Author Archives: Ben Johns

Way back when this program started, I wrote on my expectations for this summer. TL;DR I was excited about the chance to really tryout research for the first time in my life. This once far off and mysterious world was about to become my present reality. As the program wraps up, I am again asked to reflect, now on how my expectations compare to reality. My answer: I couldn’t have imagined how truly wonderful a world hid behind the doors of research!

As I look back on these past eight weeks, I am really stunned at everything I have learned and done. While I was certainly excited about mechanobiology before this summer, getting the chance to actually dive into this field has stoked a passion in me. While I knew a little bit about scientific techniques, getting to go hands-on and do my own research has greatly expanded my toolset to investigate and explore the biological realm. While I had learned a little bit about what a career in science was like, getting to see the lives and apprentice under passionate researchers who actually live in the magnificent world of research has deepened my understanding of what it means to be those who dive into the unknown and expand mankind’s understanding of the biological world.

All in all, I feel like I have finally entered this “aquarium” of research and my wonder has only grown since I stepped into its waters. And while I am still eons away from being a full researcher and there is still a lot for me to learn, I am fired up about being a researcher and am ready to bulldoze through the trials of this path to achieve this dream of mine. And so, to Curtis for his truly incredible mentorship, to Professor Hoffman for his guidance and encouragement, to Dr. Grunwald and Dr. Harrell for offering me this opportunity and strengthening me in walking this path, and to everyone who has helped me along the way, all I can say is thank you.

I knew going into the chalk talks that Misa Foster’s would be one to look forward to. From our previous conversations, I knew she was studying butterfly wing development. But even with my high expectations, she still managed to wow and amaze me, not only at her skill in speaking, but at the objective coolness of her research. Though it will be nowhere near as fascinating as her talk, I would like to relate to you all why I was so astounded and fascinated.

Misa is working in the Nijhout Lab studying the developmental biology of caterpillars, specifically their wing development. Biology 101 says creatures grow by cell division. Yet, while this is true, it doesn’t capture the whole picture. If cells were just to divide randomly in every direction, then every living thing would be a circle or a sphere. And yet, as evidenced in the magnificent beauty and architectural design of the butterfly wing, we know this is not the case. So, how do cells know when and where to divide? It is this fundamental question of developmental biology that Misa is trying to help answer.

To do so, she is extracting the imaginal disks (the precursor of the fully developed butterfly wing) from knocked out caterpillars. After staining these disks, she has to manually note and mark every mitosis event occurring in the cells. Then, with a little bit of programming, she can actually analyze where major trends of mitosis are happening in the wing. This addresses the “where” of cell division. By looking at disks in various stages of development, she can study the “when” by seeing how those spatial patterns of division change over developmental time. In addition, she can stain the wings with a different chemical to highlight DNA synthesis and see how this relates to mitosis patterns. Then, with a different program, she can map the patterns of DNA synthesis in the disks and see how they relate to mitosis trends at various stages of wing development. In total, this allows Misa to elucidate how cells grow and spread during wing development, unlocking another piece of the puzzle of how single cells can grow and develop into beautifully designed pieces of living art!

All in all, this is pretty cool! Misa is doing great work in developing our understanding of developmental biology and she did an outstanding job on Thursday presenting this radical science to all of us. Keep chugging along, Misa!!!

Most of my days begin in White Lecture Hall on East Campus. Here, I meet with my cohort to work through journal articles, talk about different aspects of research life, or hear from distinguished Duke faculty about their research and careers. You can think of this as training. We may not be learning lab techniques or getting an in-depth understanding of a field in this time, but we are training to  think, read and perceive the world as researchers. It’s really an awesome opportunity and is a great way to start the day!

