Bioelectric gene and reaction networks: computational modelling of genetic, biochemical and bioelectrical dynamics in pattern regulation
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[1] D. Kaplan,et al. Comparison of the depolarization response of human mesenchymal stem cells from different donors , 2015, Scientific Reports.
[2] P. Reddien,et al. The cellular basis for animal regeneration. , 2011, Developmental cell.
[3] Fallon Durant,et al. Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms , 2015, International journal of molecular sciences.
[4] Donald Wlodkowic,et al. Bioelectric signalling via potassium channels: a mechanism for craniofacial dysmorphogenesis in KCNJ2‐associated Andersen–Tawil Syndrome , 2016, The Journal of physiology.
[5] L. Wolpert. Positional information and the spatial pattern of cellular differentiation. , 1969, Journal of theoretical biology.
[6] Min Zhao,et al. Controlling cell behavior electrically: current views and future potential. , 2005, Physiological reviews.
[7] S. Heinemann,et al. Metabolic regulation of potassium channels. , 2004, Annual review of physiology.
[8] M. Levin,et al. Inverse drug screens: a rapid and inexpensive method for implicating molecular targets , 2006, Genesis.
[9] Michael Levin,et al. Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo , 2014, Molecular biology of the cell.
[10] V. Ganapathy,et al. Identity of the Organic Cation Transporter OCT3 as the Extraneuronal Monoamine Transporter (uptake2) and Evidence for the Expression of the Transporter in the Brain* , 1998, The Journal of Biological Chemistry.
[11] Borgens Rb,et al. Voltage gradients and ionic currents in injured and regenerating axons. , 1988 .
[12] A. Ziegelhöffer,et al. Enzyme kinetics and the activation energy of (Na,K)-ATPase in ischaemic hearts: influence of the duration of ischaemia. , 1994, General physiology and biophysics.
[13] D. Gospodarowicz,et al. Structural characterization and biological functions of fibroblast growth factor. , 1987, Endocrine reviews.
[14] R. Myers,et al. Primary structure and functional expression of the 5HT3 receptor, a serotonin-gated ion channel. , 1991, Science.
[15] Michael Levin,et al. Mathematical model of morphogen electrophoresis through gap junctions , 2006, Developmental dynamics : an official publication of the American Association of Anatomists.
[16] Michael Levin,et al. Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm , 2012, PLoS Comput. Biol..
[17] Xiaoyang Long,et al. Magnetogenetics: remote non-invasive magnetic activation of neuronal activity with a magnetoreceptor , 2015, Science bulletin.
[18] T. Miki,et al. The structure and function of the ATP-sensitive K+ channel in insulin-secreting pancreatic beta-cells. , 1999, Journal of molecular endocrinology.
[19] M. Levin,et al. Measuring resting membrane potential using the fluorescent voltage reporters DiBAC4(3) and CC2-DMPE. , 2012, Cold Spring Harbor protocols.
[20] K. Ishihara. Time-dependent Outward Currents through the Inward Rectifier Potassium Channel IRK1 , 1997, The Journal of general physiology.
[21] A. Sater. A jump-start for planarian head regeneration. , 2011, Chemistry & biology.
[22] Michael Levin,et al. Physiological controls of large‐scale patterning in planarian regeneration: a molecular and computational perspective on growth and form , 2016, Regeneration.
[23] H. Holzhütter,et al. Metabolic gradients as key regulators in zonation of tumor energy metabolism: a tissue-scale model-based study. , 2013, Biotechnology journal.
[24] G. Spinelli,et al. Early asymmetric cues triggering the dorsal/ventral gene regulatory network of the sea urchin embryo , 2014, eLife.
[25] Kenneth D. Birnbaum,et al. Slicing across Kingdoms: Regeneration in Plants and Animals , 2008, Cell.
[26] Dany S. Adams,et al. H+ pump-dependent changes in membrane voltage are an early mechanism necessary and sufficient to induce Xenopus tail regeneration , 2007, Development.
