ToxiSense Wins 2022 Venture Lab Startup Challenge

(From left to right) Startup Challenge sponsor Eric Aroesty with members of Toxisense: Aravind Krishnan, Udit Garg, Andrew Diep-Tran, and Aarush Sahni. (Image: The Wharton School)

Penn’s Venture Lab Startup Challenge awarded its 2022 prize to a sustainable and cost-effective water-testing startup. The venture, ToxiSense, was awarded at a ceremony on April 29, at Tangen Hall, Penn’s hub for student entrepreneurship and innovation.

Co-founded by four first-year students—Aravind Krishnan, Udit Garg, Andrew Diep-Tran, and Aarush Sahni—ToxiSense aims to improve the endotoxin testing required for drinking water and biopharma products through genetically engineering plants with bioluminescent properties. Biopharmaceutical products and drinking water must be tested for endotoxins, the sickness-causing molecule from bacteria. The current method relies on expensive horseshoe crab blood and is environmentally damaging. ToxiSense genetically engineered the Arabidopsis plant to luminesce based on the endotoxin concentration applied to it, serving as a sustainable, cost-effective solution.

ToxiSense was selected from a field of eight finalist teams—including DeToXyFi, Groov, Impact Local, Miren, Nemu, Ossum Technologies, and Shinkei Systems Corp.—who advanced from 30 ventures during the semi-finals portion of the competition, which consisted of a day of virtual pitching and Q&A in front of alumni entrepreneur and investor panels. For the finals, teams pitched to a panel of alumni judges and in front of a live audience of nearly 200 attendees as they competed for over $150,000 in cash and prizes to launch their startups.

“The Startup Challenge is Venture Lab’s premier yearly event, showcasing Penn’s most promising teams of student entrepreneurs,” says Lori Rosenkopf, vice dean of entrepreneurship and Simon and Midge Palley Professor at the Wharton School. “This year’s finalists included undergraduate and graduate students from across the University, and their products offered solutions for environmental, financial, health, and social challenges. These motivated teams capture the spirit of Penn entrepreneurship—innovative, interdisciplinary, inclusive—and we offer our congratulations and our optimistic wishes for their futures.”

Read more at The Wharton School.

Udit Garg (Class of 2025) is a rising second year student in Bioengineering.

Some work for this project was done in the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace, the primary teaching lab for the Department of Bioengineering.

Ossum Technologies includes Ananya Dewan, Hoang Le, Shiva Teerdhala, all students in the Vagelos Life Sciences and Management Program, Bioengineering major Karan Shah and Savan Patel, a student in the Jerome Fisher Program for Management & Technology.

How Bacteria Stores Information to Kill Viruses (But Not Themselves)

by Luis Melecio-Zambrano

A group of bacteriophages, viruses that infect bacteria, imaged using transmission electron microscopy. New research sheds light on how bacteria fight off these invaders without triggering an autoimmune response. (Image: ZEISS Microscopy, CC BY-NC-ND 2.0)

During the last few years, CRISPR has grabbed headlines for helping treat patients with conditions as varied as blindness and sickle cell disease. However, long before humans co-opted CRISPR to fight genetic disorders, bacteria were using CRISPR as an immune system to fight off viruses.

In bacteria, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) works by stealing small pieces of DNA from infecting viruses and storing those chunks in the genes of the bacteria. These chunks of DNA, called spacers, are then copied to form little tags, which attach to proteins that float around until they find a matching piece of DNA. When they find a match, they recognize it as a virus and cut it up.

Now, a paper published in Current Biology by researchers from the University of Pennsylvania Department of Physics and Astronomy shows that the risk of autoimmunity plays a key role in shaping how CRISPR stores viral information, guiding how many spacers bacteria keep in their genes, and how long those spacers are.

Ideally, spacers should only match DNA belonging to the virus, but there is a small statistical chance that the spacer matches another chunk of DNA in the bacteria itself. That could spell death from an autoimmune response.

“The adaptive immune system in vertebrates can produce autoimmune disorders. They’re very serious and dangerous, but people hadn’t really considered that carefully for bacteria,” says Vijay Balasubramanian, principal investigator for the paper and the Cathy and Marc Lasry Professor of Physics in the School of Arts & Sciences.

Balancing this risk can put the bacteria in something of an evolutionary bind. Having more spacers means they can store more information and fend off more types of viruses, but it also increases the likelihood that one of the spacers might match the DNA in the bacteria and trigger an autoimmune response.

