What is an Experiment?

What is an experiment?

Experimenting with color (source)

People use the term 'experiment' to meant a lot of things. One may say "she experimented with drugs" or "she performs experimental music". Someone might 'experiment with ones hair' or 'perform a thought experiment'.

All of these uses of the word experiment have distinct connotations, but most of them essentially mean 'to try something and see what happens'. In the examples above, most of the phrases also imply that the experiment is something new. If she experiments with her hair, she's probably trying some new style and seeing if she likes it. If she performs experimental music, she's probably not following the conventional rules for the music she is playing.

Are these kinds of 'experiments' different from the experiments that scientists do? Well yes and no.  The basic definition of an experiment as 'trying something [often new] and seeing what happens' is pretty much what scientists do. So what's different? Why isn't someones 'hair experiment' publishable in a scientific journal?

Mythbusters would have you believe that the only difference between science and screwing around is writing it down:


And that is sort of true.

But what really makes a scientific experiment scientific is controls. In our hair example, you can experiment with your hair by dying it black, and seeing if you like it. But that's not the scientific experiment. To be scientific you would have to decide how to measure how much you like your new hair color. You could do this by filling out a survey each day asking you how many times you thought you were pretty or rating your confidence on a scale of 1-10. You could fill this survey out for a week and then dye your hair and fill the survey out for another week. You could then compare the scores and decide if the new black hair had a 'significant' impact on your self-image. 

Lets say it does impact your self image and you report higher self-confidence that second week. But what if you feel different just because you have a new hair color, not because you have black hair?

Well, you would want to do a control experiment, which controls for the newness of the hair color. You could control for novelty by dying your hair yet a different color, and taking the survey for another week. Or you could take the survey two months after you dyed your hair black to see if you still report higher confidence or if your confidence has dropped back down to normal.


This is not a perfect experiment by any means, it's not even a clever or well-designed one, but it is somewhat scientific. And illustrates what I think is the most important difference between experimenting as in trying something new, and experimenting as in trying to find something out:

The control group


In addition, here is a great example of how important the control group is in science. (See the epilogue)

© TheCellularScale

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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


Micheva 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

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Is it 'Important' or is it 'valuable'?

We've recently discussed dopamine as a reward prediction signal. But that is really just the start of the complicated dopamine story.

Dopamine's role in reward and punishment (by the hiking artist)

Some research groups have also found that dopamine neurons respond to aversive stimuli, like an air puff to the face or an electric shock. This finding seems to be be completely incompatible with the idea that dopamine is a signal for reward.

Luckily some scientists took the time to try to resolve this discrepancy. Bromberg-Martin, Matsumoto, and Hikosaka (2010) have written an excellent review paper explaining that some dopamine neurons do code for value (reward), but other dopamine neurons code for salience (importance).

Differential Dopamine Coding (Bromberg-Martin et al., 2010 Fig 4)

When researchers are recording from a value coding dopamine neuron, it looks like the neuron responds to reward and actually reduces its response to the air puff. This makes sense as a 'dopamine = good' signal.

However, when a researcher is recording from a salience coding dopamine neuron, it looks like the neuron is responding equally to the good thing (reward) and the bad thing (air puff). This is confusing if you think 'dopamine = good', but makes sense if you think 'dopamine = important'. When the cue comes on (a light or a tone that signifies a reward is coming next or an air puff is coming next), these dopamine neurons fire if that cue means something.


Instead of just being confused about why sometimes dopamine would code for value and sometimes it would code for salience, Hikosaka's group showed that these two types of neurons are actually separate populations, and even seem separated in space.

(Bromberg-Martin et al., 2010 Fig 7B)

The value dopamine neurons are more ventral in the (monkey) brain, while the salience dopamine neurons are more dorsal-lateral. Importantly these two populations of neurons go to slightly different parts of the striatum and receive signals from different parts of the brain. The review paper suggests that the salience coding neurons receive their input from the central nucleus of the amygdala, while the value coding neurons receive their input from the lateral habenula-RMTg pathway.

The important thing here is that dopamine does not do just one thing to the brain. It doesn't just tell the rest of the brain 'yay, you won!' or 'you want that' etc... It says different things depending on different specific conditions. 

