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 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

Steps for defense and graduation

The journey has begun and I’m preparing to graduate this semester. In order to do that I need to have my dissertation finalized and submitted by April 15, and have defended prior to that. Here is a list of things (straight from the Office of Graduate Studies) I need to do/complete:

  1. Program of Studies – for masters.
  2. Application for Candidacy
  3. Appt of dissertation committee
  4. Announcement of Exam – also included on there is the Report of Exam
  5. Manuscript prep:
    1. Information cover sheet
    2. Certificate of final form
    3. electronic ETD release
    4. email the forms to dwein@unm.edu
  6. Register for Lobovault
    1. email dwein to confirm Lobovault registration
  7. Complete Survey of Earned Doctorates
    1. forward email of completed survey to dwein
  8. Submit Dissertation via ProQuest
    1. need to create account

Everything else via Doug:

Transmitting your manuscript to the LoboVault repository When you have completed all of your required revisions and saved your complete manuscript, including Front Matter, as a single pdf file you are ready to transmit the final electronic manuscript to the LoboVault. Here are the steps you need to follow to transmit your file:

  1. Login at “My Account” at LoboVault repository website using the same username and password that you used for registration. The “Login” will change to “Logout”.
  2. Move the cursor above to the “Browse” section and click on the “Communities & Collections” link; in the center of the page, the first heading will be “UNM Academic & Scholarly Communications”.
  3. Scroll down to “Graduate Studies Community” and select the appropriate Doctoral Dissertations Community, Master of Fine Arts Community, or Master’s Theses Community.
  4. Scroll down to the designated departmental degree collection (e.g. Anthropology or English). Click on the appropriate collection button. The website that opens will be the site where your manuscript resides, so be sure to verify that you have selected the correct department.
  5. Find the link “submit a new item to this collection”. Clicking this link initiates the actual electronic submission of the manuscript. Follow the directions on each page. The first page has an “Item Submission” heading which will move you from Initial Questions through Six Steps (Describe, Describe, Upload, Review, License, and Complete). As you proceed, complete the open fields and click on the “Next” button to move to the next page.
  6. When you click on the “Complete” button at the end of this sequence, LoboVault will deliver your manuscript to the shadow archive administered by the OGS manuscript coordinator who completes the final review of your manuscript. Within three weeks after the degree requirement deadline, you will receive a letter acknowledging the approval of your manuscript and the partial fulfillment of the program requirement for the degree. The manuscript stays in the LoboVault shadow archive until the Registrar confers the final degree, at which time the OGS manuscript coordinator electronically moves the manuscript from the shadow archive to the LoboVault open-access repository and (for doctoral students) to the ProQuest-UMI repository.

Info about Deuterium Content from Sigma-Aldrich

I emailed Sigma a couple weeks ago asking about the D content of their D2O. Here is their response:

Thank you for contacting Sigma-Aldrich Technical Service. Product 151882 is pure deuterated water with the deuterium content a minimum of 99.85% of the total hydrogen content. Although it’s not normally reported as ppm, there would be 201,198 ppm deuterium in pure deuterium oxide. Product 151882 is prepared to the chemical purity indicated, but is not sterile filtered or tested for endotoxins or nucleases, so a direct comparison with molecular biology grade water can’t be made.

 

Is it just me, or is the ppm of Deuterium a bit low? Theoretically, if there is only deuterium and oxygen in D2O then the deuterium should be 2/3 of the total molecules and so that should be something like 666,666ppm. If there is 0.15% Hydrogen that should be about 1500ppm. So if my theoretics are wrong, then I’ve become worse at math than I thought and I should return my BS in Mathematics.

But if not, then this begs the question, what else is in the water?

Incubator Down!

Aaaaahhhhh! Gotta find a small incubator to get in the shaker quickly. Some finds for now…

Incubator only:

Desktop incubator shaker: