I Swear I Did My Work…

By Marissa Totten

So probably one of the most important, non-biology, things I’ve learned this past semester is to NEVER under ANY circumstances trust that a program will actually save your work. Honestly, from now on I’m saving my documents as a new file every ten minutes. Why? Three letters and one word: DNA Master. This program made me absolutely certain that I never want to go into tech support. EVER. The problems first started with forgetting to hit post, Hunter, before moving onto another gene. Then want on to display errors that requested sums as high as $2800, Ashley. Then the best message that could pop up was the one that notified you that your previous file could not be opened. Great. Countless gene blasts lost, new ORF starts erased, and time spent waiting on HHpred function blasts (most of them turned up no known functions anyway) wasted.  Word to the wise: save a new file after every couple of annotated genes.  Do it.  After plenty of corrupt files and the phrase “I swear I finished the annotation,” I’ve learned my lesson.  I currently have 55 Phatniss files saved.  After all of this, I honestly think that annotating by hand is the best way to go.  It’s actually a lot faster because you don’t have to keep switching tabs and the only way you’re going to lose your data is by losing the papers yourself. Despite all of the annoyance and frustration this program presented, annotating is a really cool process! It was a great look into what genetics entail and what scientists have to go through to figure out gene functions.

But now we’ve started the best part of the course, of course: web lab experiments! The hands-on work in this class is the best. I’ll admit my experiment isn’t the most interesting, I wrote it up the day before it was due while I was at a soccer tournament, but I’m still super excited to be working with my phage Drac109 again (despite the fact that I have to count and measure 150-300 plaques every class). I plan on switching the top agar with agarose because agarose doesn’t contain sulfates and other molecules that are suppose to inhibit virus propagation. Proven by the entire lab last semester, many phage aren’t bother by these molecules in the top agar in the first place, so it’s possible that the agarose will actually allow plaque size to increase. Agarose doesn’t have the same nutritional content as top agar though, so I may have to throw a couple of things in there so I end up only testing one variable.

And maybe, hopefully, some things will go right on the sequencing side and I’ll be able to annotate my phage’s genome…

Posted in Uncategorized | Leave a comment

Oh How I’ve Missed My FuzzBall

By Alyssa Khan

“This semester we’re going to be annotating a genome.”
Sounds pretty cool, right? I don’t know exactly what my expectations were, but it wasn’t to be spending hours on my laptop, trying to make sense of diagrams I had never seen before. We spent the first few weeks attempting to get the necessary software to work on our laptops. Then we spent the following weeks learning how to do the annotations and doing them in groups to present. My group could only meet on Sunday morning (the best time to get work done!) and working on the annotations took hours. As the semester progressed though, it became much easier to understand how to interpret all the information we had available to us.
However overall, annotating a genome turned out to be one of those things that sounds a lot cooler than it actually is.
Last week, we returned to “wet lab” to work on individual projects. I am doing an immunity assay on my phage from last semester, FuzzBall (yes, I named my phage “FuzzBall” – if you’re planning on taking this class be sure to start thinking about your phage name early so you don’t end up choosing one that you’re slightly ashamed to tell others). When I walked into lab, I started to smile uncontrollably. I didn’t even realize how much I missed seeing my all-too-familiar ‘bullseye’ plaques on agar plates. So far, this part of the semester promises to be a lot more exciting. I’m really looking forward to seeing if the lysogens of my phage are immune to infection by other phages!

Posted in From the Phage Hunters | Tagged , , , | Leave a comment

From the Wet Lab to the Computer Lab

By Sean Melucci

When you think of biology lab work, the last thing that would come to your mind is working on a computer. However, surprisingly enough, computer software tools are an integral part to biology lab work and research. In this, the second half of the phage-hunting course, the work on the computer was indeed shown to be invaluable. What good is isolating a phage and having it sequenced, if the sequencing data cannot be interpreted and shared with the world? It was our job this semester to interpret the data and annotate the genome of the winning phage “Phatniss”.

Just as in the lab, the annotation of the genome did come with its own trials and tribulations, but in the end they helped us learn and exercise certain computer skills that are very valuable to research involving bacteria or beyond that. It would frustrate me greatly getting the Virtual Machine to install correctly, or DNA Master to start up without immediately shutting down due to failure, or even to BLAST all the genes, but in the end I pushed through it and finally got everything to work so I could begin annotating. Yes I learned important computer skills through this process, but I also learned how to think through problems and continue to persevere, just as I had done in the lab portion of this course. This course, both in the lab and outside of it, will challenge you and make you think outside of the box, all in training you to think like a researcher.

