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2022 Penn iGEM Team Wins Gold Medal in Grand Jamboree

The 2022 iGEM team from left to right: June Ahn, Shreya Villimanalan, Adiva Daniar, Wangari Mbuthia, Cristina Perez and Moses Zeidan.

Congratulations to the 2022 University of Pennsylvania iGEM Team who took home a gold medal in the iGEM Grand Jamboree. This international competition of multidisciplinary teams of graduate and undergraduate students presenting original projects in synthetic biology culminated in the in-person Jamboree event held in Paris, France in October 2022. Over 370 judges awarded prizes and medals to the 350+ teams representing over 40 countries.

The 2022 Penn team was awarded a Gold Medal for their project “Photocreate,” a toolbox to control intercellular communication using optogenetics. Their plasmid constructs are designed to control protein secretion, display and shedding using a photocleavable protein, Phocl. The full abstract reads:

Intercellular communication is primarily studied using synthetic protein-level circuits. These circuits currently lack the spatial and temporal control necessary for targeted and time-sensitive applications. To address this gap, we developed Photocrete, a toolbox of protein constructs for light-inducible control of protein display, secretion, and shedding. We expanded upon RELEASE (Vlahos et al.), a modular and generalizable protein circuit which utilizes an ER retention motif and an exogenous protease to control protein secretion. We optogenetically modified RELEASE by replacing different components with the photocleavable protein PhoCl, allowing us to control the mammalian secretion pathway at distinct nodes with finely-tuned light administration regimens. Preliminary results indicate integration of Photocrete into the secretion pathway, but more research is necessary to determine optimal light administration settings. The potential for high spatial and temporal control of Photocrete could allow researchers to perform various signaling studies and develop therapeutics at a new level of precision.

The 2022 iGEM team includes undergraduates June Ahn (B.S. in Biochemistry, Physics and Nutrition), Adiva Daniar (B.S.E. in Bioengineering, minor in Engineering Entrepreneurship), Wangari Mbuthia (B.S.E. in Bioengineering), Cristina Perez (B.S.E. in Bioengineering, minor in Physics), Shreya Vallimanalan (B.S.E. in Bioengineering, minor in Computational Neuroscience), an d Moses Zeidan (B.S.E. in Bioengineering, minor in Chemistry and Spanish). They were mentored by graduate students David Gonzalez-Martinez, Gabrielle Ho, Zikang Huang, and Will Benman. Their faculty advisor is Lukasz Bugaj, Assistant Professor in Bioengineering.

Read the full results of the 2022 iGEM Competition here.

Work for the annual iGEM competition is conducted in the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace.

We acknowledge financial support from the Bradley Gabel Memorial Fund.

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Ravi Radhakrishnan Named to the 2022 BMES Class of Fellows

Ravi Radhakrishnan, PhD

Ravi Radhakrishnan, Professor and Chair of the Department of Bioengineering and Professor in Chemical and Biomolecular Engineering, was named to the 2022 Class of Fellows of the Biomedical Engineering Society (BMES). BMES, the premier society for biomedical engineers in the U.S., recognizes individuals for their accomplishments, significant contributions and service to the Society and the field of biomedical engineering in their annual Class of Fellows. The incoming Fellows were recognized during the BMES annual meeting on October 13, 2022.

Radhakrishnan’s research interests lie at the interface of chemical physics and molecular biology. The Radhakrishnan Lab’s goal is to provide molecular level and mechanistic characterization of biomolecular and cellular systems and formulate quantitatively accurate microscopic models for predicting the interactions of various therapeutic agents with innate biochemical signaling mechanisms. Radhakrishnan was named BE’s Department Chair in January 2020. He is also a member of the Genomics & Computational Biology (GCB) Graduate Group and is the former director of the Penn Institute for Computational Science (PICS).

Read the announcement and the full 2022 BMES Award Winners and Fellows here.

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Penn Bioengineering Alumnus Named Schwarzman Scholar

Jiaqi Liu

Penn Bioengineering alumnus Jiaqi Liu has been named to the eighth class of Schwarzman Scholars and will enroll at Tsinghua University in Beijing in August.

The program’s core curriculum focuses on leadership, China, and global affairs, according to the Schwarzman program. The academic program is updated each year to align with current and future geopolitical priorities. The coursework, cultural immersion, and personal and professional development opportunities are designed to equip students with an understanding of China’s changing role in the world.

This year, approximately 151 Schwarzman Scholars were selected from a pool of 3,000 applicants from 36 countries and 121 universities.

Jiaqi Liu earned his master’s degree in bioengineering in the School of Engineering and Applied Science in 2021. After graduation, he returned to China and works in global early-stage Venture Capital. According to the Schwarzman Scholars program, Liu is passionate about promoting medical equality and affordable health care solutions and has experience in medtech startup, global pharmaceutical company, health care consulting, and health care venture capital.

