Cognitive Neuroscience Chapter 3 Methods of Cognitive Neuroscience.
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What can we measure:An experimentalist’s
perspective
Mathematical Neuroscience conference
Theoden Netoff
Assistant Professor of Biomedical Engineering
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Brain Signals that can be recorded
• Electrical• Chemical• Magnetic• Response to magnetic pulses• Changes in blood flow• Metabolic changes in cells
– Glucose consumption– Oxidative state of NADP
• Scattering properties• X-ray absorption• How Sound waves pass through the brain• Gene expression
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Multiple scales neurophysiology
homepage.mac.com/dtrapp/eChem.f/labB3.html
Ion Channels
Cells
Networks Cortex
Point mutationsUpregulationModulation
Dendritic morpohology
Mossy fiber tract sproutingChanges in stim response
Pathalogical EEG
Ramon y Cajal
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Lesions:
Pros:• Directly relates
brain area to behavior
Cons:• Mostly case
studies• Cannot be
repeated
What is the signal:• Functional loss following an injury
• Wallarian degeneration used to track pathways
Harlow 1868
Phineas Gage
Natural History Museum, Lausanne
3500 BC, Iron age Trepanation
neuraldump.com/2007/09/patient-hm.html
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The canonical neuron
• Soma• Dendrites: Inputs• Axon: Outputs
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Patch clamp recording:
Pros:• Very high fidelity
recording• Neuron can be
identified morphologically by staining
• Neuron can be stimulated
Cons:• Limited
number of cells that can be recorded
• Cell type cannot be definitively determined physiologically
What is the signal:• Glass tube filled with salt solution applied to
neuron to make low noise junction with neuron
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Electrode-Cell circuit
Axon Guide
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Patch clamp recording
Hamill et al., 1981
Single channel recording
Sakmann and Neher, 1984
http://butler.cc.tut.fi/~malmivuo/bem/bembook/04/04.htm
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Sodium and potassium channels
http://butler.cc.tut.fi/~malmivuo/bem/bembook/04/04.htmHille, 1992
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Whole cell recording
Hasselmo et al, J. Neurophysiol 2000
The “Sag” current
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Intracellular and local field potentials
Netoff and Schiff, 2002
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Local field recordings:
Pros:• Multiple cells
can be recorded at once
• Can be done in vivo
Cons:• Cell that is
being recorded cannot be positively identified
What is the signal:
• Electrode placed into the brain to record electric fields
www.berkelab.org/Techniques.html
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Tetrode Neural recordings
Slide courtesy of Adam Johnson and David Redish
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Place cells
O’Keefe, 1978
Kneirim et al., 1995 Slide courtesy of Adam Johnson and David Redish
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EEG signal source:Dendritic currents
• Apical dendrite acts as a dipole
• Dendritic currents, not action potentials, summate best
• Electrical signal is strongly attenuated at the scalp.
• Inhibitory neuron populations do not produce good dipoles
http://www.biosemi.com/pin_electrode.htm
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EEG Signal confounds correlation and activity
• Populations of cells that are synchronous and have dendrites lined up produce strong signals
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Sensitivity of neuron depends on orientation to electric field
• Rushton, 1927:
-Excitability roughly proportional to the cosine of the ange between current and nerve.
Current perpendicular to the nerve cannot stimulate an action potential.
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Degree of asymmetry of neuron determines strength of response to electric field and the field it
produces
Chan and Nicholson, 1986
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Computed Tomograpy :3d X-ray reconstruction of the head
Pros:• High spatial
resolution• Non-invasive,
but does require X-rays
Cons:• Poor constrast
between tisses• Limited to
anatomical scans
www.csmc.edu/6158.html
What is the signal:• X-rays are projected through the head. The signal is
rotated around the head and a 3D reconstruction is formed with the aid of a computer.
