The End.

By Meg Chen

“Please collect a few spoonfuls of dirt in a ziplock bag and bring the sample with you to the first day of class.

It’s been a long, yet quick journey.  The path from a random soil sample to a beautiful, unique phage feels so unreal.  But now that I come to think of it, it must have taken much longer than three months for the first researcher(s) to experiment with different procedures for isolating plaques and develop the most effective one.  For example, who came up with the idea of streaking a plaque?

One of the most important things I learned along the way was lab technique.  Early on, I would stay past 5 every day, checking my work at each step.  Yet I would still end up with contamination.  I figured that since there was no way to keep every single phage out of the microcentrifuge tubes, I resorted to methods to eliminate outside phages, such as cleaning my tools with CiDecon before putting my phage solution in and working closer to the flame.  One day, I actually worked dangerously close to the flame and burned a hole through my gloves (though the fire went out quickly and did not get to my skin).  Even though I successfully eliminated outside phages from my tubes and plates, I realized that I would have to find ways to minimize contamination instead.  For example, instead of reaching into the container to pick out microcentrifuge tubes, I learned from Dr. Fisher that I was supposed to dump them out and close them quickly.

I slowly grew accustomed to the method of sterile technique through trial and error, and by the third week, I was out of the lab by 4 most of the time.  I still remained skeptical that my plaques all came from phages in my enrichment plating and not from the surrounding air, and I saved 2 plates for each round of streaking and dilution series so that I could go back and re-streak if I run into contamination another time.  After putting top agar on my negative control plate, I would shut the lid quickly, sometimes shattering the outside of the petri dishes.  I always took one more tube to pick up the top agar with than I actually needed in case I accidentally touched the tip of one tube to a foreign surface.  When our whole class experienced contamination due to the old smeg, my plates with top agar and phage buffer alone did not have any contamination even though I had been slightly less careful.  This was when I realized that I had been too paranoid all along, and that the chance of my phage coming from the air is lower than what I originally expected.

Posted in From the Phage Hunters

Webbed Plate of Lies

By Megha Telur

I can honestly say that Phage Hunting has been my most enjoyable class this semester. Everything about the class just clicked; research, lab work, and biology. I aspire to one day be able to do genetics research at Hopkins, so being in a UTL biology lab was an absolutely amazing feeling. It seems strange to many but I love being in the lab (I also love long airplane flights!) it’s where I feel comfortable and strangely enough, at peace. The wonderful huge open windows added to the charm of my second home, the UTL.

As much as being in a Johns Hopkins lab thrilled me the first few weeks of phage hunting were overwhelming. I found that I was extremely dependent on my lab manual and the TAs to get through basic procedures. With time the process became more and more intuitive and I was able to make judgement calls on my own. I knew when I had isolated my phage,  I picked plaques to streak, and I knew when additional plating or diluting needed to be done. Nonetheless, no matter how much progress I had made, nothing could prepare for the ultimate test of patience: the webbed plate of lies.

I calculated and diluted several times to no avail. My web plates never came out right!!! Many times there was hardly any lysis much less complete lysis of the bacterial lawn on the agar plate. After weeks of no success (I plated web plates at least 4 times) and discussions with Dr. Fisher and Dr. Schildbach , I finally flooded my partially webbed plates for an HTL. It was determined the initial concentration of my phage was so high (I couldn’t successfully calculate an initial titer) that the risk in flooding partially webbed plates was minimal.

Thankfully, the risk paid off in the end. Not only was I able to quantify enough DNA, but I was able to complete the procedures on time. This experience was a quick but effective lesson in independence and strategic decision making. I realized that the manual doesn’t have all the answers and deviating from the standard procedure is sometimes necessary. If there is substantial evidence and solid reasoning creating your own path may actually lead to the best results-especially if it means avoiding a dreadful webbed plate of lies.

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A Lesson in Patience

By Isabella Zellerbach

When I went to my first Phage Hunting class, I was over the moon. We were following a lab manual that made sense, doing science-y things, and I got to use all sorts of equipment that made me feel like a real live researcher. And I was good at it! I got my enrichment culture to work, had two distinct phages that were really different, and even managed to isolate my phages in just a few streaks. And then disaster struck.

A new phage decided to pop up on my plates and I had to re-streak. And re-streak. And re-streak. And I was streaking until the end of September. I finally got my phage isolated and moved on to my MTL and things seemed like they were taking a turn for the better. I calculated the titer, got all my ducks in a row, and did the calculations for the six web plates to create the HTL. Then that mysterious, unknown contamination hit the lab.

Even though I had six beautiful webbed plates underneath all that contamination, there was no way I was going to be able to flood the plates and create an HTL. So I re-did the six plates and waited to see if the contamination was gone. Luckily, it was! And so my HTL was born.

