BIOTRANS 2020, Vol. 5
CONTENTS 3 L e t t e r f r o m t h e C o - D i r e c t o r s 4 N e w s 12 BIOTRANS Research 14 Cover Story | Linsey Marr 20 Student Profiles 23 BIOTRANS Faculty 24 F a c u l t y S p o t l i g h t 26 Alumni Corner
About BIOTRANS We are a community of biologists and engineers that collaborate to study transport in environmental and physiological systems.
Editor: Art Director: Writers: Photography:
Kristin Rose Jutras Alex Crookshanks Kristin Rose Jutras, Kendall Daniels, Rasha Aridi, James Urton, Laura Weatherford, and Alex Parrish Alex Crookshanks, Peter Means, Spencer Roberts, and Ryan Young
Photo this page: Linsey Marr in her laboratory. Photo credit: Ryan Young Cover photo: Linsey Marr wearing PPE and practicing social distancing with a couple of her laboratory assistants. Photo credit: Alex Crookshanks
DIRECTORS’ MESSAGE Rising to Meet the Challenge! Welcome to the 2020 Biological Transport (BIOTRANS) magazine, our fifth annual issue highlighting our interdisciplinary graduate education program at Virginia Tech. The BIOTRANS community consists of a highly collaborative group of life scientists and engineers who study transport in biological systems. Despite the challenge posed by the COVID-19 pandemic during the second half of the academic year, our students and faculty found ways to remain engaged and be successful. This pandemic has truly underscored the importance and value of interdisciplinary research, exemplified in the tireless work of Dr. Linsey Marr and graduate student Jin Pan. Dr. Marr is a world-renowned expert in the transmission of virus by aerosols, an issue that is perhaps the core feature of understanding and dealing with the pandemic. When the scope of the problem became clear, their lab shifted into high gear, ramping up quickly to test mask effectiveness and other scientifically relevant questions. We applaud and highlight their heroic efforts on page 16. We would like to congratulate our newest Ph.D. graduates, Dr. John (Jack) Whitehead, Dr. Nicolaas (Nico) Baudoin, and Dr. Khaled Adjerid. Their work on biological transport spans from the subcellular (chromosomes and cellular organelles) to sub-organismal (insect respiratory structures) to the organismal and environmental (ducks landing on water) level. Learn more on page 15. Our three newest trainees—Landon Bilyeu, Maria Gonzalez, and Will Snyder—completed their first-year rotations, presented their rotation work at well-attended meetings, and selected their advisors and co-advisors. You can learn more about some of their first-year experiences on pages 20-21.
Our more senior trainees received awards and published their work. To learn more, please refer to page 13 of the magazine. The work of several BIOTRANS labs caught the attention of the national news. Learn more about their work on pages 4-11. Finally, our faculty and students have continued to secure funding to support their amazing BIOTRANS research. Below is a small sample: • Dr. Linsey Marr and BIOTRANS alumnus Dr. A.J. Prussin are Co-PIs on a one-year $200K Rapid Response Research grant from the NSF to develop and test low-cost sensor platforms for SARS-CoV-2 in aerosols. • Drs. Hosein Foroutan, David Schmale, and Shane Ross were awarded a $1.1 million grant from NASA to investigate how microbes can travel across the Atlantic on dust plumes in collaboration with the U.S. Geological Survey and the University of La Laguna in the Canary Islands. • Dr. Jing Chen was awarded a $1.86 million NIH R35 (MIRA) grant to develop mathematical models to study spatiotemporal and mechanical processes in prokaryotic and eukaryotic cells. Drs. Melville and Cimini will be her experimental collaborators for the project. We would like to conclude by thanking our amazing community for remaining engaged during the spring semester, despite the challenges posed by the lockdown. We enjoyed seeing many of you via Zoom and we look forward to seeing you again in person soon. We also highly encourage interested students to consider applying to our program. In the meantime, enjoy the new issue of the magazine.
Jake Socha, Ph.D. & Daniela Cimini, Ph.D Co-Directors of BIOTRANS
BIOTRANS | NEWS
Mosquitoes are drawn to flowers as much as people - and now scientists know why Written by James Urton and Kendall Daniels
WITHOUT THEIR KEEN SENSE OF
smell, mosquitoes wouldn’t get very far. They rely on this sense to find a host to bite and spots to lay eggs. And without that sense of smell, mosquitoes could not locate their dominant source of food: nectar from flowers. “Interestingly, only females need blood. They use it to produce their eggs. However, males rely 100 percent on nectar to survive. Females also feed on nectar which increases they longevity and survival,” said Chloé Lahondère, a research assistant professor from the Department of Biochemistry in the Virginia Tech College of Agriculture and Life Sciences. Yet scientists know little about the scents that draw mosquitoes toward certain flowers, or repel them from others. This information could help develop less toxic and better repellents, more effective traps, and lead to an understanding of how the mosquito brain responds to sensory information — including the cues that, on occasion, lead a female mosquito to bite one of us. Lahondère and the rest of the research team, which includes assistant professor Clément Vinauger from the Department of Biochemistry, as well as researchers from the University of Washington and UC San Diego, have discovered the chemical cues that lead mosquitoes to pollinate a particularly irresistible species of orchid — the blunt-leaf orchid, also known as Platanthera obtusata. As they report in a paper published in the Proceedings of the National Academy of Sciences, the orchid
A mosquito on the Platanthera orchid. Note the two yellow pollen masses that are stuck on its head. Photo courtesy of Chloé Lahondère for Virginia Tech.
