Sunday, May 8, 2016

Geek version of the fat mutant labs FAQ

In the face of overwhelming demand (three people thought it sounded like a good idea), here is the geek version of the fat mutant labs FAQ, the nitty gritty about the study findings.

What gene is mutated and what does it do?

The gene itself is one of these weird ones that actually codes for multiple proteins. (Basic genetics usually assumes that one gene codes for one protein, of which there may be a few different but similar versions.) The gene in this study is POMC, or proopiomelanocortin. The “pro” means that it codes for a protein which doesn't itself do anything until it gets cut up some more. The rest of the long name describes the things it gets cut into:
  • opio: short for opioid. Opiods are potent pain relievers; the classic opioid is morphine. If you or your pet has had surgery, you’ve probably used an opioid for pain relief during or after it. (There is currently a big scandal about drug companies and opioids in the news.) In this case, two of the products snipped out of POMC are endogenous (made by the body) opiods, β-endorphin and enkephalin. They are feel-good substances.
  • melano: refers to melanocyte stimulating hormone (MSH). MSH has a bunch of different effects in different tissues, but most importantly has been associated in humans with effects in “controlling appetite,” our authors tell us.
  • cortin: the coolest thing this gene makes is ACTH, which is released into the bloodstream to tell the adrenals (down by the kidneys) to release the “stress hormone,” cortisol. This is the system I study! But it is, it turns out, not really relevant to this particular study.

What was the mutation?

It was a 14 base pair deletion. The gene itself is thousands of base pairs long; in the dogs with the obesity-associated allele, they were missing just 14 base pairs. But remember, DNA bases (nucleotides) are translated into proteins in sets of 3. (Three nucleotides codes for one amino acid; a string of amino acids makes up a protein.) If you remove a chunk of bases that is not a number divisible by 3, suddenly the translation machinery that reads the DNA and produces proteins gets completely off track. It is just reading in sets of three. Now it’s off by one or two and suddenly it's creating entirely different amino acids, so the resulting protein is completely different after this point. This is called a “missense” mutation, because a protein is still generated, it's just made with different amino acids.

For example, the sentence “mad man sat” becomes gibberish if you mess up the spaces and make  “adm ans at” after removing just one letter.

So that’s what happened here: the first chunk of the POMC protein in these dogs with this allele is fine, but the second chunk is gibberish from the body’s point of view. Since the POMC protein gets cut up into smaller proteins with actual functions, this means that some of its products were fine, and some were not. The article has a lovely illustration of the situation, highlighting in red the products that are affected by the mutation.

Image from Raffan et al., 2016

The products that are broken in dogs with this allele are β-MSH and β-endorphin. The first, you will remember, has been associated with control of appetite in humans. (And it’s apparently somewhat different in rodents, so it’s hard to test its function in laboratory mice, so it was exciting to find it in dogs so we can learn more about obesity!) The second is one of the endogenous opioids, a feel good substance.

How do these broken proteins cause obesity?

We don’t know. The authors write:

The mechanism by which reduced β-MSH and β-endorphin due to the mutation causes behavioral and weight phenotypes remains to be precisely elucidated...  However, studies of humans with POMC mutations resulting in aberrant forms of β-MSH ... have suggested that β-MSH is important in controlling appetite and obesity development in man, with hyperphagia notable in patients with both mutations... The role of β-endorphin in regulating appetite, satiety, and energy balance is less well understood, but it has been proposed to underlie oro-sensory reward in high-need states or when the stimulus is especially valuable. However, mice selectively lacking β-endorphin are hyperphagic and obese, suggesting that the loss of both neuropeptides could contribute, in combination, to the phenotype seen in dogs carrying this frameshift POMC mutation.
 So, we don’t know, but we know MSH problems make people more likely to eat a lot, and β-endorphin may have to do with the feeling of reward after eating.

How did they find the gene?

They guessed! They had a small number of genes that they thought might have to do with obesity, and they checked them out in some labs. They looked for different versions of the genes in different dogs, and then looked for alleles (versions) which were more common in fat labs than not fat labs. They found one hit — this particular allele of POMC.

This is known as a “candidate gene” approach: when you pick a gene that you think might have an effect in a particular phenotype and test it out specifically. It has historically been less productive than “hypothesis free” approaches in which you basically ask about all the genes you possibly can if they have something to do with the phenotype. This is because our guesses about which genes affect which phenotypes turn out to be wrong so often. So these authors got lucky to get a result!

Was their sample size big enough?

I hadn’t considered getting into the statistics (I hate statistics) but some people actually asked about them. Yeah, I like their numbers for a candidate gene approach. To get reliable results using some other methods they would have needed more dogs, but when you’re just asking questions about a few genes, it’s fine to have a smaller number (in this case, 310).

