Design and functional assembly of synthetic biological parts and devices

[1]  Richard I. Kitney,et al.  The Design and Construction of a Set of Modular Synthetic BioLogic Devices for Programming Cells , 2009 .

[2]  M. Win,et al.  A modular and extensible RNA-based gene-regulatory platform for engineering cellular function , 2007, Proceedings of the National Academy of Sciences.

[3]  Christina D Smolke,et al.  Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems , 2010, Proceedings of the National Academy of Sciences.

[4]  J. Collins,et al.  DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS , 2009, Nature Biotechnology.

[5]  Drew Endy,et al.  Engineering BioBrick vectors from BioBrick parts , 2008, Journal of Biological Engineering.

[6]  F. Arnold,et al.  Directed evolution: new parts and optimized function. , 2009, Current opinion in biotechnology.

[7]  Stanislas Leibler,et al.  Cooperation and Hamilton's rule in a simple synthetic microbial system , 2010, Molecular systems biology.

[8]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[9]  Zhen Xie,et al.  Rationally-designed logic integration of regulatory signals in mammalian cells , 2010, Nature nanotechnology.

[10]  James C Liao,et al.  Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde , 2009, Nature Biotechnology.

[11]  D. Endy,et al.  Refactoring bacteriophage T7 , 2005, Molecular systems biology.

[12]  M. Surette,et al.  Quorum sensing in Escherichia coli and Salmonella typhimurium. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Douglas B. Kell,et al.  System Modeling in Cell Biology From Concepts to Nuts and Bolts , 2005 .

[14]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[15]  E. Koonin.  Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.

[16]  B. Bassler,et al.  Quorum sensing in bacteria. , 2001, Annual review of microbiology.

[17]  M. Elowitz,et al.  Programming gene expression with combinatorial promoters , 2007, Molecular systems biology.

[18]  P. Swain,et al.  Accurate prediction of gene feedback circuit behavior from component properties , 2007, Molecular systems biology.

[19]  Shankar Mukherji,et al.  Synthetic biology: understanding biological design from synthetic circuits , 2009, Nature Reviews Genetics.

[20]  B. Séraphin,et al.  Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.

[21]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[22]  Kirsten L. Frieda,et al.  A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell , 2008, Science.

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

[24]  Bonnie L Bassler,et al.  Small Talk Cell-to-Cell Communication in Bacteria , 2002, Cell.

[25]  E. P. Greenberg,et al.  Metabolism of Acyl-Homoserine Lactone Quorum-Sensing Signals by Variovorax paradoxus , 2000, Journal of bacteriology.

[26]  S. Hutcheson,et al.  Lon protease functions as a negative regulator of type III protein secretion in Pseudomonas syringae , 2002, Molecular microbiology.

[27]  Jian Zhan,et al.  Develop reusable and combinable designs for transcriptional logic gates , 2010, Molecular systems biology.

[28]  O. Kuipers,et al.  Bistability, epigenetics, and bet-hedging in bacteria. , 2008, Annual review of microbiology.

[29]  S. Hutcheson,et al.  Enhancer-Binding Proteins HrpR and HrpS Interact To Regulate hrp-Encoded Type III Protein Secretion inPseudomonas syringae Strains , 2001, Journal of bacteriology.

[30]  K. Nealson,et al.  Bacterial bioluminescence: Isolation and genetic analysis of functions from Vibrio fischeri , 1983, Cell.

[31]  James J. Collins,et al.  Next-Generation Synthetic Gene Networks , 2009, Nature Biotechnology.

[32]  J. Stelling,et al.  A tunable synthetic mammalian oscillator , 2009, Nature.

[33]  B. Bassler,et al.  Quorum sensing: cell-to-cell communication in bacteria. , 2005, Annual review of cell and developmental biology.

[34]  M. Isalan,et al.  Engineering prokaryotic gene circuits , 2008, FEMS microbiology reviews.

