New Imaging Techniques 2 Flashcards
What is clarity
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
Why was clarity invented
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
What are the benefits of clarity
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
Where else is clarity used
Can be used on any organs or embryos - extremely clear (like glass)
How does clarity work
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
What did the study on fear and pleasure circuits show of mice with clarity
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
What is algebraic topology
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.
What did algebraic topology find regarding brain structure
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)
What is the order of formation (decision making) regarding the brain structure with algebraic topology
Rods (1D) –> Planks (2D) –> cubes (3D) –> complex gemoetries (4D and 5D) –> disintegration
They believe this is how decisions are made
How may these algebraic build-up patterns be used therapeutically
Brain damaged - implant these decision making structures to allow them to make informed decisions again
Why is formaldehyde used in CLARITY preparation
EXTRA READING - Geaghan-Breiner C (2013)
can facilitate attachment of the scaffolding to the proteins and nucleic acids that are to be preserved
Why is heated needed for clarity
EXTRA READING - Geaghan-Breiner C (2013)
heat is necessary to establish the actual linkages between the cellular components and the acrylamide
How does the detergent remove the lipid bilayer
EXTRA READING - Geaghan-Breiner C (2013)
Passive diffusion with detergent
OR
Accelerated with electropheresis
What is a limit of CLARITY
EXTRA READING - Shen, Helen (2013).
The immunohistochemical staining takes 6 weeks to perform
Why is detergent eelctrophoeresis unpopular
EXTRA READING - Shen, Helen (2013).
Causes 8% protein loss
