Showing posts with label brain. Show all posts
Showing posts with label brain. Show all posts

Saturday, July 23, 2016

Ruminations of a dog scientist on a 96-well plate

I've been doing a lot of bench work in the laboratory lately. This involves filling the tiny little wells on a plate with my ingredients (sample, reagents, primers) and then inserting the plate into a reader. The machine takes the plate up with whirring sounds that always fascinate me. I know there are little robot arms in there moving the plate into place, and I wish I could watch the process. But as I listen to the robot work, I sometimes think: is this the closest I get to living, moving animals now? How did I get here, so separated from fur and behaviors and emotions?

96 well PCR plate


My long term research goal is to understand the differences in how brains work in dogs who suffer from fear issues compared to resilient dogs who take life's arrows a bit more in stride. I'm doing this by studying gene expression in the brains of foxes who have been bred to be fearless (“tame”) or fearful (and aggressive — those who study them just refer to this line as “aggressive,” though).

My approach is, at the moment at least, deeply reductionist: what are the differences in gene expression in a few brain regions in these two lines of foxes? In other words, does one group make more of a certain kind of gene than the other? My hope is that I’ll be able to make some conclusions about the differences in function in these brain regions between the two lines of foxes, and that what I find will be relevant to fearful dogs. But I find myself burrowing deeper and deeper into learning about very small parts of the brain, and then very specific functions of those parts to the exclusion of other parts. Currently I’m learning about the pituitary gland — no, wait, just a particular cell type in the pituitary gland, the corticotroph — no, wait, just a particular set of processes of the corticotroph, how it releases one particular hormone into the bloodstream.

So in my daily work, I do things like take some tissue and extract all the RNA from it (throwing out DNA, proteins, cell structure, all sorts of interesting information — that's not what I'm working on or able to assess at the moment). I use PCR to extract a tiny piece of RNA from the complete transcriptome (all the RNA from that tissue), throwing out even more information. And then assess the expression level of that RNA, resulting in just one number. One number out of all that information after a day’s work.

Behavior can’t really be fully understood using this reductionist approach. If I do find a few important gene expression differences in a few small brain regions, they won’t explain the whole story of why an animal has a fearful personality. They’ll be a tiny, tiny piece of a complicated network of interactions involving genetics and life experience. But in order to get at that tapestry we have to first be able to visualize the threads that make it up. So here I am, in the trenches, doing that.

A recovering shy dog.

Monday, January 11, 2016

The future of behavior medication?

We don’t actually know how behavior medications work. We know how they change the operations of cells — for example, we know facts like “this medication makes cells slower to recycle this particular chemical.” But we don’t have a good idea of how those cellular-level changes result in behavior-level changes. We don’t know how these medications make individuals feel better.

And that’s a problem, because not every individual responds to a particular behavior med in the same way. A pathologically fearful dog might have nasty side effects on one med, no response to a second, and then respond beautifully to a third. It’s hard on owners to have to try a variety of medications before finding the right one, especially as it takes a month or two to be sure that a particular medication is or isn’t working. (Oh, yeah, and the same is true for humans who use these drugs.)

If we knew how these medications worked, we might be able to figure out who they would work on without so much cumbersome trial-and-error. Imagine taking your shy dog to a veterinary behaviorist, who would do a genetic test and prescribe the right drug based on the results, to go along with behavior modification exercises.

My current work focuses on gene networks that differ in the brain between animals who are shy and aggressive and animals who are confident and friendly. I've always felt that my requests for funding have been a little hand-wavy as I have argued that surely my findings may help us understand behavioral medications better... You know, someday. Someday maybe my findings will help us design better medications, in fact. But that day seemed a really long way off.

Until I read Ed Yong's story “CRISPR’s most exciting uses have nothing to do with gene editing”. CRISPR is a fancy new gene editing technology that has everyone talking about science fiction coming to pass: being able to edit human (and animal) genes to make designer babies (and animals). Edit out the gene variants for genetic diseases before a baby is born! (But hopefully don't slide down the slippery slope to editing height, skin color, eye color, personality...)

But it turns out that CRISPR may have a more subtle use: gene regulation. Soon, scientists may be able use it to tell individual genes to turn on and off (to make more or less of their product). Rather than permanently editing genes in embryos, we could temporarily modify the output of genes in adults. Suddenly my quest to find the sets of genes affecting shyness seems less quixotic. Maybe my discoveries (do you like how I assume I’ll have discoveries? Let’s just pretend it’s a sure thing) won't have to wait for drug discovery work to be useful. Maybe we’ll be able to directly turn the volume up or down on those particular genes, directly affecting pathological shyness.

