César de La Fuente Uses AI to Discover Germ-fighting Peptides

César de la Fuente, PhD

The impending danger of bacterial resistance to antibiotics is well-documented within the scientific community. Bacteria are the most efficient evolvers, and their ability to develop tolerance to drugs, in addition to antibiotic overuse and misuse, means that researchers have had to get particularly resourceful to ensure the future of modern medicine.  

Presidential Assistant Professor in Bioengineering, Microbiology, Psychiatry, and Chemical and Biomolecular Engineering César de la Fuente and his team are using an algorithm to search the human genome for microbe-fighting peptides. So far, the team has synthesized roughly 55 peptides that, when tested against popular drug-resistant microbes such as the germ responsible for staph infections, have proven to prevent bacteria from replicating.  

WIRED’s Max G. Levy recently spoke with de la Fuente and postdoctoral researcher and study collaborator Marcelo Torres about the urgency of the team’s work, and why developing these solutions is critical to the survival of civilization as we know it. The team’s algorithm, based on pattern recognition software used to analyze images, makes an otherwise insurmountable feat tangible.  

De la Fuente’s lab specializes in using AI to discover and design new drugs. Rather than making some all-new peptide molecules that fit the bill, they hypothesized that an algorithm could use machine learning to winnow down the huge repository of natural peptide sequences in the human proteome into a select few candidates.

“We know those patterns—the multiple patterns—that we’re looking for,” says de la Fuente. “So that allows us to use the algorithm as a search function.”

Read Max G. Levy’s An AI Finds Superbug-Killing Potential in Human Proteins” at WIRED. 

This story previously appeared in Penn Engineering Today.

Yogesh Goyal Selected as 2021 STAT Wunderkind

Yogesh Goyal, Ph.D.

Yogesh Goyal, Ph.D.,  a postdoctoral researcher in Genetics and Bioengineering, has been selected as a 2021 STAT Wunderkind, which honors the “next generation of scientific superstars.” Goyal’s research is centered around developing novel mathematical and experimental frameworks to study how a rare subpopulation of cancer cells are able to survive drug therapy and develop resistance, resulting in relapse in patients. In particular, his work provides a view of different paths that single cancer cells take when becoming resistant, at unprecedented resolution and scale. This research aims to help devise novel therapeutic strategies to combat the challenge of drug resistance in cancer.

Goyal is a Jane Coffin Childs Postdoctoral Fellow in the systems biology lab of Arjun Raj, Professor in Bioengineering and Genetics at Penn. He will begin an appointment as Assistant Professor in the Department of Cell and Developmental Biology (CDB) in the Feinberg School of Medicine at Northwestern University in spring 2022.

Read the announcement in Penn Medicine News.

BE Seminar: “Phage and Robotics-Assisted Biomolecular Evolution” (Emma Chory)

Emma Chory, Ph.D.

Speaker: Emma Chory, Ph.D.
Postdoctoral Fellow
Sculpting Evolution Laboratory
Massachusetts Institute of Technology

Date: Thursday, October 21, 2021
Time: 3:30-4:30 PM EDT
Zoom – check email for link or contact ksas@seas.upenn.edu
Room: Moore 216

Abstract: Evolution occurs when selective pressures from the environment shape inherited variation over time. Within the laboratory, evolution is commonly used to engineer proteins and RNA, but experimental constraints have limited our ability to reproducibly and reliably explore key factors such as population diversity, the timing of environmental changes, and chance. We developed a high-throughput system for the analytical exploration of molecular evolution using phage-based mutagenesis to evolve many distinct classes of biomolecules simultaneously. In this talk, I will describe the development of our open-source python:robot integration platform which enables us to adjust the stringency of selection in response to real-time evolving activity measurements and to dissect the historical, environmental, and random factors governing biomolecular evolution. Finally, I will talk about our many on-going projects which utilize this system to evolve previously intractable biomolecules using novel small-molecule substrates to target the undruggable proteome.

