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SPRING 2013

NEWS FROM THE DEPARTMENT OF BIOENGINEERING

From the Chair We are proud to announce that this year marks the 40th anniversary of the Department of Bioengineering at Penn. We take this opportunity to look back on our Department’s history and take note of our present research and accomplishments. As one of the country’s oldest departments in bioengineering, we thank the four pioneering faculty members who took a few bold steps into unmarked territory, paving the way for the nearly 20 faculty members in our Department today. In addition to our outstanding faculty, the students of bioengineering are incredibly talented in the field; additionally, they strive to create a wonderful sense of community in the department. We have some of the most active student groups on campus: the Graduate Association of Bioengineering (GABE) and the undergraduate Biomedical Engineering Society (BMES). As our alumni and friends, you reflect both the accomplishments of our past and the potential for our future. Stop by to visit whenever you are in the area, and send us news about your latest plans, as we are eager to share our collective achievements with the greater Penn community. David F. Meaney S. R. Pollack Professor and Chair

Bioengineering Students Win Senior Design Competition Pictured above is this year’s class of Bioengineering Senior Design students, who have worked throughout the academic year on self-designed projects in a wide range of topics. The students above were gathered for their final presentations this spring. At the end of April, the Penn Engineering Alumni Society sponsored the annual Senior Design Project Competition, where the top three Senior Design groups from each of the six Penn Engineering Departments competed for prizes. This year, one of the Bioengineering Senior Design groups won first prize. Seniors Nicki Blumenfeld, Anna Brzezinski, Brian Horwich, and Zach Shurden (all BSE’13) impressed the panel of judges with the vibrotactile feedback device they designed for use with elongated electrocautery tools typically used in laparoscopic surgeries. This technology provides an alternative type of feedback to the typical sensory feedback lost in laparoscopic surgeries; it has the potential to improve the 1 in 200 complication rate associated with these

“Senior Design was a true culmination of our experience in engineering, and it was really rewarding to be able to pull together the different pieces of our BE background.” — Nicki Blumenfeld, BSE’13

surgeries. The winning group, self-named HapTech, has even applied for a provisional patent for their design. Regarding the entire Senior Design process, Blumenfeld said, “Senior Design was a true culmination of our experience in engineering, and it was really rewarding to be able to pull together the different pieces of our BE background.” Horwich added, “One of the greatest things I learned through Senior Design is that you don’t realize how good it feels to design something and then have it actually work.” The group members all recalled the moment of elation after the planning and programming were complete, and the device actually functioned as intended. continued on page 3… 1

40 Years of Bioengineering at Penn The story of the Department of Bioengineering at Penn actually begins over half a century ago. Throughout the 1950s, Herman Schwann, Ph.D., a chair and professor in what would later be Penn’s Department of Bioengineering, urged for and then eventually received University approval to establish an independent Ph.D. program in biomedical electronic engineering. This was the first such Ph.D. program in the country, and made Penn the first to award a doctorate in bioengineering. Over a decade later, in 1973, the Biomedical Electronic Engineering Department, which had only included graduate studies, was renamed the Bioengineering Department, and a full undergraduate program was added to the existing graduate studies. Solomon Pollack, Ph.D., a former professor in the Department of Metallurgy and Materials Science, now called the Department of Materials Science and Engineering, had also been mentoring

graduate students in bioengineering for a number of years prior to the establishment of the formal Department. Pollack said his students felt drawn to the emerging field that focused on the interaction between materials and living systems, such as the human body. “The excitement, the importance, the newness…it resonated with them. They were adventurous,” he said. Other adventurous faculty members joined the new department at its start, including Mitchell Litt, Ph.D., from Chemical Engineering, and Abraham Noordergraaf, Ph.D., from Mechanical Engineering. These early faculty members took great risk leaving their home departments, mostly because promotion and tenure decisions were based on reputation in the field; bioengineering was a completely new field, where everyone was treading new ground, and scientists were just beginning to find collaborations and connections.

As a new Department, the first priority was developing the undergraduate program, one of the first in the nation. With such a unique field that merged so many topics, striking the balance between adequate coverage and a reasonable course load was a challenge. Drs. Litt and Pollack worked tirelessly to develop the undergraduate program: an academically demanding framework covering the basics of the engineering fields and their intersections with medicine, all with a rigorous basis in mathematics. The Department quickly flourished and grew from just a handful of undergraduates and Ph.D. students in 1975 to over 300 undergraduates, over 100 master’s students, and over 100 Ph.D. students this spring. The faculty’s interests range from optogenetics to regenerative medicine to biomimetics and more. With an average ranking of sixth in the nation over the last ten years by U.S. News & World Report, Penn’s Bioengineering Department has continued its history of growth and success.

RESEARCH ROUNDUP

New Method Measures Chromosome Structure and Gene Expression

 EEF2 intron  EEF2 mRNA  Chr. 19

iceFISH simultaneously measures chromosome structure and gene expression in a single cell. This image is of a primary human fibroblast cell with chr19 highlighted as cyan. A gene called EEF2 is shown to be actively producing RNA as the white spot within each cyan chromosome and messenger RNA for EEF in magenta are filling up the cell’s cytoplasm.

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Ph.D. student Marshall Levesque was recently published in Nature Methods. Co-authored with Arjun Raj, Ph.D., the paper is titled, “Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation.” Their research focuses on how the spatial and genomic organization of chromosomes can affect gene expression. They developed a method called intron chromosomal expression FISH (iceFISH) that assigns gene expression to individual chromosome copies within the nuclei of single cells. Using iceFISH, Levesque and Raj found that translocations, a hallmark of cancer, can cause chromosome-scale disturbances to gene expression. These measurements were not possible prior to iceFISH.

