Synthetic Switches and Regulatory Circuits in Plants1[OPEN]
暂无分享,去创建一个
Matias D Zurbriggen | Jennifer Andres | Matias D. Zurbriggen | Tim Blomeier | Tim Blomeier | Jennifer Andres
[1] Andreja Majerle,et al. A bistable genetic switch based on designable DNA-binding domains , 2014, Nature Communications.
[2] Andreja Majerle,et al. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. , 2014, Nature chemical biology.
[3] M. Fussenegger,et al. Designing cell function: assembly of synthetic gene circuits for cell biology applications , 2018, Nature Reviews Molecular Cell Biology.
[4] Jared E. Toettcher,et al. A synthetic–natural hybrid oscillator in human cells , 2010, Proceedings of the National Academy of Sciences.
[5] E. Agosin,et al. Optogenetic switches for light-controlled gene expression in yeast , 2017, Applied Microbiology and Biotechnology.
[6] M. di Bernardo,et al. A comparative analysis of synthetic genetic oscillators , 2010, Journal of The Royal Society Interface.
[7] Mauricio S. Antunes,et al. Programmable Ligand Detection System in Plants through a Synthetic Signal Transduction Pathway , 2011, PloS one.
[8] J. Hasty,et al. Synthetic gene network for entraining and amplifying cellular oscillations. , 2002, Physical review letters.
[9] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[10] Donald R. Ort,et al. Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field , 2019, Science.
[11] Alexander M. Jones,et al. Genetically Encoded Biosensors in Plants: Pathways to Discovery. , 2018, Annual review of plant biology.
[12] B. Goodwin. Oscillatory behavior in enzymatic control processes. , 1965, Advances in enzyme regulation.
[13] A. Ferré-D’Amaré,et al. Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch. , 2008, Chemistry & biology.
[14] Wilfried Weber,et al. OptoBase: A Web Platform for Molecular Optogenetics. , 2018, ACS synthetic biology.
[15] W. Reznikoff,et al. Genetic regulation: the Lac control region. , 1975, Science.
[16] Araceli M. Huerta,et al. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.
[17] M. Fussenegger,et al. Macrolide-based transgene control in mammalian cells and mice , 2002, Nature Biotechnology.
[18] Christopher A. Voigt,et al. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks , 2014, Molecular systems biology.
[19] Martin Fussenegger,et al. Synthetic RNA-based switches for mammalian gene expression control. , 2017, Current opinion in biotechnology.
[20] Michael Z. Lin,et al. Optical control of biological processes by light‐switchable proteins , 2015, Wiley interdisciplinary reviews. Developmental biology.
[21] M. Gossen,et al. Transcriptional activation by tetracyclines in mammalian cells. , 1995, Science.
[22] Trevor E Swartz,et al. Structural basis of photosensitivity in a bacterial light-oxygen-voltage/helix-turn-helix (LOV-HTH) DNA-binding protein , 2011, Proceedings of the National Academy of Sciences.
[23] The alc-GR System. A Modified alc Gene Switch Designed for Use in Plant Tissue Culture1[w] , 2005, Plant Physiology.
[24] G. Crabtree,et al. NFAT Signaling Choreographing the Social Lives of Cells , 2002, Cell.
[25] M. Gossen,et al. A chimeric transactivator allows tetracycline-responsive gene expression in whole plants. , 1994, The Plant journal : for cell and molecular biology.
[26] Detlef Weigel,et al. Highly Specific Gene Silencing by Artificial MicroRNAs in Arabidopsis[W][OA] , 2006, The Plant Cell Online.
[27] U. Sonnewald,et al. An ethanol inducible gene switch for plants used to manipulate carbon metabolism , 1998, Nature Biotechnology.
[28] K. Haynes,et al. Can the Natural Diversity of Quorum-Sensing Advance Synthetic Biology? , 2015, Front. Bioeng. Biotechnol..
[29] L. Serrano,et al. Engineering stability in gene networks by autoregulation , 2000, Nature.
[30] Karl Deisseroth,et al. The form and function of channelrhodopsin , 2017, Science.
[31] Gábor Balázsi,et al. Transferring a synthetic gene circuit from yeast to mammalian cells , 2013, Nature Communications.
