Bioengineering Round-Up (October 2019)

by Sophie Burkholder

Innovations in Advancing a Cure for Diabetes

The blue circle is the global symbol for diabetes. Wikimedia Commons.

Diabetes is one of the more common diseases among Americans today, with the American Diabetes Association estimating that approximately 9.5 percent of the population battles the condition today. Though symptoms and causes may vary across types and patients, diabetes generally results from the body’s inability to produce enough insulin to keep blood sugar levels in check. A new experimental treatment from the lab of Sha Jin, Ph.D., a biomedical engineering professor at Binghamton University, aims to use about $1.2 million in recent federal grants to develop a method for pancreatic islet cell transplantation, as those are the cells responsible for producing insulin.

But the catch to this new approach is that relying on healthy donors of these islet cells won’t easily meet the vast need for them in diabetic patients. Sha Jin wants to use her grants to consider the molecular mechanisms that can lead pluripotent stem cells to become islet-like organoids. Because pluripotent stem cells have the capability to evolve into nearly any kind of cell in the human body, the key to Jin’s research is learning how to control their mechanisms and signaling pathways so that they only become islet cells. Jin also wants to improve the eventual culture of these islet cells into three-dimensional scaffolds by finding ways of circulating appropriate levels of oxygen to all parts of the scaffold, particularly those at the center, which are notoriously difficult to accommodate. If successful in her tissue engineering efforts, Jin will not only be able to help diabetic patients, but also open the door to new methods of evolving pluripotent stem cells into mini-organ models for clinical testing of other diseases as well.

A Treatment to Help Others See Better

Permanently crossed eyes, a medical condition called strabismus, affects almost 18 million people in the United States, and is particularly common among children. For a person with strabismus, the eyes don’t line up to look at the same place at the same time, which can cause blurriness, double vision, and eye strain, among other symptoms. Associate professor of bioengineering at George Mason University, Qi Wei, Ph.D., hopes to use almost $2 million in recent funding from the National Institute of Health to treat and diagnose strabismus with a data-driven computer model of the condition. Currently, the most common method of treating strabismus is through surgery on one of the extraocular muscles that contribute to it, but Wei wants her model to eventually offer a noninvasive approach. Using data from patient MRIs, current surgical procedures, and the outcomes of those procedures, Wei hopes to advance and innovate knowledge on treating strabismus.

A Newly Analyzed Brain Mechanism Could be the Key to Stopping Seizures

Among neurological disorders, epilepsy is one of the most common. An umbrella term for a lot of different seizure-inducing conditions, many versions of epilepsy can be treated pharmaceutically. Some, however, are resistant to the drugs used for treatment, and require surgical intervention. Bin He, Ph. D., the Head of the Department of Biomedical Engineering at Carnegie Mellon University, recently published a paper in collaboration with researchers at Mayo Clinic that describes the way that seizures originating at a single point in the brain can be regulated by what he calls “push-pull” dynamics within the brain. This means that the propagation of a seizure through the brain relies on the impact of surrounding tissue. The “pull” he refers to is of the surrounding tissue towards the seizure onset zone, while the “push” is what propagates from the seizure onset zone. Thus, the strength of the “pull” largely dictates whether or not a seizure will spread. He and his lab looked at different speeds of brain rhythms to perform analysis of functional networks for each rhythm band. They found that this “push-pull” mechanism dictated the propagation of seizures in the brain, and suggest future pathways of treatment options for epilepsy focused on this mechanism.

Hyperspectral Imaging Might Provide New Ways of Finding Cancer

A new method of imaging called hyperspectral imaging could help improve the prediction of cancerous cells in tissue specimens. A recent study from a University of Texas Dallas team of researchers led by professor of bioengineering Baowei Fei, Ph.D., found that a combination of hyperspectral imaging and artificial intelligence led to an 80% to 90% level of accuracy in identifying the presence of cancer cells in a sample of 293 tissue specimens from 102 patients. With a $1.6 million grant from the Cancer Prevention and Research Institute of Texas, Fei wants to develop a smart surgical microscope that will help surgeons better detect cancer during surgery.

Fei’s use of hyperspectral imaging allows him to see the unique cellular reflections and absorptions of light across the electromagnetic spectrum, giving each cell its own specific marker and mode of identification. When paired with artificial intelligence algorithms, the microscope Fei has in mind can be trained to specifically recognize cancerous cells based on their hyperspectral imaging patterns. If successful, Fei’s innovations will speed the process of diagnosis, and potentially improve cancer treatments.

People and Places

A group of Penn engineering seniors won the Pioneer Award at the Rothberg Catalyzer Makerthon led be Penn Health-Tech that took place from October 19-20, 2019. SchistoSpot is a senior design project created by students Vishal Tien (BE ‘20), Justin Swirbul (CIS ‘20), Alec Bayliff (BE ‘20), and Bram Bruno (CIS ‘20) in which the group will design a low-cost microscopy dianostic tool that uses computer vision capabilities to automate the diagnosis of schistosomiasis, which is a common parasitic disease. Read about all the winners here.

Virginia Tech University will launch a new Cancer Research Initiative with the hope of creating an intellectual community across engineers, veterinarians, biomedical researchers, and other relevant scientists. The initiative will focus not only on building better connections throughout departments at the university, but also in working with local hospitals like the Carilion Clinic and the Children’s National Hospital in Washington, D.C. Through these new connections, people from all different areas of science and engineering and come together to share ideas.