produces a finely balanced bouquet of chemical compounds that stimulate mosquitoes’ sense of smell. “We found that this orchid emits chemicals that attract different mosquito species, including Aedes aegypti, an invasive disease vector species that is not present in the native area of the orchid. And interestingly, all these mosquitoes respond to the same volatiles that the orchid emits,” said Lahondère, who is the lead researcher for this study and an affiliated faculty member of the Global Change Center, an arm of the Fralin Life Sciences Institute at Virginia Tech. “This means that we can use this knowledge to develop new baits based on the flower scent and target a large diversity of mosquito species.” On their own, some of these chemicals have either attractive or repressive effects on the mosquito brain. When combined in the same ratio as they’re found in the orchid, they draw in mosquitoes as effectively as a real flower. The research team also found
that one of the scent chemicals that repels mosquitoes lights up the same region of the mosquito brain as DEET, a common and controversial mosquito repellant. Their findings show how environmental cues from flowers can stimulate the mosquito brain as much as a warm-blooded host — and can draw the mosquito toward a target or send it flying the other direction, said Jeffrey Riffell, a professor of biology at the University of Washington and senior author of the study. The blunt-leaf orchid grows in cool, high-latitude climates across the Northern Hemisphere. From field stations in the Okanogan-Wenatchee National Forest in Washington state, the research team verified past research showing that local mosquitoes pollinate this species, but not its close relatives that grow in the same habitat. When researchers covered the flowers with bags — depriving the mosquitoes of a visual cue for the
flower — the mosquitoes would still land on the bagged flowers and attempt to feed through the canvas. Orchid scent obviously attracted the mosquitoes. To find out why, the team turned to the individual chemicals that make up the bluntleaf orchid’s scent. “We often describe ‘scent’ as if it’s one thing — like the scent of a flower, or the scent of a person,” said Riffell. “Scent is actually a complex combination of chemicals — the scent of a rose consists of more than 300 — and mosquitoes can detect the individual types of chemicals that make up a scent.” The blunt-leaf orchid is described to have a scent that has a grassy or musky odor, while its close relatives have a sweeter fragrance. The team used gas chromatography and mass spectroscopy to identify dozens of chemicals in the scents of the Platanthera species. Compared to its relatives, the blunt-leaf orchid’s scent contained high amounts of a compound called nonanal, and smaller amounts of another chemical, lilac aldehyde. Researchers also recorded the electrical activity in mosquito antennae, which detect scents. Both nonanal and lilac aldehyde stimulated antennae of mosquitoes that are native to the blunt-leaf orchid’s habitat. But these compounds also stimulated the antennae of mosquitoes from other regions, including Anopheles stephensi, which spreads malaria, and Aedes aegypti, which spreads dengue, yellow fever, Zika, and other diseases. “Beyond the notion that mosquitoes can actually be useful in that they pollinate endangered orchids, this study also provides new knowledge on the neural circuits that regulate mosquito olfaction. Down the line, these discoveries could lead to the identification of even more targets to prevent mosquitoes from finding us,” said Vinauger, who is an affiliated faculty member of the Fralin Life
Sciences Institute and the BIOTRANS program. Experiments of mosquito behavior showed that both native and nonnative mosquitoes preferred a solution of nonanal and lilac aldehyde mixed in the same ratio as found in blunt-leaf flowers. If the researchers omitted lilac aldehyde from the recipe, mosquitoes lost interest. If they added more lilac aldehyde — at levels found in the blunt-leaf orchid’s close relatives — mosquitoes were indifferent or repelled by the scent. Using techniques developed in Riffell’s lab, the team peered directly into the brains of Aedes increpitus
can suppress activity in the region that responds to lilac aldehyde, and vice versa. Whether this “cross talk” makes a flower attractive or repelling to the mosquito likely depends on the amounts of nonanal and lilac aldehyde in the original scent. As far as future projects are concerned, Lahondère and Vinauger hope to use their recent findings from Washington to learn more about a relationship that exists between ornamental plants and invasive mosquitoes in Virginia. “Sugar feeding is one of our main projects right now. Based on our results, we hope to develop new
Chloé Lahondère, setting up the scent collection system around mosquito pollinated orchids. Photo courtesy of Clément Vinauger for Virginia Tech.
mosquitoes, which overlap with blunt-leaf orchids, and a genetically modified strain of Aedes aegypti previously developed by Riffell and co-author Omar Akbari, an associate professor at UC San Diego. They imaged calcium ions — signatures of actively firing neurons — in the antenna lobe, the region of the mosquito brain that processes signals from the antennae. These brain imaging experiments revealed that nonanal and lilac aldehyde stimulate different parts of the antenna lobe — and even compete with one another when stimulated: The region that responds to nonanal
efficient baits targeting important disease vectors, such as Ae. aegypti and Ae. albopictus, which are vectors of dengue, yellow fever, and Zika,” said Lahondère, who is also an affiliated faculty member of the BIOTRANS program. In addition to Lahondère, Vinauger, and Riffell, the co-authors of this paper are UW biology graduate students Ryo Okubo and Jeremy Chan and UW postdoctoral researcher Gabriella Wolff. The research was funded by the National Institutes of Health, the Air Force Office of Scientific Research, and the University of Washington.
BIOTRANS | NEWS insect was head-up (upright) while air sacs in the abdomen were smaller. When the animal was head-down, the opposite was true: the air sacs in the lower part of the body of the head were decreased in size while the air sacs in the thorax were greatly expanded. “No one expected that a small insect would have any type of response due to their gravitational orientation,” Socha said, who is also the director of Virginia Tech’s BIOTRANS, an interdisciplinary graduate team of biologists and engineers who work together to study transport in environmental and physiological systems. “This project started by seeing some weird things in X-ray images and asking questions.”
Jake Socha, professor in biomedical engineering and mechanics, conducts research on animal biomechanics. His recent publication in the Proceedings of the National Academy of Sciences journal discusses insects’ physiological responses to gravity. Photo by Peter Means for Virginia Tech.
X-ray images help reveal insects’ physiological responses to gravity
Written by Laura Weatherford
Written by Laura Weatherford
upside down and standing on your head. After a few seconds, you would feel pressure in your head due to an increased blood flow. Humans and other vertebrates are known to have physiological reactions to gravity with reactions increasing with body size. A new study by Jake Socha, professor in biomedical engineering and mechanics in Virginia Tech’s College of Engineering, published in the Proceedings of the National Academies of Science journal “Physiological Responses to Gravity in an Insect,” shows that insects experience similar physiological effects of gravity. With
environmental physiology at Arizona State University, and undergraduate, graduate, and postdoctoral students, Socha assessed the effect of gravity on insects and discovered an active response called functional compartmentalization. To determine the effect on schistocerca americana, commonly known as the American grasshopper, the team analyzed X-ray images at Argonne National Laboratory to observe their internal systems. In some images, the grasshoppers were head-up, and in others the grasshoppers’ heads faced the ground. When analyzing the X-ray images of grasshoppers, the researchers discovered that air sacs located in the head had greatly expanded when the
Their discoveries indicate that the pressure of gravity may affect the insect’s body and its bodily systems, just as in humans. This is counterintuitive to scientific thought and could have larger implications in future research. Socha compared this effect to diving into a deep swimming pool. As a person dives lower down into the water, there is more pressure. This same concept applies to the grasshopper’s body. The part of the body that is lower, or beneath the rest of the body, has higher blood pressure and thus, the air sacs are compressed. However, when the insect is awake, the response is different. The air sacs change less in response to orientation. To further analyze this active response, called functional compartmentalization, the researchers further examined the grasshopper. “Our findings suggest that animals had control of the inside of their bodies,” Socha said. “Earlier this year, we published a paper with a similar finding. We analyzed beetles and found they had active
Even though insects do not have a closed circulatory system with veins and arteries, most insects typically have a tube-like heart. These researchers found that the grasshopper’s heart rate would slow when head-down and beat faster when head-up, thus providing more evidence to point to insects’ systems not only being affected by gravity but having active, physiological responses to compensate for gravity’s effects, contrary to scientific prediction.
