Methods in Neuroscience Flashcards
what questions can we ask?
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?
List some methods
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.
Who is Santiago Ramon y Cajal?
father of modern day neuroscience
Lesion methods
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).
What is a lesion?
is removal of tissue but can be done in different ways
Lesion studies
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.
What shouldn’t be forgotten?
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
Animal lesion studies
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
Animal lesion models
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
Methodological limitation
correspondence between animals and humans may be low (e.g., right parietal lesions in monkeys does not produce hemi spatial neglect).
Animal lesion studies types
- high frequency radio pulse
- chemical lesions
- excitotoxic lesion
- reversible lesions
High frequency radio pulse
destroys everything.
Chemical lesions
targets specific neurotransmitters neurons.
Excitotoxic lesion
spares axons that are passing through area.
- think: head is lesion (sparing axons passing through)
Reversible lesions
anesthetic or cooling
- cooling a section of the brain
(neurons not firing as much - almost temporarily inactivating that area of the brain).
Reversible Lesions: Design Issues
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
Disadvantage of reversible lesions
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
Stereotaxic Surgery
- 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).
- BREGMA
the junction of the coronal and sagittal sutures (fontanel in infants, soft spot, young infant baby hasn’t fused yet)
Skull Sutures: Targets for Lesion or Electrode Placement
- Cut scalp of rat open so we are looking at the skill
- Use bregma as 0.00 point
- Lower an electrode so that the tip touches the edge of the skull
- We take a recording of that
- 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
- 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
Stereotaxic Atlas
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
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.
Lesion group
anesthesia
incision
lesion
suture and stitches
Sham group
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.
Stereotaxic surgery in humans.
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
Radial arm maze
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
Morris water maze
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
Bar pressing task: Effects of reinforcement…
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
Histology
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
Nissl stain
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.
myelin stain
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)
– Golgi stain
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.
Single cell neurophysiology
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.
Questions asked for single cell neurophsiology
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?
Naturally occurring lesion
no control on location, extent or cause
Name the two approaches to Human lesion models
- What function is supported by a given brain region?
- examine a group of individuals with similar lesions
- control group of patients with different lesions - 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
Double Dissociations
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).
Limitations of the lesion method
Variability in patients and lesions.
Examples of lesion variability from a study on extinction (left) and neglect (right).
Possible solutions to variability in patients and lesions:
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).
Limitations of the lesion method
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
Split-brains – disconnection syndrome.
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
Single-case vs. Group studies
Choice of single case vs. group studies depends on the nature of the brain damage and the question being asked:
Focal brain damage
e.g., from stroke, tumor, missile wound, etc.) is well suited to single case studies – no two patients are alike!
Systemic disease processes
e.g., degenerative diseases, psychiatric disorders, infections, etc.) are well suited to group studies – no two processes are alike?
Neurologically intact individuals
necessary control group.
normal functioning.
anatomical morphology (e.g., planum temporale reduced and ventricles increased in schizophrenia, hippocampal sclerosis in epilepsy, etc.).
Cognitive Psychology
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.
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.
E) All of the above are correct.
2 ) The _______ is a device used to implant an electrode or cannula into the brain.
A) stereotaxic apparatus
3 ) ______ refers to a skull landmark which also serves as a reference point for stereotaxic surgery.
C) Bregma
4 ) The ________ instrument is used to slice the brain into thin pieces for later examination.
A) microtome
5) Dyes such as cresyl violet are useful for staining
E) cell bodies
