riosa's blog
FINAL WEEK
Wow, what a week. Everything came together. Andrew revised my paper multiple times, and now it is ready to be sent in to Vanessa. My powerpoint presentation is also ready to go - I gave an informal practice talk today in front of Andrew and another lab member (this proved to be very helpful). It looks like I'm ready for my presentation tomorrow!
Week Nine
I hit one major setback this week. The 18S rRNA sequences came back and I got some unfortunate news: my sample was a SPONGE NOT an ASCIDIAN. I was in shock for a little while. I had already done a ton of literature research and had around 30 sources ready to write a solid paper about ascidians and their associated microbial communities. Now that everything was flipped, the sources and outlines I had compiled meant nothing, and I basically had to start over. This kept me extremely busy - I ate lunch next to the computer and came in on Saturday to get extra work done.
Week Eight
This past week I mostly worked on cloning. I finally have clones with the 18S rRNA gene from both ascidians and the sequences are finally ready to be anaylzed! I have also been working on cloning the archaea genes, but this has not been successful thus far. After analyzing my sequences, I will be ready to wrap up my project! In a few days, I will be hard at work on the paper and the presentation.
Week Seven
What a week. I attempted cloning two more times, but both times (oddly..) failed. At the same time, I spent the entire week struggling to amplify the 18S rRNA gene from both ascidians. Finally, by the end of the week, Andrew was able to pinpoint different, universal 18S primers that would amplify a smaller portion of the gene. The primers he gave me worked well! I purified the PCR products and began the process of cloning (for a third time). I came in on Saturday to keep my project rolling smoothly and to get a head start on week eight. Yet, surprisingly, cloning failed for a third time!
Week Six
Last week, I sent in 10 purified bacterial plasmids (that represent different bacteria present in the ascidian sample) and over week 6, I got some the sequences back! Knowing a few of the bacteria present in the sample, I am sending in 48 more bacterial plasmids for analysis (to get a wider representation of what the ascidian contains - clearly 10 isn't enough to get the big picture).
Week Five
I cannot believe I am half way through my summer internship! Here's what I've been up to week five:
Week Four
Moving forward with the DNA sample that I did obtain, I am now in the process of cloning. I ran a PCR today to make sure the clones had picked up the 16S rRNA gene. I found that about 60% of the colonies had picked up the gene I needed it to have. I am currently running a second PCR on a different plate of colonies - I'm hoping for a better percentage (somewhere between 80 - 90%).
Week Three & 1/2
I thought I would provide a little update on my project since my last blog ended with such a cliff hanger (did the second ascdian DNA extraction work?? Did everything turn out okay??)
Unfortunately, no, the DNA extraction and following PCR did not yield results. So, Andrew has advised me to move on with the project and focus my work on the ascidian sample that did yield DNA.
I am currently in the process of cloning and hope to finish that by the beginning of next week. It appears as though I may be done with my project early - so I may also be working on a second project! We'll see!
Week Three
This week has been particularly exciting because I was finally able to extract DNA from the ascidian samples. After many unsuccesful attempts to extract DNA, numerous PCRs, my disappointment turned to delight when, at last, I obtained results!
Week Two
Week two has flown by! I finally have a good grasp of what my project will be; Last week, Dr. Haygood told me that I would wake up one morning and know exactly which project to pursue, and she was right! I have chosen the second project I mentioned in my previous post. Basically, I will spend the next 8 weeks analyzing the microbial symbionts that reside in the ascidian tissue samples. For more information regarding my project, check out the link to my project description!