BE Seminar: “Understanding Spatiotemporal Cell Reprogramming for Precision Medicine” (Xiling Shen)

Xiling Shen, Ph.D.

Speaker: Xiling Shen, Ph.D.
Hawkins Family Associate Professor
Biomedical Engineering
Duke University

Date: Thursday, April 15, 2021
Time: 3:00-4:00 PM EDT
Zoom – check email for link or contact ksas@seas.upenn.edu

Abstract:

Bodily cells undergo transformations in space and time during development, disease progression, and therapeutic treatment. A holistic approach that combines engineering tools, patient-derived models, and analytical methods is needed to map cellular reprogramming and expose new therapeutic opportunities. The talk will cover our effort across the entire spectrum from bench to bedside, including organogenesis during embryonic development, epigenetic and metabolic reprogramming of cancer metastasis and COVID-19 patients, and organoid technology to guide precision- and immune-oncology.

Xiling Shen Bio:

Dr. Shen is the Hawkins Family Associate Professor in the Department of Biomedical Engineering at Duke University. He is also the director of the Woo Center for Big Data and Precision Health. He received his BS, MS, and PhD degrees from Stanford University and the NSF career award at Cornell University. He is the steering committee chair of the NCI Patient-Derived Model of Cancer Consortium. His lab studies precision medicine from a systems biology perspective. Areas of interests include cancer, stem cells, the but-brain axis, and infectious diseases.

Bioengineering Contributes to “New COVID-19 Testing Technology at Penn”

César de la Fuente, Ph.D., a Presidential Assistant Professor in Psychiatry, Microbiology, and Bioengineering, is leading a team to develop an electrode that can be easily printed at low cost to provide COVID-19 test results from your smart phone.

A recent Penn Medicine blog post surveys the efforts across Penn and the Perelman School of Medicine to develop novel says to detect SARS-CoV-2 and features several Department of Bioengineering faculty and Graduate Group members, including César de la Fuente, Presidential Assistant Professor in Psychiatry, Microbiology, and Bioengineering; Arupa Ganguly, Professor in Genetics; A.T. Charlie Johnson, Rebecca W. Bushnell Professor in Physics and Astronomy; Lyle Ungar, Professor in Computer and Information Science; and Ping Wang, Associate Professor in Pathology and Laboratory Medicine.

Read “We’ll Need More than Vaccines to Vanquish the Virus: New COVID-19 Testing Technology at Penn” by Melissa Moody in Penn Medicine News.

David Meaney Receives 2021 Lindback Award

David F. Meaney, PhD

David F. Meaney is among the recipients of the 2021 Lindback Awards.

The Lindback Awards, announced annually, are the most prestigious teaching awards that full-time faculty members at the University can receive.

Meaney is the Solomon R. Pollack Professor in Bioengineering and Senior Associate Dean of Penn Engineering and his research areas span from traumatic brain injury to brain network theory. He received his M.S. and Ph.D. in Bioengineering and Biomedical Engineering from Penn Engineering.

The Lindback Awards were established in 1961 with the help of the Christian R. and Mary F. Lindback Foundation.

Congratulations to Dr. Meaney from everyone in Penn Bioengineering for this well-deserved honor!

Read more stories on the BE blog featuring Dr. Meaney.

Originally posted in Penn Engineering Today.

BE Seminar: “Reaction-Coupled Solid-State Nanopore Digital Counting: Towards Sensitive, Selective and Fast Nucleic Acid Testing” (Weihua Guan)

Weihua Guan, PhD

Speaker: Weihua Guan, Ph.D.
Assistant Professor
Department of Electrical Engineering & Department of Biomedical Engineering (courtesy)
Pennsylvania State University, University Park

Date: Thursday, April 8, 2021
Time: 3:00-4:00 PM EDT
Zoom – check email for link or contact ksas@seas.upenn.edu

Abstract:

