Category Archives: Research

“Athlete’s Foot in Worms” goes to a regional meeting

The crowdfunded part is over, but the project lingers on. This weekend we have an opportunity to share our data at the Northwest branch meeting for the American Society for Microbiology. Two of the students who participated in the “Athlete’s Foot in Worms?” research will be presenting a poster, and I’ll be giving a short talk about crowdfunding in the sciences. We’re excited to share our experience with other educators and researchers. If you’re near the Seattle area, maybe we’ll see you there!

Research Week 5: The beauty of negative data

Last week was our final research week, and we made it count! We’ve now done infections on two different strains of C. elegans. Our results? While there are subtle phenotypes still to be explored, the obvious ones that we were looking for don’t seem to be different between the infected and control worms. What we have is some beautiful negative data.

Negative data sounds bad, doesn’t it. It’s still data, though, and it’s not really bad. If you’re getting negative data, that means that your experiment is working properly, but you’re not getting the result you were hoping for. As a mentor of mine once told me, you have to let the science tell you what’s going on. In our case, the data is lovely (excellent images, plenty of worms exposed to dermatophytes, etc). But, for what we were measuring, there just wasn’t a difference between the control and infections. So it’s good data, but it’s negative.

This is the part of science that is rarely covered in classes. We carefully design most classroom experiments so that each lab activity illustrates a particular point and you don’t end up with negative data. How nice it would be if real research worked that way! In research, asking one question might get you an answer, but it also generally leads to a million more questions. That’s how I feel at the end of this project. We’ve answered a simple question, but there are so many more I want to test. Maybe next summer.

Research weeks 3 and 4: the importance of controls

Week 3 was a bit of a shorter work-week due to the July 4th holiday. Independence of another sort was being celebrated in the lab: at this point my students were trained for lab safety and had done most of the techniques at least once, so they were able to work more on their own. They are also becoming more independent in their experimental design and have been instrumental in thinking about different ways that infection could be measured.

C. elegans on a bed of dermatophyte conidia

During week 4, we took the lessons learned from our preliminary trial runs and set up an experiment that we think will give us a good indication as to whether dermatophytes can infect C. elegans. At this point, we are using death as an endpoint, but we will look for other measurements of ill-health as well.

One thing that’s important in any experiment is to include proper controls. For example, if all our worms die, how do we know that they died because the fungi were killing them? Maybe the incubator was too hot, and that was what really killed the worms. One way that we are controlling for this is to have a group of worms that are kept under the same conditions but without exposure to the fungi. We expect these worms to be healthy at the end of our experiment. This shows us that factors other than the fungi are not causing harm to the worms, and it also gives us something to compare our “infected” worms to.

Research week 2: Science is 90% planning.

During our second week of research, we started practicing techniques that we’ll be using to do our actual experiment. These include manipulating the worms (C. elegans), treating them so that we have age-matched organisms that we can infect, and visualizing them under the microscope. We’ve also started trial runs with different infection methods. None of this is “the experiment” yet. These are considered preliminary experiments that help us determine the best conditions possible for the actual experiment.

Preliminary experiments are very common to biological science. In fact, I spend most of my time researching and planning, doing preliminary experiments, and analyzing data. I spend very little time (relatively speaking) actually doing the experiments that make it into a published article. As with many fields, biology has a lot of “behind-the-scenes” work. Surprisingly, no one has put this into a reality TV show yet!

Meet the organisms

Our project requires that we have a large quantity of each of our organisms: dermatophytes and C. elegans.

Trichophyton equinum

Dermatophytes are molds, and when growing as molds they are in multicellular filaments called hyphae. This results in a fuzzy appearance as shown on this plate, or perhaps you have also seen it on mold growing on bread that’s been around for a while. I prefer to work with dermatophyte conidia, the resting bodies they produce that are only one cell. Having single cells means we can be more quantitative (we know exactly how many conidia we add to an experiment).

Dermatophytes growing in their happy home.

To grow conidia, we plate dermatophytes on rather large plates of specialized media. In the image, they are in the incubator, next to normal plates. They will grow for about 2 weeks, then we will harvest the conidia, count them, and confirm their quality (they should be able to grow and they should be the only organism present).

The other organism we work with, C. elegans, actually eat bacteria instead of a growth medium. Last week we made small plates of medium and spotted E. coli onto the plates. We let the E. coli grow a little, then added the C. elegans. Our worms are greatly enjoying their bacterial snack and we have had plenty for our pilot experiments. As you can see from the picture, we made quite a few plates!

A “few” plates. All of them have E. coli already seeded. These will last a while!

A single plate (pen is for size). The spot in the middle is E. coli, which the nematodes will eat.

Research week 1: getting started!

Summer research has officially started! This week was spent getting things set up. We unpacked lab supplies and started working with cultures of our organisms – both the dermatophtyes and C. elegans, our worms. We also learned to use a giant pressure cooker called an autoclave and then used it to sterilize supplies and media. And perhaps most importantly, my students are getting a crash course on how to learn a new field. An important aspect of starting any new project is becoming up-to-date on what’s going on, so we’re leaving plenty of time for literature searches, reading papers, and discussions.

The Achterman lab. From left: Justin, Tony, Steven, Me.

Crowdfunding: It’s not a grant … or is it?

University research is almost exclusively funded on a “grants” model. In this model, the principle investigator (PI) sends a proposal to somewhere like the National Institutes of Health or the National Science Foundation. These large funding bodies review proposals a few times a year using a peer-review process, and a small (very small!) percentage of the proposals will be granted funding. The funding body sends the money directly to the University, which takes a cut to cover “indirect” costs like facility and equipment maintenance, library access, and other things that are necessary for research but not attributable to any one specific research project. The University then puts the remainder of the money into a fund that the PI can draw from to pay personnel and buy supplies. The funding body wants to know that the research dollars are being used appropriately. Having a specific fund for each project allows the University and the PI to keep track of how the money is spent and, presumably, show that it was spent well.

In contrast, the “Athlete’s Foot in Worms?” project, which officially started research this week, is a crowdfunded project. Crowdfunding currently lacks the accountability of the traditional grants system. The PI posts a proposal on-line using a crowdfunding platform that takes care of accepting money from funders and paying the PI  (the SciFund project I participated in used RocketHub). And then … nothing happens. When my research was funded, RocketHub took its cut, sent me a check, and said “congratulations”. They will not be checking up on me to make sure that I sent my funders their thank-you gifts. They will not be asking for  a progress report. If I spend the money on a vacation instead of lab supplies, they wouldn’t know and probably couldn’t do much about it even if they did.

What keeps me firmly in the Pacific Northwest, rather than Bermuda, isn’t RocketHub. Rather, it’s the contract I’ve made with the people who contributed through the RocketHub site: Take this money; make this project happen; honor your obligations with your thank-you gifts and by keeping us updated as the research progresses. If you do, we might fund another of your projects in the future. We might tell our friends and family that you’re worth supporting. If you don’t, you are losing some serious street cred. Some of us know you. Some of us are related to you. Don’t let us down.

This internal monologue, while extremely effective for me at least, does not fit into the University funding system. So, here’s what happened to the crowdfunding money: Rockethub sent me a check. I gave the money to the University. The University very kindly did NOT take a cut (no indirect costs were removed for the “Athlete’s Foot in Worms?” project), and they set up a fund for me to use the money. It’s a little more complicated than paying for everything myself, especially when it comes to transportation costs. However, it means that my paid undergraduate and my two volunteers are covered for liabilities. It also means that I am setting up crowdfunding at this institution as a funding mechanism that will have accountability. I think that’s probably a good thing.