Monday, January 23, 2012

I *heart* Data

PhD comics never fails to have an appropriate image. (

 A while back I said I would discuss what “comes next” after all the field work. Well, I have started the next big project: identifying all the ticks I collected from the mice and voles we trapped over the summer. This is a big project because I collected over 670 ticks, and these are larvae and nymphs, the younger life-stages of the tick, and are really small and can only be identified under a dissecting microscope. It is important to identify all these ticks to species and life-stage because there are different assumptions about previous host interactions and possible infections for each group. To catch everyone up, here is some background before we get too deep into things.

This is a diagram of the Ixodes scapularis lifecycle. It is a "cool season" tick because its adults are active in the fall. Most of the ticks in Indaina have all life-stages active in the spring and summer.

To review, ticks are ectoparasites of vertebrates that have a 4-stage life cycle: egg, larva, nymph, and adult. These parasites need to bite a host and obtain a blood meal in order to molt and transition to the next life-stage. This is somewhat unique because other common vectors like fleas and mosquitoes only feed on a host directly in the adult stage. This means ticks can have many interactions with host over their lifetime and have the opportunity to become infected or pass on infection many times. The larvae emerge from eggs uninfected, besides obligate bacterial symbionts, so the larva can pick up a pathogen infection during their first blood meal. When these larvae molt into nymphs they become infected with whatever bacteria was picked up during the previous blood meal and can transmit to an uninfected host. This same thing can happen with adult ticks, but they have had two possible times to pick up an infection. The adult female ticks then feed to produce eggs, the males mate with the females during this blood meal and they rarely feed themselves. Then the females drop of the host and lay thousands of eggs in a “mass”. The larvae then emerge in the spring and the cycle starts all over again.

Mouse with a lot of engorged nymphs on its back.

The rodent hosts that I am interested can be hosts to the larval and nymphal stages. In the part of southern Indiana where I conducted these surveys have three main species of tick, but only two have been found using rodents as hosts, Ixodes scapularis (blacklegged deer tick) and Dermacentor variabilis (American dog tick). The main character that differentiates larvae from nymphs is that larvae have 6 legs while nymphs have 8 legs (as well as the adults). Each species has some unique features that I use to discern between the two.

My lab bench

The tools I use when identifying ticks are a dissecting microscope, this is a microscope that doesn’t need a specimen to be prepared on a slide. It used an external light source to illuminate a whole sample. I manipulate the ticks mainly with a paintbrush. This is a common tool for people who handle fragile invertebrates in the lab because it can move and stick to the specimen but won’t accidentally damage it like a normal pair of forceps. There are also “soft” forceps that are made from a flexible metal that are useful for samples that are too heavy for the paintbrush to grab on to. I covered my whole bench in white bench paper. This helps keep my workspace clean, and if any ticks fall or get dropped they will show up better on the light background. My scope to chair hight ratio is still off a bit, the chair is too high so I have to hunch to look into the dissecting scope, which can be a little painful after a long time. I’m going to have to figure out the best solution to this problem (a shorter chair or raising up the scope on a platform or something).

Dermacentor is the most common tick we’ve found on the rodents, from our previous surveys and from the data I’ve collected from this past year so far. Its mouthparts are somewhat rounded, the body and legs are a light brown color, and the shield on the back (dorsal) side comes away from the body in a straight line.

Ixodes seems to be somewhat less common on these hosts, but still very present. This is of particular interest to many because this species can carry Borrelia burgdorferi, the bacteria that causes Lyme disease. These ticks have longer, straighter mouthparts, are usually darker, blacker in color (the legs in particular, especially in the larvae), and the shield is rounded all the way around. The picture I have below compares a nymph from each species. See if you can see some of the differences I listed.

These little rodents are kind of teeming with parasites, and ticks are the only ectoparasites I collected from them. Fleas and mites were fairly common, but are harder to collect because they don’t attach to the host so they are freely moving through the host’s hair and around the body while you are trying to grab them with forceps. These parasites are important because they can also carry pathogens that can infect wildlife and humans (remember theplague post?). Analyzing the blood samples we collected in 2009 showed that many hosts are infected with Bartonella, a flea-borne pathogen, so fleas may be really important in this disease community.

