Month: May 2020

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2020 Awards Season for Bioengineering Students

Each spring, the School of Engineering and Applied Science at the University of Pennsylvania gives out awards of special recognition to honor exceptional work by undergraduate and graduate students. The Department of Bioengineering is proud to announce the following awards given to students in the Class of 2020.

Bioengineering Professor and Chair Ravi Radhakrishnan says, “Congratulations to all the winners! I am so incredibly proud of your accomplishments and I thank you for enriching the Bioengineering environment with your invaluable contributions.” Keep reading below for a list of 2020 award recipients.

UNDERGRADUATE AWARDS:

Katharine Cocherl (BAS 2020), who completed a Bachelor of Applied Science degree in Bioengineering along with a second major in Cinema and Media Studies, was awarded the Ben and Bertha Gomberg Kirsch Prize. This competitive award is decided by the SEAS faculty from among the Engineering undergraduate body and distinguishes a member of the B.A.S. senior class who “in applying the flexibility of the program, has created a personal academic experience involving the most creative use of the resources of the University.”

The Hugo Otto Wolf Memorial Prize, awarded to one or more members of each department’s senior class, distinguishes students who meet with great approval of the professors at large through “thoroughness and originality” in their work. This year, BE chose to share the award between Jacqueline Peng (BSE 2020) and Vera Lee (BSE 2020). In addition to their majors, Jacqueline also minored in Computer Science and is pursuing a Master’s degree in Data Science and Vera minored in the Engineering Entrepreneurship program and is pursuing a Master’s degree in Robotics.

The Herman P. Schwan Award is decided by the Bioengineering Department and honors a graduating senior who demonstrates the “highest standards of scholarship and academic achievement.” The 2020 recipient of the Schwan Award is Alexander Silva (BSE 2020) who is also graduating with a minor in Economics.

Every year, several BE students are recognized with Exceptional Service Awards for their outstanding service to the University and their larger communities. Our winners this year are Arielle Stern (BSE 2020 with a Math minor), Lauren McLeod (BSE 2020), and Evan Paregol (BSE 2020 with an Entrepreneurship minor). Arielle and Evan are also currently in the Accelerated Master’s program, in Data Science and Bioengineering, respectively.

The Student Leadership Award is given annually to a student in Bioengineering who has demonstrated, through a combination of academic performance, service, leadership, and personal qualities, that he or she will be a credit to the Department, the School, and the University. The 2020 recipient of this award is Katherine Simms (BSE 2020 with a minor in Chemistry).

BE also distinguishes a single lab group (four students) 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 Alisa Bhakta (2020 dual degree BSE in Bioengineering and BS in Economics from Wharton), Gabriel Desantis (BSE 2020 with a minor in Math), Lauren McLeod (BSE 2020), and Caroline Raquel (2020 dual degree BSE in Bioengineering and BS in Economics from Wharton).

Of this year’s Bioengineering Senior Design teams, three groups were chosen for special recognition:

  • RelieVR with Nicole Chiou (BSE 2020 with a minor in Computer Science), Gabe Desantis (BSE 2020 with a minor in Math), Ben Habermeyer BSE 2020 with a minor in Computer Science), and Vera Lee (BSE 2020 with an Engineering Entrepreneurship minor). RelieVR also won second place at the 2020 Johns Hopkins Healthcare Design Competition and took home the Berkman Prize this past fall semester.
  • Relila with Alisa Bhakta (dual degree BSE and BS 2020), Alexander Connor (BSE 2020), Lauren McLeod (BSE 2020), Alexa Murray (BSE 2020 in Systems Science and Engineering), and Caroline Raquel (dual degree BSE and BS 2020). Relila also won second place at the annual M&T Program Lab Integration Awards summit.
  • SchistoSpot with Alec Bayliff (dual degree BAS and BS in Economics 2020), Bram Bruno (BAS 2020), Justin Swirbul (BSE 2020 in Computer Science), and Vishal Tien (BSE 2020). SchistoSpot also won the Pioneer Award at the annual Rothberg Catalyzer Makerthon.

Research for these projects was conducted in the George H. Stephenson Foundation Education Laboratory & Bio-Maker Space. The abstracts and presentation videos for each of the 2020 Senior Design Competition winners can be viewed on the BE Labs website.