The authors write, “iceFISH provides a complement to chromosome conformation assays that look for interactions at the DNA (rather than transcriptional) level. We believe that iceFISH and similar tools will allow us to determine the prevalence of these chromosome-level regulatory phenomena and uncover their underlying mechanisms.” Levesque, a native of southern California, recently presented related research at the qPCR & Next Generation Sequencing Conference, held at Technische Universität München in Munich, Germany. Levesque says of his pursuits in the field of bioengineering: “I enjoy the cross-discipline nature of the field and building tools that enhance our understanding of biology.”

Dynamic Student Activities The following sections highlight the goals and accomplishments of the tremendously active student groups in the Department of Bioengineering.

The Graduate Association of Bioengineering

GABE officers gather in Quain Courtyard, between Skirkanich and Levine Halls.

The Graduate Association of Bioengineering (GABE) aims to promote academic and social interaction among graduate bioengineering students, and works hard to improve the graduate group community. GABE hosts numerous social, academic and outreach events each year, and has a pivotal role in the graduate recruiting efforts of the Department, showing those who are considering Penn the many reasons why it is a top choice.

This year, GABE held its inaugural GABE Seminar Series, with the support of the department. The purpose of the series was to address relevant topics and skills needed by graduate students and to increase student-faculty interaction. Two faculty members were invited to each talk, and a graduate student liaison facilitated discussion over lunch. Some of this year’s topics included How to Manage Your Advisor (Dr. Kelly Jordan-Sciutto & Dr. Beth Winkelstein), How and Why to Prepare an Elevator Speech (Dr. Kristy Arbogast & Dr. Doug Smith), and How to Sit Through a Seminar You Don’t Care About (Dr. Jerry Glickson & Dr. Louis Soslowsky). GABE President Sarah Ilkhani-Pour, a Ph.D. student in the lab of Louis Soslowsky, says, “The seminar series was a success and GABE plans to continue the series next year, making it an annual tradition.”

The Biomedical Engineering Society The Biomedical Engineering Society’s mission is to expose undergraduate students to bioengineering both inside and outside of academia, and also act as liaison between faculty and students. This spring, BMES was awarded the Engineering Student Activities Council’s Club of the Year Award for its exceptional Dr. Dave Meaney and the BMES Board smile for the camera just prior to the “Pie Your programming and outreach. A few recent Professor” event March 14 (Pi Day); the event events include “Dogs & Devices,” was co-sponsored by GABE as a fundraiser where engineering students came for their American Cancer Society Relay together to build a scent wheel for the for Life team. Penn Vet Working Dog Center; periodic “study breaks” and advising sessions with advising staff; the “Pie Your Professor” event (co-sponsored by GABE); and information sessions on summer internships, graduate school (co-organized with GABE) and study abroad. Liz Feeney, BSE’14, currently serves as BMES President, and says that the BMES officers find it rewarding to plan events “emphasizing a commitment to community service, professional and academic development, and creating lasting relationships with peers and professors.”

Bioengineering Students Win Senior Design Competition continued from page 1… Although the HapTech group experienced unparalleled success, other groups in this year’s class developed a number of fascinating projects. One project resulted in a wearable device to assess the potential for injury to the ACL (anterior cruciate ligament) in the knee. Another group developed a project on red blood cell delivery mechanisms of anti-inflammatory agents for the treatment of sepsis. Yet another group developed a pipette and liquid transfer system at significantly lower cost than existing systems on today’s market. Michael Rizk, Ph.D., Senior Lecturer in Bioengineering, says, “Something that’s really neat about Senior Design is that it really runs the breadth of bioengineering. From projects in a wet lab with cells, to electrical engineering devices, to mechanical projects, you get the whole scope of bioengineering. Any two projects may look very different.” The Senior Design coursework is a requirement for all undergraduates in the Bachelor of Science in Engineering curriculum. Contrary to what the name may imply, brainstorming for the course actually begins in the spring of the junior year, when students are encouraged to think about team members and project ideas. The following fall begins with several weeks of lectures on the design process, differentiating design from research. Throughout the two semesters of senior year, Michael Rizk, Ph.D., and Beth Winkelstein, Ph.D., Professor of Bioengineering, guide the students through brainstorming the idea, doing the background research, setting the specifications, and developing the product or system. Winkelstein says, “A constant theme in our promoting Senior Design is that it’s about the students – they do the conceptualizing, the work, and the finalizing.”

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PRESORTED FIRST CLASS MAIL U.S. POSTAGE

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Department of Bioengineering

PERMIT NO. 141 WILKES-BARRE, PA

University of Pennsylvania 210 South 33rd Street Philadelphia, PA 19104-6321

Save the Date To celebrate 40 years of Bioengineering at Penn, please mark your calendar:  Thursday, October 3, 2013 40th Anniversary Symposium Plans for the day include remarks from the Department Chair, sessions with key figures in the field, and more.  Friday, October 4, 2013 Penn Bioengineering Birthday Party The celebration will continue with invited speakers, student presentations, and a picnic complete with birthday cake! Email be@seas.upenn.edu to reserve your place.

It’s easy to stay in touch with Penn Bioengineering: Find us on Facebook: facebook.com/pennbioengineering Bioengineering website: www.be.seas.upenn.edu


Department of Bioengineering Newsletter: Spring 2013