After that, I had a fairly smooth ride. My EM came out nicely, my DNA prep was a solid number, and my QC gel was bright and vibrant! It just took me until the very last day of class to get there, but I made it in the end. The entire process definitely made me re-evaluate my patience level and I’d like to think I came out of the experience way more patient than I went going in.

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To Phage or Not to Phage?

By Stephanie England

Summer before coming to Hopkins, so many things were on my mind. From trying to get to know my roommates via Facebook to making sure all my paperwork was in, the question of classes came to mind. Being one of the hundreds of pre-med kids, I wanted to try to step into the waters of research before everyone else rushed in. Phage Hunting came up on the list of recommended classes and it piqued my interest. However, so many other options were present and then I got to the freshman seminars and then timing conflicts. Overall, phage hunting was of least importance to me and it was going off the list if times conflicted or if the dreaded message came that I got wait-listed. Morning of registration came around, and luckily for me, my ideal schedule is what I got. Yet, I couldn’t help but wonder if taking phage hunting was the right decision or if I could have better used my two credits.

Now that the semester is coming to a close, I can definitely say that taking phage hunting was one of the best decisions I ever made. This lab is my favorite class and I’ve gotten to meet some of my closest friends here. The roller coaster of emotions that this class kept me on was something I never expected. Initially thinking that my enrichment failed, but then seeing plaques come from my one dot (that I had thought to be an air bubble) on my 100; this was a foreshadowing of the doubts and fears that would be dispelled from the reality of getting actual results and success.

It’s been a bumpy road, but the skills learned in this class are more than just commendable. Proper aseptic technique was definitely achieved, I mean, when there was class contamination from the old smeg and we all tested our PB and TA and not one of us contaminated our plates? Talk about impressive! Feeling the camaraderie after realizing that I wasn’t the only person who didn’t make it in time for the phage Olympics was just one of many moments that proved phage hunting a great decision. Every time I was able to streak without breaking the gel in the bottom, was such an accomplishment. I could be failing my math class in the morning, but then go to phage lab in the afternoon and just seeing plaques without contamination, would turn my day around for the better.

Later on, going in for electron microscopy was motivating, making me think that I was in the final stretch. Then a feeling of dread came when Patrick made a mistake with my sample and it had to be redone. Foreshadowing much? I hoped not. It was redone and a flood of relief came. Seeing my phage on the EM pictures, and knowing that all the streaking, all the serial dilutions, and all the hours spent were not in vain, was a moment where I could have shed a tear of happiness. My little buddy gave me such hard times in the past, but I’d do it all over again now that we’re at the end and see the results.

Now that it comes time to choose classes for next semester, phage hunting was the first class I signed up for and had to work other classes around this one. The thought of sequencing and working with DNA and genes is exciting to a nerd like me, and then being able to do our own experiments with the phages? It’s going to be great. My phage may not have made it to the phage Olympics, and it may be an equally (if not more) bumpy road next semester, but there is no doubt in my mind as to what I want to do. If this class is half as good as it was this semester, then I’d be satisfied. To Phage or Not to Phage? There is no question anymore.

Posted in From the Phage Hunters

The Call of the Phage

By Gregory Konar

For those of you who picked up on the title playing on “The Call of the Wild” by Jack London, kudos to you, you must be either a writing sems major or a very well educated other person!

But I digress, already, this post is not about Jack London or literature at all, this is about the wonderful and shockingly populous phage!

This here is a picture of a very sinister looking phage, perhaps he is participating in No Shave November? There are many other phages just like him, thousands of millions of billions of phages exist on the earth at any given moment. In fact, as you read this blog post, you might have typed on a cluster of phages hidden in bacteria on your keyboard! Eww, go clean your keyboard please! All good now? Alrighty, let’s continue on this phage journey!

Phage Hunting is an absolutely amazing class that for me runs Mondays and Wednesdays from 2:30 to 5:00. Yeah, big time commitment for a 2 credit class, but trust me when I say that it is worth it. It is single handedly the greatest class that I have taken this semester! (and no, I am not saying this just to appease the almighty powers that I call Dr. Fisher and Dr. Schildbach)

So, how do we answer the call of the phage? Well first, we had to find a phage!!!

(wise words of advice!)

Soil was our medium of choice for finding the phage, so off I galumphed searching for the perfect patch of dirt, tedious tedious work! It took me a whopping 5 minutes to locate and dig up soil necessary for the lab, and it ended up being pretty darn nice soil!

I tried 2 different methods of coaxing phages from the soil sample: Direct Plating and Enrichment. Direct Plating was like making a pizza, the agar plate was the dough, and then I added the sauce in the form of Mycobacterium smegmatis (the friendly cousin to tuberculosis) and the cheese was the dirt. Enrichment was like steroids, we juiced up the concoction with lots of food and goodies and let it fly. Low and behold, only the enrichment worked, and the pizza had nothing to show for itself.

