Automated BioPart characterisation for synthetic biology

[1]  Drew Endy,et al.  Precise and reliable gene expression via standard transcription and translation initiation elements , 2013, Nature Methods.

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

[3]  Paul S. Freemont,et al.  Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology , 2013, Nucleic acids research.

[4]  Christopher A. Voigt,et al.  A Synthetic Genetic Edge Detection Program , 2009, Cell.

[5]  Christopher A. Voigt,et al.  Genetic sensor for strong methylating compounds. , 2013, ACS synthetic biology.

[6]  Jeong-Yeol Yoon,et al.  Grand challenges for biological engineering , 2009, Journal of biological engineering.

[7]  D. Densmore,et al.  Algorithms for automated DNA assembly , 2010, Nucleic acids research.

[8]  G. Stephanopoulos,et al.  Tuning genetic control through promoter engineering. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Ron Weiss,et al.  Genetically programmable pathogen sense and destroy. , 2013, ACS synthetic biology.

[10]  B. K. Lundholt,et al.  A Simple Technique for Reducing Edge Effect in Cell-Based Assays , 2003, Journal of biomolecular screening.

[11]  Vivek K. Mutalik,et al.  Composability of regulatory sequences controlling transcription and translation in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.

[12]  J. Keasling,et al.  mRNA stability and plasmid copy number effects on gene expression from an inducible promoter system. , 1998, Biotechnology and bioengineering.

[13]  R. Weiss,et al.  Cancer Cells Multi-Input RNAi-Based Logic Circuit for Identification of Specific , 2011 .

[14]  L. Kricka,et al.  Thermal characteristics of microtitre plates used in immunological assays. , 1979, Journal of immunological methods.

[15]  Christopher A. Voigt,et al.  Genetic circuit performance under conditions relevant for industrial bioreactors. , 2012, ACS synthetic biology.

[16]  Adam Arkin,et al.  Setting the standard in synthetic biology , 2008, Nature Biotechnology.

[17]  James J. Collins,et al.  Dispersing biofilms with engineered enzymatic bacteriophage , 2007, Proceedings of the National Academy of Sciences.

[18]  L. Looger,et al.  Computational design of receptor and sensor proteins with novel functions , 2003, Nature.

[19]  Swapnil Chhabra,et al.  Biofuel alternatives to ethanol: pumping the microbial well. , 2008, Trends in biotechnology.

[20]  Jay D Keasling,et al.  BglBricks: A flexible standard for biological part assembly , 2010, Journal of biological engineering.

[21]  Drew Endy,et al.  A survey of enabling technologies in synthetic biology , 2013, Journal of biological engineering.

[22]  Nathan J Hillson,et al.  PaR-PaR laboratory automation platform. , 2013, ACS synthetic biology.

[23]  Susanna Zucca,et al.  Characterization of an inducible promoter in different DNA copy number conditions , 2012, BMC Bioinformatics.

[24]  Jacob Beal,et al.  A Method for Fast, High-Precision Characterization of Synthetic Biology Devices , 2012 .

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

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

[27]  Giovanni Bertoni,et al.  One-step high-throughput assay for quantitative detection of beta-galactosidase activity in intact gram-negative bacteria, yeast, and mammalian cells. , 2006, BioTechniques.

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

[29]  T. Hwa,et al.  Growth-rate-dependent partitioning of RNA polymerases in bacteria , 2008, Proceedings of the National Academy of Sciences.

[30]  S. Mizuno,et al.  A microplate assay for quantitation of anchorage-independent growth of transformed cells. , 1995, Analytical biochemistry.

[31]  Ruth J. Williams,et al.  Queueing up for Enzymatic Processing: Correlated Signaling through Coupled Degradation , 2022 .

[32]  H. Bujard,et al.  Context-dependent effects of upstream A-tracts. Stimulation or inhibition of Escherichia coli promoter function. , 1994, Journal of molecular biology.

