“Our Bio-MakerSpace” takes viewers on a tour inside BE’s one-of-a-kind educational laboratories.
Produced primarily on smart phones and with equipment borrowed from the Penn Libraries, and software provided by Computing and Educational Technology Services, the videos were made by rising Bioengineering junior Nicole Wojnowski (BAS ‘22). Nicole works on staff as a student employee of the BE Labs and as a student researcher in the Gottardi Lab at the Children’s Hospital of Philadelphia (CHOP), helmed by Assistant Professor of Pediatrics Riccardo Gottardi.
Sevile Mannickarottu, Director of the Educational Labs in Bioengineering, says that the philosophy of the Bio-MakerSpace “encourages a free flow of ideas, creativity, and entrepreneurship between Bioengineering students and students throughout Penn. We are the only open Bio-MakerSpace with biological, chemical, electrical, materials, and mechanical testing and fabrication facilities, all in one place, anywhere.”
Bioengineering doctoral student Dayo Adewole co-founded the company Instahub, which also took home a PIP award in 2019. Dayo also graduated from the BE undergraduate program in 2014. In this video, he discusses the helpfulness and expertise of the BE Labs staff.
Senior Associate Dean for Penn Engineering and Solomon R. Pollack Professor in Bioengineering David Meaney discusses how the Bio-MakerSpace is the only educational lab on campus to provide “all of the components that one would need to make the kinds of systems that bioengineers make.”
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.
Novel Chest X-Ray Contrast
David Cormode, Associate Professor of Radiology and Bioengineering
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).
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).
Sydney Shaffer, Assistant Professor of Bioengineering and Pathology and Laboratory Medicine
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
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.
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.
David F. Meaney, Solomon R. Pollack Professor of Bioengineering and Senior Associate Dean
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
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
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.
Konrad Kording, Penn Integrates Knowledge University Professor of Bioengineering, Neuroscience, and Computer and Information Science
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.
Konrad Kording, Penn Integrates Knowledge University Professor of Bioengineering, Neuroscience, and Computer and Information Science
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
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 email@example.com.
The George H. Stephenson Foundation Educational Laboratory and Bio-MakerSpace, more commonly known as the Bio-MakerSpace, has recently become a hub for Penn student start-ups that continue after graduation. Beyond offering a home base for projects by Bioengineering majors, the lab is also open to Penn students, regardless of major. Unlike other departmental undergraduate labs, the Bio-MakerSpace encourages interdisciplinary projects and collaborations from students across all different majors.
Even better, the lab has a neutral policy when it comes to intellectual property (IP), meaning all IP behind student projects belongs to the students instead of the lab or the engineering school. With a wide variety of prototyping equipment, coding and software programs installed on lab computers, and an extremely helpful lab staff, the Bio-MakerSpace provides students of all academic backgrounds the resources to turn their ideas into realities or even businesses, as a recent succession of start-ups founded in the lab has shown.
One of the most successful start-ups to come out of the Bio-MakerSpace in the last few years is Group K Diagnostics, founded by 2017 Bioengineering alumna Brianna Wronko. The company focuses on the use of a point-of-care diagnostic device called KromaHealthTM. Offering a variety of different tests based on the input of a small amount of blood, serum, or urine, the device induces a color change through a series of reactions that can be detected through image processing. Developed in part from Wronko’s senior design project (hence the name “Group K”) and in part from her experience working at an HIV clinic, Group K Diagnostics looks to expand access to care for all populations.
But not all start-ups from the Bio-MakerSpace have origins in senior design projects. Three start-ups from 2019, two of which won the Penn President’s Innovation Prize, all began as independent initiatives from students. InstaHub, founded by 2019 Wharton alumnus Michael Wong with help from Bioengineering doctoral candidate Dayo Adewole, is a company that focuses on the use of snap-on automation for light energy conservation. A simple and easy-to-install device with motion and occupancy sensors, InstaHub aims to reduce energy consumption in a way that’s simpler and cheaper than rewiring projects that might otherwise be required. Here, Adewole shares the way that access to the Bio-MakerSpace provided InstaHub with a helpful platform.
The second start-up from 2019 to come out of the Bio-MakerSpace and win a President’s Innovation Prize is Strella Biotechnology, founded by recent graduate Katherine Sizov (Biology 2019). In developing sensors with the ability to detect ethylene gas emitted by rotting fruits, Strella hopes to reduce the immense amount of food waste due to produce simply going bad in storage. With a patent-pending biosensor that mimics the way ripe fruits detect ethylene emissions of nearby rotting fruits, the technology behind Strella involves both biology and aspects of engineering. In this video, Sizov herself talks about the way that the Bio-MakerSpace opened its doors to her, and allowed her work to really take off with the help of resources she wouldn’t have easily found otherwise.
