The electrical activity of neurons is governed by more than 200 types of voltage gated ion channels. To model the diversity of electrical behaviors in neurons, it is necessary to characterize the biophysical properties of each individual ion channel in standardized and controlled conditions.
The Channelome project sets out to identify and quantitatively characterize all ion channels (~350) known to be expressed in the rat mammalian brain. Our analysis of existing literature on ion channel characterization (Channelpedia) revealed that previous efforts are at best anecdotal and in many cases insufficient to properly build models from the experimental data [1]. The goal of the Channelome project is to build a comprehensive and consistent set of experiments and models of all relevant ion channels.
Approach
The Channelome project consists of three main steps: 1. Creation of stable cell line library, 2. Automated biophysics characterization 3. Structured data storage.
Creation of stable cell line library starts with individual rat ion channel gene isolation using PCR, followed by insertion of the ion channel gene in a expression vector via the Gateway cloning strategy and transfection in host CHOFlpIn T-Rex cells. The transfected cell lines are then validated with immunostaining, further PCRs and electrophysiology. After successful validation, cell lines are cryopreserved for long term storage.
Automated biophysics characterization includes designing biophysical assays for each ion channel followed by automated patch clamp experiments and construction of mathematical models that best fit the data.
Channelpedia has been developed to systematically store all the data generated by the Channelome project. It uses a novel approach to manage scientific information by combining the functionality of unstructured wiki-like data with the advantage of a structured database. It is web based, freely accessible and designed to store even minor details of the Channelome project.
The initial focus of the Channelome project’s is on voltage-dependent ion channels, which upon completion will be followed by systematic mapping of ligand gated ion channels and their voltage kinetics in response to the application of relevant neurotransmitters and modulators.