Biological signal generators: integrating synthetic biology tools and in silico control
Tài liệu tham khảo
Gaudet, 2016, Redefining signaling pathways with an expanding single-cell toolbox, Trends Biotechnol, 34, 458, 10.1016/j.tibtech.2016.02.009
Purvis, 2013, Encoding and decoding cellular information through signaling dynamics, Cell, 152, 945, 10.1016/j.cell.2013.02.005
Wilson, 2017, Tracing information flow from Erk to target gene induction reveals mechanisms of dynamic and combinatorial control, Mol Cell, 67, 757, 10.1016/j.molcel.2017.07.016
Bugaj, 2018, Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway, Science, 361, 10.1126/science.aao3048
Hansen, 2013, Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression, Mol Syst Biol, 9, 10.1038/msb.2013.56
Lipan, 2005, The use of oscillatory signals in the study of genetic networks, Proc Natl Acad Sci Unit States Am, 102, 7063, 10.1073/pnas.0403790102
Melykui, 2010, Discriminating between rival biochemical network models: three approaches to optimal experiment design, BMC Syst Biol, 4
Shimizu, 2010, A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli, Mol Syst Biol, 382, 1
Wang, 2012, Diverse sensitivity thresholds in dynamic signaling responses by social amoebae, Sci Signal, 5, 10.1126/scisignal.2002449
Muzzey, 2009, A systems-level analysis of perfect adaptation in yeast osmoregulation, Cell, 138, 160, 10.1016/j.cell.2009.04.047
Apgar, 2008, Stimulus design for model selection and validation in cell signaling, PLoS Comput Biol, 4, e30, 10.1371/journal.pcbi.0040030
Olson, 2014, Optogenetic characterization methods overcome key challenges in synthetic and systems biology, Nat Chem Biol, 10, 502, 10.1038/nchembio.1559
Olson, 2014, Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals, Nat Methods, 11, 449, 10.1038/nmeth.2884
Engstrom, 2017, Transcription control engineering and applications in synthetic biology, vol. 2, 176
Uhlendorf, 2012, Long-term model predictive control of gene expression at the population and single-cell levels, Proc Natl Acad Sci Unit States Am, 109, 14271, 10.1073/pnas.1206810109
Menolascina, 2015, In-vivo real-time control of protein expression from endogenous and synthetic gene networks, PLoS Comput Biol, 10
Fiore, 2016, In vivo real-time control of gene expression: a comparative analysis of feedback control strategies in yeast, ACS Synth Biol, vol. 5, 154, 10.1021/acssynbio.5b00135
Meyer, 2018, Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors, Nat Chem Biol, 15, 196, 10.1038/s41589-018-0168-3
McIsaac, 2011, Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae, Mol Biol Cell, 22, 4447, 10.1091/mbc.e11-05-0466
Brodel, 2016, Engineering orthogonal dual transcription factors for multi-input synthetic promoters, Nat Commun, 7, 13858, 10.1038/ncomms13858
Bradley, 2015, Tools and principles for microbial gene circuit engineering, J Mol Biol, 428, 462
Fracassi, 2015, Automatic control of gene expression in mammalian cells, ACS Synth Biol, 5, 296, 10.1021/acssynbio.5b00141
Dong, 2018, Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria, Nat Commun, 9
Kundert, 2018
Hersen, 2008, Signal processing by the HOG MAP kinase pathway, Proc Natl Acad Sci Unit States Am, 105, 7165, 10.1073/pnas.0710770105
Lane, 2017, Measuring signaling and RNA-seq in the same cell links gene expression to dynamic patterns of NF-KB activation, Cell Systems, 4, 458, 10.1016/j.cels.2017.03.010
Niopek, 2014, Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells, Nat Commun, 5, 10.1038/ncomms5404
Niopek, 2016, Optogenetic control of nuclear protein export, Nat Commun, 7, 10.1038/ncomms10624
Toettcher, 2011, Light-based feedback for controlling intracellular signaling dynamics, Nat Methods, 8, 837, 10.1038/nmeth.1700
Kennedy, 2010, Rapid blue-light-mediated induction of protein interactions in living cells, Nat Methods, 7, 973, 10.1038/nmeth.1524
Gerhardt, 2016, An open-hardware platform for optogenetics and photobiology, Sci Rep, 6, 35363, 10.1038/srep35363
Kolar, 2018, OptoBase: a web platform for molecular optogenetics, ACS Synth Biol, 7, 1825, 10.1021/acssynbio.8b00120
Zhao, 2018, Optogenetic regulation of engineered cellular metabolism for microbial chemical production, Nature, 555, 683, 10.1038/nature26141
Melendez, 2014, Real-time optogenetic control of intracellular protein concentration in microbial cell cultures, Integrative Biology, 6, 366, 10.1039/c3ib40102b
Milias-Argeitis, 2016, Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth, Nat Commun, 7, 12546, 10.1038/ncomms12546
Chait, 2017, Shaping bacterial population behavior through computer-interfaced control of individual cells, Nat Commun, 8, 10.1038/s41467-017-01683-1
DelVecchio, 2011, The impact of retroactivity on the behavior of biomolecular systems, 161
Farmer, 2000, Improving lycopene production in Eschericia coli by engineering metabolic control, Nat Biotechnol, 18, 533, 10.1038/75398
Lugagne, 2017, Balancing a genetic toggle switch by real-time feedback control and periodic forcing, Nat Commun, 8, 10.1038/s41467-017-01498-0
Harrigan, 2018, Real time genetic compensation operationally defines the dynamic demands of feedback control, Cell, 175, 877, 10.1016/j.cell.2018.09.044
Benzinger, 2018, Pulsatile inputs achieve tunable attenuation of gene expression variability and graded multi-gene regulation, Nat Commun, 9, 10.1038/s41467-018-05882-2
Rullan, 2018, An optogenetic platform for real-time, single-cell interrogation of stochastic transcriptional regulation, Mol Cell, 70, 745, 10.1016/j.molcel.2018.04.012
Olson, 2017, A photoconversion model for full spectral programming and multiplexing of optogenetic systems, Mol Syst Biol, 13, 10.15252/msb.20167456
Batchelor, 2011, Stimulus-dependent dynamics of p53 in single cells, Mol Syst Biol, 7, 10.1038/msb.2011.20
Albeck, 2013, Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals, Mol Cell, 49, 249, 10.1016/j.molcel.2012.11.002
Toettcher, 2013, Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module, Cell, 155, 1422, 10.1016/j.cell.2013.11.004
Siu, 2017, Design and selection of a synthetic feedback loop for optimizing biofuel tolerance, ACS Synth Biol, 7, 16, 10.1021/acssynbio.7b00260
Lillacci, 2018, Synthetic control systems for high performance gene expression in mammalian cells, Nucleic Acids Res, 46, 9855, 10.1093/nar/gky795