Tuesday, June 2, 2009
Anyways, ever since last summer when I got the email saying that I was accepted into this lab, I was excited - maybe it was because of how exciting it sounded from the description or maybe it was because upcoming freshmen are excited about everything ;). I remember on the first day of class we were handed these awesome lab notebooks and then being told by the professors after giving a brief introduction to the class, "We have a long and busy schedule ahead of us, so lets get our hands dirty and find some phage!" Amazing.. it was only my first day in a college lab and we were already venturing out into the abyss to do fieldwork. After that, things started to get exciting. Fall term was marked with memories of using petri dishes, microcentrifuge tubes, micropipettes, and the incubator, day in and day out. Every week I would give myself a pat on the back for hitting another checkpoint in the process. Spring term, I got to run a gel for the first time (I remember using the super tiny tubes) and I got to watch the operation of an electron microscope. This term, we got to experience first hand what genome analysis was like. Finally, after having a wonderful year, we met in class for the last time today.
Even though a lot was accomplished, it doesn't even feel like the first day of class wast that long ago. Time flies when you're having fun :p
Monday, June 1, 2009
Tomorrow will be our last and final phage lab, we have gone trough so many SMEG and TA buffers to get where we are right now. Reflecting on the past months, it is incredible to think that we started out from a tiny sample of dirt, compost, or manure and now the final genome! Just shows what a team of dedicated students and experienced and passionate instructors can accomplish in a small amount of time. I am sure everyone have learned more than just the information, but also in some ways improved our communication, team work and time management skills, something’s that is very crucial to any career in the future. Lastly I would like to congratulate everyone and good luck with finals!!!
There is a link there called "Genome" that talks about Colbert a bit.
Let's chat about this in lab tomorrow!
I want to take this time to thank everyone for making this lab an enjoyable class. I made friends I probably wouldn't have made in a regular lab section, and I truly learned a lot, thanks largely to our advising faculty. Dr. Taylor, Dr. Denver, Christy, and Andrew, thank you very much for being so dedicated to helping all of us through this adventure of a research lab. :)
Saturday, May 30, 2009
So, I figured this would be a good place for updates on, as well as a sounding board for, getting Colbert (the phage) recognized by Colbert (the TV show host). Right now, my current plan is to wait until the GenBank entry has been finished and published (as that is the real legitimate proof if there being a mycobacteriophage named after Stephen Colbert), then posting the info to the Colbert Nation forum site, and hoping it gets seen by the right people, including links to our website, this blog, a contact email (I can either just create one, or we can make some sort of contact email for the lab at large), and some pictures. Thus, whoever gets informed about the GenBank entry, they should let me know, and we can get this ball rolling. Any other comments / suggestions are welcome as well.
Tuesday, May 26, 2009
Best to you all, and take care!
Saturday, May 23, 2009
Thursday, May 21, 2009
I am wondering if this lab has access to a more powerful computer that has the Phamerator on it? I would really like to see this pham circle myself and I am sure others would also.
Anyway everyone have a good long weekend!
Well - there's only 2 weeks to go in the Phage Lab! We've made it all the way through Sequencher, Apollo, GBrowse, BLAST, and Phamerator with our Colbert genome. The map of Colbert is at the right. It is pretty fun to see how it turned out and to compare it to other phage genomes - especially ones that have been discovered this year by other schools in the SEA - like UncleHowie. I hope that everyone has enjoyed this voyage of discovery as much as I have!
Thursday, May 14, 2009
We have a website url now: http://biology.science.oregonstate.edu/courses/genomics-lab
It's still under construction but should be up to running standards pretty soon-ish.
See you guys next Tuesday!
Wednesday, April 22, 2009
For many of us Phage Labbers, this has been the first time that we have truly been thrust out into the world of science without really having any idea what the outcome would be at the end of our journey. For the first time, questions arose that didn't necessarily have clear cut answers, and at that point we all heard the resounding words of Dr. Denver's coined phrase, "That's Science." Although some of us may have forgotten how we arrived where we are today, analyzing the base pairs of the Colbert genome, others are reminded of the hours a week we spent in Fall Term. Occasionally up to 7 hours a day for a few of the ambitious ones. The countless number of titrations, purification rounds, etc. that led us all where we are today. I, personally, feel quite lucky that although as a class we had a few minor setbacks, we really have gotten the job done quite nicely. Everyone stepped up when they needed to, and in the end, although only one phage was chosen to be sequenced, we were all able to make our own contributions. I just thought I would take some time to encourage people to look back the long path that we've traveled over this year. Think back to our dough-eyed expressions trying fervently to decide whether to choose the manure pile or the recycling bin. It's been a truly outPHAGEous class, wouldn't you agree?
Tuesday, April 21, 2009
We only got through a couple group presentations (maybe half) so next week will probably be the same. It is rather difficult to make this part of the class interesting because we're going through each gene called at a time, and explaining our reasoning.
Hope everyone is enjoying the weather,