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BIOTRANS 2019, Vol. 4


CONTENTS 3 L e t t e r f r o m t h e D i r e c t o r 4 N e w s 8 A M a r r i a g e o f M o s q u i t o Researchers 14 BIOTRANS Research 18 Student Profiles 23 BIOTRANS Faculty 24 B I O T R A N S F i e l d C a m p a i g n 28 Faculty Spotlight 30 Alumni Corner

DIRECTOR’S MESSAGE I t ’ s B e e n a P r o d u c t i v e Ye a r

About BIOTRANS We are a community of biologists and engineers that collaborate to study transport in environmental and physiological systems.

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Editor: Art Director: Writers: Photography:

Kristin Rose Alex Crookshanks Kristin Rose, Tiffany Trent, Kendall Daniels, Dave Guerin, and Rosaire Bushey Alex Crookshanks, Kristin Rose, and Peter Means

Photo this page: Chloé Lahondère adjusts her microscope. Photo credit: Alex Crookshanks Cover photo: Researchers Chloé Lahondère and Clément Vinauger use the mosquito flight simulator to study mosquito vision and learning. Photo credit: Alex Crookshanks

Welcome to Biological Transport (BIOTRANS) Magazine, our fourth annual issue highlighting our interdisciplinary graduate education program at Virginia Tech. We are a collaborative community of biologists and engineers who study transport in environmental and physiological systems. Our students and faculty have been hard at work in the past year!

During the week, students obtained first-hand experience with drone wind-monitoring experiments at the Kentland Experimental Aerial Systems laboratory located outside of Blacksburg.

We’d like to congratulate our newest Ph.D. graduates, Dr. Khaled Adjerid and Dr. Melissa Kenny. Dr. Adjerid has moved on to an NIH-sponsored postdoc position, working with Dr. Rebecca German at Northeast Ohio Medical University (known as NEOMED). Dr. Kenny has joined the faculty of the Department of Engineering at Wake Forest University, working as an Assistant Teaching Professor. She’ll also be returning to Virginia Tech on occasion to continue conducting research on insect flow systems.

Dr. Rafael Davalos was awarded an SBIR NIH grant for ~$250K to study the use of irreversible electroporation on ablating inoperable brain tumors.

Drs. Jonathan Boreyko and David Schmale received an $80K award from ICTAS to develop synthetic trees for water extraction and energy harvesting.

Dr. Linsey Marr received a $300K award from the Water Research Foundation to study new approaches for evaluating and treating water and wastewater quality.

We welcomed four graduate students to the BIOTRANS family in the past year: Landon Bilyeu, Maria Gonzalez, Jin Pan, and Will Snyder. Learn more about them and read about awards from our hard-working students on page 15. In the past year, our program has lent a helping hand to undergraduate research. One highlight (see page 24) was a spring break research experience hosted by Dr. David Schmale and Dr. Shane Ross, who brought students in from Morehouse College, Bennett College, and Hampden Sydney College.

Our faculty and students have received many sponsored research awards, including:

As you can see, there are so many exciting things going on with BIOTRANS, with more to follow in the coming year. Enjoy the new issue of our magazine!

Jake Socha, Ph.D. Director of BIOTRANS

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BIOTRANS | NEWS

and talented teachers he has encountered. “Even more impressive is how Dr. Marr’s students routinely exceed their personal expectations of what is possible,” Edwards said. “Students come out of her class with a life-altering experience of striving and achieving.” Marr received her bachelor’s degree from Harvard University and a Ph.D. from the University of California, Berkeley. She has published over 80 peerreviewed journal articles and more than 100 papers and presentations at conferences and professional meetings. More than one-quarter of Marr’s

papers have been published in Environmental Science & Te c h n o l o g y / E n v i r o n m e n t a l Science & Technology Letters, the leading journal in the field of environmental science and engineering. Marr always takes the opportunity to offer encouragement and advice to new teaching faculty when she can. “One thing I could recommend is aim to cover less material than you think you can in one lecture,” Marr said. “It is more important to cover material in a way that students can understand than to simply cover a lot of material.”

Linsey Marr, Ph.D.