Now, as we enter the last stage of the course being individual projects, I am more excited than ever. I feel like this course taught me a lot about the workings of a lab as well interpreting the data collected, and I feel like this final project is our chance to show the knowledge we have learned as well as learn something new about our phages. This class really has come full circle and truly prepared me to become apart of the amazing research that is being done at this great university.

Posted in From the Phage Hunters | Leave a comment

Spring Phage Lab: From Annotating to Experimenting

By Jessica Bauer

I can honestly say that this semester of Phage lab was not what I expected. Coming back from winter break, I was excited to start looking at the genome and doing whatever “annotating” entailed. I was not sure exactly what we would be doing, but I assumed it would be just as interesting and fun as being in lab was last semester. I may have been slightly disappointed. Don’t get me wrong, I liked debating start codons and staring at coding potentials just as much as everyone else, but it got boring after the 5oth or so gene. Finding SD scores, ORFs, and blast hits got really repetitive and did not have the same excitement that being in a lab and waiting for a surprising turn of events to happen gave me. Thankfully, all this annotating is mostly done though and we can finally get back to lab! Yay! I will say though that one thing I liked about annotating was how smart it made me feel to explain to someone else not in the class what I was doing. Just throwing around words like Shine Delgarno scores, ORFs, coding potential, and BLAST hits left so many of my friends with blank stares on their faces and made me feel like some mad scientific genius who does cool things like annotate a genome. Luckily they didn’t figure out how little I actually knew about what I was talking about.

Annotating is done, though, and finally we can all return to our lab benches, put on our favorite white coats, and start doing whatever we want to our phages. One thing about this semester that I am starting to really enjoy is all the different projects people are doing. We are no longer all streaking and plating and diluting, we have a wide array of topics and experiments to do. I personally have decided to do experiments testing how my phage responds to changes in pH. I figured being from Ohio, my phage is used to changing environments since weather in my town can move from spring to fall to winter to summer all in the same week. Going into lab last week I was a little worried since I was not sure on all the details of my project, but I just dove right into it and so far it has been successful. My little phage even grew in it’s titer count. This was a big surprise seeing as I was a little disappointed in him/her (it feels too impersonal to call my phage “it”) for not making it to phage olympics because of too little DNA. This growth in titer is a big accomplishment. The latest thing that I have done for my experiment up to today was make different phage buffers with an array of pH values. Word to the wise, although the name of the stuff is “phage buffer” it does not have a great buffer itself. I added just a little bit of concentrated hydrochloric acid to it and it’s pH dropped from 7.6 to almost 1.  A lot of diluting had to be done to fix that accident seeing as although I have faith that my phage will be able to survive changing pH, I don’t thing he/she would survive in that acidic of an environment. I’m excited to see where my experiment will take me in the next few days. Although surprises can be bad during an experiment, I’m kind of hoping for maybe a few harmless ones just to make things more interesting.

Although Phage Lab this semester did not start off how I thought it would, it has definitely made a turn for the better. It will be interesting  to hear about the results of everyone’s experiments and what they deduced from them. I’m not too thrilled about having to go back to finishing the annotation, but I know that it is something that we have to do so I’m fine with it. I’m also not too thrilled about it though because it will mean that Phage Lab is actually over which is a very depressing idea, probably for everyone.

Posted in From the Phage Hunters | Leave a comment

Too Small for Her Lab Coat

By Jessica Kahan

Unlike the majority of the other students in my class, I am new to Phage Hunting this semester. At first, when we were annotating genomes, everyone was new to the material, and we all learned together. However, now that we are in the lab I am totally out of my league–it’s a little intimidating! Luckily, everyone around me has already isolated a phage before and is available to answer my millions of questions. Since this is only my second week in wet lab, I’m optimistic that as the semester progresses I will get more comfortable. After all, nothing drastic has happened..yet.

Last week, I went outside to collect my soil sample. I didn’t really know where to look, so I picked a spot near a newly placed statue that looked promising. After checking out my plates today, it looks like I made the right choice! My phage was so potent that it killed all the bacteria on my first three dilutions, and I only had visible/countable plaques on my lowest dilution plate. Needless to say, I am very excited to continue isolating my phage, and I hope that my phage has yet to be discovered by another person so that I can claim it officially as my own.