[35]  R. Weiss,et al.  Directed evolution of a genetic circuit , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  A. Collmer,et al.  Negative Regulation of hrp Genes inPseudomonas syringae by HrpV , 1998, Journal of bacteriology.

[37]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[38]  Ron Weiss,et al.  Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium , 2007, Proceedings of the National Academy of Sciences.

[39]  J. Keasling,et al.  Engineering a mevalonate pathway in Escherichia coli for production of terpenoids , 2003, Nature Biotechnology.

[40]  Thomas F. Knight,et al.  Idempotent Vector Design for Standard Assembly of Biobricks , 2003 .

[41]  F. Arnold,et al.  Implications of Rewiring Bacterial Quorum Sensing , 2007, Applied and Environmental Microbiology.

[42]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , .

[43]  L. Poulsen,et al.  New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria , 1998, Applied and Environmental Microbiology.

[44]  George M Church,et al.  Towards synthesis of a minimal cell , 2006, Molecular systems biology.

[45]  Christopher A. Voigt,et al.  Genetic parts to program bacteria. , 2006, Current opinion in biotechnology.

[46]  J. Chin,et al.  Cellular logic with orthogonal ribosomes. , 2005, Journal of the American Chemical Society.

[47]  Y. Dong,et al.  AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[48]  E. Greenberg,et al.  Quorum sensing in Vibrio fischeri: essential elements for activation of the luminescence genes , 1997, Journal of bacteriology.

[49]  H. Bujard,et al.  Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. , 1997, Nucleic acids research.

[50]  Christof Teuscher.  Cellular Computing , 2004, Encyclopedia of Complexity and Systems Science.

[51]  R. Kwok.  Five hard truths for synthetic biology , 2010, Nature.

[52]  Martin Buck,et al.  Regulation of the co-evolved HrpR and HrpS AAA+ proteins required for Pseudomonas syringae pathogenicity , 2011, Nature communications.

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

[54]  Timothy S. Ham,et al.  Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. , 2008, Current opinion in biotechnology.

[55]  M. Bennett,et al.  Microfluidic devices for measuring gene network dynamics in single cells , 2009, Nature Reviews Genetics.

[56]  U. Alon,et al.  Optimality and evolutionary tuning of the expression level of a protein , 2005, Nature.

[57]  Brian F. Pfleger,et al.  Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes , 2006, Nature Biotechnology.

[58]  C. A. Hutchinson,et al.  Genome transplantation in bacteria: changing one species to another. , 2007, Nature Reviews Microbiology.

[59]  F. Blattner,et al.  Emergent Properties of Reduced-Genome Escherichia coli , 2006, Science.

[60]  Yan Niu,et al.  Construction and Enhancement of a Minimal Genetic AND Logic Gate , 2008, Applied and Environmental Microbiology.

[61]  Guy Plunkett,et al.  Engineering a reduced Escherichia coli genome. , 2002, Genome research.

[62]  Travis S. Bayer,et al.  Programmable ligand-controlled riboregulators of eukaryotic gene expression , 2005, Nature Biotechnology.

[63]  U. Bonas,et al.  Who comes first? How plant pathogenic bacteria orchestrate type III secretion. , 2006, Current opinion in microbiology.

[64]  D. Belin,et al.  Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter , 1995, Journal of bacteriology.

[65]  R. Sauer,et al.  Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA , 1996, Science.

[66]  T. Hwa,et al.  Growth Rate-Dependent Global Effects on Gene Expression in Bacteria , 2009, Cell.

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

[68]  Yiannis N. Kaznessis,et al.  Forward engineering of synthetic bio-logical and gates , 2008 .

[69]  Drew Endy,et al.  Measuring the activity of BioBrick promoters using an in vivo reference standard , 2009, Journal of biological engineering.

[70]  J. Gallivan,et al.  Guiding bacteria with small molecules and RNA. , 2007, Journal of the American Chemical Society.

[71]  R. Breaker,et al.  Regulation of bacterial gene expression by riboswitches. , 2005, Annual review of microbiology.

