…and this is a 
Ah, a solid science talk. It wasn't bad, except that it was very basic—maybe if I were a real journalist instead of a fake journalist I would have appreciated it more, but as it was, it was a nice overview of some common ideas in neuroscience, with some discussion of pretty new tools on top.
He started with a little history to outline what we know, with Ramon Y Cajal showing that the brain is made up of network of neurons (which we now know to be approxiamately 1012 neurons large). He also predicted the direction of signal propagation, and was mostly right. Each neuron sends signals outwards through an axon, and receives input from thousands of other cells on its cell body and dendrites.
Signals move between neurons mostly by synaptic transmission, or the exocytosis of transmitter-loaded vesicles induced by changes in calcium concentration. That makes calcium a very interesting ion, and makes calcium concentration an extremely important parameter affecting physiological function, so we want to know more about it. Furthermore, it's a parameter that is in constant flux, changing second by second in the cell. So how do we see an ion in real time or near real time?
The answer is to use fluorescent indicator dyes which are sensitive to changes in calcium concentration — these molecules fluoresce at different wavelenths or absorb light at different wavelengths depending on whether they are bound or not bound to calcium, making the concentration visible as changes in either the absorbed or emitted wavelength of light. There is a small battery of fluorescent compounds — Fura-2, fluo 3, indo-1 — that allow imaging of localized increases in calcium.
There's another problem: resolution. Where the concentration of calcium matters most is in a tiny microdomain, a thin rind of the cytoplasm near the cell membrane called the cortex, which is where vesicles are lined up, ready to be triggered to fuse with the cell membrane by calcium, leading to the expulsion of their contents to the exterior. This microdomain is tiny, only 10-50nm thick, and is below the limit of resolution of your typical light microscope. If you're interested in the calcium concentration at one thin, tiny spot, you've got a problem.
Most presynaptic terminals are very small and difficult to study; they can be visualized optically, but it's hard to do simultaneous electrophysiology. One way Neher gets around this problem is to use unusually large synapses, the calyx of Held synapse, which is part of an auditory brainstem pathway. It's an important pathway in sound localization, and the signals must be very precise. They have a pecial structure, a cup-like synapse that envelops the post-synaptic cell body — they're spectacularly large, so large that one can insert recording electrodes both pre- and post-synaptically, and both compartments can be loaded with indicator dyes and caged compounds.
The question being addressed is the concentration of Ca2 at the microdomain of the cytoplasmic cortex, where vesicle fusion occurs. This is below the level of resolution of the light microscope, so just imaging a calcium indicator dye won't work — they need an alternative solution. The one they came up with was to use caged molecules, in particular a reagent call Ca-DMN.
Caged molecules are cool, with one special property: when you flash UV light of just the right wavelength at them, they fall apart into a collection of inert (you hope) photoproducts, releasing the caged molecule, which is calcium in this case. So you can load up a cell with Ca-DMN, and then with one simple signal, you can trigger it to release all of its calcium, generating a uniform concentration at whatever level you desire across the entire cell. So instead of triggering an electrical potential in the synaptic terminal and asking what concentration of calcium appears at the vesicle fusion zone, they reversed the approach, generating a uniform calcium level and then asking how much transmitter was released, measured electrophysiologically at the post-synaptic cell. When they got a calcium level that produced an electrical signal mimicking the natural degree of transmitter release, they knew they'd found the right concentration.
Caged compounds don't have to be just calcium ions: other useful probes are caged ATP, caged glutamate (a neurotransmitter), and even caged RNA. The power of the technique is that you can use light to manipulate the chemical composition of the cell at will, and observe how it responds. These are tools that can be used to modify cell states, to characterize excretory properties, or to generate extracellular signals, all with the relatively noninvasive probe of a brief focused light flash.
Life Science
Brain & Behavior
Comments
Posted by: daveau
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June 30, 2009 7:56 PM
What time is it there; like 2:00 AM? what a dedicated journalist!
Go have a bier.
Seriously, interesting subject.
Seriously, go have a bier.
Posted by: maddogdelta | June 30, 2009 7:57 PM
I know this is a threadjack... and right at the start... so I will submit to any punishment PZ deems appropriate, however Thunderf00t of youtube "Why do people laugh at Creationists" fame has offered Ray Comfort an opportunity for honest debate... Everyone might find the response humorous, if expected...
// http://www.youtube.com/watch?v=ECQQbsV9g6U If I broke the link...