Image of a Melonaplus grasshopper. Photo by Jake Socha for Virginia Tech
body responses to compensate for forces on their bodies. So, we were interested in the other physiological responses of other animals.” Grasshoppers and other insects have open circulatory systems, which means that their blood is not contained in closed arteries or veins. Classic understanding of open circulatory systems is that blood flows freely within the body, like liquid in a bottle, and that pressures inside the body would all be similar. The research team discovered that these insects, in fact, could separate, or alter, internal body pressures with a flexible valving system. “This was remarkable,” Socha said. “We had been seeing odd occurrences in X-rays, so we had ideas that something was going on. Finding this gave us the evidence to conclude that grasshoppers do have a mechanism to counteract gravity, which is counterintuitive to most scientists.”
The researchers also found that grasshoppers’ heart rates change with orientation just as observed in humans. Humans sometimes feel dizzy when standing up too quickly because gravity impedes blood flow to the brain; fast-acting reflexes cause the heart to pump harder to overcome this gravity effect.
“We have multiple indicators pointing to the grasshoppers responding to its body orientation,” said Socha, who is also an affiliate faculty member in Virginia Tech’s biological sciences and mechanical engineering departments. “They respond physiologically to its orientation relative to gravity and have mechanisms inside its body to be able to deal with it. Grasshoppers are able to change their heart rate, respiratory rate, and functionally compartmentalize their bodies to control pressure.” Other Virginia Tech researchers collaborating on the project include Hodjat Pendar, research assistant professor in biomedical engineering and mechanics, and Khaled Adjerid, previously a doctoral student in the department.
Jake Socha stands in his lab in Norris Hall, where his group does experiments and does bio-inspired 7 design. Photo by Peter Means for Virginia Tech.
BIOTRANS | NEWS
Jonathan Boreyko and Brook Kennedy inspect a fog harp at Kentland Farm. Photo by Peter Means for Virginia Tech.
Virginia Tech’s fog harp harvests water even in the lightest fog Written by Alex Parrish
WHAT DO YOU GET WHEN YOU
less dense fog than its predecessors.
The development of the fog harp, a Virginia Tech interdisciplinary pairing of engineering with biomimetic design, was first reported in 2018. The hope behind the fog harp’s development was simple: in areas of the world where water is scarce but fog is present, pulling usable water from fog could become a sustainable option. While fog nets are already in use, the superior efficiency of the fog harp could dramatically increase the number of regions worldwide where fog harvesting is viable. The difference comes in the fog harp’s uncanny ability to derive water from
The partnered approach has been a combination of new design with existing science. The science initiated with Assistant Professor Jonathan Boreyko from the Department of Mechanical Engineering within the College of Engineering. His group hypothesized the harp approach and characterized the performance of the harp prototypes. Design development has been led by Associate Professor Brook Kennedy from the Department of Industrial Design in the College of Architecture and Urban Studies. Kennedy’s product development and materials knowledge brought the project to the point where it could be prototyped and tested in real-world environments. Early funding came
cross a novel approach to water harvesting with a light fog? The answer: a lot more water than you expected.
from the Institute for Creativity, Arts, and Technology. “Billions of people face water scarcity worldwide,” Kennedy said. “We feel that the fog harp is a great example of a relatively simple, lowtech invention that leverages insight from nature to help communities meet their most basic needs.” The “harp” design uses parallel wires to collect ambient water from fog, whereas current technology in use around the globe relies primarily on a screen mesh. The lab-proven theory for the new device was that parallel wires are more efficient at gathering water, avoiding clogs and enhancing drainage into the collector. The researchers’ small-scale early tests showed that in high-fog conditions, their harps outpaced those with
meshes by a factor of two to one. Testing then literally moved to the field. In the open fields of Virginia Tech’s Kentland Farm, thenundergraduate Brandon Hart built roofed structures to prevent rainfall from impacting findings. Under these coverings, fog harps were placed side-by-side with three different mesh harvesters: one with wire diameters equivalent to the harp, one with a wire size more optimal to harvesting, and one using Raschel mesh — a mesh made of flat-panel ribbons in v-shaped arrays between horizontal supports. This v-shaped mesh is currently the most popular among fog harvesting sites around the world. Whereas heavy fog conditions were used in the lab, the actual fog conditions surrounding Virginia Tech are generally much lighter. As field tests began, Boreyko and Kennedy were skeptical that the available fog would provide the feedback they
needed to do adequate testing. They were pleasantly surprised. As fog began rolling over the hills of the New River Valley, the fog harps always showed results. In thin fog, the collection pipes of the mesh collectors were completely devoid of drips. Even as fog density increased, the harps continued outperforming their companions. Depending on the density of the fog, this ranged from twice as much output to almost 20 times. Bringing together lab studies and field data, researchers determined that collection potential is the result of multiple factors. Greatest among these is the size of collectable water droplets between mesh and harp. To be harvested in both cases, water must be caught on the mesh or harp as air passes through, traveling downward into collection points by gravity. Fog harps use only vertical wires, creating an unimpeded path for mobile drops. Mesh collectors,
by contrast, have both horizontal and vertical construction, and water droplets must be significantly larger to cross the horizontal pieces. In field tests, mesh collectors routinely required droplets reaching a size roughly 100 times larger than those on harps before descending. Water that never drops will simply evaporate and cannot be collected. “We already knew that in heavy fog, we can get at least two times as much water,” said Boreyko. “But realizing in our field tests that we can get up to 20 times more water on average in a moderate fog gives us hope we can dramatically enhance the breadth of regions where fog harvesting is a viable tool for getting decentralized, fresh water.” Full publication of the field tests have been accepted by Advanced Sustainable Systems, written by lead author Weiwei Shi.
