After the Hunt Comes the Feast

By Augusto Ramirez

Phage Hunters

Wait… That can’t be right… Phage hunters don’t eat phages. Right?

Then what is this feast?

First semester, a group of inexperienced soon-to-be phage hunters gathered in a lab. Here I stood with my fellow classmates, following protocol after protocol, training my empirical skills yet oblivious to why we “capture,” “tame,” and isolate these little guys. Of course I was given a complementary manual to answer my questions, however, although dense in instruction, it only briefly explained purpose. “Why is this? Why is that?” I would constantly ask the instructors or teaching assistants when I had the chance. The answers all made sense; the general idea was there, my classmates and I obviously understood what we were doing and why, but did we really? I promise I am not willfully trying to sound either confusing or consciously attempting to appear profound. What I am saying is that although we, the phage hunters, knew what we were doing (isolating a phage for DNA sequencing) and understood the gist as to why we did it (to voluntarily contribute to the scientific community), we had not grasped the idea of what came after the hunt and why it was important.

Our ancestors, I’m speaking prehistoric Paleolithic, had a reason to hunt and gather. It was quite simple, to eat. That way, our cavemen friends could survive as a species and live long enough to evolve to what we are now. Everything we do derives from this instinct to hunt. The need to survive and prosper is naturally in our genomic composition. In a way, this applies to phage hunting, where hunting is subconsciously used as an analogy… albeit, I suppose the analogy is explicitly stated in the name for this but not explained. We hunt for phages, capture them, tame them, and isolate them; the same way a hunter would “capture” an animal to eat, a farmer would “tame” to sell and eat, and a typical human being today would go do groceries and “isolate” the food they need to eat from unnecessary products. The need to eat is the need to survive. However, when it comes to phage hunting, we don’t eat the phages; instead, we send their genetic material to a DNA sequencing facility. So where is our need to survive/eat in this scenario? Are we just hunting phages for the fun of it? Definitely not. Did I just spend this whole time writing about a theory that isn’t held constant for all things, especially not in phage hunting (which is the purpose of this post)? I hope not.

So here is where it all comes together. After all, hunting is nothing but an analogy to represent the utter instinct to survive. Think, survival of the fittest, or perhaps natural selection (a little Darwin might ring a bell). So the significance of a subject can be associated to how it is applied towards our survival. Of course, as phage hunters, we aren’t curing cancer or making breakthrough discoveries in lab everyday. However, there is great insight to be earned in the areas of genetics, epidemiology, and therapeutics from bacteriophage research. That is where the hunting analogy comes into play; because as a species we want to survive but survival is not just about having a plate to eat everyday anymore, it also is about fighting deadly pathogens and getting closer to a better and stronger society; perhaps even immortality.  In short, our need to survive as a species currently depends on being fed enough significant information. With phage hunting we will be annotating the genetic information of a phage to help contribute to a database that will perhaps be used in the future to discover “the next big thing.”

NOTE: I will now wrap up, because I just realized how I could talk about this topic for so much longer. There is actually so much more I wanted to mention but this post is very long already! Sorry!

Basically, the feast is all the genetic information we are lucky enough to annotate. Little do we know that one day our information might become a fundamental part of an era-changing breakthrough.

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The Struggles of Not Eating Lunch

By Ellie Wenneker

We are now more than three weeks into the semester and still no genome…the only major accomplishment has been the successful download and installation of all the software needed for the semester: Windows, Phamerator, and DNA Master.  It was a long fought battle between the computer and me.  The week leading up to the semester, I struggled to download and install windows onto my computer.  Cooped up in my room in Hopkins Inn, I sat in front of my 2.5 year-old MacBook Pro hoping that at least one of the programs would actually work.  None did.

The first day back in Phage Hunters, all I had eaten was some oatmeal at 9:30 that morning.  Class started at 1 PM, and I was hoping I would be in and out of UTL G89 within an hour so I could finally eat some food.  Unfortunately, downloading Windows in class proved more of a struggle than trying to download it in my dorm.  Nothing seemed to work until I got my hands on a copy of Windows XP.  I inserted the disc and it began to install!  It was already 2 pm at that point, and I was hoping the installation would go quickly.  It did not.  I waited and waited, nibbling on fruit leather I found in my bag.

