The elementary events of excitation-contraction coupling in heart muscle are Ca2+ sparks, which arise from one or more ryanodine receptors in the sarcoplasmic reticulum (SR). Here a simple numerical model is constructed to explore Ca2+ spark formation, detection, and interpretation in cardiac myocytes. This model includes Ca2+ release, cytosolic diffusion, resequestration by SR Ca2+-ATPases, and the association and dissociation of Ca2+ with endogenous Ca2+-binding sites and a diffusible indicator dye (fluo-3). Simulations in a homogeneous, isotropic cytosol reproduce the brightness and the time course of a typical cardiac Ca2+ spark, but underestimate its spatial size (approximately 1.1 micron vs. approximately 2.0 micron). Back-calculating [Ca2+]i by assuming equilibrium with indicator fails to provide a good estimate of the free Ca2+ concentration even when using blur-free fluorescence data. A parameter sensitivity study reveals that the mobility, kinetics, and concentration of the indicator are essential determinants of the shape of Ca2+ sparks, whereas the stationary buffers and pumps are less influential. Using a geometrically more complex version of the model, we show that the asymmetric shape of Ca2+ sparks is better explained by anisotropic diffusion of Ca2+ ions and indicator dye rather than by subsarcomeric inhomogeneities of the Ca2+ buffer and transport system. In addition, we examine the contribution of off-center confocal sampling to the variance of spark statistics.

Recent studies have shown that one of the parental subgenomes in ancient polyploids is generally more dominant, having retained more genes and being more highly expressed, a phenomenon termed subgenome dominance. The genomic features that determine how quickly and which subgenome dominates within a newly formed polyploid remain poorly understood. To investigate the rate of emergence of subgenome dominance, we examined gene expression, gene methylation, and transposable element (TE) methylation in a natural, <140-year-old allopolyploid (Mimulus peregrinus), a resynthesized interspecies triploid hybrid (M. robertsii), a resynthesized allopolyploid (M. peregrinus), and progenitor species (M. guttatus and M. luteus). We show that subgenome expression dominance occurs instantly following the hybridization of divergent genomes and significantly increases over generations. Additionally, CHH methylation levels are reduced in regions near genes and within TEs in the first-generation hybrid, intermediate in the resynthesized allopolyploid, and are repatterned differently between the dominant and recessive subgenomes in the natural allopolyploid. Subgenome differences in levels of TE methylation mirror the increase in expression bias observed over the generations following hybridization. These findings provide important insights into genomic and epigenomic shock that occurs following hybridization and polyploid events and may also contribute to uncovering the mechanistic basis of heterosis and subgenome dominance.

We performed intracellular recordings of relay neurons from the lateral geniculate nucleus of a cat thalamic slice preparation. We measured responses during both tonic and burst firing modes to sinusoidal current injection and performed Fourier analysis on these responses. For comparison, we constructed a minimal "integrate-and-fire-or-burst" (IFB) neuron model that reproduces salient features of the relay cell responses. The IFB model is constrained to quantitatively fit our Fourier analysis of experimental relay neuron responses, including: the temporal tuning of the response in both tonic and burst modes, including a finding of low-pass and sometimes broadband behavior of tonic firing and band-pass characteristics during bursting, and the generally greater linearity of tonic compared with burst responses at low frequencies. In tonic mode, both experimental and theoretical responses display a frequency-dependent transition from massively superharmonic spiking to phase-locked superharmonic spiking near 3 Hz, followed by phase-locked subharmonic spiking at higher frequencies. Subharmonic and superharmonic burst responses also were observed experimentally. Characterizing the response properties of the "tuned" IFB model leads to insights regarding the observed stimulus dependence of burst versus tonic response mode in relay neurons. Furthermore the simplicity of the IFB model makes it a candidate for large scale network simulations of thalamic functioning.