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Hydrogel Process Creates Transparent Brain For Research

samzenpus posted about a year and a half ago | from the I-see-what-your-were-thinking dept.

Medicine 46

First time accepted submitter jds91md writes "Scientists at Stanford have developed a technique to see the structural detail of actual brains with resolution down to the cellular and axonal/dendritic level. The process called CLARITY allows a 'transparent' view of the brain without having to slice or section it in any way. From the article: 'Even more important, experts say, is that unlike earlier methods for making the tissue of brains and other organs transparent, the new process, called Clarity by its inventors, preserves the biochemistry of the brain so well that researchers can test it over and over again with chemicals that highlight specific structures within a brain and provide clues to its past activity. The researchers say this process may help uncover the physical underpinnings of devastating mental disorders like schizophrenia, autism, post-traumatic stress disorder and others.'"

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Research proposal (4, Funny)

girlintraining (1395911) | about a year and a half ago | (#43417301)

The researchers say this process may help uncover the physical underpinnings of devastating mental disorders like schizophrenia, autism, post-traumatic stress disorder and others.'"

Can you find the center of the brain responsible for youtube comments and create a drug that turns that off? The internet will pay you. The internet will pay you a lot.

Re:Research proposal (0)

wierd_w (1375923) | about a year and a half ago | (#43417339)

I'd settle for finding the part of the brain implicated in politicians engaging in cronyism, accepting bribes, and the like.

Then we could demand legislation forcing politicians to medicate.

Re:Research proposal (5, Funny)

girlintraining (1395911) | about a year and a half ago | (#43417419)

I'd settle for finding the part of the brain implicated in politicians engaging in cronyism, accepting bribes, and the like.

I'd settle for slashmods with a sense of humo--WAIT! I haven't even posted yet and you've put me -1! Poop heads.

Re:Research proposal (-1)

Anonymous Coward | about a year and a half ago | (#43417527)

I find it particularly interesting when commenters will trot out their pet cause on completely unrelated topics.
Take a deep breath. Calm down. Take a walk outside. You'll feel better without all this stress.

Re:Research proposal (0)

Anonymous Coward | about a year and a half ago | (#43417803)

And I find it amusing when commentors with intellectual blinders on can't handle indirect applications.

Eg, "transparent brain with diagnostic protein structures intact"-->analysis of brain structure in brains of subjects with anomalous behaviors-->corelation between structure and behavioral patterns-->drugs that target those structures to alleviate abnormal behavioral impulses.

The jokes were that people being douches on youtube, and politicians being dirty and crooked were anomalous behaviors, the underlying physiology should be examined with this technique to find correlations to study drugs with, with the ultimate aims of correcting both deleterious behaviors.

Ego, the quips are indeed on-topic, your narrow sighted myopia and inability to cogitate the full implication of the discovery just prevents you from seeing that, and I find that hilarious.

Re:Research proposal (0)

Anonymous Coward | about a year and a half ago | (#43417813)

I find it particularly interesting

That will wear off and you'll be left with contempt.

Re:Research proposal (1)

Joe Snipe (224958) | about a year and a half ago | (#43417923)

Like your pet cause of stopping people from talking about completely unrelated topics?

Re:Research proposal (2)

Black Parrot (19622) | about a year and a half ago | (#43418337)

I find it particularly interesting when commenters will trot out their pet cause on completely unrelated topics.
Take a deep breath. Calm down. Take a walk outside. You'll feel better without all this stress.

So objecting to crooked politicians is a "pet cause"?

Re:Research proposal (1)

Genda (560240) | about a year and a half ago | (#43419935)

Apparently not to the wealthy and powerful...

Re:Research proposal (1)

MrLizard (95131) | about a year and a half ago | (#43421673)

I'd settle for finding the part of the brain implicated in politicians engaging in cronyism, accepting bribes, and the like.

Then we could demand legislation forcing politicians to medicate.

That's called "all of it".