Additionally, two graduating BAS seniors were awarded prizes for Best Senior Thesis:

  • Katharine Cocherl (BAS 2020 in Bioengineering and Cinema and Media Studies) for her paper “Bioethical Assessments of Film Portrayals of the Opioid Epidemic and Its Relationship with Public Discourse and Policy from the 1990s to Present.” “Insightful, original, and wide-reaching, her study of films related to the opioid epidemic in the U.S. the past 25 years was one of the best senior theses I have advised at Penn the past 15 years, ” says Katharine’s advisor Lance Wahlert, Assistant Professor of Medical Ethics & Health Policy, Program Director of the Master of Bioethics
  • Gayatri Maria Schur (BAS 2020 with a minor in Music) for her paper titled “In Vivo Assessment of OXPHOS Capacity Using 3T CrCEST MRI in Adults and Children with Friedrich’s Ataxia.” Her advisor, Shana McCormack, Assistant Professor of Pediatrics in the Perelman School of Medicine, says that Gayatri’s “work has required that she communicate with collaborators across a variety of disciplines, and has also included interaction with the community of patients we study, and she has excelled here.”

GRADUATE AWARDS:

Master’s student Kayla Prezelski was awarded an Outstanding Teaching Award for students. Kayla served as a TA for the Department of Bioengineering’s two-semester Senior Design courses (BE 495/496).

The following Master’s students were awarded recognition for their Outstanding Research:

  • Linghan Mei – advisor Andrew Tsourkas, Ph.D., Professor of Bioengineering
  • Ayush Aditya Pal – advisor Lukasz Bugaj, Ph.D., Assistant Professor of Bioengineering
  • Robert Pierson – Independent Study advisor Brian Litt, M.D., Professor of Neurology, Neurosurgery, and Bioengineering, and Thesis advisors Insup Lee, Ph.D., Cecilia Fitler Moore of Computer and Information Science and Electrical and Systems Engineering, and James Weimer, Ph.D. Research Assistant Professor of Computer and Information Science
  • Tianjia Zhu – advisor Hao Huang, Ph.D., Research Associate Professor of Radiology in the Perelman School of Medicine

And finally, The Solomon R. Pollack Award for Excellence in Graduate Bioengineering is given annually to the most deserving Bioengineering graduate student who has successfully completed research that is original and recognized as being at the forefront of its field. This year, that award goes to Jonathan Beagan, Ph.D. who recently defended his thesis. Jon conducted his research in the 3D Epigenomics and Systems Neurobiology Lab overseen by Jennifer Phillips-Cremins, Ph.D., Associate Professor of Bioengineering. Research related to Jon’s award-winning doctoral thesis was recently published in the journal Nature Neuroscience. In addition to this prestigious award, Jon was also named a National Science Foundation Graduate Research Fellow during his time at Penn. Jon’s collaborations with Dr. Cremins have been covered several times on the BE blog. “Jon is an excellent researcher — simultaneously rigorous and creative,” says Dr. Cremins. “He has been a force in the lab — reading the literature voraciously, teaching other students, and executing/designing experiments meticulously. Beyond his natural talent, it is Jon’s personal qualities that make him stand out. He is a true leader, a team player, and one of the rare people that raises the bar for everyone around him.”

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

Congratulations once again to the award winners and to all graduating students on an outstanding year of scholarship and service!

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Connecting Communities Impacted by COVID-19

Three Penn seniors combine their desire to help with their unique skill sets to create Corona Connects, an online platform that connects volunteers with organizations in need of support.

Developed by (from left) Steven Hamel from the School of Engineering and Applied Science, Megan Kyne from the Wharton School, and Hadassah Raskas from the College of Arts & Sciences, Corona Connects bridges the gap between those looking for ways to help and organizations in need of support.

by Erica K. Brockmeier

With college campuses shut due to the novel coronavirus, many students with new-found time on their hands have found themselves asking, “What can I do to help?”

To connect people with organizations that need support, three students have combined their desire to help with the skills they’ve learned both inside and outside the classroom. Developed by Penn seniors Steven Hamel from the School of Engineering and Applied Science, Megan Kyne from the Wharton School, and Hadassah Raskas from the College of Arts & Sciences, the online platform Corona Connects bridges the gap between people looking for ways to help and organizations looking for support.

