Tag: Ravi Radhakrishnan

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A Decade of BETA Day: Shaping the Success of Future Bioengineers

by Katherine Sas

Students learn about bioengineering in the BE Labs at the inaugural BETA Day (credit: Felice Macera)

Last year marked not just the 50th anniversary of the Department of Bioengineering (BE) but the 10th anniversary of Bioengineer-Teach-Aspire (BETA) Day, one of the most beloved and impactful programs run by the Graduate Association of Bioengineers (GABE).

BETA Day, an annual event in which a diverse group of Philadelphia middle school students learns about bioengineering and a variety of science, technology, engineering and math (STEM) fields from BE graduate students, has grown into an institution, one whose impact no one could have foreseen.

GABE’s original goal was to provide social opportunities for BE graduate students. While this is still an important function of the group, in the mid-2010s, students and board members found themselves looking for opportunities to provide more formalized outreach and mentorship. They wanted to have an impact on Philadelphia and cultivate the next generation of bioengineers.

The Seeds of BETA Day

Benjamin Freedman, a principal investigator at Beth Israel Deaconess Medical Center, Assistant Professor of Orthopedic Surgery at Harvard Medical School, and founder of biotech startup Limax Biosciences, earned his doctorate in Bioengineering in the lab of Louis Soslowsky, Fairhill Professor in the Department of Orthopaedic Surgery within the Perelman School of Medicine (PSOM) and in Bioengineering within the School of Engineering and Applied Science (Penn Engineering). Freedman played a key role in BETA Day’s founding. 

In 2009, Freedman, then an undergraduate at the University of Rochester, attended a talk at the City College of New York (CCNY), which sparked his interest in mentorship. Sheldon Weinbaum, a Distinguished Professor in Biomedical and Mechanical Engineering at CCNY and the Biomedical Engineering Society (BMES) inaugural diversity award winner, spoke about “fulfilling the dream” of mentorship and the struggle for inclusion in STEM fields, echoing the language of Martin Luther King Jr. 

Inspired by this encounter, Freedman got involved with a mentorship program during his senior year. He later signed up for a lunch with Weinbaum to talk about mentorship. Freedman recalls that Weinbaum’s face “lit up” when he realized that this student didn’t just want to talk science but was genuinely interested in inclusion, diversity and mentorship.

Arriving at Penn Engineering and PSOM for graduate school in 2011, Freedman joined GABE, bringing this passion and experience with him and helping GABE to shape and clarify their outreach and mentorship programs. 

From Campus to Community

Along with other GABE board members, such as Cori Riggin and Shauna Dorsey, Freedman worked over the course of a year and a half to identify the mentorship needs within BE and gauge student interest. David Meaney, Solomon R. Pollack Professor and then Chair of BE, and former BE faculty Susan Margulies, now Professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, were particularly involved in these discussions. 

Benjamin Freedman (left) addresses the first BE mentoring cohort (credit: Felice Macera)

The GABE board reorganized to include mentorship and outreach chairs, and eventually started a formal mentorship program in partnership with the Penn undergraduate Biomedical Engineering Society (BMES). The mentorship program continues to this day, creating opportunities for BE graduate students to engage with undergraduate concerns through one-on-one meetings to discuss career or graduate school advice, summer BBQ’s, roundtable discussions and monthly meetups.

With an internal mentorship program established, the team turned their focus to Philadelphia. Initially, GABE established a partnership with iPraxis, a local STEM education non-profit, to do some outreach activities in middle schools. This partnership resulted in an Outstanding Outreach Award from the national Biomedical Engineering Society in 2014. But with the department’s 40th anniversary approaching, GABE’s members wanted to do something spectacular to celebrate and give back to the community.

Service Learning in Action

By then, Ocek Eke, Director of Graduate Students Programming at Penn Engineering, had been recently appointed Director of Global and Local Service Learning Programs. Eke provided Freedman and GABE advice on setting up effective outreach programs and to determine what resources the School could contribute. “We have a role to play to fulfill our mission,” Eke says, citing Penn’s motto, “Leges Sine Moribus Vanae,” which translates to “Laws without morals are useless.”

