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Reconstruction and Simulation of Neural Tissue

Experimental Data 1
Henry Markram
Structure of the lecture

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Caveats

v Summary
Approach to study single neurons

Infrared Differential Interference Contrast Microscopy (IR-DIC); patch – clamp recordings

Approach to study single neurons

Set-up for recording from neurons in brain slices

Approach to study single neurons

Patch-clamping Neurons
Approach to study single neurons

A Stained Neuron
Approach to study single neurons

Fluorescence Staining
Approach to studying single neurons

1. Electrical profile
2. Morphological profile
3. Molecular Profile
Structure of the lecture

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Caveats

v Summary
Morphology – diversity
 Morphology – diversity

55 morphological types

Morphological Features

Soma Perimeter(µm)
Soma Area(µm²)
Dendrites max horizontal extend
Dendrites max vertical extend
Dendrite V/H
Dendrites tree number
…
…
etc

Classification based on local morphology

Morphology – repairing cut morphologies
Morphology – increasing the dataset

Average Features

v Repair Neurons

v Clone Neurons

v Synthesize Neurons
Electrophysiology

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Caveats

v Summary
Electrophysiology – electrical profiling, eCode

A battery of Stimuli

Electrical Features

1. AP Amplitude
2. AP halfwidth
3. After hyperpolarization
4. Spike train accommodation
5. …
6. …
7. etc
Electrophysiology - diversity
11 electrical types types
Morpho-electrical types
Morphological Type

Specific morphology Electrical sub-types

Morpho-electrical types
Morphological Type
Morpho-electrical Diversity
Structure of the lecture

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Caveats

v Summary
Caveats

v Brain slices; morphologies are cut

v Patch-clamp; can can only record from a

few neurons

v Classifying different morphological and

electrical types
Summary

Summary:
v Brain slices

v Patch-clamp

v How to obtain morphologies

v How to obtain electrical

properties
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Reconstruction and Simulation of Neural Tissue

Experimental Data 2
Henry Markram
Ion Channel Profiling

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Ion Channel Profiling

v Molecular Profiling

v Neuron types

v Neurons Densities

v Caveats

v Summary
Ion Channels
• 438 ion channel related genes
• 281 well characterized ion cannels
• 145 voltage-gated
OUTSIDE

INSIDE
v REST:
v K2p – open at rest, maintain the resting potential
v Kir – inward rectifying (K goes in), open on
hyperpolarization, maintain the resting potential
v DEPOLARIZATION:
v Nav- voltage gated Sodium
v Cav- voltage gated Calcium
v HYPERPOLARIZATION
v Kv- voltage-gated (K goes out), open on
depolarization, repolarize the membrane
v Kca – Calcium activated K
Source: IUPHAR/BPS Guide to Pharmacology
http://www.guidetopharmacology.org
Ion Channels – Voltage Gated K Channels

- 40 K channel genes, 12 classes (Kv1-12)

- Each gene produces a specific subunit
- Four subunits combine for form an ion channel (a tertramers)
- Same subunits combine, homotetramers
- Different subunits, heterotetramers
- Result is >> 40 different voltage-gated K channels
Voltage-gated Ion Channels
Tetrameric Structure of K Channels

Ion Selective Pore

Ion Channels – Biophysical Profiling

Ion Channel Kinetics

- Activation
- Inactivation
- Deactivation
Ion Channels – Diversity
Diversity of kinetics of Kv
channels

Opening during voltage change

Fast activating
Slow activating

Closing while voltage is on

Fast inactivating
Slow inactivation

Closing after activation

Fast deactivating
Slow deactivating
Ion Channels – Classes
Ion Channels – Classes

Channelpedia.epfl.ch
Ion Channels – Combination Determines Behavior

Toledo-Rodriguez, 2005
Ion Channel Profiling

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Ion Channel Profiling

v Molecular Profiling

v Neuron types

v Neurons Densities

v Caveats

v Summary
Combining profiles

1. Electrical profile
2. Morphological profile
3. Molecular Profile

eProfile gProfile
eP1 gP1
eP2 gP2
eP3 gP3
eP4 gP4
… …
… …
… …
… …
Combining profiles
 Ion Channels – Correlating profiles

eProfile

gProfile
A Linear Operator
Ion Channels – predict electrical features
Determinants of Electrical Properties

Location of each ion

channel
Combination of Ion Channel genes
switched on in a cell
Kinetics of each ion channel

Toledo et al., 2004

Ion Channels – Combination Determines Behavior

1. Combination
2. Distribution
3. Kinetics
4. Densities
Molecular Profiles: Molecular Diversity
Profiles: combining three profiles
Structure of the lecture

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Ion Channel Profiling

v Molecular Profiling

v Neuron types

v Neurons Densities

v Caveats

v Summary
Neuron Types

v Dimensions of the Identity of Neurons

How to name a neuron? v Location in the brain

v Local Morphology (dendritic & axonal)

v Electrical property
Location_Morph_Elect_Mol_Gen_Proj
v Molecular profile

v Gene expression

v Projection Profile
Ion Channel Profiling

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Ion Channel Profiling

v Molecular Profiling

v Neuron types

v Neurons Densities

v Caveats

v Summary
Neuron Densities
Volume, Density, Composition

Block staining
Validation
Putting all the neurons together
Validation
Structure of the Lecture

v Single Neuron Data

v Studying Single Neurons

v Morphology Profiling

v Electrophysiology Profiling

v Ion Channel Profiling

v Molecular Profiling

v Neuron types

v Neurons Densities

v Caveats

v Summary
Caveats

v Biological Data is naturally

noisy

v Experimental Data can have

many mistakes

v Classification schemes for

morphological and electrical
types are still not definitive
Summary

Summary:
v Different ion channel genes generate ion
channels with different kinetics

v Electrical property of neurons is

determined by;
v Kinetics of each ion channel
v Combination of ion channels
v Location of ion channels
v Relative conductance of each ion
channel

v If you know the ion channel genes

expressed in a neuron you an calculate
the electrical properties

v How to obtain the density of neurons