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Major Overhaul Coming!

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Now that I am done with my Doctoral program, I need to majorly revamp the site:

First, I need to reorganize all of my tags and categories for easier site navigation. I will organize the site by project first:

  • Deuterium Effects
  • Shotgun DNA Mapping
  • Open Notebook
  • Kochlab
  • Art

Next I will organize each project by organism and then experiment. For instance:

  • Deuterium Effects
    • Tobacco Seeds
      • Repeating Crumley
      • Root Hair Analysis
    • Arabidopsis
      • Seed germination
      • Root analysis
      • Plant growth
    • Yeast
      • D2O effects
    • E. coli
      • D2O Adaptation
      • D2O effects
    • Biomolecules
      • Catalase
      • Ovalbumin
      • DNA
    • Water analysis

This will make it much more intuitive to navigate for experiments that are no longer being carried out.

Second, I will also remodel the design of the site so that the design reflects (1) the high quality of science, and (2) reflects the high quality design work that I do. That will just be for fun. With the new redesign, I will also be providing a new weekly column which I’m really excited about. I’m not sure what I’m going to call it yet, but it starts tomorrow and each post will contain real scientific work that reveals exactly how science is aimed to understand the world and better it. Some posts will be very educational, others will be fun and a bit silly but scientific nonetheless, while others will highlight things you didn’t necessarily think about. Regardless, I am quite excited for the series and I hope you are too.

Third, I’ve got a few new projects to unveil. I’m not sure when those will be announced, but two of them I will get to announce this week. I’ll announce the first project tomorrow, and the other project later in the week.

Fourth, my dissertation is 99.9% done and I’m just waiting for my committee to sign the approval cover sheet in order to complete my graduation. Once that is done, I’ll be uploading the document to figshare and will make it available for download. Then after some time, I’ll be uploading a special edition version of my dissertation which will feature some graphic design styling. The special edition is the version that I’ll be getting professionally printed and bound for my advisor, myself, and my parents. I’ll upload that too in case you would rather read the more awesome version.

That is all I have to announce right now. Sorry the site has been kind of dead for the past couple of months. The dissertation work has been beastly, but ONS made it much easier than what I expected the process to be. Now I get to go back to good ole’ fashioned, and fun, science!

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.

Microorganisms, Water Type Effects on Organism Growth, Yeast

Yeast Colony Morphology

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I’m not sure what to make of these colony morphologies, but I thought I’d post them for the world to see. I started them a couple weeks ago to compare the growth to that of the E. coli morphology experiment, then just kept them growing to see what would happen.

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.

Artsy, D2O Effects on Life, DDW Effects On Life, E. Coli, Kinesin Stability in D2O, KochLab Stuff, Microorganisms, Open Notebook, Paper Summaries, Shotgun DNA Mapping, Water Analysis, Water Type Effects on Organism Growth, Yeast

The Biophysical Effects of Heavy Water – My Defense Presentation

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D2O Effects on Life, DDW Effects On Life, E. Coli, Kinesin Stability in D2O, KochLab Stuff, Microorganisms, Open Notebook, Shotgun DNA Mapping, Water Analysis, Water Type Effects on Organism Growth, Yeast

Defense Outline

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Just over a week away now…

  1. Introduction
    1. What is D2O?
    2. The history of D2O
      1. Gilbert Lewis:
        1. purification
        2. biological effects
        3. The hypothesis
      2. Joseph Katz
        1. various experiments
    3. Uses of D2O
      1. NMR, mass spec
      2. The need for a D2O adapted organism
    4. Experiments in DDW
      1. use for space travel
      2. cure for cancer?
  2. The effects on life
    1. Tobacco Seeds
      1. The Crumley experiment and repeating the experiment
      2. Tobacco seed germination rate
      3. tobacco seed growth rate in low deuterium concentration
    2. Arabidopsis
      1. arabidopsis growth rate
      2. arabidopsis morphology
    3. E. coli
      1. growth rates
      2. adaptation and adapted growth
      3. morphology
    4. Yeast
      1. growth rates
      2. adaptation – can’t adapt
      3. morphology
        1. stall during cell division
        2. microtubule stabilization in D2O
  3. Molecular effects
    1. Stabilization of biomacromolecules
      1. DLS experiments
        1. Catalase
        2. Ovalbumin
      2. YPD longevity
    2. Investigation of HD exchange
      1. mechanism and exploitation for protein struture studies
      2. FT-IR analysis
      3. Cavity ring-down analysis
        1. low cost measurement of local atmosphere isotopic composition
    3. Effect on DNA
      1. The pursuit of shotgun DNA mapping
      2. optical tweezers
      3. methods
      4. overstretching data
  4. Future Work
    1. Arabidopsis
      1. adaptation
      2. seed growth in low deuterium
    2. Tobacco growth in low D2O
    3. Yeast morphology in taxol
    4. E coli protein expression in D2O and protein structure analysis
    5. DNA
      1. overstretching in D2O with intercalators

Well there is my idea of how to present my dissertation. I’m not sure if/where I should put my discussion on open notebook science. Also there are a couple things that I could see going elsewhere. I could describe the yeast and e. coli stuff in parallel instead of one after another. Also the HD exchange stuff could easily go right after the yeast, e. coli, or even the tobacco seed stuff. What to do…

Otherwise I think the story is pretty compelling: history of D2O and the unanswered question by Lewis. Investigations into D2O effects and trying to understand low D2O concentration effects, effects on macromolecules, and the understanding of large volume/long-term HD exchange.

Any feedback you may have would be GREATLY appreciated. I’ll send you a figshare t-shirt, or if you are XL, I’ll send you a hoodie (but I only have one).

Kinesin Stability in D2O

Protein Aggregation Graphs

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I just finished some beautiful graphs by combining the aggregation data sets from the protein aggregation studies (Ovalbumin and Catalase). Check them out:

ovalbumin visual aggregation: (left) non-aggregated sample, (right) after aggregation
ovalbumin visual aggregation: (left) non-aggregated sample, (right) after aggregation
plot of ovalbumin aggregation
plot of ovalbumin aggregation
Plot of catalase aggregation
Plot of catalase aggregation
D2O Adaptation 3, Microorganisms, Water Type Effects on Organism Growth, Yeast

Feb 28 Yeast Growth

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I’ve been scratching my head about this for the past two days. I could have sworn that I did a measurement of yeast growth after adaptation and it turns out I did. Here is the data:

I’ll graph this data and publish that when I’m done (after I defend).

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

Tobacco Seed Growth Rates

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I got some awesome new data to show. The first is the compilation of all the Repeating Crumley experiments. And the second is some new data that I’ve been meaning to create and now have with the help of Koch.

Tobacco seed germination rates
Tobacco seed germination rates

The data above is the compilation of all the RC data. Each trial had different water types, but I combined the samples that were the same in every set (DDW, DI water, 33% D2O, 66% D2O, and 99% D2O). Steve adapted his R-code that applies binomial confidence intervals to a data set and used it on this data. If that makes no sense, then just know that the dotted lines are the most probable range of germination rates. For instance, in 66% D2O there is a ~70% likelihood that seeds will germinate at a rate within the dotted yellow lines.

Now it’s time for some brand new data:

tobacco seed root length
tobacco seed root length

Here we went through the pictures from Trial 5 and compared the growth rates of the roots. We calculated the lengths of various seeds in each image and tracked the changes from image to image. We chose DI, DDW, and 1% D2O, because the D2O concentrations are relatively similar and because we wanted to test a hypothesis from a while ago. It’s interesting that the seeds in DDW and D2O grow at the same rate, while seeds in DI water grow at roughly half the speed.

Do you?

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