Emma Chory Bio: Emma Chory is a postdoctoral fellow in the Sculpting Evolution Group at MIT, advised by Kevin Esvelt and Jim Collins. Emma’s research utilizes directed evolution, robotics, and chemical biology to evolve biosynthetic pathways for the synthesis of novel peptide-based therapeutics. Emma obtained her PhD in Chemical Engineering in the laboratory of Gerald Crabtree at Stanford University. She is the recipient of the NSF Graduate Research Fellowship and a pre- and postdoctoral NIH NRSA Fellowship.

Reimagining Scientific Discovery Through the Lens of an Artist

by Erica K. Brockmeier

Rebecca Kamen, Penn artist-in-residence and visiting scholar, has a new exhibition titled “Reveal: The Art of Reimagining Scientific Discovery” at American University Museum at the Katzen Arts Center that explores curiosity and the creative process across art and science. (Image: Greg Staley)

Rebecca Kamen, Penn artist-in-residence and visiting scholar, has long been interested in science and the natural world. As a Philadelphia native and an artist with a 40-plus-year career, her intersectional work sheds light on the process of scientific discovery and its connections to art, with previous exhibitions that celebrate Apollo 11’s “spirit of exploration and discovery” to new representations of the periodic table of elements.

Now, in her latest exhibition, Kamen has created a series of pieces that highlight how the creative processes in art and science are interconnected. In “Reveal: The Art of Reimagining Scientific Discovery,” Kamen chronicles her own artistic process while providing a space for self-reflection that enables viewers to see the relationship between science, art, and their own creativity.

The exhibit, on display at the Katzen Art Center at American University, was inspired by the work of Penn professor Dani Bassett and American University professor Perry Zurn, the exhibit’s faculty sponsor. The culmination of three years of work, “Reveal” features collaborations with a wide range of scientists, including philosophers at American University, microscopists at the National Institutes of Health studying SARS-CoV-2 , and researchers in Penn’s Complex Systems Lab and the Addiction, Health, and Adolescence (AHA!) Lab.

Continue reading at Penn Today.

Dani S. Bassett is the J. Peter Skirkanich Professor in the departments of Bioengineering and Electrical and Systems Engineering in the School of Engineering and Applied Science at the University of Pennsylvania. She also has appointments in the Department of Physics and Astronomy in Penn’s School of Arts & Sciences and the departments of Neurology and Psychiatry in the Perelman School of Medicine at Penn.

Rebecca Kamen is a visiting scholar and artist-in-residence in the Department of Physics & Astronomy in Penn’s School of Arts & Sciences.

David Lydon-Staley is an assistant professor in the Annenberg School for Communication at Penn and was formerly a postdoc in the Bassett lab.

Dale Zhou is a Ph.D. candidate in Penn’s Neuroscience Graduate Group.

“Reveal: The Art of Reimagining Scientific Discovery,” presented by the Alper Initiative for Washington Art and curated by Sarah Tanguy, is on display at the American University Museum in Washington, D.C., until Dec. 12.

The exhbition catalog, which includes an essay on “Radicle Curiosity” by Perry Zurn and Dani S. Bassett, can be viewed online.

Yogesh Goyal Appointed Assistant Professor at Northwestern University

Yogesh Goyal, Ph.D.

The Department of Bioengineering is proud to congratulate Yogesh Goyal on his appointment as Assistant Professor in the Department of Cell and Developmental Biology (CDB) in the Feinberg School of Medicine at Northwestern University. His lab will be housed within the Center for Synthetic Biology. His appointment will begin in Spring 2022.

Yogesh grew up in Chopra Bazar, a small rural settlement in Jammu and Kashmir, India. He received his undergraduate degree in Chemical Engineering from the Indian Institute of Technology Gandhinagar. Yogesh joined Princeton University for his Ph.D. in Chemical and Biological Engineering, jointly mentored by Professors Stanislav Shvartsman and Gertrud Schüpbach. Yogesh is currently a Jane Coffin Childs Postdoctoral Fellow in the lab of Arjun Raj, Professor in Bioengineering and Genetics at Penn.

“I am so excited for Yogesh beginning his faculty career,” Raj says. “He is a wonderful scientist with a sense of aesthetics. His work is simultaneously significant and elegant, a powerful combination.”

