Tag Archives: arabidopsis

DDW3: Day 1

Today is much better from a setup standpoint. The seeds have soaked adequately and have sunk to the bottom. I tilted the cuvettes for a little so that all the seeds would be as close to the same focal plane as possible (at the front of the cuvette). Pictures taken indicate this.

Arabidopsis vs Tobacco Seeds: A comparison

I took some macro- and microscopic images to show the size difference between the arabidopsis and the tobacco seeds. While microscopically, the arabidopsis is roughly the same size as the tobacco seed in 1 dimension, the arabidopsis is actually much smaller volume wise. While I have no concrete numbers (because I have no way to measure this stuff), it is obvious that the width and height of the tobacco seed are much greater (probably twice as wide and tall).

The scale rectangles in the microscopic images are 100um meaning each hash mark is 25um apart. These images were taken at 10x magnification on our Olympus IX71. The scale is built into a coverslip called Cellattice (which I really don’t like at all, they are made of plastic and bend very easily and thus make it hard for microscopy).

The reason that I’m showing all this is to get a sense of how difficult it is to work with these seeds. First they are small (tobacco is ~.6mm a side, and arabidopsis is ~.3mm on its smallest side). Second there is the static thing. I mentioned this before, but for some reason the seeds become charged and are repelled by the tweezers. I thought the tobacco seeds were hard to handle, but the arabidopsis go flying when I try to pick them up.

In trying to rationalize why there is a more profound effect on the smaller seeds, I thought we’d look at this physically speaking (don’t worry only basic math):

  • Electric Force is proportional to the charge of the objects divided by the distance between the objects. F_{E} = kq_{1}q_{2}/d
  • Let’s assume the charge on both the arabidopsis and tobacco seeds are the same. Then q_{1} is your seed charge and q_{2} is the charge on your tweezers. If the charges are both positive or both negative then you will get a repulsion, otherwise you get an attraction.
  • To find out which one will get flung farther if there is a repulsion then you need another equation. We can say that F_{E} = F_{a} = ma Where F_{a} is just a force due to acceleration. Both seeds will have the same F_{a} because they have the same F_{E}. This means that the tobacco seed, which has more mass (m) will have less acceleration (a) than the arabidopsis which will have a much higher acceleration.

That means less fun for me :-(

DDW Effects on Seeds: Try 3 Day 0

There are 5 seeds in each sample, but some seeds may still be floating. Hopefully the seeds will have settled by tomorrow so I can take better pictures.

Effect of Deuterium Depeleted Water on Life

Hydrogen has several isotopes and one of them, deuterium, exists quite naturally in water to form D_{2}O. In previous experiments and several papers by Gilbert Lewis, it has been found that life is hindered in the presence of D_{2}O. While this may be true, my PI Steve Koch wondered if life had found a use for it because naturally occurring water has about a 17mM (millimolar) concentration of deuterium.

To put that number into perspective, when I do a typical polymerase chain reaction of DNA I add 10mM of each base of DNA (which is less than the amount of naturally occurring deuterium) to create millions of copies of a DNA template from an amount that is 1000x less then what the reaction yields. In fact most chemicals in most of my buffers on the order of the amount of naturally occurring deuterium.

So you can see it isn’t a stretch to think that nature has found a use for D_{2}O since it is quite abundant and life has been constantly evolving for billions of years. I want to test this hypothesis in a variety of different organisms:

  1. Tobacco Seeds – to act as a foil to Lewis’ experiments in which he grew tobacco seeds in pure D_{2}O.
  2. Mustard Seeds – from what I’m told mustard seeds are the powerhouse of the botanical genetics world much like Drosophila and S. cerevisiae are in their respective genetic fields.
  3. Escherichia coli – another molecular biological powerhouse that is very easy to grow and may be easy to see results with. We just got the facilities to be able to grow E. coli and damn it I want to use them!
  4. Saccharomyces cerevisiae (Yeast) – I know a guy who grows yeast for his experiments and I’m sure it wouldn’t be a stretch to get him to do so in deuterium depeleted water.

So the idea would be to try to grow these in regular water and in deuterium depleted water (no D_{2}O), and in the case of E. coli and yeast, perhaps in pure D_{2}O because I don’t think those experiments have been carried out yet. Hopefully I will be able to conclusively state whether or not life has developed a need/use forĀ D_{2}O which would be a very interesting discovery indeed!