After that, I bike over to West Campus, where my lab is located. I work in the Hoffman Lab, located at the Center for Biomolecular and Tissue Engineering in the  Fitzpatrick Center. Once I’m in lab, I check in with my bench mentor, Curtis Shoyer, (who’s really quite a radical dude!) and get to work with my experiments. With the work I due in molecular cloning, it’s rare for me to be doing experiments all day. More often, I run an experiment and then wait for the reaction to finish or the bacteria to grow before I go on to the next path. Rinse, wash, repeat. I have a little wooden desk in the lab that I retreat to in-between experiments. I may read papers about mechanobiology that Curtis gave me, or I may start working on the computational step for a future experiment.

Throughout the day, I also get to talk to and shadow my mentor Curtis. Sometimes we’ll get lunch together and discuss a journal article to help me develop my understanding of the field. Other times, I get to shadow him on his other research as an introduction of what I’ll get to do later as I progress in the lab. And sometimes, we just talk about science or even the latest Pokémon game!

With that, my day concludes and I head back to East. Usually, I’ll read up on the protocols for the next day or keep gnawing at journal articles (although I do try to find time to get some rest in so I can come back the next day ready and raring to go)! So, this is a day in my shoes: it’s not much, but I love it!

How do professors become professors? Why not just ask one and find out? Dr. Brenton Hoffman is an associate professor of Biomedical Engineering at Duke University. One might think to be a professor, they must tailor their training from day one towards their specific field and career. But would it surprise you to know that his education is entirely in chemical engineering? Or that he never intended to go into academia until midway through grad school? Or that he never even intended to go into research when he entered graduate school? If you answered “Yes” to any of these questions, let me tell you about the unusual path of this outstanding scientist.

Dr. Hoffman began his career as a chemical engineering undergraduate student at Lehigh University in Bethlehem, PA. He actually chose this path to avoid being in lab; he was industry-bound from day one. His game plan was to go to grad school and work as a process engineer: as far from a lab as he could get. And he followed this plan… until a chance encounter with a biophysicist the first week of graduate school. While doing some exploratory rounds of different labs at the University of Pennsylvania, he ran into this professor and, simply put, “thought it was interesting.” Joining the lab, he dove headfirst into the world of polymer physics. Along the way, he was introduced to new paths, both in scientific discovery and in career avenues. It was here that he became interested in cell mechanics, the crux of his research today. He stated that for diseases with a chemical basis, because their molecular mechanisms have been studied so well, the scientific community has developed many powerful solutions and cures. But when it comes to diseases with a mechanical component like cancer, our ability to tackle these illnesses will always be lacking until we better understand the mechanisms that govern their mechanobiology. So, he decided to dedicate his professional life to understand these molecular mechanisms which allow cells to understand and interpret their physical and mechanical environment. It was also during this time that he was allured by the path of professorship. In his words, it is impossible to design a way do great science, because if research, we by definition don’t know what we are doing. Instead, the primary goal of being a professor is providing great training, with the byproduct being good and solid science. It was this hope to prepare and train the next generation of scientists to one day be his peers that drew him from industry into the halls of academia. After completing a post-doc in a cell biology lab to bolster his biological background, he accepted a faculty position at Duke University and the rest, they say, is history.

After reflecting upon his career, Dr. Hoffman offered some life advice for young students, both budding undergraduates and wizened post-docs: “Find what you’re interested in and do it.” He stressed that students often fall into a wrought in their studies and passions, getting “locked into a preconceived notion of what’s good and bad and not looking at what makes them happy.” He warned against the common notion that just because a student used to like a subject or because they started in a certain field that they are forced stick with that path, even when it no longer enthralls them. His solution? Just don’t do it. Keep revaluating what you find fascinating and chase after that. Just as his career path turned and twisted when new interests appeared before him, he encourages young scholars to remember their training isn’t a deterministic process and to adapt accordingly. With this, our interview concluded. Before I sign off, I want to break the fourth wall and offer my own advice. If you never get the chance to meet this outstanding professor, researcher, and teacher, I implore you to heed his advice and run through unexpected twists and turns to follow your fascination and study what enthralls you.