[27] D. Johnston,et al. Multiple Channel Types Contribute to the Low-Voltage-Activated Calcium Current in Hippocampal CA3 Pyramidal Neurons , 1996, The Journal of Neuroscience.
[28] R. Nuccitelli,et al. Endogenous electric fields in embryos during development, regeneration and wound healing. , 2003, Radiation protection dosimetry.
[29] Teresa Adell,et al. Planarian regeneration: achievements and future directions after 20 years of research. , 2009, The International journal of developmental biology.
[30] R B Borgens,et al. Voltage gradients and ionic currents in injured and regenerating axons. , 1988, Advances in neurology.
[31] Michael Levin,et al. Transducing Bioelectric Signals into Epigenetic Pathways During Tadpole Tail Regeneration , 2012, Anatomical record.
[32] A. M. Turing,et al. The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.
[33] J. Manzanares,et al. Electrical coupling in ensembles of nonexcitable cells: modeling the spatial map of single cell potentials. , 2015, The journal of physical chemistry. B.
[34] D C Spray,et al. Control of intercellular communication by voltage dependence of gap junctional conductance , 1983, The Journal of neuroscience : the official journal of the Society for Neuroscience.
[35] Michael Levin,et al. A chemical genetics approach reveals H,K-ATPase-mediated membrane voltage is required for planarian head regeneration. , 2011, Chemistry & biology.
[36] F. Ashcroft. ATP-sensitive potassium channelopathies: focus on insulin secretion. , 2005, The Journal of clinical investigation.
[37] D. Steiner,et al. Sequence and functional expression in Xenopus oocytes of a human insulinoma and islet potassium channel. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[38] D. Bayliss,et al. Two-Pore-Domain (Kcnk) Potassium Channels: Dynamic Roles in Neuronal Function , 2003, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.
[39] M. C. Mckay,et al. Linoleic acid both enhances activation and blocks Kv1.5 and Kv2.1 channels by two separate mechanisms. , 2001, American journal of physiology. Cell physiology.
[40] M. Andresen,et al. Differential Distribution and Function of Hyperpolarization-Activated Channels in Sensory Neurons and Mechanosensitive Fibers , 2004, The Journal of Neuroscience.
[41] R. Buhl,et al. Pharmacological inhibition of IK 1 by PA‐6 in isolated rat hearts affects ventricular repolarization and refractoriness , 2016, Physiological reports.
[42] W. Wadman,et al. On the voltage‐dependent Ca2+ block of serotonin 5‐HT3 receptors: a critical role of intracellular phosphates , 2008, The Journal of physiology.
[43] M. Levin,et al. Left-right patterning in Xenopus conjoined twin embryos requires serotonin signaling and gap junctions. , 2015, The International journal of developmental biology.
[44] R. Blakely,et al. Drosophila Serotonin Transporters Have Voltage-Dependent Uptake Coupled to a Serotonin-Gated Ion Channel , 1997, The Journal of Neuroscience.
[45] J. Sharpe,et al. Positional information and reaction-diffusion: two big ideas in developmental biology combine , 2015, Development.
[46] Laura N. Vandenberg,et al. Neurally Derived Tissues in Xenopus laevis Embryos Exhibit a Consistent Bioelectrical Left-Right Asymmetry , 2012, Stem cells international.
[47] C. Lange,et al. The mechanism of anterior-posterior polarity control in planarians. , 1978, Differentiation; research in biological diversity.
[48] Stephen H Wright,et al. Generation of resting membrane potential. , 2004, Advances in physiology education.
[49] L. Marton,et al. The Polyamine Binding Site in Inward Rectifier K+ Channels , 2006, The Journal of general physiology.
[50] K. Clarke,et al. The Energetics of Ion Distribution: The Origin of the Resting Electric Potential of Cells , 2002, IUBMB life.
[51] María Almuedo-Castillo,et al. Wnt signaling in planarians: new answers to old questions. , 2012, The International journal of developmental biology.