Flea from a mouse, most likely Orchopeas leucopus.

Fleas and mites look really different from ticks and each other. I know fewer details about these creatures, but I do know they look pretty nasty. Fleas are covered in these little hairs which make them really sticky to the host fur (and hard to handle with the paintbrush, my usual tool for this). They look like they're "swimming" through the hair when you see them on a host, its pretty crazy.

I couldn't get the whole mite in focus at once. The left picture shows its arms in focus, while the right picture shows the little hairs that cover its back.

I think mites look like little monsters with their front set of legs reaching above their head. I’m sure many of you think these guys all look like monsters, but I get so used to looking at ticks I’m not phased by them anymore (what a strange state to be in, huh?).

If I haven't completely grossed you out with this post, stay tuned for more on parasites!

Tuesday, January 3, 2012

The in-between time, or the bliss of not having students for a little while

Welcome to 2012, everyone!
Sorry I’ve been so remiss on writing the last few months, the fall semester kind of got away from me with teaching and everything else on my plate. Hence why I am writing now, when a lot of people are still on vacation, and the subject of today’s musings, what this between semester time is like.

Like I’ve mentioned before, life as a PhD student means you are almost always working on multiple things, all that should get your full attention but never do. During the semester for most of us the main things on the plate are teaching and research. Teaching pays the bills and the research is what we’re actually here for, writing a thesis to earn our degree. Our teaching obligations always seem manageable at the beginning of the semester, but invariably end up taking up far more time than we expected, eating into our time and brain power for working on our research.

This fall I would have spurts of tons of grading to work on, which I would alternate with spurts of working on a manuscript, getting a fellowship application submitted, or getting lab work done. The few times when I had a whole week or two without grading were amazing, I felt really productive, I got to really think about my science, and got a lot accomplished without having the nagging feeling that I should be working on teaching in the back of my mind. I had this same feeling a couple days after we submitted our final grades when I had uninterrupted hours to really focus on getting a near final version of a manuscript edited. I got in this great zone where things seem to make sense that didn’t before and the quality of the work was a lot higher than it had been.

When you’re an undergrad, you take your last final and then are excited to get to be on vacation, do nothing or whatever you want for a few weeks. As a grad student, you are really excited to get some time sans teaching to get some of your own important work done. This was the first year, I think probably ever, that I wasn’t ready for Christmas when the semester was over. I wanted more quiet limbo time before the holidays to get to work on what I needed to work on, not what I had to work on for teaching, meetings, other semester-related obligations.

I love this graph. I think the garland along the best-fit line is my favorite part (R^2 value is 0.69, for anyone who is interested, hehe) (

The holidays did come, but I didn’t really feel like I was on vacation until the afternoon Dec. 23rd when I sent of a manuscript draft to a collaborator in Israel (they don’t have Christmas break there, hehe). I saw a small article in Nature a few years ago discussing how scientists aren’t giving themselves enough down-time, showing that the number of papers submitted on Christmas day has been increasing (see above image). While I do think expectations for working on weekends and holidays can be a bit high, I have a new perspective on this pattern. I think submitting a paper on Christmas, or at least over the holidays, would be kind of a good idea. There wouldn’t be any scheduled meetings, classes, or students wanting to come meet with you. You have some quite down time to gather your thoughts, and then maybe nip down to present opening or Christmas dinner after your work is done. When its work on your own time it is much more enjoyable, even if it is during a holiday.

Please don’t get me wrong, I really enjoy teaching and I like interacting with students. But as I’m discovering, as a senior PhD student there is always something to do, work that needs to be done and that you actually want to do sometimes, and this makes it hard to enjoy your other professional obligations that that time away from those things. Can you put “full-time multi-tasker” on your CV?

I hope to make time for blogging this semester. I have a lot of lab work and things on my plate, so I might try writing some more detailed posts about what my research consists of these days. Good luck in the New Year!

P.S. I wanted to write about a story from This American Life that came out in the middle of November, but clearly I didn’t have time. I would highly recommend listening to the first story about the collaboration between a cancer scientist and a music professor and about how scientists and non-scientists think very differently about the same problem. If people would like to discuss it I would be happy to have this as the subject of a future post!