Penn Bioengineering and COVID-19

A message from Penn Bioengineering Professor and Chair Ravi Radhakrishnan:

In response to the unprecedented challenges presented by the global outbreak of the novel coronavirus SARS-CoV-2, Penn Bioengineering’s faculty, students, and staff are finding innovative ways of pivoting their research and academic projects to contribute to the fight against COVID-19. Though these projects are all works in progress, I think it is vitally important to keep those in our broader communities informed of the critical contributions our people are making. Whether adapting current research to focus on COVID-19, investing time, technology, and equipment to help health care infrastructure, or creating new outreach and educational programs for students, I am incredibly proud of the way Penn Bioengineering is making a difference. I invite you to read more about our ongoing projects below.

RESEARCH

Novel Chest X-Ray Contrast

David Cormode, Associate Professor of Radiology and Bioengineering

Nanomedicine and Molecular Imaging Lab

Peter Noel, Assistant Professor of Radiology and BE Graduate Group Member

Laboratory for Advanced Computed Tomography Imaging

The Cormode and Noel labs are working to develop dark-field X-ray imaging, which may prove very helpful for COVID patients. It involves fabricating diffusers that incorporate gold nanoparticles to modify the X-ray beam. This method gives excellent images of lung structure. Chest X-ray is being used on the front lines for COVID patients, and this could potentially be an easy to implement modification of existing X-ray systems. The additional data give insight into the health state of the microstructures (alveoli) in the lung. This new contrast mechanics could be an early insight into the disease status of COVID-19 patients. For more on this research, see Cormode and Noel’s chapter in the forthcoming volume Spectral, Photon Counting Computed Tomography: Technology and Applications, edited by Katsuyuki Taguchi, Ira Blevis, and Krzysztof Iniewski (Routledge 2020).

Immunotherapy

Michael J. Mitchell, Skirkanich Assistant Professor of Innovation in Bioengineering

Mitchell Lab

Mike Mitchell is working with Saar Gill (Penn Medicine) on engineering drug delivery technologies for COVID-19 mRNA vaccination. He is also developing inhalable drug delivery technologies to block COVID-19 internalization into the lungs. These new technologies are adaptations of prior research published Volume 20 of Nano Letters (“Ionizable Lipid Nanoparticle-Mediated mRNA Delivery for Human CAR T Cell Engineering” January 2020) and discussed in Volume 18 of Nature Reviews Drug Discovery (“Delivery Technologies for Cancer Immunotherapy” January 2019).

Respiratory Distress Therapy Modeling

Ravi Radhakrishnan, Professor, and Chair of Bioengineering and Professor of Chemical and Biomolecular Engineering

Radhakrishnan Lab

Computational Models for Targeting Acute Respiratory Distress Syndrome (ARDS). The severe forms of COVID-19 infections resulting in death proceeds by the propagation of the acute respiratory distress syndrome or ARDS. In ARDS, the lungs fill up with fluid preventing oxygenation and effective delivery of therapeutics through the inhalation route. To overcome this major limitation, delivery of antiinflammatory drugs through the vasculature (IV injection) is a better approach; however, the high injected dose required can lead to toxicity. A group of undergraduate and postdoctoral researchers in the Radhakrishnan Lab (Emma Glass, Christina Eng, Samaneh Farokhirad, and Sreeja Kandy) are developing a computational model that can design drug-filled nanoparticles and target them to the inflamed lung regions. The model combines different length-scales, (namely, pharmacodynamic factors at the organ scale, hydrodynamic and transport factors in the tissue scale, and nanoparticle-cell interaction at the subcellular scale), into one integrated framework. This targeted approach can significantly decrease the required dose for combating ARDS. This project is done in collaboration with Clinical Scientist Dr. Jacob Brenner, who is an attending ER Physician in Penn Medicine. This research is adapted from prior findings published in Volume 13, Issue 4 of Nanomedicine: Nanotechnology, Biology and Medicine: “Mechanisms that determine nanocarrier targeting to healthy versus inflamed lung regions” (May 2017).

