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Comment: Re:It is a brain dead application. (Score 1) 46

by Niedi (#43430949) Attached to: Hydrogel Process Creates Transparent Brain For Research

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.

Comment: Re:Clear brains is not the story (Score 2) 46

by Niedi (#43421469) Attached to: Hydrogel Process Creates Transparent Brain For Research

The headline is focusing on the wrong thingThere was already a process to make brains look like glass. 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.

Comment: Re:Really? (Score 1) 156

by Niedi (#43367393) Attached to: Firing a Laser Into Your Brain Could Help Beat a Drug Addiction

so what you are saying is that it has the potential to turn out like resident evil?

No, I was thinking of something still lethal but less freaky: cancer. Plus, even if one of the patients goes insane for whatever strange one-in-a-billion chance, it's not really infectious unless he's still capable of drilling a hole into your skull and injecting a tiny amount of purified virus into precisely the correct area of the brain (think micrometer precision). So no zombie apocalypse there, sorry.

Comment: Re:Really? (Score 1) 156

by Niedi (#43367331) Attached to: Firing a Laser Into Your Brain Could Help Beat a Drug Addiction

Adult myogenesis in skeletal muscles isn't really happening much either. As for integration into the genome, I was under the impression that you can actually chose the place in the genome it would integrate in, but that this is mostly irrelevant as adenoviral vectors are preferred over lentiviral ones.

True, but I would say that a few lost muscle cells are less problematic than a few neurons lost in the wrong part of the brain. AFAIK there is no reliable way to control the site of lentiviral integration. Plus, purifying lenti properly is nasty, the stuff can be either quite neurotoxic or not infectious at all if something goes wrong during that step.
Recombinant Adeno Associated Virus is much less problematic, it's dead simple to manufacture and only the potential protein overload problem remains (and in mice we're using them a lot without any apparent problems). However, in an adult brain, the effect of rAAV is only temporary since it doesn't integrate and gets degraded over time.

Comment: Re:Really? (Score 5, Insightful) 156

by Niedi (#43366885) Attached to: Firing a Laser Into Your Brain Could Help Beat a Drug Addiction

Gene therapy is not particularly hard, and there's clinical trials and decades old cases where it have had success. Why is this myth propagated? Did the major fuckup and misconduct in the Jesse Gelsinger case really have that much publicity?

Though I guess, every religious nut, moral-code internet warrior, environmentalist nutcase and anti-GMO opinionist would of course latch onto this outlier case and present it as a rule rather than exception, because some delusion of purity is more important than saving and improving lives.

Disclaimer: I work in neuroscience and have used viral transfection quite a lot.

Myth? It's not trivial to get the infectous titer and purity of the virus right and it's even harder (read: almost impossible) to predict the exact expression levels that the virus will cause in an actual brain. Much less if such a potential overexpression of a non-native protein will mess up regular cell trafficking/function. Even if the protein is thought to be harmless (as is the case with Channelrhodopsin or Halorhodopsin), the sheer fact that the cell now has to produce, store and process large numbers of something it usually doesn't have can cause problems and take resources away from the normal function. Plus any virus that will stably integrate into the genome can cause all kinds of fuck up down the road since you don't know WHERE it will integrate and what other function it might overwrite.

Don't get me wrong, it is interesting, it is potentially very beneficial but I'd still be cautious when applying it in the brain (as opposed to applying it in muscle or skin cells) since adult neurogenesis isn't really happening much...

Comment: Re:How Close? (Score 4, Informative) 299

by Niedi (#43005669) Attached to: How Close Is Iran, Really, To Nuclear Weapons
As interesting as ever:
Adam Curtis - The Power of Nightmares
It gives an interesting view of how this whole situation with evil states and global terrorist networks spiralled out of control.
If you have three hours of time that is... But it's definitely fascinating imho.

Comment: Re:Recipe for disaster ... (Score 3, Informative) 160

by Niedi (#42806543) Attached to: How Not To Launch a Gadget

I personally have purchased a set of gaming dice 3d printed with stainless steel.


It's a small but important distinction. The ability to print stainless steel would be revolutionary, while the ability to powder cast has been around for millennia. A hyped convolution of the mold making process is not going to change much besides the number of shitty knives and dice in pawn shop display cases.

It is indeed possible to print IN stainless steel, titanium etc.... Using a technique called selective laser sintering, fine metal powder is selectively melted/fused by a high power laser, allowing you to directly print custom parts from metal.

Comment: Re:Trade-offs (Score 5, Insightful) 384

by Niedi (#42759661) Attached to: Valve Sued In Germany Over Game Ownership
Simple solution: They shouldn't try to fool people into thinking they are actually BUYING the game. Rename it to say "license the game" or "rent for an unlimited time" or whatever. I'm fine with their non-transferable model as long as they do not try to tell me I'm actually buying the game. Because if I buy something I expect to actually own it and be able to give it away anytime I want.

Comment: Source... (Score 4, Interesting) 252

by Niedi (#42250304) Attached to: VLC Running Kickstarter Campaign To Fund Native Windows 8 App
What is the situation with the source/GPL?
"Any code touching the user interface created within this endeavor will be licensed under the GNU General Public License Version 2 or later (GPLv2+), possibly with an exception for the Windows Store if needed."
I remember vaguely that there once was a VLC for iOS around before some internal debate about whether or not this sort of port was acceptable with the GPL caused apple to remove it. Exception for Windows Store? How should that work out then?

Comment: Re:Brings patch-clamp to nobody new. (Score 1) 59

by Niedi (#41176435) Attached to: Robot Brings Patch-Clamping To the Masses
Mod parent up, it's spot on! The actual patching is not really hard, especially since it only seems to do "blind" patching (just guided by the electrical response).

The only things to add are
- Fighting with your pipette puller to deliver constant results, because either you have your own crappy little puller that is hideously unreliable or you have a fancy one which is shared, meaning there is a high risk of someone messing with the filament and/or settings. And if your pipettes are crap, neither you nor the robot are going to succeed...
- Finding out why you suddenly have massive noise in your recordings
- Not freaking out after matlab, igor et al crash halfway through your recording session taking all your data with it.

A penny saved is a penny to squander. -- Ambrose Bierce