Read the full story in Penn Today.

Vijay Balasubramanian is the Cathy and Marc Lasry Professor of Physics at the Department of Physics and Astronomy of the University of Pennsylvania, a visiting professor at Vrije Universiteit Brussel, and a member of the Penn Bioengineering Graduate Group.

Erin Berlew and Rhea Chitalia Receive Solomon R. Pollack Awards for Excellence in Graduate Bioengineering Research

The Solomon R. Pollack Award for Excellence in Graduate Bioengineering Research is given annually to the most deserving Bioengineering graduate students who have successfully completed research that is original and recognized as being at the forefront of their field. This year Penn Bioengineering recognizes the outstanding work of two graduate students in Bioengineering: Erin Berlew and Rhea Chitalia.

Erin Berlew, Ph.D. candidate in Bioengineering

Erin Berlew is a Ph.D. candidate in the lab of Brian Chow, Associate Professor in Bioengineering. She successfully defended her thesis, titled “Single-component optogenetic tools for cytoskeletal rearrangements,” in December 2021. In her research, she used the BcLOV4 optogenetic platform discovered/developed in the Chow lab to control RhoGTPase signaling. Erin earned a B.S. in Chemistry from Haverford College in 2015 and was an Americorps member with City Year Philadelphia from 2015-2016. “Erin is a world-class bioengineering with an uncommon record of productivity gained through her complementary expertise in molecular, cellular, and computational biology,” says Chow. “She embodies everything wonderful, both academically and culturally, about our graduate program and its distinguished history.” Erin’s hobbies outside the lab include spending time with family, reading mystery novels, enjoying Philadelphia, and crossword puzzles. In the future, she hopes to continue to teach for the BE department (she has already taught ENGR 105 and served as a TA for undergraduate and graduate courses) and to conduct further research at Penn.

Rhea Chitalia, Ph.D. candidate in Bioengineering

Rhea Chitalia is a Ph.D. candidate in Bioengineering and a member of the Computational Biomarker Imaging Group (CBIG), advised by Despina Kontos, Matthew J. Wilson Associate Professor of Research Radiology II in the Perelman School of Medicine. Rhea completed her B.S.E. in Biomedical Engineering at Duke University in 2015. Her doctoral research concerns leveraging machine learning, bioinformatics, and computer vision to develop computational imaging biomarkers for improved precision cancer care. In December 2021 she successfully defended her thesis titled “Computational imaging biomarkers for precision medicine: characterizing intratumor heterogeneity in breast cancer.” “It has been such a privilege to mentor Rhea on her dissertation research,” says Kontos. “Rhea has been a star graduate student. Her work has made fundamental contributions in developing computational methods that will allow us to gain important insight into tumor heterogeneity by utilizing a multi-modality imaging approach.” David Mankoff, Matthew J. Wilson Professor of Research Radiology in the Perelman School of Medicine, served as Rhea’s second thesis advisor. “It was a true pleasure for me to work with Rhea and to Chair her BE Thesis Committee,” Mankoff adds. “Rhea’s Ph.D. thesis and thesis presentation was one of the best I have had the chance to be involved with in my graduate mentoring career.” After graduation, Rhea hopes to further precision medicine initiatives through the use of real world, multi-omic data in translational industry settings. She will be joining Invicro as an Imaging Scientist. In her spare time, Rhea enjoys trying new restaurants, reading, and spending time with friends and family.

 

Strella Biotechnology Continues Scaling Up

Katherine Sizov (right) and Malika Shukurova (left) earned the 2019 President’s Innovation Prize for their startup, Strella Biotechnology.

“Fruit hacking” startup Strella Biotechnology, founded by students and faculty advisors from the School of Engineering and Applied Science (SEAS) and the School of Arts and Sciences (SAS), tackles food waste by monitoring fruit ripeness. No stranger to media coverage, Strella and co-founder Katherine Sizov have previously been spotlighted for receiving the 2019 President’s Innovation Prize, which included $100,000 of financial support, a $50,000 living stipend for both awardees, and a year of dedicated co-working and lab space at the Pennovation Center. 

Recently, Michael Birnbaum of the Washington Post spoke with Sizov about the hard work and flexibility it took to propel the company’s successful scaling endeavors: Strella is now monitoring 15 percent of all U.S. apples.  