Dopamine doesn't 'mean' anything, the cell it comes from and the cell it goes to are what determine what it does. It certainly can't be classified as the 'love molecule'

 © TheCellularScale



Bromberg-Martin ES, Matsumoto M, & Hikosaka O (2010). Dopamine in motivational control: rewarding, aversive, and alerting. Neuron, 68 (5), 815-34 PMID: 21144997

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GABA, how exciting!

I would like to thank my good friend Anonymous for asking me a great question on a previous post.

Anonymous asks:

"Are there any known transmitters in the NS that activate both inhibitory receptor subtypes AND excitatory receptor subtypes? Or does every known transmitter activate EITHER a bunch of excitatory subtypes OR a bunch of inhibitory subtypes?"

 (btw. This doesn't qualify as a LMAYQ post because it's a real true question that someone directly asked, not a search term)

While I don't know of any instances of glutamate (excitatory) activating GABA (inhibitory) receptors or of GABA activating glutamate receptors, there is an interesting little way that GABA can activate an inhibitory receptor, but actually help excite the cell. 

GABA receptor (source)

 Here's how that works: GABA(A) receptors are permeable to chloride ions, and as the picture above shows, chloride ions (Cl-) are negatively charged. When GABA binds to the receptor, the receptor opens and chloride ions rush in, bringing their negative charge with them. This hyperpolarizes the cell, meaning it brings it lower and lower in total charge (membrane potential), which brings it further and further away from the threshold where it will fire an action potential.

BUT.... if there is a lot of chloride inside the cell already (or if the cell is resting more negatively than the chloride reversal potential), chloride will actually flow out of the cell, bringing its negative charge with it. Negative ions flowing out of the cell will depolarize the neuron increasing its total charge (membrane potential), which brings it closer and closer to the threshold where it will fire an action potential.

GABA reversing at -62mV (source)

A paper published last year in the Journal of Neuroscience shows that in a model of a hippocampal neuron, when a strong excitatory (glutamate) stimulation happens right after a GABA stimulation close by on the dendrite, the cell is actually more likely to fire than when the glutamate stimulation occurs on its own. This effect is dependent on the location of the GABA stimulation along the dendrite.

Chiang et al., 2012 Figure 4E (GPSP in the dendrite)

This figure shows that a GABA stimuation (first dotted line, blue trace) can push the glutamate (excitatory) stimulation (second dotted line, red trace) up to the point of firing an action potential (green trace). This paper also showed that GABA can still inhibit the action potential in these cells, it just has to be at the soma and almost the same time as the glutamatergic input.

Chiang et al., 2012 Figure 4G (GPSP in the soma)

 So there you have it, GABA enhancing the likelihood of an action potential and acting excitatory sometimes, and acting inhibitory other times. 


 © TheCellularScale



Chiang PH, Wu PY, Kuo TW, Liu YC, Chan CF, Chien TC, Cheng JK, Huang YY, Chiu CD, & Lien CC (2012). GABA is depolarizing in hippocampal dentate granule cells of the adolescent and adult rats. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32 (1), 62-7 PMID: 22219270

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Birthing new neurons at night

By now it's well established that adults can grow new neurons.

Growing Neurons (source)

But how, when and why these neurons grow is currently under investigation. A 2008 paper attempts to answer the 'when' of neurogenesis. They labeled (PH3) cells in the mouse hippocampus (dentate gyrus to be specific), and counted how many cells were currently going through mitosis at different times of day. They found that during the dark phase, more cells were PH3-positive, indicating that more cells were growing at night.

They also tested whether neurogenesis was modulated by exercise. And it was. Mice who had access to a running wheel in their cage grew about the same number of cells during the night, but grew more cells during the day. So much so that the difference between night and day disappeared.

Tamai et al.,, 2008 Figs 1B and 2D

This figure shows the light-dark cycle (Zeitgeber time) and the number of 'growing' cells. B shows the pattern for control mice, and D shows the pattern for the running mice. Notice that the y axes are scaled differently.

So exercise helped new cells grow, but without exercise more cells grew during the night time. Now all this use of the phrase 'night time' might make you think that this neural growth is happening during sleep.

After a long night of wheel running, Jasper succumbs to a restful days sleep. (source)

But it's not. Mice are nocturnal. They sleep during the day and are wide awake at night. The paper shows that almost all the running that occurs on the running wheel happens at night. So the enhanced cell growth is happening when the mice are active. Why exercising at night causes cells to grow during the day is interesting, but the authors offer no mechanism for why that might be happening.

