Monthly Archives: May 2012

D2O1, DDW1, Microorganisms, Water Type Effects on Organism Growth, Yeast

Yeast Growth Trial 1 Data

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Here is the data courtesy of figshare:

S. cerevisiae growth in DI Water, DDW, 50% D2O, and 90% D2O. Anthony Salvagno. Figshare.
Retrieved 22:01, May 22, 2012 (GMT)
hdl.handle.net/10779/bfceb213ffb663b34149d97141755232

I would say this data is pretty exciting. Unlike the E. coli data (which was all over the place), there is a clear difference in growth rates between the D2O samples and the H2O samples. Also the growth between the DDW and DI (the H2O samples) were almost identical! That’s pretty solid.

D2O1, DDW1, E. Coli, Microorganisms, Water Type Effects on Organism Growth

A cool figure I forgot to share: E. Coli growth in Water

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the e.coli data reimagined in illustrator

I made this figure for my rockethub proposal and forgot to post it here in my notebook. Look how pretty it is!

I made this in Adobe Illustrator and if anyone is interested I would be willing to host an online workshop to teach others how to use Illustrator for science. This particular image took almost no time (maybe 30 minutes), which is a marvel because I obsess over everything I do in Illustrator (which is why there isn’t anything tangibly Illustrator on this site).

D2O1, DDW1, Microorganisms, Water Type Effects on Organism Growth, Yeast

Yeast Growth in D2O, DDW, and DI YPD: Setup

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Yesterday I created a starter colony of yeast from the lyophilized yeast that I ordered from ATCC.org. Today I’m doing growth in different water types and checking the growth every hour just like the e. coli experiments. Here is my setup:

  1. Make YPD broth with DDW and D2O.
    1. the bottles of both come in 100g quantities which means there is 90-ish ml of D2O and 100-ish ml of DDW
    2. I had 91ml of D2O –> 4.55g of YPD powder
    3. 100ml of DDW –> 5g of YPD powder
  2. suspend powder in water types and filter via syringe. DO NOT AUTOCLAVE
    1. the reason is because of deuterium exchange. The powder is ultrapure and the water is pretty pure itself, so filtering should be just fine.
  3. To make diluted cultures:
    1. I have 4 samples: 1) DI water 2) DDW 3) D2O and 4) 50% D2O in 50% DI water
    2. Put 9ml of each water type into a test tube (except for the 50/50 mix which should be 5ml of d2o and 4ml of di water)
    3. Add 1ml of starter culture (which is made from DI water)
    4. put in incubator
  4. take time points every hour in semi-micro cuvettes using nanodrop. I fill them with 0.5ml of each culture.

Simple!

Open Notebook

IGERT Limited Competition Results

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I just received word that the UNM limited competition results are in. Our IGERT proposal has been selected by UNM to proceed to the NSF letter of intent phase! That’s great news! Open science is finally being recognized by UNM as a major innovation and key for scientific development and they are going to help us push this forward to the NSF.

The letter of intent is due June 4. Any feedback I receive from the limited competition committee will be posted online.

In the meantime follow the next phase on the document which can be found here.

Microorganisms, Water Type Effects on Organism Growth, Yeast

Yeast in Water Setup

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So before I left on travel (a week and a half ago) I received a vial of dry yeast. I’ve kept it in the fridge for 2 weeks to preserve it and today I’m going to bring it to life and start a starter culture so that this week I can do time point growth, like I did with the E. coli. Here is some information about the yeast:

And here is some information on how to go from the powder to a liquid suspension and then to a culture (provided by ATCC):

  1. Open ampoule (the glass vial with the yeast powder) according to enclosed instructions (there are no instructions).
  2. From a single test tube of sterile distilled water (5 to 6ml) withdraw approx. 0.5 to 1.0ml with a sterile pipette and apply directly to the pellet. Stir to form a suspension.
  3. Aseptically transfer the suspension back into the test tube of sterile water.
  4. Let the test tube sit at room temp (25C) undisturbed for at least 2 hours; longer rehydration may increase viability of some fungi.
  5. Mix the suspension well. Use several drops to inoculate recommended solid or liquid medium. Include a control that receives no inoculation.
  6. Incubate the inoculum at the propagation conditions recommended.
  7. Inspect for growth of the inoculum strain regularly. The sign of viability is noticeable typically after 1-2 days of incubation.

And the recommended incubation temp is 30C.