Bioengineering Graduate Jason Andrechak Wins Graduate Leadership Award

Jason Andrechak

Congratulations to recent Penn Bioengineering graduate Jason Andrechak on winning a Graduate Leadership Awards for 2022. Each year a select number of students across the university are recognized for their service and lasting contributions to graduate student life at Penn. Andrechak, one of only ten recipients in 2022, won a Dr. Andy Binns Award for Outstanding Service to Graduate and Professional Student Life. This award is presented to “graduate or professional students, upon their graduation from Penn, who have significantly impacted graduate and professional student life through service involvement in student life initiatives or organizations.” Andrechak won this award for his “service and leadership in advocating for equity and accessibility during the transition to virtual operations and following a period of leadership transition within the Graduate and Professional Student Assembly (GAPSA). ”

Andrechak completed his Ph.D. in Bioengineering in 2022, where he studied macrophage immunotherapy in solid tumors in the lab of Dennis E. Discher, Robert D. Bent Professor in Chemical and Biomolecular Engineering, Bioengineering, and Mechanical Engineering and Applied Mechanics. He was named a National Science Foundation Graduate Research Fellow in 2018. He has actively led the Graduate Association of Bioengineers (GABE) as Community Service & Outreach chair from 2017-2019 and as co-President from 2019-2022. He also served as the Director of Equity & Access for the Graduate & Professional Student Assembly (GAPSA) from 2020-2021, in addition to several other service and advisory roles at the department, school, and university levels.

Learn more about the Penn Graduate Leadership Awards and read the full list of recipients on the Grad Center at Penn website.

2022 Penn Bioengineering Senior Design Teams Win Multiple Accolades

After a year of hybrid learning, Penn Bioengineering (BE) seniors were excited to return to the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace for Senior Design (BE 495 & 496), a two-semester course in which students work in teams to conceive, design and pitch their capstone projects in bioengineering. This year’s projects include tools for monitoring health, software to improve communication for the healthcare and supply chain industries, and devices to improve patient care for women and underrepresented minorities.

The year culminated in the annual Senior Design Expo on April 13 in the Singh Center for Nanotechnology, in which the students presented their pitches to a panel of alumni judges, followed by demonstrations in the George H. Stephenson  Foundation Educational Laboratory & Bio-MakerSpace which were open to the entire Penn community. This year’s winners of the Bioengineering Senior Design Competition were teams Chrysalis, Modulo Prosthetics, and ReiniSpec.

Team 11 (ReiniSpec) From L to R: Ifeoluwa Popoola, Alexa Rybicki, JeongInn Park (TA), Caitlin Frazee, Michelle White, Caroline Kavanagh (on laptop).

The three winning teams went on to compete in the annual interdepartmental Senior Design Competition sponsored by the Penn Engineering Alumni Society. BE took home two of the four interdepartmental awards: Team Modulo Prosthetics won the “Technology and Innovation Prize,” recognizing the project which best represents the highest and best use of technology and innovation to leverage engineering principles; and Team ReiniSpec won the “Leadership Prize,” which recognizes the team which most professionally and persuasively presents their group project to incorporate a full analysis of their project scope, advantages, and challenges, and addresses the commercialization and future potential of their research.

All BE teams were also required to submit their projects to local and national competitions, and were met with resounding success. “The creativity and accomplishment of this Senior Design class is really unparalleled,” said David Meaney, Solomon R. Pollack Professor in Bioengineering, Senior Associate Dean of Penn Engineering, and instructor for Senior Design. “The number of accolades received by these students, as well as the interest in transforming their ideas into real products for patients, reached a new level that makes us extremely proud.”

Keep reading for a full list of this year’s projects and awards.

Team 1 – MEViD

MEViD (Multichannel Electrochemical Viral Diagnostic) is a modular, low cost device that leverages electrochemistry to rapidly diagnose viral diseases from saliva samples.

Team members: Yuzheng (George) Feng, Daphne Kontogiorgos-Heintz, Carisa Shah, Pranshu Suri, & Rachel Zoneraich

Team 2 – MOD EZ-IO

MOD EZ-IO is a low-cost, novel intraosseous drill that uses force and RPM readings to alert the user via an LED when they have breached cortical bone and entered cancellous bone, guiding proper IO placement.

Team members: Gregory Glova, Kaiser Okyan, Patrick Paglia, Rohan Vemu, & Tshepo Yane

Team 3 – Harvest by Grapevine

Harvest by Grapevine is a user-centric software solution that merges social network communication and supply chain logistics to connect hospitals and suppliers under one unified platform.

