Category Archives: Water Type Effects on Organism Growth

Preliminary Results of YPD deterioration

Absorbance of DI YPD (pink), D2O YPD (green), and blank (red)
Absorbance of DI YPD (pink), D2O YPD (green), and blank (red)

These are the results of the experiment I stated a couple weeks ago. I have been tracking the deterioration (previously called aggregation, but I’m not entirely sure aggregation is the correct terminology) of YPD in both solvents. Today they looked pretty well degraded so I thought I’d share the results. Between the two, the DI YPD is more absorbent than the D2O YPD at nearly every wavelength measure (major uncertainty below 350nm).
I’m associating degradation with absorbance since the blank (which is also DI YPD) has an absorbance of zero at all the same frequencies.

D2O YPD also records 0 for absorbance at 600nm, which is the wavelength used for cell count studies, so there would be no interference from the solution. Whether or not the media is still usable by cells is undetermined.

I’m beginning a second experiment that would track the absorbance every few days via the same mechanism. If you recall, I began this experiment taking pictures and eventually moved toward using the nanodrop. This probe seems to do a good job so its continued use is reasonable.

Man I’ve been writing my dissertation for too long…

D2O Adapted E. coli Experimental Replication

Yesterday while writing I realized that the images of the D2O adapted E. coli that I’ve taken were grown on D2O YPD. In an effort to figure out if the morphologies are due to the YPD or the D2O, I’ve decided to redo the experiments on LB agar.

Today I made some D2O and DI LB broth:

  • 1.84g LB in 92ml of D2O
  • 1g LB in 50ml of DI water
  • Filtered broth for sterilization

Then from there I made some LB agar

  • 40ml of liquid D2O LB with 0.8g of agar (2% agar)

I already have solid LB plates with normal water (commercial).

I then incubated E. coli at 37C in liquid media so that I can streak the plates and analyze them. I used 2 different E. coli:

  1. Normal competent cells
  2. Cells from Day 33.
  3. I also had made a separate culture from an unlabeled glycerol stock that I’m pretty sure I made when I finished the experiment. I’ll check it out tomorrow after the sample has developed.

Arabidopsis Update (From March 6, 2013)

I took these images several days ago and again forgot to post them. Stupid dissertation…

Anywho, here they are. I’ll try and remember to update tomorrow when I take the images. Tomorrow will be the last day I update this experiment. I’ll be going into full dissertation mode and will be starting a new experiment when I return. I bought some larger test tubes (1in wide), which should give the plants all the room they need and should be large enough to provide more media to keep the plants alive for longer.

Arabidopsis update

This will probably be the last update. I’m going to (1) need to take a break until after I defend, and (2) need to start a new experiment because the plants are running low on media. I did just buy these awesome 1in diameter test tubes which should give the plants all the media and water they could need for a longer period of time. Anyways let’s go to the pictures:

Arabidopsis Update

Here is the update for my arabidopsis growth. It still seems to me that the plants in 10% D2O are doing better than the plants in DDW. I’ll have to make a huge purchase of D2O and DDW (still don’t understand why DDW is more expensive than D2O since one is a by product of the other) and try lower concentrations of deuterium (like 0-10% amounts).

Notice that the seeds in 99% D2O germinated (mostly likely due to D-exchange), but haven’t grown in 3 weeks.

I wanted to take images of the root growth, but my camera couldn’t see clearly enough in the agar to take decent pictures.

YPD aggregation study

Two summers ago Kenji Doering (an REU student that summer) and I did some protein aggregation studies comparing D2O and DI water. The results were pretty consistent in that proteins don’t aggregate under the same conditions in both samples. What that meant was the D2O is almost certainly better for longevity of chemicals.

A few months ago I noticed that my ypd stocks go noticeably bad after a couple of weeks. But they seemed to last longer in D2O, I just never quantified that. Well now I’m going to.

I have two cuvettes sitting on my bench. One is filled with 1ml of DI YPD and the other is 1ml of D2O YPD. They are sitting next to the benchtop cooler to supply a bit of heat to speed up the aggregation reaction. I will take daily pictures of the solutions to compare the aggregation times of each media. Here is the day=0 time point (on the left is the DI YPD sample, and the right is the 99% D2O sample):

20130219-105637.jpg

Arabidopsis Update: From Feb 13, 2013 (6 days ago)

These pictures are a bit late, but better late than never. They are an update of the growth  progress of arabidopsis in varying amounts of D2O. The group shot is inconsistent with the others because the sample captured for 0% D2O (DDW, deuterium depleted water) is different than the sample used in the individual 0% D2O image.

With that said, there are a couple morphological things I would like to point out. In my opinion the plants are growing better (bigger, faster, etc) in 10% D2O than they are in DDW. They also appear to be slightly more green. And finally there are little hairs on the leaves that seem to be more prominent than in the other samples.