Water drops are caught on the wires 9 of a fog harp. Photo by Peter Means for Virginia Tech.
BIOTRANS | NEWS
Daniela Cimini (left), Jing Chen (middle), and Nicolaas Baudoin (right) view images from a wide-field fluorescence microscope. Photo by Alex Crookshanks of Virginia Tech.
Researchers use cell imaging and mathematical modeling to understand cancer progression Written by Laura Weatherford
Written by Kendall Daniels
fundamental process that organisms need to reproduce, grow, and make repairs. But when an error disrupts this complex biological process, cellular abnormalities can lead to diseases, such as cancer, where cells are enabled to grow and divide out of control.
Using a combination of experiments and mathematical modeling, a team of researchers from the Virginia Tech Department of Biological Sciences in the College of Science and the Fralin Life Sciences Institute are beginning to unravel the mechanisms that lie behind tetraploidy - a chromosomal abnormality that is often found in malignant tumors.
Their findings were published on April 29 in eLife, an open-access journal that is dedicated to life science research. “Our study used fixed cell analysis, live cell imaging, and mathematical modeling to help us better understand the role of tetraploidy in tumor formation and progression. This work lays the foundation for future studies to really understand the link between tetraploidy and cancer. If we know what is happening in tumors, then we can have a better idea of how to develop better treatments for them,” said Nicolaas Baudoin, the lead author on the study and a recent Ph.D. graduate in the Department of Biological Sciences and the BIOTRANS program, an
interdisciplinary graduate program of biologists and engineers. Every human ‘parent’ cell holds two copies of each chromosome. Before cell division begins, every chromosome is duplicated so that the genetic information can be equally distributed between two ‘daughter’ cells. But if the parent cell fails to complete cell division, all four chromosomes are allocated into one daughter cell, thus making the cell tetraploid. When tetraploid cells acquire twice the number of chromosomes, they also acquire twice the number of centrosomes. Among their organizational and structural roles, centrosomes are key to forming microtubules and spindle fibers, which work to pull chromosomes apart during cell division. With the overabundance of centrosomes, the chromosomes are pulled in many
different directions and cell division can have abnormal results.
and cancer investigation.
member of the Fralin Life Sciences Institute and BIOTRANS.
Previous studies had suggested that these extra centrosomes may cause tumor formation, induced by tetraploidy. But then, the Virginia Tech team came across two studies in cancer progression models, which showed that the cells gained extra centrosomes initially, but ended up losing them over time.
The mathematical model also found that the only cells that could sustain long-term survival with extra centrosomes were cells that could successfully and consistently cluster these centrosomes in two groups during cell division. These predictions were tested experimentally and revealed a mechanism that explains why certain cancer cells survive despite their additional centrosome count. And if cells failed to cluster their extra centrosomes effectively, the next generation of daughter cells died.
Next, the team would like to take advantage of their model to better understand the cellular dynamics within three-dimensional cultures and real tumors.
“The main goal of our study was to verify that tetraploid cells lose the extra centrosomes, examine the dynamics of this process, and uncover the mechanism that causes this centrosome loss from tetraploid cells,” said Daniela Cimini, a professor from the Department of Biological Sciences and the codirector of BIOTRANS. Using live cell imaging and fixed cell analysis in an in vitro model, the team confirmed that tetraploid cells did lose the extra centrosomes that they had gained during tetraploidization. In experiments guided by mathematical modeling, they concluded that centrosome loss happens when dividing tetraploid cells cluster their extra centrosomes asymmetrically. As a result, one of the daughter cells will inherit one centrosome - instead of two which will allow the cell to suffer fewer cell division failures and produce more cells in the long term.
Baudoin and Cimini agree that this level of mechanistic understanding was only possible thanks to their collaboration with Jing Chen, a mathematical biologist and assistant professor of biological sciences in the Virginia Tech College of Science. “Built upon experimental measurements, the mathematical model paints a continuous and detailed picture about how the cells’ centrosome numbers change. This allows us to see information that cannot be measured by experiments.” said Chen, an affiliated faculty
In their in vitro system, the team could get a sense of what was happening within the cells by tracking and imaging them, but this cannot be done in more complex systems like real tumors. With their newest model and previous data, the team will be able to make some compelling predictions. According to Chen, the success of present and future cancer studies could be attributed to a unique, but all important, collaboration between researchers in the fields of biology and mathematics. “This hand-in-hand collaboration between experimentalist and modeler is very important - and it’s a great approach for modeling biological studies. The process requires a lot of close communication between us. When that’s done correctly, it can be very powerful,” said Chen. A tetraploid RPE-1 mitotic cell. Centrioles are displayed in green (two dots at each centrosome/spindle pole); microtubules are displayed in red; chromosomes are displayed in blue. The image was acquired on a wide-field fluorescence microscope. Image courtesy of Daniela Cimini.
