Showing posts with label student life. Show all posts
Showing posts with label student life. 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.

Wednesday, March 25, 2015

Who funds dog research?

As I move through my training and think ahead to my future career, I wonder: who will pay for all this research I want to do on dogs? I have so many questions to ask!
  • What changes happen in the canine brain as it enters, and then leaves, the socialization period?
  • How is the brain of a fearful dog different from that of a confident dog?
  • What are the genetic differences behind these variations?
  • How do environmental differences (prenatal stress, early learning, adult life) change the brain?
In other words, what are the mechanisms in the brain that differ in fearful dogs — receptors, neurotransmitters, synaptic wiring? And how can I learn about them without using invasive (painful and/or terminal) techniques?

Who are the caretakers of Dog, the species, who care about fearfulness? We as dog owners and lovers care, but dog owners and lovers aren’t the ones who are trained to heal unhealthy dogs, to perform research aimed at understanding them, and we (mostly) aren’t the ones who breed them. So who are the groups who are the caretakers of Dog, and what subsets of Dog do they care for?

Image: Who is my caretaker?


Veterinarians

We (I am a veterinarian) are trained to heal sick dogs. Relatively few veterinarians perform research compared to those who engage solely in clinical practice. But some do perform research: most commonly as faculty at veterinary schools alongside a clinical practice, or less commonly as researchers without a clinical practice at research instititutions.

Veterinary research, as a result of this strong emphasis on healing the unhealthy, is focused on clinical results. Veterinarians most commonly perform research which asks questions about the effectiveness of particular techniques — medications, surgical approaches, new equipment. Veterinary research very rarely addresses root questions about mechanisms, particularly in the area of behavior. Rather than asking “How are the brains of fearful dogs different?”, veterinary research is more likely to ask how we could fix a fearful dog: “Does this medication make a fearful dog less fearful?”

In fact, as I pursue my mechanism-based questions, I am asked if I miss being a veterinarian. The perception is that because I am engaged in basic, rather than clinical, research, I am no longer working as a veterinarian.

Basic science researchers


If veterinarians do clinical research studies, then who does basic research biomedical studies, studies that look not at how to fix problems but at how the body works? Ph.D. researchers are more likely to do this sort of research, which is why I am currently engaged in obtaining a Ph.D.

Traditionally, Ph.D. researchers have not been interested in dogs. In fact, way back in 2004 when I was originally deciding between a Ph.D. and a D.V.M., I was told by a Ph.D. animal behaviorist, “Ph.D.s don’t study domesticated animals. Veterinarians study those.” (Actually, veterinarians mostly just try to fix unhealthy domesticated animals, not study the healthy ones.)

That perception has changed in a big way in the intervening eleven years. There are now multiple laboratories studying dogs. But where does their funding come from — who cares enough about dogs as dogs, not as models for human problems, to provide the impressive funding needed for a genomics study? (The work I am doing for my Ph.D., sequencing messenger RNA, costs around $45,000.)

The U.S. federal government


The traditional source of funding for basic research is the federal government: the National Institutes of Health for health-based research and the National Science Foundation for more basic research. But these two massive institutions are very much focused on human health — as they should be, as they are funded by the tax dollars of American citizens. The economy can’t support all the research American researchers would like to do, and getting an NIH or NSF grant is becoming more and more difficult as grant funding is cut. Funding to study dogs as models of human disease? Maybe, but isn’t it easier to study laboratory rodents (on which you can perform invasive studies) or work on humans directly? Funding to study dogs as dogs? Go lie down until it passes.

In my experience, the small number of laboratories directly studying dogs are either studying them as models for questions about human health or evolution, operate on a shoestring budget, or have great trouble obtaining funding for what they want to do.

Animal welfare organizations

So who cares about dogs? Animal welfare organizations, some of which are national in scope and do perform research. Some major players in this field are the American Society for the Prevention of Cruelty to Animals (ASPCA), the Center for Shelter Dogs (CSD), and the Humane Society of the United States (HSUS). I am most familiar with the research coming out of the ASPCA and the CSD, and it is exciting stuff. But it is again mostly focused on applied questions: how can we help the shelter dogs in our care?