With a unique background in engineering, developmental biology, biophysical modeling, and single-cell biology, Yogesh develops quantitative approaches to problems in developmental biology and cancer drug resistance. As a postdoc, Yogesh developed theoretical and experimental lineage tracing approaches to study how non-genetic fluctuations may arise within genetically identical cancer cells and how these fluctuations affect the outcomes upon exposure to targeted therapy drugs. The Goyal Lab at Northwestern will “combine novel experimental, computational, and theoretical frameworks to monitor, perturb, model, and ultimately control single-cell variabilities and emergent fate choices in development and disease, including cancer and developmental disorders.”

“I am excited to start a new chapter in my academic career at Northwestern University,” Goyal says. “I am grateful for my time at Penn Bioengineering, and I thank my mentor Arjun Raj and the rest of the lab members for making this time intellectually and personally stimulating.”

Congratulations to Dr. Goyal from everyone at Penn Bioengineering!

Annenberg and Penn Bioengineering Research into Communication Citation Bias

Photo Credit: Debby Hudson / Unsplash

Women are frequently under-cited in academia, and the field of communication is no exception, according to research from the Annenberg School for Communication. The study, entitled “Gendered Citation Practices in the Field of Communication,” was published in Annals of the International Communication Association.

A new study from the Addiction, Health, & Adolescence (AHA!) Lab at the Annenberg School for Communication at the University of Pennsylvania found that men are over-cited and women are under-cited in the field of Communication. The researchers’ findings indicate that this problem is most persistent in papers authored by men.

“Despite known limitations in their use as proxies for research quality, we often turn to citations as a way to measure the impact of someone’s research,” says Professor David Lydon-Staley, “so it matters for individual researchers if one group is being consistently under-cited relative to another group. But it also matters for the field in the sense that if people are not citing women as much as men, then we’re building the field on the work of men and not the work of women. Our field should be representative of all of the excellent research that is being undertaken, and not just that of one group.”

The AHA! Lab is led by David Lydon-Staley, Assistant Professor of Communication and former postdoc in the Complex Systems lab of Danielle Bassett, J. Peter Skirkanich Professor in Bioengineering and in Electrical and Systems Engineering in the School of Engineering and Applied Science. Dr. Bassett and Bassett Lab members Dale Zhou and Jennifer Stiso, graduate students in the Perelman School of Medicine, also contributed to the study.

Read “Women are Under-cited and Men are Over-cited in Communication” in Annenberg School for Communication News.

Claudia Loebel Appointed Assistant Professor at the University of Michigan

by Mahelet Asrat

Claudia Loebel, MD, PhD (Photo/Mel Evans)

The Department of Bioengineering is proud to congratulate Claudia Loebel, M.D., Ph.D. on her appointment as Assistant Professor in the Department of Materials Science and Engineering at the University of Michigan. Loebel is part of the University of Michigan’s Biological Sciences Scholar program, which recruits junior instructional faculty in major areas of biomedical investigation. Loebel’s appointment will begin in Fall 2021.

Loebel got her M.D. in 2011 from Martin-Luther University in Halle-Wittenberg, Germany and her Ph.D. in Health Sciences and Technology from ETH Zurich, Switzerland in 2016. There she worked under her advisors Professors Marcy Zenobi-Wong from ETH Zurich and David Eglin from AO Research Institute Davos. At Penn, she conducted postdoctoral research in the Polymeric Biomaterials Laboratory of Jason Burdick, Robert D. Bent Professor in Bioengineering, and as a Visiting Research Scholar in the Mauck Laboratory of the McKay Orthopaedic Research Laboratory in the Perelman School of Medicine.

Loebel was awarded a K99/R00 Pathway to Independence Award through the National Institutes of Health (NIH), which supports her remaining time as a postdoc as well as her time as an independent investigator at the University of Michigan. Loebel is excited about training the next generation of scientists and engineers and being part of their journey in becoming independent and diverse thinkers.

Loebel’s research area is inspired by the interface between material science and regenerative engineering and how it can address specific problems related to tissue development, repair, and regeneration. By developing mechanically and strucatally dynamic biomaterials, microfabrication, and matrix manipulation techniques her works aim to recreate complex cell-matrix interactions and model tissue morphogenesis and disease. The ultimate goal of her research is to use these engineered systems to develop and translate more effective therapeutic treatments for diseases such as fibrotic, inflammatory, and congenital disorders. Her lab’s work will initially focus on developing engineering lung alveolar organoids, aiming to build models of acute and chronic pulmonary diseases and for personalized medicine.