GABE’s efforts were part of a “wave” of interest in outreach and community service in both the department and the School, Eke remembers, including the undergraduate group Access Engineering and several service learning courses which took students to Asia, Africa and Central America. He was impressed by the lack of cynicism in the BE student body. “These are students who saw a need, who are passionate about what they want to achieve. They could have just been comfortable but were willing to go and stick their necks out. They used the resources we have here in Penn Engineering to address these needs.”

A (BETA) Day to Remember

The first BETA Day took place at the Singh Center for Nanotechnology, which had only just opened. Held with the enthusiastic participation of around 70 middle schoolers, and almost as many volunteers, the event included a full day of programming, with representation from every Penn Engineering department. There were science talks, workshops, and even a drone demo with Vijay Kumar, Nemirovsky Family Dean of Penn Engineering. The entire day was student-driven and staffed by volunteers, demonstrating the students’ commitment to making a difference.

The first annual BETA Day was held in the Singh Center for Nanotechnology (credit: Felice Macera)

GABE never imagined BETA Day as an annual event, but the first instance was so successful, it became hard to imagine not repeating it. Ten years later, the GABE board continues to introduce bioengineering to a diverse and ambitious group of middle schoolers every spring. 

In recent years, the location has shifted to other venues, including Pennovation Works, in Gray’s Ferry, and BE’s own education lab, the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace. Penn’s General Robotics, Automation, Sensing and Perception (GRASP) Lab has also become a key collaborator in BETA Day. 

In 2021, during the COVID-19 lockdown, the industrious and creative GABE board even tailored BETA Day activities to be held in an entirely virtual environment. “These types of events are not as successful when they’re only initiated by faculty,” says Freedman. Generating and sustaining student involvement has been a cornerstone of BETA Day’s continued success.

The Legacy of BETA Day

GABE’s mentorship efforts have grown as well, changing to meet evolving student needs. The mentorship program now involves students being placed in “families” of around four undergraduates and two graduate students, spanning a range of class years and experience levels. A third student association, the Master’s Association in Bioengineers (MAB), was established to better foster community and facilitate opportunities for master’s students.  

The department also launched an applicant support program in 2020, enhancing BE’s mission of increasing diversity, equity and inclusion by pairing Ph.D. applicants to current doctoral students, who serve as mentors to help navigate the admissions process, giving feedback on application materials and providing other support to prospective students.

Structures of support and outreach activities like BETA Day have become a key emphasis of the department’s graduate student recruitment, helping to attract students who value the department’s core mission and increasing opportunities for underserved or underrepresented communities.

The legacy of that original BETA Day also continues in Freedman’s Lab. After graduating in 2017, having served on the GABE board and as President from 2015-2016, Freedman continued to mentor over 20 students during his postdoctoral research at Harvard. He is now building his own independent lab where diversity, mentorship and outreach are foundational pillars.

A Nebula of Inspiration

Perhaps the most consequential impact of BETA Day is the impression it makes on the middle schoolers who participate each year. “To really get to know what happens on BETA Day and what it’s true impact is, you need to experience it,” says Ravi Radhakrishnan, Herman P. Schwan Chair of the Department of Bioengineering and Professor in Bioengineering and in Chemical and Biomolecular Engineering. 

The legacy of BETA Day continues into its second decade. (credit: Afraah Shamim, BE Labs)

“I walked into the Stephenson Foundation Education Lab during BETA Day 2024,” recalls Radhakrishnan, “and what I saw was teams of teenagers tinkering with pipes that were clogged, strategizing on unclogging them without damaging them: an assignment that got them thinking in teams about how to prevent heart attacks. 

“Expose these young minds to design thinking, versatile tools, and critical problems in biomedical engineering, and the elegant solutions they brainstorm are truly mind blowing. BETA Day is like the nebula where future biomedical stars are born.”

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New Insights into the Mechanisms of Tumor Growth

by Nathi Magubane

3d render of cells secreting exosomes
A team of researchers led by the School of Arts & Science’s Wei Guo offers new insights into a mechanism that promotes tumor growth. “This information could be used to help clinicians diagnose cancers earlier in the future,” says Guo.