Linsey Marr receives Excellence in Teaching Award

Written by Dave Guerin

LINSEY MARR, THE CHARLES P. Lunsford Professor in Engineering in Virginia Tech’s College of Engineering and BIOTRANS faculty member, has earned the Excellence in Teaching Award from the Center for Excellence in Teaching and Learning (CETL). The award, presented by the CETL to approximately nine Virginia Tech faculty members each academic year, recognizes a faculty member’s effective, engaged, and dynamic approaches and achievements as an educator. “I’m incredibly honored by this 4

recognition,” Marr said. “In addition to my dedication to research, I put a lot of effort into trying to teach effectively, and I hope that students in my classes can take away knowledge and skills that they will use in the future.” Among the pillars of CETL are to help advance experiential learning at Virginia Tech and to improve student learning through research-based instructional practices and student-centered design. Marr said her personal approach to teaching parallels this philosophy as she seeks to engage students in the material

while conveying knowledge and skills that they will retain even after leaving her classes. “My teaching style combines rigorous theory with practical applications and current events,” Marr said. “To emphasize the relevance of course material to real life, I begin most of my lectures with a news story, and then I try to weave personal connections into the ensuing discussion.” Marr said the most meaningful teaching experiences are the “a-ha” moments when the student reaches a new level of understanding of the material.

“This can be something as small as figuring out the key to solving a tough homework problem or as comprehensive as appreciating what they have learned over the entire semester,” Marr said. “I find it especially rewarding to hear from students after the class is over, whether the next day or years later, that they learned a lot from my class.” Marc Edwards, University Distinguished Professor and the Charles P. Lunsford Professor in the Charles E. Via Jr. Department of Civil and Environmental Engineering, said Marr is one of the most engaging, devoted,

Marr’s research is strongly connected to the biological transport (BIOTRANS) theme. Her lab is focused on applied interdisciplinary research in air with a concentration on air quality, nanomaterials, and disease transmission.

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BIOTRANS | NEWS Dew droplets gather wheat leaf rust spores. When the droplets merge, they convert surface tension into kinetic energy and ‘jump’ from the leaf surface. If these droplets get past the boundary layer of the leaf, typically about 1 millimeter, they can be taken by the wind and deposited on other plants nearby or in other fields or even farms.

directly connects to the theme of biological transport. “Professor Schmale had seen some of the work we’ve been doing on condensation and was curious to see what we could learn about condensation on wheat leaves,” said Boreyko. “The project didn’t start with any expectations, but people already knew that rain splash and wind caused pathogenic spores to be removed from plants and spread to others, and we wanted to see if condensation might also have a role to play in spore dispersal.”

Assistant Professor Jonathan Boreyko, front, and doctoral student Farzad Ahmadi

‘Sneezing’ plants contribute to disease proliferation Written by Rosaire Bushey

VIRGINIA TECH BIOTRANS researchers discovered that wheat plants “sneezing” off condensation can vastly impact the spread of spore-borne diseases, such as wheat leaf rust, which can cause crop yield losses of up to 20 percent or more in the United States and higher than average losses in less developed agricultural nations. The study, published June 19, and featured on the cover of the Journal of the Royal Society Interface, is part of a three-year grant obtained from the U.S. Department of Agriculture’s National Institute of Food and 6

Agriculture to study the dispersal of wheat pathogens by rain splash and jumping-droplet condensation. Jonathan Boreyko, assistant professor of mechanical engineering in the College of Engineering is a co-principal investigator on the grant and David Schmale, professor of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences, is the primary investigator of the nearly $500,000 project. Both Boreyko and Schmale are BIOTRANS faculty members, and their spore dispersal research

The students involved in the study were told not to expect jumping droplets in their condensation tests, as the droplets are known to only occur on specific surfaces, namely superhydrophobic surfaces normally associated with exotic materials, such as lotus leaves and gecko skin. Superhydrophobic surfaces are non-wetting, and when spherical condensate grows, droplets merge together to release surface tension, which is converted into kinetic energy, which propels them from the surface. “Conceptually, what the plants are doing is sneezing,” Boreyko said. “The jumping droplets, at the rate of 100 or more an hour, are a violent expulsion of dew from the surface. It’s good for the plant because it is removing spores from itself, but it’s bad because, like a human sneeze, the liquid droplets are finding their way onto neighboring plants. Like a cold, it’s easy to see how a single infected plant could

(Image courtesy of the Boreyko lab.)

