Modelling Vesicular Release at Hippocampal Synapses

We study local calcium dynamics leading to a vesicle fusion in a stochastic, and spatially explicit, biophysical model of the CA3-CA1 presynaptic bouton. The kinetic model for vesicle release has two calcium sensors, a sensor for fast synchronous release that lasts a few tens of milliseconds and a separate sensor for slow asynchronous release that lasts a few hundred milliseconds. A wide range of data can be accounted for consistently only when a refractory period lasting a few milliseconds between releases is included. The inclusion of a second sensor for asynchronous release with a slow unbinding site, and thereby a long memory, affects short-term plasticity by facilitating release. Our simulations also reveal a third time scale of vesicle release that is correlated with the stimulus and is distinct from the fast and the slow releases. In these detailed Monte Carlo simulations all three time scales of vesicle release are insensitive to the spatial details of the synaptic ultrastructure. Furthermore, our simulations allow us to identify features of synaptic transmission that are universal and those that are modulated by structure

Mechanics of Vorticella Contraction

Vorticella convallaria is one of a class of fast-moving organisms that can traverse its body size in less than a millisecond by rapidly coiling a slender stalk anchoring it to a nearby surface. The stalk houses a fiber called the spasmoneme, which winds helically within the stalk and rapidly contracts in response to calcium signaling. We have developed a coupled mechanical-chemical model of the coiling process, accounting for the coiling of the elastic stalk and the binding of calcium to the protein spasmin. Simulations of the model describe the contraction and recovery processes quantitatively. The stalk-spasmoneme system is shown to satisfy geometric constraints, which explains why the cell body sometimes rotates during contraction. The shape of the collapsing and recovering stalk bounds its effective bending stiffness. Simulations suggest that recovery from the contracted state is driven by the stalk at a rate controlled by dissociation of calcium from spasmin

Dynamics and evolution of β-catenin-dependent Wnt signaling revealed through massively parallel clonogenic screening

Wnt/β-catenin signaling is of significant interest due to the roles it plays in regulating development, tissue regeneration and disease. Transcriptional reporters have been widely employed to study Wnt/β-catenin signal transduction in live cells and whole organisms and have been applied to understanding embryonic development, exploring oncogenesis and developing therapeutics. Polyclonal heterogeneity in reporter cell lines has historically been seen as a challenge to be overcome in the development of novel cell lines and reporter-based assays, and monoclonal reporter cell lines are commonly employed to reduce this variability. A375 cell lines infected with a reporter for Wnt/β-catenin signaling were screened over short (< 6) and long (> 25) generational timescales. To characterize phenotypic divergence these time-scales, a microfabricated cell array-based screen was developed enabling characterization of 1,119 clonal colonies in parallel. This screen revealed phenotypic divergence after <6 generations at a similar scale to that observed in monoclonal cell lines cultured for >25 generations. Not only were reporter dynamics observed to diverge widely, but monoclonal cell lines were observed with seemingly opposite signaling phenotypes. Additionally, these observations revealed a generational-dependent trend in Wnt signaling in A375 cells that provide insight into the pathway’s mechanisms of positive feedback and self-inhibition

Ryanodine Receptor Allosteric Coupling and the Dynamics of Calcium Sparks

Puffs and sparks are localized intracellular Ca2+ elevations that arise from the cooperative activity of Ca2+-regulated inositol 1,4,5-trisphosphate receptors and ryanodine receptors clustered at Ca2+ release sites on the surface of the endoplasmic reticulum or the sarcoplasmic reticulum. While the synchronous gating of Ca2+-regulated Ca2+ channels can be mediated entirely though the buffered diffusion of intracellular Ca2+, interprotein allosteric interactions also contribute to the dynamics of ryanodine receptor (RyR) gating and Ca2+ sparks. In this article, Markov chain models of Ca2+ release sites are used to investigate how the statistics of Ca2+ spark generation and termination are related to the coupling of RyRs via local [Ca2+] changes and allosteric interactions. Allosteric interactions are included in a manner that promotes the synchronous gating of channels by stabilizing neighboring closed-closed and/or open-open channel pairs. When the strength of Ca2+-mediated channel coupling is systematically varied (e.g., by changing the Ca2+ buffer concentration), simulations that include synchronizing allosteric interactions often exhibit more robust Ca2+ sparks; however, for some Ca2+ coupling strengths the sparks are less robust. We find no evidence that the distribution of spark durations can be used to distinguish between allosteric interactions that stabilize closed channel pairs, open channel pairs, or both in a balanced fashion. On the other hand, the changes in spark duration, interspark interval, and frequency observed when allosteric interactions that stabilize closed channel pairs are gradually removed from simulations are qualitatively different than the changes observed when open or both closed and open channel pairs are stabilized. Thus, our simulations clarify how changes in spark statistics due to pharmacological washout of the accessory proteins mediating allosteric coupling may indicate the type of synchronizing allosteric interactions exhibited by physically coupled RyRs. We also investigate the validity of a mean-field reduction applicable to the dynamics of a ryanodine receptor cluster coupled via local [Ca2+] and allosteric interactions. In addition to facilitating parameter studies of the effect of allosteric coupling on spark statistics, the derivation of the mean-field model establishes the correct functional form for cooperativity factors representing the coupled gating of RyRs. This mean-field formulation is well suited for use in computationally efficient whole cell simulations of excitation-contraction coupling