[32] Jim Haseloff,et al. Spatial control of transgene expression in rice (Oryza sativa L.) using the GAL4 enhancer trapping system. , 2005, The Plant journal : for cell and molecular biology.
[33] U. Grossniklaus,et al. A Gateway Cloning Vector Set for High-Throughput Functional Analysis of Genes in Planta[w] , 2003, Plant Physiology.
[34] Mauricio S. Antunes,et al. A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. , 2006, Plant biotechnology journal.
[35] Alexander R Leydon,et al. Synthetic hormone-responsive transcription factors can monitor and re-program plant development , 2017, bioRxiv.
[36] A. Fire,et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans , 1998, Nature.
[37] Wendell A Lim,et al. Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. , 2017, Annual review of immunology.
[38] Christopher A. Voigt,et al. Genetic programs constructed from layered logic gates in single cells , 2012, Nature.
[39] M. Fussenegger,et al. A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice , 2011, Science.
[40] Jared E. Toettcher,et al. Using Optogenetics to Interrogate the Dynamic Control of Signal Transmission by the Ras/Erk Module , 2013, Cell.
[41] Roland Eils,et al. Optogenetic control of nuclear protein export , 2016, Nature Communications.
[42] W. Hillen,et al. The role of the N terminus in Tet repressor for tet operator binding determined by a mutational analysis. , 1992, The Journal of biological chemistry.
[43] W. Filipowicz,et al. Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. , 2004, RNA.
[44] Andrew J. Millar,et al. Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs , 2013, BMC Systems Biology.
[45] 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.
[46] Matias D. Zurbriggen,et al. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. , 2016, The Plant journal : for cell and molecular biology.
[47] Jens Timmer,et al. A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells , 2013, Nucleic acids research.
[48] Markus Wieland,et al. Programmable single-cell mammalian biocomputers , 2012, Nature.
[49] Wendell A. Lim,et al. Designing customized cell signalling circuits , 2010, Nature Reviews Molecular Cell Biology.
[50] J. Medford,et al. Towards programmable plant genetic circuits. , 2016, The Plant journal : for cell and molecular biology.
[51] L. Laplaze,et al. GAL4-GFP enhancer trap lines for genetic manipulation of lateral root development in Arabidopsis thaliana. , 2005, Journal of experimental botany.
[52] Chris Parker,et al. Observations on the current status of Orobanche and Striga problems worldwide. , 2009, Pest management science.
[53] J. Liao,et al. A synthetic gene–metabolic oscillator , 2005, Nature.
[54] Alexander R Leydon,et al. Synthetic hormone-responsive transcription factors can monitor and reprogram plant development , 2017, bioRxiv.
[55] Sindy K. Y. Tang,et al. Programming self-organizing multicellular structures with synthetic cell-cell signaling , 2018, Science.
[56] T. Kagawa,et al. Phototropin and light-signaling in phototropism. , 2006, Current opinion in plant biology.
[57] W. Weber,et al. Molecular switches in animal cells , 2012, FEBS letters.
[58] J. Stelling,et al. A tunable synthetic mammalian oscillator , 2009, Nature.
[59] Bernard Chasan. Physical Biology of the Cell , 2010 .
[60] Josephine R. Chandler,et al. Bacterial Quorum Sensing and Microbial Community Interactions , 2018, mBio.
[61] Miguel Fernández-Niño,et al. A synthetic multi-cellular network of coupled self-sustained oscillators , 2017, PloS one.
[62] Katja E. Jaeger,et al. Interlocking Feedback Loops Govern the Dynamic Behavior of the Floral Transition in Arabidopsis[W][OA] , 2013, Plant Cell.
[63] Wusheng Liu,et al. Advanced genetic tools for plant biotechnology , 2013, Nature Reviews Genetics.
[64] Wusheng Liu,et al. Plant synthetic biology. , 2015, Trends in plant science.
[65] F. Lienert,et al. Synthetic biology in mammalian cells: next generation research tools and therapeutics , 2014, Nature Reviews Molecular Cell Biology.
[66] B. Cui,et al. Optogenetic control of intracellular signaling pathways. , 2015, Trends in biotechnology.
[67] J. Collins,et al. DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS , 2009, Nature Biotechnology.
[68] Kevin Thurley,et al. Modeling Cell-to-Cell Communication Networks Using Response-Time Distributions , 2018, Cell systems.