This finding can explain how certain cancers may first gain extra centrosomes during tetrapl oidiz a tio n , but then lose them at later stages. This indicates that the causal relationship between tetraploidy
BIOTRANS | RESEARCH
1. Davalos and student at worktable. 2. Schmale student gathers a water sample. 3. De Vita was honored by the American Society of Mechanical Engineers for her significant contributions as an internationally recognized expert in biomechanics. Photo credit: Emily Roediger. 4. Culex quinquefasciatus mosquito thermogram. Courtesy of Chloé Lahondère 5. Hosein Foroutan (left), David Schmale (middle), and Shane Ross (right) standing behind their drone, which is mounted with a 3D-printed sampling device Photo credit: Alex Crookshanks 6. Grants for interdisciplinary projects help new collaborations grow. Erica Corder for Virginia Tech. 7. Dr. Chloé Lahondère handling a frog at Mountain Lake Biological Station. 12 credit: Joanna Reinhold Photo
B I O T R A N S | S T U D E N T AWA R D S Hyunggon Park Liviu Librescu Memorial Fellowship awarded by Engineering Mechanics
Sussman Fellowship Virginia Tech Department of Biological Sciences Robert and Marion Patterson Scholarship for excellence in research
Virginia Tech Graduate Student Development Award, Fall 2019
SELECT LIST OF 2020 PUBLICATIONS BY BIOTRANS LABS:
LahondĂ¨re C., Vinauger C., Okubo R.P., Wolff G.H., Chan J.K., Akbari O.S., Riffell J.A. (2020). The olfactory basis of orchid pollination by mosquitoes. Proceedings of the National Academy of Sciences, 117: 708-716. doi: 10.1073/pnas.1910589117 Harrison J.F., Adjerid K., Kassi A., Klok C.J., VandenBrooks J.M., Duell M.E., Campbell J.B., Talal S., Abdo C.D., Fezzaa K., Pendar H., Socha J.J. (2020). Physiological responses to gravity in an insect. Proceedings of the National Academy of Sciences, 117: 2180-2186. doi: 10.1073/pnas.1915424117 Lin K., Marr L.C. (2020). Humidity-dependent decay of viruses, but not bacteria, in aerosols and droplets follows disinfection kinetics. Environmental Science & Technology, 54: 1024-1032. doi: 10.1021/acs.est.9b04959 Baudoin N.C., Nicholson J.M., Soto K., Martin O., Chen J., and Cimini D. (2020). Asymmetric clustering of centrosomes defines the early evolution of tetraploid cells. eLife, 9: e54565. doi: 10.7554/eLife.54565 Graybill P.M., Davalos R.V. (2020). Cytoskeletal disruption after electroporation and its significance to pulsed electric field therapies. Cancers, 12: 1132. doi: 10.3390/cancers12051132 Yeaton I.J., Ross S.D., Baumgardner G.A., Socha J.J. (2020). Undulation enables gliding in flying snakes. Nature Physics, 16: 974â€“982. doi: 10.1038/s41567-020-0935-4
BIOTRANS | COVER STORY
Spurred by COVID-19, BIOTRANS researcher Linsey Marr evaluates efficacy of sterilized N95 respirators and alternative mask materials
- Written by Suzanne Irby, Eleanor Nelsen, and Kendall Daniels
SINCE MARCH, VIRGINIA TECH PROFESSOR
Linsey Marr, an expert in the airborne transmission of infectious disease, has been testing the efficacy of sterilized N95 respirators and alternative mask materials in filtering out particles. The science experiments conducted by Marr’s team aim to quantify how well different forms of personal protective equipment and homemade face coverings shield their wearers against COVID-19, especially in the face of shortages and sluggish PPE supply chains. Because of these shortages, the medical community and the wider public have turned to improvisation. Some hospitals have worked to extend the use of their stores of N95 respirators by sterilizing them. Members of the public, advised by the Centers of Disease Control and Prevention to wear cloth face coverings in public places, are also exploring creative solutions by sourcing off-the-shelf materials for homemade masks. As people adapt, Marr’s team is working to supply them with insights grounded in science. “Since I understand how the coronavirus moves around in air, I knew how important it was for health care workers to have proper respiratory protection,” said Marr, the Charles P. Lunsford Professor of Civil and Environmental Engineering. “I knew my lab could help by testing N95s after sterilization to ensure that they could be reused safely. I quickly wrote up a procedure, and my students reconfigured our equipment to start running experiments.” Marr’s lab broadly looks at the sources, transformations, and fate of air pollutants. Over the years, she’s focused on engineered nanomaterials and viral aerosols — mainly those of the flu for the latter — and how they can be physically and chemically transformed in the environment. When testing sterilized N95 respirators, Marr and graduate students Jin Pan and Charbel Harb found that the respirators retained their ability to filter particles after up to 10 cycles of sterilization with hydrogen peroxide vapor and ethylene oxide.
Lindsey Marr (center) with Charbel Harb (left) and Jin Pan (right) 15 practicing social distancing and wearing PPE. Photo by Alex Crookshanks for Virginia Tech
BIOTRANS | COVER STORY
Lindsey Marr. 16 by Alex Crookshanks for Virginia Tech Photo
“We are testing the effectiveness of different homemade mask materials in limiting airborne particles of different sizes from being inhaled by the wearer. We do that under ideal conditions and realistic conditions, where we use a mannequin to simulate mask fit to a human face. We are also testing the effectiveness of these materials in blocking particles that are exhaled by humans,” said Charbel Harb, a Ph.D. Student in the Department of Civil & Environmental Engineering and a member of the fellow civil and environmental engineering professor Hosein Foroutan’s Applied Interdisciplinary Research on Flow Systems (AIRFlowS) Laboratory. “After realizing how many people died in this pandemic and how many healthcare workers were sacrificed in this war, I can no longer sit still. I am eager to help by using my own knowledge and I am glad that I can do it with funding from the IGEP program and support from my advisor, Dr. Marr,” said Jin Pan, a Ph.D. Candidate in Marr’s Applied Interdisciplinary Research in Air (AIR2) Laboratory and the BIOTRANS program. Since 2010, Marr has been an affiliated faculty member of BIOTRANS, an interdisciplinary Ph.D. program at Virginia Tech that brings biologists and engineers together to study transport in environmental and physiological systems. “Trying to understand the transmission of COVID-19, and other diseases, is a great example of an interdisciplinary problem that demands an understanding of the biology of pathogens and of their transport through the
environment as they are moving between people,” said Marr. As she’s pivoted in recent months to apply her insights to the novel coronavirus, Marr has weighed in on subjects that have captured national media attention, such as the possibility of transmission by inhalation, the 6-foot distance recommendation for running outside, and how virus particles may or may not land on a person’s clothes or other surfaces. “Because this is such a public health problem, it is really important to communicate science to the public and to the public health agencies that are providing messages about COVID-19 to the public and developing policies. I realized early on that I was one of a small number of people in the world who have expertise on airborne viruses. And so I realized that it was very important for me to share my research in a way that people could understand,” said Marr. In their examination of homemade mask materials, Marr’s team has tested items that have emerged in the public eye in recent months, such as: Shop-Vac bags, HVAC filters, T-shirts, microfiber cloth, felt, auto shop rags and towels, and coffee filters. A few top performers and busts emerged from their tests. Microfiber cloth, a material used to clean eyeglasses, filtered out at least 80 percent of particles under optimal conditions. But a heavyweight cotton t-shirt, a shop towel, and a shop rag filtered out only about 10 percent of the hardest particles to remove and about 50 percent of the larger ones. HVAC filters removed a low of 20 percent of particles; Shop-Vac
bags removed at least 60 percent. Some of the alternative mask materials arrived in Marr’s lab for testing via Matt Hull, a research scientist at the Institute for Critical Technology and Applied Science and Marr’s colleague on the institute’s NanoEarth team. Hull recognized that amid the COVID-19 pandemic, there would be a strain on supply chains for protective materials with specialized properties, including materials that the medical community might eye for lastresort use in PPE. He dropped off potential candidates at the Kelly Hall headquarters of the Institute for Critical Technology and Applied Science. What was once a conference room has now been transformed into a staging area for piles of material destined for testing in Marr’s lab down the hall. The experiments are ongoing, but Marr has been releasing the results in real time on Twitter. She also shared the procedure behind the tests on Twitter, and other aerosol science labs around the country have since adopted these methods to help test materials in their regions. “Twitter is time consuming, but I learn a lot from it. I learn about new scientific papers and I get to see different perspectives. I also have interesting scientific discussions and exchanges with other experts. The general public has really great questions that force us to think more deeply about the problem,” said Marr. As for now, Marr’s team will continue to run experiments as new ideas for mask materials emerge.