In many instances, the physical manifestation of cancers and the ways they are subsequently diagnosed is via a tumor, tissue masses of mutated cells and structures that grow excessively. One of the major mysteries in understanding what goes awry in cancers relates to the environments within which these structures grow, commonly known as the tumor microenvironment.

These microenvironments play a role in facilitating tumor survival, growth, and spread. Tumors can help generate their own infrastructure in the form of vasculature, immune cells, signaling molecules, and extracellular matrices (ECMs), three-dimensional networks of collagen-rich support scaffolding for a cell. ECMs also help regulate cellular communications, and in the tumor microenvironment ECMs can be a key promoter of tumor growth by providing structural support for cancerous cells and in modulating signaling pathways that promote growth.

Now, new research led by the School of Arts & Science’s Wei Guo and published in the journal Nature Cell Biology has bridged the complex structural interactions within the tumor microenvironment to the signals that trigger tumor growth. The researchers studied cancerous liver cells grown on ECMs of varying stiffness and discovered that the stiffening associated with tumor growth can initiate a cascade that increases the production of small lipid-encapsulated vesicles known as exosomes.

“Think of these exosomes as packages that each cell couriers out, and, depending on the address, they get directed to other cells,” says Ravi Radhakrishnan, professor of bioengineering in the School of Engineering and Applied Science and a co-author of the paper.

“By recording the number of packages sent, the addresses on these packages, their contents, and most importantly, how they’re regulated and generated, we can better understand the relationship between a patient’s tumor microenvironment and their unique molecular signaling signatures, hinting at more robust personalized cancer therapies,” Radhakrishnan says.

While studying exosomes in relation to tumor growth and metastasis has been well-documented in recent years, researchers have mostly focused on cataloging their characteristics rather than investigating the many processes that govern the creation and shuttling of exosomes between cells. As members of Penn’s Physical Sciences Oncology Center (PSOC), Guo and Radhakrishnan have long collaborated on projects concerning tissue stiffness. For this paper, they sought to elucidate how stiffening promotes exosome trafficking in cancerous intracellular signaling.

“Our lab previously found that high stiffness promotes the secretion of exosomes,” says Di-Ao Liu, co-first author of the paper and a graduate student in the Guo Lab. “Now, we were able to model the stiffening processes through experiments and identify molecular pathways and protein networks that cause this, which better links ECM stiffening to cancerous signaling.”

Read the full story in Penn Today.

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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 Anti-Cancer Engineering Center Will Delve Into the Disease’s Physical Fundamentals

by Evan Lerner

A colorized microscope image of an osteosarcoma shows how cellular fibers can transfer physical force between neighboring nuclei, influencing genes. The Penn Anti-Cancer Engineering Center will study such forces, looking for mechanisms that could lead to new treatments or preventative therapies.

Advances in cell and molecular technologies are revolutionizing the treatment of cancer, with faster detection, targeted therapies and, in some cases, the ability to permanently retrain a patient’s own immune system to destroy malignant cells.

However, there are fundamental forces and associated challenges that determine how cancer grows and spreads. The pathological genes that give rise to tumors are regulated in part by a cell’s microenvironment, meaning that the physical push and pull of neighboring cells play a role alongside the chemical signals passed within and between them.

The Penn Anti-Cancer Engineering Center (PACE) will bring diverse research groups from the School of Engineering and Applied Science together with labs in the School of Arts & Sciences and the Perelman School of Medicine to understand these physical forces, leveraging their insights to develop new types of treatments and preventative therapies.

Supported by a series of grants from the NIH’s National Cancer Institute, the PACE Center is Penn’s new hub within the Physical Sciences in Oncology Network. It will draw upon Penn’s ecosystem of related research, including faculty members from the Abramson Cancer Center, Center for Targeted Therapeutics and Translational Nanomedicine, Center for Soft and Living Matter, Institute for Regenerative Medicine, Institute for Immunology and Center for Genome Integrity.

Dennis Discher and Ravi Radhakrishnan

The Center’s founding members are Dennis Discher, Robert D. Bent Professor with appointments in the Departments of Chemical and Biomolecular Engineering (CBE), Bioengineering (BE) and Mechanical Engineering and Applied Mechanics (MEAM), and Ravi Radhakrishnan, Professor and chair of BE with an appointment in CBE.