[69] Mauricio Barahona,et al. Computational Re-Design of Synthetic Genetic Oscillators for Independent Amplitude and Frequency Modulation , 2017, bioRxiv.
[70] Brian F. Volkman,et al. Agrochemical control of plant water use using engineered abscisic acid receptors , 2015, Nature.
[71] M. Mahfouz,et al. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. , 2015, Plant biotechnology journal.
[72] Diego Orzaez,et al. DNA assembly standards: Setting the low-level programming code for plant biotechnology. , 2018, Plant science : an international journal of experimental plant biology.
[73] Mett,et al. Controlled cytokinin production in transgenic tobacco using a copper-inducible promoter , 1998, Plant physiology.
[74] James M. Carothers,et al. Digital logic circuits in yeast with CRISPR-dCas9 NOR gates , 2017, Nature Communications.
[75] B. Bassler,et al. Quorum sensing in bacteria. , 2001, Annual review of microbiology.
[76] W. J. Brammar,et al. Control of gene expression in tobacco cells using a bacterial operator‐repressor system. , 1992, The EMBO journal.
[77] James A. Stapleton,et al. Quantitative and simultaneous translational control of distinct mammalian mRNAs , 2013, Nucleic acids research.
[78] Jens Timmer,et al. Multi-chromatic control of mammalian gene expression and signaling , 2013, Nucleic acids research.
[79] N. Rockwell,et al. The Structure of Phytochrome: A Picture Is Worth a Thousand Spectra , 2006, The Plant Cell Online.
[80] R. W. Davis,et al. A steroid-inducible gene expression system for plant cells. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[81] R. Quatrano,et al. Use of Bacterial Quorum-Sensing Components to Regulate Gene Expression in Plants1[W] , 2006, Plant Physiology.
[82] Lukas C. Kapitein,et al. Optogenetic control of organelle transport and positioning , 2015, Nature.
[83] M. Freeman. Feedback control of intercellular signalling in development , 2000, Nature.
[84] B. Goodwin. Temporal Organization in Cells; a Dynamic Theory of Cellular Control Processes , 2015 .
[85] Stuart L. Schreiber,et al. SnapShot: Ca2+-Calcineurin-NFATSignaling , 2009, Cell.
[86] Daniel F. Voytas,et al. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation1[OPEN] , 2015, Plant Physiology.
[87] Matias D Zurbriggen,et al. Red Light-Regulated Reversible Nuclear Localization of Proteins in Mammalian Cells and Zebrafish. , 2015, ACS synthetic biology.
[88] Viktor Stein,et al. Synthetic protein switches: design principles and applications. , 2015, Trends in biotechnology.
[89] M. White,et al. Characterization of the ethanol-inducible alc gene-expression system in Arabidopsis thaliana. , 2001, The Plant journal : for cell and molecular biology.
[90] M. Fussenegger,et al. Novel pristinamycin-responsive expression systems for plant cells. , 2001, Biotechnology and bioengineering.
[91] Sung Mi Park,et al. Translation initiation mediated by RNA looping , 2015, Proceedings of the National Academy of Sciences.
[92] Klaus Palme,et al. A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics , 2013, Scientific Reports.
[93] James J. Collins,et al. Next-Generation Synthetic Gene Networks , 2009, Nature Biotechnology.
[94] C. Gersbach,et al. A light-inducible CRISPR/Cas9 system for control of endogenous gene activation , 2015, Nature chemical biology.
[95] Matias D. Zurbriggen,et al. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. , 2017, Trends in plant science.
[96] Matias D. Zurbriggen,et al. A Green-Light-Responsive System for the Control of Transgene Expression in Mammalian and Plant Cells. , 2018, ACS synthetic biology.
[97] Alexander M. Jones,et al. Quantitative imaging with fluorescent biosensors. , 2012, Annual review of plant biology.
[98] Matias D. Zurbriggen,et al. Optogenetics in Plants: Red/Far-Red Light Control of Gene Expression. , 2016, Methods in molecular biology.
[99] M. Gossen,et al. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[100] C. Gatz,et al. Stringent repression and homogeneous de-repression by tetracycline of a modified CaMV 35S promoter in intact transgenic tobacco plants. , 1992, The Plant journal : for cell and molecular biology.