This story is by Amanda Mott. Read more about the Schwarzman Scholars at Penn Today.

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Dani Smith Bassett Receives 2022-23 Heilmeier Award

by Olivia J. McMahon

Dani Bassett, Ph.D.

Dani Smith Bassett, J. Peter Skirkanich Professor in Bioengineering and in Electrical and Systems Engineering in Penn Engineering, has been named the recipient of the 2022-23 George H. Heilmeier Faculty Award for Excellence in Research for “groundbreaking contributions to modeling and control of brain networks in the contexts of learning, disease and aging.”

The Heilmeier Award honors a Penn Engineering faculty member whose work is scientifically meritorious and has high technological impact and visibility. It is named for the late George H. Heilmeier, a Penn Engineering alumnus and member of the School’s Board of Advisors, whose technological contributions include the development of liquid crystal displays and whose honors include the National Medal of Science and Kyoto Prize.

Bassett, who also holds appointments in Physics & Astronomy in Penn Arts & Sciences and in Neurology and Psychiatry in the Perelman School of Medicine, is a pioneer in the field of network neuroscience, an emerging subfield which incorporates elements of mathematics, physics, biology and systems engineering to better understand how the overall shape of connections between individual neurons influences cognitive traits. They lead the Complex Systems lab, which tackles problems at the intersection of science, engineering and medicine using systems-level approaches, exploring fields such as curiosity, dynamic networks in neuroscience, and psychiatric disease.

Bassett will deliver the 2022-23 Heilmeier Award Lecture in Spring 2023.

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‘Organ-on-a-Chip’ Device Provides New Insights into Early-Stage Pregnancy

by Scott Harris

Dan Huh’s BIOLines Lab develops several different kinds of organ-on-a-chip systems, such as this blinking-eye-on-a-chip.

If you’d read about it in a science fiction novel, you might not have believed it. Human organs and organ systems — from lungs to blood vessels to blinking eyes — bio-miniaturized and stored on a plastic chip no larger than a matchbook.

But that’s the breathing, blinking reality at the Biologically Inspired Engineering Systems (BIOLines) Laboratory in the Department of Bioengineering in the School of Engineering and Applied Sciences at the University of Pennsylvania, a bona fide pioneer of what is now widely known as “organ-on-a-chip” technology. Proponents hope these devices can one day help scientists around the world learn more about the body’s inner workings and ultimately improve disease prevention and treatment.

“The century-old practice of cell culture is to grow living cells isolated from the human body in hard plastic dishes and keep them bathed in copious amounts of culture media under static conditions, and that is drastically different than the complex, dynamic environment of native tissues in which these cell reside,” said Dan Dongeun Huh, Ph.D., BIOLines’ principal investigator and an associate professor of Bioengineering in Penn’s School of Engineering and Applied Science. “What makes this organ-on-a-chip technology so unique and powerful is that it enables us to reverse-engineer living human tissues using microengineered devices and mimic their intricate biological interactions and physiological functions in ways that have not been possible using traditional cell culture techniques. This represents a major advance in our ability to model and understand the inner workings of complex physiological systems in the human body.”

Generally speaking, organ-on-a-chip devices are made of clear silicone rubber — the same material used to make contact lenses — and can vary in size and design. Embedded within are microfabricated three-dimensional chambers lined with different human cell types, arranged and propagated to ultimately form a structure complex enough to actually mimic the essential elements of a functioning organ.

With partners at the Perelman School of Medicine, BIOLines recently developed a newer variation of the organ-on-a-chip: one that replicates the interface between maternal tissue and the cells of the placenta at the critical moments in early pregnancy when the embryo is implanting in the uterus. Huh and Penn Medicine physicians led a study using the “implantation-on-a-chip” to observe things that would otherwise have been virtually unobservable.

The study findings appeared this spring in the journal Nature Communications.

Continue reading at Penn Medicine News.

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Grace Hopper Distinguished Lecture: “How Memory Guides Value-Based Decisions” (Daphna Shohamy, Columbia University)

We hope you will join us for the 2022 Grace Hopper Distinguished Lecture by Dr. Jennifer Lewis, presented by the Department of Bioengineering and hosted by Dani S. Bassett, J. Peter Skirkanich Professor in Bioengineering, Electrical and Systems Engineering, Physics & Astronomy, Neurology and Psychiatry.

Date: Thursday, December 8, 2022
Start Time: 3:30 PM EST
Location: Glandt Forum, Singh Center for Nanotechnology, 3205 Walnut Street, Philadelphia, PA 19104

Join us after the live lecture for a light reception!

Daphna Shohamy, Ph.D.