[52] R. Nusse,et al. Wnt proteins. , 2012, Cold Spring Harbor perspectives in biology.
[53] L. Britto,et al. Neurotransmitter regulation of neural development: acetylcholine and nicotinic receptors. , 2002, Anais da Academia Brasileira de Ciencias.
[54] Michael Levin,et al. Induction of Vertebrate Regeneration by a Transient Sodium Current , 2010, The Journal of Neuroscience.
[55] Michael Levin,et al. Bioelectric signaling regulates head and organ size during planarian regeneration , 2013, Development.
[56] C. McCaig,et al. Electrical dimensions in cell science , 2009, Journal of Cell Science.
[57] Kirsten Morris,et al. What is Hysteresis , 2011 .
[58] K. Magleby,et al. Single-channel kinetics of BK (Slo1) channels , 2014, Front. Physiol..
[59] M. Levin,et al. Transmembrane voltage potential is an essential cellular parameter for the detection and control of tumor development in a Xenopus model , 2013, Disease Models & Mechanisms.
[60] Julio A. Hernández,et al. A possible role for membrane depolarization in epithelial wound healing. , 2005, American journal of physiology. Cell physiology.
[61] M. Boyett,et al. A difference in inward rectification and polyamine block and permeation between the Kir2.1 and Kir3.1/Kir3.4 K+ channels , 2005, The Journal of physiology.
[62] A. Noma,et al. Voltage‐dependent magnesium block of adenosine‐triphosphate‐sensitive potassium channel in guinea‐pig ventricular cells. , 1987, The Journal of physiology.
[63] L. Gentile,et al. The planarian flatworm: an in vivo model for stem cell biology and nervous system regeneration , 2010, Disease Models & Mechanisms.
[64] Michael Levin,et al. smedinx-11 is a planarian stem cell gap junction gene required for regeneration and homeostasis , 2007, Development.
[65] Javier Cervera,et al. Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics , 2016, Scientific Reports.
[66] Y Schiffmann,et al. An hypothesis: phosphorylation fields as the source of positional information and cell differentiation--(cAMP, ATP) as the universal morphogenetic Turing couple. , 1991, Progress in biophysics and molecular biology.
[67] T. Morgan,et al. An examination of the problems of physiological “polarity” and of electrical polarity in the earthworm , 1904 .
[68] Metabolic Gradients: A New System for Old Questions , 2008, Current Biology.
[69] Erik P. Hoel,et al. Quantifying causal emergence shows that macro can beat micro , 2013, Proceedings of the National Academy of Sciences.
[70] Leonardo Beccari,et al. The logic of gene regulatory networks in early vertebrate forebrain patterning , 2013, Mechanisms of Development.
[71] Frank Jülicher,et al. Scaling and regeneration of self-organized patterns. , 2014, Physical review letters.
[72] Cunshuan Xu,et al. Protein expression profiling in head fragments during planarian regeneration after amputation , 2015, Development Genes and Evolution.
[73] Y. Schiffmann. Segmentation and zooid formation in animals with a posterior growing region: the case for metabolic gradients and Turing waves. , 2004, Progress in biophysics and molecular biology.
[74] H. W. Beams,et al. Electrical control of morphogenesis in regenerating Dugesia tigrina. I. Relation of axial polarity to field strength. , 1952, Journal of cellular and comparative physiology.
[75] M. Levin,et al. Gap junctional signaling in pattern regulation: Physiological network connectivity instructs growth and form , 2017, Developmental neurobiology.
[76] M. Levin,et al. Regulation of cell behavior and tissue patterning by bioelectrical signals: challenges and opportunities for biomedical engineering. , 2012, Annual review of biomedical engineering.
[77] Michael Levin,et al. Transmembrane voltage potential controls embryonic eye patterning in Xenopus laevis , 2012, Development.