Diagnostics

Sydney Shaffer, Assistant Professor of Bioengineering and Pathology and Laboratory Medicine

Syd Shaffer Lab

Arjun Raj, Professor of Bioengineering

Raj Lab for Systems Biology

David Issadore, Associate Professor of Bioengineering and Electrical and Systems Engineering

Issadore Lab

Arjun Raj, David Issadore, and Sydney Shaffer are working on developing an integrated, rapid point-of-care diagnostic for SARS-CoV-2 using single molecule RNA FISH. The platform currently in development uses sequence specific fluorescent probes that bind to the viral RNA when it is present. The fluorescent probes are detected using a iPhone compatible point-of-care reader device that determines whether the specimen is infected or uninfected. As the entire assay takes less than 10 minutes and can be performed with minimal equipment, we envision that this platform could ultimately be used for screening for active COVID19 at doctors’ offices and testing sites. Support for this project will come from a recently-announced IRM Collaborative Research Grant from the Institute of Regenerative Medicine with matching funding provided by the Departments of Bioengineering and Pathology and Laboratory Medicine in the Perelman School of Medicine (PSOM) (PI’s: Sydney Shaffer, Sara Cherry, Ophir Shalem, Arjun Raj). This research is adapted from findings published in the journal Lab on a Chip: “Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip” (Issue 15, 2015). See also United States Provisional Patent Application Serial No. 14/900,494 (2014): “Methods for rapid ribonucleic acid fluorescence in situ hybridization” (Inventors: Raj A., Shaffer S.M., Issadore D.).

HEALTH CARE INFRASTRUCTURE

Penn Health-Tech Coronavirus COVID-19 Collaborations

Brian Litt, Professor of Bioengineering, Neurology, and Neurosurgery

Litt Lab

In his role as one of the faculty directors for Penn Health-Tech, Professor Brian Litt is working closely with me to facilitate all the rapid response team initiatives, and in helping to garner support the center and remove obstacles. These projects include ramping up ventilator capacity and fabrication of ventilator parts, the creation of point-of-care ultrasounds and diagnostic testing, evaluating processes of PPE decontamination, and more. Visit the Penn Health-Tech coronavirus website to learn more, get involved with an existing team, or submit a new idea.

BE Labs COVID-19 Efforts

BE Educational Labs Director Sevile Mannickarottu & Staff

BE Educational Labs staff members Dana Abulez (BE ’19, Master’s BE ’20) and Matthew Zwimpfer (MSE ’18, Master’s MSE ’19) take shifts to laser-cut face shields.

The George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace staff have donated their PPE to Penn Medicine. Two staff members (Dana Abulez, BE ’19, Master’s BE ’20 and Matthew Zwimpfer, MSE ’18, Master’s MSE ’19) took shifts to laser-cut face shields in collaboration with Penn Health-Tech. Dana and Matthew are also working with Dr. Matthew Maltese on his low-cost ventilator project (details below).

Low-Cost Ventilator

Matthew Maltese, Adjunct Professor of Medical Devices and BE Graduate Group Member

Children’s Hospital of Philadelphia Center for Injury Research and Prevention (CIRP)

Dr. Maltese is rapidly developing a low-cost ventilator that could be deployed in Penn Medicine for the expected surge, and any surge in subsequent waves. This design is currently under consideration by the FDA for Emergency Use Authorization (EUA). This example is one of several designs considered by Penn Medicine in dealing with the patient surge.

Face Shields

David F. Meaney, Solomon R. Pollack Professor of Bioengineering and Senior Associate Dean

Molecular Neuroengineering Lab

Led by David Meaney, Kevin Turner, Peter Bruno and Mark Yim, the face shield team at Penn Health-Tech is working on developing thousands of rapidly producible shields to protect and prolong the usage of Personal Protective Equipment (PPE). Learn more about Penn Health-Tech’s initiatives and apply to get involved here.