 

Speaker: Daphna Shohamy, Ph.D.
Kavli Professor of Brain Science, Co-Director of the Kavli Institute for Brain Science, Professor in the Department of Psychology & Zuckerman Mind Brain Behavior Institute
Columbia University

Title: “How Memory Guides Value-Based Decisions”

Zoom link
Passcode: 704696

 

Lecture Abstract:

From robots to humans, the ability to learn from experience turns a rigid response system into a flexible, adaptive one. In the past several decades, major advances have been made in understanding how humans and other animals learn from experience to make decisions. However, most of this progress has focused on rather simple forms of stimulus-response learning, such as automatic responses or habits. In this talk, I will turn to consider how past experience guides more complex decisions, such as those requiring flexible reasoning, inference, and deliberation. Across a range of behavioral contexts, I will demonstrate a critical role for memory in such decisions and will discuss how multiple brain regions interact to support learning, what this means for how memories are used, and the consequences for how decisions are made. Uncovering the pervasive role of memory in decision-making challenges the way we think about what memory is for, suggesting that memory’s primary purpose may be to guide future behavior and that storing a record of the past is just one way to do so.

Dr. Shohamy Bio:

Daphna Shohamy, PhD is a professor at Columbia University where she co-directs the Kavli Center for Neural Sciences and is Associate Director of the Zuckerman Mind, Brain Behavior Institute. Dr. Shohamy’s work focuses on the link between memory, and decision-making. Combining brain imaging in healthy humans with studies of patients with neurological and psychiatric disorders, Dr. Shohamy seeks to understand how the brain transforms experiences into memories; how memories shape decisions and actions; and how motivation and exploration affect human behavior.

Information on the Grace Hopper Lecture:
In support of its educational mission of promoting the role of all engineers in society, the School of Engineering and Applied Science presents the Grace Hopper Lecture Series. This series is intended to serve the dual purpose of recognizing successful women in engineering and of inspiring students to achieve at the highest level.

Rear Admiral Grace Hopper was a mathematician, computer scientist, systems designer and the inventor of the compiler. Her outstanding contributions to computer science benefited academia, industry and the military. In 1928 she graduated from Vassar College with a B.A. in mathematics and physics and joined the Vassar faculty. While an instructor, she continued her studies in mathematics at Yale University where she earned an M.A. in 1930 and a Ph.D. in 1934. Grace Hopper is known worldwide for her work with the first large-scale digital computer, the Navy’s Mark I. In 1949 she joined Philadelphia’s Eckert-Mauchly, founded by the builders of ENIAC, which was building UNIVAC I. Her work on compilers and on making machines understand ordinary language instructions lead ultimately to the development of the business language, COBOL. Grace Hopper served on the faculty of the Moore School for 15 years, and in 1974 received an honorary degree from the University. In support of the accomplishments of women in engineering, each department within the School invites a prominent speaker for a one or two-day visit that incorporates a public lecture, various mini-talks and opportunities to interact with undergraduate and graduate students and faculty.

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Student Spotlight: Bella Mirro

Bella Mirro (BE 2023)

Bella Mirro, a fourth year student in Bioengineering who also minors in Chemistry, spoke with 34th Street Magazine about her many roles at Penn, including being Co–President of Shelter Health Outreach Program (SHOP), a Research Assistant in lab of Michal A. Elovitz, the Hilarie L. Morgan and Mitchell L. Morgan President’s Distinguished Professor in Women’s Health at Penn Medicine, and a Penn Engineering Council Marketing Team Member. In this Q&A, she discusses her research in women’s health and her passions for accessible healthcare, serving Philadelphia’s homeless community, and good food.

Read “Ego of the Week: Bella Mirro” in 34th Street.

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Listen: ‘Curious Minds’ on NPR’s ‘Detroit Today’

by Ebonee Johnson

Twin siblings and scholars Dani S. Bassett of Penn and Perry Zurn of American University collaborated over half a dozen years to write “Curious Minds: The Power of Connection.” (Image: Tony and Tracy Wood Photography)

Twin academics Dani S. Basset, J. Peter Skirkanich Professor and director of the Complex Systems Lab, and Perry Zurn, a professor of philosophy at American University, were recently featured as guests on NPR radio show “Detroit Today” to discuss their new book, “Curious Mind: The Power of Connection.”

In their book, Basset and Zurn draw on their previous research, as well as an expansive network of ideas from philosophy, history, education and art to explore how and why people experience curiosity, as well as the different types it can take.

Basset, who holds appointments in the Departments of Bioengineering and Electrical and Systems Engineering, as well as the Department of Physics and Astronomy in Penn Arts & Science, and the Departments of Neuroscience and Psychiatry in Penn Perelman’s School of Medicine, and Zurn spoke with “Detroit Today” producer Sam Corey about what types of things make people curious, and how to stimulate more curiosity in our everyday lives.