[101] J. V. Van Etten,et al. Human Pumilio Proteins Recruit Multiple Deadenylases to Efficiently Repress Messenger RNAs* , 2012, The Journal of Biological Chemistry.
[102] U. Schopfer,et al. Chemically Regulated Zinc Finger Transcription Factors* , 2000, The Journal of Biological Chemistry.
[103] S. Cutler,et al. A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration. , 2017, ACS chemical biology.
[104] Daniel Karcher,et al. Inducible gene expression from the plastid genome by a synthetic riboswitch , 2010, Proceedings of the National Academy of Sciences.
[105] B. Séraphin,et al. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion , 2001, The EMBO journal.
[106] Mingqi Xie,et al. Self-adjusting synthetic gene circuit for correcting insulin resistance , 2016, Nature Biomedical Engineering.
[107] N. Chua,et al. A glucocorticoid-mediated transcriptional induction system in transgenic plants. , 1997, The Plant journal : for cell and molecular biology.
[108] G. Balázsi,et al. Negative autoregulation linearizes the dose–response and suppresses the heterogeneity of gene expression , 2009, Proceedings of the National Academy of Sciences.
[109] J. Szostak,et al. In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.
[110] M. Bennett,et al. A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.
[111] Carl Troein,et al. Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock , 2014, PLoS Comput. Biol..
[112] Kole T. Roybal,et al. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors , 2016, Cell.
[113] Thomas Lübberstedt,et al. Need for multidisciplinary research towards a second green revolution. , 2005, Current opinion in plant biology.
[114] Martin Fussenegger,et al. BioLogic gates enable logical transcription control in mammalian cells , 2004, Biotechnology and bioengineering.
[115] E. Greenberg,et al. Quorum sensing in bacteria: the LuxR-LuxI family of cell density-responsive transcriptional regulators , 1994, Journal of bacteriology.
[116] Ralf Reski,et al. A red light-controlled synthetic gene expression switch for plant systems. , 2014, Molecular bioSystems.
[117] A. Tramontano,et al. A synthetic biology approach allows inducible retrotransposition in whole plants , 2010, Systems and Synthetic Biology.
[118] Stefanie Widder,et al. A generalized model of the repressilator , 2006, Journal of mathematical biology.
[119] R. Weiss,et al. Multi-input Rnai-based Logic Circuit for Identification of Specific , 2022 .
[120] Moritoshi Sato,et al. CRISPR-Cas9-based photoactivatable transcription system. , 2015, Chemistry & biology.
[121] Nicholas J. Guido,et al. A bottom-up approach to gene regulation , 2006, Nature.
[122] Mauricio S. Antunes,et al. Quantitative characterization of genetic parts and circuits for plant synthetic biology , 2015, Nature Methods.
[123] S. Cutler,et al. Chemical manipulation of plant water use. , 2016, Bioorganic & medicinal chemistry.
[124] M. Fussenegger,et al. Prosthetic gene networks as an alternative to standard pharmacotherapies for metabolic disorders. , 2015, Current opinion in biotechnology.
[125] Mustafa Khammash,et al. Design of a synthetic integral feedback circuit: dynamic analysis and DNA implementation , 2016, ACS synthetic biology.
[126] T. Tuschl,et al. Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.
[127] Brendan M Ryback,et al. Design and analysis of a tunable synchronized oscillator , 2013, Journal of biological engineering.
[128] Vladislav V Verkhusha,et al. An optogenetic system based on bacterial phytochrome controllable with near-infrared light , 2016, Nature Methods.
[129] K. Gardner,et al. An optogenetic gene expression system with rapid activation and deactivation kinetics , 2013, Nature chemical biology.
[130] Peter Hedden,et al. Gibberellin biosynthesis and its regulation. , 2012, The Biochemical journal.
[131] C. Robertson McClung,et al. Plant Circadian Rhythms , 2006, The Plant Cell Online.
[132] Ivan Razinkov,et al. Sensing array of radically coupled genetic biopixels , 2011, Nature.
[133] R. Poethig,et al. GAL 4 GFP enhancer trap lines for analysis of stomatal guard cell development and gene expression , 2009 .
[134] Nicola J Patron,et al. DNA assembly for plant biology: techniques and tools. , 2014, Current opinion in plant biology.