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

[34]  H. Aiba,et al.  Transcriptional terminator is a positive regulatory element in the expression of the Escherichia coli crp gene. , 1991, The Journal of biological chemistry.

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

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

[37]  Juhyun Kim,et al.  The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes , 2012, Nucleic Acids Res..

[38]  W. Reznikoff,et al.  Anaerobically expressed Escherichia coli genes identified by operon fusion techniques , 1991, Journal of bacteriology.

[39]  J. Altenbuchner,et al.  Optimization of an E. coli L-rhamnose-inducible expression vector: test of various genetic module combinations , 2008, BMC biotechnology.

[40]  F. Srienc,et al.  Minimal Escherichia coli Cell for the Most Efficient Production of Ethanol from Hexoses and Pentoses , 2008, Applied and Environmental Microbiology.

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

[42]  Tanja Kortemme,et al.  Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. , 2011, Journal of molecular biology.

[43]  Douglas Densmore,et al.  Automated assembly of standard biological parts. , 2011, Methods in enzymology.

[44]  Javier Macía,et al.  Synthetic protocell biology: from reproduction to computation , 2007, Philosophical Transactions of the Royal Society B: Biological Sciences.

[45]  D. G. Gibson,et al.  Enzymatic Assembly of Overlapping DNA Fragments , 2011, Methods in Enzymology.

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

[47]  H. Bremer,et al.  Control of the Escherichia coli rrnB P1 promoter strength by ppGpp , 1995, The Journal of Biological Chemistry.

[48]  Deepak Chandran,et al.  TinkerCell: modular CAD tool for synthetic biology , 2009, Journal of biological engineering.

[49]  Drew Endy,et al.  Measurement and modeling of intrinsic transcription terminators , 2016, Nucleic acids research.

[50]  Christopher A. Voigt,et al.  Characterization of 582 natural and synthetic terminators and quantification of their design constraints , 2013, Nature Methods.

[51]  David Tollervey,et al.  Coding-Sequence Determinants of Gene Expression in Escherichia coli , 2009, Science.

[52]  Francesca Ceroni,et al.  Rational design of modular circuits for gene transcription: A test of the bottom-up approach , 2010, Journal of biological engineering.

[53]  R Y Tsien,et al.  Wavelength mutations and posttranslational autoxidation of green fluorescent protein. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Nicola Zamboni,et al.  Genome engineering reveals large dispensable regions in Bacillus subtilis. , 2003, Molecular biology and evolution.

[55]  Joan L. Slonczewski,et al.  pH of the Cytoplasm and Periplasm of Escherichia coli: Rapid Measurement by Green Fluorescent Protein Fluorimetry , 2007, Journal of bacteriology.

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

[57]  D. Ron,et al.  Luciferase reporter gene assay in mammalian cells. , 1992, Methods in enzymology.

[58]  India G. Hook-Barnard,et al.  Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters , 2007, Gene regulation and systems biology.

[59]  Carola Engler,et al.  A One Pot, One Step, Precision Cloning Method with High Throughput Capability , 2008, PloS one.

[60]  D. Hanahan,et al.  Plasmid transformation of Escherichia coli and other bacteria. , 1991, Methods in enzymology.

[61]  Jochen Büchs,et al.  Advances in understanding and modeling the gas–liquid mass transfer in shake flasks , 2004 .

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

[63]  H. Goossens,et al.  Antibiotic resistance—the need for global solutions , 2013, BDJ.

[64]  B. Hall,et al.  Growth rates made easy. , 2014, Molecular biology and evolution.

[65]  Gabriel C. Wu,et al.  Synthetic protein scaffolds provide modular control over metabolic flux , 2009, Nature Biotechnology.

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

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

[68]  Christopher A. Voigt,et al.  Ribozyme-based insulator parts buffer synthetic circuits from genetic context , 2012, Nature Biotechnology.

