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The Biological Physics, Structure and Design program was created to unite biophysical work on biomolecules and their complexes across campus. The program builds on two previous programs (Biomolecular Structure and Design and the Physiology and Biophysics Departmental program), and that is reflected in the composition of the current students. This new program will facilitate interactions among a broader community and provide incoming students with a broad set of labs to consider for their thesis work.

Aaron Williams

Aaron Williams

I joined the Physiology and Biophysics Department as a graduate student in September of 2009. I grew up in the San Francisco Bay Area (San Jose), and did my undergraduate work in Bioengineering at the University of California, San Diego. I graduated from UCSD in 2002, and worked in the biotech industry (at Vertex Pharmaceuticals) for the following seven years. While I was working in industry, I also completed an MS degree in Cell and Molecular Biology at San Diego State University. I spent most of my time in industry working in teams developing treatments for diseases associated with ion channel function (or dysfunction). Most of industry’s R&D focus is in Development, though, and I found that I wanted to spend more of my career on Research- therefore, my decision to pursue a PhD.

When I was evaluating graduate programs, I was impressed with the breadth and caliber of the research going on in the PBio department. During my first year, I rotated through the labs of Sharona Gordon, Greg Horwitz, and Nicholas Poolos; I joined the Poolos lab at the end of my first year. The research in the Poolos lab is focused on the specific mechanisms leading from traumatic brain injury to temporal lobe epilepsy. There is a latent (epileptogenic) phase between brain insult and the onset of spontaneous seizures; during this phase, the ion channels responsible for regulating neuronal excitability in the hippocampus (hyperpolarization-activated cyclic nucleotide-gated, or HCN, channels) are downregulated. The downregulation of HCN channels leads to neuronal hyperexcitability. However, the mechanisms leading to this downregulation are unknown- in the Poolos lab, we’re using electrophysiology, biochemistry, and animal behavior monitoring to investigate these mechanisms.

Another reason that I was drawn to the program was the quality of life in Seattle. I’m really into snowboarding, and there are a lot of great resorts around Seattle. In the summer, I get to spend a lot of time kayaking on Lake Union and Lake Washington, and there’s excellent camping and hiking nearby (Olympic National Park, San Juan Islands, Lake Chelan…). The snowboarding’s great around here, too. Seattle’s proximity to Vancouver and Portland makes for the nice occasional diversion. Did I mention the snowboarding?

 

Edward ChengEdward Cheng

The ancients once believed that the heart was the domicile of the soul, that the inexorable beats propelled the vital humours through our sinews, endowing us with humanity. While physiologists going back to Vesalius have completely disproved this romantic Aristotelian notion, those inexorable beats of life, and the catastrophes that ensue when they are no longer, held deep fascination for an aspiring physician scientist as I sat through two years of interminably dry medical school lectures before pursuing my thesis. While it is easy to dismiss the heart as a simple mechanical pump governed by the primordial autonomic drives, as it was sometimes taught in my undergraduate bioengineering courses, its complexity and elegance can only be revealed using the approaches of classic physiology-quantitative, hypothesis driven experiments that seek to understand the intricate clockwork of the heart in situ. I joined the Santana lab in the Physiology and Biophysics Department because I get to apply the latest techniques in electrophysiology and imaging to answer some of these classic problems in physiology; for example, how does the excitation-contraction machinery maintains the fidelity that exceeds those of the finest Swiss timepiece, and how this finely tuned mechanism fails in pathophysiology.

The pursuit of science is a road filled with moments of triumph and deep despair; however, the occasional moments of despair are somewhat ameliorated by the beauty of Seattle and its numerous diversions. When I was deciding between different institutions to pursue my MD-PhD degree, I chose Seattle partly because it is one of the few cities where a graduate student does not have to be cloistered in a dank closet of an apartment like a medieval monk, nor does he or she have to be a hermit, away from the allures of civilization. The other, less trivial factor, was that the University of Washington and Seattle offer an intellectually stimulating environment where one, fueled by El Diablo Espresso and Manny’s Pale Ale, can truly mature intellectually.

 

Ray Y.-R. WangRay Y.-R. Wang

I grew up in Taipei City, Taiwan, where the weather is also known to be gloomy and rainy during wintertime. For that, we even have a ballad entitled "Come to Taipei in winter to visit the beauty of drizzle." In this respect, Seattle always makes me feel at home.