After returning to her hometown of Silver Spring, Maryland, Raskas was eager to find some way to help but noticed that it was difficult to find opportunities online. With friends and colleagues voicing similar struggles, Raskas reached out to University of Maryland junior Elana Sichel and started putting together a list of organizations in need of help. Then, after reaching out on the Class of 2020 Facebook page about the project, Hamel, from Philadelphia, and Kyne, from Pittsburgh, offered their support to get an online platform up and running.

The team of students quickly realized that there was both a large number of individuals who wanted to find ways to help alongside an unprecedented level of need from numerous types of organizations. “We knew there was need, and we knew there was an availability of people, but the connection was missing, so we built Corona Connects to bridge this gap,” says Raskas.

Continue reading on Penn Today.

Steven Hamel graduated with his B.S.E. in Bioengineering and a Math minor in in 2020 and is currently pursuing a Master’s in Bioengineering.

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To Err is Human, to Learn, Divine

Researchers develop a new model for how the brain processes complex information: by striking a balance between accuracy and simplicity while making mistakes along the way.

By Erica K. Brockmeier

New research finds that the human brain detects patterns in complex networks by striking a balance between simplicity and complexity, much like how a pointillist painting can be viewed up close to see the finer details or from a distance to see its overall structure.

The human brain is a highly advanced information processor composed of more than 86 billion neurons. Humans are adept at recognizing patterns from complex networks, such as languages, without any formal instruction. Previously, cognitive scientists tried to explain this ability by depicting the brain as a highly optimized computer, but there is now discussion among neuroscientists that this model might not accurately reflect how the brain works.

Now, Penn researchers have developed a different model for how the brain interprets patterns from complex networks. Published in Nature Communications, this new model shows that the ability to detect patterns stems in part from the brain’s goal to represent things in the simplest way possible. Their model depicts the brain as constantly balancing accuracy with simplicity when making decisions. The work was conducted by physics Ph.D. student Christopher Lynn, neuroscience Ph.D. student Ari Kahn, and Danielle Bassett, J. Peter Skirkanich Professor in the departments of Bioengineering and Electrical and Systems Engineering.

This new model is built upon the idea that people make mistakes while trying to make sense of patterns, and these errors are essential to get a glimpse of the bigger picture. “If you look at a pointillist painting up close, you can correctly identify every dot. If you step back 20 feet, the details get fuzzy, but you’ll gain a better sense of the overall structure,” says Lynn.

To test their hypothesis, the researchers ran a set of experiments similar to a previous study by Kahn. That study found that when participants were shown repeating elements in a sequence, such as A-B-C-B, etc., they were automatically sensitive to certain patterns without being explicitly aware that the patterns existed. “If you experience a sequence of information, such as listening to speech, you can pick up on certain statistics between elements without being aware of what those statistics are,” says Kahn.

To understand how the brain automatically understands such complex associations within sequences, 360 study participants were shown a computer screen with five gray squares corresponding to five keys on a keyboard. As two of the five squares changed from gray to red, the participants had to strike the computer keys that corresponded to the changing squares. For the participants, the pattern of color-changing squares was random, but the sequences were actually generated using two kinds of networks.

The researchers found that the structure of the network impacted how quickly the participants could respond to the stimuli, an indication of their expectations of the underlying patterns. Responses were quicker when participants were shown sequences that were generated using a modular network compared to sequences coming from a lattice network.

Continue reading on Penn Today.

This paper was also profiled on the website Big Think.

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Penn Postdoctoral Researcher David Lydon-Staley Appointed Assistant Professor in Annenberg School for Communication

by Sophie Burkholder

A Penn Bioengineer will soon join the Annenberg School for Communication as an Assistant Professor of Communication. David Lydon-Staley, Ph.D., recently completed two years as a Postdoctoral Researcher in Penn’s Complex Systems Lab, led by Danielle Bassett, Ph.D., the J. Peter Skirkanich Professor of Bioengineering and Electrical and Systems Engineering.

David Lydon-Staley, Ph.D.

Lydon-Staley started out studying English and Psychology in his undergraduate education, going on to pursue a Ph.D. from Penn State University in Human Development and Family Studies. What brought him to Bassett’s lab was his interest in using cognitive neuroscience to understand the brain patterns and behaviors behind substance abuse and addiction. There, Lydon-Staley examined networks of nicotine withdrawal behaviors, how those behaviors impact each other, and what information they might hold about how to help smokers in their quit attempts. “David’s breadth of interest is only rivalled by his expansive expertise and bottomless enthusiasm,” says Bassett. “I feel incredibly lucky to have had the chance to work with him.”