Team members: Nicole Bedanova, Kerry Blatney, Blake Grimes, Brenner Maull, & Lukas Yancopoulos

Team 4 – CliniCall

CliniCall helps streamline and centralize communication channels, offering a real-time monitoring device that enables on-site/attending physicians to communicate with on-call physicians through a livestream of patients and data.

Team members: Neepa Gupta, Santoshi Kandula, Sue Yun Lee, & Ronil Synghal

Team 5 – PneuSonus

PneuSonus is a low-cost, user-friendly wearable strap that aids in detecting pediatric pneumonia by using frequency analysis of sound waves transmitted through the lungs to identify specific properties related to fluid presence, a valid indicator specific to pneumonia.

Team members: Iman Hossain, Kelly Lopez, Sophia Mark, Simi Serfati, & Nicole Wojnowski

Team 6 – Chrysalis

Chrysalis is a smart swaddle system comprising an electric swaddle and accompanying iOS application that comforts neonatal abstinence syndrome infants via stochastic resonance and maternal heartbeat vibrational patterns to reduce opioid withdrawal symptoms without pharmacological intervention or constant nurse oversight as well as streamlines the Eat, Sleep, Console documentation process for nurses.

Team members: Julia Dunn, Rachel Gu, Julia Lasater, & Carolyn Zhang

Team 7 – EquitOx

EquitOx is a revolutionized fingertip pulse oximeter designed for EMS that addresses racial inequality in medicine through the use of one-off tongue-calibrated SpO2 measurements.

Team members: Ronak Bhagia, Estelle Burkhardt, Juliette Hooper, Caroline Smith, & Kevin Zhao

Team 8 – Modulo Prosthetics

Modulo Prosthetic is an adjustable, low-cost, thumb prosthetic with integrated haptic feedback that attaches to the metacarpophalangeal (MCP) joint of partial hand amputees and assists in activities of daily living (ADLs).

Team members: Alisha Agarwal, Michelle Kwon, Gary Lin, Ian Ong, & Zachary Spalding

Team 9 – Cor-Assist By Cygno Technologies

COR-ASSIST by Cygno Technologies is a low-cost intra-aortic balloon enhancement that directly supports heart function by increasing cardiac output to 2.8L/min, at a much lower cost and bleeding risk than the current Impella cardiac assist device.

Team members: Francesca Cimino, Allen Gan, Shawn Kang, Kristina Khaw, & William Zhang

Team 10 – Pedalytics

Pedalytics Footwear is a rechargeable sandal that continuously monitors foot health and prevents diabetic foot ulcer formation by novelly tracking three key metrics indicative of ulceration, temperature, oxygen saturation, and pressure, and sending alerts to patients via the Pedalytics app when metric abnormalities are detected.

Team members: Samantha Brosler, Constantine Constantinidis, Quincy Hendricks, Ananyaa Kumar, & María José Suárez

Team 11 – ReiniSpec

ReiniSpec is a redesigned speculum to improve the gynecological exam experience, increasing patient comfort with a silicone shell and using motorized arm adjustments to make it easily adjustable for each patient, while also incorporating a camera, lights, and machine learning to aid in better diagnosis by gynecologists.

Team members: Caitlin Frazee, Caroline Kavanagh, Ifeoluwa Popoola, Alexa Rybicki, & Michelle White

Learn more about the 2022 Senior Design projects, including full abstracts and photo gallery, on the Stephenson Bio-MakerSpace website.

Watch all the 2022 project pitches on the BE Labs Youtube channel 2022 Senior Design Playlist:

Grapevine Wins 2022 President’s Innovation Prize

William Kohler Danon and Lukas Yancopoulos of Grapevine (Photos Eric Sucar)

University of Pennsylvania Interim President Wendell Pritchett announced the recipients of the 2022 President’s Engagement, Innovation, and Sustainability Prizes. Awarded annually, the Prizes empower Penn students to design and undertake post-graduation projects that make a positive, lasting difference in the world. Each Prize-winning project will receive $100,000, as well as a $50,000 living stipend per team member.

A Penn Bioengineering student is behind one of the prize-winning projects. Grapevine, winner of the President’s Innovation Prize, aims to increase resilience within the healthcare supply chain. BE senior Lukas Achilles Yancopoulos and his partner William Kohler Danon created Grapevine, and Lukas went on to adapt the Grapevine software into his award-winning senior design project Harvest by Grapevine along with team members Nicole Bedanova, Kerry Blatney, Blake Grimes, Brenner Maull.

