Tag Archives: data

Arabidopsis growth after 2 weeks

These pictures are a few days delayed. I tried to take the images on Monday, but realized my iPhone camera was glitching (purple spots on CCD). I’ve got a brand new iPhone now and retook the images on Tuesday and finally got them into WordPress for you all to see. Let’s talk about what we are seeing here.

If you recall, I setup this experiment a couple of weeks ago. The first few pictures are from the original arabidopsis growth experiment about 2 months ago. The rest are from the most recent protocol. This experiment was inspired by a paper I read a few months ago where they grew arabidopsis in heavy water and cultivated seeds from each generation growing it in higher amounts of heavy water. The purpose was to test for adaptation.

Some notes:

  • The paper reported visible morphology changes in the plant growth in high amounts of D2O. I don’t remember the details, but the obvious changes include leaf discoloration and flowering at earlier stages. The expected (and observed) change was delay in growth of plant in presence of high levels of D2O.
  • For the most part I’m not observing these color changes. The plants are still too young to determine flowering capabilities. The delay of growth in D2O has been noticed, although growth in 10% D2O has been pretty similar to growth in DDW. Perhaps that level of concentration results in very little effect.
  • The most astounding thing is that the seeds germinated in 99% D2O media. In my Repeating Crumley experiment this never occurred. There could be several factors related to this, but the most obvious factor is deuterium exchange. Since the test tubes are sealed with breathable tape, there is air transfer between the samples and the environment. From what I’ve seen D-exchange is mostly a surface interaction type problem and since the seeds are near the surface there would be considerably more exchange during early germination than at any other point in the life cycle. I expect that as the roots grow it will become incredibly difficult for the plant to sustain life. The interesting thing to mention is that Bhatia and Smith (of the aforementioned paper) note they never were able to grow seeds in anything over 70% D2O. I don’t understand how.
  • In the 99% D2O samples, one plant has grown its first leaves (cotyledon), while the other samples have begun to sprout a root (radicle). I’ll keep observing to see if these plants develop further.
  • I’m actually very surprised to see the 60% D2O plants do fairly well.
  • I’m wondering if the presence of the MS media has given the plants an advantage that Gilbert Lewis didn’t think of.
  • Evaporation of my gel is a huge problem. The two month old sample is running out of media and there is no way that I know of to replenish the supply. The other samples will have this happen in time. I will test a small batch of samples to see if I can use a rubber stopper to get the plants to grow in an effort to reduce evaporation. Other setups have the advantage of keeping the plants in a moisture controlled environment. If I had $1,000,000, I could create a grow house that cycles heavy water mixtures into a chamber to keep the plants in an environment to reduce evaporation. Maybe this would be a worthwhile grant?
  • Equipment to create my own D2O and DDW from tap water would be crucial so I wouldn’t need to spend thousands buying 100g bottles from Sigma. Think of the experiments I could run!

I think that’s all I have for now. I’m potentially about to come upon some money so I hope to spend a bunch of it on water before I run out and then I’ll run a series of experiments that should take me through the semester.

Yeast morphology in 80% D2O

Yeast Colonies in 60% D2O YPD

So I suck at my own microscopy technique of taking pictures and combining them. In each case I left out a pretty sizable portion of the colony. 🙁 Oh well. I’m going to do these experiments again (cause I made 2 sets of each type of solid media, 0%-100% D2O) and will be taking new images then. Can’t wait!!

DNA Overstretching Data

For the past few days, Pranav’s been hard at work collecting DNA tweezing data. The first set of experiments revolve around DNA overstretching (which I’ll explain later, but you should feel free to google it). We’re planning on analyzing force differences between DNA in D2O and H2O through overstretching. Hopefully eventually we’ll be working towards DNA unzipping, but that is less likely given our time constraints (graduation!!). Regardless there are a lot of interesting studies to be done here.

DNA overstretching, several force profiles are overlapping. Notice the repeatability.

Here is the link to the notes. And here is the folder where all the data is stored.

Yeast grown in 60% D2O