In his new role at Annenberg, Lydon-Staley will launch the Addiction, Health, and Adolescence Lab, or “AHA!” for short. “My recent work examines engagement with new media during the course of daily life, and how the information sought and encountered relates to both curiosity and substance use,” he says. Lydon-Staley’s new lab will use methods like experience-sampling and functional Magnetic Resonance Imaging to understand brain and behavior, while drawing on theories and tools from  communication, psychology, cognitive neuroscience, network science, and more.

Even though Lydon-Staley will be working out of a new school at Penn, he still has plans to continue collaborating with the Bassett Lab. One ongoing project he has with the lab involves studying how curiosity works in everyday life, and another looks at moment-to-moment patterns of cigarette withdrawal in daily smokers. “Working in the Bassett Lab gave me the confidence and ability to stretch my wings, chase ideas across traditional disciplinary lines, learn new skills, and collaborate with creative and capable scientists every day,” says Lydon-Staley. Those are opportunities he hopes to keep chasing and fostering in his new position.

Beyond continuing his prior research from a communication-based angle, Lydon-Staley is also excited to develop new classes in the Annenberg School. “Annenberg is a very special place. It is an active school, with frequent seminars and many vibrant research centers,” he says. Informed and inspired by the breadth of research from Annenberg scholars, Lydon-Staley hopes that he can create classes that focus on the psychology of time and timing in everyday life—topics that he spends a lot of time thinking about himself.

Above all, Lydon-Staley is excited by the opportunity to stay at Penn and continue the kind of versatile and multi-faceted studies that have been the bedrock of his research so far. He hopes to continue expanding his previous work with not only the Engineering School, but the School of Medicine and the Graduate School of Education as well. “The opportunities for interdisciplinary collaboration at Penn are unrivaled, and I am constantly in awe of the quality of students here.”

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Language in Tweets Offers Insight Into Community-level Well-being

In a Q&A, researcher Lyle Ungar discusses why counties that frequently use words like ‘love’ aren’t necessarily happier, plus how techniques from this work led to a real-time COVID-19 wellness map.

By Michele W. Berger

Lyle Ungar, Ph.D. (Photo: Eric Sucar)

People in different areas across the United States reacted differently to the threat of COVID-19. Some imposed strict restrictions, closing down most businesses deemed nonessential; others remained partially open.

Such regional distinctions are relatively easy to quantify, with their effects generally understandable through the lens of economic health. What’s harder to grasp is the emotional satisfaction and happiness specific to each place, a notion ’s has been working on for more than five years.

In 2017, the group published the , a free, interactive tool that displays characteristics of well-being by county based on Census data and billions of tweets. Recently, WWBP partnered with ’s Center for Digital Health to create a , which reveals in real time how people across the country perceive COVID-19 and how it’s affecting their mental health.

That map falls squarely in line with a paper published this week in the by computer scientist , one of the principal investigators of the World Well-Being Project, and colleagues from Stanford University, Stony Brook University, the National University of Singapore, and the University of Melbourne.

By analyzing 1.5 billion tweets and controlling for common words like “love” or “good,” which frequently get used to connote a missing aspect of someone’s life rather than a part that’s fulfilled, the researchers found they could discern subjective well-being at the county level. “We have a long history of collecting people’s language and asking people who are happier or sadder what words they use on Facebook and on Twitter,” Ungar says. “Those are mostly individual-level models. Here, we’re looking at community-level models.”

In a conversation with Penn Today, Ungar describes the latest work, plus how it’s useful in the time of COVID-19 and social distancing.

Read Ungar’s Q&A at .

Dr. Lyle Ungar is a Professor of Computer and Information Science and a member of the Department of Bioengineering Graduate Group.

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En Garde!: The Fencers of Penn Engineering

By Patricia Hutchings

Senior Akshay Malhotra (center) pumps up Penn Fencing. He is one of several Engineering students on the team, including senior Alexandre Amice, sophomores Kristina Khaw and Jerry Wu, and freshman Enzo Bergamo. (Photos courtesy of Penn Athletics)

What were the chances? Captivated by a fencing demonstration at his elementary school in St. Louis, MO, an American-born son of French parentage went straight home and announced his desire to learn the sport. Meanwhile, an internationally recognized fencer, who had once coached the Egyptian National team, had settled in St. Louis and was busy making plans to establish a fencing club there. Two dreams collided: The Fencers Academy of St. Louis took shape and the boy learned to fence, and to fence well. Meet Alexandre Amice (BSE’20, MSE’20).