This image shows a flying snake (common name: paradise tree snake; scientific name: Chrysopelea paradisi) gliding through the air. The snake transforms itself by flattening, a shape that can be seen in the view of the snakeâ€™s belly. In addition to flattening, the snake undulates in the air, a motion that looks like swimming. A recent paper in Nature Physics demonstrated that this behavior is a critical component of the snakeâ€™s ability to glide. Without it, the snake would be unstable and would tumble out of the sky. This study was lead by former BIOTRANS graduate Dr. Isaac Yeaton (now at the Johns Hopkins University Applied Physics Laboratory) and was co-authored by faculty members Drs. Shane Ross and Jake Socha. 18
BIOTRANS | RESEARCH
BIOTRANS | CURRENT STUDENTS education, it seemed like the BIOTRANS experience would be very beneficial to my future work,” Will said.
WILL SNYDER ADVISOR: RAFFAELLA DE VITA CO-ADVISOR: RAFAEL DAVALOS Will Snyder graduated from Virginia Tech with a B.S. in mechanical engineering. During his senior year, he took a class taught by Raffaella De Vita and joined her lab as part of a class project. Will found himself enjoying the work, and ultimately decided to join De Vita’s lab through the BIOTRANS program. “Given that I had very little exposure to life sciences during my mechanical engineering
WHAT WAS THE ROTATION PROCESS LIKE? My first rotation was with Dr. Schmale analyzing the elastic response of wheat leaves following water droplet impacts to understand how the structural mechanics of the leaves contributes to the dispersal of disease spores during rainstorms. Next, I worked in Dr. Davalos’ lab learning how to model a passive cell separation technique known as pinched flow fractionation with COMSOL, their preferred finite element software. Finally, I rotated in Dr. De Vita’s lab, where I began using COMSOL to recreate a biaxial stress-strain experiment, which involved the inflation of rat vaginal tissue to investigate its mechanical properties. HOW DID YOU KNOW WHICH LAB TO CHOOSE? It was really always going to be Dr. De Vita’s lab — I had been working with her before I graduated, and I already felt like
a part of her team. She’s one of the main reasons I decided to pursue graduate level education in the first place, so it wasn’t a difficult choice. WHAT ARE YOU STUDYING NOW? The focus of my research is to apply the reduced order modeling techniques I learned during my rotation to a more complex model. We believe we can eventually apply this more complex reduced order model to perform inverse finite element analysis, whereby the mechanical properties of a real material can be determined by matching the model to experimental stressstrain results for said material. WHAT ARE YOU MOST LOOKING FORWARD TO IN THE BIOTRANS PROGRAM? I am most looking forward to having colleagues from a myriad of different disciplines who can provide unique perspectives informed by the nuances of their respective fields. I feel like I am constantly learning just by stepping outside of my limited engineering bubble, and I hope to continue that trend.
LANDON BILYEU ADVISOR: DAVID SCHMALE, COADVISOR: SHANE ROSS Landon Bilyeu graduated from the University of Missouri with a degree in biological engineering. In his search for a Ph.D. program, he originally applied to Virginia Tech’s Department of Biology. “Somebody reached out to me about BIOTRANS and recommended me to apply, since it is a combination of biology and engineering. I thought it would be a good fit, and I have had a good experience with both science and engineering professors,” Landon said.
WHAT WAS THE ROTATION PROCESS LIKE? Overall, I enjoyed my rotation process. It wasn’t a lot of time in each lab, but I did enjoy all my different lab experiences. With Dr. Ross, I worked on creating a predictive model for Red Tide events in Florida where we attempted to determine which beaches would experience less of a potentially harmful algal blooms (HABs). With Dr. Schmale, I analyzed HAB data we had collected over the summer and went to Florida to collect Red Tide HAB data. With Dr. Boreyko, I mixed it up and did work on jumping droplets that occur on wheat leaves and their potential for fungal spore dispersal. HOW DID YOU KNOW WHICH LAB TO CHOOSE? I had a good idea
that I wanted to work with algae blooms and during my rotations I found that I enjoyed the field aspect of Dr. Schmale’s lab and that pushed me into asking to work with him. WHAT ARE YOU STUDYING NOW? I look at how weather conditions impact the severity of HABs, and I would like to learn how to apply the data we collect to a model that could map the impact area of a HAB. WHAT ARE YOU MOST LOOKING FORWARD TO IN THE BIOTRANS PROGRAM? I am looking forward to continuing to work with people from different departments and combining multiple fields to the work I will do, as I think interdisciplinary research allows for much more to be discovered.
B I O T R A N S | R E C E N T G R A D U AT E S
DR. KHALED ADJERID ADVISOR: JAKE SOCHA CO-ADVISOR: RAFFAELLA DE VITA Khaled Adjerid earned his Ph.D. in December 2019. He is now a postdoctoral research fellow in anatomy and neurobiology at the Northeast Ohio Medical University, where he works in Rebecca German’s lab. He studies deficiencies in preterm infant drinking, swallowing, and respiration. “While it is a departure from my engineering background, as well as my insect biomechanics doctoral studies, programs like BIOTRANS prepared me to jump into a role like this and speak with experts, read papers, and learn techniques outside of my primary disciplinary,” said Khaled. He ultimately hopes to move into a full-time academic position.