Loebel says, “I am grateful to all my Ph.D. and postdoc mentors for their continuous support and especially Jason who, over the last few years, has trained me in becoming an independent scientist and mentor. This transition would not have been possible without such a great mentor team behind me.”

Congratulations Dr. Loebel from everyone at Penn Bioengineering!

“New Biosealant Can Stabilize Cartilage, Promote Healing After Injury”

New research from Robert Mauck, Mary Black Ralston Professor in Orthopaedic Surgery and Bioengineering and Director of Penn Medicine’s McKay Orthopaedic Research Laboratory, announces a “new biosealant therapy may help to stabilize injuries that cause cartilage to break down, paving the way for a future fix or – even better – begin working right away with new cells to enhance healing.” Their research was published in Advanced Healthcare Materials. The study’s lead author was Jay Patel, a former postdoctoral fellow in the McKay Lab and now Assistant Professor at Emory University and was contributed to by Claudia Loebel, a postdoctoral research in the Burdick lab and who will begin an appointment as Assistant Professor at the University of Michigan in Fall 2021. In addition, the technology detailed in this publication is at the heart of a new company (Forsagen LLC) spun out of Penn with support from the Penn Center for Innovation (PCI) Ventures Program, which will attempt to spearhead the system’s entry into the clinic. It is co-founded by both Mauck and Patel, along with study co-author Jason Burdick, Professor in Bioengineering, and Ana Peredo, a PhD student in Bioengineering.

Read the story in Penn Medicine News.

Postdoctoral Fellow Linden Parkes Wins BBRF Young Investigator Grant

Linden Parkes, PhD

The Department of Bioengineering at Penn is thrilled to congratulate Linden Parkes on receiving a Brain & Behavior Research Foundation (BBRF) Young Investigator Grant for 2021-2022. This grant will support Parkes’ continued postdoctoral research under the supervision of Danielle S. Bassett, J. Peter Skirkanich Professor of Bioengineering and Electrical and Systems Engineering in the School of Engineering and Applied Science (SEAS),  Theodore D. Satterthwaite, Associate Professor of Psychiatry in the Perelman School of Medicine (PSOM), and Raquel E. Gur, the Karl and Linda Rickels Professor of Psychiatry in PSOM.

Originally from Australia, Parkes did his undergraduate B.Sc. (Hons.) in Psychology and Psychophysiology at the Swinburne University of Technology in Melbourne. He went on to receive his Ph.D. in Neuroscience from the Turner Institute for Brain and Mental Health at Monash University (also in Melbourne) under the supervision of Murat Yucel, Professor of Psychology, Alex Fornito, Professor of Psychology, and Ben Fulcher, Senior Lecturer in the School of Physics at the University of Sydney. After finishing his doctorate, Parkes moved to Philadelphia to take up a position as a postdoctoral fellow in Danielle Bassett’s Complex Systems Lab.

Parkes will use the BBRF’s support to continue his research examining the link between the symptoms of mental illness and the brain. In particular, he seeks to uncover how individual patterns of abnormal neurodevelopment link to, and predict, the emergence of psychosis symptoms through childhood and adolescence using longitudinal data. In turn, Parkes’ work will discover prognostic biomarkers for the psychosis spectrum that will help inform clinical outcome tracking.

“I am honored to have been selected for a Young Investigator Grant from the BBRF this year,” Parkes says. “This award will support me to conduct research that I believe will make real inroads into understanding the pathways that link abnormalities in neurodevelopment to the symptoms of psychosis. I feel grateful for the opportunity to complete my postdoctoral training at Penn. Penn has connected me with wonderful people who I’m sure will be lifelong mentors, colleagues, and peers.”

The BBRF Young Investigator Grants are valued at more than $10.3 million and are awarded annually to 150 of the world’s most promising young scientists to support the work of early career investigators with innovative ideas for groundbreaking neurobiological research seeking to identify causes, improve treatments, and develop prevention strategies for psychiatric disorders.

