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Week 6- Cruise Prep and Mass Cloning

This week I was working on a variety of little projects in order tobe ready to mail the mass cloning plates away and to help Suzanne prepare for the sampling cruise that she will be going on next week.  On Monday, Suzanne and I got packing material from Nancy Christie and got dry ice from the primate center.

Week 5- Mystery Meat and Columbia River Samples

This week was a sucessful week for Suzanne and I. We started off the week by decideing to send out samples for the Columbia River site back tothe primate center to make sure that a mistake wasn't made since out first sequencing came back as P. Putida.  We knew that this just meant a mistake was made or somewhere along the line our sample was contaminated.

Week 3 & 4: Environmental Sample Extraction

During these two weeks my time was spent trying to get my newly extracted CR-20 samples to amplify.  We discovered that the problem was our primers.  Somehow the general bacterial primers we were using had degraded.  We ordered new primers during week four.  Because we had bad results when we sent our first set of CR-20 samples to the primate center for sequencing we decided to clone them again and send them back to make sure a mistake was not made.  If this comes back with the results that don't show contamination, than we won't have to amplify the samples that we

Week 2 - PCR and Cloning

This week I have been working on getting the samples from the LP-6, the NH-10 and the CR-20 to amplifiy using a general bacterial primer. Suzanne and I got the cleaned SIP samples to amplify and then went on to PCR cleaning.  We introduced the vector into our samples and cloned them so we could send them over to the primate center for sequencing.

Week 1- Extractions

I started on the Tuesday of this week working with Suzanne Delorenzo. This is my second year working witha CMOP graduate student and I am really excited to be back. I am continuing my work  in Brad Tebo and Peter Zuber's lab. This week I extracted DNA from samples that Suzanne had collected during May of this year and set up the Stable Isotope Probing (SIP) using an aerchea called halobacterium.

Week 9 - Denaturing Gradient Gel Electrophoresis (DGGE)

At the beginning of this week I finished up amplifying my samples and started the DGGE process.

Week 8

This week I is my seventh week because I wasn't here for the first week.  That means I have three weeks to finish up my project, write my paper, and create my final presentation.  Yikes.  I can't believe how fast this summer internship has gone.  This next week I will be moving on to the DGGE.  If we get it right the first time I should be a great place to work on my paper at the end of next week because Suzanne will be gone and I will have data to write my paper on.  If we have troubles with the procedure which is possible because it i

Week 7

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

Week 6 - Presentations

This week we gave our midway presentations.  I spoke about what I had accomplished so far including sampling, DNA extraction, and stable isotope probing.

Week 5- PCR Troubles

This week has been a week of learning with some frustrations.  We have been trying to run PCR on two of our samples and we jsut can't seem to get the results we are looking for.  The first time ran a the PCR we had no aplification and the second time we ran it the positive didn't amplify.  The third time we ran the same PCR we had more amplification but some of the 12 C labels didn't amplify and they are supposed to always amplify.  This was concerning because it could have meant that we didn't have any DNA after cleaning the SIP.  So I ran a gel to be sure tha


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