Have you ever tried to get a group to work together? If so, how many were you trying to reconcile? With that image in your head, imagine trying to do that with hundreds or even thousands of people. Now, make those people cells which can’t speak and who each want to move in a random direction independent of the group, and you’ll begin to see the wonder that is collective cell migration.

This summer, I am working in the Hoffman Lab studying collective cell migration (CCM). CCM is the process by which hundreds (if not thousands!) of cells move together as sheets, groups, or chains in the same direction with the same velocity. However, each cell is independent and can generate propulsive forces without needing outside help. So, how then can so many cells all stay connected and coordinate their movements? Our lab wants to discover the molecular mechanisms that enable this incredible phenomenon.

Specifically, we are interested in how mechanotransduction, or the conversion of mechanical forces into biochemicals signals, mediates this process.  Many key proteins have been identified that deform when the proper force is applied, changing their structure and function. These force-dependent conformations can regulate biochemical pathways that influence complex cellular processes, like the cell coordinating its movement with the larger group. These “mechanosensitive” proteins allow the cell to turn local forces into chemical signals that can impact and influence the entire cell!

But one of the big challenges facing this field is identifying which proteins are involved and how this process is regulated. Much of the actual molecular mechanics of it all is still poorly understood. Until we really have a tighter grasp on these mechanisms, we are hindered in our ability to manipulate CCM, both to understand it better and harness it for future applications in cancer biology, wound healing, and regenerative medicine.

This is where I come in! This summer I am using molecular cloning to engineer fusion proteins which will allow us to study the dynamics of some of these mechanosensitive proteins in live cells. You can think of fusion proteins as the Frankenstein’s monsters of the protein world. By cutting and pasting the DNA using traditional molecular cloning techniques, we can take the mechanosensitive proteins we are interested in and attach a fluorescent protein to the end of it. Because this protein is fluorescent (lights up when hit by the right wavelength of light), we can use this “biosensor” to see the protein in live cells! With this, we can better understand its localization and dynamics in the cell and its involvement in CCM. Additionally, by creating biosensors where the mechanosensitive protein has a single amino acid substitution whose effect on the protein is already known, we can further study the function of our protein in CCM by examining the mutant’s effects relative to the normal biosensor.

So, that’s my plan for the summer. Stay tuned to see if I can actually brighten up the world a bit!

Bonus: These fluorescent proteins lets us take really beautiful pictures of cells and cell sheets! Photo courtesy of Hoffman Lab.

Aquariums are kind of awesome. Before you ask, no, my research this summer has nothing to do with aquariums or any kind of aquatic life. And no, I did not choose a random title because I’ve been banging my head against the wall, trying to figure out how to write this post (although I’d be lying if it wasn’t a tempting option). The reason I bring up aquariums is because they act as a powerful medium through which I can explain to you the complicated jumble of expectations and hopes I have for this summer. Doubtful? Watch this.

As I tried to solidify this soup of thoughts, I noticed a common theme that stood out from the rest: the hope of what could be. I’ve always loved science for as long as I can remember: I devoured any book or video I could get my hands on as a kid. As I think upon it, my fascination with science was like that first step into an aquarium. I am talking about the wonder and amazement of seeing that weird but entrancing underwater world, from the might and power of its apex predators to the mystery and oddity of its glowing deep-water residents. My yearning to understand science was like that of the child pressing their face against the glass, trying their best to pop through and embrace the unknown. This summer, I hope, I’ll finally be on the other side of the glass. In the readings, experiments, and conversations that this fellowship can facilitate, I will no longer be staring through aquarium walls but swimming alongside these wonderful and mysterious beasts known as science and research. I would no longer be the child sitting by the wayside, astounded by but alien to these wonders, but instead become the diver, with a robust understanding of the creatures I swim by and, because of this, an even greater awe at these beasts of the watery deep.

So yeah, aquariums are kind of awesome. But science, research and the possibility of entering them that this fellowship offers me: They are more awesome.