Saturday, April 27, 2013

LMAYQ: Mirror Neurons

Mirror neurons really excite people. They've been hyped as the root of empathy and essential to human nature. I've addressed some of this hype, but questions remain. So for this edition of Let Me Answer Your Questions, we will focus on mirror neurons. As always, the LMAYQ series can be found here.

Escher's Mirror (source)

1. "What do mirror neurons look like?" 
Good question, and guess what? I have addressed this directly.

2. "Do mirror neurons fire when you die?"
Another good question. Ultimately, all neurons stop firing when you die including mirror neurons. But this doesn't happen immediately. In fact, if the death is due to something traumatic such as decapitation, the neurons might fire more when the nerves are severed between the spinal cord and the brain. But this just brings up questions about the moment of death. Is it when the heart stops, the head is severed? or is it when the neurons stop firing? Can a 'person' be dead when some of their cells are still alive?

In a lot of cellular-level research, cells are kept alive after the animal that they came from has died. Electrophysiologists keep slices of brain alive for hours to record electrical signals from their neurons. Still other projects involve culturing neurons that have been extracted from an animal. These neurons are carefully tended for days, weeks, and even months. These neurons not only stay alive in little dishes, but they can also grow and even control robots.

There are living neurons in there (source)
3. "what does it mean to have a mirrored brain?"
Well. nothing really. I have never heard the term 'mirrored brain' before, and it sounds like something that might be in a pseudo-scientific quiz along the lines of Are you left brained or right brained?  "Do you have a mirrored brain? take our quiz and find out"

4. "Is love nothing but mirror cells?"
I love and hate these kinds of questions. The idea that love is nothing if it can be explained by a biological mechanism really gets me. If love is just neurons firing (mirror or otherwise), so what? Why would that make LOVE any less meaningful?

Heart Mirror (source)
On the other hand, this is a really interesting question if it is asking whether mirror neurons have anything to do with love. Again mirror neurons are neurons that fire when you do something and also when you see someone else do that thing. Specifically, they were discovered in monkeys when monkeys reached for something and then saw other hands reach for something. Then the concept got hyped up. It's easy to imagine that if you have neurons that fire when you do something and when you see some one else do that same thing, that those might have something to do with 'feeling another's pain' and thus empathy. So it's not a huge step to take from there to think that maybe mirror neurons could have something to do with building relationships and love.

But the speculation here is WAY beyond the science. There isn't good solid evidence for mirror neurons controlling empathy, and certainly not for being the basis of love.

 © TheCellularScale

Monday, April 22, 2013

Connecting Form and Function: Serial Block-face EM

The retina is a beautiful and wondrous structure, and it has some really weird cells.

Retina by Cajal (source)
Retinal Ganglion Cells (RGC) have all sorts of differentiating characteristics. Some are directly sensitive to brightness (like rods and cones), while some are sensitive to the specific direction that a bar is traveling.

I am discussing really amazing new techniques to see inside cells this month, and have already posted about the magic that is Array Tomography. Today we'll look at another amazing new technique that (like array tomography) combines nano-scale detail with a scale large enough to see many neurons at once. This technique is called Serial Block-face Electron Microscopy (SBEM), and was recently used to investigate how starburst amacrine cells control the direction-sensitivity of  retinal ganglion cells.

Serial Block-face EM (source)

SBEM images are acquired by embedding a piece of tissue (like a retina) in some firm substance and slicing it superthin (like 10s of nanometers thick) with a diamond blade. The whole slicing apparatus is set up directly under a scanning electron microscope, so as soon as the blade cuts, an image is taken of the surface remaining. Then another thin slice is shaved off and the next image is taken, and so on.

Using this technique, Briggman et al. (2011) are able to trace individual neurons and their connections for a (relatively) large section of retina. What is so great about this paper is that before they sliced up the retina, they moved bars around in front of it and measured the directional selectivity of a bunch of neurons. Then, using blood vessels and landmarks to orient themselves, they were able to find the exact same cells in the SBEM data and trace them.

Briggman et al. (2011) Fig1C: Landmark blood vessels
The colored circles above represent the cell bodies and the black 'tree' shape are the blood vessel landmarks.

Once they found the cell bodies, the could trace the cells through the stacks of SBEM data. What is really neat is that you can try your hand at this yourself. This exact data set has been turned into a game called EYEWIRE by the Seung lab at MIT.