Finally after 40 minutes, Windows had downloaded.  Ready to get up and get food, I was then told I needed to download DNA Master as well.  Frustrated and starving, I opened my computer and ran Windows.  When I clicked to download DNA Master, it said I needed 1 gigabyte of storage, but I only had 512 megabytes.  I had to shut it all down and change the storage amount in Windows.  I had no problem with the Internet before, but this second time when I tried to get on the Internet in Windows, it no longer worked. I spent at least 30 minutes struggling with the Internet settings in Windows, testing every possible combination of proxies and connection types.  When I was ready to quit, the TA changed one setting I missed…“Cable Connected.”  With this, I was finally able to download DNA Master.

As soon as DNA Master downloaded, I booked it out of there to fill myself up on mediocre food from the FFC.

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A new old world, or an old new world

By Andrew Greenhaugh

Welcome back fellow Phage Hunters! I hope the long winter’s cold and the intersession’s boredom did not reduce you to a state of an utter academic and intellectual pulp. A lot has changed since last semester, and it’s not just the year. It’s the way we approach things in The Lab of Phages. Everyday last semester, the routine was familiar: come in, put your lab coat on, see if you had plaques, cry if you didn’t, cry if you did, and repeat, all the while leading up to the culminating steps of creating an HTL, preparing a sample for DNA prep, and ultimately viewing your masterpiece under a $300,000 microscope.

But now, the tides have changed. We sit in a room about 1/3 as large as the lab we were in. Instead of putting lab coats on, we turn computers on. Instead of crying over plaques, we cry over getting windows on Mac computers. Ultimately, we experiment with computer software instead of agar plates and “smeg”. It may seem like an entirely different game, but the fact of the matter is is that we’re going into this semester the same as we did last, with no knowledge of what’s ahead. And that is the beauty of this class. We explore the smallest bundles of DNA and RNA which have the biggest impact on the world, and can contribute to an ever growing database of information on these little “dudes.” So HOP (haha I made a funny) on board the Phage Train 2. We will look even more inside the phage this semester than we ever have before . . .

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A necessity for science: technology

By Hunter Richer

So here comes the second semester, round two of our phage research. Each of us has isolated a phage, voted on the one we wanted sequenced and now we begin preparations for the annotation of this genome.

Granted, a bacteriophage’s genome is one of simplest that there is, but, still, analyzing and annotating it would be an enormous computational challenge without computers. That being said, it became apparent to me while trying to install the profoundly disagreeable Phamerator software that I literally don’t know a single thing about computers.

For someone aspiring to a career in the biological sciences, this is an issue.

I mean, sure, I can follow directions and am not ashamed to bother the TAs with endless questions about any hiccup, no matter how minute, that may arise while using an unfamiliar program (shoutout to Tegan). But eventually there won’t be directions or TAs to help. What then?

Considering the increasing dependence that scientists have on computers as tools in data analysis and representation, I think it is only a matter of time that some degree of computer science education is incorporated into the curriculum of science majors.

This realization has convinced me to take at least one intro level course in the subject before I graduate. Others who are equally ignorant on the matter should probably consider doing the same.

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Ride of the (Ph)ages

By Winston Jin

It seems like it was yesterday that I dug up pieces of dirt from the AMR II courtyard and looked like a crazy person in front of my peers during the first week of classes. Here I am now, sitting in phage lab for the last time in 2013, holding the product of a semester’s hard work in a micro-centrifuge tube, and writing about my experiences as a professional phage hunter (at least I’d like to think so) at the end of my first semester of my freshman year in college.

They say time flies when one’s having fun. That was certainly the case with my time here at Phage Hunting lab. Thankfully, all of my experiences were recorded in my lab notebook. It’s the first time I’ve kept a personal diary of my feelings every other day (trust me, it’s nothing short of an emotional one). My mood of the day depended on how my phage would behave, and I must say, Wentao (my phage) has taken me on an emotional roller coaster ride all semester long, with the scariest descents on two occasions.

The first of the spine tinglers took place when a completely new “target” morphology showed up in all of my MTL dilution plates, which forced me to redo the entire dilution until I obtained a consistent plaque morphology. This incident has had a traumatic effect on my psyche. Ever since then I would streak all of my plates mindlessly round after round, paranoid that another mysterious morphology would show up. Thankfully none ever did.