Amice’s passion for the sport remained strong throughout high school, and the year he walked on to the Penn Fencing Team as a freshman engineering student, he was voted by the captains and coaches as Most Dedicated Fencer.

Of the three types of fencing swords: the épée, the foil and the sabre, Amice’s weapon of choice is the light and flexible foil. In foil bouts, the target area for scoring touches is limited to the torso, requiring the fencers to remain closely engaged and in constant motion. Amice characterizes his fencing style as “athletic,” with his build and skillset well-matched with his weapon.

Amice cites his measured and deliberate competition strategy as useful in his intellectual life. As he concurrently works toward his undergraduate degree in electrical engineering and mathematics and a master’s in robotics, Amice clearly is not one to waste energy.

The sabre is the weapon of choice for Penn World Scholar and freshman electrical engineering major, Enzo Bergamo. At an early age, he determined the discipline of sabre fencing to be “the cool one,” with its reputation for quickness, aggression, slashing touches and split-second decision making. Compared in speed and spirit to Formula 1 racing by Olympic sabre fencer Daryl Homer, the target area for the discipline is the entire torso, the head, and the arms up to the wrist.

Andy Ma, Penn’s head fencing coach, also serves as sabre coach, and Bergamo feels fortunate to be able to work with him one-on-one in lessons once or twice a week. After twelve years of high-level fencing in Sao Paulo, Brazil, Bergamo attributes his renewed love for the sport to Ma’s influence and attentive demeanor. For Bergamo, being able to face down frustration and maintain physical and emotional balance are valuable attributes, with or without a sword in his hand.

Bergamo notes that he and his teammates are known as “student athletes,” not “athlete students,” and, with an electrical engineering concentration in data science and a minor in computer and information science, he envisions a master’s degree in his future. Bergamo’s overarching goal, he states, is “making a positive impact in my home country.”

At 5’3,” Kristina Khaw, a sophomore bioengineering major, fences with the épée, the largest and heaviest of fencing swords. Bouts in épée have been described as “aggressive defensive,” and points can be scored with touches anywhere on the body. Fencers train especially hard to perfect their skills in counter moves.

Obeying her mother’s directive to put her books aside in favor of exercise now and again, Khaw followed her sister, Kathryn (ENG’19), onto the fencing strip. She admits that, as a seventh grader, her greatest incentive to take up the sport was watching Kathryn delightedly stab their cousin with impunity in club practice.

As Khaw describes it, the muscle memory to succeed in épée came easily to her. Her stats provide proof: From the USA Fencing Nationals in the summer of her high school sophomore year, Khaw brought back to her Plainsboro, NJ, home the title of Division ll Women’s Épée Champion. Other notable wins and honors followed.

Khaw is a problem solver by nature and believes that her strategizing as a fencer creates new brain connections, enhancing her ability to think about things in new ways. Accordingly, she finds myriad applications of her athletic training to her life as a Penn Engineer.

“One touch at a time” is Khaw’s fencing mantra and, as she continues her studies on the pre-med track, her calm and logic will undoubtedly inform her journey.

Read the full story on the Penn Engineering blog.

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A Record 15 BE Students Receive 2020 NSF Graduate Research Fellowships

The Department of Bioengineering at Penn is incredibly proud of its fifteen current and future graduate student recipients of the 2020 National Science Foundation Graduate Research Fellowship Program (NSF GRFP). This total surpasses last year’s record of twelve students. In addition, one current student was selected for honorable mention and one additional incoming student has been named a Fullbright Scholar.

The prestigious NSF GRFP program recognizes and supports outstanding graduate students in NSF-supported fields. Further information about the program can be found on the NSF website. BE is thrilled to congratulate our excellent students on these well-deserved accolades! Continue reading below for a list of 2020 recipients and descriptions of their research.

Current Students:

William Benman

William Benman is a Ph.D. student in the lab of Assistant Professor of Bioengineering, Lukasz Bugaj. His work in the Bugaj lab focuses on developing novel optogenetic tools to control and study cell function.

Paul Gehret

Paul Gehret is a Ph.D. student and Ashton Fellow in the lab of Riccardo Gottardi, Assistant Professor of Pediatrics at the Perelman School of Medicine. Paul works on pediatric cartilage and airway tissue engineering for children with subglottic stenosis. He and his team apply classic tissue engineering principles to the airway.