© TheCellularScale


Tamai S, Sanada K, & Fukada Y (2008). Time-of-day-dependent enhancement of adult neurogenesis in the hippocampus. PloS one, 3 (12) PMID: 19048107

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JoVE: god of thunder, journal of techniques

If you don't know about the Journal of Visualized Experiments, now is the time to learn.

god of thunder, journal of techniques (source)

Methods sections of papers should contain enough detail that a scientist reading it could replicate the results of the paper. But this is rarely the case. Research in computational neuroscience has an advantage because the actual code used to run the simulations can be deposited and downloaded. But for experimental work, the nuances of exactly how to do each step in a process can get lost.

Protocol papers are often able to fully describe a process, but nothing can beat actually seeing the researchers performing the technique. For this there is JoVE.

You can get lost on their website watching fascinating 10 minute video after fascinating 10 minute video. For example, the very first video listed under 'neuroscience' when I checked it is called "Optogenetic activation of zebrafish somatosensory neurons using ChEF-tdTomato" and it shows you how stimulate the zebrafish neurons with light. But it doesn't just show you someone doing it, it shows each step in detail. How to modify the optic cable, how to position the zebrafish embryo, and even to be careful when using lasers. (Also, it taught me what the Pasteur Pipette can be used for.)

I think this is a great addition to scientific literature, and will be useful to many people. However, I still have some doubts about how easy it would be to replicate these techniques from the video alone. But fortunately accompanying the videos are detailed protocols with more details and equipment specs. 

I'd be interested to know if anyone has used a JoVE article and their sole resource and been able to replicate a technique successfully. 

© TheCellularScale

Palanca, A., & Sagasti, A. (2013). Optogenetic Activation of Zebrafish Somatosensory Neurons using ChEF-tdTomato Journal of Visualized Experiments (71) DOI: 10.3791/50184

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LMAYQ: Let me do your homework for you

Sometimes reading the textbook is just too hard. And sometimes it's much easier just to type your exact homework question into a search engine and find the answer. Before we get started you might want to take a look at Smith and Wren (2010) "What is Plagiarism and how can I avoid it?" 

This edition of Let Me Answer Your Questions will address 'homework questions.' As always, you can find previous LMAYQ questions here.

Tough Homework Questions are for the Internet (source)

1. "cells that fire together a) wire together. b) definitely don’t wire together. c) become overheated and die. d) wire with inactive cells." Ok, student. If you have to turn to the Internet for this multiple choice question, you need a serious lesson in test-taking skills. Here's a tip. If you don't know the answer, eliminate some because they are obviously not the right answer. A good rule to follow is if it says definitely or all or always in the answer it is unlikely that that is the right one. So we can eliminate B. If you know anything about neurons from your class, you should at least know that neurons fire. If they didn't fire they wouldn't 'work'. So you can eliminate C. If all the cells that fired together overheated and died, you would basically not have any neurons left in your brain after reading this sentence. Now you have a 50-50 chance of guessing it correctly. Not too bad. But seriously, if one answer creates a cute little rhyme with the question... it's probably going to be that one. So yes, neurons that fire together wire together. 2. "explain simply where the hippocampus is" The hippocampus is one of the most famous brain structures because it has to do with encoding new memories. It's name comes from the Greek hippo (horse) and campus (sea), because it looks like a seahorse: Hippocampus = Seahorse (source) (By the way, potamus=river, so a hippopotamus is a 'river-horse'). Back to the hippocampus: It is a structure in the brain and it is located subcortically meaning under the cortex. Specifically it's located under the temporal lobe of the cortex. There are two of them, one on each side of brain. 3. "Why are neurons and blood cells structured and shaped differently from each other?" Neuron and Blood cell Knitting (by Estonia76) This is a great question, but it has the ring of 'I need help with my homework' about it. I talk a lot about the shapes of neurons in this blog, usually speculating on why different neurons would be shaped differently from each other. But this is a good question, why do neurons have dendrites and axons in the first place? Well basically neurons need to receive and transfer information, while blood cells need to physically move to transfer oxygen. Neurons stay in place, while blood cells travel all over the body. Blood cells need to be small and hydrodynamic to float through your blood vessels. Neurons need to 'cover space' to contact many other neurons, so they have branching dendrites and axons. © TheCellularScale Smith N Jr, & Wren KR (2010). Ethical and legal aspects part 2: plagiarism--"what is it and how do I avoid it?". Journal of perianesthesia nursing : official journal of the American Society of PeriAnesthesia Nurses / American Society of PeriAnesthesia Nurses, 25 (5), 327-30 PMID: 20875892

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The Cellular Guide to Pipettes

What is a pipette?

