Losing the Battle to Win the War: Plant massacres and program fails

I’ve taken a fair few Ls in the past few weeks here in Puzey lab, but I know they’ve all been for the best. In my last post, I wrote about the measures we were taking to beat back thrips and spider mites; in this post, I must write that I was unable to control the insects on my plants, and had to make the decision to cut them all back. The spider mite populations were huge, and I was having to wipe down the leaves and stems of my plants every day to kill them. Misting with water and even bleach didn’t help, and on top of that, thrips were still present. I couldn’t use insecticidal soaps on the plants, because we had released so many predatory insects to help. So, I cut every single plant back to its roots. This sounds traumatic for the plants, but milkweed has such extensive root systems that they regrow quickly and healthily. Now I just have to wait for everything to grow—and then I can start executing my experiment!

We’ve finally started getting significant amounts of data for the microsatellite project, and currently my labmates and I are working to prepare it for presentation at an upcoming conference. The grad student who works on the project with us, Angie, will be giving a talk at the Botany 2018 conference. We’re really excited that our work will be shared with other scholars, but we’re also scrambling to get analyses done in time for it! Our last week has been spent researching different software and R packages that we can use to calculate the statistics we need. R is a programming language mostly used for statistical computation, and is widely used by biologists. I’ve had to blow the dust off my R skills, but they were already pretty limited, and I’ve definitely learned a lot in the past week! Currently my extracurricular project for lab is making a map of Virginia to show where our study sites are—my first attempt was pretty shoddy, but it took me half a day! One of the most frustrating things about this part of the project is how long everything takes for very minimal progress. We’re reading papers, installing software, troubleshooting infiles, and running tests on a bunch of different programs, just to find out that most of them have some particular flaw or shortcoming that prevents us from using them for our project. It can feel like the failures are just piling up and up and up. Yesterday, however, we had a big breakthrough. We’re now finally generating results with the program SPAGeDi, (which we all pronounce spaghetti.)  Though we still have plenty of PCR and genotyping to do to fill in the holes in our data, seeing our preliminary results is incredibly exciting

va map with study sites

My very first R map! Pretty sad, huh?

milkweed massacre

My plants after the chop

Comments

  1. kastahl says:

    Very nice map! R is definitely very challenging.

  2. egeichenberger says:

    Can’t wait to share my next map update with you! Keep an eye out for an upcoming blog post!

  3. mjhudson says:

    I’m so sorry to hear about your plants! It has got to be disheartening to have to cut everything back so far, especially after all the work you put in to try to avoid just that. How long do you expect the milkweed to take to regrow enough that you can get going with the rest of your experiment? I hope it doesn’t take too long (both because I want you to be able to move on with your work, but also because your project sounds fascinating and I selfishly want to hear more about it!!) Good luck with everything going forward. I hope things go more smoothly from here on out!

  4. egeichenberger says:

    Thanks for the kind words! Milkweed is an incredible plant; as long as the root system is healthy, the plants can begin regrowing almost instantaneously. I saw new shoots coming up as soon as two days after I cut them back. In the greenhouse we’ve observed that cutting back the plants seems to encourage clonal growth– some of my pots which only had one or two stems before have as many as 10 growing now! Milkweed performs “adventitious budding,” which means root buds, the predecessors to stem growth, can appear anywhere the plant “decides” to form them along the roots. This gives the plants more freedom to propagate than those that clone via below-ground rhizomes or above-ground stolons, both of which are actually modified stems and not true roots. In those cases, new clones can only appear at set intervals called nodes. I will begin my experiment this coming Monday, and most of my plants are at least a foot tall.

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