Re:Research proposal (1)

noh8rz10 (2716597) | about a year and a half ago | (#43417423)

does the article and submittor even know what a "transparent brain" is??!? Very insensitive to throw around that term so casually.

Re:Research proposal (1)

Penguinisto (415985) | about a year and a half ago | (#43417429)

Depends on whose brain they used as the template.

For the typical youtube commenter, I think they would have had to refer to, oh I dunno, a dachshund?

Re:Research proposal (1)

Genda (560240) | about a year and a half ago | (#43419955)

It said Abby! Abby Normal.. Damn your eyes! Too Late!

Oh, and Gesundheit!

Re:Research proposal (1)

interkin3tic (1469267) | about a year and a half ago | (#43417487)

Pretty sure that's a software issue, not a hardware issue...

Re:Research proposal (1)

kermidge (2221646) | about a year and a half ago | (#43419969)

There's a rich field of puns available, aye. One I liked from the first article linked was at the end:

Dr. Reid agreed that Clarity had applications in many fields. “It could permeate biology,” he said.

(only trick is one had to read the article, which describes the method....)

Re:Research proposal (1)

noh8rz10 (2716597) | about a year and a half ago | (#43417747)

Can you find the center of the brain responsible for youtube comments and create a drug that turns that off? The internet will pay you. The internet will pay you a lot.

I use the ShutUp plug in for Safari, but there are ones for other browsers too. It hides comments on any page in an intelligent way. I started using it because of the horrible Yahoo News comments, but it will work for Youtube too. you can activate it with a white list, so slashdot comments are ok, although maybe we'd be better off without those too. as they say, easier to put on blinders than to change the world. http://stevenf.com/shutup-css [stevenf.com] . Slashgods take note - a constructive comment from noh8rz!

Re:Research proposal (1)

AndyKron (937105) | about a year and a half ago | (#43417753)

I make very rational, intelligent comments on YouTube, you meandering crotch sniffer! /s

Re:Research proposal (1)

Genda (560240) | about a year and a half ago | (#43419967)

I beg your pardon! I never meander while crotch sniffing. Everyone knows a trollop is called for. La la la la la lalala la lala la...

Hooray! (0)

Anonymous Coward | about a year and a half ago | (#43417345)

Alpha-levels, here we come!

ZomBee (1)

fazil (62946) | about a year and a half ago | (#43417425)

This is obviously how the Zombies start.

Clear brains is not the story (5, Interesting)

interkin3tic (1469267) | about a year and a half ago | (#43417445)

The headline is focusing on the wrong thingThere was already a process to make brains look like glass. [gizmag.com] It was really cheap and easy too: it's just urea basically.

The real story is the second part. You can stain for proteins and see where the localize. With SCALE, the previous method, you couldn't do that easily. Probably anyway, I never tried. You had to have fluorescent proteins expressing in the tissue, which isn't possible in human tissue samples from deceased patients unless you're trying some weird shit. Alternatively, you could stain sections, but that doesn't give you as good a 3D image of the 3D structure.

It's really interesting work. If it doesn't cost too much, I may have to try it in my lab (though I don't work on brains.)

Re:Clear brains is not the story (3, Interesting)

wierd_w (1375923) | about a year and a half ago | (#43417519)

Since it achieves the transprency the same basic way (washout of the lipids in the bilayers), it should work on neary all soft tissues, not just neuronal tissue.

So, unless you are researching diseases of adipose tissue, this should still be of real value.

Re:Clear brains is not the story (0)

Anonymous Coward | about a year and a half ago | (#43417761)

unless you're trying some weird shit

As opposed to all the rest of that perfectly normal stuff?

Re:Clear brains is not the story (2)

Niedi (1335165) | about a year and a half ago | (#43421469)

The headline is focusing on the wrong thingThere was already a process to make brains look like glass. [gizmag.com] It was really cheap and easy too: it's just urea basically.