Update 4/29/20: The Penn Engineering community has sprung into action over the course of the past few weeks in response to COVID-19. Dr. Meaney shared his perspective on those efforts and the ones that will come online as the pandemic continues to unfold. Read the full post on the Penn Engineering blog.

OUTREACH & EDUCATION

Student Community Building

Yale Cohen, Professor of Otorhinolaryngology, Department of Psychology, BE Graduate Group Member, and BE Graduate Chair

Auditory Research Laboratory

Yale Cohen, and Penn Bioengineering’s Graduate Chair, is working with Penn faculty and peer institutions across the country to identify intellectually engaging and/or community-building activities for Bioengineering students. While those ideas are in progress, he has also worked with BE Department Chair Ravi Radhakrishnan and Undergraduate Chair Andrew Tsourkas to set up a dedicated Penn Bioengineering slack channel open to all Penn Bioengineering Undergrads, Master’s and Doctoral Students, and Postdocs as well as faculty and staff. It has already become an enjoyable place for the Penn BE community to connect and share ideas, articles, and funny memes.

Undergraduate Course: Biotechnology, Immunology, Vaccines and COVID-19 (ENGR 35)

Daniel A. Hammer, Alfred G. and Meta A. Ennis Professor of Bioengineering and Chemical and Biomolecular Engineering

The Hammer Lab

This Summer Session II, Professor Dan Hammer and CBE Senior Lecturer Miriam R. Wattenbarger will teach a brand-new course introducing Penn undergraduates to a basic understanding of biological systems, immunology, viruses, and vaccines. This course will start with the fundamentals of biotechnology, and no prior knowledge of biotechnology is necessary. Some chemistry is needed to understand how biological systems work. The course will cover basic concepts in biotechnology, including DNA, RNA, the Central Dogma, proteins, recombinant DNA technology, polymerase chain reaction, DNA sequencing, the functioning of the immune system, acquired vs. innate immunity, viruses (including HIV, influenza, adenovirus, and coronavirus), gene therapy, CRISPR-Cas9 editing, drug discovery, types of pharmaceuticals (including small molecule inhibitors and monoclonal antibodies), vaccines, clinical trials. Some quantitative principles will be used to quantifying the strength of binding, calculate the dynamics of enzymes, writing and solving simple epidemiological models, methods for making and purifying drugs and vaccines. The course will end with specific case study of coronavirus pandemic, types of drugs proposed and their mechanism of action, and vaccine development.
Update 4/29/20: Read the Penn Engineering blog post on this course published April 27, 2020.

Neuromatch Conference

Konrad Kording, Penn Integrates Knowledge University Professor of Bioengineering, Neuroscience, and Computer and Information Science

Kording Lab

Dr. Kording facilitated Neuromatch 2020, a large virtual neurosciences conferences consisting of over 3,000 registrants. All of the conference talk videos are archived on the conference website and Dr. Kording has blogged about what he learned in the course of running a large conference entirely online. Based on the success of Neuromatch 1.0, the team are now working on planning Neuromatch 2.0, which will take place in May 2020. Dr. Kording is also working on facilitating the transition of neuroscience communication into the online space, including a weekly social (#neurodrinking) with both US and EU versions.

Neuromatch Academy

Konrad Kording, Penn Integrates Knowledge University Professor of Bioengineering, Neuroscience, and Computer and Information Science

Kording Lab

Dr. Kording is working to launch the Neuromatch Academy, an open, online, 3-week intensive tutorial-based computational neuroscience training event (July 13-31, 2020). Participants from undergraduate to professors as well as industry are welcome. The Neuromatch Academy will introduce traditional and emerging computational neuroscience tools, their complementarity, and what they can tell us about the brain. A main focus is not just on using the techniques, but on understanding how they relate to biological questions. The school will be Python-based making use of Google Colab. The Academy will also include professional development / meta-science, model interpretation, and networking sessions. The goal is to give participants the computational background needed to do research in neuroscience. Interested participants can learn more and apply here.

