Good company makes for good conversation: the 2014 SEA-PHAGES Symposium

Just about a week ago, I had the wonderful privilege of attending the 6th annual SEA-PHAGES Symposium. Situated on the gorgeous Janelia Farm Research Campus in Virginia, the symposium lasted for a whole weekend and hosted more than 240 students and faculty from over 75 colleges around the nation.

I was pleasantly surprised that everyone who attended was as excited about bacteriophages and research as I was. During dinner, Laura (one of my peers from Dr. Schildbach’s section) and I chatted with Carnegie Melon phage hunters about different ways to perform genomic sequencing. We couldn’t stay and talk for long, as we were quickly swept into a whirlwind of presentations and talks. Students, faculty, and even Dr. Graham Hatfull himself (a celebrity in the phage hunting world – he founded the national Phage Hunting program) gave captivating presentations about their own experiments and experiences with research. The guest speaker this year was Dr. Martin Chalfie, a Nobel laureate who shared the 2008 Nobel Prize in Chemistry with two other scientists for discovering and developing the green fluorescent protein (GFP). His presentation was not a lecture on the wondrous studies and experiments he had performed (which I am sure there are many), but rather he weaved a fascinating story about his path of scientific discovery and its implications on society as well as his own life. He did briefly discuss the logistics of his experiment and how it led to the ultimate discovery that GFP can be used to identify cells expressing specific proteins – his clarity of presentation was astounding to me, as even I could easily understand what a man of his caliber was teaching. However, the thing that struck me the most was his description about starting out as a young scientist, not unlike the ones sitting in front of him. He made it sound like research was easy to pursue as long as you were curious and determined enough. This opened up my eyes to a plethora of possibilities because, to be honest, I was never really quite certain that I would be able to find solace in the intimidating field of biological research.

However, my job at the symposium was not to just simply listen to and soak in all of these wonderful presentations – I also had the opportunity to present a poster about the experiments performed by my class during the school year. There were two sessions in order to accommodate the multitude of posters that were being presented. I was scheduled for the second session, so I used my free time during the first to talk to a few presenters and see what other schools were doing. Some schools decided to pursue independent projects in the wet lab, like we did, while others focused more on bioinformatics or applications of phage therapy. One of my favorite posters included a presentation from North Carolina State University, where the students there were working on finding a phage that could target Paenibacillus larvae, a type of bacteria that can infect and kill honeybee larvae, as a means of rescuing the dwindling honeybee population. It was so fascinating and inspiring to see that the research we are doing has an immediate application to the real world.

symposium2

The second poster session, during which I presented, sailed by smoothly enough, probably because our class had a poster presentation right before the semester ended, which left me feeling confident that I was relatively well prepared for any questions headed my way. I remember that one of the researchers asked me what the most interesting thing I learned throughout the course was. Looking back on it, he might have been asking me for an interesting fact about phages or even a question that our experiments left unanswered, but before I could reflect on his intent, I blurted out that I learned how hard research was. All the experiments we performed had procedures and guidelines and even expected results; however, along the way, plates got contaminated, HTL ran out, and many of my experiments failed. Despite not everything working out as expected, the most important thing I learned in class was that a contaminated plate is not the end of the world- you’re going to stumble a few times before you end up with the results that you want.

I am so thankful to have had the opportunity to participate in the Phage Hunting Symposium as well as the class itself – from dealing with contamination to actually getting to see my phage under the electron microscope to meeting people equally as excited about science as I am, I have been able to learn something from every single one of the ups and downs I’ve experienced in this class. Thank you to Dr. Fisher, Katie, and all the Mon/Wed Phage Hunters for making this class one of my most rewarding freshman year experiences!

sympos1

Posted in From the Phage Hunters, Uncategorized | 1 Comment

Ode to Scientific Method

By Aviana Duca

Over my spring break, I was helping my little brother with his middle school science fair project, titled Ode to Snot. His project was about the effects that nasal mucus has on odor perception. For those that didn’t hear my brother’s hypothesis and abstract at the dinner table for a week straight, who knew that the much-neglected nasal mucus has such an important role in transporting odorants to receptors in the nose? He designed his experiment to have a control group, a test population, and a well thought out procedure to determine the accuracy of his hypothesis. I was able to shed some light on the scientific process and help him analyze and interpret data. Working with him allowed me to realize how far I have come as a scientist and this only excites me as I begin to work on my own experiment.

Working with my brother helped me to realize that no matter what age you are, what your experiment is, or what you are trying to prove, the scientific thought process is universal. The scientific method is a logical thought process that is used by scientists to acquire and interpret data. Experiments involve observation and two different kinds of reasoning strategies, inductive and deductive reasoning. Inductive reasoning is when broad generalizations are made from specific observations. This is helpful when designing an experiment and coming up with what to test. Deductive reasoning is when a scientist starts out with a general statement and preforms an experiment to reach a conclusion. The scientific method uses deduction to support or disprove the hypotheses.

What makes the scientific method so attractive is that it can be applied to both complicated problems and everyday occurrences. It is a step-by-step process that leads to a conclusion. While my brother’s experiment and my own are at two different levels, the steps we follow are fundamental to our success. Working with my brother helped me to organize ideas for my project and the direction that I want to take. I look forward to getting back into the lab and moving to more hands-on experimentation. I also look forward to see what results and data will be obtained and what discoveries will be made. Watching him go through the process of testing a hypothesis reconfirmed my love for science.