Types of Pipettes (I took this picture)

There are lot of things that fall under the category of "pipette" and I found this a source of much confusion in my early graduate school days. Even after I knew by context what 'hand me the pipette' meant, I had a hell of a time trying to order the right type of pipette from scientific supply companies. 

So I am going to do you all a service, and give you a guide to pipette types: 

Labeled pipette types (I took this picture)

Basically, things that are long and skinny and can suck up certain amounts of liquid are called pipettes. 

Pipet-Aid: I think this is the brand name, but I didn't know what else to call it. It is battery powered and sucks liquid through an electrical vacuum. 

Serological pipet: This attaches to the pipet-aid and is calibrated for certain amounts of liquid. We use it for 10-25 mL volumes. 

Pipettor/pipette tip: This is the thing that I find most commonly referred to as a 'pipette.' They usually take smaller amounts (from microliters up to 5 milliliters) than the pipet-aid.

Pen: Do not try to use this as a pipette...or a pen. It's more 'cute' than it is 'able to write.'

Large transfer pipettes: These are plastic with squeeze-bulbs at the end.  They are not good for precise volumes of liquid like the others so far, but they are a quick easy way to transfer liquid from one place to another. We cut off the tip of the larger kind and use it to gently transfer brain slices into incubation chambers. 

Small transfer pipettes: I bought these on accident trying to replenish our supply of large transfer pipettes (#overlyhonestmethods). Now we use them to remove bubbles from the incubation chamber.

Pasteur pipette: These are glass and have detachable squeeze bulbs. I am not really sure what people use them for generally, but we have them in the lab left over from previous experiments. I use them to fill my pH meter with KCl and that's about it.  

Micropipette: This is a tiny pipette used for electrophysiology. The tip is so small that you can only see the opening under a relatively powerful microscope. The opening is smaller than the soma of a neuron, and I use these to patch onto brain cells. 

So there you have it: the ultimate guide to types of pipettes. I hope that one day this guide will save someone 20 minutes of online searching. 

If I missed some kind of pipette, please let me know! 

© TheCellularScale

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why you shouldn't wash your brain with soap

I can't think of any situation where you might be inclined to soap up your brain (except maybe if you had recently been trepanned), but it is still a bad idea.

you can actually buy soap shaped like a brain here. (It smells like bubble gum!)

When used on say, an oily frying pan, soap + scrubbing will trap the oil in little units which can be rinsed off. Without soap, using only water, the oil which is hydrophobic (meaning it would rather stick to anything besides water) will stick to the pan rather than the water. 

Soap + shaking = trapped oil (source)

How does this relate to the brain? Well the cell membrane which helps give the shape to the neurons is made up of a lipid bilayer. These lipids have a hydrophobic tail (which hides in the middle of the layer) and a hydrophilic head which faces outward, just like the oil particles above.

Cell membrane (source)

So basically if you scrubbed your brain cells with soap, the membrane that holds the neuron together would be disrupted. Scientists actually use this principle to get stuff (like DNA) out of a neuron. In DNA extraction, there is a lysis step in which a detergent (like SDS) is applied to the tissue and given a good shake. This disrupts the membrane and allows access to the contents of the neuron.

You can wash your skin with soap because the living skin cells are protected by an outer dead skin cell layer. Though if you soap up too much, you can actually dry out yours skin by stripping it of lipids faster that they can be replenished. See "How much should you shower" for an excuse to stay in bed tomorrow morning rather than get up and shower.


© TheCellularScale

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LMAYQ: Relationship Advice

We have reached the part of our program where I answer your important google questions. As always, these are real true questions that I found on my 'keyword search terms'. You can see all of these posts and the questions they answer here. 