WHY DID YOU CHOOSE TO BE PART OF THE BIOTRANS PROGRAM? “I found that the aspect that really sold me on BIOTRANS was the crossdiscipline collaboration. The BIOTRANS program was built upon the idea that the greatest advances in sciences are to be made at interfaces of disciplines by researchers who are able to communicate fluently across disciplinary boundaries. This was evident at every social gathering, student activity, class, and seminar.” WHAT WAS THE FOCUS OF YOUR RESEARCH? “I studied how insects control the flows of fluids around their bodies. We looked at the unexpected degree of control that insects have of the pressure regimes in their body. Then we examined the structure and movement of the small tubes
that control air throughout their bodies. Finally, we studied the material properties of those tubes possibly explaining how they selectively collapse creating valves and pathways for airflow in the body. ” WHAT IS YOUR FAVORITE MEMORY FROM YOUR TIME IN BIOTRANS? “My favorite memory was the BIOTRANS retreat where the current and past students gathered at Mountain Lake to discuss ways in which crossdisciplinary collaborations could be better facilitated for the students and faculty. While it was fun to be in the mountain air sharing our research experiences and getting advice from senior students, later seeing our input in a new and evolving program being considered and implemented by the faculty was satisfying.”
Khaled Adjerid presenting at an outreach event. Photo courtesy of Khaled Adjerid
B I O T R A N S | FA C U LT Y Nicole Abaid Jonathan Boreyko Jing Chen Daniela Cimini
Rafael Davalos Raffaella De Vita Hosein Foroutan Chloé Lahondère
Linsey Marr Steve Melville Shane Ross David Schmale
BIOTRANS FACULTY members are located in ten different
Eva Schmelz Jake Socha
departments and programs across three different colleges at Virginia Tech. Their research, which sits at the interface of biology and engineering, loosely falls into three categories: transport at the
Ann Staples Mark Stremler
cellular scale, transport at the organismal scale, and transport at the environmental scale. During the application process, students must indicate three BIOTRANS faculty whose research most interests them.
B I O T R A N S | FA C U LT Y S P O T L I G H T
An Interview with Jonathan Boreyko Written by Kendall Daniels
WHAT IS THE FOCUS OF YOUR RESEARCH? I run the NatureInspired Fluids & Interfaces (NIFI) laboratory in the Department of Mechanical Engineering in the College of Engineering. I tell my students that they have to pass three rules to do a project: It has to be inspired by some kind of natural phenomenon, have something to do with fluid mechanics or heat transfer in some way, and have something that is different, fun, and awesome. To give more concrete examples, we work with redwood inspired-fog harvesting, mangrove-inspired water purification, and beetle-inspired anti-frosting aircraft surfaces. WHY DID YOU CHOOSE VIRGINIA TECH TO CONTINUE YOUR CAREER? First of all, I married a southern girl, so I was required to be somewhere warm. So that ruled out a lot of major universities in New England or places like that. That was definitely a big factor. Also, our families are all in North Carolina. It is nice because we are two hours away from our extended family. And that’s been great because the kids get to see their grandparents a lot. For me, in particular, I was raised in a mountain village in New Hampshire. So, I am a very small town kind of person. I feel much more at home having all of the trails and mountains and rivers. So Blacksburg has that cozy small town feel that I am accustomed to. And then I just kept hearing how high the morale is here, like students love being 24
Hokies. It was like a genuine pride. I think that all of those things put together was why Virginia Tech was my top choice when I was interviewing for colleges. WHAT DO YOU ENJOY ABOUT BEING AN AFFILIATED FACULTY MEMBER WITH THE BIOTRANS PROGRAM? It’s really neat getting to see different disciplines coming together and helping each other out. One day Professor Schmale brought some wheat leaves over to my lab and he said ‘Hey, I’ve been looking at how rainsplash affects disease on wheat and I know that you do condensation stuff. Why don’t you just try growing some dew droplets on the wheat leaf and see what happens?’ It turned out that we discovered a new mechanism for how disease spreads among wheat crops. So we found that there are these jumping dew drops that explosively jump off of the surface, powered by their surface tension, and
they are taking these spores with them. So this jumping dew is this completely unknown transport mechanism for spreading disease among wheat crops and if we can understand it, we can maybe control it and help promote better health for the farmers’ crops. So just having those random people come together and put ideas together has been really neat. You have to have that curiosity to have that openness to cross borders and work with new people and new topics and mush two different fields together. It’s that passionate curiosity that unites all of us despite the fact that we come from very different backgrounds. WHAT ADVICE DO YOU HAVE FOR PROSPECTIVE GRADUATE STUDENTS? I encourage students to realize that in graduate school, grades don’t really matter. It’s really about having this mindset of discovery, creativity, and patience and applying that to research,
where you are failing a whole lot and then discovering something cool and then exploiting that to get some big breakthrough. It’s those creative, research-based accomplishments that are really going to define your graduate career. My advice is to just get out of the grade-oriented mindset and get into something that you find really cool and then you can find a professor that is doing something that connects to your passions.
WHAT HAS BEEN YOUR MOST MEMORABLE EXPERIENCE SINCE JOINING VIRGINIA TECH OR MOVING TO BLACKSBURG? I’ve been really wanting to create what are called “synthetic trees,” which are basically trees that you make out of tubing and pores and other engineering materials that can copy the transpiration cycle of natural trees. It can pump water against gravity and things like that. I think that the coolest moment so far was when a senior project team made a ten
foot tall synthetic tree that was also scalable to any area that you wanted it to be. So, it could be very tall and very wide. This was exciting because current synthetic trees are almost all much smaller, for example built onto a silicon chip. So to have these undergraduates, with no prior research experience, come in and expand on this idea of building trees from a tiny chip to a massive ten foot tall tree is really neat to see. That’s my favorite one so far, but I have lots of other ones too.
EDUCATIONAL BACKGROUND: Ph.D. in Mechanical Engineering and Materials Science, Duke University, 2012
the coronavirus pandemic, I also tried to play chess and squash once a week with friends on campus. I also enjoy playing Beethoven on the piano, I find his works transcendent.”
utmost passion to what you do in life to find the fullest expression of who you are as a person.”