Once the enrichment provided some putative phage plaques (no, not the bad plaque that forms on your teeth), I went forward and plated and replated and replated the phage 4 times until the plaques were all nice and stable in morphology. Then the titering began…

And as chemistry cat so eloquently puts it, I needed the concentration of phages present on the plates. So the plates were flooded and liquid stocks of the phages were created. This was done once on a small scale to get the MTL and then again on a much larger scale to get the HTL. From the HTL the real fun began!

The HTL unlocked a whole new world of possibilities! From there I did a whole host of things ranging from DNA Preps to Restriction Enzyme digests to Electron Microscopy! The possibilities were endless, and everything was amazing and fun and eye opening! My phage baby  had a 48nm head and a 160nm tail, which I thought was pretty darn awesome!

Konar_EM

I haven’t ever used an electron microscope before, so this was a new experience for me!

As of the time in which I write this blog, I am busily preparing for the Phage Olympics on top of an RNA presentation, Chem Test, and panic over class registration. So, it will be a fun and great experience on Monday at the Olympics, hopefully my baby will be in tip top shape for that and will bring home the gold! Let’s see if it can answer the call of the phage!

Oh, did I mention that its name is Cell-Fie?

Until next time! Phage out!

Posted in From the Phage Hunters

The Race to Phage Olympics

By Stephanie Hernandez

Less than two weeks until we find out whose phage is the king of all phages. We must choose the very best to represent phage-hunters everywhere. I have moved away from streaking and dilution series to focus on DNA prep and Electron Microcopy. The DNA prep was a nice change from the usual streaking and dilutions, although it was even more stressful because there was more room for error. Decanting the supernatant liquid was probably the most stressful part of lab because you couldn’t disturb the pellet, which sounds easy. Mind you the pellet is very hard to distinguish against the liquid and the tube was tiny. However, the result from quantifying my DNA was encouraging. Using the EM machine was one of the highlights of my phage hunting experience. Even observing the preparation of the copper EM grid was fascinating. The images shown of my phages by the EM machine were so microscopic you could see individual phages. Viewing my phages was mind blowing. I could spend hours looking at bacteria under that microscope. Now all I have to do is convince my class how awesome my phages are.

Posted in From the Phage Hunters

Phage Hunting: An Experience

By Daniel Choi

I still remember that fateful day when I registered for Phage Hunting, not knowing at all what to expect from it. To be perfectly honest, I had initially only registered for the class because it counted two hours towards the research requirement for my intended major, but, in a short amount of time and with a little bit of patience, I grew to love it sincerely and appreciate it for what it was and all that it was willing to offer me.

After I had registered for the class, in a blink of an eye, I somehow ended up in a conference room filled with a bunch of people I didn’t know in a place miles away from what felt like my only home at the time, discussing the importance of manifesting a willingness to fail, which, at the time, seemed more like a bad omen than the invaluable life lesson that I eventually came to appreciate, a life lesson that, for a time, my experiences in Phage Hunting would not allow me to forget.

I will admit that there have been times in Phage Hunting when I would feel frustrated, to say the very least. There were times when it seemed as though everyone in the laboratory except me was moving perfectly along. There were times when I felt as though I was getting left behind. There were times when I felt that I had made no progress that day. There were times when I felt like a burden to my lab partner and the T.A.’s, times when I felt like they secretly detested me for my apparent inabilities. There were times when I felt as though I didn’t belong in Phage Hunting or even at Johns Hopkins. I remember, for a while, always being the very last one to leave the laboratory everyday, always preventing the professor and the T.A.’s from moving on with their lives, always being a burden.

Still, I held on and kept going not because I had any hope of making what I could call legitimate progress but because it was what was expected of me, unbeknownst to me that, one day, the former would come true.

Still, when all is said and done, I can honestly and easily say that there have been more times in Phage Hunting when I would feel inexplicable amounts of happiness than times when I would feel frustration. I still remember my excitement, my first day, when I got my very own lab coat and goggles. I felt like a real scientist, and that made me very happy.

Whenever I did make progress, I felt an inexplicably overwhelming amount of joy that would just seem to force a moment of giddiness and sometimes a much needed smile on my face. It was a joy that drove all the self-doubt away and made me feel so very proud of myself. At one point, I even learned to smile and laugh at the mistakes that I made, and they made me look forward to doing better all the next times. It seems as though, now, that all that bad was worth it just to make the good all that much better. Now, I truly feel like I belong, like a real Phage Hunter.

At first, those two words really didn’t seem as though they had any business being next to each other, but now, it seems that they have made all the difference for my first semester of college at Johns Hopkins University, and I wouldn’t have or want them any other way. For Phage Hunting, I will eternally be grateful, and I can’t help but feel giddy, whenever I think about taking Phage Hunting II in the spring semester.

I guess the point of Phage Hunting is to understand that it’s perfectly okay for something to rain on your parade because “when it rains, you put on a coat.”

Posted in From the Phage Hunters