Today's theme: Relationships

1. "Is there a difference in dopamine level between men and women?"

Great question.  In my post "Neurosexism and Delusions of Gender", I present a graph from Di Liberto et al., 2012 showing that female and male (mice) brains show no difference in the amount of dopamine transporter (DAT) in the striatum.

No Difference in Male and Female Dopamine Transporter

This question is particularly interesting in light of the recent reactions to Naomi Wolf's new book: "Vagina: a New Biography"  (See also Here and Here) In "Vagina", Naomi Wolf explains that "Dopamine is the ultimate feminist chemical in the female brain." ... Which is a a pretty ridiculous simplification of what dopamine is... in that it is completely untrue. First of all, men have dopamine too. And while their may be some differences in dopamine positive cells in the hypothalamus (Lansing and Lonstein 2006), the hypothalamus is  not the brain's main source of dopamine. Basically, the death of the Substantia Nigra (which feeds tons of dopamine into the striatum), results in Parkinson's Disease for men just like it does for women.

Second of all, dopamine doesn't have anything to do with your worldview (except maybe to help color it rosy). Misogynists have dopamine just like feminists do, and there is no reason to think that the amounts differ between them.

Dopamine: the Love molecule... a grossly simplified necklace (source)

However, having not read the book, I am guessing that Naomi Wolf claims dopamine is a feminist chemical because it is released during sex. But guess what, it's released during sex for both males and females, and it's not ONLY released during sex, it is also released when you eat food, do cocaine, or talk about yourself. It is a very complex molecule, with many receptors (at least 5 different kinds).  And dopamine literally does OPPOSITE things depending on whether it binds to the D1 type receptors or the D2 type receptors.


2. "Why are all women bitches?"

Look, you sound like a "Nice Guy", so I'll give you a tip: Some women do bitchy things sometimes, just like some guys do bitchy things sometimes, but your attitude that all women are bitches is probably one of the main reasons that most women are bitches to you. For a couple of reasons:

1. Self-fulfilling prophecy: If you expect to be screwed over by every woman you meet, you will see 'bitchiness' in their actions no matter what, and will probably act preemptively defensive. This will result in women acting on average more bitchy to you.

2. You are an asshole.


 3. "Do guys like cerebral women?"

Yes, guys like cerebral women.  Do all guys like cerebral women? probably not, some might be threatened by a woman who is smart.  But that's their loss.  Those guys probably end up asking the Internet questions like "why are all women bitches?"  But really, most guys I've met do not want vapid self-absorbed or shallow ladies in their lives.

One of my favorite fantasy authors, Robert Jordan has a moderately related quote:

"When I was a boy, just old enough to be starting to date in a fumbling way, I complained something about girls. And my father said to me, “Would you rather hunt leopards or would you rather hunt rabbits? Which is going to be more fun?” And I decided I’d rather hunt leopards." -Robert Jordan

Guys don't want wide eyed rabbit easy to get simple women, they want a challenge. If you are a cerebral woman, I am sure that you are smart enough to know that acting stupid to get a guy is basically the worst possible thing you could do to yourself. You don't want a guy who would fall for that crap.

But the real advice I want to give you is to stop caring what guys like. Do what you like, find yourself an awesome cause and fight for it, or an awesome project and do it. Check out cool things like Girls Who Code and play some Mass Effect. If you are really worried about 'having a partner' doing the things that you love to do will put you near other people who like doing those same things. In my opinion that is the best way to start a deep relationship anyway.

For more on gender et cetera, see the XX tab. 

© TheCellularScale


Lansing SW, & Lonstein JS (2006). Tyrosine hydroxylase-synthesizing cells in the hypothalamus of prairie voles (Microtus ochrogaster): sex differences in the anteroventral periventricular preoptic area and effects of adult gonadectomy or neonatal gonadal hormones. Journal of neurobiology, 66 (3), 197-204 PMID: 16329116

Di Liberto V, Mäkelä J, Korhonen L, Olivieri M, Tselykh T, Mälkiä A, Do Thi H, Belluardo N, Lindholm D, & Mudò G (2012). Involvement of estrogen receptors in the resveratrol-mediated increase in dopamine transporter in human dopaminergic neurons and in striatum of female mice. Neuropharmacology, 62 (2), 1011-8 PMID: 22041555

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Fire Together Wire Together

Fire together Wire together (source)

Synaptic plasticity, the strengthening and weakening of neuronal connections, is thought to be the cellular correlate of learning and memory. Neurons that are active around the same time (fire together) will generally strengthen the connection between them (wire together). 