“Sizov, 24, wants to eliminate food waste one fruit at a time. In central Washington, it was an effort that required almost as much quick footwork as the épée squad she captained as a championship fencer in college. One moment, she was trying to beam the sensor’s WiFi signal through the reception black hole of millions of apples, which cause transmission issues because of their high water content. The next, she was sitting down with laconic apple growers with orchards planted generations ago, trying to convince them she could help them avoid wasted fruit. By day’s end, she might be folding her 6-foot frame into the passenger seat of a rental car, balancing her laptop on her knees and trying to win over Silicon Valley investors on Zoom calls using skills she had picked up partly by watching YouTube tutorials.”

Read Michael Birnbaum’s Fighting food waste, one apple at a time” for more about Sizov’s motivation, background and process.

Strella Biotechnology was founded by Penn alumna Katherine Sizov (Bio 2019) and was initially developed in the George H. Stephenson Foundation Educational Laboratory, the biomakerspace and primary teaching lab of the Department of Bioengineering. Sizov and Penn Bioengineering alumna Malika Shukurova (BSE 2019) won a President’s Innovation Prize in 2019. Read more BE blog stories featuring Strella Biotechnology.

BE Seminar: “Ionic Liquid-based Therapeutics” (Samir Mitragotri)

Samir Mitragotri, Ph.D.

Speaker: Samir Mitragotri, Ph.D.
Hiller Professor of Bioengineering and Hansjorg Wyss Professor of Biologically Inspired Engineering
John A. Paulson School of Engineering and Applied Sciences
Harvard University

Date: Thursday, November 18, 2021
Time: 3:30-4:30 PM EST
Zoom – check email for link or contact ksas@seas.upenn.edu
This seminar will be held virtually, but students registered for BE 699 can gather to watch in Moore 216.

Abstract: Ionic liquids, the liquid salts comprising organic anions and cations, offer exciting opportunities for several therapeutic applications. Their tunable properties offer control over their design and function. Starting with biocompatible ions, we synthesized a library of ionic liquids and explored them for various drug delivery applications. Ionic liquids provided unique advantages including overcoming the biological transport barriers of skin, buccal mucosa and the intestinal epithelium. At the same time, they also stabilized proteins and nucleic acids and enabled the delivery of biologics across these barriers. Ionic liquids also provided unique biological functions including adjuvancy towards vaccines and antimicrobial function. I will present an overview of the design features of ionic liquids and novel biomedical applications enabled by these unique materials.

Samir Mitragotri Bio: Samir Mitragotri is the Hiller Professor of Bioengineering and Wyss Professor of Biologically Inspired Engineering at Harvard University. His research is focused on transdermal, oral, and targeted drug delivery systems. He is an elected member of the National Academy of Engineering, National Academy of Medicine and National Academy of Inventors. He is also a foreign member of Indian National Academy of Engineering. He is also an elected fellow of AAAS, CRS, BMES, AIMBE, and AAPS. He is an author of over 350 publications, an inventor on over 200 patent/patent applications, and a Clarivate Highly Cited Researcher. He received his BS in Chemical Engineering from the Institute of Chemical Technology, India and a PhD in Chemical Engineering from the Massachusetts Institute of Technology. He is the Editor-in-Chief of AIChE’s and SBE’s journal Bioengineering and Translational Medicine.

Interact, Adapt, Repeat

Sophomores Linda Wu and Nova Meng spent the summer studying coevolution among plants, mutualistic bacteria, and parasitic nematodes in Corlett Wood’s biology lab.

by Katherine Unger Baillie

To study coevolution, the responsibilities of Nova Meng and Linda Wu included caring for plants in the Penn greenhouse. (Image: From July 2021, when masks were not required)

Coevolution is all around us. Think of the elongated blooms that perfectly accommodate a hummingbird’s slender mouth parts. But not all examples of species influencing one another’s evolutionary course accrue benefits to all parties. Tradeoffs are part of the game.

This summer, sophomores Linda Wu of Annandale, Virginia, and Nova Meng of Akron, Ohio, researched an coevolutionary scenario with benefits as well as costs for the species involved. Their work, supported by the Penn Undergraduate Research Mentoring Program (PURM) and conducted in the lab of biology professor Corlett Wood, has examined the relationship among plants in the genus Medicago, beneficial bacteria that dwell in their roots, and parasitic nematodes that try to steal the plants’ nutrients.