[78] Michael Levin,et al. Inferring Regulatory Networks from Experimental Morphological Phenotypes: A Computational Method Reverse-Engineers Planarian Regeneration , 2015, PLoS Comput. Biol..
[79] I. So,et al. ATP-sensitive K(+) channels composed of Kir6.1 and SUR2B subunits in guinea pig gastric myocytes. , 2002, American journal of physiology. Gastrointestinal and liver physiology.
[80] John M. Allen,et al. Regeneration in Invertebrates: Model Systems , 2016 .
[81] F. Kortüm,et al. Mutations in KCNH1 and ATP6V1B2 cause Zimmermann-Laband syndrome , 2015, Nature Genetics.
[82] Ryan D Morrie,et al. V‐ATPase‐dependent ectodermal voltage and ph regionalization are required for craniofacial morphogenesis , 2011, Developmental dynamics : an official publication of the American Association of Anatomists.
[83] Jean Dimmitt,et al. Electrical control of morphogenesis in regenerating Dugesia tigrina. II. Potential gradient vs. current density as control factors. , 1952, Journal of cellular and comparative physiology.
[84] H. G. Ferreira,et al. Determination of ionic permeability coefficients of the plasma membrane of Xenopus laevis oocytes under voltage clamp. , 1989, The Journal of physiology.
[85] Michael Levin,et al. General principles for measuring resting membrane potential and ion concentration using fluorescent bioelectricity reporters. , 2012, Cold Spring Harbor protocols.
[86] A. Haghighi,et al. Neuronal Nicotinic Acetylcholine Receptors Are Blocked by Intracellular Spermine in a Voltage-Dependent Manner , 1998, The Journal of Neuroscience.
[87] M. Arnone,et al. A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin , 2014, Development.
[88] Sigrid A. Langhans,et al. Cancer as a channelopathy: ion channels and pumps in tumor development and progression , 2015, Front. Cell. Neurosci..
[89] David L. Kaplan,et al. Membrane Potential Controls Adipogenic and Osteogenic Differentiation of Mesenchymal Stem Cells , 2008, PloS one.
[90] A. Mathews. ELECTRICAL POLARITY IN THE HYDROIDS , 1903 .
[91] James Sharpe,et al. Data-driven modelling of a gene regulatory network for cell fate decisions in the growing limb bud , 2015, Molecular systems biology.
[92] A. Sater,et al. Analysis of growth factor signaling in embryos , 2006 .
[93] E. Bates,et al. Ion channels in development and cancer. , 2015, Annual review of cell and developmental biology.
[94] Hans Meinhardt,et al. Models of biological pattern formation: from elementary steps to the organization of embryonic axes. , 2008, Current topics in developmental biology.
[95] F. Ashcroft,et al. How ATP Inhibits the Open KATP Channel , 2008, The Journal of general physiology.
[96] Michael Levin,et al. A linear-encoding model explains the variability of the target morphology in regeneration , 2014, Journal of The Royal Society Interface.
[97] Takashi Gojobori,et al. Long-range neural and gap junction protein-mediated cues control polarity during planarian regeneration. , 2010, Developmental biology.
[98] Deepali Jhamb,et al. Network based transcription factor analysis of regenerating axolotl limbs , 2011, BMC Bioinformatics.
[99] J. Taylor,et al. Epidermal growth factor. Physical and chemical properties. , 1972, The Journal of biological chemistry.
[100] E. J. Lund. Experimental control of organic polarity by the electric current. IV. The quantitative relations between current density, orientation, and inhibition of regeneration , 1924 .
[101] A. Alcaraz,et al. Membrane potential bistability in nonexcitable cells as described by inward and outward voltage-gated ion channels. , 2014, The journal of physical chemistry. B.
[102] B. Jansson. Potassium, sodium, and cancer: a review. , 1996, Journal of environmental pathology, toxicology and oncology : official organ of the International Society for Environmental Toxicology and Cancer.
