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.

Sunday, January 24, 2016

Dog parks: tools to be used for good or evil

Dog parks can be valuable ways to exercise and socialize your dog. They can also be dangerous places where dogs can get hurt. And so we ask ourselves: are dog parks a good thing or a bad thing? I argue that they are neither. Like retractable leashes, they are just a tool that can be used well or badly.

Park design

The design of a dog park can have a lot to do with how well it functions. I think the size of the park is incredibly important. At my local park, we have a lot of space. And I use this space with my dogs. If there is a group of dogs that my dogs aren’t getting along well with, and I see trouble brewing, I move on to a different part of the park. In a small park, this wouldn't be possible.

Jenny at my fabulous local park

My local park also has a smaller area, separately fenced. It’s a great place to take a smaller dog when the park is full of big dogs, or to take a dog who needs a cooling down period after he's been acting like a bully. I don’t use this space much with my dogs, but it’s extremely helpful for a friend of mine who’s trying to teach her six month old to restrain his enthusiasm around other dogs by giving him time outs when he fails to control himself appropriately.

Park timing

I don’t go to the park when it’s crowded. Of course, it’s crowded at the times that are the most convenient for the most people: late afternoon, weekends, when the weather is lovely. I go in the mornings during the week. I lead a lifestyle which makes that possible (though I have to push back at work to protect that time). If you can only go to the park when it’s crowded, it might not be worth going at all. Tempers run high when dogs are packed in together with no real room to get away.

Dog management

This is the important one for me: I am always alert and managing my dogs. I keep an eye on them. One of them can have a short temper with other dogs, and I keep her moving, away from groups. If I see her meeting another dog, I am watching closely for her to get tense, and if I don't think it's going well, I call her away before something goes wrong.

This kind of management is hard for a lot of owners who don’t understand dog body language well. For this reason, I’ve founded a group at my local park with the goal of (among other things) providing educational material at the park to help owners understand how to identify and avoid problems before they start. Not everyone will be interested in this material, and that’s why it’s also important to me to attend a large park during low occupancy times.

Stuff happens

My dogs have been attacked at the park. One of my dogs has also been attacked while I was walking him on leash on a sidewalk. And once he got away from me and was almost hit by a car. That’s life. Is it more dangerous at the park than on a leash on the sidewalk? Possibly, though I’d love to see evidence one way or the other. Is it more dangerous to a young dog to fail to get his crazies out on leash, and then be at risk of being surrendered by a frustrated owner? Again, I can’t say, but there are risks to any choices about how we manage our dogs.

At the park, there are no cars, no cats, no children, no bicycles, no terrifying joggers just begging to be bitten. One of my park friends walked her dog on leash until he bit a roller blader who passed too close. Without the park, she would be unable to exercise her dog safely. My shy dog Jenny has made canine and human friends at the park that she is unable to make in situations in which she's restrained. She has made incredible gains in confidence. That has come at a risk, but to me, with a lot of careful management of the dog park environment, at the right park, with these dogs, it’s worth it.

Thursday, January 14, 2016

Too many pairs: DNA, chromatin, and chromosomes

Some facts:
  • Molecules of DNA are double-stranded, each strand a perfect complementary copy of the other.
  • Humans have 23 pairs of chromosomes.
  • Chromosomes are made of DNA.
  • We have two copies of each gene.
Where do these two copies of each gene come from — the complementary DNA? Or the pairs of chromosomes? In fact, what is the relationship between DNA and chromosomes? These questions have proven thorny for students in the past, so I'll try here to describe the two different ways in which genetic information is duplicated in a cell.

1. Complementary copies of DNA strands

Molecules of DNA duplicate the information they carry. Each base in a DNA strand is bonded to its complement on the opposite strand: A bonds to T, C bonds to G. It’s like a backup mechanism: if something happens to one part of the strand, the other half is there with the complement of the information. So that’s the first way in which genetic information is paired. And the important part about this pairing is that the pairs are exact complements of each other, like mirror images: the information is duplicated precisely and does not vary.