Reconstructing the cells, they could not only tell which cells connected to which other cells, but they could also see exactly where on the dendrites the cells connected. This is the really amazing part. They found that specific dendritic areas made synapses with specific cells.

Briggman et al. (2011) Fig4: dendrites as the computational unit

This starburst amacrine cell overlaps with many retinal ganglion cells (dotted lines represent the dendritic spread of individual RGCs)...BUT its specific dendrites (left, right, up down etc) synapse selectively onto RGCs sensitive to a particular direction. Each color represents synapses onto a specific direction-sensitivity. e.g. yellow dots are synapses from the amacrine cell onto RGCs which are sensitive to downward motion.

This suggests that each individual dendritic area of these starburst amacrine cells inhibits (probably) a specific type of RGC, and that these dendrites act relatively independently of one another.

"The specificity of each SAC dendritic branch for selecting a postsynaptic target goes well beyond the notion that neuron A selectively wires to neuron B, which is all that electrophysiological measurements can test. Instead the dendrite angle has an additional, perhaps dominant, role, which is consistent with SAC dendrites acting as independent computational units."  -Briggman et al (2011)(discussion)

These cells are weird for so many reasons, but the ability of the dendrites to act so independently of one another is a new and exciting development that I hope to see more research on soon.

© TheCellularScale
Briggman KL, Helmstaedter M, & Denk W (2011). Wiring specificity in the direction-selectivity circuit of the retina. Nature, 471 (7337), 183-8 PMID: 21390125

Wednesday, April 17, 2013

Van Gogh was afraid of the moon and other lies

I remember the first time I realized just how easily false information gets spread about.

A terrifying starry night
I was in French class in high school. Our homework had been to find out 1 interesting fact about Van Gogh and tell it to the class. When it was my turn, I said some boring small fact that I no longer remember. My friend sitting behind me, however, had a fascinating fact: When Van Gogh was a young child, he was actually afraid of the moon.

The teacher and the class were all quite impressed and thought about how interesting that was and how that fact might be reflected in the way that he paints the Starry Night. Though this fact was new to everyone, including the teacher, no one even thought to question its truth.

In fact, the teacher was so enthralled by this idea that she passed the information on to all the other French classes that day.

When talking to my friend later that day, he admitted that he had not done the assignment, and just made the 'fact' up. I was completely surprised, not only that someone had not done their homework *gasp*, but that I hadn't even thought to question whether this was true or not. 
The best lies have an element of truth (source)
 Misinformation like this spreads like wildfire and is exceptionally difficult to undo. The more things you can link this piece of information to in your brain, the more true you might think it and even after your learn that it's not true, you still might inadvertently believe it or fit new ideas into the context it creates. Myths like the corpus callosum is bigger in women than in men is just one of those things that is easy to believe.

An interesting paper by Lewandowsky et al. (2012) explains how this kind of persistent misinformation is detrimental to individuals and to society with the example of vaccines causing autism. This particular piece of misinformation is widely believed to be true despite numerous attempts to publicize the correct information and the most recent scientific findings showing no evidence for a link between the two

The authors of this paper give some recommendations for making the truth more vivid and effectively replacing the misinformation with new, true information. For example:
"Providing an alternative causal explanation of the event can fill the gap left behind by retracting misinformation. Studies have shown that the continued influence of misinformation can be eliminated through the provision of an alternative account that explains why the information was incorrect." Lewandowsky et al. (2012)
Misinformation can be replaced with information, but it takes more work to replace a 'false fact' than to just have the truth out there in the first place. It is much better when misinformation is not spread around in the first place, than when it is retroactively corrected.

This paper is also covered over at The Jury Room.

© TheCellularScale
Lewandowsky, S., Ecker, U., Seifert, C., Schwarz, N., & Cook, J. (2012). Misinformation and Its Correction: Continued Influence and Successful Debiasing Psychological Science in the Public Interest, 13 (3), 106-131 DOI: 10.1177/1529100612451018

Saturday, April 13, 2013

Seeing Inside Cells: Array Tomography

I wrote a lot about dopamine and its complicated nature last month after coming back from the IBAGs conference, so for a change of pace, I'll talk about some truly amazing new techniques that allow us to see inside cells with unprecedented resolution and at unprecedented volumes.