[103] F. Cornelius,et al. Investigation of the enzymatic activity of the Na+,K+-ATPase via isothermal titration microcalorimetry. , 2010, Biochimica et biophysica acta.
[104] M. Levin,et al. Exploring Instructive Physiological Signaling with the Bioelectric Tissue Simulation Engine , 2016, Front. Bioeng. Biotechnol..
[105] Teresa Adell,et al. Gradients in planarian regeneration and homeostasis. , 2010, Cold Spring Harbor perspectives in biology.
[106] A. Masotti,et al. Keppen-Lubinsky syndrome is caused by mutations in the inwardly rectifying K+ channel encoded by KCNJ6. , 2015, American journal of human genetics.
[107] David L. Kaplan,et al. Genome‐wide analysis reveals conserved transcriptional responses downstream of resting potential change in Xenopus embryos, axolotl regeneration, and human mesenchymal cell differentiation , 2015, Regeneration.
[108] David L. Kaplan,et al. Role of Membrane Potential in the Regulation of Cell Proliferation and Differentiation , 2009, Stem Cell Reviews and Reports.
[109] M. L. Ujwal,et al. Divalent metal-ion transporter DMT1 mediates both H+ -coupled Fe2+ transport and uncoupled fluxes , 2005, Pflügers Archiv.
[110] S. Angers,et al. Glutamate Transporter Coupling to Na,K-ATPase , 2009, The Journal of Neuroscience.
[111] T. Keku,et al. IGF-I and TGF-beta1 have distinct effects on phenotype and proliferation of intestinal fibroblasts. , 2002, American journal of physiology. Gastrointestinal and liver physiology.
[112] W. R. Lieb,et al. The two-pore-domain K(+) channels TREK-1 and TASK-3 are differentially modulated by copper and zinc. , 2004, Molecular Pharmacology.
[113] Guy Karlebach,et al. Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.
[114] Swati S. More,et al. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin , 2010, Pharmacogenetics and genomics.
[115] M. Levin,et al. Light-activation of the Archaerhodopsin H+-pump reverses age-dependent loss of vertebrate regeneration: sparking system-level controls in vivo , 2013, Biology Open.
[116] M. Levin,et al. Serotonin Signaling Is a Very Early Step in Patterning of the Left-Right Axis in Chick and Frog Embryos , 2005, Current Biology.
[117] V. Ganapathy,et al. Cloning and Functional Characterization of a Potential-sensitive, Polyspecific Organic Cation Transporter (OCT3) Most Abundantly Expressed in Placenta* , 1998, The Journal of Biological Chemistry.
[118] Hans Meinhardt,et al. Beta‐catenin and axis formation in planarians , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.
[119] Stephen L. Johnson,et al. Bioelectric Signaling Regulates Size in Zebrafish Fins , 2014, PLoS genetics.
[120] T. Moos,et al. Divalent metal transporter 1 (DMT1) in the brain: implications for a role in iron transport at the blood-brain barrier, and neuronal and glial pathology , 2015, Front. Mol. Neurosci..
[121] H. Kilbinger,et al. Release of non‐neuronal acetylcholine from the isolated human placenta is mediated by organic cation transporters , 2001, British journal of pharmacology.
[122] Jin Han,et al. The direct modulatory activity of zinc toward ion channels , 2015, Integrative medicine research.
[123] J. Bayascas,et al. Planarian Hox genes: novel patterns of expression during regeneration. , 1997, Development.
[124] Arthur Konnerth,et al. Early postnatal switch in magnesium sensitivity of NMDA receptors in rat CA1 pyramidal cells , 1999, The Journal of physiology.
[125] M. A. Stolow,et al. Xenopus sonic hedgehog as a potential morphogen during embryogenesis and thyroid hormone-dependent metamorphosis , 1995, Nucleic Acids Res..
[126] J. Cooke,et al. Scale of body pattern adjusts to available cell number in amphibian embryos , 1981, Nature.