Yet another start-up to use the Bio-MakerSpace as a launch pad for innovation is BioAlert Technologies, comprised of a group of Penn engineering undergraduate and graduate students, including 2019 Bioengineering alumnus Johnny Forde and current Biotechnology student Marc Rosenberg, who is the startup’s CEO and founder. BioAlert’s innovations are in what they call continuous infection monitoring (CIM) systems, designed to detect infections in patients with diabetic foot ulcers. Often, even when properly bandaged by a doctor, these ulcers run the risk of bacterial infection once a patient returns home and continues to care for the wound. BioAlert uses their platform to assess whether or not a bacterial infection might occur in a given patient’s wound, and uses an app to alert both patients and doctors of it, so that patients can receive the proper response treatment and medication as quickly as possible.
Though each of these start-ups used the resources of the Bio-MakerSpace, they are each interdisciplinary approaches to solving real-world problems today. Paired with other student resources at Penn like courses offered under an Engineering Entrepreneurship minor, knowledge from the nearby Wharton business school professors, and competitions like the Rothberg Catalyzer, the Bio-MakerSpace allows for any student to transform their idea into a reality, and potentially take it to market.
As technology and hands-on activities continue to become a larger part of education at all levels, a new movement of do-it-yourself projects is on the rise. Known as the “MakerSpace Movement,” the idea is that with the use of devices like 3-D printers, laser cutters, and simple circuitry materials, students, classes and communities can apply topics discussed in the classroom to real-life projects. Especially popular among STEM educators, the MakerSpace Movement is one that’s taken over labs in engineering schools around the country. Here at Penn, our own Stephenson Foundation Bioengineering Educational Lab and Bio-MakerSpace is equipped with all of the tools needed to bring student designs to fruition. In particular, the Stephenson Lab is the only lab on Penn’s campus that is open to all students and has both mechanical and electrical rapid prototyping equipment, as well as tools for biological and chemistry work.
Though Penn helps to fund the lab’s operation, many of the technologies and materials used in the Stephenson Lab and Bio-MakerSpace to help students throughout different class and independent projects are actually relatively affordable. Sevile Mannickarottu, Director of the Educational Laboratories, recently presented a paper describing the innovations and opportunities available to students through the MakerSpace attributes of the lab.
The Stephenson Lab mostly looks to support bioengineering majors, particularly in their lab courses and seniors design projects, but also encourages students of all disciplines to use the space for whatever MakerSpace-inspired ideas they might have, whether it be fixing a bike or measuring EMG signals for use in a mechanical engineering design.
Believe it or not, however, some of the best parts of the Bio-MakerSpace can actually be purchased for a total of under $1500. Though that number is probably far beyond the individual budget of most students, it might be more affordable for a student club or dorm floor that receives additional funding from Penn. While the idea of building a MakerSpace from nothing might sound intimidating, the popularity of the movement actually helps to provide a wide range of technology and affordable options.
One of the hallmarks of the MakerSpace at the Stephenson Lab, and of any MakerSpace, is the 3-D printer. Certainly, the highest quality 3-D printers on the market are incredibly expensive, but the ones used in the Stephenson Lab are actually only $750 per printer. Even better, most spools of the PLA filaments used in printers like this one can be found online for under a price of $30 each. With access to free CAD-modeling services like OpenScad and SketchUp, all you need is a computer to start 3-D printing on your own.
But if you can’t afford a 3-D printer, or want to add more electric components to the plastic designs the printer can make, the Stephenson Lab also has NI myDAQ devices, external power sources, wires, resistors, voltage meters, Arduino kits, and other equipment that can all be purchased by students for less than $500.
The most expensive device is the NI myDAQ, which costs $200 for students, but $400 for everyone else. With access to software that includes a digital multimeter, oscilloscope, function generator, Bode analyzer, and several other applications, the myDAQ is essential to any project that involves data with electronic signals. But even without the myDAQ, components like breadboards, wire cutters, resistors, voltage regulators, and all of the other basic elements of circuitry can typically be found online for a total price of under $100.
The Stephenson Lab also provides students with Arduino Kits, which are a combination of hardware and software in circuitry and programming that can be purchased for under $100 from the Arduino website. With sensors, breadboards, and other essential circuit elements, the Arduino Kits also allow users to control their designs through a software code that corresponds to hands-on setup. Particularly for those new to understanding the relationship between codes and circuitry, an Arduino Kit can be a great place to start.
Using all of these items, you can easily start your own MakerSpace for under $1500, especially if you can take advantage of student pricing. At the heart of the MakerSpace movement is the notion that anyone, anywhere can bring their own ideas and innovations to reality with the right equipment. So if you have a project in mind, get started on building your own MakerSpace, with these tools or your own — it’s cheaper than you’d think!