One theory is that neurons strengthen their synapses based on the specific timing between receiving a signal and firing an action potential. This is called Spike Timing Dependent Plasticity (STDP). The basic premise is that if neuron A fires first, and then neuron B fires, neuron A is probably partly responsible for neuron B firing. If this is the case then the signal from A to B probably contains meaningful information.

Neurons Connecting (modified from here)

The action potential in B coming right after a signal from A is a trigger for the cell to strengthen that synapse. The most common hypothesis is that it does this by causing a calcium surge inside the dendrite.

And the opposite? What if neuron B fires before neuron A? It could be a meaningful signal or it could just be random noise. Maybe neuron A fired for no good reason (or even just a little vesicle of glutamate popping out untriggered). Many studies show that when B fires before A, the connection was actually weakened.

So the saying perhaps should be 'neurons that fire one right after the other wire together' ... But that just doesn't flow off the tongue the way 'fire together wire together' does.

STDP is incredibly complex and even though this A before B = strengthening and B before A = weakening explanation makes intuitive sense, there is an exception for every rule.  Some studies find just the opposite! And some studies find that both directions strengthen the synapse (A-B and B-A). 

Dan and Poo (2006) have a nice table explaining these exceptions and the parts of the brain where they are found.
© TheCellularScale


Bi G, & Poo M (1999). Distributed synaptic modification in neural networks induced by patterned stimulation. Nature, 401 (6755), 792-6 PMID: 10548104

Dan Y, & Poo MM (2006). Spike timing-dependent plasticity: from synapse to perception. Physiological reviews, 86 (3), 1033-48 PMID: 16816145

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A little stress goes a long way

.... toward preventing PTSD symptoms.

Post Traumatic Stress Disorder

This may surprise you as the S in PTSD stands for STRESS.  How on earth could stress prevent it? But you heard correctly. A new paper by Rao et al., (2012) from Biological Psychiatry shows that a little stress in the form of glucocorticoids, prior to an acute stress event actually prevents PTSD-like symptoms in rats.

First of all how do you tell if a rat has PTSD?
This study uses two measures: one behavioral and one cellular.

To test anxiety in a rat, you can put in on an Elevated Plus Maze (EPM). Rats don't love heights, and they do love dark corners. But, they are also somewhat naturally curious. The EPM makes use of these rat characteristics to test how anxious the rat is.

Elevated Plus Maze (source)

The EPM has four arms, two are open (but far enough off the ground that the rat can't just step off the maze) and two are enclosed with walls. Normal rats tend to explore all the arms of the maze roughly equally, but anxious rats tend to strongly avoid the open arms. The amount of time spent in the open arm area is a generally accepted measure of how anxious the rat is.

An earlier paper from the same lab, found that rats who had undergone the single stress event were more anxious (spent less time in the open arms of the EPM) 10 days after the event, but NOT 1 day after the event.  The single event stress and the delay of symptom onset are why this study is more relevant for PTSD than for chronic stress. 

Rao et al., 2012 Fig 4B

As interesting as the behavioral experiments are, the cellular level experiments are where it gets really cool (The Cellular Scale is not biased or anything). They used the Golgi stain to visualize neurons in the Amygdala. They measured how long the dendrites were and also how many spines they had on them. (Spines are the little protrusions that come of dendrites to receive synaptic inputs).


They found that the stressed rats had more dendritic spines on the amygdala neurons than the non-stressed rats.  Not only that, but this increase in spine density was apparent 10 days after the stress event, but not 1 day after.  


You might think dendritic spine growth is a good thing, and likely signifies synaptic plasticity and pathway strengthening... but remember this is the amygdala, a structure critical for FEAR learning, more spines here may not be beneficial. Stronger pathways to these amygdala neurons likely means that they fire more easily.


Now that we understand how PTSD is measured in a rat, we can move on to how they 'cured' it in this paper.  

Rao et al found that when they injected vehicle (a fancy science term for 'nothing' or 'placebo' or 'saline') into the rat 30 minutes before the 2 hour stress event, the rat no longer showed either the increased in anxiety (fewer open arm entries on the EPM) or the increase in dendritic spine density.