“This year’s Prize recipients have selflessly dedicated themselves to improving environmental, health, and educational outcomes for others,” said Pritchett. “From empowering young people through free creative writing education to building robotics that minimize fish waste to reducing microfiber pollution in the ocean, these outstanding and inspiring projects exemplify the vision and passion of our Penn students, who are deeply committed to making a positive difference in the world.”

William Kohler Danon and Lukas Achilles Yancopoulos for Grapevine: Danon, a history major in the College of Arts and Sciences from Miami, and Yancopoulos, an environmental studies major in the College and a bioengineering major in the School of Engineering and Applied Science from Yorktown Heights, New York, will work to increase resilience across the health care supply chain, with a particular focus on small-to-medium businesses. Grapevine builds upon Danon and Yancopoulos’sinspiring work with Pandemic Relief Supply, a venture that delivered $20 million of health care supplies to frontline workers at the height of the COVID-19 pandemic. They are mentored by David F. Meaney, the Solomon R. Pollack Professor of Bioengineering and senior associate dean for Penn Engineering.

Read about all the winning projects at Penn Today

2022 Undergraduate Awards for Bioengineering Students

2022 Bioengineering student award winners

Congratulations to the Bioengineering undergraduate student recipients of awards from the School of School of Engineering and Applied Science  for the 2021-2022 academic year. These  awards are given annually by the school and the department in recognition of outstanding scholarship and service. Read the full list of Bioengineering undergraduate award winners below.

The Wolf-Hallac Award: Neepa Gupta (BAS 2022). This award was established in October 2000 to recognize the graduating female senior from across Penn Engineering’s departments who is seen as a role model, has achieved a high GPA (in the top 10% of their class), and who has demonstrated a commitment to school and/or community.

The Hugo Otto Wolf Memorial Prize: Ian Ong (BSE 2022) and Iman Hossian (BSE 2022). This prize is awarded to one or more members of each department’s senior class, distinguishing students who meet with great approval of the professors at large through “thoroughness and originality” in their work.

The Herman P. Schwan Award: George Feng (BSE and Jerome Fisher Program in Management & Technology 2022). This department award honors a graduating senior who demonstrates the “highest standards of scholarship and academic achievement.”

Exceptional Service Awards recognize students for their outstanding service to the University and their larger communities: Estelle Burkhardt (BSE 2022), Khristina Khaw (BSE 2022), Zachary Spalding (BSE 2022), and Nicole Wojnowski (BSE 2022).

The Student Leadership Award: Kerry Blatney (BSE 2022). This award is given annually to a student in Bioengineering who has demonstrated, through a combination of academic performance, service, leadership, and personal qualities, that they will be a credit to the Department, the School, and the University.

The Engineering Alumni Society E. Stuart Eichert, Jr. Student Award: Gloria Lee (BSE 2023). This award is given annually by the Engineering Alumni Society to a Penn Engineering third-year student who best exemplifies the characteristics of selfless service to the University and the community.

Additionally, the Bioengineering Department  also presents a single lab group with the Albert Giandomenico Award which reflects their “teamwork, leadership, creativity, and knowledge applied to discovery-based learning in the laboratory.” This year’s group consists of Caitlin Frazee (BSE 2022), Ifeoluwa Poppola (BSE 2022), Alexa Rybicki (BSE 2022), and Michelle White (2022).

Three Bioengineering Senior Design teams were chosen for recognition in the Bioengineering Senior Design Competition:

Team Chrysalis: Team members Julia Dunn, Rachel Gu, Julia Lasater, & Carolyn Zhang. Chrysalis is a smart swaddle system comprising an electric swaddle and accompanying iOS application that comforts neonatal abstinence syndrome infants via stochastic resonance and maternal heartbeat vibrational patterns to reduce opioid withdrawal symptoms without pharmacological intervention or constant nurse oversight as well as streamlines the Eat, Sleep, Console documentation process for nurses.

Team Modulo Prosthetics: Team members Alisha Agarwal, Michelle Kwon, Gary Lin, Ian Ong, & Zachary Spalding. Modulo Prosthetic is an adjustable, low-cost, thumb prosthetic with integrated haptic feedback that attaches to the metacarpophalangeal (MCP) joint of partial hand amputees and assists in activities of daily living (ADLs).

Team ReiniSpec: Team members Caitlin Frazee, Caroline Kavanagh, Ifeoluwa Popoola, Alexa Rybicki, & Michelle White. ReiniSpec is a redesigned speculum to improve the gynecological exam experience, increasing patient comfort with a silicone shell and using motorized arm adjustments to make it easily adjustable for each patient, while also incorporating a camera, lights, and machine learning to aid in better diagnosis by gynecologists.

Research for these projects was conducted in the George H. Stephenson Foundation Education Laboratory & Bio-Maker Space. Read the full abstracts and watch the pitch videos for all the 2022 Senior Design projects on the Stephenson Bio-MakerSpace website.

A full list of SEAS award descriptions and recipients can be found here.

The Changing Face of Portraiture at Penn

by Katherine Unger Baillie

One of the new portraits in Leidy depicts Jane Hinton, one of the first two Black women to earn a doctorate in veterinary medicine from Penn. Captions on the photos chronicle the achievements of those displayed, but also, in some cases, the challenges they faced due to their race or gender.

A grand split staircase inside the entrance to Leidy Labs invites visitors into the home of the School of Arts & SciencesBiology Department. As students ascend or descend on their way to lab meetings and classes, a set of faces looks down on them—not the old, gilt-framed portraits that long hung in the stairwell, but 14 new photos in chestnut-colored wooden frames, depicting scientists who have close connections to Penn and the department. The gallery now highlights a more diverse suite of individuals, such as Emily Gregory, the first female teaching fellow at Penn, and Roger Arliner Young, the first African American woman to earn a doctorate in zoology.

The new art is part of a collective effort by the department, working with guidance from the University Curator’s office, to rethink how portraiture and representation operate in the halls of their buildings. Many other University departments, schools, and leaders are in the process of undertaking similar initiatives, driven in part by the question: How can the walls of campus buildings better reflect the communities they serve?

“We have about 1,500 to 1,600 portraits in our collection,” says University curator Lynn Marsden-Atlass. “Most of them are paintings by white men of white men. Since I have been the University curator, my goal has really been to bring in more visible diversity to our art collection. And now we’ve been getting increasing numbers of requests, like from the Biology Department, to take on some of this themselves.”

The changes are meant to enhance a sense of inclusion for all at Penn, notably students, says history of art professor Gwendolyn DuBois Shaw. “There are certain contexts that students, in particular, want to assert that they belong,” she says, “that they are not just at Penn, but they’re of Penn.”

Pushing against homogeny

At Penn and many institutions like it, portraits find their way onto walls through a variety of means. Portraits honor department chairs, deans, or others who have ascended to the top ranks of the academy. Sometimes they depict thought leaders in a field, who may or may not have a direct connection to the University. And occasionally donors write into their gift agreement that a portrait will be hung in recognition of their philanthropy.

The result, however, can mean building walls that function like memorials or museums, highlighting the past but not the current community, or a hoped-for future one.

Located at one of the unofficial “entrances” to Penn’s campus at 34th and Walnut streets, the 16-foot-tall bronze form of Brick House, by artist Simone Leigh, makes a statement. Installed in November 2020, it is the first campus sculpture of and by a Black woman.

“I’ve had such an interesting set of conversations about what the walls of Penn are for,” says Dani Bassett, a professor in the School of Engineering and Applied Science. “We as an institution have used the walls to display our history. But there’s a sense in which the students who walk the halls feel that, especially when those faces are not diverse, this kind of art can be really oppressive, saying that, ‘This space is not for me, it’s only for white men.’ So, the question is, how do we venerate our history without hurting our students? Are our walls the place for history or the place for the future?”

In June 2020, amid widespread Black Lives Matter protests, Bassett, together with Junhyong Kim, chair of the Biology Department, as well as other faculty and staff, addressed an open letter requesting institutional and financial support for diversifying portraiture at Penn.

“Many spaces at Penn reflect its history but do not reflect our core values of diversity and inclusion, nor do they accurately reflect the student, staff, and faculty bodies that comprise the Penn of today, or those we envision to comprise the Penn of tomorrow,” they wrote. More than 430 members of the Penn community signed the letter.

Bassett has felt the need to act—and felt it most viscerally—when they interact with students, who have identified the issue of portraiture as an area that makes them feel uncomfortable, even unwelcome. For example, Bassett notes, one room in which students present their thesis proposals (and later defend their Ph.D. theses) is lined with portraits of white men. “The students walk into this room and think, ‘Here is this space where I will be evaluated and I will be evaluated, most likely, by people who are not like me,’” Bassett says. “It was those conversations with students that made me realize this is so important to address.”

Read the full story in Penn Today.