Rebecca Haley

Rebecca Haley is a Ph.D. student in the lab of Michael J. Mitchell, Skirkanich Assistant Professor of Innovation in Bioengineering. Her current project aims to use polymer and/or lipid nanoparticles for the intracellular delivery of proteins. Successful delivery of proteins (such as antibodies) in this fashion may allow for targeting of previously undruggable intracellular targets.

Patrick John Mulcahey

Patrick John Mulcahey is a Research Assistant and Graduate Student in the Children’s Hospital of Philadelphia (CHOP) Epilepsy Research Lab of Douglas A. Coulter, Professor of Pediatrics at the Perelman School of Medicine. His work focuses on developing techniques that combine electrophysiology with two-photon excitation microscopy to study a potential biomarker of the seizure onset zone in models of drug-refractory epilepsy.

Catherine Porter

Catherine Porter is a Ph.D. student in the lab of Alex J. Hughes, Assistant Professor of Bioengineering. She is working on developing high-throughput methods to produce and characterize human-cell-derived kidney organoids for disease modeling and genetic screening. Currently, she is focused on engineering physicochemical control to improve organoid homogeneity.

Sarah Shepherd

Sarah Shepherd is a Ph.D. student who is co-advised in the Michael J. Mitchell lab and the lab of David Issadore, Associate Professor of Bioengineering and Electrical and Systems Engineering (ESE). Her research aims to combine microfabrication with biomaterial design of lipid nanoparticles to address major shortcomings in the field of nanomedicine. Currently, she is prototyping a scale-up microfluidic device to produce lipid nanoparticles for gene therapy.

Michael Tobin

Michael Tobin is a Ph.D. student in the lab of Dennis E. Discher, Robert D. Bent Professor of Chemical and Biomolecular Engineering (CBE), Bioengineering, and Mechanical Engineering and Applied Mechanics (MEAM). His current research examines phenomena leading to mechano-induced genomic variation in multiple cell subtypes. Through better understanding of characteristic pathways and subsequent cell responses, he hopes to improve treatments for malignant solid tumors.

John Viola, a Ph.D. student in the Hughes lab, was listed as an honorable mention.

Incoming Students:

Additionally, eight NSF GRFP honorees from other institutions will be joining our department in the fall of 2020. We congratulate them as well and look forward to welcoming them to Penn:

Finally, incoming Ph.D. student Dora Racca was awarded a Fullbright Scholarship. Dora will will have rotations in the BIOLines Laboratory of Dongeun (Dan) Huh, Associate Professor of Bioengineering and the McKay Orthopaedic Research Laboratory of Robert Mauck, Mary Black Ralston Professor of Orthopaedic Surgery and Professor of Bioengineering.

We would like to send congratulations once again to all our current and future graduate students on another year of outstanding research!

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Bomyi Lim Receives KIChE President Young Investigator

Bomyi Lim, Ph.D.

Bomyi Lim, Assistant Professor in the Department of Chemical Biomolecular Engineering, has been selected by the U.S. Chapter of the Korean Institute of Chemical Engineers (KIChE) as the recipient of the KIChE President Young Investigator Award. As a recipient of this Award, Lim will be invited to present a research talk at the KIChE Open Forum during the AIChE Conference.

KIChE is an organization that aims “to promote constructive and mutually beneficial interactions among Korean Chemical Engineers in the U.S. and facilitate international collaboration between engineers in the U.S. and Korea.”

Read more on the Penn Engineering blog. Dr. Lim is a member of the Department of Bioengineering Graduate Group.

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David Meaney on Responding to the COVID-19 Crisis

David F. Meaney, the Senior Associate Dean of Penn Engineering and Solomon R. Pollack Professor of Bioengineering, is known for his scholarship and innovation in neuroengineering and concussion science, his leadership as former Chair of the Department of Bioengineering, and for his marshaling of interdisciplinary research between Penn Engineering and the University’s health schools.

The Penn Engineering community has sprung into action over the course of the past few weeks in response to COVID-19. Meaney shared his perspective on those efforts and the ones that will come online as the pandemic continues to unfold.

David F. Meaney, Ph.D.