B.S., Mechanical Engineering, Trinity College, 2007 B.S., Physics, Trinity College (Hartford, CT), 2007 HONORS & AWARDS: 2020 - Faculty Fellow Award, College of Engineering Dean’s Awards, Virginia Tech 2019 - Outstanding Early Career Award, ASME ICNMM 2018 - Outstanding New Mechanics Educator, ASEE 2018 - Junior Faculty Award, ICTAS, Virginia Tech 2017 - CAREER Award, National Science Foundation HOBBIES: “Right now I’m really enjoying going on bike rides and hikes with my four young children. Before
FAVORITE THING TO DO AROUND BLACKSBURG: “We just moved from Christiansburg to Blacksburg, and there’s some amazing trails accessible from our house. I have been taking my 2-year daughter in a jogging stroller and going on long runs with my three boys on bikes (5-year old twins on pedal bikes and a 3-year old on a balance bike). The other day we managed a five mile excursion, all the way to campus and back!” FAVORITE QUOTE: “My favorite quote is from the novelist Fyodor Dostoevsky, who, while writing The Brothers Karamazov, said that ‘I’d die happy if I could finish this final novel, for I would have expressed myself completely.’ I think there’s a wonderful mindset here, about giving your
FAVORITE TYPE OF MUSIC OR ARTIST: “Classical music all the way. My favorites are Beethoven, Rachmaninoff, and I’m increasingly appreciating the more subtle brilliance of Bach.” FAVORITE BOOK OR BOOK SERIES: “My favorite book is The Brothers Karamazov by Fyodor Dostoevsky. I love how Dostoevsky is not afraid to dig deep regarding the big questions in life. Why are we here? Is there a God? How do you define what is good and moral in life? How would the answers to these questions affect how we live? To explore these questions in the form of a novel is something I find fascinating. I can’t seem to convince anyone else this is fascinating; everyone I’ve ever gifted the book to has never been able to finish it.”
BIOTRANS | ALUMNI CORNER
After BIOTRANS Melissa Kenny, Ph.D. Written by Rasha Aridi
MELISSA KENNY RECEIVED HER Ph.D. in biomedical engineering from Virginia Tech in May 2019. As part of her research, she studied the structural and physical characteristics of insect flow systems and worked to understand how insects circulate blood and breathe air at minute scales. Melissa was advised by Dr.
the introductory class that all the engineering undergraduates take. I think Dr. Socha started to notice that I was putting more time and effort into those teaching opportunities than I was into my research, so it helped cement for me that I really love teaching. I also really like research, and I continue to do it, but I actually applied for
As someone who thinks like both a scientist and an engineer, Melissa enjoys the discovery that comes with being a scientist and also the real-world applications of being an engineer. She says that BIOTRANS was an opportunity to fuse biology and engineering together and operate under both mindsets.
WHAT DO YOU DO NOW AT WAKE FOREST UNIVERSITY? I’m an assistant teaching professor in the engineering program at a liberal arts university, which is unique. What I really like about it is that the engineering department here is basically brand new, so I’m involved in building this program. Our oldest students are now rising seniors, so we’ll graduate our first class next May. I’m considered a founding faculty member, so I get to develop brand new courses and advise students.
Jake Socha and co-advised by Dr. Mark Stremler, both professors in the Department of Biomedical Engineering and Mechanics in the College of Engineering.
Before coming to Virginia Tech, Melissa earned her B.S. in biological engineering from Cornell University and then began her Ph.D. at Virginia Tech later that year. She now works as an assistant teaching professor at Wake Forest University’s Department of Engineering, where she is a founding faculty member and able to help shape the new department. LOOKING BACK, HOW HAVE THINGS TURNED OUT SINCE COMPLETING YOUR PH.D.? During my time at VT, I taught 26
only teaching positions in my final year because I’m interested in engineering education research and improving how we teach future engineers.
HOW DO YOU SEE YOUR BIOTRANS EXPERIENCE PLAY OUT AS AN ASSISTANT TEACHING PROFESSOR? In Dr. Socha’s lab, we had biomedical engineering students, biology students, a neuroscientist, and a couple of mechanical engineers, among others. It was really cool because you got to
see all different perspectives. Dr. Socha himself is a biologist and physicist, as well as an engineer, working in biomechanics, and so our lab was really interdisciplinary the whole time. I see a lot of parallels between work and BIOTRANS because when you work with people in a certain discipline, you get used to the quirks and the lifestyle and how things are done. When you have to work with other disciplines, it can feel awkward or it puts everyone out of their comfort zone. I think having worked with BIOTRANS, I learned really quickly that engineers think a little differently than biologists who think a little differently than even other engineers or natural scientists. In this position, I work with sociologists, psychologists, and historian who help with our courses and bring new perspectives. I see a lot of parallels
there, and I really like having had that experience of working with and presenting to professors across different disciplines. I feel like I’ve been out of my comfort zone and expanded it, so now I’m in a job where I’m expanding it even more. WHAT IS YOUR FAVORITE PART OF YOUR CURRENT JOB? I really love working with students, especially first-year students, because I think a lot of the ways we teach engineering aren’t necessarily encouraging to a lot of young students. I strive really hard to make engineering more approachable. We have a small program of approximately 40 graduating students in general
engineering. I like that there’s a research emphasis at WFU, but there’s a huge teaching emphasis that you don’t see at every school. WHAT ADVICE WOULD YOU GIVE TO STUDENTS CONSIDERING THE BIOTRANS PROGRAM? I had no idea what I wanted to do with my life until I was about five years into my Ph.D., and that’s okay. Having this opportunity to rotate through labs and explore other areas helps you figure out where you want to be. For me, I see the world like an engineer, but I also see it like a scientist. Finding that space where I could do both was really helpful, but it also gave me the opportunity to
explore more in grad school, which not everyone gets to do. If you’re looking for a unique experience where you get to merge natural science and engineering, BIOTRANS is awesome. The biggest advice I give anyone going into a Ph.D. program is to pick your advisor. It’s not just about the science, you can give a little there because that changes and develops over time. Get to know your advisor before you decide to work with them. I’m really fortunate to have had the advisor that I did because he was supportive and helpful throughout my entire journey, and I think we worked well together. more.
Left to right: Drs. Melissa Kenny, Jake Socha, and Khaled Adjerid. 27 Photo courtesy of Melissa Kenny.
Fralin Life Sciences Institute Steger Hall 1015 Life Science Circle Blacksburg, VA 24061
Jin Pan and Charbel Harb of Marrâ€™s lab. Her graduate students are evaluating how well N95 respirators retain their efficacy post-sterilization using various techniques, as well as the particle filtration efficacy of improvised mask materials. Photo by Linsey Marr for Virginia Tech.