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Magnetic Resonance Imaging :Interaction with tissue and magnetic field
Pros:• High spatial
resolution• Non-invasive• Good white/Gray
matter contrast
Cons:• Water signals do
not provide good temporal signals, but other signals can be measured
• Expensive to run
http://en.wikipedia.org/wiki/Image:MRI_head_saggital.jpg
What is the signal:• Hydrogen atoms are pumped to high energy state with
Electromagnetic wave. • Turn off EMF wave and measure time of relaxation to low
energy state• Strength of signal varies with water density. Gray matter
has higher water density than white matter• Frequency is different as field strength falls off allowing
for depth imaging
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Functional MRI:MRI of signals that change over time
Pros:• Medium spatial
resolution with depth• Non-invasive• Flexibility in signals
that can be measured• Can be laid directly
over an anatomical scan
Cons:• Slow temporal scale• Assumes relation of
activity to blood flow, but what causes increase in metabolism is not a unique set
• Expensive to runen.wikipedia.org/wiki/Positron_emission_tomography
What is the signal:• Changes in MR signal with time.• Depending on the RF pulse frequency, different
molecules can be imaged besides hydrogen.• BOLD- hemoglobin changes from paramagnetic to
diamagnetic when oxygenated
MRI Imaging signals:HemoglobinCholine
http://www.cem.msu.edu/~reusch/VirtTxtJml/Spectrpy/nmr/nmr1.htm
CreatineLactateN-acetlyaspartate
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Positron Emission Tomography:Sequestration of radioactive isotopes in tissue
Pros:• Medium spatial
resolution with depth
• Non-invasive• Flexibility in signals
that can be measured
Cons:• Only slow
metabolic activity can be imaged
• Exposure to radiation
• Very Expensive to run
en.wikipedia.org/wiki/Positron_emission_tomography
What is the signal:• Radioactive isotope of a molecule is developed using an
accelerator• A neurotransmitter or glucose are made with the isotope
and injected into the subject• The brain sequesters the radioactive molecules into
active spots where it makes hot spots of gamma • Using a scintillator material gamma radiation is converted
to light and imaged.
PET molecules:Fluorodeoxyglucose2-Deoxy glucoseWaterAmmoniaDopamineSeretonin
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Magnetoencephalography:Magnetic signals from the brain
Pros:• Non-invasive• Source localization
is done to estimate depth from signal
• Provides signals that cannot be measured in any other way
Cons:• Low spatial
resolution with respect to EEG
• Low signal to noise with respect to EEG
www.acoustics.org/press/153rd/hertrich.html
What is the signal:• Magnetic fields generated by electrical activity of the brain• SQUIDs detect magnetic signal
en.wikipedia.org/wiki/Magnetoencephalography
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Intrinsic Optical Imaging:Reflectance of the brain
Pros:• Does not require
dye• High spatial
resolution
Cons:• Signal not well
understood• Requires
exposing the brain
• Signal is slow and on the order of a metabolic signal
• Cannot be used to resolve single cells
Cerne and Haglund
Neuroscience Letters(2002)
What is the signal:• Infrared light is used to illuminate the tissue• CCD camera detects changes in brightness of tissue over
time• Caused by changes extracellular space volume
(scattered light) or by changes in blood flow to the area (absorbed light)
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Intrinsic Optical Imaging:Flavoprotein imaging
Pros:• Does not
require dye• High spatial
resolution
Cons:• Signals are of
metabolic processes, not limited to neuronal activity
• Slow, on order of metabolic demand
What is the signal:• Excitation light is used to illuminate brain tissue• Autofluorescent flavoproteins (such as NADH) change fluorescence with
oxidative state. This is a direct measurement of the metabolic process
Reinert et al, J Neurosci Research, 2007
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Non-invasive optical imaging:Optical reflectance and scattering
Pros:• Non-invasive
recording• Useful on children• Useful in MRI
where electrode leads can be difficult to deal with
Cons:• Very low resolution
spatially and low signal to noise ratio
• Signal, not very well understood
What is the stimulus:• Bright long wavelength light is shined onto the surface of the scalp
penetrating to the brain• Photo sensors detect reflected and scattered light• Signal changes caused by bloodflow or swelling of cells increasing
reflectance
http://rabi.nmr.mgh.harvard.edu/DOT/research/probe-gallery.htm
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Voltage dye imaging:Directly imaging membrane voltage
Pros:• Signal is very fast• Direct measure of
neuronal activity
Cons:• Voltage dyes stain
all membranes, neurons are only a small fraction
• To keep SNR high light must be very bright
• Cannot be used to image large numbers with single cell resolution
• Dyes can be toxic
What is the signal:• Membranes are stained with a fluorescent protein that indicates voltage
change
Zochowski, et al.