Associate Professor of Penn Bioengineering Dani Bassett, Ph.D., recently sat down with the Penn Integrates Knowledge University Professor Duncan Watts, Ph.D., for an interview published in Penn Engineering. Bassett discusses the origins of network science, her research in small-world brain networks, academic teamwork, and the pedagogy of science and engineering. You can read the full interview here.

An all-female group of researchers from Northern Illinois University developed a device for use by occupational therapists that can capture three-dimensional images of a patient’s hand, helping to more accurately measure the hand or wrist’s range of motion. The group presented the abstract for their design at this year’s meeting of the Biomedical Engineering Society here in Philadelphia, where Penn students and researchers presented as well.

Students’ Innovative Orthotic Device Wins Rothberg Catalyzer

NB: Penn Bioengineering would like to congratulate one of its current Senior Design teams (Alec Bayliff, Bram Bruno, Justin Swirbul, and Vishal Then) which took home the $500 Pioneer Award at this year’s Rothberg Catalyzer competition this past weekend! Keep reading for more information on the competition, awards, and winners.

Penn Health-Tech’s Rothberg Catalyzer is a two-day makerthon that challenges interdisciplinary student teams to prototype and pitch medical devices that aim to address an unmet clinical need.

The Catalyzer’s third competition was held last weekend and was won by MAR Designs, a team of Mechanical Engineering and Applied Mechanics graduate students: Rebecca Li, Ariella Mansfield and Michael Sobrepera.

MAR Designs took home the top prize of $10,000 for their project, an orthotic device that children with cerebral palsy can more comfortably wear as they sleep.

According to the team’s presentation, existing wrist orthoses “improve function and treat/prevent spasticity. However, patients report that these devices are uncomfortable which leads to lack of compliance and may also prevent patient’s eligibility for surgeries.” MAR Designs’ device initially allows full range of motion, but gradually straightens the wrist as the child is falling asleep.

In second place was Splash Throne. Team members Greg Chen, Nik Evitt, Jake Crawford and Meghan Lockwood proposed a toilet safety frame intended for elderly users. Embedded sensors track basic health information, like weight and heart-rate, as part of a preventative health routine.

Integrated Product Design students Jonah Arheim, Laura Ceccacci, Julia Lin and Alex Wan took third place with ONESCOPE, an untethered, hands-free laproscope designed to make minimally-invasive surgeries faster and safer.

Finally, SchistoSpot took home the Catalyzer’s Pioneer Award. Bioengineering and Computer and Information Science seniors Alec Bayliff, Bram Bruno, Justin Swirbul and Vishal Then designed a low-cost microscopy system that can aid in the diagnosis of the parasitic disease schistosomiasis by detecting eggs in urine samples, eliminating the need for a hospital visit.

The event was made possible by a three-year donation by scientist and entrepreneur Jonathan Rothberg, with the intent of inspiring the next generation of healthcare innovators.

Originally posted on the Penn Engineering Medium blog.

Penn Researchers’ Model Optimizes Brain Stimulation Therapies, Improving Memory in Tests

The researchers’ model involves mapping the connections between different regions of an individual’s brain while they performed a basic memory task, then using that data to predict how electrical stimulation in one region would affect activity throughout the network. Individuals’ improved performance on the same memory task after stimulation suggests the model could eventually be generalized toward a variety of stimulation therapies.

Brain stimulation, where targeted electrical impulses are directly applied to a patient’s brain, is already an effective therapy for depression, epilepsy, Parkinson’s and other neurological disorders, but many more applications are on the horizon. Clinicians and researchers believe the technique could be used to restore or improve memory and motor function after an injury, for example, but progress is hampered by how difficult it is to predict how the entire brain will respond to stimulation at a given region.

In an effort to better personalize and optimize this type of therapy, researchers from the University of Pennsylvania’s School of Engineering and Applied Science and Perelman School of Medicine, as well as Thomas Jefferson University Hospital and the University of California, Riverside, have developed a way to model how a given patient’s brain activity will change in response to targeted stimulation.

To test the accuracy of their model, they recruited a group of study participants who were undergoing an unrelated treatment for severe epilepsy, and thus had a series of electrodes already implanted in their brains. Using each individual’s brain activity data as inputs for their model, the researchers made predictions about how to best stimulate that participant’s brain to improve their performance on a basic memory test.

The participants’ brain activity before and after stimulation suggest the researchers’ models have meaningful predictive power and offer a first step towards a more generalizable approach to specific stimulation therapies.

Danielle Bassett and Jennifer Stiso.

The study, published in the journal Cell Reports, was led by Danielle Bassett, J. Peter Skirkanich Professor in Penn Engineering’s Department of Bioengineering, and Jennifer Stiso, a neuroscience graduate student in Penn Medicine and a member of Bassett’s Complex Systems Lab.

Read the full post on the Penn Engineering Medium blog. Media contact Evan Lerner.

Bioengineering Round-Up (September 2019)

by Sophie Burkholder

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

REACT 2019 students and Grenoble summer program interns, including undergraduate Rebecca Zappala (third from left, front), pose in front of the Chartreuse Mountains after completing a challenging ropes course. (Photo: Hermine Vincent)

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.”

Read the rest of the story on Penn Today. 

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.

