Estimating the synaptic current in a multiconductance AMPA receptor model

Redundancy principle and the role of extreme statistics in molecular and cellular biology

The paradigm of chemical activation rates in cellular biology has been shifted from the mean arrival time of a single particle to the mean of the first among many particles to arrive at a small activation site. The activation rate is set by extremely rare events, which have drastically different time scales from the mean times between activations, and depends on different structural parameters. This shift calls for reconsideration of physical processes used in deterministic and stochastic modeling of chemical reactions that are based on the traditional forward rate, especially for fast activation processes in living cells. Consequently, the biological activation time is not necessarily exponentially distributed. We review here the physical models, the mathematical analysis and the new paradigm of setting the scale to be the shortest time for activation that clarifies the role of population redundancy in selecting and accelerating transient cellular search processes. We provide examples in cellular transduction, gene activation, cell senescence activation or spermatozoa selection during fertilization, where the rate depends on numbers. We conclude that the statistics of the minimal time to activation set kinetic laws in biology, which can be very different from the ones associated to average times.

The First 100 nm Inside the Pre-synaptic Terminal Where Calcium Diffusion Triggers Vesicular Release

Calcium diffusion in the thin 100 nm layer located between the plasma membrane and docked vesicles in the pre-synaptic terminal of neuronal cells mediates vesicular fusion and synaptic transmission. Accounting for the narrow-cusp geometry located underneath the vesicle is a key ingredient that defines the probability and the time scale of calcium diffusion to bind calcium sensors for the initiation of vesicular release. We review here the time scale, the calcium binding dynamics and the consequences for asynchronous versus synchronous release. To conclude, three-dimensional modeling approaches and the associated coarse-grained simulations can now account efficiently for the precise co-organization of vesicles and Voltage-Gated-Calcium-Channel (VGCC). This co-organization is a key determinant of short-term plasticity and it shapes asynchronous release. Moreover, changing the location of VGCC from few nanometers underneath the vesicle modifies significantly the release probability. Finally, by modifying the calcium buffer concentration, a single synapse can switch from facilitation to depression.

Neuronal activity controls transsynaptic geometry

The neuronal synapse is comprised of several distinct zones, including presynaptic vesicle zone (SVZ), active zone (AZ) and postsynaptic density (PSD). While correct relative positioning of these zones is believed to be essential for synaptic function, the mechanisms controlling their mutual localization remain unexplored. Here, we employ high-throughput quantitative confocal imaging, super-resolution and electron microscopy to visualize organization of synaptic subdomains in hippocampal neurons. Silencing of neuronal activity leads to reversible reorganization of the synaptic geometry, resulting in a increased overlap between immunostained AZ and PSD markers; in contrast, the SVZ-AZ spatial coupling is decreased. Bayesian blinking and bleaching (3B) reconstruction reveals that the distance between the AZ-PSD distance is decreased by 30 nm, while electron microscopy shows that the width of the synaptic cleft is decreased by 1.1 nm. Our findings show that multiple aspects of synaptic geometry are dynamically controlled by neuronal activity and suggest mutual repositioning of synaptic components as a potential novel mechanism contributing to the homeostatic forms of synaptic plasticity.

Presynaptic architecture of the larval zebrafish neuromuscular junction

This article shows the ultrastructural architecture of larval zebrafish (Danio rerio) neuromuscular junctions in three dimensions. We compare classical electron microscopy fixation techniques with high-pressure freezing followed by freeze substitution (HPF/FS) in combination with electron tomography. Furthermore, we compare the structure of neuromuscular junctions in 4- and 8-dpf zebrafish larvae with HPF/FS because this allows for close-to-native ultrastructural preservation. We discovered that synaptic vesicles of 4-dpf zebrafish larvae are larger than those of 8-dpf larvae. Furthermore, we describe two types of dense-core vesicles and quantify a filamentous network of small filaments interconnecting synaptic vesicles as well as tethers connecting synaptic vesicles to the presynaptic cell membrane. In the center of active zones, we found elaborate electron-dense projections physically connecting vesicles of the synaptic vesicle pool to the presynaptic membrane. Overall this study establishes the basis for systematic comparisons of synaptic architecture at high resolution in three dimensions of an intact vertebrate in a close-to-native state. Furthermore, we provide quantitative information that builds the basis for diverse systems biology approaches in neuroscience, from comparative anatomy to cellular simulations.

Control of flux by narrow passages and hidden targets in cellular biology

Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small spatial scales. These may be small binding sites inside or on the surface of the cell, or narrow passages between subcellular compartments. The great disparity in spatial scales is the key to controlling cell function by structure. We report here recent progress on resolving analytical and numerical difficulties in extracting properties from experimental data, from biophysical models, and from Brownian dynamics simulations of diffusion in multi-scale structures. This progress is achieved by developing an analytical approximation methodology for solving the model equations. The reported results are applied to analysis and simulations of subcellular processes and to the quantification of their biological functions.

Synaptic transmission in neurological disorders dissected by a quantitative approach

Synaptic transmission depends on several molecular and geometric components, such as the location of vesicular release, the number of released neurotransmitter molecules, the number and type of receptors, as well as the synapse organization. Our goal here is to illustrate how synaptic modeling allows extracting quantitative information in the context of neurological diseases and associated therapies. Combining electrophysiology with simulation tools, we first evaluate the reduction in synaptically released glutamate molecules induced by a ketogenic diet. In a second part, because the scaffolding molecule Shank3 is disrupted at the postsynaptic density in Autism Spectral Disorders, we present a numerical simulation of the synaptic response where this disruption leads to an alteration of the excitatory AMPA receptor trafficking. The take home message is that combining recent experimental findings with modeling approaches allows obtaining precise quantitative properties of what was still unapproachable a decade ago.