Methods in brain research 1.Structure a. Morphology b. Pathways 2. Function

1.Sacrificing the animal / or post-mortem studies 2.Replace the blood with saline (physiologic water) 3.Fixation – injection of formaline Dissection

Grey matter White matter frontal section horizontal section ventricles Thalamus

Nissl stain Staining of cell bodies Histology

Staining of axon fibers Hard to see individual cells

Golgi stain Individual cells

Microscopy 1.Light (up to x1500 magnification) 2.Electron Microscopy (EM; magnification of ~10 8 in tissue slices) 1.Transmission EM (high resolution 2d information) 2.Scanning EM – lower resolution but provides 3d information 3. Confocal microscopy – Uses laser and fluorescent dyes. Higher resolution than light microscopy Thicker slices (3d) in living tissue

Neural pathways Anterograde labeling – chemicals that enter the cells (through dendrites), and travel along the axons to the terminal buttons 1.Injection of PHA-L 2.Substance is transported throughout the cell 3.Animal is sacrificed and brain is perfused 4.Histology – PHA-L is made visible through use of immunocytochemical methods

Autoradiography – using radioactive markers for labeling

Retrograde labeling – chemicals that enter the terminal buttons, and travel through the axons to the cell bodies

Auditory pathway Tracer in the thalamus

Imaging techniques to study structure Computerized Tomography (CT) Magnetic Resonance Imaging (MRI)

Computed Tomography

X ray

Computed Tomography X ray

Brain damage Stroke Hemorrhage

Computed Tomography X ray Advantages of CT Accessible (and cheap) Efficient in detecting Stroke Hemorrhages Tumors Uses X-Ray No separation between white/grey matter Can only take horizontal sections Drawbacks of CT

Good spatial resolution (~1mm) Separation between grey/white matter Magnetic Resonance Imaging Very strong magnetic field. Earth is ~0.5 Gauss 10,000 Gauss is 1 Tesla Typical scanner today has a magnetic field of 3 Tesla

Magnetic resonance angiography (MRA)

04-12a Measuring proton density (from water molecules) with MRI

Advantages: Non-invasive (and can be used in the living brain) High spatial resolution (~1mm) Safe (Does not damage tissue)

Diffusion Tensor Imaging (DTI) Can NOT tell from _X_ to_Y_ - but gives the general direction of the fibers

Tools to study brain function 1.Manipulating brain function (e.g. by lesions) and inferring a region’s role in behavior/cognition 2.Manipulating behavior and measuring changes in brain activity

Naturally occurring lesions (stroke) or accidents (e.g. gun wounds etc.) Broca

Phineas Gage’s lesion reconstructed (H. Damasio and R. Frank, 1992)

Experimental ablation (removal of brain tissue)

1.Suction of brain tissue 2.Destruction of brain tissue Electrically (general) Chemically (more specific) for example – use of kianic acid to over-excite cells until they die 3. Temporary lesions (cooling)

Recording of electrical activity / electrical stimulation of brain tissue Spike trains

Free recall demo for hippocampal re-activation Gelbard-Sagiv, Mukamel, Harel, Malach & Fried. Science 2008

Quiroga, Mukamel, Isham, Malach & Fried. PNAS 2008

Positron emission tomography (PET) – Enables tracking metabolic processes in various brain regions Involves injection of a radio-active tracer Enables scanning in multiple planes

1.Seeing words 2.Listening to words 3.Saying words 4.Generating verbs PET-Positron Emission tomography

Functional Magnetic Resonance Imaging

What does the BOLD fMRI signal measure? Hemoglobin has two states: Oxygenated (diamagnetic), and De-Oxygenated (paramagnetic) The BOLD fMRI signal is sensitive to the ratio between Oxy and De- oxy hemoglobin in a manner that an increase in Oxygenated blood results in an increase in the fMRI signal.

Following neural activation: Consumption of oxygen Overcompensation with fresh oxygenated blood fMRI signal

Advantages of fMRI over PET Higher temporal resolution (seconds vs min) No radioactive radiation cheaper