Junior Bioengineering Students Filter ECG Signals for Use in Astronaut Fatigue-Monitoring Device

by Sophie Burkholder

Every undergraduate student pursuing a B.S.E. in Bioengineering participates in the Bioengineering Modeling, Analysis, and Design Laboratory I & II courses, in which students work together on a series of lab-based design challenges with an emphasis on model development and statistical analysis. Recently, junior undergraduates enrolled in this course taught by Dr. Brian Chow and Dr. David Issadore (both of whom recently received tenure) completed a project involving the use of electrocardiography (ECG) to innovate a non-invasive fatigue-monitoring device for astronauts that tend to fall asleep during long operations in space.

Using ECG lead wires and electrodes with a BioPac M-35 data collection  apparatus, students collected raw data of their own heart and respiration rates, and loaded the data into MATLAB to analyze and calculate information like the heart rate itself, and portions of it like the QT-interval. “I think it was cool that we could measure signals from our own body and analyze it in a way that let us use it for a real-world application,” said junior Melanie Hillman about the project.

After taking these preliminary measurements, students used a combination of circuitry, MATLAB, and data acquisition boards to create both passive and active filters for the input signals. These filters helped separate the user’s breathing rate, which occurs at lower frequencies, from the heart rate, which occurs at higher frequencies, allowing for the data to be read and analyzed more easily. In their final design, most students used an active filter circuit chip that combined hardware with software to create bandpass filters of different frequency ranges for both input signals.

“It was nice to be able to do a lab that connected different aspects of engineering in the sense that we both electronically built circuits, and also modeled them theoretically, because normally there’s a separation between those two domains,” said junior Emily Johnson. On the final day of the project, Demo Day, groups displayed their designs ability to take one input from the ECG cables connected to a user, and filter it out into recognizable heart and respiration rates on the computer. This project, conducted in the in the Stephenson Foundation Bioengineering Educational Laboratory here at the University of Pennsylvania’s Department of Bioengineering, is just one of many examples of the way this hallmark course of the bioengineering curriculum strives to bring together all aspects of students’ foundational engineering coursework into applications with significance in the real world.

Penn BE Undergrads Make Biology More Accessible with Open-Source Plate Reader

The annual International Genetically Engineered Machine (iGEM) competition challenges students to expand the field of synthetic biology to solve tangible problems. While most iGEM projects involve imbuing microorganisms with useful new traits and adding them to a global toolkit, Penn Engineering students took a unique approach to the iGEM challenge by creating an open-source blueprint for a mechanical instrument that could make biological research more accessible.

Penn Bioengineering undergraduate Andrew Clark and recent graduates Karol Szymula, now a research assistant in Penn’s Complex Systems Lab, and Michael Patterson, now the lab engineer for Penn Bioengineering’s Instructional Laboratories, contributed to the project that originated through the 2017 iGEM challenge. Graduate student Michael Magaraci, who started Penn’s iGEM program as an undergraduate, and Sevile Mannickarottu, director of Instructional Laboratories, also participated. Brian Chow, Assistant Professor in Bioengineering at Penn, who helped create the iGEM competition when he was an MIT graduate student, oversaw the project.

Read the full story at Penn Engineering’s Medium Blog. Media contacts Evan Lerner and Lauren Salig.

Penn BE Undergraduates’ Plate Reader Design Published

Microplate reader, Wikimedia Commons

In a paper recently published in Biochemistry, a group of University of Pennsylvania Bioengineering students describe the results of their work designing a new, open-source, low-cost microplate reader. Plate readers are instruments designed to measure light absorption and fluorescence emission from molecules useful for clinical biomarker analyses and assays in a diverse array of fields including synthetic biology, optogenetics, and photosensory biology. This new design costs less than $3500, a significantly lower price than other commercially available alternatives. As described in the paper’s abstract, this design is the latest in a growing trend of open-source  hardware to enhance access to equipment for biology labs. The project originated as part of the annual International Genetically Engineering Machine Competition (iGEM), an annual worldwide competition focusing on “push[ing] the boundaries of synthetic biology by tackling everyday issues facing the world” (iGEM website).

The group consists of current junior Andrew Clark (BSE ’20) and recent graduates Karol Szymula (BSE ’18), who works in the lab of Dr. Danielle Bassett, and Michael Patterson (BSE ’18), a Master’s student in Bioengineering and Engineer of Instructional Laboratories. Assistant Professor of Bioengineering Dr. Brian Chow served as their faculty mentor alongside Director of Instructional Labs Sevile Mannickarottu and Michael Magaraci, a Ph.D. candidate in Bioengineering, all of whom serve as co-authors on the published article. The research and design of the project was conducted in the Stephenson Foundation Bioengineering Educational Laboratory here at the University of Pennsylvania’s Department of Bioengineering.

Chow Wins NIH Grant for Brain Study

Chow R01
Brian Chow, Ph.D.

The National Institutes of Health (NIH) has awarded a grant to Brian Chow, Ph.D., an assistant professor in the Department of Bioengineering, to study ultrafast genetically encoded voltage indicators (GEVIs). GEVIs are proteins that can detect changes in the electrical output of cells and report those changes by emitting different color light. His research seeks to create GEVIs that can report these changes much more rapidly – in fact, more than a million times more quickly than the velocity of the changes themselves – and apply these ultrafast GEVIs to the study of the brain.

The NIH-funded research will build on earlier research, employing de novo fluorescent proteins (dFPs) created in Dr. Chow’s lab. These dFPs, which are totally artificial and unrelated to natural proteins, report voltage changes in neurons by changing in brightness. Working with a team of investigators that includes faculty members from the Departments of Biochemistry & Biophysics and Neuroscience, Dr. Chow hopes to develop these ultrafast GEVIs.

“Monitoring thousands of neurons in parallel will shed new light on cognition, learning and memory, mood, and the physiological underpinnings of nervous system disorders,” he says.

Phytoplankton Research Earns Award


The Scripps Institution of Oceanography at the University of California, San Diego, announced last week that one of its faculty members, Andrew Barton, PhD, received a Simons Foundation Early Career Award to study phytoplankton — a type of algae that requires sunlight to survive and that serves as the basis for much of the marine food chain.

Dr. Barton’s research will use the Scripps Plankton Camera System, which provides real-time photographic images to monitor these phytoplankton. While not exactly offering the excitement or cuteness factor of the Golden Retriever Puppy Cam, this sort of technology is incredibly important to better understanding certain aspects of marine biology.

“This is an interesting project that brings cutting edge image-processing technology to the natural habitat to study complex organismal dynamics in the real-world setting,” says Brian Chow, PhD, assistant professor of bioengineering at the University of Pennsylvania. “Establishing the critical interplay between an organism’s form and function and the forces of its local and global environments are important problems in physical biology in general. Diatoms have long been studied by bioengineers interested in self-assembly, programmed assembly, biomineralization, and biomimicry, so the work may lead to some novel insights for our field.”

Congratulations to Dr. Barton on receiving this prestigious award.