I've previously discussed some traditional techniques for visualizing specific details in neurons, and this month I'm going to talk about some of the newest fanciest ways to look at cellular scale information. 

First off, Array Tomography! 

Micheva et al. 2010 Figure 1 Array Tomography

Array Tomography combines the enhanced location information of the electron microscopy with the scale and context of immunohistochemistry or in situ hybridization. Not only that, but Array Tomography is done in such a way that the same preparation can be stained for 100s of different proteins.  This is a priceless gift to those who want to study protein co-localization.  Do certain receptors 'flock together', and if so does a mutation, or drug treatment alter their abundance or proximity to one another?

Micheva et al. 2010 Figure 4 spine head and neck locations of specific proteins

And just how do they accomplish this feat?

The trick is in the slicing. Using an ultramicrotome these guys can slice a section of brain 70 nm thin. That's 70 NANOmeters, which is really really thin. (Compare it to 'thick section staining' which works on sections 350,000 nanometers thin). The smallest cellular features, the necks of spines can be as thin as 50-100nm, so 70nm can really capture a lot of detail.

Here is a 'fly through' video of the cortical layers in a cortical column. The red dots are identified synapses, and around 2:11 of the video you get to the pyramidal cell bodies (green) which is pretty stunning.

While "Array Tomography" doesn't quite capture the public imagination like "neurons activated by light", it is huge leap forward in the domain of cellular neuroscience. With array tomography, it becomes possible to investigate co-localization of many proteins in a relatively large section of brain tissue. 

© TheCellularScale

ResearchBlogging.orgMicheva KD, Busse B, Weiler NC, O'Rourke N, & Smith SJ (2010). Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron, 68 (4), 639-53 PMID: 21092855

Sunday, April 7, 2013

LMAYQ: Scales

The word "scale" can mean many things, and The Internet can't yet use context to tell the difference. So for this issue of Let Me Answer Your Questions, here are questions about scales that The Internet thinks The Cellular Scale can answer. As always these are real true search terms, and all the posts in the LMAYQ series can be found here

A Question of Scale (source)

1. "Can you give a rat scales?"

 I have never thought to ask this question, but it is an interesting one. If you can grow weird things on mice, like ears, then why not scales? Well here's the thing, the 'ear mouse' is growing skin like it normally does, the skin is just growing over an ear-shaped mold. It would actually be harder to make a rat grow scales. If it is possible, it would take some mastery in genetic manipulation...

Bee-Rat, the ultimate achievement in genetic manipulation (source)

Some sniffing around on wikipedia taught me that scales have evolved several times (fish, reptiles, arthropods, etc). It might be possible to make a rat (or mouse) grow scales by isolating the scale gene from these other animals and inserting it into the rat genome. However, since rats already grow fur, teeth, and nails, which are related to scales, it might be possible to manipulate those features already in the rat to become more scale-like.

But to answer your question, no. I am pretty sure we can't give a rat scales yet.

2. "Does the giant squid have scales?"

Another interesting question. The quick answer is no, giant squid and colossal squid (like their normal squid counterparts) have smooth skin that does not contain scales. This isn't too surprising because squid aren't fish, they are cephalopods (like octopus and cuttlefish). Cephalopods sometimes have shells, but not scales. 

Zoomed in view of Squid Skin (source)
Instead of protective scales, cephalopods use pigment in their skin to camouflage themselves or confuse predators.

Blue Octopus, Eilat Israel (I took this picture)
This octopus turning blue sure confused me.

3. "How to turn your cell phone into a scale."

There are a couple of ways that you might think a cell phone could be used as a scale. One is by the touch screen sensor. However, most smart phones now have capacitive touch screens which respond to the electric change your finger induces on the screen. That means that the amount of pressure applied doesn't matter. So you couldn't use a smart phone as a scale in that way.

Another way is through the accelerometer. Smart phones also have accelerometers, which you could possibly use to measure the force of something moving. But this wouldn't tell you the mass of the object unless you already knew the acceleration. (force = mass * acceleration). 

But really the only way that seems to actually work (albeit slowly and with questionable accuracy) is using the 'tilt sensor' of the smart phone.

But really you just as well make your own if you are weighing out small amounts of something.