[72]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[73]  O. White,et al.  Global transposon mutagenesis and a minimal Mycoplasma genome. , 1999, Science.

[74]  E. Greenberg,et al.  Signalling: Listening in on bacteria: acyl-homoserine lactone signalling , 2002, Nature Reviews Molecular Cell Biology.

[75]  E. Raineri,et al.  Evolvability and hierarchy in rewired bacterial gene networks , 2008, Nature.

[76]  Christopher A. Voigt,et al.  Environmentally controlled invasion of cancer cells by engineered bacteria. , 2006, Journal of molecular biology.

[77]  Alain Dufour,et al.  Two acid‐inducible promoters from Lactococcus lactis require the cis‐acting ACiD‐box and the transcription regulator RcfB , 2005, Molecular microbiology.

[78]  Martin Fussenegger,et al.  Synthetic ecosystems based on airborne inter- and intrakingdom communication , 2007, Proceedings of the National Academy of Sciences.

[79]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

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

[81]  Haisu Ma,et al.  Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch , 2010, Molecular systems biology.

[82]  Priscilla E. M. Purnick,et al.  The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.

[83]  R. D'Amato,et al.  Exogenous control of mammalian gene expression through modulation of RNA self-cleavage , 2004, Nature.

[84]  Frances H Arnold,et al.  Synthetic gene circuits: design with directed evolution. , 2007, Annual review of biophysics and biomolecular structure.

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

[86]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[87]  D. Bose,et al.  A second paradigm for gene activation in bacteria. , 2006, Biochemical Society transactions.

[88]  M. Chandler,et al.  An in vivo transposase-catalyzed single-stranded DNA circularization reaction. , 1995, Genes & development.

[89]  S Falkow,et al.  FACS-optimized mutants of the green fluorescent protein (GFP). , 1996, Gene.

[90]  Farren J. Isaacs,et al.  Computational studies of gene regulatory networks: in numero molecular biology , 2001, Nature Reviews Genetics.

[91]  Jared R. Leadbetter,et al.  Directed Evolution of Vibrio fischeri LuxR for Improved Response to Butanoyl-Homoserine Lactone , 2007, Applied and Environmental Microbiology.

[92]  S. Basu,et al.  Spatiotemporal control of gene expression with pulse-generating networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[93]  S. He,et al.  Type III protein secretion in Pseudomonas syringae. , 2003, Microbes and infection.

[94]  R. Weiss,et al.  Advances in synthetic biology: on the path from prototypes to applications. , 2005, Current opinion in biotechnology.

[95]  Jeff Hasty,et al.  Monitoring dynamics of single-cell gene expression over multiple cell cycles , 2005, 2006 Bio Micro and Nanosystems Conference.

[96]  James J. Collins,et al.  A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells , 2007, Cell.

[97]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[98]  Joseph H. Davis,et al.  Design, construction and characterization of a set of insulated bacterial promoters , 2010, Nucleic acids research.

[99]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[100]  D. Fouts,et al.  Pseudomonas syringae Hrp type III secretion system and effector proteins. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[101]  Christopher A. Voigt,et al.  Environmental signal integration by a modular AND gate , 2007, Molecular systems biology.

[102]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[103]  Virginia W Cornish,et al.  Transcription factor logic using chemical complementation. , 2008, Molecular bioSystems.

[104]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[105]  C. Hutchison,et al.  Essential genes of a minimal bacterium. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[106]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[107]  R. Weiss,et al.  Optimizing genetic circuits by global sensitivity analysis. , 2004, Biophysical journal.

[108]  Wendell A Lim,et al.  Synthetic biology: lessons from the history of synthetic organic chemistry , 2007, Nature Chemical Biology.

[109]  James C. Hu,et al.  Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[110]  Bonnie L Bassler,et al.  Chemical communication among bacteria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[111]  A. deMello,et al.  Opportunities for microfluidic technologies in synthetic biology , 2009, Journal of The Royal Society Interface.

[112]  Ryan T Gill,et al.  Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides , 2010, Nature Biotechnology.