Abstract
Modeling biophysical processes in general requires knowledge about underlying biological parameters. The quality of simulation results is strongly influenced by the accuracy of these parameters, hence the identification of parameter values that the model includes is a major part of simulating biophysical processes. In many cases, secondary data can be gathered by experimental setups, which are exploitable by mathematical inverse modeling techniques. Here we describe a method for parameter identification of diffusion properties of calcium in the nuclei of rat hippocampal neurons. The method is based on a Gauss–Newton method for solving a least-squares minimization problem and was formulated in such a way that it is ideally implementable in the simulation platform uG. Making use of independently published space- and time-dependent calcium imaging data, generated from laser-assisted calcium uncaging experiments, here we could identify the diffusion properties of nuclear calcium and were able to validate a previously published model that describes nuclear calcium dynamics as a diffusion process.
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References
Allbritton N, Meyer T, Stryer L (1992) Range of messenger action of calcium ion and inositol 1,4,5-trisphosphate. Science 258: 1812–1815
Bading H, Ginty DD, Greenberg ME (1993) Regulation of gene expression in hippocampal neurons by distinct calcium signaling pathways. Science 260: 181–186
Bastian P, Wittum G (1994) Adaptive multigrid methods: the UG concept. In: Notes on numerical fluid mechanics. Vieweg
Cruzalegui FH, Bading H (2000) Calcium-regulated protein kinase cascades and their transcription factor targets. Cell Mol Life Sci 57: 402–410
Eder A, Bading H (2007) Calcium signals can freely cross the nuclear envelope in hippocampal neurons: somatic calcium increases generate nuclear calcium transients. BMC Neurosci 8: 57
Ghosh A, Greenberg M (1995) Calcium signaling in neurons: molecular mechanisms and cellular consequences. Science 268: 239–247
Hagenston AM, Bading H (2011) Calcium signaling in synapse-to-nucleus communication.Cold Spring Horbor Perspect Biol (in press)
Milner B, Squire LR, Kandel ER (1998) Cognitive neuroscience and the study of memory. Neuron 20: 445–468
Nocedal J, Wright SJ (2000) Numerical optimization. Springer
Queisser G, Wittmann M, Bading H, Wittum G (2008) Filtering, reconstruction, and measurement of the geometry of nuclei from hippocampal neurons based on confocal microscopy data. J Biomed Opt 13: 014,009
West AE, Chen WG, Dalva MB, Dolmetsch RE, Kornhauser JM, Shaywitz AJ, Takasu MA, Tao X, Greenberg ME (2001) Calcium regulation of neuronal gene expression. Proc Natl Acad Sci USA (PNAS) 98: 11,024–11,031
Wittmann M, Queisser G, Eder A, Wiegert JS, Bengtson CP, Hellwig A, Wittum G, Bading H (2009) Synaptic activity induces dramatic changes in the geometry of the cell nucleus: interplay between nuclear structure, histone h3 phosphorylation, and nuclear calcium signaling. J Neurosci 29(47): 14,687–14,700
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Queisser, G., Wittum, G. A method to investigate the diffusion properties of nuclear calcium. Biol Cybern 105, 211–216 (2011). https://doi.org/10.1007/s00422-011-0452-8
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DOI: https://doi.org/10.1007/s00422-011-0452-8