Week 7

This week I have been tying loose ends that I have been working on for the last few weeks.

• First I had to re-spin the samples and clean them again so I could be sure that the SIP product was good.  I really need to have the rest of the samples amplify and having clean SIP product will only help me do this.  My 2:20 pm samples are amplified and Suzanne showed me exactly low she cleaned them to get them.  I cleaned my samples just like she did so I should be able to amplify the rest at the beginning of next week.  I have set up alot of DGGE PCRs but have not had great luck with them so now that I have good cleaned SIP I should not have problems. 
• I am also doing a DGGE PCR on the on the control samples before the SIP to amplify the control DNA that we extracted.  This is the samples that have not been enriched with Sodium Bicarbonate.  
• Also with the control samples I ran an archaeal PCR to see if there was archaea in the sample to begin with.  I found that there was archaea in most of the samples so we would like to try and pull out bands of archaea from our control samples using stable isotope probing.  
• In order to pull archaea bands out, we would want to use a carrier to bring out the bands more.  When we pulled bacterial DNA from the bands, we used sulfolobus (12C and 13C).  Now that we are trying to pull out archaeal DNA, we are going to use an archaeal carrier.  We will use Pseudomonas Putida. So, this week I made M9 minimal salts which is the media that the Pseudomonas Putida grows in.  Using some plates that Christina graciously let me use, I cultured some of my own P. Putida both 12C and 13C and let them grow for 3 days. 
• I extracted the DNA from the samples of p. putida that I cultured and I yielded a large amount of DNA.  I was really excited that I cultured so much DNA because I had never made the media before and wasn't even sure if I was making it correctly. 
• Having strong yields of p. putida DNA will give me a strong start to pulling out archaeal bands.  We aren't too sure if we will be able to pull bands out of the control but having a good carrier will help. 

For next week I have to get the rest of my samples to amplify at the beginning of the week.  Also I have to extract the sulfolobus that Suzanne got from Portland State University.  I plan to do this Monday.  I would also like to set the contol SIP up for the archaea.

I enjoyed the brown bag this week.  We had a great speaker who talked all about how he went about picking what he wanted to do as a career.  We watched a movie that closely related to the topics we have been learning about in our Tribal Law class.  Vanessa always invites interesting people to come speak with us during our brown bag lunches!