 

Week in BioE (August 16, 2019)

by Sophie Burkholder

Electrode Arrays and Star Wars Help to Inspire a New Prosthetic Arm

Brain-controlled prosthetic arm, Wikimedia commons

After nearly fifteen years of work, a new high-tech prosthetic arm from researchers at the University of Utah allows hand amputees to pluck grapes, pick up eggs without breaking them, and even put on their wedding rings. Named after Luke Skywalker’s robotic hand in the Star Wars saga, the LUKE Arm includes sensors that better mimic the way the human body sends information to the brain, allowing users to distinguish between soft and hard surfaces and to perform more complicated tasks. The arm relies heavily on an electrode array invented by University of Utah biomedical engineering professor Richard A. Normann, Ph.D., which is a bundle of microelectrodes that enable a computer to read signals from connected nerves in the user’s forearm.

But the biggest innovation in the use of these electrode arrays for the LUKE Arm is in the way they allow the prosthetic to mimic the sense of feeling on the surface of an object that indicates how much pressure should be applied when handling it. Gregory Clark, Ph.D., an associate professor of biomedical engineering at the University of Utah and the leader of the LUKE Arm project, says the key to improving these functions in the prosthetic was by more closely mimicking the path that this information takes to the brain, as opposed to merely what comprises that sensory information. In the future, Clark hopes to improve upon the LUKE Arm by including more inputs, like one for temperature data, and on making them more portable by eliminating the device’s need for computer connection.

Philly Voice Recognizes the Cremins Lab’s Innovations in Light-Activated Gene-Folding

While technological advancements over the past few decades have opened doors to understanding the topological structures of DNA, we still have far more to learn about how these structures impact and contribute to genome function. But here at Penn, the Cremins Laboratory in 3D Epigenomes and Systems Neurobiology hopes to fix that. Led by Jennifer E. Phillips-Cremins, Ph.D., members of the lab use light-activated dynamic looping (LADL) to better understand the way that genome topological properties and folding can affect protein translation. Cremins and her lab use this technique to force specific genome folds to interact with each other, and create temporary DNA loops that can then be bound together in the presence of blue light for certain proteins in the Arabidopsis plant. Using the data from these tests, researchers can better understand the genome structure-function relationships, and hopefully open the door to new treatments for diseases in which expression or mis-expression of certain genes is the cause.

Artificial Cells Can Deliver Molecules Better than the Real Thing

From pills to vaccines, ways to deliver drugs into the body have been constantly evolving since the early days of medicine.

Now, a new study from an interdisciplinary team led by researchers at the University of Pennsylvania provides a new platform for how drugs could be delivered to their targets in the future. Their work was published in the Proceedings of the National Academy of Sciences.

The research focuses on a dendrimersome, a compartment with a lamellar structure and size that mimic a living cell. It can be thought of as the shipping box of the cellular world that carries an assortment of molecules as cargo.

The scientists found that these dendrimersomes, which have a multilayered, onion-like structure, were able to “carry” high concentrations of molecules that don’t like water, which is common in pharmaceutical drugs. They were also able to carry these molecules more efficiently than other commercially available vessels. Additionally, the building block of the cell-like compartment, a janus dendrimer, is classified as an amphiphile, meaning it contains molecules that don’t like water and also molecules that are soluble in water, like lipids, that make up natural membranes.

“This is a different amphiphile that makes really cool self-assembled onions into which we were able to load a bunch of molecular cargos,” says co-author Matthew Good.

Read the rest of the story on Penn Today.

A Warm Evening Bath Could Improve Sleep Quality

In a recent review of over 5,000 sleep studies, biomedical engineering researchers at the University of Texas at Austin found a connection between water-based passive body heating and sleep onset latency, efficiency, and quality. Using meta-analytical tools to compare all of the studies and patient data, lead author and Ph.D. candidate Shahab Haghayegh and his team found that a warm bath in the temperature range of 104-109 degrees Fahrenheit taken 1-2 hours before bed has the ability to improve all three considered sleep categories. This makes sense considering that our body’s Circadian rhythms govern both our sleep cycles and temperature, bringing us to a higher temperature during the day and a lower one at night during sleep. In fact, this lowering of body temperature before sleep is what helps to trigger the onset of sleep, so taking a warm bath and allowing your body to cool down from it before going to sleep enhances the body’s own efforts of naturally cooling down before we go to bed. With this new and comprehensive review, those who suffer from poor sleep quality may soon find solace in temperature regulation therapy systems.

People & Places

With the recent 50th anniversary of the first moon landing by Americans Neil Armstrong, Buzz Aldrin, and Michael Collins in 1969, ABC News looked back at one of the women involved in the project. Judy Sullivan was a biomedical engineer at the time of the project, and served as the lead engineer of the biomedical system for Apollo 11. In this role, she led studies on the astronauts’ breathing rates and sensor capabilities for the devices being sent into space to help the astronauts monitor their health. For the Apollo 11 mission and a lot of Sullivan’s early work at NASA, she worked on teams of all men, as women were often encouraged to become teachers, secretaries, or homemakers over other professions. Today, Sullivan says she’s thrilled that women have more career options to choose from, and wants to continue seeing more women getting involved in math and science.

We would like to congratulate Sanjay Kumar, M.D., Ph.D., on his appointment as the new Department Chair of Bioengineering at the University of California, Berkeley. Since joining the faculty in 2005, Kumar has received several prestigious awards including the NSF Career Award, the NIH Director’s New Innovator Award, the Presidential Early Career Award for Scientists and Engineers, and the Berkeley student-voted Outstanding Teacher Award.

