Methods in Neuroscience

Question 1

what questions can we ask?

Answer 1

Santiago Ramon y Cajal said we can ask how but not why questions.

But how questions can be asked on many different levels.

Cellular – how do neurons communicate?

Anatomical – how are different areas interconnected (cytoarchitectonics)?

Functional – how do certain areas mediate certain behaviors?
- How do we know occipital cortex plays big role in vision?

Systemic – how do disease processes affect brain function?
- What does Parkinson do, Alzheimer’s do?

Question 2

List some methods

Answer 2

Cellular – histology and staining.
- Ways to prepare tissue so they can be seen under microscope

Anatomical – autopsy of healthy and diseased brains.

Functional methods; human (natural/rarely induced - stroke, bullet wound, car accident etc.) and animal (induced - specific areas) brain lesions.

neural stimulation – animal studies (single units) and human studies (disruption to networks – TMS).
- TMS = transcranial magnetic stimulation - way of temporary lesioning or existing cells

Systemic – neuroimaging – the brain in action.

Question 3

Who is Santiago Ramon y Cajal?

Answer 3

father of modern day neuroscience

Question 4

Lesion methods

Answer 4

removal of tissue (ablation), radio frequency lesions, chemical lesions(can target certain transmitters), reversible chemical lesions, cooling(reversible, can use animal as own control subject).

Question 5

What is a lesion?

Answer 5

is removal of tissue but can be done in different ways

Question 6

Lesion studies

Answer 6

Assume that if cognition X is disrupted by a lesion to a brain area Y then region Y “supports” function X.

If an area of the brain like occipital cortex if lesioning it affects vision then then that area is linked to vision

Modular concept of brain organization – a place for everything and everything in its place.

Question 7

What shouldn’t be forgotten?

Answer 7

Shouldn’t forget that many functions are highly distributed throughout the brain!

Damaging a particular area may affcet behaviour but doesn’t mean only that area is involved in that behviour a network could be involved

Question 8

Animal lesion studies

Answer 8

experimental ablation.(removal of tissue)

caution in interpretation – change in behavior after a lesion could be due to many things:

a) the loss of function supported by that particular region.
b) the loss of a sub-component necessary for the behavior caused by disruption to the network.

c) co-existing behavioural changes unrelated to the particular region.
- Stress of surgery or something else

Question 9

Animal lesion models

Answer 9

Lesions may also change behaviour (adaptation to the deficit).

Monkeys deprived of sensory feedback to one limb will favour use of the other limb.

When deprived of sensory feedback to both limbs they will not favour one over the other.

• haven’t knocked out the ability for that monkey to use that limb, but it’s had a preference now for using the other limb
• but if you knock out sensory feedback, it uses both

Question 10

Methodological limitation

Answer 10

correspondence between animals and humans may be low (e.g., right parietal lesions in monkeys does not produce hemi spatial neglect).

Question 11

Animal lesion studies types

Answer 11

• high frequency radio pulse
• chemical lesions
• excitotoxic lesion
• reversible lesions

Question 12

High frequency radio pulse

Answer 12

destroys everything.

Question 13

Chemical lesions

Answer 13

targets specific neurotransmitters neurons.

Question 14

Excitotoxic lesion

Answer 14

spares axons that are passing through area.

- think: head is lesion (sparing axons passing through)

Question 15

Reversible lesions

Answer 15

anesthetic or cooling
- cooling a section of the brain
(neurons not firing as much - almost temporarily inactivating that area of the brain).

Question 16

Reversible Lesions: Design Issues

Answer 16

Within-subjects designs

test with the lesion and without

increased statistical power

Subject is testing as its own control

Test same animal with brain cool and brain normal

Question 17

Disadvantage of reversible lesions

Answer 17

don’t euthanize the animal, stain the brain, and determine that the lesion was in the desired location.
- hard to know if you hit the right area

Question 18

Stereotaxic Surgery

Answer 18

• helmet like mount on a person’s shaved head
• purpose: so surgeon can use a map of the brain to know where they’re doing the implantation
• use a particular seam in the skull (a SUTURE) as a landmark.
• BREGMA - the junction of the coronal and sagittal sutures (fontanel in infants).

