March 8, 2012
2011/12 REU Daily Feed, DDW (Deuterium Depleted Water effects), RC (Repeated Cromley Experiment)
Wow, it’s been almost two weeks since my last post! It’s almost spring break, and I’ve been studying like mad for midterms. I’ve been in the lab very little the past two weeks. <sad face>
Monday Anthony and I went on a little excursion to the Bosque looking for tardigrade habitats. Read his post here. It was an interesting experience. Anthony had mentioned tardigrades a few months ago. I did a Google search and found lots of interesting information about these little creatures:
Tardigrade (or water bear), the toughest creature on Earth.
- They are found everywhere in the world, from the Himalayas to the Artic. They live in Hot Springs and Forests.
- They can survive in extreme environments because they can pause their metabolism and enter a state of suspended animation, called cryptobiosis.When they are in this state they are in a tun.
- They can survive without water for over 100 years while in tun.
- They can withstand 1000 times more radiation than any other living creature known.
- They can also survive in space (without space suites or spaceships).
All in all they are very impressive little critters.
So why were we looking for them? Well, since I’ve been here, all our research on D2O and DDW has been with tobacco and Arabidopsis seeds. We are now moving into the next phase of research, using yeast and e.coli. One day we were talking about this next phase, and Anthony mentioned that it would be cool to see what effects D2O and DDW have on other life forms. Since Tardigrades are so adaptable, we started looking into getting some for our experiments. Since they are found everywhere we decided to go on a Tardigrade hunt.
The following steps are how to find them (taken from Sarah Bordenstein’s page at Carleton College):
- Collect a clump of moss or lichen (dry or wet) and place in a shallow dish, such as a Petri dish.
- Soak in water (preferably rainwater or distilled water) for 3-24 hours.
- Remove and discard excess water from the dish.
- Shake or squeeze the moss/lichen clumps over another transparent dish to collect trapped water.
- Starting on a low objective lens, examine the water using a stereo microscope.
- Use a micropipette to transfer tardigrades to a slide, which can be observed with a higher power under a compound microscope.
Today we started step 2.
Bosque Samples in water, awaiting for Tardigrade extraction
January 31, 2012
2011/12 REU Daily Feed, DDW (Deuterium Depleted Water effects), FTIR, Protein Stability, R, RC (Repeated Cromley Experiment)
Some Background: My long term goal is to complete a BS CompE and an MBA under the UNM 3+2 program, expected May 2015. I’ve got a ton of work experience in project management; I’m really good at it, and I love it. I came back to school so I could eventually get into management.
Anthony and I have been talking quite a bit about the best fit for me here in the BioPhysics Lab. I really enjoy learning about everything, and it is all really interesting, and Anthony and I all work well together. One morning we were talking about all the projects we have going on and Anthony asked if I wanted to be the project manager for them. What a great fit for my goals and experience. We decided that I would work as a Research Assistant, focusing on the project management side of our work.
So, the semester is started, and I’ve finally gotten a regular lab schedule worked out. Anthony and I met today about all of our ongoing projects. The synopsis of current and upcoming happenings in our lab is posted on Google Docs.
P.S. I’ve had to shelve my R learning project for now. I’ve gotten a fair understanding of the language… enough to basically understand code already written and edit it if needed. I’ve also gotten the hang of the syntax. Had to put it down for a bit though, this semester I’ve got 4 classes with 4 languages to learn. I didn’t want to push my brain over the edge.
January 13, 2012
2011/12 REU Daily Feed, DDW (Deuterium Depleted Water effects), ONS (Open Notebook Science), R, RC (Repeated Cromley Experiment), Uncategorized
Today was presentation day at CHTM. All the REU students (me included) gave a 20 minute presentation about what we have been doing for our research. I don’t know why, but I get extremely nervous for these presentations. The strange thing is I have a lot of experience speaking to crowds of people. I used to teach continuing education classes, and was never even a little bit nervous. I wonder what is going on?
Anyway, all this week Dr. Koch, Anthony and I have been working on my Mind Map presentation. I wanted to do something different from the standard PowerPoint presentation. Don’t get me wrong, PowerPoint is a good tool, I just wanted to do something different. We decided a Mind Map would be a good way to show case one of the many tools/applications that we use here in Kochlab.
In addition, I handed out little cards with a qr code and a short link to a google docs spreadsheet with links to many of the tools we use for our ONS. My Mind Map also had links to most of the information that I used for my research and presentation.
After it was all over I realized that I had forgotten to show the really cool, time lapse growth images that Anthony had put together for the D2O experiments.
Next presentation I will take Dr. Koch’s suggestion and practice, out loud, the entire presentation. If I do this several times I might not get stage fright quite so bad.
I’m really grateful for the opportunities that have come my way since I’ve been working here at CHTM and KochLab. Dr. Koch and Anthony have been absolutely great to work with. Linda Bugge has been a good friend and really helpful with all the administrative “stoof.” It is an honor to have been selected to be a part of the NSF grant. I’m meeting some really awesome and brilliant people here. I’m super lucky.
November 2, 2011
2011/12 REU Daily Feed, RC (Repeated Cromley Experiment)
Today I helped Anthony set up Trial 4 of the Repeating Crumley (RC) experiment (this will be the third set of usable data). We use four types of water: Deionized (DI), 33% D2O, 66% D20, and 99% D20; with two species of seeds: Virginia Gold #1 tobacco and Columbia Arabidopsis . Previously he had DDW water also, but we are eliminating that portion of the experiment for this trial.
I counted out tobacco seeds, Anthony handled the Arabidopsis seeds. We need 30 seeds for each analyslide. It was more difficult than it looked, as Anthony has previously posted.
First we put out four sheets of 4×4 weighing paper and fold each sheet in half. Next I tapped what looked like 30 seeds (turned out to be almost 60) out of the envelope that holds the seeds. Then, using the tweezers, I proceeded to count the seeds by attempting to move them with the tweezers to an empty portion of the weighing paper. The seeds and the tweezers seemed to have the same charge, so the tweezers never touched the seeds. The seeds where repelled by the tweezers, so I had to be very careful, otherwise the seeds would jump right off of the paper into Elsewhere.
While I was counting the first set of 30 seeds, Anthony gave me a tip for the next three sets:
Tobacco seeds are fairly large (compared to Arabidopsis seeds), so if I gently tap the little envelope, they will come out a few at a time and I can count them as they fall. By the last set I had the hang of it and was able to get the 30 seeds out without using the tweezers!
We were out of D2O, delivery came later in the day, so Anthony completed the setup on Tuesday.
—— Aside ——
Wednesday, 11/2/2011 — I learn that after I left the lab on Monday, Anthony was careless with his Arabidopsis seeds and they got lost in Elsewhere (see link above). So he trashed everything and had to recount Arabidopsis and tobacco seeds all-by-himself on Tuesday. Trial 4 is now underway.