I’d be more concerned about where their dogs came from. They tell us:

Labrador retriever samples were collected from dogs from a large assistance dog breeding colony (n = 81) or that were pet dogs from the UK (n = 310). Pet dogs were recruited either after their owners volunteered in response to an email from the UK Kennel Club sent to over 15,000 Labrador retriever owners, or via participating veterinary practices.
This sounds reasonable enough. But if I wanted to play devil’s advocate, I’d suggest that they were biasing themselves to a particular kind of owner, the kind of owner who responds to UK Kennel Club email. These owners may be more likely to breed and/or show labs, and therefore these labs may have a slightly different genetic background than some other group of labs. For example, perhaps some famous show lab sire who sired thousands of puppies happened to have this mutation. And then perhaps labs that are shown are more likely to be fat than labs who are not (because UK judges actually reward obesity in show labs — don’t get me started on that). If that happened, it would throw off the statistics and you might see a spurious correlation between the mutation and obesity.

That’s just me spinning tales. I think their methods are pretty standard; it’s hard to recruit pet dogs to these kinds of studies and they did it the usual way. It's quite interesting that they found a mutation which is so clear in its loss of function of the protein. If the correlation is indeed spurious, subsequent studies using different populations of labs should show us.

Any more questions?

What else do you guys want to know? I tend to focus on stuff in studies that I find interesting. What do you find interesting?

Learn more genetics

As before, I will shamelessly take the opportunity to plug my upcoming genetics class. It is not too late to sign up; it starts Monday, May 9, but you can sign up several days late.

Raffan, Eleanor, et al. "A Deletion in the Canine POMC Gene Is Associated with Weight and Appetite in Obesity-Prone Labrador Retriever Dogs." Cell Metabolism (2016).

Saturday, May 7, 2016

Fat mutant labradors FAQ

The study about a mutation associated with obesity in labrador retrievers has received massive news coverage for a dog genetics article (and you can see how happy the researchers are about it at @GODogsProject). So what does it mean for your dog?

Image: Raffan et al., 2016

  • Do all labs have this mutation? No. They tested 383 UK labs and found that of 383 Labrador retrievers from the UK, 78% of them didn't have this mutation at all; 20% had one copy of the mutation (were heterozygous); and 2% had two copies (the maximum number you can have; they were homozygous). They tested some US labs as well and found similar frequencies.
  • Do any other breeds have this mutation? Yes, it was also found in flat-coated retrievers, a breed closely related to the lab. The researchers tested 38 other breeds, testing 8-55 dogs per breed. (The list of breeds they tested is provided.) They tested 55 golden retrievers, another closely related breed to the lab, without finding this mutation. That doesn’t mean it’s not out there, but it does suggest that if it is present in other breeds, it’s much less common in them than in labs.
  • If my dog has this mutation, does it mean my dog is doomed to be fat? No. They did show an association between the mutation and weight: dogs who have one copy of the mutation are, on average, 1.90 kg (4.18 lbs) heavier than dogs who have no copies. Dogs who have two copies are on average 3.8 kg heavier than dogs who have no copies. (This is in labs, but the numbers in flatties are very similar.) But that’s an average. It’s not all about genetics. Some dogs who have this mutation won’t put on that much extra weight, and some dogs who have it will put on more. The gene they studied will interact with other genes to affect your dog’s eating habits and metabolism, and of course in weight gain as in behavior, the environment (food type, food amount, exercise) is a huge factor.
  • If my dog is fat, does it mean my dog probably has this mutation? Not necessarily. There are lots of reasons to get fat.
  • Is this “the gene” for weight gain? In dogs as in humans, multiple genes control weight. This is just one, albeit one with a pretty impressive effect in this breed. And again, remember the importance of environmental factors!
  • How does this mutation cause weight gain? It may have to do with causing dogs to want to eat more (certainly a trait we’ve all seen in labs!). It may also change their metabolism directly, affecting how they turn calories into energy.
  • Where did the mutation come from? Both labs and flat-coats are descended from the St. John’s water dog, a breed which is no longer around. The researchers have reason to believe that the mutation dates back to that breed.
  • Does this mutation make labs easier to train? Possibly. The researchers tested a population of labs who are used as breeding stock for assistance dogs, and found that many more of them carried the mutation than in the general population: 23% had zero copies, 64% had one copy, and 12% had two copies. Additional genetic analysis suggested that these dogs are being actively selected for this mutation (unbeknownst to the people who are selecting them!). This suggests that something about this mutation makes dogs better at assistance work — perhaps making them more food motivated and easier to train.
  • Does this mutation make flat-coats fat, too? It does, and yet flatties aren’t known for obesity the way labs are. It’s a bit of a head scratcher.
  • What's the big deal? Didn’t we already know that labs are food-obsessed mutants? I know, right?
Raffan, Eleanor, et al. "A Deletion in the Canine POMC Gene Is Associated with Weight and Appetite in Obesity-Prone Labrador Retriever Dogs." Cell Metabolism (2016). It’s open access and, as modern genetics papers go, not that hard a read. Check it out!

