The yeast has spread into colonies (yay), but the E. coli have not. I don’t get what is happening there, but I’ll try growing them in liquid media and seeing what happens. Tomorrow I’ll check on the e. coli and decide what to do from there. In the mean time, I’ll also start a liquid media batch of yeast to grow side-by-side with the e. coli.
Let’s get it…
and poop to some extent…
Ahem! I started cultures of e. coli and s. cerevisiae streaking cells on some plates to be incubated overnight and beyond. From here I will pick colonies and grow flasks of them to get familiar with the growth rates so I can take data. If all goes according to plan, I’ll be getting some preliminary results by the end of the week!
Here is some info about my cells:
E. coli: XL1-Blue MRF’ competent cells that are designed to replicate pBluescript
Yeast: S. cerevisiae of the variety g160/2d
Sorry for the lack of notebooking today. I had to send a bunch of emails this morning, catch up on teaching work, and then had to write an informal CV this afternoon. Wanna see it?
Anyways, I’m doing the prep work for the E. coli studies and showing Alex how to use an autoclave. I also am getting into sterile technique and Alex will have something up later about all of this to which I will link.
Tomorrow we are going to mess around (and get triple doubles) in a safe environment and grow some e.coli and see what happens. I also hope to get my hands on some yeast. There are a few barriers before we can get any serious data. First I have to successfully grow microscopic creatures in small containers. I have to get acclimated to using the nanodrop as an OD measuring device. Then I have to do all this with different water types.
Fun times ahead.
Another page for project outlining that will change over time.
UPDATE: I changed the embed code so the map has live update capabilities.
I spoke with Kelly Trujillo about cell synchronizing after Koch had mentioned to me that we may need this for ddw yeast studies. He mentioned that he was going to be synchronizing for a study that he was setting up and that I could come learn the process. So I took him up on his offer.
I have to say, the protocol is surprisingly simple. Kelly grew a colony, diluted it to about 0.1 OD and then let it divide up to 0.4 OD. We looked at the asynchronous growth and then he added some mating pheromone (details to come) to some of the culture to halt the cells in G1 phase of cell division. From here, he could synchronize them to enter S phase by using hydroxyurea (HU) after washing out the mating pheromone. The remaining culture was arrested in G2/M phase with the drug Nocodazole.
We paused during each step to look at each culture (asynch, G1, S, and G2) but I have no pictures. I do have the knowledge to do it myself and hope to incorporate this in the DDW experiments shortly. A preplanning thread will come soon.
Hydrogen has several isotopes and one of them, deuterium, exists quite naturally in water to form 
To put that number into perspective, when I do a typical polymerase chain reaction of DNA I add 10mM of each base of DNA (which is less than the amount of naturally occurring deuterium) to create millions of copies of a DNA template from an amount that is 1000x less then what the reaction yields. In fact most chemicals in most of my buffers on the order of the amount of naturally occurring deuterium.
So you can see it isn’t a stretch to think that nature has found a use for
.So the idea would be to try to grow these in regular water and in deuterium depleted water (no