Meanwhile, in 60% D2O the plants are very yellow in appearance. It is interesting that more plants sprouted in that sample, but they are significantly behind in development.

I’ll update tomorrow for the weekly update. And this time I’ll upload the images in real-time. Promise!

Looking into hydrogen-deuterium exchange

H-D exchange (or D-exchange as I’ve sometimes referred to it) has been a problem I’ve dealt with in the lab for some time. It is essentially something that I need to minimize but can never actually stop. It is also a process that I know almost nothing about other than it happens, it occurs somewhat instantaneously, but may be mediated by evaporation rates (when dealing with DDW and 99% D2O). Now I’m perusing the internet looking for some information. Come take a walk with me:

  • At ScienceOnline 2013, I met a person who pointed me in the direction of a Dr. Richard Zare. She told me he was very knowledgable in the field and so I looked up his papers. He had five papers relevant to exchange reactions, all of which are way above my head. So I’ll start on Wikipedia and work my way up.
  • For those unaware, hydrogen-deuterium exchange is a reaction where a covalently bonded hydrogen is replaced with a deuterium atom. In the case of my experiments this happen with water. If I have deuterium depleted water and I keep it in contact with the environment (which has deuterium in it at around 16mM), eventually it will reach equilibrium and the deuterium level (of the DDW) will rise. The mechanism that causes this, I presume, is D-exchange.
  • Apparently the reaction is pH dependent. It can be quenched around pH 2.6, but seems to work best at pH 7.0-8.0. That’s really interesting to me. The pH levels that I’m normally working around are optimal for these reactions. Unfortunately there is nothing I can do about that.
  • The reaction may also be quite slow. According to Wikipedia, exchange is slow/unlikely intramolecularly, but is quite rapid via exposed surface hydrogen bonds. For the purposes of NMR, in vivo deuterium incorporation would be valuable and is hard to attain by dissolving proteins in D2O.
  • The first person to measure H-D exchange was Kaj Ulrik Linderstrøm-Lang, and I would read some of his stuff right now but they are locked down. The mechanism he used to study D-exchange was pretty interesting and involved a density gradient tube. If I read this correctly, KULL filled a long tube with oils of different desities. He could place a drop of water, with a small amount of proteins in the drop, into the oils to determine the density. As reactions occur, the density would change and the drop would move accordingly.

Ok I’ve reached the limit of what I can do tonight without using the UNM network for access to papers. I’ll try to look for more information this weekend. The quest for a basic understanding of H-D exchange continues…

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.

Arabidopsis growth setup

I don’t believe I have time this semester to adapt Arabidopsis to D2O, but I might as well get started and hope I can carry out my experiments this summer and beyond. With that said, I’ll also be looking for morphological affects of D2O on the plants. So I’m starting the growth now and let’s see what observations I can make by March.

Cleaning the seeds (protocol provided by Pedro Nunes):

  1. Place seeds in microcentrifuge tube.
  2. Wash with 4:1 ethanol to bleach solution. (I used 1ml of this mixture)
  3. Let sit for 10 min.
  4. Pipette out mixture.
  5. Wash twice with 100% ethanol, and discard ethanol.
  6. Let the ethanol evaporate.

The seeds will sink to the bottom so it is fairly easy to pipette any liquid in the tube. After step 6 I’ll add some water so I can pipette the seeds into their growth media.

Preparing the growth media:

I originally intended to grow seeds in 5 different mixtures of D2O/DDW, but I spilled one so now I’m doing 4: 0% D2O, 10% D2O, 60% D2O, and 99.9% D2O (I spilled the 5% D2O mixture).

  1. Measure 50ml of D2O and 50ml of DDW
  2. Add 0.22g of MS media to each tube
  3. Mix water in 15ml amounts in small beakers/flasks
    • 0% D2O – 0ml D2O, 15ml DDW
    • 10% D2O – 1.5ml D2O, 13.5ml DDW
    • 60% D2O – 9ml D2O, 6ml DDW
    • 99.9% D2O – 15ml D2O, 0ml DDW
  4. Add 0.15g agar (to make 1% gel)
  5. Heat to dissolve agar
  6. Pour 5ml amounts into test tubes
  7. Allow to cool for gel to solidify

There are three samples per water mixture. Make sure you label your tubes.

Planting the seeds:

After cleaning the seeds use a pipetter to add 3 seeds to each sample. The seeds are small enough to fit in the tiny tips. I’ve read that you can place the seeds on the surface of the growth media, but in my (limited) experience that doesn’t work. As an alternative, I plunge the tip a few millimeters below the surface and drop the seeds there.