Want to know more about dogs and genetics? I have a class on it starting Monday, May 9! We will learn concepts like homozygosity and heterozygosity, and I will be happy to discuss this study in more depth.

Thursday, May 5, 2016

Dogs and hugs FAQ

Stanley Coren, well known and respected author on dog cognition, recently published a blog post about dogs not enjoying hugs. Now that I have been asked to weigh in on his post by my father ("that can't be true!"), my lab mate ("Jessica will have some useful insights about this!"), and multiple dog park friends, I feel compelled to spread my wisdom across the internet for the benefit of all, whether they want it or not.

Source: The Data Says "Don't Hug the Dog!", Stanley Coren, Psychology Today

  1. Does your dog enjoy being petted by you? Almost certainly.
  2. Does your dog enjoy being grabbed and squeezed? Probably not.
  3. Do any dogs enjoy being grabbed and squeezed? I am sure there are some. I know some dogs who enjoy all interactions with humans up to and including getting whacked up side the head (I live with one). But as a species generalization, I believe they mostly don't.
  4. Should you hug random dogs when you meet them? Absolutely not. But you knew that already, right?
  5. Should you hug your own dog? Sure. I do it to my dogs sometimes. Just be aware that you are doing it for your own enjoyment, not theirs. My dogs tolerate the occasional squoze. I tolerate being punched in the butt when I get home from work.
  6. How can it be that dogs, who love us so much, don't enjoy hugs, which we enjoy so much? Well, note that primates really love pressing our tummies against each other, but canids don't (except when they are initiating sex or displaying poor manners). They display affection other ways: licking you in the face, sitting next to you, leaning on you. With someone who moves at the same pace they do, you sometimes see them walking or running shoulder to shoulder. I would love to hear from people about what they think their dogs do instead of hugging.
  7. Was Coren's study a good study? It wasn't actually a study, and Coren didn't say it was; in his blog post, he refers to it as data. This data set was pretty interesting and it was nice of him to share it with us. It would be even nicer if someone did a study using similar approaches, but with a control group, maybe having the person scoring the dog body language blinded to the group the dog is in (editing out the human so you can't see the hug?), and published it in a peer reviewed journal. Oh, and while I'm asking, make it an open access journal, please.
  8. Where can I learn more about dogs and hugs? In my mind the best resource is Dr. Patricia McConnell's coverage in her classic book, The Other End of the Leash. Which is a must-read for oh so many reasons.

Saturday, April 23, 2016

From the genetics of dog breeds to stress and reproduction

The other morning I was talking to my husband in bed in an attempt to help him wake up.

Me: So I ran into our friend who walks those three goldens separately yesterday and we had a nice conversation. She said she’d read my blog and had a dog genetics question for me.

Him: mmmppphh

Me: She said she’d heard that 1% of dog genes account for all the differences between breeds and asked me if it was true. I pointed out that 1% of 20,000 is still a lot of genes, and also explained that it's really hard to use statistics like that to describe genomic differences, because you can measure those differences in so many different ways.

Him: Did you tell her that humans and chips are 98% similar genetically?

Me: Yes I did.

Him: But I’ve been seeing that for at least 10, maybe 20 years. Is it still true?

I consulted the internet on my phone.

Me: Let's see... The Smithsonian Institute says we're 1.2% different from them. I think I'll skip this link to the Institute for Creation Research -- is that really the second hit on “human chimp genetic similarity”?! Ah, Wikipedia gives more information: “The alignable sequences within genomes of humans and chimpanzees differ by about 35 million single-nucleotide substitutions. Additionally about 3% of the complete genomes differ by deletions, insertions and duplications. Since mutation rate is relatively constant, roughly one half of these changes occurred in the human lineage.” Well, that’s not true.

Him: What?

Me: Mutation rate isn’t constant.

Him: It’s not?

Me: Well it is closer to constant in specific areas, like parts of the mitochondrial DNA, which we like to use as clocks. But over the whole genome, which is what they're talking about here, no. Different areas evolve at different rates. There are hotspots that go faster. And then the whole species might change faster when its environment suddenly changes. Like if you're in a lovely sunny valley and you're well adapted to it and then suddenly an Ice Age starts and your valley fills with ice and you suddenly have intense selection pressure to change your coat length and thickness and your diet and things like that. The stress itself can change your mutation rate.

Him: Stress can’t change your mutation rate! How would that even work? If a female is stressed, it’s too late, her eggs are already made.

Me: Her grandkids then? Or only sperm have more mutations? Hmm, that’s good point.

I consult the internet again. I find and discard an article about yeast evolving more quickly under stressful conditions. Yeast don't make eggs or sperm as part of their reproductive process.