It is remarkable to think that a little more than a month ago I was saying an early goodbye to students for their spring break. In the first week of March, I was wishing everyone a happy and safe break, emphasizing safe, not knowing how prophetic that word would be. I was also looking forward to my own spring break, traveling for the first time in many years over this part of the academic calendar.

And then our campus — and world — changed.

COVID-19 is among us, in ways that we can’t exactly measure. It is among us in ways that we feel — we probably know someone that has tested positive for the virus, and others that are living with someone that is sick. And we all realize the virus will be with us for some time; the exact amount we don’t know.

Which brings up the question — what can we do to fight this pandemic? Many of us are trying to find ways to keep our connections with others vibrant and strong in the world of Zoom, Hangout, and BlueJeans. That is important. Let me also say that I can’t wait to reconnect with everyone in person, and close my laptop for a week.

But staying connected is what everyone should do. I often think about what can engineers do?

As the Senior Associate Dean, I want to let you know what I’m seeing on a quiet, but not shuttered, Penn campus. Examples of our response to the pandemic include our faculty designing personal protective equipment for health care workers, and our students, faculty and staff volunteering to assemble it. Other faculty are inventing COVID-19 test kits that can be completed at home, with the results available in less than an hour. Professors are sharing their creative mask designs with the world, for free, to make sure that we can all feel comfortable walking outside. And yet others that are collaborating to make a vaccine that will help us put COVID-19 behind us, permanently.

All of this is happening at speeds we have never seen before. Ideas move to prototypes and testing in days, not months, and to product in a week. We are not alone — our colleagues across campus are working at light speed to generate better tests, treatments, and models to fight COVID-19. This time, Nature has given us the problem. Time for us to solve it.

It’s more important than ever that we amplify one another’s voices and we want to hear from you. Learn more about Penn Engineering’s Share Your Story project here, and read entries here. You can also keep up-to-date on Penn Engineering’s pandemic response efforts here.

Originally posted on the Penn Engineering blog. Media contact Evan Lerner.

Learn more about the Department of Bioengineering’s COVID-19 projects in our recent blog post.

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The Optimal Immune Repertoire for Bacteria

by Erica K. Brockmeier

Transmission electron micrograph of multiple bacteriophages, viruses that infect bacteria, attached to a cell wall. New research describes how bacteria can optimize their “memory” of past viral infections in order to launch an effective immune response against a new invader. (Image: Graham Beards)

Before CRISPR became a household name as a tool for gene editing, researchers had been studying this unique family of DNA sequences and its role in the bacterial immune response to viruses. The region of the bacterial genome known as the CRISPR cassette contains pieces of viral genomes, a genomic “memory” of previous infections. But what was surprising to researchers is that rather than storing remnants of every single virus encountered, bacteria only keep a small portion of what they could hold within their relatively large genomes.

Work published in the Proceedings of the National Academy of Sciences provides a new physical model that explains this phenomenon as a tradeoff between how much memory bacteria can keep versus how efficiently they can respond to new viral infections. Conducted by researchers at the American Physical Society, Max Planck Institute, University of Pennsylvania, and University of Toronto, the model found an optimal size for a bacteria’s immune repertoire and provides fundamental theoretical insights into how CRISPR works.

In recent years, CRISPR has become the go-to biotechnology platform, with the potential to transform medicine and bioengineering. In bacteria, CRISPR is a heritable and adaptive immune system that allows cells to fight viral infections: As bacteria come into contact with viruses, they acquire chunks of viral DNA called spacers that are incorporated into the bacteria’s genome. When the bacteria are attacked by a new virus, spacers are copied from the genome and linked onto molecular machines known as Cas proteins. If the attached sequence matches that of the viral invader, the Cas proteins will destroy the virus.

Bacteria have a different type of immune system than vertebrates, explains senior author Vijay Balasubramanian, but studying bacteria is an opportunity for researchers to learn more about the fundamentals of adaptive immunity. “Bacteria are simpler, so if you want to understand the logic of immune systems, the way to do that would be in bacteria,” he says. “We may be able to understand the statistical principles of effective immunity within the broader question of how to organize an immune system.”

Read more on Penn Today.

Vijay Balasubramanian is the Cathy and Marc Lasry Professor in the Department of Physics and Astronomy in the School of Arts & Sciences at the University of Pennsylvania and a member of the Department of Bioengineering Graduate Group. 

This research was supported by the Simons Foundation (Grant 400425) and National Science Foundation Center for the Physics of Biological Function (Grant PHY-1734030).