Question 19

• BREGMA

Answer 19

the junction of the coronal and sagittal sutures (fontanel in infants, soft spot, young infant baby hasn’t fused yet)

Question 20

Skull Sutures: Targets for Lesion or Electrode Placement

Answer 20

1. Cut scalp of rat open so we are looking at the skill
2. Use bregma as 0.00 point
3. Lower an electrode so that the tip touches the edge of the skull
4. We take a recording of that
5. If we use that as our 0 point, we can then use a map/altus of the brain to figure out how far down/left or right, forward or back etc. we have to go to hit the area we want to hit
6. Have to figure out where to drill the hole & how far down do we have to send it in order to target that specific area of interest

Question 21

Stereotaxic Atlas

Answer 21

like goggle maps of brain
Breaks brain down into diff quadrant

So you can figure out how to adjust stereotaxic device to leison the areas your testing

Answer 22

Rats are anesthetized, place the rat so that ear bars go into ears and tightly lock the skull into position, bite bar is put Infront of front teeth so that skull is in position, make sure its in level, holes are drilled and the tip of the electrode is sunk down to the level specified in the stereotaxic atlas.

Current is turned on, ablating the structure.

Rat is sutured and is tested after a couple of days.

Question 23

Lesion group

Answer 23

anesthesia
incision
lesion
suture and stitches

Question 24

Sham group

Answer 24

anesthesia
incision
sutures and stitches
Note the incision in the sham group includes lowering the electrode or cannula to the appropriate depth.
control animals must undergo all aspects of the lesion study except the lesion itself.

Question 25

Stereotaxic surgery in humans.

Answer 25

Take skull

screwing devices into skull

Align skull so its in the same posiiton as in the atlas so you can use the atlas to figue out where to go

Question 26

Radial arm maze

Answer 26

Remembering places visited.

-good for spatial memory learning of roots

Animal will learn to go only down the wells with only food

Always have the same wells with food then mouse will always go same

Will ignore the wells with no food but at first will go to all of them but after a while will make a map

After you perform surgery you can see if animal still uses that map or runs down arms that never ahd food bc it got confused

Question 27

Morris water maze

Answer 27

Spatial orientation and spatial memory…
Tub with water in it

Hide a platform with pexiglass platform that cant be seen

And rat would be placed inside this water maze

Would bump and find platform

Would get very good at finding the platform not bc they are always put in the same location but bc they use the room cues- create a spatial map

Then do a surgery and see of behaviour is affected

Neocortical control lesion- doesn;’t affect they find their way to the platform

Hippocampal lesion- animal is swimming around until they find platform

Trail 9- rat has learned spatial layout of room and swims right to platform

Question 28

Bar pressing task: Effects of reinforcement…

Answer 28

For learning

Animal press on bar to stp electric shock or reward

Problem; Animal was having pleasure zone stimulated and when they lesioned the zone they stopped pressing the bar so scientists thought oh we found the zone

Another group of scientsits had holes and animal had to stick its nose thru the hole and even after the lesion the animal would still stick its nose thru the hole

Question 29

Histology

Answer 29

licing and staining the brain

to determine if lesions were made in the correct location (or that the appropriate cells were targeted) the brain is fixed, sliced and stained.

1st process is fixing the brain

Destroy autolytic enzymes that will turn the deceased brain into mush.

Place the brain in a fixative, formalin- Add fermeldahyde
halts autolysis
kills micro-organisms
hardens the fragile brain

Perfusion: draining the blood and replacing it with another fluid.

Then freeze the brain

And slice it using a microtome- sharp razor blade that makes thin sections of the brain

Question 30

Nissl stain

Answer 30

tissue section is placed in various chemical solutions to highlight specific details.

Nissl (German neurologist) stain – highlights cell bodies – assumption is if the lesion was in the right place the cell count should be low.

methylene blue or cresyl violet.

shows off the different layers of the cortex.

shows off nuclei.

Question 31

myelin stain

Answer 31

specifically stains myelin.

not too useful for tracing pathways in any detail.

Just shows everything as black (black shows myelin connection, not useful for looking at cell bodies)

Question 32

– Golgi stain

Answer 32

shows up the neuron in great detail including dendritic branches.

for reasons unknown it only stains a small number of cells at a time making easy to examine them in detail.