Journal of Biomedical Engineering Call for Review Articles

Beth Winkelstein, Vice Provost for Education and Eduardo D. Glandt President’s Distinguished Professor of Bioengineering

Spine Pain Research Lab

The American Society of Medical Engineers’ (ASME) Journal of Biomechanical Engineering (JBME), of which Dr. Winkelstein is an Editor, has put out a call for review articles by trainees for a special issue of the journal. The call was made in March 2020 when many labs were ramping down, and trainees began refocusing on review articles and remote work. This call continues the JBME’s long history of supporting junior faculty and trainees and promoting their intellectual contributions during challenging times.
Update 4/29/20: CFP for the special 2021 issue here.

Are you a Penn Bioengineering community member involved in a coronavirus-related project? Let us know! Please reach out to ksas@seas.upenn.edu.

April 10, 2020

Danielle Bassett Named AIMBE Fellow

Danielle Bassett, J. Peter Skirkanich Professor of Bioengineering, has been named an American Institute for Medical and Biological Engineering (AIMBE) Fellow.

Election to the AIMBE College of Fellows is among the highest professional distinctions accorded to a medical and biological engineer. College membership honors those who have made outstanding contributions to “engineering and medicine research, practice, or education” and to “the pioneering of new and developing fields of technology, making major advancements in traditional fields of medical and biological engineering, or developing/implementing innovative approaches to bioengineering education.”

Bassett was nominated, reviewed, and elected by peers and members of the College of Fellows for “significant contributions to the application of neural network theory for understanding both physio and patho-physiological brain function.”

As a result of health concerns, AIMBE’s annual meeting and induction ceremony scheduled for March 29–30, 2020, was cancelled. Under special procedures, Bassett was remotely inducted along with 156 colleagues who make up the AIMBE College of Fellows Class of 2020.

Originally posted on the Penn Engineering blog.

April 3, 2020April 3, 2020

Five Tips to Stay Positive and Healthy During Social Isolation

Though the coronavirus situation is changing daily, even hourly, by now the need for physical separation from those not in your household is clear. That doesn’t mean it’s easy, says Penn psychologist Melissa Hunt.

“We’re social animals,” says Hunt, associate director of clinical training in Penn’s Psychology Department. “We have an entire neuroendocrine system that responds to touch and social proximity with people we care about, that contributes to our sense of well-being and connection in the world. Losing out on that is really hard.”

It’s also not something we’ve really been asked to do before, says Lyle Ungar, a Penn computer scientist who is part of the World Well-Being Project, an initiative that uses social media language to measure psychological well-being and physical health. “This is an experiment on a scale that we’ve never seen in the United States,” he says.

Ungar and Hunt offer some suggestions to stay positive and healthy in the face of this new social isolation.

1. Maintain a connection with the people you love, even if it can’t be a physical one.

“Social distance does not mean no social contact,” Ungar says. Psychologically, face-to-face conversations are best, but right now they’re not likely possible. Instead, Ungar suggests video calls. “They’re second best in terms of emotional bonding,” he says. “Phone calls aren’t as good as video chats, and texting is even worse. But of course, being totally isolated is the worst.”

Read the full five tips at Penn Today. Media contact Michele W. Berger.

Melissa G. Hunt is the associate director of clinical training in the Department of Psychology in the School of Arts and Sciences at the University of Pennsylvania.

Lyle Ungar is a professor in the departments of Bioengineering and Computer and Information Science in the School of Engineering and Applied Science, in the Graduate Group in Genomics and Computational Biology in the Perelman School of Medicine, in the Department of Operations, Information, and Decisions in the Wharton School, and in the Department of Psychology in the School of Arts and Sciences.

March 25, 2020March 25, 2020

The Optical Society Names Nader Engheta the 2020 Max Born Award Recipient

The Optical Society (OSA) has named Nader Engheta, H. Nedwill Ramsey Professor in the Department of Electrical and Systems Engineering, as the 2020 recipient of the Max Born Award.

