Tag Archives: brainstorming

Defense Outline

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).

D2O Adaptation Try 3 – Project Plan

Now that the lab is clean, I’m going to collect my thoughts and write a plan to follow. While the first two experiments were unsuccessful, there were some interesting results that can’t be disregarded. But in the pursuit of science more results are required! So let’s get this party started…

D2O adaptation: Based on the paper I read yesterday, it seems that a slow adaptation is the right way to go. Yeast grown in pure D2O seemed to endure too much stress to adapt and the adaptation might be way slower compared to a progressive adaptation plan. So each week I’ll increase the amount of D2O by 20% starting with 20% D2O YPD:

  1. 20% D2O
  2. 40% D2O
  3. 60% D2O
  4. 80% D2O
  5. 100% D2O


  1. Every Monday I plan on running a time trial experiment comparing the growth of yeast in DI YPD to the increased D2O YPD concentration and to the previous D2O concentration.
  2. Every Friday I’ll run a time trial of the yeast growth in that week’s D2O concentration.
  3. Every day, yeast will be provided new medium for growth and daily nanodrop readings will be recorded to analyze the 24 hour growth. Also a microscope analysis will also be done to ensure there is no contamination.
  4. Weekly glycerol stocks will be created in case of contamination.
  5. Agar plates of each D2O concentration will be created to analyze colony morphology. Inoculation onto solid media will take place each week, and right now I’m not sure when the best day to do this is, but I’m thinking Wednesdays might be best.


Planning for #scio13 – The impact of electronic/open notebooks on science #opennotebookscience

I’m starting this thread for anyone to comment on to drop some ideas about what we should all talk about when it comes to electronic and open notebook science. I have some goals for the session that I’ll jot down below, and I hope you all share what you’re goals for the session are. If you can come to ScienceOnline 2013 I hope you’ll come¬†talk¬†with us, and if not then I hope you’ll join the conversation on twitter. Either way, share your thoughts on the future of ONS below!

Deuterium exchange analysis experimental planning

The future direction of the experiment using the ring down cavity spectroscopy device will be planned here. This should be a fun collaboration between Scott Jasechko (Earth and Planetary Sciences) and myself (Physics). Join the conversation!


5k for science (and other fundraising endeavors)

With all the hoopla for crowdfunding science, #SciFund and petridish.org (among others) I started wondering, “How come there was no traditional form of raising money for science?” And by traditional I don’t mean PI’s applying for grants. I look at crowdfunding for science more as like a charity type of situation. So why hasn’t there been any traditional type of fundraising for science?

Maybe someone has done this, but I haven’t heard of such a venture so I’m proposing a 5k for science. And for those who want to have a ton of fun, what about a pub crawl for science!

The idea would be simple, set up an event. Get a ton of people to register for the event and charge a $10-20 admission fee. Then let them run/drink themselves silly. The money would go directly towards labs for research. On the research end, graduate students could write microgrants that would be awarded with the money from the 5k (for instance).

Alternatively, those wishing to be funded via the 5k could submit posters to the 5k for display along the trail. The money would be evenly distributed among those posters’ “presenters” (since no one would actually be there alongside the poster).

If crowdfunding can work for science, than why can’t this?

This idea originally sprung up because I was thinking about how to engage the local commuinity (ABQ in my case) and entice them to contribute directly to research in their own backyard. A crowdfunding site dedicated to research at UNM was one avenue, but I wanted something that allowed students and researchers to interact directly with the community. Thus the idea of a 5k popped up. A pub crawl would probably be more “profitable”. And some kind of science day at a local museum would be more fitting (where ticket sales would be donated to researchers participating in the event). It might even be worth it for scientists to host their own educational opportunities where visitors would provide a donation for the researcher’s time. This would be most fun for those who do field work (ecologists, anthropologists, some biologists, and some very exciting physicists).

Anyway, the ideas are very rough, but could provide some interesting outside the box funding options for labs in the same mold that crowdfunding has provided.

If you have heard of such endeavors, please share your stories in the comments!

Yeast and E. coli Growth: What’s next?

There are several things I can do with the yeast experiments:

  • Another but longer time trial experiment (data every hour)
  • Time Trials in larger quantities: maybe 100ml or 50ml – I want to see if the growth in such small volumes affects the measurements any
  • Adapt yeast to D2O and then grow in DDW – I’ll have to do cultures daily in D2O and see if they begin to grow faster in D2O over time. I’m thinking this will let me know they’ve adapted to their environment. I can also try to grow cultures in less D2O (like 10%) and incrementally increase it over time to see if that causes adaptation. Both methods seem viable.

I’m open to suggestions as to what to do next as well.

As for E. coli, those experiments are very inconclusive even in 99% D2O and I wouldn’t have the foggiest as to how to deal with this. Suggestions would be much appreciated here. Ayuda me!

The Open IGERT Proposal

I’ve been saying for months that I want to submit a proposal to the NSF for an open science IGERT. Well the call for such a proposal dropped into my lab a week ago and UNM is doing a limited competition to pick the best proposal to send into the NSF.

Since I’m an open notebook scientist and everything, I’m going to write this proposal openly despite my actual fears about doing so. Because it’s best to be open!

Some key aspects of the proposal are that the NSF is looking to train students in the ways of data management and to do science in the 21st century. So I’m pairing with UNM Library Scientist Rob Olendorf to design an open science repository for UNM students (for data, blogs, notebooks, etc) and we are going to train students on modern data management techniques and how to do science openly, online.

Right now, these thoughts are still being hashed out but you can see the progress we’re making in this document:

IGERT Proposal

And if you haven’t checked out my rockethub project please do so!