Transmitter release is evoked with low probability predominately by calcium flux through single channel openings at the frog neuromuscular junction.

The quantitative relationship between presynaptic calcium influx and transmitter release critically depends on the spatial coupling of presynaptic calcium channels to synaptic vesicles. When there is a close association between calcium channels and synaptic vesicles, the flux through a single open calcium channel may be sufficient to trigger transmitter release. With increasing spatial distance, however, a larger number of open calcium channels might be required to contribute sufficient calcium ions to trigger vesicle fusion.

An excess-calcium-binding-site model predicts neurotransmitter release at the neuromuscular junction.

Despite decades of intense experimental studies, we still lack a detailed understanding of synaptic function. Fortunately, using computational approaches, we can obtain important new insights into the inner workings of these important neural systems. Here, we report the development of a spatially realistic computational model of an entire frog active zone in which we constrained model parameters with experimental data, and then used Monte Carlo simulation methods to predict the Ca(2+)-binding stoichiometry and dynamics that underlie neurotransmitter release.

High-resolution reconstruction of fluorescent inclusions in mouse thorax using anatomically guided sampling and parallel Monte Carlo computing.

We present a method for high-resolution reconstruction of fluorescent images of the mouse thorax. It features an anatomically guided sampling method to retrospectively eliminate problematic data and a parallel Monte Carlo software package to compute the Jacobian matrix for the inverse problem. The proposed method was capable of resolving microliter-sized femtomole amount of quantum dot inclusions closely located in the middle of the mouse thorax.

Single-pixel optical fluctuation analysis of calcium channel function in active zones of motor nerve terminals.

We used high-resolution fluorescence imaging and single-pixel optical fluctuation analysis to estimate the opening probability of individual voltage-gated calcium (Ca(2+)) channels during an action potential and the number of such Ca(2+) channels within active zones of frog neuromuscular junctions. Analysis revealed ∼36 Ca(2+) channels within each active zone, similar to the number of docked synaptic vesicles but far less than the total number of transmembrane particles reported based on freeze-fracture analysis (∼200-250). The probability that each channel opened during an action potential was only ∼0.

Free-space fluorescence tomography with adaptive sampling based on anatomical information from microCT.

Image reconstruction is one of the main challenges for fluorescence tomography. For in vivo experiments on small animals, in particular, the inhomogeneous optical properties and irregular surface of the animal make free-space image reconstruction challenging because of the difficulties in accurately modeling the forward problem and the finite dynamic range of the photodetector. These two factors are fundamentally limited by the currently available forward models and photonic technologies.

Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models.

Spatially realistic diffusion-reaction simulations supplement traditional experiments and provide testable hypotheses for complex physiological systems. To date, however, the creation of realistic 3D cell models has been difficult and time-consuming, typically involving hand reconstruction from electron microscopic images. Here, we present a complementary approach that is much simpler and faster, because the cell architecture (geometry) is created directly in silico using 3D modeling software like that used for commercial film animations.

FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.

Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.

Interoperability of neuroscience modeling software: current status and future directions.

Neuroscience increasingly uses computational models to assist in the exploration and interpretation of complex phenomena. As a result, considerable effort is invested in the development of software tools and technologies for numerical simulations and for the creation and publication of models. The diversity of related tools leads to the duplication of effort and hinders model reuse.

An introduction to simulation and visualization of biological systems at multiple scales: a summer training program for interdisciplinary research.

Advances in biomedical research require a new generation of researchers having a strong background in both the life and physical sciences and a knowledge of computational, mathematical, and engineering tools for tackling biological problems. The NIH-NSF Bioengineering and Bioinformatics Summer Institute at the University of Pittsburgh (BBSI @ Pitt; www.ccbb.

Evidence for ectopic neurotransmission at a neuronal synapse.

Neurotransmitter release is well known to occur at specialized synaptic regions that include presynaptic active zones and postsynaptic densities. At cholinergic synapses in the chick ciliary ganglion, however, membrane formations and physiological measurements suggest that release distant from postsynaptic densities can activate the predominantly extrasynaptic alpha7 nicotinic receptor subtype. We explored such ectopic neurotransmission with a novel model synapse that combines Monte Carlo simulations with high-resolution serial electron microscopic tomography.

Spatial Distribution of Calcium Entry Evoked by Single Action Potentials within the Presynaptic Active Zone.

The nature of presynaptic calcium (Ca(2+)) signals that initiate neurotransmitter release makes these signals difficult to study, in part because of the small size of specialized active zones within most nerve terminals. Using the frog motor nerve terminal, which contains especially large active zones, we show that increases in intracellular Ca(2+) concentration within 1 msec of action potential invasion are attributable to Ca(2+) entry through N-type Ca(2+) channels and are not uniformly distributed throughout active zone regions. Furthermore, changes in the location and magnitude of Ca(2+) signals recorded before and after experimental manipulations (omega-conotoxin GVIA, diaminopyridine, and lowered extracellular Ca(2+)) support the hypothesis that there is a remarkably low probability of a single Ca(2+) channel opening within an active zone after an action potential.

THE VIRTUAL INSTRUMENT: SUPPORT FOR GRID-ENABLED MCELL SIMULATIONS.

Ensembles of widely distributed, heterogeneous resources, or Grids, have emerged as popular platforms for large-scale scientific applications. In this paper we present the Virtual Instrument project, which provides an integrated application execution environment that enables end-users to run and interact with running scientific simulations on Grids. This work is performed in the specific context of MCell, a computational biology application.

Novel delta subunit mutation in slow-channel syndrome causes severe weakness by novel mechanisms.

We investigated the basis for a novel form of the slow-channel congenital myasthenic syndrome presenting in infancy in a single individual as progressive weakness and impaired neuromuscular transmission without overt degeneration of the motor endplate. Prolonged low-amplitude synaptic currents in biopsied anconeus muscle at 9 years of age suggested a kinetic disorder of the muscle acetylcholine receptor. Ultrastructural studies at 16 months, at 9 years, and at 15 years of age showed none of the typical degenerative changes of the endplate associated with the slow-channel congenital myasthenic syndrome, and acetylcholine receptor numbers were not significantly reduced.