 

Penn Engineering’s Blinking Eye-on-a-Chip Used for Disease Modeling and Drug Testing

By Lauren Salig

Rachel Young, a graduate student in Huh’s lab, holds up the new eye-on-a-chip device. The latest iteration of the lab’s eye-on-a-chip has a mechanical eyelid to simulate blinking, and was used to test an experimental drug for dry eye disease. By incorporating human cells into an engineered scaffolding, the eye-on-a-chip has many of the benefits of testing on living subjects, while minimizing risks and ethical concerns.

People who spend eight or more hours a day staring at a computer screen may notice their eyes becoming tired or dry, and, if those conditions are severe enough, they may eventually develop dry eye disease (DED). DED is a common disease with shockingly few FDA-approved drug options, partially because of the difficulties of modeling the complex pathophysiology in human eyes. Enter the blinking eye-on-a-chip: an artificial human eye replica constructed in the laboratory of Penn Engineering researchers.

This eye-on-a-chip, complete with a blinking eyelid, is helping scientists and drug developers to improve their understanding and treatment of DED, among other potential uses. The research, published in Nature Medicine, outlines the accuracy of the eye-on-a-chip as an organ stand-in and demonstrates its utility as a drug testing platform.

Dan Huh and Jeongyun Seo

The study was led by Dan Huh, associate professor in the Department of Bioengineering, and graduate student Jeongyun Seo.

They collaborated with Vivian Lee, Vatinee Bunya and Mina Massaro-Giordano from the Department of Ophthalmology in Penn’s Perelman School of Medicine, as well as with Vivek Shenoy, Eduardo D. Glandt President’s Distinguished Professor in Penn Engineering’s Department of Materials Science and Engineering. Other collaborators included Woo Byun, Andrei Georgescu and Yoon-suk Yi, members of Huh’s lab, and Farid Alisafaei, a member of Shenoy’s lab.

Huh’s lab specializes in creating organs-on-a-chip that provide microengineered in vitro platforms to mimic their in vivo counterparts, including lung and bone marrow proxies launched into space this May to study astronaut illness. The lab has spent years fine-tuning its eye-on-a-chip, which earned them the 2018 Lush Prize for its promise in animal-free testing of drugs, chemicals, and cosmetics.

In this study, Huh and Seo focused on engineering an eye model that could imitate a healthy eye and an eye with DED, allowing them to test an experimental drug without risk of human harm.

The Huh lab’s eye-on-a-chip attached to a motorized, gelatin-based eyelid. Blinking spreads tears over the corneal surface, and so was a critical aspect to replicate in the researchers’ model of dry eye disease. cells. The cells of the cornea grow on the inner circle of scaffolding, dyed yellow, and the cells of the conjunctiva grow on the surrounding red circle. Artificial tears are supplied by a tear duct, dyed blue.

To construct their eye-on-a-chip, Huh’s team starts with a porous scaffold engineered with 3D printing, about the size of a dime and the shape of a contact lens, on which they grow human eye cells. The cells of the cornea grow on the inner circle of scaffolding, dyed yellow, and the cells of the conjunctiva, the specialized tissue covering the white part of human eyes, grow on the surrounding red circle. A slab of gelatin acts as the eyelid, mechanically sliding over the eye at the same rate as human blinking. Fed by a tear duct, dyed blue, the eyelid spreads artificial tear secretions over the eye to form what is called a tear film.

“From an engineering standpoint, we found it interesting to think about the possibility of mimicking the dynamic environment of a blinking human eye. Blinking serves to spread tears and generate a thin film that keeps the ocular surface hydrated. It also helps form a smooth refractive surface for light transmission. This was a key feature of the ocular surface that we wanted to recapitulate in our device,” says Huh.

For people with DED, that tear film evaporates faster than it’s replenished, resulting in inflammation and irritation. A common cause of DED is the reduced blinking that occurs during excessive computer usage, but people can develop the disease for other reasons as well. DED affects about 14 percent of the world’s population but has been notably difficult to develop new treatments for, with 200 failed clinical drug trials since 2010 and only two currently available FDA-approved drugs for treatment.

Huh’s lab has been considering the drug-testing potential of organs-on-a-chip since their initial conceptualization, and, because of its surface-level area of impact, DED seemed the perfect place to start putting their eye model to the test. But before they started a drug trial, the team had to ensure their model could really imitate the conditions of DED.

“Initially, we thought modeling DED would be as simple as just keeping the culture environment dry. But as it turns out, it’s an incredibly complex multifactorial disease with a variety of sub-types,” Huh says. “Regardless of type, however, there are two core mechanisms that underlie the development and progression of DED. First, as water evaporates from the tear film, salt concentration increases dramatically, resulting in hyperosmolarity of tears. And second, with increased tear evaporation, the tear film becomes thinner more rapidly and often ruptures prematurely, which is referred to as tear film instability. The question was: Is our model capable of modeling these core mechanisms of dry eye?”

The answer, after much experimentation, was yes. The team evoked DED conditions in their eye-on-a-chip by cutting their device’s artificial blinking in half and carefully creating an enclosed environment that simulated the humidity of real-life conditions. When put to the test against real human eyes, both healthy and with DED, the corresponding eye-on-a-chip models proved their similarity to the actual organ on multiple clinical measures. The eyes-on-a-chip mimicked actual eyes’ performance in a Schirmer strip, which tests liquid production; in an osmolarity test, which looks at tear film salt content; and in a keratography test, which evaluates the time it takes for a tear film to break up.

Having confirmed their eye-on-a-chip’s ability to mirror the performance of a human eye in normal and DED-inducing settings, Huh’s team turned to the pharmaceutical industry to find a promising DED drug candidate to test-drive their model. They landed on an upcoming drug based on lubricin, a protein primarily found in the lubricating fluid that protects joints.