I went to National Taiwan University with a major in Biochemistry. While in college, I became fascinated by the versatility of proteins and all those splendid illustrations of proteins structures. I then joined a structural biology lab under the advisements of Drs. Andrew H.-J. Wang and Kai-Fa Huang in Academia Sinica, Taiwan. The lab primarily utilized X-ray crystallography combined with other biophysical and biochemical techniques to study proteins of interest, basically enzymes. During my later half of college life, I was involved in studies of human glutaminyl cyclase (HQC), which is related to the progression of Alzheimer's disease. Meanwhile, I studied a HQC isozyme from bacteria, which surprisingly was able to carry out comparable catalytic activity to HQC even in extreme environments. After a year of enlisting in the military service, I went to work in another X-ray crystallography lab for Dr. Che Ma as a technician, working on membrane protein structural studies. In the mean time, I started applying to graduate schools in the States. These research experiences not only confirmed my passion for structural biology, but also pushed me thousands of miles away from home to pursue expertise and do cutting-edge research in this field.

Among all the Ph.D. programs I applied to, the BMSD program in UW had always been my first choice, mostly because it was totally structurally orientated and composed of prominent faculty members covering all sorts of approaches in structural biology, where I would be able to weigh the tastes from NMR, X-Ray Crystallography, CryoEM, Molecular Dynamics Simulations, and Rosetta Modeling. Moreover, I could even have a combo from any of those different disciplines where the research met. In BMSD, it is common to find faculty members cooperating in exploring a topic, exploiting different approaches to solve a problem.

After doing my first two rotations in purely computational projects in the labs of Phil Bradley and David Baker, I went to work with Bill Schief to do some wet lab work. Finally, I found that my passion lies in determining protein structure in a more elegant way -- computer-aided prediction. It was probably because I had suffered enough from laborious work of membrane protein crystallography and was eager to find a better way to circumvent this long-standing problem. Participation in the CASP9 competition right after joining the Baker lab affirmed my goal of dealing with problems of protein structure prediction.

I had never been a great lover of outdoor activities before I moved to Seattle. This summer, I went hiking several times. People would easily become addicted to the beauty of magnificent nature in Washington State once the try it. I cannot wait to plan my first ski trip this winter.

 

Chris KingChris King

My torrid love affair with biological macromolecules began at the University of Texas while pursuing a degree in Biomedical Engineering, where I began my research in molecular modeling and simulation, which I quickly became enamored with. Through my undergraduate classwork, I also became fascinated with the prospects of nanotechnology, and found myself loving the creative processes of engineering design. By the time I graduated, I had decided that a career in computational protein design could probably keep me pretty thoroughly entertained and satisfied for the foreseeable future. Given that I felt this whole field was so awesome, I decided that I should probably just go ahead and get a PhD at the number one place for protein design in the world, which, according to my research, is the BMSD program at UW.

I applied to the program, got an interview, and was very impressed with the diversity of expertise that BMSD attracts. Problems in macromolecular design require a many-faceted, concerted approach that covers a broad range of disciplines, and BMSD has some of the top people in the world working on every facet. I also like how the department, rather than being centered around a single discipline or field, is centered around a certain problem, and then uses every approach available to attack it.

Besides the school, I instantly fell in love with Seattle. The weather is actually pretty nice, the city is beautiful and full of parks, sustainable lifestyle is the rule rather than the exception, local politics are intelligent and progressive, and the music and art scene is huge.

I came to UW specifically to work with David Baker but did rotation projects with Valerie Daggett, Phil Bradley, and David Baker. I really loved all three labs, but had to narrow it down, and eventually chose David Baker and Phil Bradley as co-advisors, as their research both overlapped most with my long-term goals. My current research concerns the computational prediction and design of protein-peptide binding specificity, with the more general goal of developing new algorithms for de novo design of protein interactions.

When not working, I spend my time making music on my laptop, riding my bike, and enjoying the prolific electronic music scene here.

 

Andy McMillanAndy McMillan

I joined the BMSD program in 2006 after graduating from the University of Colorado with a double major in biochemistry and molecular, cellular and developmental biology. I am interested in how biology works at fundamental levels, and while I felt I had a good grounding in biology I wanted a better grounding in chemistry and physics when I went to grad school. BMSD seemed to be good fit; while being focused on things I was interested in, it also gave enough flexibility since I still wasn't sure what exactly I wanted to work on.

After my rotations during my first year I went back to work with Bill Parson studying how a polymorphism in the Catechol O-Methyltransferase gene affects the structure and physical properties of this protein. Bill has been very good to work with, very knowledgeable and willing to help me, but also giving me the freedom to figure things out on my own. I've recently expanded my project to include more theoretical studies of fluorescence, which has meant collaborating with members of Niels Andersen's group where I did my third rotation and doing computational work which I was first exposed to in my rotation with Valerie Daggett.

As much as I enjoy the science, I've found Seattle to be a great place to live when I get away from the lab too. Being in a major city provides plenty of opportunities for things to do (in my case I can frequently be found checking out some random band I've never heard of before) while it's still relatively easy to escape from the city and enjoy the outdoors as well.

