The Indiana University Graduate and Professional Student Organization (GPSO) and University Graduate School (UGS) congratulate our November student of the month, Erkin Kuru. Erkin is part of the Biochemistry Interdisciplinary Graduate Program. His research interests focus on analyzing bacterial cell walls in order to design much needed antibiotics. Erkin was born and raised in Istanbul, Turkey. He recalls “I was constantly at the heart of one of the most sophisticated cities in the world, but I also realized early on, that I needed to become an experimental biologist, who would combine the analytical thinking of an engineer with biological sciences. Thus, I went on studying the biological sciences and bioengineering program at the Sabanci University. During my time in college, it became clear that I would not be able to fully contemplate biological systems without a fair intuition about the chemistry of their macromolecular components.” Erkin’s academic interests always had a biological component to them, but he found biological systems too complex and unpredictable. Therefore, he has sought ways to simplify biological systems in order to increase our understanding and our control on them. “This 'obsession' about increasing control was probably founded very early on, when me and my colleagues reinvented and discussed overly simplified versions of chaos theory and mechanistic determinism on a philosophical level,” he explains. “Much more recently, I have discovered that this approach to biology is shared by many great minds, whose vision can now be classified within the scope of a fairly popular field: synthetic biology. I think my whole academic interest can perfectly be summed up by one of the last entries that the great physicist Richard Feynman had on his black board: ‘What I cannot create, I do not understand.’”
When asked about his accomplishments of which he is most proud, Erkin offered this fascinating mini-lesson in his field: “When came to IU, I joined to Prof. Michael VanNieuwenhze's organic chemistry group, mostly because Mike posed a great biological problem for me to solve: Developing universal chemical tags to label the cell walls of bacteria, namely their peptidoglycan. Peptidoglycan is an essential megamolecule that is also specific to bacteria; therefore most of the antibiotics we currently rely on target the peptidolgycan assembly. However, the resistance of bacteria to these antibiotics is on the rise and we need to increase our understanding of peptidoglycan biosynthesis in order to be a few steps ahead of these dangerous multi-drug resistant bacteria. Unfortunately, until now we had only a limited set of tools to probe peptidoglycan in vivo. Basically, I have developed the first non-toxic and universal methods to probe the peptidoglycan synthesis real-time and in live bacteria. In the process of design, I have looked at molecular signatures of peptidoglycans,that are common to all bacterial species and noticed from the literature that some of these molecules can readily be exchanged by seemingly bizarre but natural derivatives in diverse bacteria. Recognizing this inherent tolerance, I have designed a variety of unnatural and modular derivatives, which allowed us to probe cell walls of virtually all bacteria without perturbing their growth. In other words, we have discovered the Achilles' heel of the bacteria! Therefore, this concept definitely carries the potential to facilitate countless experiments involving basic peptidoglycan research. On the other hand, since peptidoglycan biosynthesis is an essential process and is tightly related to the bacterial growth, we are currently designing new probes that may directly have diagnostic and/or antimicrobial applications.”
Erkin identifies art as a key component of his life. “I cannot read, write or do lab work if I don’t listen to good music, preferably jazz or classical music,” he reflects. But his chief artistic passion is photographic, a craft he learned while assisting Nazif Topcuoglu, a renowned Turkish art photographer, in Istanbul. Erkin finds any excuse to take pictures, and recently used his talents to photograph his friends in their Halloween costume in his studio.
Taking a moment to reflect upon his graduate school experience thus far, Erkin explains “Graduate school is an amazing place to learn how to cope with failure! Graduate school, similar to any other ambitious endeavors in life, is full of failures. And there is no doubt that this is very depressing. Thus, although considering to give up is sometimes inevitable, I believe my example tells that persistence and stubbornness about your project can pay off. The trick is in taking the right attitude in order to keep yourself constantly motivated.” He also pointed out that “thinking widely and interdisciplinary was definitely a must for [his] case.”On that inspirational note, we ask the final, most important question that faces all graduate students: cake or pie? Erkin responds: “Unless it is cheesecake, I would definitely choose pie! I usually hate cake, because I am not a big fan of frosting. There is a lot of sugar and foamy cream to get though until reaching to the core of a cake. Obviously, cheesecake is an exception and therefore I love it! Pie is another story. I don’t think I have ever eaten a real pie until I got to States. Surprisingly, the pie concept as a desert does not exist in the Turkish cuisine. I love the substance that its crust gives to a pie. I also like my fruits in a desert!”