“When people think of DED, they normally treat it as a chronic disease driven by inflammation,” says Huh, “but there’s now increasing evidence suggesting that mechanical forces are important for understanding the pathophysiology of DED. As the tear film becomes thinner and more unstable, friction between the eyelids and the ocular surface increases, and this can damage the epithelial surface and also trigger adverse biological responses such as inflammation. Based on these observations, there is emerging interest in developing ophthalmic lubricants as a topical treatment for dry eye. In our study, we used an lubricin-based drug that is currently undergoing clinical trials. When we tested this drug in our device, we were able to demonstrate its friction-lowering effects, but, more importantly, using this model we discovered its previously unknown capacity to suppress inflammation of the ocular surface.”

By comparing the testing results of their models of a healthy eye, an eye with DED, and an eye with DED plus lubricin, Huh and Seo were able to further scientists’ understanding of how lubricin works and show the drug’s promise as a DED treatment.

Similarly, the process of building a blinking eye-on-a-chip pushed forward scientists’ understanding of the eye itself, providing insights into the role of mechanics in biology. Collaborating with Shenoy, director of the Center for Engineering MechanoBiology, the team’s attention was drawn to how the physical blinking action was affecting the cells they cultivated to engineer an artificial eye on top of their scaffolding.

“Initially, the corneal cells start off as a single layer, but they become stratified and form multiple layers as a result of differentiation, which happens when these cells are cultured at the air-liquid interface. They also form tight cell-cell junctions and express a set of markers during differentiation,” Huh says. “Interestingly, we found out that mechanical forces due to blinking actually help the cells differentiate more rapidly and more efficiently. When the corneal cells were cultured under air in the presence of blinking, the rate and extent of differentiation increased significantly in comparison to static models without blinking. Based on this result, we speculate that blink-induced physiological forces may contribute to differentiation and maintenance of the cornea.”

In other words, human cornea cells growing on the scientists’ scaffold more quickly became specialized and efficient at their particular jobs when the artificial eyelid was blinking on top of them, suggesting that mechanical forces like blinking contribute significantly to how cells function. These types of conceptual advances, coupled with drug discovery applications, highlight the multifaceted value that engineered organs-on-a-chip can contribute to science.

Huh and Seo’s eye-on-a-chip is still just dipping its toes into the field of drug testing, but this first step is a victory that represents years of work refining their artificial eye to reach this level of accuracy and utility.

“Although we have just demonstrated proof-of-concept,” says Seo, “I hope our eye-on-a-chip platform is further advanced and used for a variety of applications besides drug screening, such as testing of contact lenses and eye surgeries in the future.”

“We are particularly proud of the fact that our work offers a great and rare example of interdisciplinary efforts encompassing a broad spectrum of research activities from design and fabrication of novel bioengineering systems to in vitro modeling of complex human disease to drug testing,” says Huh. “I think this is what makes our study unique and representative of innovation that can be brought about by organ-on-a-chip technology.”

This work was supported by the National Institutes of Health through grants 1DP2HL127720–0, R01EY026972 and K08EY025742–01, the National Science Foundation through grants CMMI:15–48571, and Research to Prevent Blindness.

Originally posted on the Penn Engineering Medium blog.

New data reveals cell size sparks genome awakening in embryos

Awakening of the zygote genome over time as decreasing individual cell size triggers early embryo transcription. (Image: Hui Chen, Penn Medicine; Cell Press)

There is a transition during early development when an embryo undergoes biochemical changes, switching from being controlled by maternal molecules to being governed by its own genome.

For the first time, a team from the Perelman School of Medicine found in an embryo that activation of its genome does not happen all at once, instead it follows a specific pattern controlled primarily by the various sizes of its cells. The researchers published their results as the cover story in Developmental Cell.

In an early embryo undergoing cell division, maternally loaded RNA and proteins regulate the cell cycle. The genomes of the zygote—a term for the fertilized egg—are initially in sleep mode. However, at a point in the early life of the embryo, these zygotic nuclei “wake up” and expression from their genomes takes biochemical control over subsequent embryo development. But how an embryo “recognizes” when to undergo this transition has remained unknown.

“How an embryo ‘hands over’ control of development from mother to zygote is a fundamental question in developmental biology,” says senior author Matthew C. Good, an assistant professor of both cell and developmental biology and bioengineering. “Previously it was not appreciated that different regions of a vertebrate embryo can undergo genome activation at different times, or how directly cell size regulates the awakening of a zygote’s genome.”

Read more at Penn Medicine News.

Week in BioE (July 26, 2019)

by Sophie Burkholder

New 3D Tumor Models Could Improve Cancer Treatment

New ways of testing cancer treatments may now be possible thanks to researchers at the University of Akron who developed three-dimensional tumor models of triple-negative breast cancer. Led by Dr. Hossein Tavana, Ph. D., an associate professor of biomedical engineering at the university, the Tissue Engineering Microtechnologies Lab recently received a $1.13 million grant from the prestigious National Cancer Institute (NCI) of the National Institute of Health (NIH) to continue improving these tumor models. Tumors are difficult to fully replicate in vitro, as they are comprised of cancerous cells, connective tissue, and matrix proteins, among several other components. With this new grant, Tavana sees creating a high-throughput system that uses many identical copies of the tumor model for drug testing and better understanding of the way tumors operate. This high-throughput method would allow Tavana and his lab to isolate and test several different approaches at once, which they hope will help change the way tumors are studied and treated everywhere.