Due to their conceptual simplicity, the nanopore sensors have attracted intense research interest in electronic single molecule detection. While considerable success has been achieved, the solid-state nanopores still face three significant challenges, including repeatable nanopore size control, introduction sensing specificity, and prolonged sensor response time at low concentrations. In this talk, I will discuss a calibration-free solid-state nanopore counting method and two representative applications in nucleic acid testing. One is an isothermal amplification-coupled nanopore counting for malaria analysis. The other is the CRISPR-cas12a-coupled nanopore counting for HIV analysis. Finally, I will also discuss how we can develop a fully integrated ‘sample-to-result’ nucleic acid testing device using the solid-state counting strategy. I believe the reaction-coupled solid-state nanopore digital counting could open a new avenue towards compact, robust, low-cost electronic nucleic acid testing at the point of care.

Weihua Guan Bio:

Weihua Guan received his Ph.D. degree in Electrical Engineering from Yale University in 2013 and did his postdoctoral training at Johns Hopkins University from 2013 to 2014. He joined the Department of Electrical Engineering at Pennsylvania State University in Jan 2015. He also held a courtesy appointment in the Department of Biomedical Engineering at Penn State. Dr. Guan’s research interests are in the multidisciplinary areas of micro- and nanotechnology, micro/nanofluidics, bioMEMS, lab-on-a-chip devices, and point-of-care devices. Dr. Guan’s research group at Penn State focuses on developing micro and nanoscale devices as well as novel sensing principles towards advanced medical diagnostics and testing. Dr. Guan is a member of IEEE, Engineering in Medicine and Biology Society, Biophysical Society, and American Physics Society. Among other honors, Dr. Guan is a recipient of the HHMI International Research Fellowship and NSF CAREER award.

“This is What a Data Scientist Looks Like”

Speakers at the second annual Women in Data Science @ Penn Conference.

Last month, the second annual Women in Data Science (WiDS) @ Penn Conference virtually gathered nearly 500 registrants to participate in a week’s worth of academic and industry talks, live speaker Q&A sessions, and networking opportunities.

Hosted by Penn Engineering, Analytics at WhartonWharton Customer Analytics and Wharton’s Statistics Department, the conference’s theme — “This is What a Data Scientist Looks Like” – emphasized the depth, breadth, and diversity of data science, both in terms of the subjects the field covers and the people who enter it.

Following welcoming remarks from Erika James, Dean of the Wharton School, and Vijay Kumar, Nemirovsky Family Dean of Penn Engineering, the conference began with a keynote address from President of Microsoft US and Wharton alumna Kate Johnson.

Conference sessions continued throughout the week, featuring panels of academic data scientists from around Penn and beyond, industry leaders from IKEA Digital, Facebook and Poshmark, and lightning talks from students speakers who presented their data science research.

All of the conference’s sessions are now available on YouTube and the 2021 WiDS Conference Recap, including a talk titled “How Humans Build Models for the World” by Danielle Bassett, J. Peter Skirkanich Professor in Bioengineering and Electrical and Systems Engineering.

Read more about the conference at Wharton Stories: “How Women in Data Science Rise to the Top.

Originally posted in Penn Engineering Today.

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.

Manuela Raimondi Appointed Visiting Professor in Bioengineering

Manuela Raimondi, PhD

Manuela Teresa Raimondi was appointed Visiting Professor in Bioengineering in the Associated Faculty of the School of Engineering and Applied Science for the 2020-2021 academic year. Raimondi received her Ph.D. in Bioengineering in 2000 from Politecnico di Milano, Italy. She is currently a Full Professor of Bioengineering at Politecnico di Milano in the Department of Chemistry, Materials and Chemical Engineering “G. Natta”, where she teaches the course “Technologies for Regenerative Medicine” in the Biomedical Engineering graduate program.