Pretty weird, considering they were injecting vehicle prior to the stress event.  How could inactive saline (essentially nothing) cure PTSD symptoms?

They figured out that the actual injection process was stressing the rat out a little bit. When animals (including humans) are stressed, they release a hormone called cortisol.

Rao et al., 2012 Fig 1C,D,E

They found that the 2 hour stress event caused a huge rise in corticosterone (right and left panels), while the injection (vehicle) alone caused a small rise (middle panel). 

Because they were injecting nothing, they hypothesized that the corticosterone produced by the small stress of being injected was somehow protecting against the large 2 hour stress event.

The rest of their paper is basically confirming this. They add corticosterone to the water of the rats and this also prevents the PTSD-like symptoms.  They find that all their manipulations isolating the corticosterone confirm that this is what is protecting the rats from the delayed impact of the stress event.  

Interestingly there is evidence that 'small stress' can help prevent 'big stress' in humans too. They cite clinical studies reporting that intensive care unit (ICU) patients who receive injections of stress-level cortisol during treatment are less likely to develop ICU-related PTSD symptoms.

It is a puzzling paradox at the moment, but the next step is to figure out how exactly this little stress can reduce big stress.


Epilogue: 

I was lucky enough to see Dr. Chattarji, the principle investigator of this study, give a talk at a conference a few months ago.  And one interesting piece of information that you can get from a talk, but will never read in a paper is how the scientists originally stumbled upon their finding.  In this case, Chattarji's lab didn't start their study by injecting vehicle. They were actually testing a real drug that they thought might help alleviate PTSD.  They had a beautiful result showing that when you injected "drug X" before the 2 hour stress event, you eliminated the PTSD symptoms. The natural conclusion is to think that "drug X" is a new cure for PTSD.

 But therein lies the importance of the control group. To control for any effects of simply injecting the rat, they injected vehicle. When they saw that the vehicle prevented the PTSD symptoms just like the actual drug, they were crushed! This is the ultimate demise of an experiment.  The control group shows the same thing as the drug group, which means that the drug does not work! Luckily they were flexible and smart enough to investigate what they did see, that the injection alone could protect against the PTSD symptoms.

Also, if someone would like to explain the difference between cortisol and corticosterone, please do. I clearly do not have a full understanding here.

© TheCellularScale




Rao RP, Anilkumar S, McEwen BS, & Chattarji S (2012). Glucocorticoids Protect Against the Delayed Behavioral and Cellular Effects of Acute Stress on the Amygdala. Biological psychiatry PMID: 22572034

Mitra R, Jadhav S, McEwen BS, Vyas A, & Chattarji S (2005). Stress duration modulates the spatiotemporal patterns of spine formation in the basolateral amygdala. Proceedings of the National Academy of Sciences of the United States of America, 102 (26), 9371-6 PMID: 15967994

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In defense of pink microscopes

I know I am late to the party here, as the "Science is a girl thing" video (embedded below) came out Friday and has already been ripped to shreds by many a blog. But I just couldn't stop thinking about it, so here's my opinion on that video and pinkifying science in general.

Hello Kitty Microscope

I am reminded of a quote from Pres. Obama's initial campaign.  He said (something like) "We need to shatter the blasphemy that says a black child with a book is acting white." 

It is equally true that "we need to shatter the blasphemy that says a woman in science is acting masculine."

Sometimes women in science dress down and wear less make up on purpose because they are worried that they won't be taken seriously if they look 'girlie' or even 'attractive'. Or specifically, "If I look like I took a long time doing my hair, nails, and make up, people might think I am not spending time doing science."

It is just as sexist to think that a woman wearing heels in the lab is less capable or less dedicated to science as it is to think that women shouldn't be in a lab in the first place. What a woman wears to the lab (within lab safety guidelines anyway) has NOTHING to do with how good she is at science or with how seriously she takes her work.  NOTHING.  The woman who wears heels and makeup, the woman who wears the same sweatpants 3 days in a row, and the woman who wears a t-shirt with jeans should all be taken equally seriously as scientists and judged on their work and not their appearance. 

Being 'masculine' does not help you be a better scientist and for crissake women, do not brag about having a 'masculine brain'. You are not helping inspire young girls to success when you attribute your intelligence and ability to being like a man.