Noise-Induced Hearing Loss Poses Greater Threat to Neural Processing

Even though we all know we probably shouldn’t listen to music at high volumes, most of us typically do it anyway. But researchers at Purdue University recently found that noise-induced hearing loss could cause significant changes in neural processing of more complex sound inputs. Led by Kenneth Henry, Ph.D., an assistant professor of otolaryngology at the University of Rochester Medical Center, and Michael Heinz, Ph.D., a professor of biomedical engineering at Purdue University, the study shows that when compared with age-related hearing loss, noise-induced hearing loss will result in a greater decrease in hearing perception even when the two kinds of hearing loss appear to be of the same degree on an audiogram. This is because noise-induced hearing loss occurs because of physical trauma to the ear, rather than the long-term electrochemical degradation of some components that come happen with age. The evidence of this research is yet another reason why we should be more careful about exposing our ears to louder volumes, as they pose a greater risk of serious damage.

Increasing the Patient Populations for Research in Cartilage Therapy and Regenration

Despite the great progress in research of knee cartilage therapy and regeneration, there are still issues with the patient populations that most studies consider. Researchers often want to test new methods on patients that have the greatest chance of injury recovery without complications – often referred to as “green knees” – but this leaves out those patient populations who suffer from conditions or defects that have the potential to cause complications – often referred to as “red knees.” In a new paper published in Regenerative Medicine, the Mary Black Ralston Professor for Education and Research in Orthopaedic Surgery and secondary faculty in the Department of Bioengineering at Penn, Robert Mauck, Ph.D., discusses some cartilage therapies that may be suitable for red knee populations.

Working with James Carey, M.D., the Director of the Penn Center for Cartilage Repair and Osteochondritis, Mauck and his research team realized that even those with common knee cartilage conditions such as the presence of lesions or osteoarthritis were liable to be excluded from most regeneration studies. In discussing alternatives methods and structures of studying cartilage repair and regeneration, Mauck and Carey hope that future therapies will be applicable to a wider range of patient populations, and that there will soon be more options beyond full joint replacement for those with red knee conditions.

Plant-Like Superhydrophobicity Has Applications in Biomedical Engineering

Researchers in the Department of Biomedical Engineering at Texas A&M University recently found ways of incorporating the superhydrophobic properties of some plant leaves into biomedical applications through what they’re calling a “lotus effect.” The Gaharwar Lab, led by principal investigator and assistant professor of biomedical engineering Akhilesh Gaharwar, Ph.D., developed an assembly of two-dimensional atomic layers that they describe as a “nanoflower” to help control surface wetting in a biomedical setting. A recent paper published in Chemical Communications describes Gaharwar and his team’s work as expanding the use of superhydrophobic surface properties in biomedical devices by demonstrating the important role that atomic vacancies play in the wetting characteristic. While Gaharwar hopes to research the impact that controlling superhydrophobicity could have in stem cell applications, his work already allows for innovations in self-cleaning and surface properties of devices involving labs-on-a-chip and biosensing.

People and Places

Nader Engheta, H. Nedwill Ramsey Professor in Electrical and Systems Engineering, Bioengineering and Materials Science and Engineering, has been inducted into the Canadian Academy of Engineering (CAE) as an International Fellow. The CAE comprises many of Canada’s most accomplished engineers and Engheta was among the five international fellows that were inducted this year.

The Academy’s President Eddy Isaacs remarked: “Over our past 32 years, Fellows of Academy have provided insights in the fields of education, infrastructure, and innovation, and we are expecting the new Fellows to expand upon these contributions to public policy considerably.”

Read the full story on Penn Engineering’s Medium Blog. 

We would like to congratulate Anthony Lowman, Ph.D., on his appointment as the Provost and Senior Vice President for Academic Affairs at Rowan University. Formerly the Dean of Rowan’s College of Engineering, Lowman helped the college double in size, and helped foster a stronger research community. Lowman also helped to launch a Ph.D. program for the school, and added two new departments of Biomedical Engineering and Experiential Engineering Education in his tenure as the dean. Widely recognized for his research on hydrogels and drug delivery, Lowman was also formerly a professor of bioengineering at Temple University and Drexel University.

Lastly, we would like to congratulate Daniel Lemons, Ph.D., on his appointment as the Interim President of Lehman College of the City University of New York. Lemons, a professor in the Department of Biology at City College, specializes in cardiovascular and comparative physiology, and was also one of the original faculty members of the New York Center for Biomedical Engineering. With prior research funded by both the National Institute of Health (NIH) and the National Science Foundation (NSF), Lemons also holds patents in biomechanics teaching models and mechanical heart simulators.

 

Week in BioE (July 12, 2019)

by Sophie Burkholder

DNA Microscopy Gives a Better Look at Cell and Tissue Organization

A new technique that researchers from the Broad Institute of MIT and Harvard University are calling DNA microscopy could help map cells for better understanding of genetic and molecular complexities. Joshua Weinstein, Ph.D., a postdoctoral associate at the Broad Institute, who is also an alumnus of Penn’s Physics and Biophysics department and former student in Penn Bioengineering Professor Ravi Radhakrishnan’s lab, is the first author of this paper on optics-free imaging published in Cell.