Scary? Yeah, it's not something I foresee being used therapeutically in the next few years, not until we understand the brain well enough to be able to predict side effects. But it’s really cool to imagine that some day we may have this sort of fine-tuned control over psychological diseases.

Monday, March 9, 2015

Contexts and cues: the reactive dog brain


A dog on leash, seeing another dog, explodes into a fury of barking and lunging. Reactive dogs, dogs who respond with arousal or aggression to what should be innocuous stimuli, can be very difficult for their owners to manage safely. I've written previously about hormonal changes in individuals experiencing this kind of arousal. But why do their brains trigger the stress response in such inappropriate situations in the first place?


Learning and memory

Past learning, stored as memories, has a lot to do with current behavior. If a dog has made bad associations with something in the past, he has a good chance of expecting a similarly unpleasant experience the next time he encounters it or something that reminds him of it. How he chooses to deal with this situation — aggression or withdrawal — is one interesting question, but right now I’m writing about how he makes associations in the first place and how he retrieves them later.

Learning and memory can mean a lot of different things depending on their context. I’ll be using them in a very narrow sense.

Learning: making an association between a stimulus and a consequence
Memory: the ability to retrieve a previously-formed association
So if a puppy is attacked by another dog, he may learn to associate other dogs with pain and fear. When he later encounters another dog, he uses his memory to retrieve that association. Two parts of the brain which are deeply associated with this type of learning and memory are the amygdala and the hippocampus.

The amygdala is associated with threat evaluation: is that twisty shape I see out of the corner of my eye a stick, or a poisonous snake? Is the dog I am greeting friendly, or about to attack me? People with damage to their amygdalas may have difficulty evaluating threats, to the extent that they may not be able to feel fear. As a result, the amygdala functions in emotional learning: people told scary stories remember them better than less exciting stories partly because of the emotional contributions of their amygdala, which tells them that an experience has some level of threat and should be recorded in memory with particular care.

The hippocampus, on the other hand, is famous for its contributions to learning different locations. London cab drivers must spend years memorizing the twisty street map of their city, and when they are done, their hippocampuses are actually larger in size compared to people who haven’t gone through the training.

When they work well, these two brain structures are an important part of the process of identifying appropriate threats and discarding stimuli that aren’t threatening, based on previous experience. So what exactly is going on when they operate as they should?

Fear conditioning: contexts and cues

The most effective studies that have been done to determine exactly how the hippocampus and amygdala function in learning and memory have used fear conditioning, often in laboratory rodents. Dog trainers use classical conditioning to associate stimuli that a dog considers threatening with something positive, to change the dog’s emotional response to that stimulus — for example, to teach a dog who fears other dogs that they will reliably get food when other dogs approach, so that the dog comes to look forward to the approach of another dog as a chance to get a treat. Fear conditioning researchers do the opposite, teaching a laboratory rat that something previously benign (like the sound of a bell) predicts something aversive (like an electric shock).

It’s unfortunate that so much research has been done on how to teach fear, something we don’t actually want to do in real life. However, what we learned from these studies should translate to the types of classical conditioning we do with dogs, and be even more relevant to helping us understand how fear-based behavior issues come about in the first place.

These studies have shown that that contexts and cues are important in classical conditioning. If you put a rat into a blue cage and then repeatedly play a bell right before shocking him, he will learn to fear the sound of the bell. The blue cage is the context; the bell is the cue. If you move the rat into a purple cage and play the tone without a subsequent shock, the rat will learn that the purple cage represents a different context, and that he does not need to fear the cue in that context. So the cue and the context contribute differently to classical conditioning.

Source:  Nature Reviews Neuroscience 14, 417–428 (2013)


In the case of a reactive dog, we might imagine that this dog spent time in a rough playgroup as a puppy, and learned to associate other dogs with being bullied. Here, the cue is another dog, and the context is the room the playgroup was in.

The hippocampus: learning in context

One of the jobs of the hippocampus is to encode contexts. Those London cab drivers with oversized hippocampuses have countless contexts encoded to represent many different locations around London. The hippocampus of the puppy who had a tough time at playgroup encoded the room where playgroup happened as a context.

In the case of our laboratory rats, the hippocampus encodes the blue cage as one context and the purple cage as another. With a healthy hippocampus, the rat can differentiate between the two contexts, and is fearful of the cue only in the appropriate context. But with a damaged hippocampus, the rat can’t differentiate between the blue and the purple cage. Although he was trained that the bell only predicts a shock in the blue cage, he fears both cages, because his hippocampus is unable to properly represent the context of the blue cage.