Dani Bassett is the J. Peter Skirkanich Professor, with appointments in the Departments of Bioengineering and Electrical & Systems Engineering in the School of Engineering and Applied Science, the Department of Physics & Astronomy in the School of Arts & Sciences, and the Departments of Neurology and Psychiatry in the Perelman School of Medicine.

 

Decoding a Material’s ‘Memory’

by Erica K. Brockmeier

A suspension of particles of different sizes during shearing experiments conducted in the lab of Paulo Arratia, with arrows indicating particle “flow” and trajectories. In a new study published in Nature Physics, researchers detail the relationship between a disordered material’s individual particle arrangement and how it reacts to external stressors. The study also found that these materials have “memory” that can be used to predict how and when they will flow. (Image: Arratia lab)

New research published in Nature Physics details the relationship between a disordered material’s individual particle arrangement and how it reacts to external stressors. The study also found that these materials have “memory” that can be used to predict how and when they will flow. The study was led by Larry Galloway, a Ph.D. student in the lab of Paulo Arratia, and Xiaoguang Ma, a former postdoc in the lab of Arjun Yodh, in collaboration with researchers in the labs of Douglas Jerolmack and Celia Reina.

A disordered material is randomly arranged at the particle-scale, e.g. atoms or grains, instead of being systematically distributed—think of a pile of sand instead of a neatly stacked brick wall. Researchers in the Arratia lab are studying this class of materials as part of Penn’s Materials Research Science & Engineering Center, where one of the program’s focuses is on understanding the organization and proliferation of particle-scale rearrangements in disordered, amorphous materials.

The key question in this study was whether one could observe the structure of a disordered material and have some indication as to how stable it is or when it might begin to break apart. This is known as the yield point, or when the material “flows” and begins to move in response to external forces. “For example, if you look at the grains of a sand castle and how they are arranged, can I tell you whether the wind can blow it over or if it has to be hit hard to fall over?” says Arratia. “We want to know, just by looking at the way the particles are arranged, if we can say anything about the way they’re going to flow or if they are going to flow at all.”

While it has been known that individual particle distribution influences yield point, or flow, in disordered materials, it has been challenging to study this phenomenon since the field lacks ways to “quantify” disorder in such materials. To address this challenge, the researchers collaborated with colleagues from across campus to combine expertise across the fields of experimentation, theory, and simulations.

Read the full story in Penn Today.

The authors are Larry Galloway, Erin Teich, Christoph Kammer, Ian Graham, Celia Reina, Douglas Jerolmack, Arjun Yodh, and Paulo Arratia from Penn; Xiaoguang Ma, previously a postdoc at Penn and now at the Southern University of Science and Technology in Shenzhen, China; and Nathan Keim, previously a postdoc at Penn and now at Pennsylvania State University.

Arjun Yodh is the James M. Skinner Professor of Science in the Department of Physics and Astronomy in Penn’s School of Arts & Sciences and a member of the Penn Bioengineering Graduate Group.

Paulo Arratia is a professor in the departments of Mechanical Engineering and Applied Mechanics and Chemical and Biomolecular Engineering in the School of Engineering and Applied Science at the University of Pennsylvania.

Douglas Jerolmack is a professor in the Department of Earth and Environmental Science in Penn’s School of Arts & Sciences and in the Department of Mechanical Engineering and Applied Mechanics at Penn Engineering.

Celia Reina is the William K. Gemmill Term Assistant Professor in the Department of Mechanical Engineering and Applied Mechanics at Penn Engineering.

Refining Data into Knowledge, Turning Knowledge into Action

by Janelle Weaver

Heatmaps are used by researchers in the lab of Jennifer Phillips-Cremins to visualize which physically distant genes are brought into contact when the genome is in its folded state.

More data is being produced across diverse fields within science, engineering, and medicine than ever before, and our ability to collect, store, and manipulate it grows by the day. With scientists of all stripes reaping the raw materials of the digital age, there is an increasing focus on developing better strategies and techniques for refining this data into knowledge, and that knowledge into action.

Enter data science, where researchers try to sift through and combine this information to understand relevant phenomena, build or augment models, and make predictions.

One powerful technique in data science’s armamentarium is machine learning, a type of artificial intelligence that enables computers to automatically generate insights from data without being explicitly programmed as to which correlations they should attempt to draw.

Advances in computational power, storage, and sharing have enabled machine learning to be more easily and widely applied, but new tools for collecting reams of data from massive, messy, and complex systems—from electron microscopes to smart watches—are what have allowed it to turn entire fields on their heads.