[127] T. Lau,et al. Expression of divalent metal transporter 1 (DMT1) isoforms in first trimester human placenta and embryonic tissues. , 2005, Human reproduction.
[128] Dany S. Adams,et al. Use of genetically encoded, light-gated ion translocators to control tumorigenesis , 2016, Oncotarget.
[129] J. Miller,et al. Electrophoretic repatterning of charged cytoplasmic molecules within tissues coupled by gap junctions by externally applied electric fields. , 1989, Developmental biology.
[130] Michael Levin,et al. Morphogenetic fields in embryogenesis, regeneration, and cancer: Non-local control of complex patterning , 2012, Biosyst..
[131] M. Levin,et al. The ATP-sensitive K(+)-channel (K(ATP)) controls early left-right patterning in Xenopus and chick embryos. , 2010, Developmental biology.
[132] A. Mathie,et al. Recovery of Current through Mutated TASK3 Potassium Channels Underlying Birk Barel Syndrome , 2014, Molecular Pharmacology.
[133] Konstantinos Sousounis,et al. Organ repair and regeneration: an overview. , 2012, Birth defects research. Part C, Embryo today : reviews.
[134] R. Kramer,et al. Optogenetics in Developmental Biology: using light to control ion flux-dependent signals in Xenopus embryos. , 2015, The International journal of developmental biology.
[135] Bioelectric patterning during oogenesis: stage-specific distribution of membrane potentials, intracellular pH and ion-transport mechanisms in Drosophila ovarian follicles , 2015, BMC Developmental Biology.
[136] J. R. Sachs. Kinetic evaluation of the Na‐K pump reaction mechanism. , 1977, The Journal of physiology.
[137] K. Williams,et al. Binding of spermine and ifenprodil to a purified, soluble regulatory domain of the N‐methyl‐d‐aspartate receptor , 2008, Journal of neurochemistry.
[138] J. Steinbach,et al. Voltage‐dependent block by magnesium of neuronal nicotinic acetylcholine receptor channels in rat phaeochromocytoma cells. , 1991, The Journal of physiology.
[139] Néstor J. Oviedo,et al. Bioelectrical regulation of cell cycle and the planarian model system. , 2015, Biochimica et biophysica acta.
[140] Jonathan Slack,et al. Establishment of spatial pattern , 2014, Wiley interdisciplinary reviews. Developmental biology.
[141] A. VanDongen,et al. Activation Mechanisms of the NMDA Receptor , 2009 .
[142] J. Rossant,et al. Mouse embryonic chimeras: tools for studying mammalian development , 2003, Development.
[143] Tsung-Han Lee,et al. Sodium or potassium ions activate different kinetics of gill Na, K-ATPase in three seawater- and freshwater-acclimated euryhaline teleosts. , 2005, Journal of experimental zoology. Part A, Comparative experimental biology.
[144] K. Igarashi,et al. Different intracellular polyamine concentrations underlie the difference in the inward rectifier K+ currents in atria and ventricles of the guinea‐pig heart , 2005, The Journal of physiology.
[145] T. Narahashi,et al. Fipronil Is a Potent Open Channel Blocker of Glutamate-Activated Chloride Channels in Cockroach Neurons , 2004, Journal of Pharmacology and Experimental Therapeutics.
[146] M. Levin,et al. HDAC Activity Is Required during Xenopus Tail Regeneration , 2011, PloS one.
[147] Michael Levin,et al. Characterization of innexin gene expression and functional roles of gap-junctional communication in planarian regeneration. , 2005, Developmental biology.
[148] M. Levin,et al. Transmembrane potential of GlyCl-expressing instructor cells induces a neoplastic-like conversion of melanocytes via a serotonergic pathway , 2010, Disease Models & Mechanisms.
[149] M. Levin,et al. Endogenous Gradients of Resting Potential Instructively Pattern Embryonic Neural Tissue via Notch Signaling and Regulation of Proliferation , 2015, The Journal of Neuroscience.