The associative amygdala

One of the jobs of the amygdala, on the other hand, is to encode associations. It encodes the association between cue and stimulus (bell predicts shock) and between context and stimulus (the shock only happens in the context of the blue cage). When humans were tested with functional MRI to see which regions of their brain became more active during a fear conditioning trial, the amygdala and hippocampus responded in different situations. When humans were trained to associate a cue with a shock, their amygdala activated in response to the cue. When they were trained to associate only a context with a shock, both their amygdala and their hippocampus activated when they were exposed to that context. The amygdala activated in both cases because the association was being recalled in both cases, but the hippocampus was only activated when the particular context was recalled. Fascinatingly, this study also found that humans with larger hippocampus volume had greater fear responses in fear conditioning trials. There was no association between amygdala size and fear response.

Prefrontal cortex as mediator

We are not, thankfully, completely at the mercy of the whims of our hippocampus and amygdala, subject to uncontrollable fears based on past bad experiences. We have some ability to take a step back and calm ourselves down. One of the parts of the brain involved in this higher-order cognition is the prefrontal cortex (PFC). This region of the brain has direct connections to both the hippocampus and the amygdala and appears able to mediate some of the signals coming from those two regions. Functional MRI studies tell us that while fear acquisition involves the amygdala, fear extinction (learning to let go of a fear) involves the PFC as well. We also know that people who have thicker PFCs are better at extinguishing fear associations. This mediation by the PFC is what lets us take a deep breath and choose not to give in to our fears.

Do dogs have this ability to take a step back and try consciously to decrease their fears? Certainly they are not as good at this skill as humans are, but I wonder if they do have some ability to do this. In a recent post at Reactive Champion, a reactive dog owner describes a situation in which she believes her reactive dog did just that.

PTSD: failure to contextualize?

When this system goes wrong, how does it go wrong? One hypothesis suggests that post-traumatic stress disorder (PTSD) is a disease of failure to contextualize. Humans with PTSD report having flashbacks to previous trauma unexpectedly and uncontrollably, and in inappropriate contexts. If you were in a drugstore during a robbery, it would be appropriate for you to remember that traumatic event when you returned to that location, and even to feel trepidation about entering that store again. You’d probably think about the event a lot for the first days, weeks, perhaps months afterwards, in many other contexts, as well. But your brain should recover, and you should eventually come to not think of it constantly, and only be reminded of it in similar contexts, such as the same or similar locations.

People with PTSD, however, may have trouble limiting their recall of traumatic events to similar contexts, so that they may be retrieving these memories (often vividly) in any and all contexts, years after the trauma has passed. The problem may lie with their hippocampus, which may have difficulty limiting recall by context. And indeed, studies have shown that people with PTSD often have smaller sized hippocampuses compared to the healthy population.

The perspective of the reactive dog

On to the realm of pure speculation, then, because studies haven’t been done in hippocampus function in reactive dogs. But I think the story of the person involved in a trauma who can’t appropriately contextualize her memories is similar to the story of the dog who was involved in a trauma (dog attack, overwhelming experience in a crowded area as a puppy) and can’t contextualize the experience. A dog who is attacked by other dogs at a dog park may learn to fear the dog park, but if never attacked outside of the dog park, should he learn to fear all dogs, everywhere? I’d argue that that’s an inappropriate association for his brain to make, and that the mechanism of failure might have to do with a failure of the hippocampus to appropriately contextualize, just as in someone with PTSD.

I’m certainly not saying that all reactive dogs have PTSD, but I am speculating that the mechanisms might be similar. Does hippocampal function vary across a spectrum, with some individuals having high-functioning hippocampuses and others not so effective ones? Do dogs with hippocampuses on one end of that spectrum have difficulty limiting their negative associations, such that they are more likely to suffer from fearfulness and possibly fear aggression? I don’t know, and I don’t know if the research will ever be done, but it’s an intriguing story to consider.

References

  • Maren, Stephen, K. Luan Phan, and Israel Liberzon. "The contextual brain: implications for fear conditioning, extinction and psychopathology." Nature Reviews Neuroscience 14.6 (2013): 417-428. [PDF]
  • Feder, Adriana, Eric J. Nestler, and Dennis S. Charney. "Psychobiology and molecular genetics of resilience." Nature Reviews Neuroscience 10.6 (2009): 446-457. [HTML]

Tuesday, March 3, 2015

Brain regions and their functions

https://magic.piktochart.com/output/4811521-brain-regions

[Note: this infographic is intended for use in my online class, The Canine Brain: From Neurons to Behavior, which starts tomorrow (March 3, 2015). Check it out if dog brains interest you, and/or if you're a dog trainer looking for CEUs!]