Detail of 1seed.11



Project
Title
BDML file for quantiative information about the simple stochastic model of Ca2+ increasing in the spine volume
Description
NA
Release, Updated
2018-11-15
License
NA
Kind
Quantitative data based on Simulation
File Formats
Data size
11.3 MB

Organism
-
Strain(s)
-
Cell Line
-

Datatype
molecular dynamics
Molecular Function (MF)
Biological Process (BP)
-
Cellular Component (CC)
neuron spine ( GO:0044309 )
Biological Imaging Method
XYZ Scale
-
T scale
1 millisecond for each time interval

Image Acquisition
Experiment type
-
Microscope type
-
Acquisition mode
-
Contrast method
-
Microscope model
-
Detector model
-
Objective model
-
Filter set
-

Summary of Methods
See details in Fujii et al. (2017) Biophys J., 112(4): 813-8286.
Related paper(s)

Masashi Fujii, Kaoru Ohashi, Yasuaki Karasawa, Minori Hikichi, Shinya Kuroda (2017) Small-Volume Effect Enables Robust, Sensitive, and Efficient Information Transfer in the Spine., Biophysical journal, Volume 112, Number 4, pp. 813-826

Published in 2017 Feb 28

(Abstract) Why is the spine of a neuron so small that it can contain only small numbers of molecules and reactions inevitably become stochastic? We previously showed that, despite such noisy conditions, the spine exhibits robust, sensitive, and efficient features of information transfer using the probability of Ca(2+) increase; however, the mechanisms are unknown. In this study, we show that the small volume effect enables robust, sensitive, and efficient information transfer in the spine volume, but not in the cell volume. In the spine volume, the intrinsic noise in reactions becomes larger than the extrinsic noise of input, resulting in robust information transfer despite input fluctuation. In the spine volume, stochasticity makes the Ca(2+) increase occur with a lower intensity of input, causing higher sensitivity to lower intensity of input. The volume-dependency of information transfer increases its efficiency in the spine volume. Thus, we propose that the small-volume effect is the functional reason why the spine has to be so small.
(MeSH Terms)

Contact
Shinya Kuroda, Masashi Fujii , Graduate School of Sciences, University of Tokyo , Department of Biological Sciences , Systems Biology (Kuroda Lab)
Contributors
Masashi Fujii, Kaoru Ohashi, Yasuaki Karasawa, Minori Hikichi, Shinya Kuroda

Local ID
1seed.11
BDML ID
3a4fd91e-cc29-461f-b51e-355574612712
BDML/BD5