Category Archives: KochLab Stuff

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:

 

Lab Contamination!!!

This morning while setting up for a time trial experiment, I noticed the 20% yeast sample didn’t smell like yeast anymore. It smelled like a mixture of yeast and something else. So I setup the experiment, took initial measurements, and then analyzed the sample in the microscope. This is what I saw:

Surrounding my slightly modified yeast are these tiny things, that look like super small e. coli so they are probably some bacteria or perhaps they are some kind of spore. Regardless that was not at all in the sample from yesterday (see above), and looks nothing like the e. coli that I temporarily believed was adapted yeast.

So I began a mission to decontaminate the lab. After the cleaning I just did, nothing is alive! Not even myself! In fact I’m not even writing this… (Note to dead future self: Sorry :-\)

Anyways, I began by bleaching the fuck out of everything. The incubator got it the worst as I basically drowned it in bleach. I scrubbed real hard with this super awesome huge bristle brush. I let the bleach sit for about 10 minutes and then wiped it down with clean rags.

Next I used the Activeion Ionator EXP, which was loaned to me by the custodial staff here at CHTM. It’s a spray that ionizes water to clean and disinfect, and supposedly can kill viruses and bacteria. After the bleach treatment on the incubator, I Ionated it and wiped it down and allowed it to air dry.

Then I used the Ionator EXP to clean all the bench tops and all my lab equipment (pipetters, racks, scales, hot plate, etc). I finished by emptying my current supply of YPD and made new stocks for use tomorrow. I feel sad that I had to throw about $80 worth of D2O down the drain, but I gotta be careful in the lab and so it had to go.

Tomorrow I will start the D2O adaptation experiment again (Round 3!) and let’s hope the contamination issues are behind me.

 

All #SciFund Expenditures

I’ve been posting my expenditures as I buy them, but I thought it would be beneficial to everyone (myself included) to document the total spent. So, here it is for your viewing pleasure:

If you have any questions about any of the line items, ask in the comments!

#SciFund Expenditure!

Today I bought some goodies to help me analyze and control my experiments:

  1. light timer to control the lights for the plants. Over the thanksgiving break I was unable to come into the lab and since I doubt anyone else was in here, I’m sure the plants saw no light for 4 days. This will remedy that!
  2. A Macro/wide angle lens.
  3. A zoom lens and tripod.
  4. A microscope objective.
  5. Deuterium depleted water (from Sigma).

I bought the iPhone accessories to make my data collection process more efficient. Since they were relatively inexpensive it wasn’t a big gamble.

Microscope Pixel Calibration

It is important to provide scale when showing microscope images. Personally I’m not a huge fan of scale bars and would prefer to know the dimensions of an image and the conversion factor. For our camera/microscope at 10x magnification it’s almost exactly 1um/px. This calibration was performed by Andy Maloney using a 60x objective. See below for details.