Fold-change detection in biological systems

Current Opinion in Systems Biology - Tập 8 - Trang 81-89 - 2018
Miri Adler1, Uri Alon1
1Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel

Tài liệu tham khảo

Goentoro, 2009, The incoherent feedforward loop can provide fold-change detection in gene regulation, Mol Cell, 36, 894, 10.1016/j.molcel.2009.11.018 Shoval, 2010, Fold-change detection and scalar symmetry of sensory input fields, Proc Natl Acad Sci, 107, 15995, 10.1073/pnas.1002352107 Russo, 2011, Symmetries, stability, and control in nonlinear systems and networks, Phys Rev E, 84, 041929, 10.1103/PhysRevE.84.041929 Shoval, 2011, Input symmetry invariance, and applications to biological systems, 2233 Shoval, 2011, Symmetry invariance for adapting biological systems, SIAM J Appl Dyn Syst, 10, 857, 10.1137/100818078 Fechner, 1860 Barkai, 1997, Robustness in simple biochemical networks, Nature, 387, 913, 10.1038/43199 Bargmann Eldar, 2002, Robustness of the BMP morphogen gradient in Drosophila embryonic patterning, Nature, 419, 304, 10.1038/nature01061 Iglesias, 2012, A systems biology view of adaptation in sensory mechanisms, 499 Levchenko, 2002, Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils, Biophys J, 82, 50, 10.1016/S0006-3495(02)75373-3 Ma, 2009, Defining network topologies that can achieve biochemical adaptation, Cell, 138, 760, 10.1016/j.cell.2009.06.013 Lazova, 2011, Response rescaling in bacterial chemotaxis, Proc Natl Acad Sci, 108, 13870, 10.1073/pnas.1108608108 Alon, 1999, Robustness in bacterial chemotaxis, Nature, 397, 168, 10.1038/16483 Sourjik, 2002, Receptor sensitivity in bacterial chemotaxis, Proc Natl Acad Sci, 99, 123, 10.1073/pnas.011589998 Mesibov, 1973, The range of attractant concentrations for bacterial chemotaxis and the threshold and size of response over this Range Weber law and related phenomena, J Gen Physiol, 62, 203, 10.1085/jgp.62.2.203 Edgington, 2014, Fold-change detection in a whole-pathway model of Escherichia coli chemotaxis, Bull Math Biol, 76, 1376, 10.1007/s11538-014-9965-3 Kojadinovic, 2013, Response kinetics in the complex chemotaxis signalling pathway of Rhodobacter sphaeroides, J R Soc Interface, 10, 20121001, 10.1098/rsif.2012.1001 Masson, 2012, Noninvasive inference of the molecular chemotactic response using bacterial trajectories, Proc Natl Acad Sci, 109, 1802, 10.1073/pnas.1116772109 Menolascina, 2017, Logarithmic sensing in Bacillus subtilis aerotaxis, NPJ Syst Biol Appl, 3, 16036, 10.1038/npjsba.2016.36 Norris, 2014, The effect of reversals for a stochastic source-seeking process inspired by bacterial chemotaxis, 3411 Hamadeh, 2013, Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis, J R Soc Interface, 10, 20120935, 10.1098/rsif.2012.0935 Youk, 2014, Secreting and sensing the same molecule allows cells to achieve versatile social behaviors, Science, 343, 1242782, 10.1126/science.1242782 Takeda, 2012, Incoherent feedforward control governs adaptation of activated ras in a eukaryotic chemotaxis pathway, Sci Signal, 5, 10.1126/scisignal.2002413 Kamino, 2017, Fold-change detection and scale invariance of cell–cell signaling in social amoeba, Proc Natl Acad Sci, 114, E4149, 10.1073/pnas.1702181114 Larsch, 2015, A circuit for gradient climbing in C. elegans chemotaxis, Cell Rep, 12, 1748, 10.1016/j.celrep.2015.08.032 Lee, 2014, Fold change of nuclear NF-κB determines TNF-induced transcription in single cells, Mol Cell, 53, 867, 10.1016/j.molcel.2014.01.026 Cohen-Saidon, 2009, Dynamics and variability of ERK2 response to EGF in individual living cells, Mol Cell, 36, 885, 10.1016/j.molcel.2009.11.025 Frick, 2017, Sensing relative signal in the Tgf-β/Smad pathway, Proc Natl Acad Sci, 114, E2975, 10.1073/pnas.1611428114 Alon, 2007, Network motifs: theory and experimental approaches, Nat Rev Genet, 8, 450, 10.1038/nrg2102 Skataric, 2012, Exploring the scale invariance property in enzymatic networks, 5511 Lan, 2013, The cost of sensitive response and accurate adaptation in networks with an incoherent type-1 feed-forward loop, J R Soc Interface, 10, 20130489, 10.1098/rsif.2013.0489 Marquez-Lago, 2011, Stochastic adaptation and fold-change detection: from single-cell to population behavior, BMC Syst Biol, 5, 22, 10.1186/1752-0509-5-22 Skataric, 2012, A characterization of scale invariant responses in enzymatic networks, PLoS Comput Biol, 8, e1002748, 10.1371/journal.pcbi.1002748 Skataric, 2014, Scale-invariance in singularly perturbed systems, 3035 Skataric, 2015, Fundamental limitation of the instantaneous approximation in fold-change detection models, IET Syst Biol, 9, 1, 10.1049/iet-syb.2014.0006 Inoue, 2011, Weber's law for biological responses in autocatalytic networks of chemical reactions, Phys Rev Lett, 107, 10.1103/PhysRevLett.107.048301 Tu, 2008, Modeling the chemotactic response of Escherichia coli to time-varying stimuli, Proc Natl Acad Sci, 105, 14855, 10.1073/pnas.0807569105 Kamino, 2016, Rescaling of spatio-temporal sensing in eukaryotic chemotaxis, PLos One, 11, 10.1371/journal.pone.0164674 Adler, 2017, Optimal regulatory circuit topologies for fold-change detection, Cell Syst, 4, 171, 10.1016/j.cels.2016.12.009 Hironaka, 2014, Cellular sensory mechanisms for detecting specific fold-changes in extracellular cues, Biophys J, 106, 279, 10.1016/j.bpj.2013.10.039 Olsman, 2016, Allosteric proteins as logarithmic sensors, Proc Natl Acad Sci, 113, E4423, 10.1073/pnas.1601791113 Adler, 2014, Logarithmic and power law input-output relations in sensory systems with fold-change detection, PLoS Comput Biol, 10, e1003781, 10.1371/journal.pcbi.1003781 Iyengar, 2016, Properties of composite feedback-feedforward pulse generating motifs, bioRxiv Iglesias, 2014, Comparison of adaptation motifs: temporal, stochastic and spatial responses, IET Syst Biol, 8, 268, 10.1049/iet-syb.2014.0026 Sontag, 2017, A dynamic model of immune responses to antigen presentation predicts different regions of tumor or pathogen elimination, Cell Syst, 4, 231, 10.1016/j.cels.2016.12.003 Lang, 2017, Zeros of nonlinear systems with input invariances, Automatica, 81, 46, 10.1016/j.automatica.2017.03.030 Hironaka, 2012, Encoding and decoding of positional information in morphogen-dependent patterning, Curr Opin Genet Dev, 22, 553, 10.1016/j.gde.2012.10.002 Rahi, 2017, Oscillatory stimuli differentiate adapting circuit topologies, Nat Methods, 14, 1010, 10.1038/nmeth.4408 Clausznitzer, 2014, Predicting chemical environments of bacteria from receptor signaling, PLoS Comput Biol, 10, e1003870, 10.1371/journal.pcbi.1003870 Kim, 2014, Synthetic circuit for exact adaptation and fold-change detection, Nucleic Acids Res, 42, 6078, 