Saturday, May 30, 2009

Hey everybody,

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

Thanks and Farewell

Hi guys! I couldn't agree more with Rachel- it's crazy how this lab is really coming to an end. I feel like I have learned SO much over the course of this year not only in terms of phage genomics and working with these highly specialized computer programs like Phamerator and Mega4 but also in terms of wet lab protocol which will be particularly useful for me in future science courses (i.e Microbiology and Cell Molec). In particular, I really enjoyed the DNA extraction process when we used the centrifuge and syringe/column apparatus to remove impurities from the DNA sample. And even though certain aspects of this lab may have been...less optimal to say the least (haha j/k), I appreciate the challenges that this lab presented me with because I know that they have influenced how I will approach problems in the future. I've had a blast this year working with you all and getting to know many of you very well. Lets stay in touch...facebook, of course haha. Special thanks to Dr. Denver, Dr. Taylor, Christy and Andrew; without all of you, none of this would have been possible.

Best to you all, and take care!


Saturday, May 23, 2009

pham 1419

i found that about 4 of the 6 genes i looked at in class last time were in pham 1419, which had a total of over 600 members...and yet, the pham that contained my tapemeasure protein only had 6 members. i'd have thought that one tapemeasure protein would perhaps have more in common with other tapemeasure proteins...any thoughts on that?


Thursday, May 21, 2009

Wow! I can't believe that we're almost done with this lab :( I have learned so much about genetics and bioinformatics! For the microbiology task force, we're currently investigating if the phage that has been sitting on the bench top for the past month is still alive and active! We're also starting a DNA prep, to see if we can improve the yield.

Pham 1432

I don't know about all of you but I am curious about the infamous pham 1432. Which if you don't remember has the largest number of members, 792 total.

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!

~Jon S.

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! 
Also - we are looking for students to help out with the lab next year as undergraduate teaching interns. You can get credit for this. If you are interested - come talk to me!  

Wednesday, May 20, 2009

FML phamily has 792 members.

Thursday, May 14, 2009


We still only have 8 followers! We're are all the people in this lab? I know you guys are out there, I've seen you in lab.


We have a website url now:

It's still under construction but should be up to running standards pretty soon-ish.

See you guys next Tuesday!

- Tamsen.