DDW4: Day 7 cropped photos of Arabidopsis (and some pics from DDW3)

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Here are the cropped photos. I used a program called JPEGcrops to mass crop the images from day 7. It was sweet and quick. I also included (uncropped) photos of the DI and tap water samples from Trial 3 of the DDW experiment. I don’t know if the curviness is real or not so I’ll let you comment below if you think it’s real. My money is on yes!

  • http://stevekochscience.blogspot.com Steve Koch

    I agree that the arabidopsis in DDW are very curly!  And appear to be much more so than in tap water.  Also than in DI, but the number of images in DI, unfortunately is too limited.  I agree with what you see but want exact side-by-side controls.

    And the point Bill brought up about temperature control is a big deal.  As a minimum, they need to be next to each other to be sure to be at the (variable) room temperature.  Temperature-controlled would be better.  Measuring the (room) temperature (maybe use Andy’s software and an old computer) also important as an intermediate goal, and probably not too tough.  You could just log the data to a public folder on the server for now.

    AND, now that we have the three separate preliminary indications of DDW phenotypes (tobacco seeds root hairs in DDW; tobacco seeds less germination in DDW; and arabidopsis seeds curly roots in DDW), we’re back to the burning question: is the only difference between DDW and DI water the deuterium content?  Or could there be trace contaminants in either / or?  That’s a tough question we may need help with?

    • http://www.iheartanthony.com Anthony Salvagno

      Can you describe what you mean by side by side? Like literally touching a ddw with a di/tap water image next to each other?

      It is a tough question and we may need help with it. I’ll contact Sigma and Thermo to ask about how the DDW/DI (respectively) are produced.

      I think contaminants wouldn’t be a proper explanation. Worst case scenario is that DDW is made from tap water (right?) so there should be similarities between the water types, but the root hairs is such a different development than in either of the other two samples. The interesting thing was that in the first trial the DI water had some root hairs but as time went on they receded. What could cause that? Perplexing!

      I’m so excited and so confused that I can’t think straight.

      • http://stevekochscience.blogspot.com Steve Koch

        I agree exciting!  By side-by-side, I meant the actual experiments.  Matching conditions of different samples as closely as possible, with only variable being water type.  So, starting at the same time, same initial condition of seeds, and having same temperature throughout.  As far as temperature goes, that means being next to each other and not near any kind of other equipment or different kind of lighting.

        • http://www.iheartanthony.com Anthony Salvagno

          I managed to find references to some ddw life science experiments while reading a paper on how to produce ddw (trying to figure out differences between do water and ddw) :

          Sinyak, Y.; Grigoriev, A.; Gaydadimov, V.; Gurieva, T.; Levinskih, M.; Pokrovskii, B. Deuterium-free water (1H 2 O) in complex life-support systems of long-term space missions Acta Astronaut. 2003, 52, 575– 580 [CrossRef], [PubMed], [CAS]

          Gleason, J. D.; Friedman, I. Oats may grow better in water depleted in oxygen-18 and deuterium Nature 1975, 256, 305– 305 [CrossRef], [PubMed], [CAS]

          Pricope, F.; Ştefă̆nescu; Tiţescu, G.; Cărăuş, I.; Ureche, D. Effect of deuterium-depleted water on reproduction of rainbow trout Environ. Chem. Lett. 2003, 1, 149– 151 [CrossRef], [CAS]

          Seki, K.; Usui, T. Process for promoting growth of agricultural products and aquatic animals, and for treating pancreatic disease, involves using deuterium-depleted water having specific deuterium concentration. Patent JP2005328812-A, 2005.

          I’m pasting them to look them up later (I’m on my tablet) .
          On Dec 10, 2011 11:48 AM, “Disqus”

          • http://stevekochscience.blogspot.com Steve Koch

            Awesome finds!  I think it’s time to start thinking about a coherent story to publish (PLoS ONE) w/ preliminary data.  Not that we’re ready yet, but we need to start collecting these references.  Mendeley is the best option.  Unfortunately, I think we will need to share PDFs, and thus a private collection is the only option (we can copy the collection and make it public manually along the way, but I don’t think there’s a way to sync the references to public collection automatically).  Can you please create the Mendeley shared library (deuterium depletion effects on living systems)?  Invite me and Alex.  Also, invite Bill Hooker in case he wants to write with us.  I think there is a “star” option in Mendeley.  We should use stars to mark papers that we will cite for sure.  Basically any paper that has studied deuterium-depletion in living systems.  You found a bunch of new ones that I hadn’t found and I’m excited to read them!

            Another thing to know about is http://www.papercritic.com/ .  It ties in with Mendeley and allows you to rate and post comments.  It’s not a perfect option (I don’t think it works well for collaboration, e.g.), but I think we should try it out. There will be duplication of effort, but I think you should post summaries as you read papers in a number of places: (1) on your blog, (2) in the notes section of Mendeley, and (3) using PaperCritic.

            Thanks again for finding these!  Hopefully I will have time soon to read these, but don’t let that stop you from getting ahead of me.

        • http://www.iheartanthony.com Anthony Salvagno

          And here is the paper that I found them from :

          http://pubs.acs.org/doi/full/10.1021/ie101820f#references
          On Dec 11, 2011 5:11 PM, “Anthony Salvagno”

  • http://stevekochscience.blogspot.com Steve Koch

    This goes through much more of the life cycle of arabidopsis than you are probing, but looks useful for a little info on phenotypes so I’m linking here: 
    http://www.arabidopsis.org/portals/education/boyes2001.pdf

    • http://stevekochscience.blogspot.com Steve Koch
    • http://stevekochscience.blogspot.com Steve Koch
    • http://stevekochscience.blogspot.com Steve Koch

      More searching via terms looks helpful: arabidopsis germination phenotypes

    • http://www.iheartanthony.com Anthony Salvagno

      I was almost pissed with this paper because there were no methods but they turned out to be at the very end. There wasn’t much for me to take back except that they used certified plates during germination and grew them in petrified dishes. They also put the seeds in the fridge for 3 days to sync growth. Finally they used ethanol and bleach to sterilize the seeds. Honestly I don’t think I should do that part but it is good to know.