I reviewed some of the research these two organizations have performed on how to identify and treat food aggression in shelter dogs in my story for the Bark on shelter behavioral assessments. This was ground-breaking research and I am really glad to see it published. But it doesn’t ask the basic (i.e., non-applied) research questions I am interested in: what is it about the brains of these dogs that differs from the brains of dogs without food aggression? That kind of research doesn’t have immediate applied benefit. You can’t take it to a shelter worker with a recommendation about whether or not to put a food aggressive dog on the adoption floor. It is incredibly impressive that these shelter-focused organizations perform any research at all, and it is absolutely appropriate that the research they perform should have a highly applied focus, with clear questions that, when answered, will provide guidance on how to improve the lives of shelter dogs, immediately. They do not have the resources to pursue these sort of mechanism questions that I want to ask, which do not have immediate applicability.

So who cares about understanding how dog brains work, with the hope that that information will provide a base for future applied research? Who cares about the whole species, not just the subset in shelters or the subset in hospitals?

Breed organizations

Breed organizations care very much about the health and welfare of dogs, and in fact have provided funding into the mechanisms behind health issues specific to their breed. A recent paper about associations between spay/neuter status and health issues in Golden Retrievers was partially funded by the American Kennel Club’s Canine Health Foundation (AKC/CHF), and a similar study on Vizslas was funded by the Vizsla Club of America Welfare Foundation. (I blogged about these studies elsewhere.)

These organizations can fund basic research on how and why particular diseases occur in their breeds, and may even be willing to fund expensive genetic studies, such as a recent one on the genetics of cancer in Golden Retrievers, supported in part by both the AKC/CHF and the Golden Retriever Foundation. However, their focus is very much on the problems of a particular breed. My questions are broader: why do dogs of all breeds have different personalities, some more or less fearful? These organizations are really the caretakers of breed subsets of Dog, not of Dog itself.

Who, then?

Who does that leave as a group willing to fund studies on Dog? On problems common to all breeds? On problems which may or may not provide good models for humans? If I hope to one day run a laboratory which studies these problems, who can I hope to help pay for the research?

I would be remiss if I did not mention Morris Animal Foundation here. While their important Golden Retriever Lifetime Study happens to focus on the health issues of a single breed, their mission is to fund research into studies of small animals (dogs and cats), livestock, and wild animals, with no breed limitations. This group is doing important work, and I applaud them.

But one organization is not enough for a laboratory to depend on for survival, especially in these times with research funding so hard to come by. And so I wonder: are we, the dog lovers of the world, the ones to start supporting research into what it is to be a dog? We, who own dogs of all breeds and mixes, with all sorts of problems, who know what problems most plague us as owners — not just medical problems, but behavioral ones?

And so I leave you with my dreams of crowdfunding, in which a researcher proposes a study and asks the public to support it through donations. Such an approach allows the dog community to take the task of answering basic questions about Dogness into their own hands. This direct connection between a researcher and the community affected by their research is a new benefit of this age of social media. Is this approach right for this particular problem? Time will tell.

Image: Will crowdfunding work?

Saturday, March 15, 2014

The state of the Zombieverse: spring 2014

No matter how many times I resolve that I will post at least once a week, life always seems to get in the way. So I figured I’d make lemonade from the lemons and tell you guys about what I’ve been up to. I know a lot of you enjoyed the posts about life as a shelter medicine intern, but I’ve been suspicious that life in the lab would be less interesting. (“Today I found the perfect set of pipetters! It was awesome!”) Still, it seems possible that there are people out there who wonder what first year PhD students spend their time doing, so here it is.
Me escaping from lab for Scio!