 

Kate StollKate Stoll

I grew up in small towns in Wyoming and Washington, and went to Reed College in Portland, Oregon. I have always had an interest in biology, but at Reed I gained an appreciation of chemistry and found the chemical underpinnings of biology to be the most intriguing. During my Reed education and a summer research experience at UW in Rachel Klevit's lab, I developed an interest in structural biology. During my last year at Reed, under the advisement of Arthur Glasfeld, I completed an undergraduate thesis characterizing the DNA and metal ion specificity of the Streptococcal cell adhesion protein Regulator, ScaR, and got my feet wet in the field of crystallography. After graduation from Reed in 2004, I moved to England to work for Jane Clarke at the University of Cambridge, where I was as a lab technician studying the small aβ protein domain, LysM.

I joined the BMSD program in 2005. BMSD was a good fit for me because of its emphasis on structural research, its flexible curriculum, the collaborative nature of both faculty and students, and the variety of labs in which I could train. BMSD encompasses research groups from six different departments and many specialties, including NMR, crystallography, and even EM so it was easy to find a lab that matched my research interests. After rotating in the Klevit, Varani, and Xu labs, I chose the Klevit lab in part because of its balance of structural and biochemical techniques. I typically use NMR, yeast genetics, and enzymatic assays among other techniques to explore BRCA1 mediated ubiquitination. My current projects include solving the structure of the breast cancer protein (BRCA1) in complex with the E2 protein Ubc13, and investigating ubiquitination pathways in yeast. While at UW I've had the chance to pursue extra-curricular interests through my participation in a student initiative called the Forum On Science Ethics & Policy (FOSEP). FOSEP is an organization of graduate students and post docs whose mission is to increase dialogue between scientists, policy makers, and the general public about the role of science in society. I am currently a director of FOSEP and recently co-organized a public forum on US energy policy (www.fosep.org/pastevents.php).

Outside of the lab, I find plenty of fun activities in Seattle. It is the ideal city for me because of its bikeability, its music, food, and arts scene, but mostly because of its access to so many surrounding mountains and wilderness areas. I enjoy backpacking in the summer and snowshoeing in the winter in places like the Olympic Peninsula, Mt. Rainier, the Northern Cascades, and Snoqualmie Pass.

 

Ryan EatonRyan Eaton

Reading the profiles of my senior classmates, I prefer those that convey personality. I, myself, am of the "just-the-facts-ma'am" mentality so I describe myself here accordingly. I grew up in a small town in northern California and studied physics at UC Davis. Lack of opportunity in the high-energy physics field and my increasing fascination with information processing in neurobiology motivated my shift to neuroscience, having convinced myself (naïvely) my background in physics would be an asset. For the next three years I toiled as a research assistant at Oregon Health and Science University using transcranial magnetic stimulation to evaluate disease progression in patients with movement disorders (Parkinson's disease, essential tremor and ALS). Through research assistantship I gained skills and patience to carry out experiments, but I longed for more theory and wanted to design experiments to address my own inquiries. Graduate school was in the cards for me.

I researched many neuroscience graduate programs and the Department of Physiology & Biophysics (PBio) at the University of Washington stood out among the lot. The diversity and caliber of research described in the faculty profiles impressed me most of all. Within a few minutes of digging I had already found several labs researching topics overlapping my somewhat scattered interest in neuroscience. My interview experience only strengthened my impression: faculty and students were enthusiastic and welcoming, I met four of the seven of my incoming class that weekend and many of us became good friends. Coursework proved both challenging and relevant. I rotated through labs of Fetz (explored attractor dynamics in neural network models of short term memory), Binder (compared white noise-elicited firing patterns of a cortical neuron and a simplified model) and Jagadeesh (tested the role of perceptual masks in object recognition). In their second year, most PBio students serve as TAs in a two-quarter general physiology course for dental and nursing students. While I dreaded the prospect of leading discussion sessions, I learned a great deal of physiology and became more confident through the experience.

At the end of my first year, Eb Fetz graciously took me on as his student. My project investigates recruitment of muscle-related, and pre-motoneuronal, cortical neurons during muscle contraction. In conjunction, we stimulate the medial forebrain bundle--a pathway intimately involved in reward-related behaviors---to reinforce cortical and muscle-activity operants in the freely-behaving primate. These days I work alongside four post- and two other pre-doctoral fellows; my research has benefited from the talents and insights of each. Opportunities to meet visiting scientists, participate in department committees and present findings at scientific conferences are but a few of the benefits enjoyed by PBio graduate students.

Contrary to whatever impression the above may have formed, there is more to life than one's career. To appease my creative urges (and to blow off steam) I play drums in a rock band (my second since moving to Seattle). Seattle is a great place to go running in the summer months and it is never hard to find fun things to do.

 

   

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