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Measuring the Brain:
How We Learn About It
by Bill Trowbridge
for Future Salon, Boulder, CO 2013-02-09
• The evolution and anatomy of the brain, this organ that
operates on several different hierarchical scales (very
briefly, as background),
• The techniques and tools we use to measure the brain
from macro-scale: autopsy, fMRI imaging, micro-scale
firing neurons in-vivo using lasers, and more.
• Some recent papers/discoveries to discuss as time
permits.
• Information and images are used for
educational purposes according to Copyright
Act of 1976, section 107.
• References to sources are in the notes of the
slideshow.
Anatomy
• Quick review
– Body
– Central Nervous System
– Neurons
– Synapses
– Molecular Mechanisms
Spinal Cord
Cross Section
Embryonic development
early – 4 week – 6 week
Cortical Column
6 layers
Rat: ~10K neurons
and ~ 100,000 columns
Human: ~100K neurons
and 2 millions columns
Cellular Level
• Neurons
• Glial cells
• Blood Supply
"there are as many as 10,000 specific types of neurons in the human brain"
Synapse
• Chemical synapse (common)
• Gap synapse (rarer, faster)
directly connects cytoplasm
Synaptic
Vesicle
electron
microscope
image
Transport (Mitochondrial)
Neurotransmitters
• acetycholine (neuromuscular: nicotinic receptor;
autonomic/parasympathetic nervous system: muscarinic; central
nervous system);
• the catecholamines:
– Dopamine,
– norepinephrine (noradrenaline),
– epinephrine (adrenaline);
Used in central nervous system & in autonomic/sympathetic nervous
system for smooth muscle & organs, alpha & beta receptors
tyrosine --> dopa --> dopamine --> norepinephrine --> epinephrine
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serotonin;
GABA (gamma-aminobutyric acid) (inhibitory);
glutamate (exitatory)
many more
Neurotransmitters
• Neurotransmitters broken down, or removed by re-uptake pumps.
• Many drugs are receptor blockers (i.e. beta blockers: propranolol, etc.)
• SSRIs (Selective Serotonin Reuptake Inhibitors) anti-depressants Zoloft,
Lexipro, Prozac.
• Ligand gated ion channels: Sodium channels, yields instant voltage change.
• Ligand Gated Ion Channel Second Messenger Activation: enables gradual
metabolic changes (activates/inactivates enzyme), complex
• Adenylyl Cyclase, ATP --> cAMP e.g. neurotransmitter can activate adenylyl
cyclase to convert ATP (energy source) to cyclic AMP (cAMP).
• phosphodiesterase (PDE) breaks down cAMP to 5'AMP, caffeine inhibits
PDE, thus increasing cAMP levels.
• Sodium(out)/potassium(in) ATPase pumps -- always running -- create
sodium gradient == capacitor
• Used to transport other molecules: e.g. glucose, tyrosine, amino acids
Evolution
• Neurotransmitters (some in single-cell organisms)
• Synapses (Protosynapse in unicellular organisms.
Even yeast have ~20% of signaling complex
proteins, used for regulating cell response to
environment. Post-synaptic density in sensory
cells of early multi-cellular animals.)
• Nerves and muscles (all animals but sponges)
• Spinal cord (vertebrates)
• “Mammal brain” (more emotions, behaviors)
• Highly expanded cortex (primates, humans)
Common Animal Models
• Nematode roundworm
(Caenorhabditis elegans)
• Fruit Fly (Drosophila melanogaster)
• Zebrafish
• Mouse
• Rat
• Cat
• Rhesus Monkey (Rhesus Macaque)
Measurement -- Early
• Surgery (animal, cadaver)
• Brain Damage (lesions)
H.M. lost hippocampus, amygdala, entorhinal & perirhinal cortices on both sides
Phineas Gage, mining accident, rod through frontal cortex & eye
• Microscope (w/stains) (Golgi)
• X-Rays (skull, not brain)
Measurement – Then and Now
• EEG (electroencephalography)
voltage sensors on scalp, measuring brain
• EMG (electromyography)
measures electrical activity of muscles
• Drug studies
• Behavioral tests
NIH Toolbox
www.nihtoolbox.org
“to help scientists measure the ways we think, move, feel and sense the world is ready for
use in studies assessing neurological and behavioral outcomes” (2 hrs)
http://nihrecord.od.nih.gov/newsletters/2012/10_26_2012/story8.htm
Measurement
• Nerve Tracing (started with tetanus &/or rabies virus/toxin)
• Microelectrodes (inserted in single neurons)
• Genetics
– Knockout genes ( story: proprioception, diptheria toxin story )
(http://www.youtube.com/watch?v=B1uO_d3hi5w )
• Microscopy
– Light, Electron
– Confocal (optical sectioning, 3d reconstruction,
one-photon, two-photon(multi-photon), multi-pinhole
spinning disk )
– … & many more
Measurement -- Imaging
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CAT (Computerized Axial Tomography)
PET (Positron Emission Tomography)
SPECT (Single-Photon Emission-Computed Tomography)
MRI (Magnetic Resonance Imaging)
fMRI (functional MRI)
DSI (Diffusion Spectrum Imaging)
ICE (Intra-Cranial Electrophysiology)
CAT (Computerized Axial Tomography)
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3-D structural image of brain
Invented 1972 by Hounsfield & Cormack
They got 1979 Nobel for that.