Most importantly it's helpful to know what some typical objects around the house weigh, so you can use them to calibrate a phone or homemade scale.  Here are some useful weights:

1. US penny 2.5g
2. US nickel 5 g
3. 1ml water 1g
4. Euro 7.5g
5. British pound 9.5 g

4. "What is the scale on the cellular level?" 

Finally a relevant question! Most cells are measured in microns, with a blood cell being about 6-8 microns in diameter.

blood (source)
Neurons on the other hand can have somas (cell bodies) ranging from tiny (5 micron diameter) to large (50 micron diameter). But even for neurons with small somas, the dendritic or axonal arbors can be gigantic. 

Some neurons in the aplysia (snail) can get up to 1mm (1,000 microns) in diameter. Which is ridiculously huge for a neuron. For perspective, C. Elegans, a nematode frequently used for neuroscience research, is about 1mm in length. The whole animal! Including its 302 neurons! 

© TheCellularScale

Thursday, April 4, 2013

Neurons and New Newt Legs

Salamanders are amazing and mystical creatures.
Salamanders and their amazing leg-growing superpower (source)
Not because they can survive in fire (they can't), but because they can regrow amputated limbs.
A paper in 2007 investigates exactly what neural signals are required for this amazing superpower.

Newt Amputee (Kumar et al., 2007)
This paper brings together two interesting things about salamander (newt) leg growth.

1. The salamander arm 'knows' where it was cut. If it is cut at the wrist it only grows a hand (paw?...foot?), if it is cut at the shoulder, it grows the whole leg/arm. So one question is HOW does the arm know?

The answer is surprisingly simple: there is a small protein called Prod 1 that is highly concentrated at the shoulder and progressively decreases along the arm. This protein could tell the new bud of growing cells where it is, and what it should grow into.


2. To regenerate, the arm needs intact nerve endings at the point of the cut. That is, the nerve fiber that goes down the arm has to be attached to the nervous system. If the nerve is cut further up than the arm cut, the arm will not regenerate.

Kumar et al., 2007 Author Summary Figure
Kumar et al. (2007) found a molecule that ties these two interesting things together, completing the newt leg regeneration story. They find a molecule, nAG (n for newt and AG for anterior gradient) which binds to Prod 1, and is secreted by the nerve sheath (the Schwann cells that surrounds nerve fibers).

They show that when they cut the nerve further up the arm (denervation), they don't get nAG expression and they don't get limb regeneration. But, when they artificially supply nAG, (see D and E above), the amputated and denervated limb starts to grow. 

This is a really neat 'rescue experiment' suggesting that the reason the nerve is necessary for regeneration is because it triggers nAG release which binds to Prod 1 and says "GROW".

One thing that they don't do (because genetically manipulating salamanders is not really a thing yet) is remove nAG, but keep the nerve intact. This would show that the only important thing the nerve fiber is doing is triggering nAG.

This study is also a small step towards limb regeneration in humans, not because injecting nAG into an amputated human limb could regenerate it (It couldn't), but because the more we understand about how the system works, the more likely we can figure out a way to engineer a similar system in humans. 

© TheCellularScale
Kumar A, Godwin JW, Gates PB, Garza-Garcia AA, & Brockes JP (2007). Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate. Science (New York, N.Y.), 318 (5851), 772-7 PMID: 17975060

Tuesday, April 2, 2013

Reviewers and Citations: an update

A few weeks ago, I asked whether reviewers should be required to cite sources in their summary statements for submitted journal articles.
I heart citations (source)
I was frustrated about my paper reviews (not an uncommon sentiment) because one reviewer made some serious claims against my basic assumptions, but did not include any citations to back these claims up. A few people in the comments suggested that I write to the editor.

So I did. I wrote a nice polite letter saying that citations from the reviewer would be helpful. The editors wrote to the reviewer and then wrote back to me with the reviewers reply. I was actually surprised at this because I had a feeling that once the editor puts the paper on the 'will not consider for publication' list, that they might not even respond. But I got some citations from the reviewer, so I could find out where I got lost in my own literature search. And much to my delight, after scouring the papers the reviewer cited, I still feel that I am right and that my paper has a sound foundation. I have now re-submitted this paper (to another journal), and feel pretty confident about it. 

Though of course I always feel more confident about a submitted paper than I should.

Submitting a beautifully written paper for review (what should we call grad school)

© TheCellularScale