Part of a DNA strand, demonstrating complementary bases in matching colors
This double-stranded molecule of DNA, then, is wrapped up tightly around proteins called histones, and this set of spools of DNA and histones all together is a material called chromatin.
Chromatin: light blue/green strands of DNA wrapped around bright blue histones.

2. Two copies of each chromosome

Chromosomes are made out of chromatin. In a lot of the pictures of chromosomes in which you can see the chromatin that makes it up, the chromatin looks sort of like yarn woven into a sweater. That’s a reasonable way to think of chromosomes: big structures (big enough that we can see them with a not-too-powerful microscope) made from this yarn-like chromatin.

Cartoon of chromosome made of yarn-like chromatin. (Image by Magnus Manske at Wikipedia.)
 A particular gene is always on a particular chromosome in a given species. For example, the gene for oxytocin, OXT, is always on chromosome 24 in dogs and chromosome 20 in humans. So your chromosomes are very orderly, each one containing a specific set of genes.

Humans have 23 pairs of chromosomes. Dogs have 39 pairs. In fact, Wikipedia has a whole page devoted to the number of pairs of chromosomes in different species. We think of chromosomes as looking like big X. The X is actually the two separate chromosomes in a pair, stuck together during the process of cell division. Usually those two arms of the X are separate in the cell.

Image by JWSchmidt at Wikipedia

In a pair of chromosomes, one chromosome is made of chromatin from one (double) strand of DNA and proteins, which you got from your mother; and the other chromosome is made of chromatin from another (double) strand of DNA and proteins, which you got from your father. So you have, for example, two copies of chromosome 20, one from your mother and one from your father.

Human chromosomes: 23 pairs.
These pairs of chromosomes are the second way in which your genetic information is paired. But this is very different from the exact copy pairing of strands of DNA. Your version of the OXT gene on the chromosome you got from your mother may be slightly different from your version of the OXT gene on the chromosome you got from your father. Where her version had a G-C, his version may have an A-T. (Or it may be just the same.)

DNA differences on two different copies of the same chromosome (see the difference highlighted in blue).
So we have two versions of each gene, one on each chromosome in a matched pair. For a particular gene, we may have two identical copies (in which case we are “homozygous” for that gene) or we may have two different versions (in which case we are “heterozygous” for that gene).

So, yes, we essentially have four instances of each gene in each cell. That’s four instances, but a maximum of two versions of the gene (the doubled instances on a double strand of DNA are always identical complements; it’s only when you compare instances between chromosomes that you may see differences).

In the minds of geneticists, it’s the two versions in the pair of chromosomes which really count. That’s the pair that could differ, after all. And that’s why you'll hear that we have “two” copies of each gene, even though the gene is paired both in the DNA and again between chromosomes.

Wednesday, January 13, 2016

Science for the people

One of my students in the online genetics class I’m teaching commented to me that it was a little sad that we were marketing the class as “not too difficult.” Science is only as hard as you make it, she said. It shouldn’t be something scary.

It shouldn’t be, but for a lot of people it is. As a freshman in college I figured I should take college level biology as an elective so that I had a solid groundwork in how life works. (I was a medieval studies major.) But talking to my pre-med friends convinced me otherwise. Science classes were for people who were all in: they were only for scientists, not dabblers. They were hard work. Lots of hard work.

When I decided to go back to school to become a veterinarian, I took that introductory biology course, and a lot of other science courses. I learned a lot of information I’d never use again (and have since forgotten), particularly in chemistry and physics. I wasn’t eligible to learn the things I wanted to learn until I’d jumped through these hoops.

I hope that these days, with online classes, the tide is starting to turn. I don’t think people should have to take a year of basic biology in order to learn a little about genetics. I don’t think people should have to learn about photosynthesis and the difference between monocots and dicots (those are groups of plants, by the way) in order to learn neurobiology. It is perfectly possible to design science courses for people who are not pre-med or pre-vet undergraduates. But sometimes, when I’m telling people about this great new genetics course I'm teaching and they look slightly alarmed, I'm saddened by the history of how we've traditionally taught science courses.

More than thirty people signed up for the genetics course. I hope I’ve designed something that’s worth their while.