propagate a disease across an entire crop.” The paper, co-first-authored by Saurabh Nath and Farzad Ahmadi, engineering mechanics graduate students in Boreyko’s lab, showed the jumping droplets can dramatically increase the dispersal of disease spores. “We wanted to find out, first if the condensation droplets can carry spores, and while 90 percent of them carry only a single spore, we have seen instances where a droplet has carried as many as 11,” Ahmadi said. “We also looked at how high the spores can jump and whether they can get past the boundary layer of the leaf.” The boundary layer, which is about a millimeter thick, is the region of air near the leaf’s surface where the wind doesn’t affect the droplet. If the kinetic energy from merging moves the jumping droplet above the boundary layer, the droplet can be taken by the wind. Depending upon the wind speed, it’s feasible

for the droplet to then be moved great distances, including to neighboring fields or farms. “Using water-sensitive paper we measured how high the droplets can jump,” Ahmadi said. “A blue dot on the paper shows us a droplet, and a reddish dot shows us a spore, so in this way we can calculate both the height and the number of spores in the droplet.” The droplets in Ahmadi’s tests routinely jumped from 2-5 millimeters from the surface of the leaf, well above the distance necessary to be taken by the wind to be re-deposited elsewhere. “It’s important to realize these droplets are microscopic in size,” explained Boreyko. “Each droplet is about the same size as the thickness of a human hair – about 50 micrometers – so this is all happening at a scale we don’t notice. A 0.1 meter per second wind can support the weight of a jumping droplet, whereas a droplet directly on the leaf requires a wind of 10 meters per

second – 100 times stronger to be removed. Once it’s in the wind, there is, hypothetically, no limit to how far it can be carried.” The low wind speed needed to carry the droplets means that the spore-ridden dew drops can have a large impact on crop health over a very wide area. “We know now that wind and rain aren’t the only factors in the spread of disease among crops,” Boreyko said. The next phase of the continuing experiment for Boreyko and his team is to see how far the wind can carry the spore-bearing droplets. Using water-sensitive paper spread out in varying distances from a wheat leaf, the team will use fans to simulate wind and collect data on droplet and spore dispersal.

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BIOTRANS | COVER STORY

The Mechanisms of Love: A Marriage of Mosquito Researchers Written by Tiffany Trent

CHLOÉ LAHONDÈRE AND CLÉMENT VINAUGER are no strangers to the vicissitudes of mosquito research. They thrive upon it. They’ve built a research partnership and a marriage upon it, in fact. Meeting in graduate school in France, they’ve traveled around the world trying to understand how mosquitoes and other blood-feeding insects such as tsetse flies and kissing bugs target humans and, thus, how they transport pathogens and parasites to their human victims. This, in fact, was what brought them after a sojourn at the University of Washington to the Department of Biochemistry and BIOTRANS program at Virginia Tech.

“We like being faculty members of the BIOTRANS program because it gives us an opportunity to meet new collaborators and talented interdisciplinary researchers,” said Lahondère, a research assistant professor in the Department of Biochemistry in the College of Agriculture and Life Sciences. They could not have chosen a better place. With collaborators in every aspect of engineering and biology, Lahondère and Vinauger have been able to develop some projects with some truly groundbreaking possibilities. Image, this page: LED Mosquito flight simulator. Photo credits: Alex Crookshanks. Images, previous page, far left: CHLOÉ LAHONDÈRE AND CLÉMENT VINAUGER with 3D printer; LAHONDÈRE adjusts her microscope; 9 Vinauger examines the electrophysiology of a mosquito. Photo credits: Alex Crookshanks and Kristin Rose.


BIOTRANS faculty members are located in ten different 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 cellular scale, transport at the organismal scale, and transport at the environmental scale. Lahondère and Vinauger’s interdisciplinary research combines methods from biochemistry, neuroscience, bioengineering, and chemical ecology, and spans across these different scales. They identify epidemiologically relevant behaviors and investigate the chemical, neural, and mechanical processes that underlie these behaviors. A recent proposal, for example, promises understanding of the mechanisms behind mosquitoborne infection, especially with regards to how mosquitoes feed. They have also been working very intensely on “understanding how mosquitoes navigate space and time,” according to Vinauger, an assistant professor in the Department of Biochemistry in the College of Agriculture and Life Sciences. While much has been studied about the mosquito’s sense of smell and how it targets CO2 exhalations to find victims, very little is understood about how the mosquito uses vision. In a recent publication in Current Biology, Vinauger has gained insight into how the visual and olfactory centers of the mosquito 10