The Center for Undergraduate Research & Fellowships provides students in the PURM program awards of $4,500 during the 10-week summer research internship. Wu and Meng stayed busy through those weeks. Whether evaluating plants in a soybean field in Michigan or tending to hundreds—even thousands—of plants in the greenhouse at Penn, these aspiring researchers built a foundation for future scientific endeavors with hands-on practice.

“It’s been an amazing experience,” says Wu. “I’ve always been interested in genetics and evolution and have found parasitic relationships in particular really interesting. I like reading about weird parasites. This summer I’ve gotten to participate in lab meetings, read books about coevolution, and expand my knowledge about the topic.”

Mentored by Ph.D. student McCall Calvert, Wu spent the summer focused on the parasites in the Medicago model system the Wood lab uses. “I’m trying to see if those nematodes are specialists or generalists, if they’re locally adapted to their host plant or open to parasitizing on different species,” Wu says.

To do so, she’s grown pots and pots of plants in the Penn greenhouse, experimentally infecting Medicago plants as well as other species, such as carrot and daisy plants, with nematodes, to measure the degree to which the parasites flourish.

Meng, who is pursuing a bioengineering major, is examining how bacteria that dwell in plant roots affect the plants’ susceptibility to parasites.

Meng’s project looked at the bacterial side of the coevolutionary relationship. Overseen by lab manager and technician Eunnuri Yi, Meng looked at four strains of bacteria, known as rhizobia. Two strains are nitrogen-fixing, giving their associated plants a crucial nutrient to promote growth, while the other two do not seem to contribute nitrogen to the plants, and instead exist as parasites in the plants’ roots. “I’m looking at what happens when we infect the plants with nematode parasites,” Meng says, “to see if the plants that are open to mutualistic rhizobia are more susceptible to the nematode parasites.”

Read the full story in Penn Today.

Linda Wu is a sophomore pursuing an uncoordinated dual degree in business, energy, environment, and sustainability in the Wharton School and in biology with a concentration in ecology and evolution in the College of Arts and Sciences at the University of Pennsylvania.

Nova Meng is a sophomore majoring in bioengineering in the School of Engineering and Applied Science at Penn.

BE Seminar: “Dynamics of 3D Cell Migration and Organ Formation” (Kenneth Yamada)

Our next Penn Bioengineering seminar will be held on zoom next Thursday.

Kenneth Yamada, MD, PhD

Speaker: Kenneth Yamada, M.D., Ph.D.
NIH Distinguished Investigator
Cell Biology Section
National Institute of Dental and Craniofacial Research, National Institutes of Health (NIH)

Date: Thursday, September 9, 2021
Time: 3:30-4:30 PM EDT
Zoom – check email for link or contact ksas@seas.upenn.edu
Location: Moore Room 216, 200 S. 33rd Street

Abstract: Real-time microscopy of the dynamics of cells and tissues in 3D environments is opening new windows to understanding the biophysical mechanisms of complex biological processes. Direct visualization is allowing us to explore fundamental questions in more depth that include: How do cells migrate in 3D? How do cancer cells invade? How is the extracellular matrix assembled? How are organs formed? Visualizing how cells move and organize into tissues is not only providing descriptive insights, but is also leading to the identification of novel, unexpected physical and mechanical mechanisms relevant to tissue engineering. Cells can use varying combinations of cell adhesion to adjacent cells and to the surrounding extracellular matrix with localized cellular contractility to migrate, invade, and produce the complex tissue architecture needed for organ formation.

Kenneth Yamada Bio: Kenneth Yamada has been an NIH Distinguished Investigator since 2011. He received MD and PhD degrees from Stanford. He was a Section Chief at the National Cancer Institute for 10 years and has been a Section Chief at NIDCR since 1990. He is an elected Fellow of the AAAS and American Society for Cell Biology. His research focuses on discovering novel mechanisms and regulators of cell interactions with the extracellular matrix and their roles in embryonic development and cancer. His research group focuses on the mechanisms by which three-dimensional (3D) extracellular matrix mediates key biological events, including cell migration, tissue morphogenesis, and cancer cell invasion. His research places particular emphasis on characterizing the dynamic movements of cells and their extracellular matrix as tissues are remodeled in 3D in real time. The biological systems they study include human primary cells migrating in 3D, human tumor cells and tissues, and mouse organ development. He places particularly high priority on developing future independent research leaders.

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!

