Category Archives: KochLab Stuff

The Biophysical Effects of Heavy Water – My Defense Presentation

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).

Chapter 1: Open Notebook Science

View in Google Drive.

The link above should give you access to the chapter in all it’s glory. Currently it is pretty much done barring revisions, the addition of figures, and moving the references from side comments to an end of chapter reference section. I’m providing an embed below in case you don’t care about all the cool references enclosed and just want to read. If you are reading via mobile, click the link.

“The biophysical effects of deuterium oxide on biomolecules and living cells through open notebook science”

…My dissertation title. What do you think?

The entire story of my scientific career

This article is actually the introduction to my dissertation and I thought I’d share it with the world officially rather than let it die in an electronic archive somewhere. I’ve shared this story in some form or another several times already, but I’ve never provided the entire account like this. And so, it is with great pleasure that I share with you, the story of how I became the scientist that I am today…

I joined the KochLab in the Spring of 2007. It was a brand new lab that, at the time, was comprised of Dr. Koch, myself, and my best friend Larry Herskowitz (who is now Dr. Herskowitz). In our first lab meeting, Dr. Koch discussed his scientific endeavors up to that point (some of which are continued in this dissertation) and introduced the concept of open science.

Open science was, and still is, an emerging paradigm, and is not to be confused with a particular field of science. The core concept of open science is providing access information and it is through the opening of scientific research that many new endeavors have become possible. Many of these endeavors have changed the way scientists approach research and acquire data. Citizen science, for instance, has brought a mass scale of human analysis to previously unsolvable problems. Even sharing data has led to new forms of collaboration. Data repositories have allowed scientists to share data with the world in hopes of finding new uses for the shared data. Tools like DataOne have emerged to provide some organization to the new data. Meanwhile, open notebook science has emerged to open the entire scientific process and practitioners make every stage of research accessible including protocols, raw data, data analysis, and much more open to scrutiny.
Continue reading The entire story of my scientific career

Tracking my stress through weight

Since I’ve been told that stress is a factor in weight gain/loss I’m going to openly track my weight over the next few weeks until I defend and submit my dissertation, and potentially after that. Hopefully I can maintain a stable weight or lose a few lbs and avoid gaining weight as I approach the day. Check it out:

Dissertation guidelines

(This is rewritten in Anthony language for my own clarification. If anyone else finds this useful than awesome!)

Dissertation guidelines via OGS:

  1. Deadline: April 15 for Spring
  2. Formatting rules:
    1. Letter Size, 8 ½ X 11 inch
    2. The left margin of each page must be 1 1/2 inches, and the top, right, and bottom margins 1 inch.
    3. paginate your manuscript; upper right hand corner and bottom center
      1. If your page numbers are at the bottom, leave two blank line spaces between the last line of text and the line on which the page number is placed.
      2. Whether they are at the top or the bottom, page numbers should appear just outside the 1-inch margins (.5 to .8 inches from the top or bottom edge of the page).
      3. Use lower-case Roman numerals for the front matter (which is all pages before the body of research), create section break and continue (beginning again with page “1”) with Arabic numerals for the remainder of the manuscript, including the text, illustrations, appendices and references.
    4. Your manuscript should be double-spaced and single-sided.
    5. References may be single-spaced with a double space between each reference. Indented quotations may also be single-spaced.
    6. Font size for your text should be 12 point; headings may be up to 14 point. Fonts for tables, figures, and appendices may range from 8 to 12 point.

Latex format

MS Word format