10.1093/nar/gku233 Kello, 2010, Scaling laws in cognitive sciences, Trends Cognit Sci, 14, 223, 10.1016/j.tics.2010.02.005 Brown, 2007, A temporal ratio model of memory, Psychol Rev, 114, 539, 10.1037/0033-295X.114.3.539 Shepard, 1987, Toward a universal law of generalization for psychological science, Science, 237, 1317, 10.1126/science.3629243 Chater, 2008, From universal laws of cognition to specific cognitive models, Cognit Sci, 32, 36, 10.1080/03640210701801941 Chater, 1999, Scale-invariance as a unifying psychological principle, Cognition, 69, B17, 10.1016/S0010-0277(98)00066-3 Levy, 2011, Comparing apples and oranges: using reward-specific and reward-general subjective value representation in the brain, J Neurosci, 31, 14693, 10.1523/JNEUROSCI.2218-11.2011 Tobler, 2005, Adaptive coding of reward value by dopamine neurons, Science, 307, 1642, 10.1126/science.1105370 Hart, 2013, Comparing apples and oranges: fold-change detection of multiple simultaneous inputs, PLos One, 8, e57455, 10.1371/journal.pone.0057455 Treisman, 1996, The binding problem, Curr Opin Neurobiol, 6, 171, 10.1016/S0959-4388(96)80070-5 Buijsman, 2014, Efficient fold-change detection based on protein-protein interactions, Phys Rev E, 89, 10.1103/PhysRevE.89.022712 De Palo, 2013, Unraveling adaptation in eukaryotic pathways: lessons from protocells, PLoS Comput Biol, 9, 10.1371/journal.pcbi.1003300 Gorbonos, 2017, Stable swarming using adaptive long-range interactions, Phys Rev E, 95, 10.1103/PhysRevE.95.042405 Gorbonos, 2016, Long-range acoustic interactions in insect swarms: an adaptive gravity model, New J Phys, 18, 10.1088/1367-2630/18/7/073042 Sontag, 2015, Incoherent feedforward motifs as immune change detectors, bioRxiv Sontag, 2016, Two-zone tumor tolerance can arise from a simple immunological feedforward motif that estimates tumor growth rates, bioRxiv Furusawa, 2012, Adaptation to optimal cell growth through self-organized criticality, Phys Rev Lett, 108, 208103, 10.1103/PhysRevLett.108.208103 Lang, 2016, Scale-invariant systems realize nonlinear differential operators, 6676 Zechner, 2016, A molecular implementation of the least mean squares estimator, 5869 Savageau, 2001, Design principles for elementary gene circuits: elements, methods, and examples, Chaos Interdiscip J Nonlinear Sci, 11, 142, 10.1063/1.1349892 Arrieta, 2017, Phototaxis beyond turning: persistent accumulation and response acclimation of the microalga Chlamydomonas reinhardtii, Sci Rep, 7, 10.1038/s41598-017-03618-8 Goentoro, 2009, Evidence that fold-change, and not absolute level, of β-catenin dictates Wnt signaling, Mol Cell, 36, 872, 10.1016/j.molcel.2009.11.017 Lyashenko, 2017, Receptor-based mechanism of relative sensing in mammalian signaling networks, bioRxiv Gildor, 2015, Comparative study of regulatory circuits in two sea urchin species reveals tight control of timing and high conservation of expression dynamics, PLoS Genet, 11, e1005435, 10.1371/journal.pgen.1005435 Wartlick, 2011, Dynamics of Dpp signaling and proliferation control, Science, 331, 1154, 10.1126/science.1200037 De Palo, 2013, Common dynamical features of sensory adaptation in photoreceptors and olfactory sensory neurons, Sci Rep, 3, 10.1038/srep01251 Fain, 2001, Adaptation in vertebrate photoreceptors, Physiol Rev, 81, 117, 10.1152/physrev.2001.81.1.117