Question 33

Single cell neurophysiology

Answer 33

Looking at how cells respond to particular stimuli

Electrode in monkeys brain that’s recording from neuron, train the monkey to only stare and fixation point not supposed to move eyes from point then put white bar on screen if they keep eyes at fixation point the bar falls in receptive field(area of space that cell is tuned for) they are recording in

record response of single neuron (or multiple neurons) to specific tasks.

can also stimulate one neuron and examine the effect of stimulation on a neuron in a different brain region.

Question 34

Questions asked for single cell neurophsiology

Answer 34

do single cell responses reflect what happens at the population level?

to what extent are human and monkey brains alike?

high degree of training required for the monkey to perform a given task – ecological validity?

Question 35

Naturally occurring lesion

Answer 35

no control on location, extent or cause

Question 36

Name the two approaches to Human lesion models

Answer 36

1. What function is supported by a given brain region?
   - examine a group of individuals with similar lesions
   - control group of patients with different lesions
2. What brain regions support a given cognitive function?
   - examine a group of individuals with similar cognitive impairment
   - can then examine the brain regions common to this deficit

Question 37

Double Dissociations

Answer 37

Patient with damage to area X is impaired for cognition A but not cognition B.

Patient with damage to area Y is impaired for cognition B but not cognition A.

e.g., lesion to Broca’s area (X) impairs speech production (A) but not comprehension (B).

Question 38

Limitations of the lesion method

Answer 38

Variability in patients and lesions.

Examples of lesion variability from a study on extinction (left) and neglect (right).

Question 39

Possible solutions to variability in patients and lesions:

Answer 39

group studies can control for age, IQ, handedness etc.

compare a group of patients with different lesions (assumptions made about the region of overlap for the ‘critical’ lesion).

Question 40

Limitations of the lesion method

Answer 40

Must infer the functions of the damaged region from observed impairments.

Can determine if region X is “critical” for cognition A? (i.e., does the lesion disrupt the cognition?)

But other brain regions may also be critical (i.e., area X may be necessary but not sufficient for cognition A).

Disconnections – area X may not participate directly in cognition A but may disconnect two critical brain regions that are critical for cognition A.

More than one way to skin a cat! Cognition A could be performed by multiple brain regio

Question 41

Split-brains – disconnection syndrome.

Answer 41

Severing the white matter fibres of the corpus collosum leads to certain cognitive impairments.

But it’s not the corpus collosum that carries out these functions!

• picking out outfit with right hand left hand is stopping you

Question 42

Single-case vs. Group studies

Answer 42

Choice of single case vs. group studies depends on the nature of the brain damage and the question being asked:

Question 43

Focal brain damage

Answer 43

e.g., from stroke, tumor, missile wound, etc.) is well suited to single case studies – no two patients are alike!

Question 44

Systemic disease processes

Answer 44

e.g., degenerative diseases, psychiatric disorders, infections, etc.) are well suited to group studies – no two processes are alike?

Question 45

Neurologically intact individuals

Answer 45

necessary control group.

normal functioning.

anatomical morphology (e.g., planum temporale reduced and ventricles increased in schizophrenia, hippocampal sclerosis in epilepsy, etc.).

Question 46

Cognitive Psychology

Answer 46

reaction time – mental chronometry

accuracy

mental operations – (e.g., visually process letter, match to template, make category decision, execute action).

parallel vs. serial processing

exploring the limits on information processing (e.g., capacity limits, automatic vs. controlled processes, etc.).

RED- your brain has hard time saying its red bc it green

Cognitive psychology helps determine the processes involved in a given cognition, the limits to information processing (i.e., boundary conditions) and the normal patterns of performance.

Question 47

1 ) An advantage of a reversible lesion is that

A) axons of passage are not affected by reversible procedures

B) each animal can serve as its own control

C) cell bodies are not affected by reversible procedures

D) such lesions affect brain tissue near the tip of the lesion device

E) All of the above are correct.

Answer 47

E) All of the above are correct.

Question 48

2 ) The _______ is a device used to implant an electrode or cannula into the brain.

Answer 48

A) stereotaxic apparatus

Question 49

3 ) ______ refers to a skull landmark which also serves as a reference point for stereotaxic surgery.

Answer 49

C) Bregma

Question 50

4 ) The ________ instrument is used to slice the brain into thin pieces for later examination.

Answer 50

A) microtome

Question 51

5) Dyes such as cresyl violet are useful for staining

Answer 51

E) cell bodies