Posted by: PZ Myers
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June 30, 2009 8:06 PM
Are you kidding? I just got back from dinner -- two dinners, actually, both hosted by Lindau, one an affair with a couple of Nobelists and the other for the press -- and they were serving FREE BEER. I had a couple of dunkels, a weissbier, and some pils, and some other stuff which all started to run together.
And yeah, it's 2am.
Posted by: daveau
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June 30, 2009 8:13 PM
Having been to Europe several times, I know your body knows it's really only 7:00 PM, and you're just getting started.
Wow! That sounds pretty exciting.
Posted by: Patricia, OM
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June 30, 2009 8:15 PM
Beer, phooey. I want to hear about the sausages.
Posted by: Qwerty | June 30, 2009 8:17 PM
Patricia OM - I think PZ drank his dinner.
Posted by: Shirakawasuna | June 30, 2009 8:23 PM
Make sure you drink a Schwarzbier for me! And every other commenter!
Also, caged compounds are extremely cool, thanks for the interesting article!
Posted by: Umkomasia | June 30, 2009 8:35 PM
And people will like him.
Posted by: Natrina | June 30, 2009 8:35 PM
Neurotransmitters developments! Oh how I remember trying to make an assignment on those and not finding any consensus on what a given neurotransmitter actually did. I mostly had access to old books anyway, though.
Posted by: Abie | June 30, 2009 8:43 PM
Considering the cooing sound I made while reading the beginning of this post, I have to admit it to myself : I am secretly in love with Santiago Ramon y Cajal...
The story of his Nobel Price shared with Golgi is priceless : go and read their acceptance speech, and you'll see why they couldn't talk the same day!
http://nobelprize.org/nobel_prizes/medicine/laureates/1906/
Posted by: Leukocyte | June 30, 2009 8:43 PM
@ Natrina:
What a given neurotransmitter does depends entirely on what type and number of receptors are on the postsynaptic cell. Glutamate, for example, can be excitatory, inhibitory or modulatory depending on the receptors.
Posted by: Leukocyte | June 30, 2009 8:48 PM
@ Abie
I am more than secretly in love with Ramon y Cajal. His "Advice for a Young Investigator" is still stellar advice today. I would be more annoyed with how cliche it is to start every general neuroscience talk with Ramon y Cajal, except that it still blows my mind after hearing it dozens of times.
Posted by: peter | June 30, 2009 8:55 PM
BTW - the spelling should be Erwin Neher.
That's the German way.
Posted by: NickS | June 30, 2009 9:11 PM
/method-gasm
My mind's a spinning at all the possible uses of those caged compounds, cheers!
Posted by: Christoph Geisler | June 30, 2009 9:48 PM
This microdomain is tiny, only 10-50 µmthick. Shouldn't that be in nm?
Posted by: Felix | June 30, 2009 10:03 PM
ah, wonderful spam.
no, beer is still better.
and yes, in Germany we do drink our meals - beer is generally referred to as 'Flüssigbrot', liquid bread. I'll have another right now. 4:00 AM. not tired.
Prost!
Posted by: Rorschach | June 30, 2009 10:59 PM
Now this is not advisable.
That's headache territory !
A real German(TM) would know that...:-)
Sort of ruins the breakfast of pastries the next day,too..;)
Posted by: Paul Burnett | June 30, 2009 11:20 PM
PZ wrote: "...the brain is made up of network of neurons (which we now know to be approxiamately 10^12 neurons large)."
A Pentium chip contains 4.5 x 10^6 transistors. How long before Intel makes a chip with 10^12 transistors?
Posted by: Nameless Cynic | June 30, 2009 11:23 PM
Well, that may seem basic to you, but some of us don't have your science background.
I've got some guy beating me up about global warming, and I'm going to be in over my head soon. Would anybody like to step in with some real scientific understanding on the subject? I'd appreciate it.
http://www.leftcoastrebel.com/2009/06/is-liberal-left-actually-open-minded.html
Posted by: katie | June 30, 2009 11:26 PM
Strangely enough...my boyfriend literally just defended his thesis on the synthesis and mechanisms of some of these compounds :) I just showed him this article!
It always blows my mind at what useful things real scientists can come up with.
Posted by: Brian | June 30, 2009 11:35 PM
Nice to see that the subscripts are working again.
Posted by: MadScientist | June 30, 2009 11:53 PM
Awesome. :) So the cryptands *do* have their uses. That sounds like a pretty neat tool to play around with in biological studies. I wonder if anyone's trying to use the general technique for targeted release of drugs (such as achieving better targeting with some types of chemotherapy).