Discher, an expert in mechanobiology and in delivery of cells and nanoparticles to solid tumors, and Radhakrishnan, an expert on modeling physical forces that influence binding events, have long collaborated within the Physical Sciences in Oncology Network. This large network of physical scientists and engineers focuses on cancer mechanisms and develops new tools and trainee opportunities shared across the U.S. and around the world.

Lukasz Bugaj, Alex Hughes, Jenny Jiang, Bomyi Lim, Jennifer Lukes and Vivek Shenoy (Clockwise from upper left).

Additional Engineering faculty with growing efforts in the new Center include Lukasz Bugaj, Alex Hughes and Jenny Jiang (BE), Bomyi Lim (CBE), Jennifer Lukes (MEAM) and Vivek Shenoy (Materials Science and Engineering).

Among the PACE Center’s initial research efforts are studies of the genetic and immune mechanisms associated with whether a tumor is solid or liquid and investigations into how physical stresses influence cell signaling.

Originally posted in Penn Engineering Today.

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2021 Graduate Research Fellowships for Bioengineering Students

We are very pleased to announce that ten current and future graduate students in the Department of Bioengineering have received 2021 National Science Foundation Graduate Research Fellowship Program (NSF GRFP) fellowships. 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 2021 recipients and descriptions of their research.

Current Students:

Puneeth Guruprasad

Puneeth Guruprasad is a Ph.D. student in the lab of Marco Ruella, Assistant Professor of Medicine in the Division of Hematology/Oncology and the Center for Cellular Immunotherapies at the Perelman School of Medicine. His work applies next generation sequencing methods to characterize tumors and study the genetic basis of resistance to cancer immunotherapy, namely chimeric antigen receptor (CAR) T cell therapy.

Gabrielle Ho

Gabrielle (Gabby) Ho is a Ph.D. student in the lab of Brian Chow, Associate Professor in Bioengineering. She works on design strategies for engineering near-infrared fluorescent proteins and tools.

 

Abbas Idris

Abbas Idris is a Master’s student in the lab of Lukasz Bugaj, Assistant Professor in Bioengineering. His work focuses on using optogenetic tools to develop controllable protein assemblies for the study of cell signaling behaviors.

 

 

Incoming Students:

Additionally, seven NSF GRFP honorees from other institutions will be joining our department as Ph.D. students in the fall of 2021. We congratulate them as well and look forward to welcoming them to Penn:

Congratulations again to all our current and future graduate students on their amazing research!

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Penn, CHOP and Yale Researchers’ Molecular Simulations Uncover How Kinase Mutations Lead to Cancer Progression

by Evan Lerner

A computer model of a mutated anaplastic lymphoma kinase (ALK), a known oncogenic driver in pediatric neuroblastoma.

Kinases are a class of enzymes that are responsible for transferring the main chemical energy source used by the body’s cells. As such, they play important roles in diverse cellular processes, including signaling, differentiation, proliferation and metabolism. But since they are so ubiquitous, mutated versions of kinases are frequently found in cancers. Many cancer treatments involve targeting these mutant kinases with specific inhibitors.

Understanding the exact genetic mutations that lead to these aberrant kinases can therefore be critical in predicting the progression of a given patient’s cancer and tailoring the appropriate response.

To achieve this understanding on a more fundamental level, a team of researchers from the University of Pennsylvania’s School of Engineering and Applied Science and Perelman School of Medicine, the Children’s Hospital of Philadelphia (CHOP) and researchers at the Yale School of Medicine’s Cancer Biology Institute, have constructed molecular simulations of a mutant kinase implicated in pediatric neuroblastoma, a childhood cancer impacting the central nervous system.

Using their computational model to study the relationship between single-point changes in the kinase’s underlying gene and the altered structure of the protein it ultimately produces, the researchers revealed useful commonalities in the mutations that result in tumor formation and growth. Their findings suggest that such computational approaches could outperform existing profiling methods for other cancers and lead to more personalized treatments.

