Category Archives: D2O Effects on Life

D2O Effects on Life, RCPub, Water Type Effects on Organism Growth

Repeating Crumley Publication Prep

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  1. I need a title for the paper. I’ve always called it Repeating Crumley, and maybe it makes sense to continue that trend, but is there a more fitting/descriptive name? Does it even matter?
  2. I think it makes sense to create .gifs from all the plant germination images for each sample of each experiment.
    1. From RC1-4 I had slideshows, which allowed you to click through each sample at your own pace. Then after I had started making .gifs (especially since that was around the time of memes on the web).
    2. I still think it makes sense to have all the data as pictures as well. If they aren’t already there, I will upload all the images to figshare, and have a separate dataset as gifs.
  3. Should the gifs be stored via my notebook (and thus the Winnower), or figshare?
    1. Both?
    2. Since the Winnower can actively display the .gifs, this has my preference, but I’m not sure. Maybe both… just because.
  4. Making a citation list for every notebook entry may be tiring, but it must be done.
  5. I’ll have to go through my figshare profile to see what data is currently up there.
  6. I worry that I don’t remember some of the data analysis methods. I think the only one I have absolutely no recollection of is the root length vs time graph. I remember it happening but I don’t remember going from Point A to B. I think of this like getting in the car and driving to work. You remember getting in the car, but you have no recollection of the in-between time because you were lost in thought. This is what happens when your brain is in Dissertation/Defense mode.
  7. The primary focus on this paper is going to be about the replication of the Crumley experiment through my methods and the difference in our results. I will include some of the cooler data, but won’t be able to write a follow-up (yet) since there is insufficient data on some of the cooler experiments. But I can show preliminary stuff!

I think that’s all I got now. I’ll keep adding notes like this when I get more ideas, come across roadblocks, or something else.

D2O Effects on Life, Open Notebook, RC1, RC2, RC3, RC4, RC5, RCD, RCW, Water Type Effects on Organism Growth

The Repeating Crumley-ONS Project: Next Steps

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Slightly over a month ago, I came across the Winnower and began a project in open notebook science. The concept was to upload notes from my notebook to the Winnower, archive the notes, and get DOI’s for each post. Then I would write 2 papers: one to summarize the experiment and the other to theorize a complete publication system that would incentive open documentation of real-time research (open notebook science). I chose the Repeating Crumley experiment for this experiment in ONS, and you can read about the reasoning here.

Well I’m happy to say that I’ve completed Steps 1, 2, and 3! I’ve posted every notebook entry in the RC series (there’s a physics pun there somewhere) to the Winnower and received DOI’s for almost every post. A few posts didn’t translate, at all, on the platform. They are uploaded, but I didn’t bother with the DOI. Regardless, you can go on any of my Winnower posts and get a DOI (or click through to my notebook),  or look through the RC entries and click the DOI to get to the Winnower archive of that post.

One cool side effect of this project was that a Twitter friend noticed a post that had embedded .gifs and I think I am now credited with being the first to publish a scientific paper with embedded .gif’s.

Now it’s time to write the paper based on all this research. I got the process started a couple years ago with a Google Doc about the project. I think I never followed through, because I didn’t value the traditional publication process. I think open science and peer review publication are on a course to merge and the incentives for ONS will shift, but this is a topic for another time.

Anyway, here is the previous write-up which I’ll work on, merge with some info from my dissertation, and to which add some new thoughts.

This part may take some time…

This post is open to read and review on The Winnower.

Arabidopsis Adaptation, D2O Effects on Life, Water Type Effects on Organism Growth

Arabidopsishttp://t.co/ZM1LINP0Sm Growth Try 4: Week 5

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The latest updates are in. Between last week and this week, plants grown in 0% D2O, 30% D2O, 70% D2O, and 80% D2O have died. While this is expected for the larger concentrations, I can’t explain why the 0% D2O sample or 30% D2O sample has died. But I did just think of an interesting effect:

Because the plants are more-or-less sealed from the environment, I have minimized the effects of evaporation and transpiration. I’m not sure if transpired water is harmful to the plants because it basically is their excrement. Regardless, the water in the solid media (the agar) should have a slight rise in D2O concentration due to transpiration processes in the leaves and evaporation of water from the solid media. I’ll have to find the reference for a paper I have that verifies this.

Arabidopsis Adaptation, D2O Effects on Life, Water Type Effects on Organism Growth

Arabidopsis Growth Try 4: Week 5

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Arabidopsis Adaptation, D2O Effects on Life, Water Type Effects on Organism Growth

Arabidopsis Growth Try 4: Week 3

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D2O Effects on Life, DDW Effects On Life, RC4, Water Type Effects on Organism Growth

Growth of Arabidopsis in heavy water

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Arabidopsis seeds in DI water (0.0156% D2O).
Arabidopsis seeds in DI water (0.0156% D2O).
Arabidopsis seeds in 33% D2O.
Arabidopsis seeds in 33% D2O.
Arabidopsis seeds in 66% D2O.
Arabidopsis seeds in 66% D2O.
Arabidopsis seeds in 99% D2O.
Arabidopsis seeds in 99% D2O.

