The PLOS ONE Synthetic Biology Collection: Six Years and Counting

Since it was launched in 2006, PLOS ONE has published over fifty articles illustrating the many facets of the emerging field of synthetic biology. This article reviews these publications by organizing them into broad categories focused on DNA synthesis and assembly techniques, the development of libraries of biological parts, the use of synthetic biology in protein engineering applications, and the engineering of gene regulatory networks and metabolic pathways. Finally, we review articles that describe enabling technologies such as software and modeling, along with new instrumentation. In order to increase the visibility of this body of work, the papers have been assembled into the PLOS ONE Synthetic Biology Collection (www.ploscollections.org/synbio). Many of the innovative features of the PLOS ONE web site will help make this collection a resource that will support a lively dialogue between readers and authors of PLOS ONE synthetic biology papers. The content of the collection will be updated periodically by including relevant articles as they are published by the journal. Thus, we hope that this collection will continue to meet the publishing needs of the synthetic biology community.

[1]  H. Sauro,et al.  Standard Biological Parts Knowledgebase , 2011, PloS one.

[2]  Jan Marienhagen,et al.  OmniChange: The Sequence Independent Method for Simultaneous Site-Saturation of Five Codons , 2011, PloS one.

[3]  Tom Ellis,et al.  Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology , 2012, PloS one.

[4]  Timothy S. Ham,et al.  Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory , 2008, PloS one.

[5]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[6]  In Vitro Assembly of Multiple DNA Fragments Using Successive Hybridization , 2012, PloS one.

[7]  Tau-Mu Yi,et al.  Synthetic Morphology Using Alternative Inputs , 2009, PloS one.

[8]  Raik Grünberg,et al.  A Biobrick Library for Cloning Custom Eukaryotic Plasmids , 2011, PloS one.

[9]  Marten Veenhuis,et al.  An Engineered Yeast Efficiently Secreting Penicillin , 2009, PloS one.

[10]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[11]  J. Peccoud,et al.  Targeted Development of Registries of Biological Parts , 2008, PloS one.

[12]  J. Gonçalves,et al.  Bimodal and Hysteretic Expression in Mammalian Cells from a Synthetic Gene Circuit , 2008, PloS one.

[13]  Mehrdad Nourani,et al.  Statecharts for Gene Network Modeling , 2010, PloS one.

[14]  A. Oudenaarden,et al.  Cellular Decision Making and Biological Noise: From Microbes to Mammals , 2011, Cell.

[15]  Stanislas Leibler,et al.  Printing Multistrain Bacterial Patterns with a Piezoelectric Inkjet Printer , 2007, PloS one.

[16]  M. Elowitz,et al.  Build life to understand it , 2010, Nature.

[17]  M. Grabherr,et al.  Exploiting Nucleotide Composition to Engineer Promoters , 2011, PloS one.

[18]  Albert Sorribas,et al.  Two Component Systems: Physiological Effect of a Third Component , 2012, PloS one.

[19]  Ying-jin Yuan,et al.  An Environment-Sensitive Synthetic Microbial Ecosystem , 2010, PloS one.

[20]  Z. Cai,et al.  Chemical Synthesis of Bacteriophage G4 , 2011, PloS one.

[21]  M. A. Jensen,et al.  DMSO and Betaine Greatly Improve Amplification of GC-Rich Constructs in De Novo Synthesis , 2010, PloS one.

[22]  R. Weiss,et al.  Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks , 2011, PloS one.

[23]  Jun Wang,et al.  Reverse Engineering of Bacterial Chemotaxis Pathway via Frequency Domain Analysis , 2010, PloS one.

[24]  A. Kossiakoff,et al.  Characterization of Engineered Actin Binding Proteins That Control Filament Assembly and Structure , 2010, PloS one.

[25]  D. Wishart,et al.  The Bacterial Nanorecorder: Engineering E. coli to Function as a Chemical Recording Device , 2011, PloS one.

[26]  Ernst Weber,et al.  A Modular Cloning System for Standardized Assembly of Multigene Constructs , 2011, PloS one.

[27]  Michael H. Hecht,et al.  De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth , 2011, PloS one.