Posted in From the Phage Hunters | Leave a comment

The Mysteries of Phage Hunting

By Lizzy Glass
Last week, we started our individual projects in Phage Hunting. We were all finally back in the lab using pipettes and microcentrifuge tubes, and I could not have been more excited. For my individual project, I chose to study how an absence of calcium affects the growth of my bacteriophage Calkins. I hypothesized that calcium would inhibit the growth of plaques on my plates. The first day I did a serial dilution to calculate my titer after having my HTL sit in the fridge since November. The next day, I was ready to compare the calcium-rich sample and the calcium deficient sample. I plated dilutions using calcium and without using calcium.

LG2LG1

However, when I came into lab the day after these plates were made, I noticed some interesting results: there were more plaques on the plates without calcium than with calcium. This was the opposite of my hypothesis. I redid my procedure from the day before and left lab feeling puzzled.
Sometimes the things that happen in Phage Hunting do not make sense, and they go against what you had thought was ever possible. However, my favorite part of Phage Hunting is when results don’t necessarily add up because then you get to try again and look at new results. And if something turns out to actually be different, you may have found something unique.

Posted in From the Phage Hunters | Leave a comment

The winding road of discovery

By Alexa Potts

Dr. Fisher’s voice floats over the sterilized lab benches and around the flames of Bunsen burners as she explains the art of streaking to a group of new phage hunters. My lab partner and I listen with pride, as if we are mothers wondering at a child’s first bike ride. But wait. We were there ourselves only last semester. Was it really just a few months ago that I could not tell the difference between 10 µl and 100 µl on the various pipette dials? Did I actually agonize over not making bubble baths when plating, which I can now do without a second thought, carefully maneuvering test tubes of smeg, plastic caps, and TA bottles between my fingers while not letting go of the automated pipette? It seems as though we always knew how to speak of plaques and high titer lysates, siphoviridae morphotypes and phage phams in nonchalant voices; when months ago this was just a baffling foreign language. Yet for all the knowledge and happiness we have discovered in lab there is always more to uncover. Plates are checked and the results are not what we expected. Something new goes awry. The winding road of discovery continues on as we work through different challenges and deal with old enemies (horrendous morphology changes, evil negative controls with plaques, misplaced HTLs). Lab time has its fair share of frustration and disappointments, but the joy of gorgeous web plates and beautiful ten-fold serial dilutions, the pride of seeing the EM images of your very own phage for the first time, far surpass the upset of strange results. And in true Hopkins style, we wouldn’t be telling the truth if we did not admit that some part of us relishes in the challenge of figuring out why certain results were funky and what our next course of action should be. There is nothing like floating through the lab, empowered by the sense of ownership and independence that comes from taking charge of your project and your darling phages. This lab has its own special magic, and it certainly is good to be back.

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

The End of the Year

By Andrew Greenhalgh

We survived. From the first day where we were so afraid to break plates to today where we were masters of laboratory work, each and everyone of us has survived this together. And I have had the pleasure to watch each and everyone of you progress into the scientist you are today. To be honest, this was my most fun class of the year. I was able to progress not only as a scientist, but as a person, all because of the amistad that bound us so close together. Thank you all for an incredible freshmen year, and I look forward to seeing you in the fall.

Signing off,

Andrew

Posted in From the Phage Hunters | Leave a comment

We’ve reached the end!

By Justin Decker

From the start of the semester to this very busy week, the Phage Hunting course is over.  Left though is a bittersweet feeling.  While it is nice to have isolated a novel bacteriophage in the wet lab, it’s sad that I won’t be able to work more in the lab and with the same people.  Everyone contributed to a relaxed, amicable feeling in lab, and it really added to the excitement each time.  It was a pleasure to work with my peers, as they were always willing to help and always so cheerful.  I’ll miss seeing and working with some of the new friends I made there.

In the culmination of the experiments conducted in wet lab, there was an event in the Mudd commons where groups of students in phage lab presented posters on their work.  Not only that, but there were also posters that other students had made from different classes on myriad, scientific topics.  I had never known that students could get so involved in certain research projects at Johns Hopkins, but seeing all the posters on display, it quickly became apparent that it is possible!  The event was so much fun, and there was even pizza.

In the end, phage lab was so much fun, and it was a delight to work with the other students, Dr. Fisher, and Dr. Schildbach.  I’m so happy to have had this opportunity!

Posted in From the Phage Hunters | Leave a comment

Crossing the Finish Line

By Sarah Cohen

Unfortunately, as the semester ends, so does our time with our phages that we worked so hard to nurture and keep alive (as college students it’s hard enough to keep ourselves alive). Our final class period was spent presenting our projects instead of working further with the phages. As sad as it was to not be in lab, it was exciting to see all of the work come together.

As I frantically studied up on my procedure before the big presentation, for the first time, I fully understood everything that had been done in lab in order to arrive at my isolated phage– Swimmie (named after my sister’s goldfish). It was nice to see it all come together and mean something. Also comforting was the teamwork that I encountered as my group helped each other gather up the courage to speak about these formerly abstract ideas. Phage lab not only helped me learn about bacteriophages and valuable laboratory techniques, but it also helped make friends that I would never have met otherwise. Overall, my experience as a phage hunter was a great one.

Posted in From the Phage Hunters | Leave a comment