[69]  Y. Choi,et al.  Microbial production of short-chain alkanes , 2013, Nature.

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

[71]  Jay D Keasling,et al.  Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression , 2011, Science.

[72]  Christopher A. Voigt,et al.  Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca , 2012, Proceedings of the National Academy of Sciences.

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

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

[75]  M Grunberg-Manago,et al.  Messenger RNA stability and its role in control of gene expression in bacteria and phages. , 1999, Annual review of genetics.

[76]  Markus Wieland,et al.  Engineering molecular circuits using synthetic biology in mammalian cells. , 2012, Annual review of chemical and biomolecular engineering.

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

[78]  Thomas H Segall-Shapiro,et al.  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome , 2010, Science.

[79]  C. Gross,et al.  The anti-initial transcribed sequence, a portable sequence that impedes promoter escape, requires sigma70 for function. , 2001, Journal of Biological Chemistry.

[80]  Alistair Elfick,et al.  A pH-based biosensor for detection of arsenic in drinking water , 2011, Analytical and bioanalytical chemistry.

[81]  A S Verkman,et al.  Green fluorescent protein as a noninvasive intracellular pH indicator. , 1998, Biophysical journal.

[82]  Nathan J Hillson,et al.  j5 DNA assembly design automation software. , 2012, ACS synthetic biology.

[83]  J. Kittleson,et al.  Rapid optimization of gene dosage in E. coli using DIAL strains , 2011, Journal of biological engineering.

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

[85]  Gary J. Lye,et al.  Modelling surface aeration rates in shaken microtitre plates using dimensionless groups , 2005 .

[86]  Matthew W. Lux,et al.  Essential information for synthetic DNA sequences , 2011, Nature Biotechnology.

[87]  S. Klumpp Growth-Rate Dependence Reveals Design Principles of Plasmid Copy Number Control , 2011, PloS one.

[88]  Meghdad Hajimorad,et al.  BglBrick vectors and datasheets: A synthetic biology platform for gene expression , 2011, Journal of biological engineering.

[89]  F. Blattner,et al.  Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications , 2010, Microbial cell factories.

[90]  Tom Ellis,et al.  One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy , 2013, Nucleic acids research.

[91]  Baojun Wang,et al.  Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology , 2011, Nature communications.

[92]  T. Wreghitt,et al.  An ELISA test for the detection of antibodies to Legionella pneumophila. , 1982, Journal of clinical pathology.

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

[94]  Uri Alon,et al.  Invariant Distribution of Promoter Activities in Escherichia coli , 2009, PLoS Comput. Biol..

[95]  Christopher A. Voigt,et al.  Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.

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

[97]  Arif Ali,et al.  Bioluminescent bioreporter for assessment of arsenic contamination in water samples of India , 2013, Journal of Biosciences.

[98]  Stefano Cardinale,et al.  Effects of genetic variation on the E. coli host-circuit interface. , 2013, Cell reports.

[99]  Hiroshi Mizoguchi,et al.  Escherichia coli minimum genome factory , 2007, Biotechnology and applied biochemistry.

[100]  G. Unden,et al.  Control of FNR function of Escherichia coli by O2 and reducing conditions. , 2002, Journal of molecular microbiology and biotechnology.

[101]  U. Alon,et al.  Diverse two-dimensional input functions control bacterial sugar genes. , 2008, Molecular cell.

[102]  R. Schleif,et al.  A regulatory cascade in the induction of rhaBAD. , 1993, Journal of molecular biology.

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

[104]  Paul Freemont,et al.  Synthetic biology – the state of play , 2012, FEBS letters.

[105]  F. Rombouts,et al.  Modeling of the Bacterial Growth Curve , 1990, Applied and environmental microbiology.

[106]  Igor L. Medintz,et al.  Self-assembled TNT biosensor based on modular multifunctional surface-tethered components. , 2005, Analytical chemistry.

[107]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

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