True, but the level of transparency wasn't that impressive with that method, it only worked up to 1-3mm of depth. BABB based protocols were a lot better in that regards.

The real story is the second part. You can stain for proteins and see where the localize. With SCALE, the previous method, you couldn't do that easily. Probably anyway, I never tried. You had to have fluorescent proteins expressing in the tissue, which isn't possible in human tissue samples from deceased patients unless you're trying some weird shit. Alternatively, you could stain sections, but that doesn't give you as good a 3D image of the 3D structure. It's really interesting work. If it doesn't cost too much, I may have to try it in my lab (though I don't work on brains.)

Hell yes, that's the big one here. Plus, expressed fluorescent proteins in the tissue don't get degraded as much as with BABB et al. Definitely give it a shot, you probably have all the ingredients around the lab anyway. The clearing is done with PFA, acrylamide, bis-acrylamide, VA044 and PBS. The slices should then be immersed in glycerol, so nothing special there as far as I can see it. You only need to build a custom electrophoresis chamber to stain the brain, but even that shouldn't be too hard.

I See What You Did There (1)

Anonymous Coward | about a year and a half ago | (#43417553)

*writes on clipboard*

It is a brain dead application. (4, Informative)

140Mandak262Jamuna (970587) | about a year and a half ago | (#43417755)

The brain is real, but not alive. MRI works on living brains, but usually still pictures. Functional MRI gives movies of activity on living brains, but at a lower resolution. This technique carefully washes away some parts of the brain leaving the fat cells, neurons etc intact. Then they apply electric current and study the connectivity.

Re:It is a brain dead application. (4, Informative)

Anthony Castanza (2881747) | about a year and a half ago | (#43418463)

fMRI doesn't really track brain activity, it tracks blood oxygenation which is used as a reasonably good approximation of actual activity. Just a little nitpick.

Re:It is a brain dead application. (1)

m-kirkcaldie (979966) | about a year and a half ago | (#43419309)

Ah, no, fMRI doesn't give "movies of activity". As Anthony mentioned it tracks blood flow changes and give you a map of where it changed most when the subject performed a task. Nothing moves in the image. Nor does this technique leave cells intact, and nor can you use electric currents to "study the connectivity". You may want to check up on some basics.

Re:It is a brain dead application. (1)

QQBoss (2527196) | about a year and a half ago | (#43419505)

Ah, I thought this was somehow working on living tissue, even after casually examining the Nature abstract.

Since it does require dead tissue, I have an IT admin here with a brain he isn't using that could be donated to help with this research. Really, I insist.

Re:It is a brain dead application. (1)

Genda (560240) | about a year and a half ago | (#43420037)

He'll have to take his rightful turn after thousands of Politicians, Religious Fundamentalists and Bankers.

Re:It is a brain dead application. (2)

lxs (131946) | about a year and a half ago | (#43420161)

MRI works fine on dead brains, which is a bit of a problem really. [discovermagazine.com]

Re:It is a brain dead application. (1)

c0lo (1497653) | about a year and a half ago | (#43420845)

This technique carefully washes away some parts of the brain leaving the fat cells, neurons etc intact.

Fat cell intact but without fat. TFA:

Dr. Chung said the hydrogel forms a kind of mesh that permeates the brain and connects to most of the molecules, but not to the lipids, which include fats and some other substances. The brain is then put in a soapy solution and an electric current is applied, which drives the solution through the brain, washing out the lipids.

Now, about...

Then they apply electric current and study the connectivity.

Perhaps the technique has some value in allowing particular protein staining be applied, but I really doubt that one can still consider the brain prepared as such a functional one.