Posted by: Gruesome Rob | July 1, 2009 12:04 AM
If Moore's law continues to hold, 30 years.
10^6 ~= 2^20. 20 doublings, in 18 months per doubling = 30 years
Posted by: antistokes
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July 1, 2009 12:30 AM
Yeaaah, caged compounds are ok, but recall that they do require UV wavelengths for excitation, which if used over long periods can photodamage the cell. One way around this is to employ two photon excitation at an IR wavelength.
Also, this is kind of a pet peeve of mine, but fluorophores are still great huge honking organic molecules (well, 'cept the quantum dots, that's a whole different story) as I'm sure you know. These dyes can interfere with cellular machinery (don't even get me started on the GFPs). (I'm working on doing in vivo measurements on murine brains with NO labels and high spatiotemporal resolution (about a micron), so I get all persnickety about using dyes.)
For interesting fluorescence work on beating the diffraction barrier, check out the STED technique developed by S. Hell's lab (also German!), there was a recent short highlight article in nature about his work.
Posted by: MadScientist | July 1, 2009 12:39 AM
[OT] - and I apologize in advance to this long OT post.
@Nameless Cynic: What specific issues do you want addressed?
Having a quick look through:
"CO2 doesn't pile up in the atmosphere because of the oxygen and other trace gasses that are far lighter than CO2."
That is simply not true, and CO2 will not sink down to the ground and into the ground. Be grateful that it doesn't or most people in big cities would be dead due to automobile exhaust. "Gravitational settling" of CO2 is absolutely insignificant when compared to molecular diffusion of CO2 in air and other transport mechanisms (convection, turbulent mixing, etc). CO2 will not settle, it will mix. Looking at the atmospheric composition, we have an almost constant mix of 78% nitrogen, 21% oxygen, and 385ppm CO2 in the atmosphere. I say "almost constant" because you can get significant fluctuations at ground level but in the long term CO2 mixes rather than settling to the ground via gravitation. Having said that, if you release a large amount of cold CO2 under very still conditions it will maintain an invisible (and hazardous) 'pool' for quite some time. This is due to the fact that molecular diffusion of CO2 is only on the order of 5cm/second whereas mixing even in a very light breeze is much greater. The temperature difference in this case also ensures that there is no convective mixing (diffusion is dominant). Of course if you release such a pool uphill, the buoyancy will lead to that pool traveling downhill. So indeed we can observe CO2 "going down", but it is incorrect to believe that CO2, by virtue of its molecular mass, will always drift towards and into the earth.
Damn - that's getting long and it's only 1 point. Is that idiot seriously suggesting there's a "CO2 rain" effect?
As for his "candle demonstration", the hot gas from the flame causes convective mixing thus forcing CO2 down and extinguishing the candle; the CO2 is not flowing towards the ground "because it is heavy".
Now why hasn't barometric pressure increased with increasing CO2? Simple - the CO2 has increased 25% from pre-industrial levels but it is still a trace gas whose increase would at most contribute a few tens of parts per million change in pressure.
His "water" argument doesn't stand; you can get a beaker with 100% CO2 in gas form, but in a room habitable by humans you cannot get a beaker with 100% water vapor and at ambient air pressure - it just doesn't happen. If you're lucky maybe you can get a beaker with 4% water vapor - that's an awful big effective dilution compared to the CO2 case. His "experiments" require some imagination but no thought and only demonstrate a severe misunderstanding of basic behavior of gases. As with CO2 he gets the water vapor behavior all wrong - water does not fly up and away. If it did then most of the water would be way up in the sky, but that simply is not the case. Most of the water in the atmosphere is near the surface - unless of course you make silly and meaningless comparisons such as the sahara desert during the day vs. a rain cloud.
"If plants couldn't take it [CO2] in as fast, the oxygen in our air would be diluted." Well, yes, we can say "our oxygen is diluted", but we're talking a few parts per million. If all industrial CO2 emissions were not scrubbed at all by nature, perhaps we'd be close to 500ppm CO2 by now - that's 0.0005% CO2 vs 21% O2 - big dilution eh? I suspect he's trying to conflate "immediate health risk to humans" and "nasty effect on global climate".
"CO2 emission causing global warming theory has been debunked" - a popular claim amongst the ignoramuses, but no evidence whatsoever to support it.