Engheta, who also has appointments in the departments of Bioengineering and Materials Science and Engineering, is honored for pioneering contributions to optical metamaterials and nanoscale optics.

“The Born Award recognizes Nader Engheta’s exceptional contributions to the fields of metamaterials, transformation optics and nanophotonics,” said 2020 OSA President Stephen D. Fantone, founder and president of Optikos Corporation. “This honor is emblematic of the pioneering work he has done in near-zero index metamaterials.”

Read the full story on the Penn Engineering blog.

February 17, 2020February 17, 2020

Penn Nanoparticles are Less Toxic to T Cells Engineered for Cancer Immunotherapy

An artist’s illustration of nanoparticles transporting mRNA into a T cell (blue), allowing the latter to express surface receptors that recognize cancer cells (red). (Credit: Ryan Allen, Second Bay Studios)

New cancer immunotherapies involve extracting a patient’s T cells and genetically engineering them so they will recognize and attack tumors. This type of therapy is not without challenges, however. Engineering a patient’s T cells is laborious and expensive. And when successful, the alterations to the immune system immediately make patients very sick for a short period of time, with symptoms including fever, nausea and neurological effects.

Now, Penn researchers have demonstrated a new engineering technique that, because it is less toxic to the T cells, could enable a different mechanism for altering the way they recognize cancer, and could have fewer side effects for patients.

The technique involves ferrying messenger RNA (mRNA) across the T cell’s membrane via a lipid-based nanoparticle, rather than using a modified HIV virus to rewrite the cell’s DNA. Using the former approach would be preferable, as it only confers a temporary change to the patient’s immune system, but the current standard method for getting mRNA past the cell membrane can be too toxic to use on the limited number of T cells that can be extracted from a patient.

Michael Mitchell, Margaret Billingsley, and Carl June

The researchers demonstrated their technique in a study published in the journal Nano Letters. It was led by Michael Mitchell, Skirkanich Assistant Professor of Innovation of bioengineering in the School of Engineering and Applied Science, and Margaret Billingsley, a graduate student in his lab.

They collaborated with one of the pioneers of CAR T therapy: Carl June, the Richard W. Vague Professor in Immunotherapy and director of the Center for Cellular Immunotherapies in the Abramson Cancer Center and the director of the Parker Institute for Cancer Immunotherapy at the Perelman School of Medicine.

Read more at Penn Engineering blog.

February 3, 2020January 31, 2020

Alex Hughes Receives the First MIRA Award of Penn SEAS

by Sophie Burkholder

We would like to congratulate Assistant Professor in Bioengineering Alex Hughes, Ph.D., on receiving the Maximizing Investigators’ Research Award (MIRA) from the National Institutes of Health (NIH), which funds investigators to create flexible and forward-thinking research programs. Hughes is the first recipient of this award in Penn’s School of Engineering and Applied Science, marking a major accomplishment for him and his lab.

The award recognizes Hughes’ efforts to create new tools used for tissue engineering, in particular by fusing concepts from developmental biology into tissue construction efforts. Hughes believes this approach will have impacts on fundamental understanding human disease, leading to new strategies to combat them. Hughes and his lab specifically focus on kidney disease. As Hughes says, “defects in the kidney and urinary tract account for up to a third of all birth defects.” Furthermore, because kidney development involves many different kinds of cell interactions, there’s a gap in understanding exactly how these defects occur.

Unlike other grants that focus on funding projects, the MIRA prioritizes the people behind the research, giving them funding as a sign of faith in the future work they’ll choose to do. “The MIRA has allowed us significant leeway to integrate several complementary approaches here,” Hughes says. Because of this flexibility, Hughes and his lab thinks it will allow them to reach for more innovative and risky approaches in their research, in the hopes that this will lead to a better understanding of kidney defects and modes of treatment for them.