“This is where data science comes in,” says Susan Davidson, Weiss Professor in Computer and Information Science (CIS) at Penn’s School of Engineering and Applied Science. “In contrast to fields where we have well-defined models, like in physics, where we have Newton’s laws and the theory of relativity, the goal of data science is to make predictions where we don’t have good models: a data-first approach using machine learning rather than using simulation.”

Penn Engineering’s formal data science efforts include the establishment of the Warren Center for Network & Data Sciences, which brings together researchers from across Penn with the goal of fostering research and innovation in interconnected social, economic and technological systems. Other research communities, including Penn Research in Machine Learning and the student-run Penn Data Science Group, bridge the gap between schools, as well as between industry and academia. Programmatic opportunities for Penn students include a Data Science minor for undergraduates, and a Master of Science in Engineering in Data Science, which is directed by Davidson and jointly administered by CIS and Electrical and Systems Engineering.

Penn academic programs and researchers on the leading edge of the data science field will soon have a new place to call home: Amy Gutmann Hall. The 116,000-square-foot, six-floor building, located on the northeast corner of 34th and Chestnut Streets near Lauder College House, will centralize resources for researchers and scholars across Penn’s 12 schools and numerous academic centers while making the tools of data analysis more accessible to the entire Penn community.

Faculty from all six departments in Penn Engineering are at the forefront of developing innovative data science solutions, primarily relying on machine learning, to tackle a wide range of challenges. Researchers show how they use data science in their work to answer fundamental questions in topics as diverse as genetics, “information pollution,” medical imaging, nanoscale microscopy, materials design, and the spread of infectious diseases.

Bioengineering: Unraveling the 3D genomic code

Scattered throughout the genomes of healthy people are tens of thousands of repetitive DNA sequences called short tandem repeats (STRs). But the unstable expansion of these repetitions is at the root of dozens of inherited disorders, including Fragile X syndrome, Huntington’s disease, and ALS. Why these STRs are susceptible to this disease-causing expansion, whereas most remain relatively stable, remains a major conundrum.

Complicating this effort is the fact that disease-associated STR tracts exhibit tremendous diversity in sequence, length, and localization in the genome. Moreover, that localization has a three-dimensional element because of how the genome is folded within the nucleus. Mammalian genomes are organized into a hierarchy of structures called topologically associated domains (TADs). Each one spans millions of nucleotides and contains smaller subTADs, which are separated by linker regions called boundaries.

Associate professor and Dean’s Faculty Fellow Jennifer E. Phillips-Cremins.

“The genetic code is made up of three billion base pairs. Stretched out end to end, it is 6 feet 5 inches long, and must be subsequently folded into a nucleus that is roughly the size of a head of a pin,” says Jennifer Phillips-Cremins, associate professor and dean’s faculty fellow in Bioengineering. “Genome folding is an exciting problem for engineers to study because it is a problem of big data. We not only need to look for patterns along the axis of three billion base pairs of letters, but also along the axis of how the letters are folded into higher-order structures.”

To address this challenge, Phillips-Cremins and her team recently developed a new mathematical approach called 3DNetMod to accurately detect these chromatin domains in 3D maps of the genome in collaboration with the lab of Dani Bassett, J. Peter Skirkanich Professor in Bioengineering.

“In our group, we use an integrated, interdisciplinary approach relying on cutting-edge computational and molecular technologies to uncover biologically meaningful patterns in large data sets,” Phillips-Cremins says. “Our approach has enabled us to find patterns in data that classic biology training might overlook.”

In a recent study, Phillips-Cremins and her team used 3DNetMod to identify tens of thousands of subTADs in human brain tissue. They found that nearly all disease-associated STRs are located at boundaries demarcating 3D chromatin domains. Additional analyses of cells and brain tissue from patients with Fragile X syndrome revealed severe boundary disruption at a specific disease-associated STR.

“To our knowledge, these findings represent the first report of a possible link between STR instability and the mammalian genome’s 3D folding patterns,” Phillips-Cremins says. “The knowledge gained may shed new light into how genome structure governs function across development and during the onset and progression of disease. Ultimately, this information could be used to create molecular tools to engineer the 3D genome to control repeat instability.”

Read the full story in Penn Today.

Penn Bioengineering Senior Raveen Kariyawasam Named 2022 Rhodes Scholar

2022 Rhodes Scholar, Raveen Kariyawasam

One of the two University of Pennsylvania seniors who were awarded Rhodes Scholarships for graduate study at the University of Oxford is Penn Engineering‘s own Raveen Kariyawasam, from Colombo, Sri Lanka.