Going back to the other idiot again - as a gas, CO2 is 100% miscible in the atmosphere (which is a gas). It's a well-known property of gases and has been stated a few hundred years ago. CO2 will never "supersaturate" and magically precipitate out of the air. (Well, in truth it does when you compress and cool the air by a huge amount - but that will not happen in our atmosphere.) Also, we use a variety of spectroscopic techniques to measure CO2 in the air - attempting to measure a change in barometric pressure is just silly - pressure is not species-specific, not to mention it's a challenge to detect parts per million change when a few parts per thousand change can occur over a few hours. It just demonstrates that the guy hasn't got a clue what he's talking about. (There are other usable non-spectroscopic techniques such as gas chromatography, but that's too much detail.)
Posted by: Alan Kellogg | July 1, 2009 2:40 AM
Paul Burnett, #18
When somebody comes up with a network of 1012 computers is when you'll get something like the human brain. Oh, and massively multiprocessor computers at that.
Posted by: Brg | July 1, 2009 3:41 AM
Quite interesting. All of this can be found in the bible, too, right? Probably not in such a confusing language as you have put it above, but in passages and parables that can be understood clearly and beautifully if we just decide to open out hearts to Jebus, right?
Posted by: Marc Abian | July 1, 2009 5:04 AM
This is the first I've heard of caged molecules. Sounds brilliant.
Posted by: Carl Troein | July 1, 2009 5:07 AM
Regarding the number of transistors: The first Pentium chips had 3.1*106 transistors, says Wikipedia, but that was 16 years ago! Today's (quad-core) CPUs have something like 7*108 transistors. That's a 200-fold increase in about 10 doubling times - the missing factor of 5 or so would be the improved performance per transistor.
Posted by: Peter Ashby | July 1, 2009 5:34 AM
Alan Kellog is right, you cannot compare transistors with neurons, a neuron is way more complex and has lots more inputs and potentially outputs than a transistor. Neurons are also analogue in the sense that they can vary their output. They vary not just in signal strength or frequency as well but the pattern of the signals can be important too. We are not too good at modelling the activity of just single neurons in all ways yet, put more than a few neurons into a network and things get n hard very quickly. So sorry HAL is not just around the corner even if all you need is complexity, which is wrong. Without cell death and connection pruning you would be a vegetable.
Posted by: mo | July 1, 2009 6:24 AM
...and don't forget the new hip thing for zebrafish people:
Caged MORPHOLINOS
Posted by: Tantalus Prime | July 1, 2009 9:02 AM
"the brain is made up of network of neurons (which we now know to be approxiamately 10^12 neurons large)."
I thought current estimates were 10^11 neurons? Since the glia:neuron ratio in humans is about 10:1, that would be about 10^12 cells total. Am I missing some information?
Posted by: katie | July 1, 2009 10:13 AM
@antistokes:
Photocages don't have to be big, and they don't have to be proteins like GFP (which is meant just for labelling, not photoreleasing). A photocage can be something like a phenylacetic acid, which can be as small as 166 M. And you can design photocages to release at a variety of wavelengths, not just UV (even without two photon absorption).
The tricky part is designing a photocage that fulfills a wishlist of requirements: innocuous by-products, aqueous solubility, high quantum yield, etc.
Posted by: antistokes | July 1, 2009 10:50 AM
Yes, I know, and I have no doubt that valuable discoveries will be made, much like the GFP case (I'm looking forward to Tsien's talk tomorrow, I did a lot of protein engineering with GFPs). But, personally, I don't like going beyond isotopic labeling (I do a lot of vibrational spectroscopy), if that. 166 M, as I'm sure you're aware, is the size (if not the composition of) many biologically active compounds.
Another tricky bit, like you say, is controlling the photophysics (such as side reactions in the excited state) of the cages, which is not a trivial task.
Posted by: Matt | July 1, 2009 11:16 AM
At #19 / Nameless Cynic
Left Coast Rebel named Michelle Bachman as "one of the only pols in the entire country that I like."
StarTribune.com:
Posted by: Matt | July 1, 2009 11:29 AM
At #25 / MadScientist:
Wll done sir, I'm printing out that thorough debunk.
PS: Sorry for OT
Posted by: trrll | July 1, 2009 6:43 PM
The other really nice thing about caged compounds is that it is possible to produce a localized "spike" of concentration on a time scale that is comparable to synaptic release of a neurotransmitter, which is something that is very tricky to achieve otherwise. This is because you don't have to worry about things being slowed down by diffusion through an unstirred layer, which is always a problem when you try to physically change solutions. The molecule is already there, and the "uncaging" can be very fast.