The primary goal of the study was to find a way of improving analysis of the spatial organization of cells and tissues in terms of their molecules like DNA and RNA. The DNA microscopy method that Weinstein and his team designed involves first tagging DNA, and allowing the DNA to replicate with those tags, which eventually creates a cloud of sorts that diffuses throughout the cell. The DNA tags subsequent interactions with molecules throughout the cell allowed Weinstein and his team to calculate the locations of those molecules within the cell using basic lab equipment. While the researchers on this project focused their application of DNA microscopy on tracking human cancer cells through RNA tags, this new method opens the door to future study of any condition in which the organization of cells is important.

Read more on Weinstein’s research in a recent New York Times profile piece.

Penn Engineers Demonstrate Superstrong, Reversible Adhesive that Works like Snail Slime

A snail’s epiphragm. (Photo: Beocheck)

If you’ve ever pressed a picture-hanging strip onto the wall only to realize it’s slightly off-center, you know the disappointment behind adhesion as we typically experience it: it may be strong, but it’s mostly irreversible. While you can un-stick the used strip from the wall, you can’t turn its stickiness back on to adjust its placement; you have to start over with a new strip or tolerate your mistake. Beyond its relevance to interior decorating, durable, reversible adhesion could allow for reusable envelopes, gravity-defying boots, and more heavy-duty industrial applications like car assembly.

Such adhesion has eluded scientists for years but is naturally found in snail slime. A snail’s epiphragm — a slimy layer of moisture that can harden to protect its body from dryness — allows the snail to cement itself in place for long periods of time, making it the ultimate model in adhesion that can be switched on and off as needed. In a new study, Penn Engineers demonstrate a strong, reversible adhesive that uses the same mechanisms that snails do.

This study is a collaboration between Penn Engineering, Lehigh University’s Department of Bioengineering, and the Korea Institute of Science and Technology.

Read the full story on Penn Engineering’s Medium blog. 

Low-Dose Radiation CT Scans Could Be Improved by Machine Learning

Machine learning is a type of artificial intelligence growing more and more popular for applications in bioengineering and therapeutics. Based on learning from patterns in a way similar to the way we do as humans, machine learning is the study of statistical models that can perform specific tasks without explicit instructions. Now, researchers at Rensselaer Polytechnic Institute (RPI) want to use these kinds of models in computerized tomography (CT) scanning by lowering radiation dosage and improving imaging techniques.

A recent paper published in Nature Machine Intelligence details the use of modularized neural networks in low-dose CT scans by RPI bioengineering faculty member Ge Wang, Ph.D., and his lab. Since decreasing the amount of radiation used in a scan will also decrease the quality of the final image, Wang and his team focused on a more optimized approach of image reconstruction with machine learning, so that as little data as possible would be altered or lost in the reconstruction. When tested on CT scans from Massachusetts General Hospital and compared to current image reconstruction methods for the scans, Wang and his team’s method performed just as well if not better than scans performed without the use of machine learning, giving promise to future improvements in low-dose CT scans.

A Mind-Controlled Robotic Arm That Requires No Implants

A new mind-controlled robotic arm designed by researchers at Carnegie Mellon University is the first successful noninvasive brain-computer interface (BCI) of its kind. While BCIs have been around for a while now, this new design from the lab of Bin He, Ph.D.,  a Trustee Professor and the Department Head of Biomedical Engineering at CMU, hopes to eliminate the brain implant that most interfaces currently use. The key to doing this isn’t in trying to replace the implants with noninvasive sensors, but in improving noisy EEG signals through machine learning, neural decoding, and neural imaging. Paired with increased user engagement and training for the new device, He and his team demonstrated that their design enhanced continuous tracking of a target on a computer screen by 500% when compared to typical noninvasive BCIs. He and his team hope that their innovation will help make BCIs more accessible to the patients that need them by reducing the cost and risk of a surgical implant while also improving interface performance.

People and Places

Daeyeon Lee, professor in the Department of Chemical and Biomolecular Engineering and member of the Bioengineering Graduate Group Faculty here at Penn, has been selected by the U.S. Chapter of the Korean Institute of Chemical Engineers (KIChE) as the recipient of the 2019 James M. Lee Memorial Award.

KIChE is an organization that aims “to promote constructive and mutually beneficial interactions among Korean Chemical Engineers in the U.S. and facilitate international collaboration between engineers in U.S. and Korea.”

Read the full story on Penn Engineering’s Medium blog.

We would also like to congratulate Natalia Trayanova, Ph.D., of the Department of Biomedical Engineering at Johns Hopkins University on being inducted into the Women in Tech International (WITI) Hall of Fame. Beginning in 1996, the Hall of Fame recognizes significant contributions to science and technology from women. Trayanova’s research specializes in computational cardiology with a focus on virtual heart models for the study of individualized heart irregularities in patients. Her research helps to improve treatment plans for patients with cardiac problems by creating virtual simulations that help reduce uncertainty in either diagnosis or courses of therapy.

Finally, we would like to congratulate Andre Churchwell, M.D., on being named Vanderbilt University’s Chief Diversity Officer and Interim Vice Chancellor for Equity, Diversity, and Inclusion. Churchwell is also a professor of medicine, biomedical engineering, and radiology and radiological sciences at Vanderbilt, with a long career focused in cardiology.

Penn Engineers’ ‘LADL’ Uses Light to Serve Up On-demand Genome Folding

Every cell in your body has a copy of your genome, tightly coiled and packed into its nucleus. Since every copy is effectively identical, the difference between cell types and their biological functions comes down to which, how and when the individual genes in the genome are expressed, or translated into proteins.

Scientists are increasingly understanding the role that genome folding plays in this process. The way in which that linear sequence of genes are packed into the nucleus determines which genes come into physical contact with each other, which in turn influences gene expression.

