002-05-15       Impact factor: 16.971

10.  Mutant loxP vectors for selectable marker recycle and conditional knock-outs.

Authors:  H Arakawa; D Lodygin; J M Buerstedde
Journal:  BMC Biotechnol       Date:  2001-09-26       Impact factor: 2.563

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  35 in total

1.  Focus Issue Editorial: Synthetic Biology.

Authors:  Andrew D Hanson; Julian M Hibberd; Mattheos A G Koffas; Joachim Kopka; Eleanore T Wurtzel
Journal:  Plant Physiol       Date:  2019-03       Impact factor: 8.340

2.  Computer-Aided Design and Pre-validation of Large Batches of DNA Assemblies.

Authors:  Valentin Zulkower
Journal:  Methods Mol Biol       Date:  2021

3.  Usage of Digital Twins Along a Typical Process Development Cycle.

Authors:  Peter Sinner; Sven Daume; Christoph Herwig; Julian Kager
Journal:  Adv Biochem Eng Biotechnol       Date:  2021       Impact factor: 2.635

Review 4.  Stress-tolerant non-conventional microbes enable next-generation chemical biosynthesis.

Authors:  Sarah Thorwall; Cory Schwartz; Justin W Chartron; Ian Wheeldon
Journal:  Nat Chem Biol       Date:  2020-01-23       Impact factor: 15.040

Review 5.  The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology.

Authors:  Troy E Sandberg; Michael J Salazar; Liam L Weng; Bernhard O Palsson; Adam M Feist
Journal:  Metab Eng       Date:  2019-08-08       Impact factor: 9.783

6.  Challenges to Ensure a Better Translation of Metabolic Engineering for Industrial Applications.

Authors:  Fayza Daboussi; Nic D Lindley
Journal:  Methods Mol Biol       Date:  2023

7.  Effects of DNA template preparation on variability in cell-free protein production.

Authors:  Eugenia Romantseva; Nina Alperovich; David Ross; Steven P Lund; Elizabeth A Strychalski
Journal:  Synth Biol (Oxf)       Date:  2022-08-13

8.  AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms.

Authors:  Yi Yang; Yufeng Mao; Ruoyu Wang; Haoran Li; Ye Liu; Haijiao Cheng; Zhenkun Shi; Yu Wang; Meng Wang; Ping Zheng; Xiaoping Liao; Hongwu Ma
Journal:  Nucleic Acids Res       Date:  2022-05-26       Impact factor: 19.160

Review 9.  The future of biologically inspired next-generation factories for chemicals.

Authors:  Claudia Schmidt-Dannert
Journal:  Microb Biotechnol       Date:  2017-08-14       Impact factor: 5.813

Review 10.  Recent Advances in Heterologous Synthesis Paving Way for Future Green-Modular Bioindustries: A Review With Special Reference to Isoflavonoids.

Authors:  Moon Sajid; Shane Ramsay Stone; Parwinder Kaur
Journal:  Front Bioeng Biotechnol       Date:  2021-07-01
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