Kariyawasam is a double major in Engineering’s Department of Bioengineering, with concentrations in computational medicine and medical devices, and in the Wharton School, with concentrations in finance and entrepreneurship and innovation.

“We are so proud of our newest Penn Rhodes Scholars who have been chosen for this tremendous honor and opportunity,” said President Amy Gutmann. “The work Raveen has done in health care innovation and accessibility and Nicholas has done to support student well-being while at Penn is impressive, and pursuing a graduate degree at Oxford will build upon that foundation. We look forward to seeing how they make an impact in the future.”

The Rhodes is highly competitive and one of the most prestigious scholarships in the world. The scholarships provide all expenses for as long as four years of study at Oxford University in England.

According to the Rhodes Trust, about 100 Rhodes Scholars will be selected worldwide this year, chosen from more than 60 countries. Several have attended American colleges and universities but are not U.S. citizens and have applied through their home country, including Kariyawasam in Sri Lanka.

With an interest in health care innovation and accessibility, Kariyawasam is involved in several research projects, including his Wharton honors thesis that focuses on optimizing a low-cost electronic medical record system in Sri Lanka and the Philippines. He has received several research grants, including the Vagelos Undergraduate Research Grant, the Berkman Opportunity Fund grant, and the National Science Foundation’s Innovation Corps grant. At Penn, he is editor-in-chief of Synapse, a student-run health care magazine and is vice president of the Phi Sigma Biological Honor Society. He is a disc jockey for the student-run radio station, WQHS, and an executive board member of the Wharton Undergraduate Healthcare Club. He also is a former student ambassador at the Penn Health-Tech Center for Health Devices and Technology. At Oxford, Kariyawasam plans to pursue a D.Phil. degree.

Read more at Penn Today.

Penn’s 2021 iGEM Team Takes Home Multiple Prizes

Four of Penn’s 2021 iGEM team (left to right): Juliette Hooper, Grace Qian, Saachi Datta, and Gloria Lee.

The University of Pennsylvania’s 2021 iGEM team has been awarded several distinctions in this year’s highly competitive iGEM Competition. The International Genetically Engineered Machine Competition is the largest synthetic biology community and the premiere synthetic biology competition for both university and high school level students from around the world. Each year, hundreds of interdisciplinary teams of students combine molecular biology techniques and engineering concepts to create novel biological systems and compete for prizes and awards through oral presentations and poster sessions.

The Penn team’s project, “OptoReader,” is a combined light-simulation device and plate reader, which makes optogenetic experiments more powerful and accessible. The abstract reads:

“Metabolic engineering has the potential to change the world, and optogenetic tools can make metabolic engineering research easier by providing spatiotemporal control over cells. However, current optogenetic experiments are low-throughput, expensive, and laborious, which makes them inaccessible to many. To tackle this problem, we combined a light-stimulation device with a plate reader, creating our OptoReader. This device allows us to automate ~100 complex optogenetic experiments at the same time. Because it is open source and inexpensive, our device would make optogenetic experiments more efficient and available to all.”

Watch the team’s presentation on OptoReader here.

This year’s Penn team was mentored by Lukasz Bugaj, Assistant Professor in Bioengineering. In addition, the team was supported by Brian Chow, Associate Professor in Bioengineering. Chow has supported previous undergraduate iGEM teams at Penn, and was involved in the creation of the iGEM program during his time as a graduate student at MIT.

OptoReader took home the top prizes in three of the four categories in which it was nominated. These prizes include:

  • Best Foundational Advance (best in track)
  • Best Hardware (best from all undergraduate teams)
  • Best Presentation (best from all undergraduate teams)

They were also awarded a Gold Medal Distinction and were included in the Top 10 Overall (from all undergraduate teams, and the only team from the United States to make the top 10) and Top 10 Websites (from all undergraduate teams).

The awards were announced during iGEM’s online Jamboree Award Ceremony on November 14, 2021 (watch the full award ceremony here).

In addition to the outstanding awards recognition, OptoReader was also selected for an iGEM Impact Grant which awards teams $2,500 to continue development of their projects. This new initiative from the iGEM Foundation was announced earlier this year, and with the support of the Frederick Gardner Cottrell Foundation, is distributing a total of $225,000 in grant funds to 90 iGEM teams during the 2021 competition season. Learn more about the Impact Grant and read the full list of winning teams here.