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Calcium dye imaging :Directly imaging membrane voltage
Pros:• Intracellular
measurement of activity
• Bath or intracellular application
• Very bright changes
Cons:• Slow• Indirect measure
of activity
What is the signal:• Cells stained with fluorescent dyes that indicate changes in intracellular
calcium concentration.
http://probes.invtrogen.com
Ikegaya et al, Neuroscience Research, 2005
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Calcium dyes:Bath applied AM dyes
Badea, et al. J. Neurobiol, 5;48(3):215-27 (2001)
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Multiple cell recordings using Calcium dyes
• Imaging population over time and parsing image up results in time series from multiple neurons
Cossart et al, Cell Calcium (2005)
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4-AP induced Seizure activity in CA1
DIC
100 μm
Str. Pyr Str. Ori
Str. Rad
Resting Fluorescence
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Calcium imaging of seizures in the hippocampus
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Ion sensitive electrodes
Pros:• Measure many
different signals:– Gasses:O2
– pH– Salts: K+, Na+,
Ca++
Cons:• Slow• Low spatial
resolution• Interference
across ion species
What is the signal:Ion selective exchange across membrane creates voltage. Membranes can be made of glass, crystal, resin or polymer. Enzyme electrodes
Potassium concentrations after stimulationGorji et al, Epilepsia, 2006
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Stimulating the brain
• Patch electrode:– can be used for
recording and stimulating
• Extracellular electrodes:– Playing back
measured signal is like playing a tape recording of planes taking off at the airport to make planes take off.
Walter Freeman
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Deep brain stimultion
http://www.sctimst.ac.in/hospital/neurology/movementdisorder.htm
mcrais.googlepages.com/implants.htm
en.wikipedia.org/wiki/Image:Parkinson_surgery.jpg
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Electroconvulsive therapy:Electric fields and the brain
Pros:• Non-invasive
stimulation• Used for
treating depression
Cons:• Not localized• Mechanism?
Inducing Seizures!
What is the stimulus:• Current is applied to the head to induce seizures
http://www.humanillnesses.com/Behavioral-Health-Br-Fe/Electroconvulsive-Therapy.html
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Transcranial magnetic stimulation:Magnetic fields and the brain
Pros:• Non-invasive
stimulation• Short duration• Some localization of
field• Used in place of
electroconvulsive therapy
Cons:• Localization is
poor (compared with an implanted electrode)
• Effects not well understood
What is the stimulus:• Short pulse of magnetic field induces small current flows in the brain.
www.princeton.edu/~napl/methods_h.htm
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Stimulating neurons: Caged compounds
Rothman et al, Epilepsy Research 74(2):201-209 (2007)Jin et al, J. Neuroscience 26(18):4891-4900 (2006)
Caged glutamate stimulation Caged GABA
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Closing the loop
• Dynamic clamp• Brain Machine/Computer Interface• Neurotransmitter uncaging• Photosensitive ion channels
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Dynamic clamp:Real time computer interfaced with a neuron
Pros:• Flexible system for
complex protocols• Simulation of ion
channels• Simulation of
synapses• Simulation of
neurons to make “hybrid” networks
Cons:• Limited number
of channels
What is the stimulus:• Voltage measurement can be used to calculate current to inject
Vm
Iapp
Iapp
Vm
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Phase Response Curve
500 1000 1500 2000 2500 3000 3500 4000 4500 5000-50
-40
-30
-20
-10
0
10
mV
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50.6
0.65
0.7
0.75
0.8
0.85
sec
nA
T
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Phase Response Curve
500 1000 1500 2000 2500 3000 3500 4000 4500 5000-50
-40
-30
-20
-10
0
10
mV
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50.6
0.65
0.7
0.75
0.8
0.85
sec
nA
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Phase Response Curve
500 1000 1500 2000 2500 3000 3500 4000 4500 5000-50
-40
-30
-20
-10
0
10
mV
0 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.50.6
0.65
0.7
0.75
0.8
0.85
sec
nA
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Phase Response Curve
Stimulus time (since last spike)
Per
turb
atio
n fr
om p
erio
d
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Optical stimulation:Real time computer interfaced with a neuron
Pros:• Single cell
resolution of 100s of cells
• Millisecond time scale
Cons:• Requires
genetic alteration of cells
What is the stimulus:Channel rhodposin-2 a light sensitive cation channel activated by yellow light
Boyden et al, Nature Neuroscience (2005)
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Inhibiting neurons
• Light driven chloride pump
• Genetically spliced to cell type specific promoter
• Shining light hyperpolarizes the cell with msec time constants
• Single action potentials can be inhibited.
Han and Boyden, PLoS ONE, 2007
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Summary
Churchland and Sejnowski, 1988