The study, published in the Proceedings of the National Academy of Sciences, was led by Ravi Radhakrishnan, Professor and chair of Penn Engineering’s Department of Bioengineering and professor in its Department of Chemical and Biomolecular Engineering, and Mark A. Lemmon, Professor of Pharmacology at Yale and co-director of Yale’s Cancer Biology Institute. The study’s first authors were Keshav Patil, a graduate student in Penn Engineering’s Department of Chemical and Biomolecular Engineering, along with Earl Joseph Jordan and Jin H. Park, then members of the Graduate Group in Biochemistry and Molecular Biology in Penn’s Perelman School of Medicine. Krishna Suresh, an undergraduate student in Radhakrishnan’s lab, Courtney M. Smith, a graduate student in Lemmon’s lab, and Abigail A. Lemmon, an undergraduate in Lemmon’s lab, contributed to the study. They collaborated with Yaël P. Mossé, Associate Professor of Pediatrics at Penn Medicine and in the division of oncology at CHOP.

“Some cancers rely on the aberrant activation of a single gene product for tumor initiation and progression,” says Radhakrishnan. “This unique mutational signature may hold the key to understanding which patients suffer from aggressive forms of the disease or for whom a given therapeutic drug may yield short- or long-term benefits. Yet, outside of a few commonly occurring ‘hotspot’ mutations, experimental studies of clinically observed mutations are not commonly pursued.”

Read the full post in Penn Engineering Today.

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Ravi Radhakrishnan Adapts Multiscale Modeling Course

 

Ravi Radhakrishnan, PhD

Ravi Radhakrishnan, Professor and Chair of the Department of Bioengineering and Professor in Chemical and Biomolecular Engineering, is among the many faculty who quickly adapted their courses to an online format in the wake of the COVID-19 pandemic. Now, a recent publication in the American Institute of Chemical Engineers (AIChE) Journal reflects one of these revamped courses. The course BE 559: “Multiscale Modeling of Chemical and Biological Systems” provides theoretical, conceptual, and hands-on modeling experience on three different length and time scales: (1) electronic structure (A, ps); (2) molecular mechanics (100A, ns); and (3) deterministic and stochastic approaches for microscale systems (um, sec). During the course, students gained hands-on experience in running codes on real applications together with the following theoretical formalisms: molecular dynamics, Monte Carlo, free energy methods, deterministic and stochastic modeling. The transition to the online format was greatly facilitated by a grant from the Extreme Science and Engineering Discovery Environment (XSEDE) which provided cloud and supercomputing resources to the students facilitating the computational laboratory experience. Radhakrishnan’s article, “A survey of multiscale modeling: Foundations, historical milestones, current status, and future prospects,” reviews the foundations, historical developments, and current paradigms in multiscale modeling (MSM).

Radhakrishnan aspires to modernize computational science, integrating Multiscale Modeling and Data Science for Biological and Biomedical Science & Engineering. His team does so by integrating multiphysics modeling, computing, data science to tackle applications. The integrative approach is pictorially depicted here in terms of modeling different length and timescales using techniques such as molecular dynamics of atomistic systems, Brownian dynamics of coarse-grained systems, and field equations governing continuum scales of macroscopic systems.

Read the full article in the AIChE Journal: https://doi.org/10.1002/aic.17026

Funding source: National Institutes of Health, Grant/Award Number: CA227550

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Penn Alumnus Peter Huwe Appointed Assistant Professor at Mercer University

Peter Huwe, Ph.D.

Peter Huwe, a University of Pennsylvania alumnus and graduate of the Radhakrishnan lab, was appointed Assistant Professor of Biomedical Sciences at the Mercer University School of Medicine beginning this summer 2020 semester.