DOI: 10.15200/winn.142722.25163 provided by The Winnower, a DIY scholarly publishing platform

D2O Effects on Life, DDW Effects On Life, RC5, Water Type Effects on Organism Growth

Growth of tobacco seeds in low concentrations of deuterium

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Growth of tobacco seeds in DDW.
Growth of tobacco seeds in DDW (0.0001% D2O).
Growth of tobacco seeds in DI water.
Growth of tobacco seeds in DI water (0.0156% D2O).
Growth of tobacco seeds in 1% D2O.
Growth of tobacco seeds in 1% D2O.
tobacco seed root length
Tobacco seed root length growth.

DOI: 10.15200/winn.142801.10415 provided by The Winnower, a DIY scholarly publishing platform

D2O Effects on Life, DDW Effects On Life, RC4, Water Type Effects on Organism Growth

Growth of Tobacco Seeds in Heavy Water

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Growth of tobacco seeds in DI water.
Growth of tobacco seeds in DI water.
Growth of tobacco seeds in DDW.
Growth of tobacco seeds in DDW.
Growth of tobacco seeds in 33% D2O.
Growth of tobacco seeds in 33% D2O.
Growth of tobacco seeds in 66% D2O.
Growth of tobacco seeds in 66% D2O.
Growth of tobacco seeds in 99% D2O.
Growth of tobacco seeds in 99% D2O.

DOI: 10.15200/winn.142722.25159 provided by The Winnower, a DIY scholarly publishing platform

Arabidopsis Adaptation, D2O Effects on Life, Water Type Effects on Organism Growth

Arabidopsis Growth Try 4: Week 2

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The plants are one week old! They seem to be doing really well, for the most part. As expected, as the concentration of D2O increases the plants develop slower. Also as expected the plants also exhibit leaf decolorization. Notice how in 60, and 70% D2O the leaves are a pale green. In 80% the plants are too small to notice growth. It also seems that the plant in 5% D2O is growing the fastest, which seems to be in line with my observations from the last trial run, and also with hypotheses from my dissertation (to be posted as soon as it is all finished). I will have to record some observations of the plants in DDW and compare them to 5% D2O and 10% D2O.

Arabidopsis Adaptation, D2O Effects on Life, Water Type Effects on Organism Growth

Arabidopsis Growth Try 4: Setup

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I’ve got larger test tubes (1in diameter and about a ft in height), I’ve got plenty of water, and I’ve got a PhD. Looks like I’m ready to grow some plants! Here is the protocol ( adapted from Jan 22):

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 growing seeds in 10 different mixtures of D2O/DDW: 0% D2O, 5% D2O, 10% D2O, 20% D2O, 30% D2O, 40% D2O, 50% D2O, 60% D2O, 70% D2O, and 80% D2O. I’m not doing a 99.9% D2O sample this time. Each sample will have 20ml of water total.

  1. I used 1 bottle of D2O (100g), 1 fresh bottle of DDW (100g), and one old bottle of DDW (~50g, from 1/22/13, stored in desiccator).
  2. Add 0.22g per 50ml of water of MS media
  3. Mix water in 20ml amounts in test tubes
    • 0% D2O – 0ml D2O, 20ml DDW
    • 5% D2O – 1ml D2O, 19ml DDW
    • 10% D2O – 2ml D2O, 18ml DDW
    • 20% D2O – 4ml D2O, 16ml DDW
    • 30% D2O – 6ml D2O, 14ml DDW
    • 40% D2O – 8ml D2O, 12ml DDW
    • 50% D2O – 10ml D2O, 10ml DDW
    • 60% D2O – 12ml D2O, 8ml DDW
    • 70% D2O – 14ml D2O, 6ml DDW
    • 80% D2O – 16ml D2O, 4ml DDW
  4. Add 0.2g agar (to make 1% gel)
  5. Heat to dissolve agar
  6. Allow to cool for gel to solidify

Planting the seeds:

Normally, I use a pipetter that one would use for small volumes to deposit the seeds, but because the tubes are so much bigger than the ones in the past I need to alter my method. Today I used a glass Pasteur pipet with a very nice long tip. I used the wrong kind of bulb, so it was more challenging than expected, but worked well enough.

Also because my test tubes are much bigger than before, I made the mistake of not purchasing a test tube holder. So I had to fashion one from spare lab components. Check out my system:

Test tube holder fr 25mm diameter tubes.
Test tube holder for 25mm diameter tubes.

It’s made from the breadboard that has become my plant station, screws, and nuts. Pretty simple, and works amazingly well.