I went to ScienceOnline Together 2014, which was a great deal of fun. The head of my lab smiled tolerantly and let me go — she doesn’t do much layperson-level science communication herself, but she knows I love that stuff and figures there’s probably a good reason for me to get better at it. I went to a discussion about engaging undergraduates in science (run by two undergraduates), where I learned that Facebook is the Thing right now but Twitter might be catching up; a brainstorming session about providing explanations of various scientific concepts to people at a variety of levels, elementary school through expert; and an intergalactic gala, where I met Malcolm Reynolds, the Doctor, and an inflatable Dalek, and ate carbonated ice cream which was made before my eyes.

Back home but still on the science communication track, I have been kicking around ideas with another science blogger here about improving science communication education at UIUC. Let me tell you a story about how much the world needs help training aspiring scientists about science communication! I was in class with some undergrads, and they were talking about our recent midterm. One said: “I didn’t really understand that question where we were supposed to explain the findings as if to a scientist, and then as if to a non-scientist. What did that mean?” The other replied: “I don’t know, so I just wrote the same thing twice.” Ouch.

So yeah, I had some midterms. The one mentioned above was for an excellent class on genes and behavior. I really dig the structure of this class: every week we read some articles, then discuss them on the message board. We come to class already understanding the articles fairly well, and we discuss them more in person, both in small groups and as a full class with the professor. It’s a great design, though it does suffer around midterm time when the students are too tired to muster the energy to do paper analysis. Still, it is always better to read articles than a text book!

I also had a project for a statistics class. Statistics can be mind-bogglingly boring, but it is really essential to understand it if you want to be able to analyze your data well. In my experience doing my Master’s work, asking a statistician for help will lead to some terrifyingly complicated analyses that you will only understand during the moments that he is explaining them, and will immediately become completely opaque when you are trying to explain them to your advisor the next day. Anyways, this stats class was designed for grad students, not undergrads, and this project was to do some analysis of our own data. I am a first year student, so what do I not have yet? Data. I have a bunch of RNA which had been sitting in the sequencing machine for weeks. My hope was that sequencing would finish up in time for me to analyze that data for the class. Nope. So, with the teacher’s permission, I made up the data. It was kind of fun. Not enough significant results? Let me just change those numbers... This is apparently not something we are supposed to do in real life, unfortunately.

Did you hear me mention RNA in the sequencer? Yes, I am also doing research! Last semester was a lot of time at the bench, doing ridiculously finicky extraction work to get RNA out of tissue samples. RNA, you will remember from high school biology or some such, is a single-stranded copy of DNA. The cell makes these single stranded copies for use in making proteins, so RNA is part of the whole translation mechanism whereby DNA turns into an organism. Because RNA is single stranded, it isn’t as stable as DNA (which is double stranded), so handling RNA is a really annoying process involving gloves and this magic spray bottle which kills the evil RNA-eating demons which apparently live in the air, your hands, on counters, and on the mobile phones that undergraduates like to leave in your work area.

But once you get the RNA extracted into teeeeny little vials, you can send it off to be sequenced. What I will get back (what I got back a few days ago, but which involves a lot of processing before I can extract useful information from it) is information about which genes are expressed at different levels in particular tissues. I am using tissues from foxes selected for tameness versus foxes selected for aggression. (Remember, I work on the tame fox project.) Why is that interesting? Well, it seems likely that a lot of the differences that we see in tame foxes aren’t due to changes in their actual genes, but changes in how those genes are regulated. So maybe tame foxes express more of a particular gene rather than a different form of that gene. If I know which genes are expressed at higher or lower levels in tame foxes, I can start to guess at the functions of those genes, in foxes and, eventually, in dogs and humans.

What else? Helping the head of my lab teach her class in domestic animal behavior. I have been working behind the scenes to find good papers for students to read and writing questions to assess the students’ understanding of those papers. It’s the perfect job for me. I get to read a lot of papers about domestic animal behavior, and I get paid to do it.

Finally, I’ve been working on another project which is days (DAYS, I tell you) away from being ready to be announced here. I think it’s safe to say I find it more exciting than you will, but I still think you should check this blog daily in breathless anticipation!