BIOTRANS | COVER STORY

brain interact to help mosquitoes better track their prey. When mosquitoes encounter CO2 , they become attracted to dark, visual objects like their hosts, and the presence of CO2 enhances their accuracy in hunting us down. Vinauger and his research team were able to determine this by fitting the mosquitoes with tiny helmets and tethering them in a LED flight simulator, exposing the mosquitoes to puffs of CO2 . “We monitored the mosquitoes’ responses to visual and olfactory cues by tracking wingbeat frequency, acceleration, and turning behavior,” said Vinauger. Using calcium imaging experiments, the research team found CO2 modulates mosquito neural responses to discrete visual stimuli. It has become obvious to Lahondère and Vinauger that interaction between the olfactory and visual processing centers of the mosquito brain helps the insects target their victims very accurately. It’s been found that mosquitoes are changing hunting routines in response to host cues; they now recognize when people emerge from bednets in Africa and have begun hunting more often during the day than at night. Understanding how mosquitoes process information and learn, therefore, is crucial to figuring out how to create better baits and traps. Projects like this have naturally brought Lahondère and Vinauger closer together. What many people may not realize is that

Image: Vinauger and Lahondère use a 3D printer to create helmets which they fit onto mosquitoes to study their brain activity. Photo courtesy of Vinauger and Lahondère

their partnership also relies heavily on their individual specialties and how they bring these to bear on project development after forays at the bench and in the field. Vinauger and Lahondère are eager to take on new graduate students from the BIOTRANS program; they have a multitude of projects that would fit within the theme of biological transport. Lahondère currently has two graduate students, an undergraduate student, and

a post-bac student in her lab, while Vinauger has two graduate students, a postdoc fellow and four undergraduate students in his lab. Lahondère has many projects on her docket. She’s currently trying to understand how mosquitoes who specialize in cold-blooded animals, especially frogs and snakes, are attracted to them. What are the mechanisms of attraction? She is also working on a project analyzing how local plants can be

used to keep mosquitoes away, and whether or not ornamental plants attract them. “This is definitely a project that will interest all residents of Virginia,” Lahondère said. This potentially dovetails with another field project of Lahondère’s, in which she’s trapping populations throughout Virginia to see how global change will affect their populations at various elevations. For instance, Aedes japonicus, an invasive mosquito that is a vector for West

Nile virus among other diseases, is now found at Mountain Lake Biological Station in Pembroke, Virginia. Lahondère, who is affiliated with the Global Change Center, and Vinauger have teamed up with the Philosophy department and with the department of Fish and Wildlife Conservation to understand how Virginians perceive mosquitoes and what their expectations regarding mosquitoes will be as the climate continues to change. “Currently, we’ve been amazed


BIOTRANS | COVER STORY to discover that only 49% of Virginians believe that climate change will have any effect. “We’re hoping to use the spread of mosquitoes as disease vectors to help people understand the effects of climate change,” Lahondère noted. Vinauger prefers to work in the lab, and with his collaborators, he is working on several projects to understand fluid mechanics as

Image this page, 3D printed helmet on a mosquito. Photo courtesy of Vinauger and Lahondère labs. Images opposite page, clockwise: Lahondère adjusts her microscope; 3D printer; Graduate student Nicole Wynne. Photo credit: Alex Crookshanks.

they pertain to mosquito feeding and the extent to which the neurophysiology of mosquitoes fluctuates with time-of-day.

“It’s hard to turn work off,” Vinauger said, “but having a child makes you realize you need to be home and spend time with him.”

Whether they work separately or alone, one lovely thing has come of this partnership – a son, Timotey, now almost two years old. Born at the end of their postdoctoral phase, their son has made them realize the importance of work-life balance.

Despite the frenetic nature of their professional lives, the family still finds time to maintain its center. Negotiating that balance has become one of the most important mechanisms of their professional careers and their love.


BIOTRANS | RESEARCH

B I O T R A N S | S T U D E N T AWA R D S

Talia Weiss won a renewal of the NASA-Virginia Space Grant Consortium Graduate STEM Research Fellowship to complete her study of interfacial locomotion in skittering frogs.

Erica Pack won Graduate Research Development Program (GRDP) award from Virginia Tech for work on swine reproductive tissues.

Hyunggon Park won the Outstanding Poster Award at the Annual Symposium of Center for Soft Matter and Biological Physics for his work on rain splash-induced spore dispersal.

Nico Baudoin was awarded a GSDA fellowship by the Department of Biological Sciences for fall 2019. The award was based on Nico’s consistently high performance as a graduate student and on the quality of his work on the in vitro evolution of tetraploid cells.