I fully support feminine scientists and pink science equipment. There is no reason that a microscope shouldn't be pink and there is no reason that a girl shouldn't be able to have her own Computer Engineer Barbie if she wants one. 

Computational Neuroscientist Barbie

The message that you can both care about shoes and be a successful working scientist is important. It helps shatter the stereotype that scientific women are or should be masculine.

Recently a study by Betz and Sekaquaptewa (2012) investigated the influence of overtly feminine cues (such as pink clothes, makeup, etc) on middle-school girls' interest in math as a future career. They had the students read an magazine-style interview with a feminine woman (pictured as wearing make up and pink and described as liking fashion magazines), and a neutral woman (pictured with dark clothes and glasses and described as liking reading).

The finding that has been the focus of this paper's blog coverage is that for the girls that did not label math or science as their favorite subject, the feminine cues significantly reduced their self-reported interest in math as a career. They attribute this to the girls thinking that the feminine women are 'too good' and thus being discouraged because they don't see themselves as ever reaching those heights.

While this is an interesting hypothesis, a closer look at the study is merited.  First of all, there is not un-gendered control study. Might a similar effect might show up for middle school boys when shown either a muscular, athletic man who likes football or a neutral man who isn't particularly muscular, wears glasses and likes reading? This could be a general 'attractivity' thing where kids are intimidated by role models who 'have it all' or 'are too good'. Maybe it's not really a gender issue.

Secondly, what hasn't been discussed much is that 54% of the girls initially listed math or science as their favorite subject! And for those girls, the femininity of the woman in the article had no statistically significant effects on their interest in science and math. 

54% ! more than half of the girls in this study reported science, math, or both as their FAVORITE subject! and while there were no significant effects, there was a trend (p=0.19) toward the femininity of the role model increasing these girls' report of how 'attainable' both her femininity and scientific success might be.

Betz and Sekaquaptewa, 2012 Figure 3

This graph shows the "self-reported likelihood of attaining role model femininity and STEM (science, tech, engineering, and math) success" If anything the feminine role model slightly increased the attainability of these characteristics for girls who already like science (not significant, p=0.19).   

Regardless, I think the conclusion that feminine-looking science is bad for girls is not on sound footing. And again, I defend pink microscopes.

If you have already seen the It's a girl thing video, you might be now expecting me to support it.  But don't worry, I think it is as idiotic and every other scientist on the planet does. 


Far from showing feminine scientists, it is showing a scientist (the man) and separate from that a bunch of giggly girls dropping things. NOT HELPFUL. The only part I liked was the girl looking like she was concentrating and writing equations on the clear board. She looked feminine and pretty and she was 'doing' science.  If these girls had been actually doing science through the entire video (sitting at microscopes like the guy did, for example), I might actually have liked it.

The thing that is wrong with this video is not that these girls are wearing heels (though short skirts do violate lab safety codes), or that they look feminine or pretty. That's all fine. The problem is that they are not doing science, they are giggling and blowing kisses. If your goal is to combine femininity and prettiness with science, you have to COMBINE them, not present them as two completely separate things.


In conclusion, I'll leave you with one of the best comments so far: Cartomancer on Pharyngula suggests some equally stereotypical and offensive videos to promote diversity in science:

"67. cartomancer says:

22 June 2012 at 10:41 am

I want to see what they’d come up with to get more LGBT people and ethnic minorities into science. “Science: it’s a gay thing!” featuring Abercrombie and Fitch models, bare-chested apart from an open lab coat, playing with unfeasibly suggestive phallic test tubes. Cut to discotheque-esque laser equipment and the word “science” with the C as a big rainbow.
Or how about “Science: it’s a black thing!” – grinding hip-hop beats accompanying blinged-up rapper types in pimped-out lab goggles, gold-rimmed petri dishes, Neil DeGrasse Tyson with a ridiculous posse behind him, research grants delivered in unmarked bills… yeah, you get the idea.
Well it amused me anyway."

© TheCellularScale

Diana E. Betz, & Denise Sekaquaptewa (2012). My Fair Physicist? Feminine Math and Science Role Models Demotivate Young Girls Social Psychological and Personality Science DOI: 10.1177/1948550612440735

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