According to the twin experts, curiosity is not a standalone facet of one’s personality. Basset and Zurn’s work has shown that a person’s capacity for inquiry is very much tied to the overall state of their health.

“There’s a lot of scientific research focusing on intellectual humility and also openness to ideas,” says Bassett. “And there are really interesting relationships between someone’s openness to ideas, someone’s intellectual humility and their curiosity and also their wellbeing or flourishing,”

Listen to “What makes people curious and how to encourage the act” at “Detroit Today.”

Register for a book signing event for “Curious Minds: The Power of Connection,” on Friday, December 9th at the Penn Bookstore.

This story originally appeared in Penn Engineering Today.

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Book Discussions and Bonding at the Bioengineering Retreat

by Brittany H. Scheid

Retreat participants in Mitchell Hall at the College of Physicians

This year, the lineup of new student orientation activities included a new event:  the first bioengineering retreat for incoming Ph.D. graduate students.  Sitting in the historic Mitchell Hall at the College of Physicians, the 2022 Ph.D. cohort participated in a fun and educational half-day program that included a series of bonding activities, small-group conversations, and panel discussions. Current members of the Graduate Association of Bioengineers (GABE) planned the program to strengthen personal connections among students and to lend some advice to the newcomers as they embarked on their scholastic journey.

Prior to the retreat, participants read The Immortal Life of Henrietta Lacks by Rebecca Skloot, a work that delves into the human story of Henrietta Lacks, a Black woman from Virginia whose cancer cells were obtained for scientific study in the early 1950s without her knowledge. Today, “HeLa” cells have become one of the most significant tools in cell biology, enabling the development of polio vaccines, research into radiation effects, and even research on COVID-19. Together at the retreat, we discussed the intersection of ethics and scientific discovery, and reflected on our responsibility as scientists to consider the impact of our work beyond the immediate scientific question.

“Surviving the PhD 101” Panel Discussion. From left to right: Aoifa O’Farrell, Mosha Deng, David Mai, Lasya Sreepada

Current Ph.D. students volunteered their afternoons to share in two additional activities. Aoife O’Farrell, David Mai, Lasya Sreepada, and Mosha Deng imparted sage advice about using on-campus resources, handling advisor-advisee conflicts, and finding the best bites in Philly in the “Surviving the Ph.D. 101” panel discussion. Seven other students presented a series of flash talks about their research areas and musings on the best hypothetical mascot to represent their lab. The afternoon finished with an after-hours visit to the Mütter Museum, which holds an extensive and unique collection of anatomical specimens and antique medical equipment previously used for medical education.

If the WhatsApp group formed by the new cohort during the event is any indication, the retreat was an overall success! GABE looks forward to continuing the event in the future.

Brittany H. Scheid is a Ph.D. candidate studying Bioengineering in the lab of Brian Litt, Professor in Bioengineering and Neurology, and she is Co-President of GABE at Penn.

 

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Toothbrushing Microbots on Walter Isaacson’s ‘Trailblazers’ Podcast

by Holly Wojcik

An infographic explains the magnetic and catalytic properties of the iron oxide nanoparticles and their assembly into bristle and floss-like forms. (Image: Melissa Pappas/Penn Engineering)

Penn Dental Medicine’s Michel Koo, Co-Director and Co-Founder of the Center for Innovation & Precision Dentistry (CiPD), was among a panel of researchers, engineers, and business founders invited to be part of a recent Trailblazers with Walter Isaacson Podcast titled “Dentistry: An Oral History of Disruption.”

Koo shared findings from one of his recent studies conducted in collaboration with Penn Engineering, which showed that a shapeshifting robotic microswarm can brush and floss teeth.

“Routine oral care is cumbersome and can pose challenges for many people, especially those who have a hard time cleaning their teeth” says Koo. “You have to brush your teeth, then floss your teeth, then rinse your mouth; it’s a manual, multistep process. The big innovation here is that the robotics system can do all three in a single, hands-free, automated way.”

The building blocks of these microrobots are iron oxide nanoparticles that have both catalytic and magnetic activity. Using a magnetic field, researchers could direct their motion and configuration to form either bristlelike structures that sweep away dental plaque from the broad surfaces of teeth, or elongated strings that can slip between teeth like a length of floss.

“Nanoparticles can be shaped and controlled with magnetic fields in surprising ways,” says Edward Steager, a senior research investigator at Penn Engineering and co-corresponding author. “We form bristles that can extend, sweep, and even transfer back and forth across a space, much like flossing. The way it works is similar to how a robotic arm might reach out and clean a surface. The system can be programmed to do the nanoparticle assembly and motion control automatically.”

Listen to “Dentistry: An Oral History of Disruption” to learn more about Toothbrushing Microbots.

This story originally appeared in Penn Engineering Today.