823 days: A tale of parasite publication

It’s unusual that I can pick exactly how long a project took from beginning to end. This time, I can: 823 days.

Day 1: 4 July 2009

Since 2006, I’d been examining the nervous system of shrimp (for a project that is still ongoing – sigh). When I looked at the nerve cords under the microscope, I kept seeing odd little bits that I thought were caused by some problem with the fixation or clearing process. I realized that was wrong when on 4 July 2009, I took this video:



Okay, those slight odd looking bits in the nerve cord didn’t have anything to do with staining. They were moving. They were something alive inside the nerve cord.

Well. That was unexpected. Also, slightly freaky.

Here’s my notebook entry for the day:

(And yes, I am well aware of my terrible handwriting and other problems, thank you very much.)

Soon after, I went down the hall and showed this stuff to the man on the right in the photo below.

This is my co-author Brian Fredensborg, who is a real parasitologist. He had joined our department a couple of years previously. I showed him what I had. He didn’t immediately say, “Oh, yes, that’s a [name], and it’s well known that they live in the nervous systems of crustaceans. Not very interesting at all.” This was a good sign. We were both interested, for different reasons, in what the heck was going on here.

Day 4: 7 July 2009

Brian gives me a tentative ID of the beasts we’re dealing with: larval tapeworms. I record in my notebooks, “Possibly PROCHRISTIANELLA PENAEI or PARACHRISTIANELLA or POLYPOCEPHALUS.” Brian seeks out some help in narrowing down the possibilities from a colleague, and he hears from one of his colleagues that the last guess is the right one.

But the project had to wait. Neither of us had the time to follow it up immediately, and all our students at the time were already deep in working on projects of their own.

Enter the woman on the left.

Day 59: 31 August 2009

The last day of August in 2009 is the first day of class for the Fall semester. I am teaching my neurobiology class, and though I didn’t know it at the time, one of the students registered for the class is Nadia Carreon. We had some good conversations in that semester. This good relationship in class helps paves the way...

Day 200-317: Spring 2010

After the semester is over and neurobiology is done, Nadia comes into my office and asks about the possibility of doing a research project before she graduates. We sit down in my office, and I throw out a whole whack of half-baked ideas that could be turned into research projects, including the mystery shrimp parasites. Nadia thinks the parasite project is cool, so we walk down to Brian’s office and I introduce them to each other.

Everything looks good, so we start to plan a project that Nadia can complete over the summer that will, we hope, be publishable.

Days 318-422: Summer, 2010

And we are go for data collection! We plot, we plan, and we set up a way to gather data at the Coastal Studies Lab. We fiddle with webcams. We figure out ways to tag the animals so we can track them individually. I pull out a big honkin’ heavy mechanical cell counter – made of metal and that makes a very satisfying click every time you press one of the keys – to aid in the counting of all those parasites.

(For the record, I wish to apologize to Nadia publicly: I had no idea just how many parasites were going to be in those shrimp. I never expected that one shrimp alone might have 500 parasites infecting it.)

Proving the old adage, “If it weren’t for the last minute, nothing would get done,” much of the planning takes place in May and June, while a lot of the actual data collection happens late in August.

Day 451: 27 September 2010

We do get a first pass at data gathered over the summer, and get it together in time for a poster at the HESTEC science symposium. The poster wins third place in the undergraduate poster competition.

The analysis and writing continues at a slow but steady pace through the fall semester.

One moment I particularly liked was when I finally got the big, massive spreadsheet of all the behavioural data. For whatever reason, in my research, there are very few “Aha!” moments. There’s a lot more sneaking suspicions followed by a long period of trying to convince myself that what I think I’m seeing is actually what I’m seeing.

As it happened, we had a little bit of data destruction problem. Some of the last video shot was unusable. Brian and Nadia and I had talked about whether we might need to run some more behavioural tests on shrimp, but we still had a decent sized number of animals. We decided that if we didn’t see significant differences, we might run some more. But if it was significant, but it saw significant differences with the smaller sample, we could start writing up in earnest.

There was so much data here, there was no way to get a sense of whether there were going to be any trends associated with infection rates. So I was quite excited to run the first analysis, because I had no idea how it was going to turn out. ... and see significant differences in behaviour!

Day 533: 18 December 2010

Nadia graduates with her bachelor’s degree in biology!

Brian and I are committed to writing and finishing this manuscript before the year is out. The main reason is that Brian is expecting to become a father for the first time in very early January. This gave us very strong incentive to finish, because, as I said to several people, “I don’t know of anyone who has ever said, ‘Yes, we just had a baby. And my productivity has gone through the roof!’”

Day 545: 30 December 2010

Manuscript submitted! Happy New Year!

Day 609: 4 March 2011

Nadia gives the first presentation of this story to the larger scientific community at the Texas Academy of Science meeting. This poster later appears on the Better Posters blog.

Day 633: 28 March 2011

The manuscript is accepted. On the first submission, without any revisions. This has never happened to me before. Holy cow. And the pre-print goes up the same day!

Day 704: 7 June 2011

I present an updated version of the Texas Academy of Science poster at The Crustacean Society meeting in Honolulu. The new data makes this poster 33% bigger than its predecessor.

Day 823: 4 October 2011

The paper finally moves from “pre-print” to published status! And now, I have a paper in a parasitology journal, which was never something I expected to happen. Hooray for collaboration and academic freedom.

Day 824: 5 October 2011

“And on the eight-hundredth and twenty-fourth day, he blogged.”

But wait! We’re not quite done yet! Nadia continued working on this project a bit on a volunteer basis through 2011 after she graduated. We have more data, that we hope will eventually become part of the first follow-up paper.

Day 864: 14 November 2011

Come meet Nadia and myself at the poster session for the Faculty for Undergraduate Neuroscience at the Neuroscience meeting! 6:45-8:45 pm in the Grand Ballroom Central and North in the Renaissance Hotel.

There you have it. The long, winding road from an initial observation to a final, pretty, published article, with brushes along the way of both the thrill of victory (“No revisions?!”) and the agony of defeat (“The video’s gone?!”). It’s also fairly typical of research at undergraduate universities, I think, in that things can wait for a long time because you’re just waiting for a student to pick up the project. And I was surprised in writing up this retrospective to be reminded that stuff gathered even early in the project can be useful:

I took the picture in Figure 1a on Day 1.

Reference

Carreon N, Faulkes Z, Fredensborg BL. 2011. Polypocephalus sp. infects the nervous system and increases activity of commercially harvested white shrimp (Litopenaeus setiferus). Journal of Parasitology 97(5): 755-759. DOI: 10.1645/GE-2749.1

Faulkes Z. 2007. Motor neurons involved in escape responses in white shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 47(Supplement 1): e178. DOI: 10.1093/icb/icm105