From A Different Perspective

After the last day of classes and labs, I had thought that it would finally sink in that all too soon we would be leaving Baylor and going home to relax (and take more classes!) for the summer. However, this proved to be untrue. These past two weeks have been so insanely busy that it does not ever seem like the year could possibly be drawing to a close. Looking back, we, as a class, have made so much progress this year. We went from being completely clueless, if highly enthusiastic, at the beginning of each semester to confidently isolating and annotating both bacteriophage and maize genes by the end of the year. (I must admit, I was *really* not expecting to have anything to do with maize genomics…ah well. It was an interesting change of pace, at any rate.) I am going to miss spending time in wet labs and computer labs with everyone next year. Hopefully we will all continue to have classes with each other over the next few years and can keep in touch as we progress through our studies. Thank you all for making this such a wonderful year!

After finishing the functional annotations after lab today, it finally fully dawned on me that the year is almost over. While yes, I am excited to see all of the work that our class has done throughout the year come to a cumulation, I am also saddened to know that after this year our class of twenty-four amazing people will scatter throughout Baylor. (However it does seem like there is a fairly large percentage in my chemistry class next semester!) Anyway, good luck to everyone as we finish with Benedict and start work on the corn genomic honors project!

Yay! Halfway through the functional annotation of my nine genes! I have to admit, while being shown how to use phamerator and the other functional annotation software, I was completely lost at first. (There was a weird feeling of deja vu reminiscent of the first day of wet lab and the first couple days of the genomic annotation.) Fortunately however, all my assigned genes are at the end of the genome and the vast majority had no match in BLAST, making my job comparatively easy. Hopefully the rest of the genes go as smoothly!

As I finish annotating Benedict’s gene sequences that were assigned to me, I have to reflect on the differences between our lovely Etude and Benedict. First, the gene calls on Etude were, by comparison, much easier than the gene calls on Benedict. There were few overlapping sequences, and tons of one to one blastx matches. Benedict, on the other hand, seems to revel in causing the class to develop headaches. Just as we decipher one of his puzzles, he presents us with an entirely new challenge! Every single one of the eight genes in my section of his genome were in reverse, half of them had overlapping sequences, all but one of them had not a single match in blastx, and the Glimmer and GeneMark calls on most of them were vastly disparate, with evidence that could point either way! Nevertheless, those eight genes have now been annotated! Victory is mine! In only a short while we shall see how my calls compare with the overlapping sequence in another student’s assignment…Hopefully all goes well!

This past week the class completely annotated the gene location of Etude and, much to our surprise, pretty much every gene that we called was correct to the best of our knowledge! We also found out that our bacteriophage, Benedict, was finally ready! I cannot wait to start working on annotating his genome! I wonder when we start working…

I have to admit, at the beginning of the semester, I wasn’t really sure what to expect. I honestly did not believe that this semester could possibly be nearly as fun as the first semester of labs was. How could it be? Our biology lab is in a library and we are working solely with computers, which has never really been one of my strengths. However, I was very pleasantly surprised when I showed up (after getting lost in the basement of the library, unable to find the designated classroom) and we immediately began playing with a sample DNA sequence, Etude.
It was by no means simple to work with, but I was reminded of the first day of lab last semester in which the whole class looked with dismay at the various procedures and equipment which we were informed that we would have to learn to use effectively, all while minimizing contamination by outside pathogens. Just like last semester though, I slowly began learning how to use the software provided and was delighted by the sheer coolness of what we were doing! To me at least, annotating a gene is comparable to a cross between a wordsearch and a jigsaw puzzle, two things I am rather fond of. Now, after annotating several of Etude’s genes, I impatiently await the arrival of Benedict. This semester is suddenly looking fascinating!

After a less than sucessful first attempt at plating and growing the bacteriophage (due to several possible causes), a second attempt was made. Although it was a disappointing moment watching the first set of plates set aside to be autoclaved, it did have some upsides, including the elimination of some, shall we say…interesting odors emerging from some of the contaminated plates. Allowing a few minutes of mourning for the class upon the revelation and disposal of the plates, we soon enough jumped back into the experiment and started all over–what fun! The whole class–well, me at any rate–was rather pleasantly surprised that the process of capturing the phage and plating it that had taken us a whole week to get right the first time now could be accomplished in a single lab period! What a relief. As I finished up and prepared to leave the lab, I left the seven new plates awaiting inspection in the incubator as well as a mountain of prayer and a million hopes for positive results on the morrow. Combined with the rest of the class’s plates and hopes, I am honestly not quite sure how everything fit in that incubator…

The next day, I walked with great trepidation into the lab, opened the incubator, and YES! There were small (and some not-so-small) plaques! I am confident that I have never been so excited about seeing clear circles in bacteria! The atmosphere in the lab went from almost tangibly tense to complete euphoria in a matter of seconds as everyone began exclaiming over their phages and exhibiting them to everyone in the vicinity. This feeling of victory persisted throughout the day as we selected different plaques to try and isolate the bacteriophage from (a surprisingly tough choice). As soon as that was done, we slowly drifted out of the lab, but on my way out I could not help but think “Wow, now this is science!” I can not wait to eventually see the large variety of phage living in the seeminly dead and inert soil as we progress throughout the year!

With great joy,

Rachel

Ok, so this is my first post.  Ever.  It is an odd feeling, realizing that setting up a blog and keeping it updated actually makes me more anxious than anything in a lab…I would never have guessed before starting this that that would be the case.  Ah well, c’est la vie. 

So, for lack of anything else to write about, I shall discuss my dirt.  Sounds like so much fun, eh?  Anyway, I collected my soil from my backyard.  It is pretty much typical Abilene dirt–dry, dusty, and red.  However, in the rush to get everything packed for moving in to Baylor, I left my dirt sitting in my room.  As a result, I had to request that my mom mail my dirt to me before class on Monday!  While waiting for my dirt to arrive, I checked my mailbox everyday (sometimes more often!).  This behavior, to those students not enrolled in this bio class, seemed a little odd.  When asked why I was so preoccupied with the postal office here at Baylor, I had to explain that I was waiting for my dirt to arrive in the mail.  You can imagine the number of incredulous expressions people wore when I mentioned that!  Horrible…However, on the bright side, I met many wonderful people while trying to explain exactly why I needed soil sent to me in the mail when it is so ubiquitous here at Baylor!   In conclusion, I finally did get my dirt and have loved every minute in the lab and cannot wait to (hopefully) find some bacteriophages lurking within the soil!

Until next time,

Rachel