Although I was nervous at first about the prospect of wet lab, I’ve found that it is highly engaging and fun. The hours fly by, and I always feel satisfied after accomplishing the day’s work. Phage Hunting is definitely the highlight of my week, and I can tell that each day I am learning more about phages and lab research in general. I’m looking forward to completing the semester!

Posted in From the Phage Hunters | Leave a comment

Missing the Wet Lab

By Matthew Williams

I am not the biggest fan of genome annotation. It’s not that I don’t find genetics interesting; although I know little about genetics, I find the topic fascinating. The problem lies within the cut and dry process of annotating.

For starters, I had to download Virtual Box because the programs only work on Windows, and I own a Mac. The interface on Virtual Box is just poor. The screen that I can work on in Virtual box is about 1/4 of my entire computer screen. There might be a way to better this situation, but I am not the best with technology, so it is frustrating for me.

Next, I find the annotation process repetitive and boring. I was never able to blast the entire genome, so I have to copy and paste the amino acid sequence for each gene and personally blast them using the blastp website. It just gets old after awhile. It would be nice if I could just copy and paste the results into DNA Master, but of course it doesn’t work that way. That would just make too much sense.

To continue, I don’t understand how HHPred can predict the function of a gene. My understanding is that the program compares the amino acid sequence of a gene to a bunch of databases and magically can predict the folds in the protein, and as a result determines its function. To HHPred’s credit, I do not understand a lot about genetics or how folds work in proteins. But all I am saying is that if I understood how it worked, the annotation process would be more enticing…. Maybe…

Yes, the source of most of my complaining lies in my own incompetence. I do want to learn more about genetics, and I will do so when I have free time. I could probably fit it in my free time in between my two-a-day training sessions for soccer, 16 credit course load, or my 15 hours worth of research I do every week.

But in all seriousness, I do have a problem with the annotation process. It seems like whenever we come across something new or different, we are supposed to change it to be similar to the other genomes that have been annotated. For example “TTG start sites are less common.” Well if everyone annotating a genome has this mentality and therefore changes the start site to fit the mold, then of course TTG start sites are going to be less common. Also predicting the function of genes based on earlier annotations seems sketchy. While the people who developed the DNA Master Annotation Guide have way more experience and knowledge about genetics and annotation than I do, I would like to pose a question for them. Does their “guidelines for annotation” foster the potential for diversity in phage genomes?

To conclude, I miss the wet lab. I want to develop an experiment to quantify the diffusion rate of Phatniss. I am having some trouble developing a protocol to do so, but I thought it would be cool to compare the difference of diffusion rates in different densities of agar. In a practical sense, this would relate to the diffusion rate in different densities of soil.

 

Posted in From the Phage Hunters | Leave a comment

A Whole New World

By Taylor Veralli

Ugh, I’m just going to say it. Phage Hunting went from my favorite class last semester to my least favorite this semester. I dread the potentially 2.5 hours spent discussing gene annotation every Tuesday and Thursday. The professor and my classmates are honestly the worst, I don’t know what happened (I used to think everyone was great, but now they are just so lame). I sit in class just hoping it will end soon, just so that I can go back to my dorm and annotate more genes. To be honest I wish I had the foresight to drop this class and explore other options.

April Fools :)

In reality, the second semester of Phage Hunting is quite different from the first semester, yet still very enjoyable. Working in the lab was definitely fun, (I’d be lying if I said I wouldn’t rather be there on most days) however, gene annotation (while tedious and confusing at first) is actually quite interesting. We all learned so many practical lab skills last semester, it was nice to learn the science of the genes that make up my little phage. As a class we were also able to learn just how difficult getting Windows and Linux operating systems onto a Mac. (On that note, my non-computer science major self feels like such a badass when running three operating systems simultaneously). The actual process of gene annotation is a rather tedious and repetitious after a while, but I’m assuming the end result is well worth it.

This semester is also interesting because I am literally watching, and actively participating in the picking apart and labeling of what became my child during the first semester. It is a really weird feeling seeing the thing you harvested over many long hours in the lab, just quantified into a computer file of just A,T,C, and Gs. Then multiple programs and undergraduates had to further analyze just what makes your baby phage unique. Honestly the whole thing is almost worthy of an existential crisis. As if this wasn’t unsettling enough, I also cringe with slight embarrassment at every mention at the name “Phatniss” because everyone is painfully aware at how obsessed I am with the Hunger Games.

Just to be explicit: I still adore this class and all of the amazing things that I have gotten out of it.

Posted in From the Phage Hunters | Tagged , , , , | Leave a comment