January 29, 2020January 29, 2020

Danielle Bassett Among Science’s ‘Favorite Photos of 2019’

Among shots of a towering thunderstorm reaching into the stratosphere, the moon Daphnis peeking through Saturn’s rings, and an extremely close-up of a highly-endangered pangolin in Mozambique, one of Science’s favorite photos of 2019 was taken in Penn Engineering’s Raisler Lounge.

There, Danielle Bassett, J. Peter Skirkanich Professor in the Department of Bioengineering, poses underneath a giant visualization of the brain’s structural connections, projected on the wall behind her. Bassett’s research combines elements of physics, mathematics, engineering and neuroscience to provide a new look at how brain function arises from these networks of neurons.

Kelly Servick of Science profiled Bassett last year, revealing how a child whose parents discouraged her from attending college went on to become a pioneer in a highly interdisciplinary way of understanding the brain.

Read Bassett’s profile in Science here, and see the rest of the journal’s favorite photos of the year here.

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

January 28, 2020January 27, 2020

Ravi Radhakrishnan Named Chair of the Department of Bioengineering

The Department of Bioengineering would like to congratulate and welcome our new Chair, Dr. Ravi Radhakrishnan! Read the post below, originally posted on the Penn Engineering blog, and visit the Radhakrishnan Lab’s website for more information on his research.

Ravi Radhakrishnan has been named Chair of the Department of Bioengineering.

Radhakrishnan holds joint appointments in the Department of Bioengineering and the Department of Chemical and Biomolecular Engineering. He is a founding member and the current Director of the Penn Institute for Computational Science, as well as a member of the Penn Physical Sciences in Oncology Center, Institute for Translational Medicine and Therapeutics, and several graduate groups, including Materials Science and Engineering, Genomics and Computational Biology, and Biochemistry and Molecular Biophysics.

In addition to these roles at Penn, Radhakrishnan holds many editorial board positions in the research community, including Nature Publishing’s Scientific Reports.

Beyond being a passionate teacher and advocate for his students, Radhakrishnan’s research interests lie at the interface of chemical physics and molecular biology. His 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.

January 27, 2020January 27, 2020

David Meaney Named Senior Associate Dean of Penn Engineering

David F. Meaney, Solomon R. Pollack Professor of Bioengineering, has been named the Senior Associate Dean of Penn Engineering, effective January 1, 2020. This newly created leadership position will have oversight responsibilities in budget, space and infrastructure planning; facilities and research services; and will create and cultivate new interschool partnerships that will expand Penn Engineering’s footprint on campus.

Meaney is well known not only for his scholarship and innovation in neuroengineering and concussion science, but also for his leadership during his highly successful tenure as Chair of the Department of Bioengineering.

“Dave’s strong connections to the health schools will help strengthen Penn Engineering’s initiatives throughout campus,” says Vijay Kumar, Nemirovsky Family Dean of Penn Engineering. “He will have oversight of Penn Health-Tech, the Center for Engineering MechanoBiology and other efforts between engineering and the health schools, and Dave brings his unique creativity, energy and leadership experience to these collaborative efforts.”

Read the full story on the Penn Engineering blog.

January 15, 2020January 14, 2020

Danielle Bassett Receives New Scholarly Chair

Danielle Bassett has been named the J. Peter Skirkanich Professor of Bioengineering.

Dr. Bassett is a Professor in the department of Bioengineering at the School of Engineering and Applied Science. She holds a Ph.D. in Physics from the University of Cambridge and completed her postdoctoral training at the University of California, Santa Barbara, before joining Penn in 2013.

Dr. Bassett has received numerous awards for her research, including an Alfred P Sloan Research Fellowship, a MacArthur Fellowship, an Office of Naval Research Young Investigator Award, a National Science Foundation CAREER Award and, most recently, an Erdos-Renyi Prize in Network Science to name but a few. She has authored over 190 peer-reviewed publications as well as numerous book chapters and teaching materials. She is the founding director of the Penn Network Visualization Program, a combined undergraduate art internship and K-12 outreach program bridging network science and the visual arts.

Continue reading at the Penn Engineering blog.