Me: Here you go. Flies. Close enough to mammals for you? Stress does cause flies to have offspring with more mutations. It makes sense because if you’re stressed, it means you're probably not well adapted to your environment, so you should do the random shuffle with your kids’ genetics in the hopes that something, anything, different will give them a better shot. Mostly they’ll be worse off, but at that point it’s worth if it a few are better off and can pass on those genes.

Him: But how does it work with female flies having already made their eggs before they’re stressed?

Me: I dunno... Hang on... Here we are. OK, so the researchers mutated the males, their sperm.

The reason the researchers mutated the males has to do with how DNA is fixed in male and female fruit flies. There is almost no DNA repair in sperm. But the egg can repair DNA in any sperm that fertilizes it.

So the researchers were basically asking how much of the mutated DNA from the male could slip through the repair processes in the egg. The answer was that eggs from stressed females let a lot more mutations through.

Why would stressed female eggs not fix DNA as well? Probably because fixing DNA perfectly costs lots of energy. And these stressed females may not have had enough energy to spare.

There are two different kinds of DNA repair out there. The one that fixes the DNA perfectly costs a lot of energy. The other kind gets rid of any gross problems but leaves errors behind. This costs less energy but leads to more mutations.

The idea is that stressed females can't afford to use the perfect DNA repair system. So they use the other one. Their kids survive but they have more mutations.

—Stanford at the Tech, Understanding Genetics
 Me: Oh crap now I’m late to take Jack to physical therapy.

...Kind of makes you wonder about puppies conceived in puppy mills or animals conceived in hoarding situations, doesn’t it? Might they have more mutations than animals conceived in less stressful environments?

Saturday, March 19, 2016

Why are puppy vaccination schedules so crazy?

Next week I'm giving on a webinar about puppy vaccine schedules. I'm aiming the webinar at people who have to explain to puppy owners why the crazy schedule, why they can't go to the dog park even though they have all the vaccines they need at this point, why they should socialize but be cautious... We will start with a whirlwind tour of the immune system to give you guys a good grounding to understand why puppy vaccines have to be given every 3-4 weeks. There will be scary parvo stories and photos of cute puppies and cute immune cells and fun biology facts and suggestions on what to do about that vet who thinks socialization isn't all that important. It will be a blast, you should come and ask me lots of questions!

When: Wednesday, March 23, 8-9pm ET
Where: sign up with the Pet Professional Guild
CEUs: Yes, 1!

Questions about whether this webinar will be helpful for you? Ask me here or on Twitter (@dogzombieblog).

Sunday, February 7, 2016

Being the one who remembers: humane housing in shelters

A cat who is clearly not in a shelter.

Last night I wrote the first draft of a document on appropriate housing for shelter animals for IAABC’s new shelter division. Before getting into the nitty gritty details, I wrote as part of the general overview:
Housing for any shelter animal should be clean and safe: easy to sanitize; no sharp edges that could injure the animal; no gaps or broken latches that could allow the animal to escape. Animals should not be housed in temporary enclosures like airplane crates for more than a few hours while longer term housing is located.
I wondered: Is this too basic to even cover? Will readers stop reading the document at this point, thinking it’s worthless?

But then I remembered the story of a cat I encountered at a shelter during my internship. I was working in the kitten house, a small house dedicated to raising kittens during The Season. The cages were mostly roomy enough for moms with their litters; smaller cages were reserved for litters of orphan kittens. But one small cage had an elderly adult cat in it.

This cage was just too small for this cat. Now, some shelters keep all their cats in cages like this. But the thing was, this was a really excellent shelter. They did a great job of providing their cats with roomy housing. And their vet knew the importance of good housing and advocated for it, and moreover had enough authority to make it happen (sadly, a bit of a rarity in many shelters). So what was going on here?

I asked. Turns out, the cat had been adopted by a staff member but had proven to have behavoral issues that made it difficult for her to live in a home. So she had come back to the shelter. She also had a disease or two which made her expensive to keep and difficult to adopt. But the shelter wasn’t willing to euthanize her, so they put her in a spare cage in the kitten house and planned to figure out the situation later. And hadn’t figured it out yet, because in a shelter, there’s always some more pressing problem that has to be figured out today.

What it took for this cat to get good housing was for someone to notice and make her a priority. We moved her into the bathroom for a few days so she could have more legroom, and she hung out with me in the guest bedroom at night. I found a roomy wire crate intended for litters of kittens and we set that up for her for her evenings long term, and during the days she got to hang out on the desk of the kitten house manager.

And that is often the job of the person at a shelter who works on animal behavior and welfare. Not training. Not making plans for Kong programs. Not fighting to change whole banks of cat cages out for something better. But noticing one single animal who got forgotten in an airline crate in a corner. Being the advocate for the little things. Being the one who remembers.