The second of the heart droppers occurred when my NanoDrop analysis showed an absurdly low number of DNA found in my purified sample. Challenged by adversity, I performed DNA purification two additional times, but the outcomes stayed disappointing. Although the results were less than satisfactory, I’ve learned a valuable lesson of coping with failure, something I’ve never been good at.

Phage hunting lab has been a thrilling ride to say the least. But with the accompaniment and support from my fellow phage hunters and instructors, it was indeed a fulfilling experience. I look forward to embarking on another ride next semester!

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My Pride and Joy

By Celina Cisneros

Back in pre-school, after a long day of finger-painting and reciting the ABC’s, I would eagerly run home to present to my mother the lovely piece of art I had ‘skillfully’ painted for her. Of course, as we all know, a child’s art is far from Van Gogh or da Vinci. It usually consists of a few scribbles and undecipherable stick figures. Nonetheless, my parents would always take it and proudly display it on the refrigerator for all to see. Over the course of the semester, through all the ups and downs I have experienced with my phage, I too have become a proud parent.

Jumping right into lab work on the first day of class was overwhelming to say the least. It was all just a whirlwind of soil, pipettes, and phage buffer. Although direct plating proved unsuccessful, after enrichment plating, I was able to see my phage for the first time. However, the journey from the enrichment sample to DNA prep was not easy for me, and many others. I battled fierce contamination, fluctuating morphologies, and inadequate DNA concentration. Streaking my plaques to conclude that I had a pure morphology seemed to go on without end. Overall, I streaked eight times (yes, eight!) before I was confident that my morphology was indeed pure. But perhaps in part due to these struggles, I was even more proud when I was able to see my phage illuminated on the screen after Professor McCaffery placed it in the electron microscope. Honestly, it looked the same as all of my other classmates’ phages, but I was immeasurably proud nonetheless. And like any proud parent, I wanted to tell as many people as possible about my pride and joy.

Calling home at the end of the week, my parents always ask, as they have since pre-school, “what did you learn today?” I usually launch into my recent discoveries in phage lab, sharing accomplishments after a good week or venting to them after a bad one. Although my parents usually have very little idea of what I am talking about, they listen and feign interest as I ramble on about streaking, dilutions, and top agar. On the other hand, as I shared my work with my older brother, he appeared openly disinterested, commenting on my EM picture, “What is it? It looks like a lollipop”. Studying theatrical set and film design, my brother is not exactly the ‘science-y’ type, but still, I took offense to his blatant disinterest. I could not comprehend how someone could find the project that I devoted an entire semester to, uninteresting. It was at this point that I realized how attached I had gotten to my phage and phage hunting in general.

Phage lab was the perfect beginning to my scientific adventure at Johns Hopkins. It reminds me why I love science, biology specifically. Decked out in a white lab coat and shiny safety glasses, I transitioned from mere high school science student to dedicated college scientist. Although, I still have much to learn in the lab, I can now say that I am quite handy with the pipette and am not too shabby at streaking. There is something wonderful about working in a lab, and finally seeing your dedication and work come to fruition.

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Struggles of Phage Hunting

By Eric Kang

Throughout the semester I have experienced the ups and downs of phage hunting to the greatest extent. In just the past few weeks I have been frustrated beyond compare because of endless contamination that comes out of nowhere, bad top agar, and plainly not getting the results I need. However, these negative experiences were very constructive. For the next four years I will be spending hours upon hours in the lab doing research and similarly to my experience in phage hunting, everything will not always go according to plan. Facing all the obstacles that I did throughout this semester gave me increased patience and attention to detail that will surely help me in the coming years. Also, when I am working with much more dangerous and expensive materials/equipment I will appreciate all the pain that I went through in this class with the contamination, aseptic procedure and whatnot. Although there was frustration during the course there was also great joy. For example, seeing the EM images of my phage was incredible. Not only is it mind-blowing to see such a small organism, but also this was my phage, the one I isolated all on my own. I like to compare the experience of a father seeing his unborn child’s ultrasound. However, seeing my phage was not nearly as life changing. Other joys come from succeeding after so many attempts. Being able to finally harvest an HTL after so many failed attempts and so much contamination I was jumping for joy. Lastly, being in this lab setting allowed me to collaborate and interact with my fellow classmates in a way that none of my other classes allow. Looking back the only thing I regret is not being able to get enough DNA to be in the phage Olympics, especially since I know my phage would have kicked all the other phage’s butts (tails). I look forward to another semester of phage hunting.

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