Read more about the BBRF 2020 Young Investigators here.

Penn Bioengineering Postdoc Brittany Taylor Appointed Assistant Professor at University of Florida

 

Brittany Taylor, PhD

The Department of Bioengineering is proud to congratulate Postdoctoral Researcher Brittany Taylor, PhD on her appointment as a tenure-track Assistant Professor in the J. Crayton Pruitt Family Department of Biomedical Engineering of the Herbert Wertheim College of Engineering at the University of Florida. Taylor’s appointment will begin in January 2021 after four years as a postdoc in Penn Medicine’s McKay Orthopaedic Research Laboratory where she worked under the supervision of Louis Soslowsky, Fairhill Professor in Orthopaedic Surgery and Professor in Bioengineering.

Taylor got her BS in Biomedical Engineering from the University of Virginia where she conducted research under Drs. Cato Laurencin and Edward Botchwey (the latter got his PhD in Penn Bioengineering in 2002). She went on to complete her PhD in Biomedical Engineering in 2016, studying with Dr. Joseph Freeman, in the Musculoskeletal Tissue Regeneration Laboratory at Rutgers University. During her time at Penn, she served as the Co-President of the Biomedical Postdoctoral Council, worked with the Perelman School of Medicine’s PennVIEW program on postdoctoral diversity recruitment, and spearheaded the mentoring circles program, which brings together postdoctoral researchers, graduate students, and undergraduates in informal groups that allow mentorship and learning to flow freely.

The foundation for Taylor’s research interests is a combination of her training in bone tissue engineering, bioactive biomaterials, and tendon injury and repair. Her graduate research focused on a three-dimensional biomimetic pre-vascularized scaffold that simultaneously promoted osteogenic and angiogenic differentiation of human mesenchymal stem cells in vitro and cellular infiltration and neovascularization in vivo without the addition of growth factors of cells. As a postdoctoral fellow, in addition to investigating the role of collagen type V on tendon inflammation and remodeling in a mouse patellar tendon injury model, she also elucidated the biological and mechanical implications of an implantable bilayer delivery system (BiLDS) for controlled and localized release of non-steroidal anti-inflammatory drugs (NSAIDs) to modulate tendon inflammation in a rat rotator cuff injury and repair model. This collection of work exploits the ability of these transformative technologies to provide physical and chemical regenerative cues without the use of exogenous cells; hence avoiding possible complications associated with autologous and allogeneic cell sources and simplifying the regulatory pathway towards clinical application. Taylor’s future research program at the University of Florida will focus on tailored cell-free combinatorial strategies, such as decellularized matrices, tunable delivery systems, and modified extracellular vesicles, to complement and improve the native musculoskeletal tissue regenerative and reparative process.

“Brittany has been an amazing postdoctoral fellow,” says her mentor Louis Soslowsky. “She has learned a lot and contributed to various projects in an exemplary manner. She has been a leader in many arenas here at Penn and I am so proud of what she has done so far. I look forward to following her continued accomplishments at the University of Florida! I know she’ll do great!”

In the course of her pre-faculty career, Taylor achieved an impressive list of accomplishments. She received a Postdoctoral Fellowship for Academic Diversity from the Office of the Vice Provost for Research; a Postdoctoral Enrichment Program (PDEP) award from the Burroughs Wellcome Fund; and a UNCF Bristol-Myers Squibb E.E. Just Postgraduate Fellowship. Additionally, she was named a Rising Star in Cell Mentor’s list of “100 inspiring Black scientists in America” in February 2020 and was given a Rising Star in Biomedical Science Award from MIT in 2019.

“I am grateful for the opportunity to complete my postdoctoral training at Penn,” Taylor says:

“[P]articularly in a lab that is affiliated with the Penn Bioengineering program and the Department of Orthopaedic Surgery, where I had the unique experience of addressing basic science questions using translational animal models, while utilizing my engineering background and having a direct interaction with clinicians. Additionally, I connected with some amazing people here at Penn who had a significant impact on my time at Penn, and will be lifelong friends, colleagues, and mentors.”

Congratulations Dr. Taylor from everyone at Penn Bioengineering!