A New Sprayable Gel Can Help Prevent Surgical Adhesions
Adhesions are a common kind of scar tissue that can occur after surgery, and though usually not painful, they have the potential to result in complications like chronic pain or decreased heart efficiency, depending on where the scar tissue forms. Now, a sprayable gel developed by researchers at Stanford University will help to prevent adhesions from forming during surgical procedures. The gel, called PNP 1:10 in reference to its polymer-nanoparticle structure, has a similar stiffness to mayonnaise and achieves an ideal balance of slipperiness and stickiness that allows it to adhere easily to tissue of irregular shapes and surfaces. The flexible gel will actually dissolve in the body after two weeks, which is about how long most adhesions take to heal. Though lead author Lyndsay Stapleton, M.S., and senior authors Joseph Woo, M.D., and Eric Appel, Ph.D., have only tested the gel in rats and sheep so far, they hope that human applications are not too far in the future.
Learning to Understand Blood Clots in a New Model
Blood clots are the source of some of the deadliest human conditions and diseases. When a clot forms, blood flow can be interrupted, cutting off supply to the brain, heart, or other vital organs, resulting in potentially serious damage to the mind and body. For patients with certain bleeding disorders, clotting or the lack thereof can hold tremendous importance in surgery, and affect some of the typical procedures of a given operation. To help plan for such situations, researchers at the University of Buffalo created an in vitro model to help better illustrate the complex fluid mechanics of blood flow and clotting. Most importantly, this new model better demonstrates the role of shear stress in blood flow, and the way that it can affect the formation or destruction of blood clots – an aspect that current clinical devices often overlook. Led by Ruogang Zhao, Ph.D., the model can allow surgeons and hematologists to consider the way that certain chemical or physical treatments can affect clot formation on a patient-to-patient basis. The two key factors of the model are its incorporation of blood flow, and its relationship to shear stress, with clot stiffness through microfabrication technology using micropillars as force sensors for the stiffness. Going forward, Zhao and his research team hope to test the model on more patients, to help diversify the different bleeding disorders it can exhibit.
Training the Next Generation of Researchers
Rebecca Zappala, a junior from Miami, Florida who is majoring in bioengineering, worked in Grenoble this summer on new ways to harvest water from fog. She describes her research project as a “futuristic” way to collect water and says that she’s thankful for the opportunity to work on her first independent research project through the Research and Education in Active Coatings Technology (REACT) program.
After learning the technical skills she needed for her project, Zappala spent her summer independently working on new ways to modify her material’s properties while working closely with her French PI and a post-doc in the lab. She was surprised to see how diverse the lab was, with researchers working on everything from biomolecular research to energy in the same space.
“I learned a lot,” she says about being in such an interdisciplinary setting. “I hadn’t been part of a research team before, and I got a lot of exposure to things that I wouldn’t have been exposed to otherwise.”
Virginia Tech Course Addresses the Needs of Wounded Veterans
A new course at Virginia Tech encourages students to apply engineering skills to real-life problems in the biomedical world by designing medical devices or other applications to assist veterans suffering from serious injuries or illnesses. Funded by the National Institute of Health, faculty from the Department of Biomedical Engineering and Mechanics hope that the course will allow students to see how theoretical knowledge from the classroom actually works in a clinical setting, and to understand how different stakeholder interests factor into designing a real device. What makes this new class unique from other traditional design-focused courses at other universities is its level of patient interaction. Students at Virginia Tech who choose to take this class will have the chance to gain input from field professionals like clinicians and engineers from the Salem Veterans Affairs Medical Center, while also being able to get direct feedback from the patients that the devices will actually help. Beginning in the spring of 2020, students can take the new course, and volunteer in the veterans clinics to gain even more experience with patients.
People and Places
Sevile Mannickarottu, the Director of the Educational Laboratories in Penn’s Department of Bioengineering and recent recipient of the Staff Recognition Award from the School of Engineering and Applied Sciences, presented a paper to highlight the Stephenson Foundation Bioengineering Educational Lab and Bio-Makerspace at the 126th annual conference of the American Society for Engineering Education. Thanks to the dedication of Mannickarottu and the lab staff to creating a space for simultaneous education and innovation, the Bioengineering Lab continues to be a hub for student community and projects of all kinds.
A week-long program for high school girls interested in STEM allows students to explore ideas and opportunities in the field through lab tours, guest speakers, and hands-on challenges. A collaboration across the University of Virginia Department of Biomedical Engineering, Charlottesville Women in Tech, and St. Anne’s Belfield School, the program gave this year’s students a chance to design therapies for children with disorders like hemiplegia and cerebral palsy, in the hopes that these interactive design challenges will inspire the girls to pursue future endeavors in engineering.
We would like to congratulate Nancy Albritton, Ph.D., on her appointment as the next Frank & Julie Jungers Dean of the College of Engineering at the University of Washington. Albritton brings both a deep knowledge of the research-to-marketplace pipeline and experience in the development of biomedical microdevices and pharmacoengineering to the new position.
We would also like to congratulate Jeffrey Brock, Ph.D., on his appointment as the dean of the Yale School of Engineering and Applied Science. Already both a professor of mathematics and a dean of science in the Faculty of Arts and Sciences at Yale, Brock’s new position will help him to foster collaborations across different departments of academia and research in science and engineering.