Huwe earned dual B.S. degrees in Biology and Chemistry in 2009 from Mississippi College, where he was inducted into the Hall of Fame. At Mississippi College, Huwe had his first exposure to computational research in the laboratory of David Magers, Professor of Chemistry and Biochemistry. He went on to earn his Ph.D. in Biochemistry and Molecular Biophysics in 2014 in the laboratory of Ravi Radhakrishnan, Chair of the Bioengineering Department at Penn. As an NSF Graduate Research Fellow in Radhakrishnan’s lab, Huwe focused his research on using computational molecular modeling and simulations to elucidate the functional consequences of protein mutations associated with human diseases. Dr. Huwe then joined the structural bioinformatics laboratory Roland Dunbrack, Jr., Professor at the Fox Chase Cancer Center as a T32 post-doctoral trainee. During his post-doctoral training, Huwe held adjunct teaching appointments at Thomas Jefferson University and at the University of Pennsylvania. In 2017, Huwe became an Assistant Professor of Biology at Temple University, where he taught medical biochemistry, medical genetics, cancer biology, and several other subjects.

During each of his appointments, Huwe became increasingly more passionate about teaching, and he decided to dedicate his career to medical education. Huwe is very excited to be joining Mercer University School of Medicine as an Assistant Professor of Biomedical Sciences this summer. There, he will serve in a medical educator track, primarily teaching first and second year medical students.

“Without Ravi Radhakrishnan and Philip Rea, Professor of Biology in Penn’s School of Arts & Sciences, giving me my first teaching opportunities as a graduate guest lecturer at Penn, I may never have discovered how much I love teaching,” says Huwe. “And without the support and guidance of each of my P.I.’s [Dr.’s Magers, Radhakrishnan, and Dunbrack], I certainly would not be where I am, doing what I love.  I am incredibly thankful for all of the people who helped me in my journey to find my dream job.”

Congratulations and best of luck from everyone in Penn Bioengineering, Dr. Huwe!

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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.

 

 

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Penn Bioengineering Former Postdoc Whelton Miller Appointed Assistant Professor Loyola University

 

Whelton Miller, Ph.D.

The Department of Bioengineering is proud to congratulate Whelton Miller, Ph.D., a former BE Postdoctoral Fellow, on his appointment as an Assistant Professor in the Department of Medicine in the Health Sciences Division at Loyola University. Miller’s appointment began in January 2020.

Miller received his B.S. in Biochemistry in 2001 from the University of Delaware where he worked under the supervision of Dr. Douglass F. Taber. After graduation, he worked in industry as a synthetic organic chemist for a pharmaceutical company. After three years of industry experience, he returned to academia to complete a Ph.D. in Theoretical/Computational Chemistry from the University of the Sciences in Philadelphia in 2012.

After graduate school, he was given a unique opportunity through Penn’s Postdoctoral Opportunities in Research and Teaching (PennPORT) program, an NIH-sponsored, Institutional Research and Academic Career Development Award (IRACDA) postdoctoral fellowship. In addition to Miller’s responsibilities through the PennPORT program, he served on the Biomedical Postdoctoral Council (BPC), as well as chair of the Engineering PostDoc Association (EpoD). He has worked closely with the Physician Scientist Training Program (PSTP) as a mentor to a high school student, as well as a program guest speaker. This allowed Miller to be a Postdoctoral Research Fellow in the Department of Bioengineering at Penn in the Radhakrishnan Lab – led by BE Department Chair Ravi Radhakrishnan – which focuses on the interface between chemical physics and molecular biology.

Miller has also gained experience in various affiliated appointments, serving as an Assistant Professor in the Department of Chemistry and Physics at Lincoln University (2015-2019), and is currently an Adjunct Assistant Professor in the Department of Chemical and Biomolecular Engineering (CBE) at Penn and an Adjunct Professor in Biomedical Engineering at the University of Ghana in Accra.

Miller joined Loyola University in Chicago, IL in the summer of 2019. Now in his new faculty position, Miller continues to work on collaborative research projects and include colleagues at Instituto Tecnológico de Santo Domingo, the University of Pennsylvania, Lincoln University, University of Ghana, and the University of the Sciences. His current research involves using computational chemistry techniques for theoretical design and study of organometallic and inorganic compounds, protein ligand interactions, and structural electronic effects. His goal is to employ several computational techniques to understand, as well as predict, molecular interactions, such as protein-ligand interactions and protein-protein interactions. Miller says he is always looking forward to more opportunities for minority student development and enrichment in the STEM-related disciplines. Congratulations, Dr. Miller!