Alumni Spotlight: Jane Shmushkis

Jane graduated in Fall 2017 with both a B.S.E. in Bioengineering (with a Medical Devices Concentration) and M.S.E. in Bioengineering. Jane is currently an Automation Engineer at Mosa Meat (Maastricht, Netherlands) working on laboratory tools to scale up cultured beef production. Formerly, she was a Research & Development Engineer at Opentrons (Brooklyn, New York) working on affordable robots for life sciences research. She is also an instructor with Genspace Community Biology Lab (Brooklyn, New York).

Jane Shmushkis (BSE/MSE 2017)

“While at Penn, I worked in the Stephenson Foundation Educational Laboratory and Bio-MakerSpace and in the Chow Lab as a student researcher. The educational lab was a free space to mess around with rapid prototyping tools, including 3D printing, laser cutting, Arduino, and much more. The experience in synthetic biology research encouraged me to think of biology with an engineering lens and to have the confidence to plan my own experiments. The people I got to work with at the BioMakerSpace and the Chow Lab kept me optimistic through challenging semesters and excited to learn.

With this excitement to keep learning, I decided to submatriculate into the Bioengineering Master’s program. Because of the program’s flexibility, I could choose from a mix of project-based courses, like Biomechatronics and Modeling Biological Systems, and literature-based courses, like Tissue Engineering and Musculoskeletal Bioengineering. Outside of Bioengineering, I took classes to sharpen skills in part fabrication (Machine Design and Manufacturing) and programming (Computer Vision & Computational Photography). This breadth helped me realize how much I could do with a foundation in coding and mechanical design and an understanding of the life sciences.

Beyond Penn Engineering, I was involved in Penn Dance Company, CityStep Penn, and the Science & Technology Wing. Penn Dance was a necessary break for my body and mind. CityStep was a way to connect with the larger Philadelphia community through performing arts. STWing showed me how playful engineering can be. After a couple years on campus, I also built up the confidence to bike off campus. If you have a good helmet and quick reflexes, I really recommend it to explore more of Philly!”

This post is part of BE’s Alumni Spotlight series. Read more testimonies from BE Alumni on the BE website.

2021 CAREER Award recipient: Alex Hughes, Assistant Professor in Bioengineering

by Melissa Pappas

Alex Hughes (illustration by Melissa Pappas)

The National Science Foundation’s CAREER Award is given to early-career researchers in order to kickstart their careers in innovative and pivotal research while giving back to the community in the form of outreach and education. Alex Hughes, Assistant Professor in Bioengineering and in Cell and Developmental Biology, is among the Penn Engineering faculty members who have received the CAREER Award this year.

Hughes plans to use the funds to develop a human kidney model to better understand how the development of cells and tissues influences congenital diseases of the kidney and urinary tract.

The model, known as an “organoid,” is a lab-grown piece of human kidney tissue on the scale of millimeters to centimeters, grown from cultured human cells.

“We want to create a human organoid structure that has nephrons, the filters of the kidney, that are properly ‘plumbed’ or connected to the ureteric epithelium, the tubules that direct urine towards the bladder,” says Hughes. “To achieve that, we have to first understand how to guide the formation of the ureteric tubule networks, and then stimulate early nephrons to fuse with those networks. In the end, the structures will look like ‘kidney subunits’ that could potentially be injected and fused to existing kidneys.”

The field of bioengineering has touched on questions similar to those posed by Hughes, focusing on drug testing and disease treatment. Some of these questions can be answered with the “organ-on-a-chip” approach, while others need an even more realistic model of the organ. The fundamentals of kidney development and questions such as “how does the development of nephrons affect congenital kidney and urinary tract anomalies?” require an organoid in an environment as similar to the human body as possible.

“We decided to start with the kidney for a few reasons,” says Hughes. “First, because its development is a beautiful process; the tubule growth is similar to that of a tree, splitting into branches. It’s a complex yet understudied organ that hosts incredibly common developmental defects.

“Second,” he says, “the question of how things form and develop in the kidney has major medical implications, and we cannot answer that with the ‘organ-on-a-chip’ approach. We need to create a model that mimics the chemical and mechanical properties of the kidney to watch these tissues develop.”

The fundamental development of the kidney can also answer other questions related to efficiency and the evolution of this biological filtration system.

“We have the tendency to believe that systems in the human body are the most evolved and thus the most efficient, but that is not necessarily true,” says Hughes. “If we can better understand the development of a system, such as the kidney, then we may be able to make the system better.”

Hughes’ kidney research will lay the foundation for broader goals within regenerative medicine and organ transplantation.

Read the full story in Penn Engineering Today.