Models that contain the Modeling Application : NeuroRD (Home Page)

("Computationally efficient, neuronal reaction-diffusion stochastic simulator (pronounced NeurRDS). Java program which runs on any platform. The algorithm is based on Gillespie's tau-leap reaction algorithm, and the stochastic diffusion algorithm of Blackwell. It uses XML-based model specifications.")
Re-display model names without descriptions
    Models   Description
1.  Biochemically detailed model of LTP and LTD in a cortical spine (Maki-Marttunen et al 2020)
"Signalling pathways leading to post-synaptic plasticity have been examined in many types of experimental studies, but a unified picture on how multiple biochemical pathways collectively shape neocortical plasticity is missing. We built a biochemically detailed model of post-synaptic plasticity describing CaMKII, PKA, and PKC pathways and their contribution to synaptic potentiation or depression. We developed a statistical AMPA-receptor-tetramer model, which permits the estimation of the AMPA-receptor-mediated maximal synaptic conductance based on numbers of GluR1s and GluR2s predicted by the biochemical signalling model. We show that our model reproduces neuromodulator-gated spike-timing-dependent plasticity as observed in the visual cortex and can be fit to data from many cortical areas, uncovering the biochemical contributions of the pathways pinpointed by the underlying experimental studies. Our model explains the dependence of different forms of plasticity on the availability of different proteins and can be used for the study of mental disorder-associated impairments of cortical plasticity."
2.  Dopamine activation of signaling pathways in a medium spiny projection neuron (Oliveira et al. 2012)
Large scale stochastic reaction-diffusion model of signaling pathways in a medium spiny projection neuron dendrite with spines to investigate whether the critical function of anchoring is to locate PKA near the cAMP that activates it or near its targets, such as AMPA receptors located in the post-synaptic density. Simulations, implemented in NeuroRD, show that PKA colocalization with adenylate cyclase, either in the spine head or in the dendrite, leads to greater phosphorylation of DARPP-32 Thr34 and AMPA receptor GluA1 Ser845 than when PKA is anchored away from adenylate cyclase.
3.  Gq coupled signaling pathways involved in striatal synaptic plasticity (Kim et al. 2013)
Model of Gq coupled signaling pathways underlying synaptic plasticity in striatal medium spiny projection neurons. Reactions and diffusion are implemented stochastically in a dendrite with one or more diffusionally coupled spines. Simulations demonstrate that theta burst stimulation, which produces LTP, increases the ratio of PKC:2AG as compared to 20 Hz stimulation, which produces LTD.
4.  Hippocampus CA1: Simulations of LTP signaling pathways (Kim M et al. 2011)
This is a multi-compartmental, stochastic version of the Kim et al. 2010 paper. There are a few additional reactions, and some of the rate constants have been updated. It addresses the role of molecule anchoring in PKA dependent hippocampal LTP.
5.  Signaling pathways In D1R containing striatal spiny projection neurons (Blackwell et al 2018)
We implemented a mechanistic model of signaling pathways activated by dopamine D1 receptors, acetylcholine receptors, and glutamate. We use our novel, computationally efficient simulator, NeuroRD, to simulate stochastic interactions both within and between dendritic spines. Results show that the combined activity of several key plasticity molecules correctly predicts the occurrence of either LTP, LTD or no plasticity for numerous experimental protocols.
6.  Signaling pathways underlying LTP in hippocampal CA1 pyramidal cells (Jedrzejewska-Szmek et al 2017)
" ...We investigated whether the diverse experimental evidence can be unified by creating a spatial, mechanistic model of multiple signaling pathways in hippocampal CA1 neurons. Our results show that the combination of activity of several key kinases can predict the occurrence of long-lasting forms of LTP for multiple experimental protocols. ..."

Re-display model names without descriptions