Raimondi is the founder and Director of the Mechanobiology Lab and of the Interdepartmental Live Cell Imaging lab. She has pioneered the development of cutting edge tools for cell modelling, ranging from micro-engineered stem cell niches, to miniaturized windows for in vivo intravital imaging, to microfluidic culture systems to engineer tissue-equivalents and organoids for cell modelling and drug discovery. Her platforms are currently commercialized by her start-up, MOAB srl. Her research is funded by the European Research Council (ERC), by The National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), by the European Commission, and by the European Space Agency.

“Getting to Penn was quite the challenge with the various travel restrictions and the pandemic, but I am used to overcoming adverse odds and I am really excited to be here now,” says Dr. Raimondi. “In this challenging time, when many new barriers are coming up, I think building bridges and new scientific collaborations is even more important. I very much look forward to being part of the Penn research community.”

Dr. Raimondi with host Riccardo Gottardi, PhD on Smith Walk

During her sabbatical at Penn, Raimondi is investigating her hypothesis that stem cells pluripotency reprogramming can be guided by mechanical cues. Over the past five years, she has cultured many different stem cell types in the “Nichoids,” the synthetic stem cell niche she developed, and gathered robust evidence on how physical constraints at the microscale level upregulate pluripotency. Raimondi is hosted in the Bioengineering and Biomaterials Lab of Riccardo Gottardi, Assistant Professor in Bioengineering and in Pediatrics at the Perelman School of Medicine, where she is helping to refine human stem cell sources that could be minimally manipulated for translational tissue engineering for a safe and effective use in regenerative therapies, as a key issue for clinical translation is the maintenance or enhancement of multipotency during cell expansion without exogenous agents or genetic modification.

“Dr. Raimondi is a trailblazer in Italy in regenerative medicine who has introduced many new concepts in a sometimes musty academic environment and has shattered a number of glass ceilings,” says Dr. Gottardi. “I think her sabbatical at Penn is a great opportunity for her and for the Penn community to build new and exciting trans-Atlantic collaborations.”

BE Seminar: “Deciphering the Dynamics of the Unconscious Brain Under General Anesthesia” (Emery Brown)

Emery Brown, MD, PhD

Speaker: Emery N. Brown, MD, PhD
Edward Hood Taplin Professor of Medical Engineering and of Computational Neuroscience, MIT
Warren M. Zapol Professor of Anaesthesia, Harvard Medical School
Massachusetts General Hospital

Date: Thursday, April 1, 2021
Time: 3:00-4:00 PM EDT
Zoom – check email for link or contact ksas@seas.upenn.edu

Title: “Deciphering the Dynamics of the Unconscious Brain Under General Anesthesia”

Abstract:

General anesthesia is a drug induced state that is critical for safely and humanely allowing a patient to undergo surgery or an invasive diagnostic procedure. During the last 10 years the study of the neuroscience of anesthetic drugs has been an active area of research. In this lecture we show how anesthetics create altered states of arousal by creating oscillation that impede how the various parts of the brain communicate. These oscillations, which are readily visible on the electroencephalogram (EEG), change systematically with anesthetic dose, anesthetic class and patient age. We will show how the EEG oscillations can be used to monitor the brain states of patients receiving general anesthesia, manage anesthetic delivery and learn about fundamental brain physiology.

EMERY BROWN BIO:

Emery N. Brown is the Edward Hood Taplin Professor of Medical Engineering and Professor of Computational Neuroscience at Massachusetts Institute of Technology. He is the Warren M. Zapol Professor of Anaesthesia at Harvard Medical School and Massachusetts General Hospital (MGH), and an anesthesiologist at MGH.

Dr. Brown received his BA (magna cum laude) in Applied Mathematics from Harvard College, his MA and PhD in statistics from Harvard University, and his MD (magna cum laude) from Harvard Medical School. He completed his internship in internal medicine at the Brigham and Women’s Hospital and his residency in anesthesiology at MGH. He joined the staff at MGH, the faculty at Harvard Medical School in 1992 and the faculty at MIT in 2005.