You see, that fat (myelin mainly) that makes the brain opaque... it has quite a big role: it's an electrical insulator. And one just replaced that insulation with hydrogel, which, containing water, is conductive (unless one eliminates all the ions inside the brain - especially those pesky highly mobile Na, K and Ca ones; hang-on, aren't they required to actually have electrical conduction inside neurons? if one succeeds, the result would be making all the neurons non-conductive). Mind you, the loss of only a small percentage of that myelin [wikipedia.org] is pretty nasty
Applying the procedure it's pretty much like sinking you computer in water: can't really expect it to work afterwards... but maybe I'm wrong so, please, do elaborate on how can one expect a functional brain.

Re:It is a brain dead application. (1)

Niedi (1335165) | about a year and a half ago | (#43430949)

Then they apply electric current and study the connectivity.

Nope, that's no longer possible on such a brain. What you do is you inject special tracer substances (while the mouse is still alive). These substances will stain neurons at the site of injection and then cross the synapse to connected cells, either in the direction of the information flow or opposed to it, depending on the system used. These tracers are then imaged using the method that this article is about. To further aid you, you can do different stainings to see what type/subtype of neurons you are looking at. By combining this information with known functional properties of the found neuronal types, you can try to infer what is actually happening in the area you examine.

Interesting... (0)

houbou (1097327) | about a year and a half ago | (#43417775)

This is really cool. Guess it won't be too long when they will be able to do the same with live brains. Which would more than likely result in the ability to cure many forms of mental issues and illness.

Re:Interesting... (4, Informative)

wierd_w (1375923) | about a year and a half ago | (#43417879)

Doing this to a living brain would be "horribly unethical" in just about every way.

This technique makes the brain transparent by gelling up the cytoplasm with a synthetic molecule, then washing out all the lipids.

Lipids are fundementally necessary for proper neural function, and are the primary duty of glial cells to produce and deposit. Mylein is predominantly comprised of lipids. Without it, you would be a quivering and drooling moron. (On a good day.)
[Glial cells chaparone the long axons of neural whitematter, and are the cells that wrap the axon in mylein, among other duties.]

Doing this to a living brain would cause unbelievable neural harm.

Re:Interesting... (0)

Anonymous Coward | about a year and a half ago | (#43418153)

No it would cause believeable harm. Because I believe it.

Re:Interesting... (1)

ankhank (756164) | about a year and a half ago | (#43418373)

like, fatal.

Next up, a process that removes everything _but_ the lipids, which will probably reveal a fascinating complex of varying resistances and processes that go through changes passing through the fat, too.

Also like completely fatal.
Kids, do not do this at home.

Re:Interesting... (1)

MrLizard (95131) | about a year and a half ago | (#43421719)

Ah, but could you do it to a recently deceased brain, then use a 3-D bioprinter to replicate each neuron and its connections, then place the result in a new host?

Intresting tech (4, Funny)

LordZardoz (155141) | about a year and a half ago | (#43417833)

Sounds like an optimal way to clear your mind.

END COMMUNICATION

SCIENCE!! (1)

Intrepid imaginaut (1970940) | about a year and a half ago | (#43417907)

Fuck yeah.

Re:SCIENCE!! (1)

Black Parrot (19622) | about a year and a half ago | (#43418355)

There's an xkcd for that.

Re:SCIENCE!! (2)

jkflying (2190798) | about a year and a half ago | (#43420689)

It works, bitches.

New, improved Clarity (0)

Anonymous Coward | about a year and a half ago | (#43418843)

It really depends on whether this is the customary Clarity, or the new and improved one.

Fringe S01E01 (2)

badkarmadayaccount (1346167) | about a year and a half ago | (#43420011)

Seriously, nobody here made the connection?

How About Brain Investigations For the Rest of Us? (1)

LifesABeach (234436) | about a year and a half ago | (#43422531)

Could this be the path that allows me to backup my brain? A method that would allow me go back and search for significant things like my wife's birthday? Or where I saw/experienced that last place I put my car keys? These are things that matter.

Also serves to diagnose death... (1)

gweihir (88907) | about a year and a half ago | (#43427953)

... as I guess the person owning that brain should be dead before the procedure and certainly is so afterwards.

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