[28]  P. Oldham,et al.  Synthetic Biology: Mapping the Scientific Landscape , 2012, PloS one.

[29]  Marc D. Riedel,et al.  Rate-Independent Constructs for Chemical Computation , 2011, Pacific Symposium on Biocomputing.

[30]  Jay D. Keasling,et al.  High-Level Production of Amorpha-4,11-Diene, a Precursor of the Antimalarial Agent Artemisinin, in Escherichia coli , 2009, PloS one.

[31]  Sylvestre Marillonnet,et al.  Assembly of Designer TAL Effectors by Golden Gate Cloning , 2011, PloS one.

[32]  Jean Peccoud,et al.  Strengths and limitations of the federal guidance on synthetic DNA , 2011, Nature Biotechnology.

[33]  Karin Schroën,et al.  A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis , 2012, PloS one.

[34]  Jingdong Tian,et al.  Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways , 2009, PloS one.

[35]  P. Stafford,et al.  A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells , 2009, PloS one.

[36]  Frances H. Arnold,et al.  Self-Organization, Layered Structure, and Aggregation Enhance Persistence of a Synthetic Biofilm Consortium , 2011, PloS one.

[37]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[38]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[39]  A. Granell,et al.  GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules , 2011, PloS one.

[40]  Mauricio S. Antunes,et al.  Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway , 2011, PloS one.

[41]  Carola Engler,et al.  Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes , 2009, PloS one.

[42]  Jürgen Kurths,et al.  Timing Cellular Decision Making Under Noise via Cell–Cell Communication , 2009, PloS one.

[43]  L. Serrano,et al.  Reconstitution of Mdm2-Dependent Post-Translational Modifications of p53 in Yeast , 2008, PloS one.

[44]  Fabrizio Gelain,et al.  Designer Self-Assembling Peptide Nanofiber Scaffolds for Adult Mouse Neural Stem Cell 3-Dimensional Cultures , 2006, PloS one.

[45]  S. Sørensen,et al.  Design and Synthesis of a Quintessential Self-Transmissible IncX1 Plasmid, pX1.0 , 2011, PloS one.

[46]  Javier Macía,et al.  Monomeric Bistability and the Role of Autoloops in Gene Regulation , 2009, PloS one.

[47]  M. di Bernardo,et al.  How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator, or a Bistable Switch , 2009, PloS one.

[48]  Alan Villalobos,et al.  Design Parameters to Control Synthetic Gene Expression in Escherichia coli , 2009, PloS one.

[49]  J. Bae,et al.  Synthetic Biology of Proteins: Tuning GFPs Folding and Stability with Fluoroproline , 2008, PloS one.

[50]  Oliver Purcell,et al.  A Multi-Functional Synthetic Gene Network: A Frequency Multiplier, Oscillator and Switch , 2011, PloS one.

[51]  Michel M. Maharbiz,et al.  A Modified Consumer Inkjet for Spatiotemporal Control of Gene Expression , 2009, PloS one.

[52]  Drew Endy,et al.  Gemini, a Bifunctional Enzymatic and Fluorescent Reporter of Gene Expression , 2009, PloS one.

[53]  K. Kaneko,et al.  Adaptive Response of a Gene Network to Environmental Changes by Fitness-Induced Attractor Selection , 2006, PloS one.

[54]  Gilles Charvin,et al.  A Microfluidic Device for Temporally Controlled Gene Expression and Long-Term Fluorescent Imaging in Unperturbed Dividing Yeast Cells , 2008, PloS one.

[55]  Yu Tanouchi,et al.  Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology , 2010, PloS one.

[56]  J. Mielenz,et al.  High-Yield Hydrogen Production from Starch and Water by a Synthetic Enzymatic Pathway , 2007, PloS one.

[57]  Henrike Niederholtmeyer,et al.  Towards a Synthetic Chloroplast , 2011, PloS one.

[58]  Emma M. B. Weeding,et al.  Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems , 2011, PloS one.

[59]  M. Bradley,et al.  Microarray Generation of Thousand-Member Oligonucleotide Libraries , 2011, PloS one.