Dr. Brown is an anesthesiologist-statistician recognized for developing signal processing algorithms for neuroscience data analysis and for defining the neurophysiological mechanisms of general anesthesia.

Dr. Brown was a member of the NIH BRAIN Initiative Working Group. He is a fellow of the IEEE, the AAAS, the American Academy of Arts and Sciences and the National Academy of Inventors. Dr. Brown is a member of the National Academy of Medicine, the National Academy of Sciences and the National Academy of Engineering. He received an NIH Director’s Pioneer Award, the National Institute of Statistical Sciences Sacks Award, the American Society of Anesthesiologists Excellence in Research Award, the Dickson Prize in Science, the Swartz Prize for Theoretical and Computational Neuroscience and a Doctor of Science (honoris causa) from the University of Southern California.

Watch the Inaugural Joseph Bordogna Forum Lecture by Dr. John Brooks Slaughter

The inaugural Joseph Bordogna Forum took place on Wednesday, February 24 and featured a talk from John Brooks Slaughter, Deans’ Professor of Education and Engineering at USC’s Viterbi School of Engineering and Rossier School of Education, entitled a “Call to Action for Racial Justice and Equity in Engineering.”

Dr. Slaughter was joined by panelists Jennifer R. Lukes, Professor in Mechanical Engineering and Applied Mechanics, Oladayo Adewole, an alumnus in Robotics who recently defended his doctoral dissertation in Bioengineering, and CJ Taylor, Raymond S. Markowitz President’s Distinguished Professor in Computer and Information Science and Associate Dean, Diversity, Equity and Inclusion, who moderated the talk.

Dr. Slaughter talked about how microaggressions can often be a barrier to student success and emphasized on the importance of mentorship for underrepresented minorities: “If faculty members seek to improve the retention of underrepresented minorities, often times more has to be done than introducing science and math principles early on in their education, but instead, the unique backgrounds of these students must be understood.”

Originally posted in Penn Engineering Today.

“The Bio-MakerSpace — Fostering Learning and Innovation Across Many Disciplines”

Penn Bioengineering’s BioMakerSpace in action (photo taken pre-pandemic)

Writing for the Penn Health-Tech blog, Hannah Spector profiled the George H. Stephenson Foundation Educational Laboratory and Bio-MakerSpace, the primary teaching lab for the Department of Bioengineering at Penn Engineering. This interdisciplinary Bio-MakerSpace (aka BioMakerSpace) is open to the entire Penn community for independent research and has become a hub for student startups in recent years:

One example is Strella Biotechnology, founded in 2019 by Katherine Sizov (Biology 2019 & President’s Innovation Prize winner). Strella is developing sensors with the ability to reduce the amount of food waste due to going bad in storage. “Having a Bio-MakerSpace that gives you the functionalities of both a wet lab and a traditional electronics lab is extremely helpful in developing novel technologies” says Sizov on the BE Labs Youtube channel.

The Bio-MakerSpace provides students of all academic backgrounds the resources to turn their ideas into realities, including highly knowledgeable lab staff. Seth Fein (BSE ’20, MSE ’21) has worked at the lab since Fall 2020. “Because bioengineering spans many fields, we encourage interdisciplinary work. Students from Mechanical, Electrical, and Chemical Engineering have all found valuable resources in the lab,” says Fein.

The article also discusses the many resources the BioMakerSpace provides to Penn students and their efforts to keep the lab functional, safe, and open for research and education during the current semester.

Penn Health-Tech is an interdisciplinary center launched in 2017 to advance medical device innovation across the Perelman School of Medicine and the School of Engineering and Applied Sciences by forging collaborative connections among Penn researchers and providing seed funding to incubate novel ideas to advance health care.

Continue reading “The Bio-MakerSpace — Fostering Learning and Innovation Across Many Disciplines” at the Penn Health-Tech blog.

Read more BE blog posts featuring the BioMakerSpace.