LADL combines CRISPR/Cas9 and optogenetics to bring two distant points in a linear gene sequence into physical contact, forming a folding pattern known as a “loop.” Looping interactions influence gene expression, so the researchers envision LADL as being a powerful tool for studying these dynamics.

Jennifer Phillips-Cremins, assistant professor in Penn Engineering’s Department of Bioengineering, is a pioneer in this field, known as “3-D Epigenetics.” She and her colleagues have now demonstrated a new technique for quickly creating specific folding patterns on demand, using light as a trigger.

The technique, known as LADL or light-activated dynamic looping, combines aspects of two other powerful biotechnological tools: CRISPR/Cas9 and optogenetics. By using the former to target the ends of a specific genome fold, or loop, and then using the latter to snap the ends together like a magnet, the researchers can temporarily create loops between exact genomic segments in a matter of hours.

The ability to make these genome folds, and undo them, on such a short timeframe makes LADL a promising tool for studying 3D-epigenetic mechanisms in more detail. With previous research from the Phillips-Cremins lab implicating these mechanisms in a variety of neurodevelopmental diseases, they hope LADL will eventually play a role in future studies, or even treatments.

Jennifer Phillips-Cremins, Ji Hun Kim and Mayuri Rege

Alongside Phillips-Cremins, lab members Ji Hun Kim and Mayuri Rege led the study, and Jacqueline Valeri, Aryeh Metzger, Katelyn R. Titus, Thomas G. Gilgenast, Wanfeng Gong and Jonathan A. Beagan contributed to it. They collaborated with associate professor of Bioengineering Arjun Raj and Margaret C. Dunagin, a member of his lab.

The study was published in the journal Nature Methods.

“In recent years,” Phillips-Cremins says, “scientists in our fields have overcome technical and experimental challenges in order to create ultra-high resolution maps of how the DNA folds into intricate 3D patterns within the nucleus. Although we are now capable of visualizing the topological structures, such as loops, there is a critical gap in knowledge in how genome structure configurations contribute to genome function.”

In order to conduct experiments on these relationships, researchers studying these 3D patterns were in need of tools that could manipulate specific loops on command. Beyond the intrinsic physical challenges — putting two distant parts of the linear genome in physical contact is quite literally like threading a needle with a thread that is only a few atoms thick — such a technique would need to be rapid, reversible and work on the target regions with a minimum of disturbance to neighboring sequences.

The advent of CRISPR/Cas9 solved the targeting problem. A modification of the gene editing tool allowed researchers to home in on the desired sequences of DNA on either end of the loop they wanted to form. If those sequences could be engineered to seek one another out and snap together under the other necessary conditions, the loop could be formed on demand.

Cremins Lab members then sought out biological mechanisms that could bind the ends of the loops together, and found an ideal one in the toolkit of optogenetics. The proteins CIB1 and CRY2, found in Arabidopsis, a flowering plant that’s a common model organism for geneticists, are known to bind together when exposed to blue light.

“Once we turn the light on, these mechanisms begin working in a matter of milliseconds and make loops within four hours,” says Rege. “And when we turn the light off, the proteins disassociate, meaning that we expect the loop to fall apart.”

“There are tens of thousands of DNA loops formed in a cell,” Kim says. “Some are formed slowly, but many are fast, occurring within the span of a second. If we want to study those faster looping mechanisms, we need tools that can act on a comparable time scales.”

As shown in a 2013 Nature Methods paper by fellow Penn bioengineer Lukasz Bugaj, the optical response of the CRY2 protein is a key component of LADL. When the blue light is turned on, CRY2 proteins in cell immediately find one another and bind together into clumps large enough to be seen under magnification. When the light is turned off, the clumps begin to dissolve away.”

Fast acting folding mechanisms also have an advantage in that they lead to fewer perturbations of the surrounding genome, reducing the potential for unintended effects that would add noise to an experiment’s results.

The researchers tested LADL’s ability to create the desired loops using their high-definition 3D genome mapping techniques. With the help of Arjun Raj, an expert in measuring the activity of transcriptional RNA sequences, they also were able to demonstrate that the newly created loops were impacting gene expression.

The promise of the field of 3D-epigenetics is in investigating the relationships between these long-range loops and mechanisms that determine the timing and quantity of the proteins they code for. Being able to engineer those loops means researchers will be able to mimic those mechanisms in experimental conditions, making LADL a critical tool for studying the role of genome folding on a variety of diseases and disorders.

“It is critical to understand the genome structure-function relationship on short timescales because the spatiotemporal regulation of gene expression is essential to faithful human development and because the mis-expression of genes often goes wrong in human disease,” Phillips-Cremins says. “The engineering of genome topology with light opens up new possibilities to understanding the cause-and-effect of this relationship. Moreover we anticipate that, over the long term, the use of light will allow us to target specific human tissues and even to control looping in specific neuron subtypes in the brain.”

The research was supported by the New York Stem Cell Foundation; Alfred P. Sloan Foundation; the National Institutes of Health through its Director’s New Innovator Award from the National Institute of Mental Health, grant no. 1DP2MH11024701, and a 4D Nucleome Common Fund, grant no. 1U01HL1299980; and the National Science Foundation through a joint NSF-National Institute of General Medical Sciences grant to support research at the interface of the biological and mathematical sciences, grant no. 1562665, and a Graduate Research Fellowship, grant no. DGE-1321851.

Originally published on the Penn Engineering Medium blog.