Basically: X-ray + computer-imaging
Find tumors, clots, fractures, cysts, infections.
Useful for trauma, osteoporosis, lung cancer.
Cannot precisely capture movement (heartbeat)
Note: Combined PET/CT machines are available.
CAT
PET (Positron Emission Tomography)
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Invented 1973, Phelps at UCLA
Measures chemical function, level of activity
Has injection of radioactive tracing solution
Good to detect cancer, blocked/narrowed
vessels, detect source of epilepsy condition,
diagnose Alzheimer’s
• Slow. 1 min to capture image. Very expensive.
Radioactivity precludes frequent re-use.
PET
SPECT (Single-Photon Emission-Computed Tomography)
• 1970s
• Cheaper than PET, less detail.
• Detects absorption of radionuclides into tissue
and can distinguish between healthy and
diseased.
• Similar strengths, weaknesses as PET.
SPECT
MRI (Magnetic Resonance Imaging)
• (1980s) Provides 3-D Structural Image
• Measures “rebound” of magnetized spinning
protons, typically in H2O, but tunable to other.
• 1991 Kwong & Belliveau – “moving” picture
• Safe. Multipurpose: structure, blood O2,
diffusion, perfusion, spectroscopy. High
resolution (higher as magnet Teslas increase)
• Expensive. Loud. Cannot be used for patients
with certain metallic implants.(old pacemaker)
MRI
fMRI (functional MRI)
• Early 1990s, Ogawa noticed that oxygenated
and de-oxygenated blood were affected
differently, allowing mapping brain activity.
• BOLD == blood-oxygen-level-dependent signal
• To ~1mm resolution. 2-6 sec time resolution.
• Can only measure O2 use of populations of
neurons, not even close to single neurons.
fMRI
fMRI
Math
technique to
inflate and
flatten image,
so that patients
are comparable
on a coordinate
system.
(warp-align)
DSI (Diffusion Spectrum Imaging)
• Measures the direction of the structures (i.e.
axons), by determining the direction the water
molecules can move.
• Reveals the nerve tracts in the brain.
DSI (Diffusion Spectrum Imaging)
(tractography, color-coded direction)
Long Distance Brain Network Macaque PNAS
ICE (Intra-Cranial Electrophysiology)
• Similar to EEG
• But, only for brain-surgery patients
(with consent).
• Electrodes are placed directly on brain during
the surgery.
• Very high temporal and spatial resolution.
• Up to 20,000 samples per second.
ICE
Other Imaging Techniques
• Optical Tomography – Forms image using
scattered light thru translucent structures.
• PEPSI (Proton Echo-Planar Spectroscopic Imaging)
– Trace activities of specific brain chemicals in
real time. 32 times faster than fMRI.
• MEG (Magnetoencephalography) Records
magnetic field produced by actively firing
neurons. Can follow the exact time sequence of
firing events.
Optical
Tomography
PEPSI
MEG
Fluorescent Proteins w/Microscopy
• GFP (Green Fluorescent Protein) used in:
– 30,000 published articles
– 65% of articles in major cell bio journals
• FRAP (florescence recovery after photo-bleaching)
• FRET (Förster resonance energy transfer) Detect energy
transfer between nearby fluorescent chromophores,
<10 nm, uses: measure distance and detect molecular
interactions, measure distances between domains of a
single protein to confirm conformation.
• Also, Optogenetics
• BrainBow (on next slide)
Projects
• Human Connectome Project
http://www.humanconnectomeproject.org/about/
• NIH Blueprint for Neuroscience Research
http://www.neuroscienceblueprint.nih.gov/
• Human Brain Project (Blue Brain Project is a partner)
Long term goal: Simulate complete human brain http://www.humanbrainproject.eu/
To date: studies of neuron morphological and electrical types and on the cortical column, and
simulation of rat corical column.
• Whole Brain Project http://www.wholebrainproject.org/
(open source Mouse: http://www.wholebraincatalog.org/ )
Local -- Colorado
• BioFrontiers Advanced Imaging Resource
Brain Studies\Downloaded\Home — BioFrontiers.mht
http://cimb.colorado.edu/core-facilities/microscopy-core
Studies/Papers
• Light-Gated Glutamate Receptor
http://www.cup.uni-muenchen.de/oc/trauner/Publication/71.pdf
• See additional downloaded links