Penn’s 2021 iGEM team was made up of an interdisciplinary group of women undergraduates from the School of Engineering and Applied Science (SEAS) and the School of Arts and Sciences (SAS):

  • Saachi Datta (B.A. in Biology and Religious Studies 2021)
  • Juliette Hooper (B.S.E. and M.S.E. in Bioengineering 2022)
  • Gabrielle Leavitt (B.S.E. in Bioengineering 2021 and current Master’s student in Bioengineering)
  • Gloria Lee (B.A. in Physics and B.S.E. in Bioengineering 2023)
  • Grace Qian (B.S.E. in Bioengineering 2023)
  • Lana Salloum (B.A. in Neuroscience 2022)

They were mentored by three doctoral students in Bioengineering: Will Benman (Bugaj Lab), David Gonzalez Martinez (Bugaj Lab), Gabrielle Ho (Chow Lab). Saurabh Malani, a graduate student in the Avalos Lab at Prince University, was also very involved in mentoring the team.

OptoReader

The graduate mentors were instrumental in quickly bringing the undergraduates up to speed on a diverse array of skills needed to accomplish this project including circuit design, optics, optogenetics, programming, and additive manufacturing. They then coached the team through building and testing prototypes, as well as accomplishing other objectives required for success at iGEM. These other objectives included establishing collaborations with other iGEM teams, performing outreach, and effectively communicating their project through a website and online presentations.

“This team and their work is outstanding,” said William Benman. “Not only did they sweep several awards, but they did it all with a small team and while working with technology they had no prior experience with. They created a device that not only increases accessibility to optogenetics but also allows optogenetic systems to interface directly with computer programs, allowing for completely new research avenues within the field. They are truly a remarkable group.”

Due to the COVID pandemic, the team operated virtually through the summer of 2020, and then continued in person in the summer of 2021 as the project progressed and more students returned to Penn’s campus. Upon return to campus, the work was conducted in both the Bugaj lab in the Stephenson Foundation Educational Laboratory & Bio-MakerSpace, the primary teaching laboratory in Penn Bioengineering and an interdisciplinary makerspace open to anyone at Penn. The team also collaborated with the Avalos Lab at Princeton University, which conducts research in the application of optogenetics to optimize production of valuable  chemicals in microbes.

“I’m beyond excited about this phenomenal showing from team Penn at the iGEM Jamboree awards ceremony,” said faculty mentor Lukasz Bugaj. “This is truly outstanding recognition for what the team has accomplished, and it wouldn’t have happened without essential contributions from everyone on the team.”

Brian Chow added that this achievement is “no small feat,” especially for a hardware project. “The iGEM competition leans toward genetic strain engineering, but the advances in the field made by these incredible students were undeniable,” he said.

Going forward, the team plans to publish a scientific article and file a patent application describing their device. “It’s clear that there is excitement in the scientific community for what our students created, and we’re excited to share the details and designs of their work,” said Bugaj.

Congratulations to all the team members and mentors of OptoReader on this incredible achievement! Check out the OptoReader project website and Instagram to learn more about their project.

This project was supported by the Department of Bioengineering, the School of Engineering and Applied Science, and the Office of the Vice Provost for Research (OVPR). 

Penn Takes Part in National Science Foundation’s First I-Corps Hubs

by Evan Lerner

A decade ago, the National Science Foundation started its Innovation Corps program to help translate academic research into the wider world. Functioning as a national start-up accelerator, I-Corps provides training and funding to researchers who have a vision for applying their ideas, starting businesses and maximizing social impact. 

Several successful start-ups launched by Penn Engineering students, including Strella BiotechnologyInventXYZ, and Percepta AI have participated in the I-Corps program.

Now, to further develop innovation ecosystems and share regional resources, the NSF has launched a network of five I-Corps Hubs.

Penn is a member of the Mid-Atlantic Hub, which will be led by the University of Maryland at College Park, and include Carnegie Mellon University, George Washington University, Howard University, Johns Hopkins University, North Carolina State University, Penn State, University of North Carolina at Chapel Hill, and Virginia Tech.

The Penn Center for Innovation is currently accepting applications to join the next I-Corps cohort, which begins in October 2021. Teams will receive up to $2,000 to support their start-up, and can apply online.

This story originally appeared in Penn Engineering Today.

N.B.:  Founded by Penn alumna Katherine Sizov (Bio 2019) and winner of a 2019 President’s Innovation Prize, Strella Biotech seeks to reduce food waste through innovative biosensors, and was initially developed in the George H. Stephenson Foundation Educational Laboratory, the bio-makerspace and primary teaching lab of the Department of Bioengineering. Read more BE blog stories featuring Strella Biotechnology.