[135] Duško Lainšček,et al. A Synthetic Mammalian Therapeutic Gene Circuit for Sensing and Suppressing Inflammation. , 2017, Molecular therapy : the journal of the American Society of Gene Therapy.
[136] Wendell A Lim,et al. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators , 2016, Nature Methods.
[137] J. Barbé,et al. A multifunctional gene (tetR) controls Tn10-encoded tetracycline resistance , 1982, Journal of bacteriology.
[138] Randall J. Platt,et al. Optical Control of Mammalian Endogenous Transcription and Epigenetic States , 2013, Nature.
[139] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[140] R. Eils,et al. Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells , 2014, Nature Communications.
[141] A. Webb,et al. GAL4 GFP enhancer trap lines for analysis of stomatal guard cell development and gene expression , 2008, Journal of experimental botany.
[142] L. Tsimring,et al. A synchronized quorum of genetic clocks , 2009, Nature.
[143] M. Savageau. Comparison of classical and autogenous systems of regulation in inducible operons , 1974, Nature.
[144] A. Ninfa,et al. Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.
[145] M. Fussenegger,et al. An engineered epigenetic transgene switch in mammalian cells , 2004, Nature Biotechnology.
[146] D. C. Nelson,et al. Smoke and Hormone Mirrors: Action and Evolution of Karrikin and Strigolactone Signaling. , 2016, Trends in genetics : TIG.
[147] David A. Drubin,et al. Rational design of memory in eukaryotic cells. , 2007, Genes & development.
[148] Christopher A. Voigt,et al. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.
[149] K. Akiyama,et al. Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi , 2005, Nature.
[150] Barbara Fink,et al. Molecular analysis of a synthetic tetracycline-binding riboswitch. , 2005, RNA.
[151] E. Farcot,et al. Modeling plant development: from signals to gene networks. , 2015, Current opinion in plant biology.
[152] Jonathan S. Dordick,et al. Radio-Wave Heating of Iron Oxide Nanoparticles Can Regulate Plasma Glucose in Mice , 2012, Science.
[153] T. Wandless,et al. General method for regulating protein stability with light. , 2014, ACS chemical biology.
[154] Jens Timmer,et al. Dual-controlled optogenetic system for the rapid down-regulation of protein levels in mammalian cells , 2018, Scientific Reports.
[155] G. Howe,et al. Control of Carbon Assimilation and Partitioning by Jasmonate: An Accounting of Growth–Defense Tradeoffs , 2016, Plants.
[156] Homme W Hellinga,et al. Engineering key components in a synthetic eukaryotic signal transduction pathway , 2009, Molecular systems biology.
[157] J. Monod,et al. Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.
[158] B. J. Clark. Control of Gene Expression , 2004 .
[159] A. Trewavas. Green plants as intelligent organisms. , 2005, Trends in plant science.
[160] R. Breaker. Riboswitches and the RNA world. , 2012, Cold Spring Harbor perspectives in biology.
[161] J. Collins,et al. Programmable cells: interfacing natural and engineered gene networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[162] Paolo Sassone-Corsi,et al. A Web of Circadian Pacemakers , 2002, Cell.
[163] Wilfried Weber,et al. Synthetic biological approaches to optogenetically control cell signaling. , 2017, Current opinion in biotechnology.
[164] R. Weiss,et al. Programmed population control by cell–cell communication and regulated killing , 2004, Nature.
[165] N. Chua,et al. Technical advance: An estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. , 2000, The Plant journal : for cell and molecular biology.
[166] Christina D Smolke,et al. Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins , 2010, Science.
[167] Arp Schnittger,et al. Phenotypes on demand via switchable target protein degradation in multicellular organisms , 2016, Nature Communications.
[168] E. Bateman,et al. Autoregulation of eukaryotic transcription factors. , 1998, Progress in nucleic acid research and molecular biology.
[169] Matias D Zurbriggen,et al. Optogenetics for gene expression in mammalian cells , 2015, Biological chemistry.
[170] Maria Karlsson,et al. A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication , 2015, BMC Systems Biology.
[171] Christopher A. Voigt,et al. Principles of genetic circuit design , 2014, Nature Methods.
[172] W. Stec,et al. Differences among mechanisms of ribozyme-catalyzed reactions. , 2000, Current opinion in biotechnology.