New Imaging Techniques 2 Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

What is clarity

A

Methodology that removes the opaque elements of the brain (absorb or scatter light) to make them translucent and use microscopy to look at the brain in 3D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Why was clarity invented

A

The brain is extremely opaque - a lump of fatty tissue which light is poorly penetrated and scattered. This makes it difficult to understand what is going on inside

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the benefits of clarity

A

Able to label lots of molecules in the whole brain
Trace cells through a forest of other cells
Dont have to slice the brain to look at sections

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Where else is clarity used

A

Can be used on any organs or embryos - extremely clear (like glass)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

How does clarity work

A

The lipid bilayer of each brain cell of obscures the view.
This cannot be removed without replacing its structure therefore it is placed with a hydrogel mesh (not binding to fats so can be removed) then the lipid bilayer is removed with sodium dodecyl sulfate (SDS) gel.
It is transparent to light now however markers can be added to specific molecules to look at various features or follow a specific cell.

Takes 8 days

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What did the study on fear and pleasure circuits show of mice with clarity

A

Mice given cocaine, or electric shocks + Clarity + dyes to highlight cells that fired

shows which networks of neurons corresponded to pleasure, or to fear

both emotions are laid down in the medial prefrontal cortex

but stored along different pathways or axonal projections

And they are connected to different regions in the brain – better understanding of the localisation of these emotions

Increasing the likelihood of more targeted treatments for psychiatric disease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is algebraic topology

A

A mathematical model of helping us ask the big questions -
How do we make a decision?
What and where is consciousness?
Can we image these things happening?

It answers these by analysing the neural networks and their firing patterns.

Essentially, it is translating the chaotic brain activty to something we can interpret and understand.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What did algebraic topology find regarding brain structure

A

Mutli-dimensional geometrical structures and spaces within brain networks - allowing us to look at a large picture in very fine detail.
This detail is made up by recording the communication between the neurons and and buidling up a stucture of cliques (families of neurons)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the order of formation (decision making) regarding the brain structure with algebraic topology

A

Rods (1D) –> Planks (2D) –> cubes (3D) –> complex gemoetries (4D and 5D) –> disintegration

They believe this is how decisions are made

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

How may these algebraic build-up patterns be used therapeutically

A

Brain damaged - implant these decision making structures to allow them to make informed decisions again

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Why is formaldehyde used in CLARITY preparation

EXTRA READING - Geaghan-Breiner C (2013)

A

can facilitate attachment of the scaffolding to the proteins and nucleic acids that are to be preserved

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Why is heated needed for clarity

EXTRA READING - Geaghan-Breiner C (2013)

A

heat is necessary to establish the actual linkages between the cellular components and the acrylamide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How does the detergent remove the lipid bilayer

EXTRA READING - Geaghan-Breiner C (2013)

A

Passive diffusion with detergent
OR
Accelerated with electropheresis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is a limit of CLARITY

EXTRA READING - Shen, Helen (2013).

A

The immunohistochemical staining takes 6 weeks to perform

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Why is detergent eelctrophoeresis unpopular

EXTRA READING - Shen, Helen (2013).

A

Causes 8% protein loss

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How is algebraic topology transfered into neural connections

EXTRA READING - Reimann 2017

A

neurons as the vertices (dots) and the synaptic connections directed from pre- to postsynaptic neurons as the edges (lines), which can be analyzed using elementary tools from algebraic topology

17
Q

How does a clique determine its dimension in algebraic topology

EXTRA READING - Reimann 2017

A

The number of neurons in a clique determines its size, or more formally, its dimension.

18
Q

What are cavities in algebraic topology and what do they show

EXTRA READING - Reimann 2017

A

When cliques share neurons this means no more geometric dimensions form leaving “holes” or cavities.

19
Q

What do cliques show

EXTRA READING - Reimann 2017

A

Local networking

20
Q

What do cavities show

EXTRA READING - Reimann 2017

A

Global networking