NEW STUDENTS:

Jin Pan earned bachelor’s and master’s degrees in civil and environmental engineering from Tsinghua University and the University of California, Berkeley, respectively. She completed her laboratory rotations and is now working with co-advisors Dr. Linsey Marr and Dr. David Schmale. The other students are currently conducting rotations and will choose advisors in the spring. Landon Bilyeu is a graduate of the University of Missouri with a bachelor’s degree in bioengineering. Maria Gonzalez graduated from Wellesley College with a bachelors in physics and minoring in women’s and gender studies. In addition to BIOTRANS, she’s also a McNair Scholar and part of the New Horizons program. Images, top: Product design research at W.L. Gore and Associates where former BIOTRANS student Adwoa Baah-Dwomoh, Ph.D., currently works. Image, middle: The Schmale and Ross labs brought six undergraduate students from partnering colleges to Virginia Tech to conduct data and decisions research in March during spring break. Photo credit: Peter Means. Image, bottom left: High resolution microscopy image of fluorescent proteins in Clostridium perfringens. Photo courtesy of Steve Melville. Image, bottom right: Visiting 14 student Bryan Bloomfield downloading data from a drone. Photo credit: Peter Means.

Will Snyder is a graduate of mechanical engineering here at Virginia Tech, and will likely be working on some aspect of tissue mechanics. 15


BIOTRANS | RESEARCH

Image, 16 this page: Dye tracking experiment at the Blacksburg quarry. Photo courtesy of the Schmale lab.

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BIOTRANS | CURRENT STUDENTS group collaborates with many researchers on this project. But my research focus has shifted to other projects,” says Pan.

Jin Pan received her bachelor’s of science in civil and environmental engineering from Tsinghua University in 2017. The following year, Pan graduated with a master’s in civil and

WHAT WAS THE ROTATION PROCESS LIKE? “For me, it was incredibly fun and educational. I rotated in three labs and each lab has a different research focus. There were things that I would have never had the chance to do if I did not do the rotations. It was definitely a very special experience and it is very beneficial for any young researcher. In my first lab rotation, I analyzed correlations between reported flu incidence and indoor environmental conditions or meteorological conditions. This research is still ongoing and we hope to find

environmental engineering from the University of California, Berkeley. Now at Virginia Tech, she is doing data scraping on meteorological data from different countries and regions. Currently, she is on track to get a Ph.D. in environmental engineering. “This is a large project and our

some common patterns of data reported from different regions. In my second lab rotation, I investigated how raindrops impact biofilms, and how they are able to break biofilm into fragments and transport them into the air. We grew biofilm by using a mixture of Legionella surrogate, a type of bacteria,

JIN PAN 2ND YEAR PH.D. STUDENT IN LINSEY MARR’S LAB CO-ADVISOR: DAVID SCHMALE

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and Anabaena, a type of algae. Then, we recorded the process of impaction through a high-speed camera. During my third lab rotation, I modeled the impaction process using computer programming. Modeling would be a good approach to explore the unknowns that cannot be figured out by experiments. We calculated the trajectory of droplets with biofilm fragments and found out that they might suspend in the air under certain circumstances, which may pose threats to human health when breathed in.” HOW DID YOU KNOW WHICH LAB YOU WANTED TO CHOOSE? “I discussed with my primary advisor and she gave me some recommendations based on my

NICOLAAS (NICO) BAUDOIN 7TH YEAR PH.D. CANDIDATE IN DANIELA CIMINI’S LAB CO-ADVISOR: RAFAEL DAVALOS Nico Baudoin graduated from George Mason University with a bachelor’s degree in biology. He is also the co-founder of Mycobiome, a company that is developing a “living mulch that can be applied to soil contaminated with pesticides, petroleum products, heavy metals, or other environmental contaminants” says Baudoin. He says that the rotations in the BIOTRANS program are unique because “they get you to step outside of your home department and let you see a new way of thinking about problems.’’ WHAT WAS THE ROTATION PROCESS LIKE? “Rotations allow you to explore the research that is being done in different labs within your field and [you] get a better feel for the work before you join. They can help you gain a broader perspective before joining a lab and diving more deeply into a research program. As a biologist, I was introduced to some knowledge and tools from the engineering

discipline that have really helped me out in my research. I think that what I learned, and the relationships I built, will help me succeed and build interdisciplinary collaborations in the future.” HOW DID YOU KNOW WHICH LAB TO CHOOSE? “I knew that I wanted to work on cell biology, and the Cimini lab does good cell biology research. It seemed like the best fit, as far as my interests and career trajectory were concerned. Dr. Cimini and the students in the lab were very welcoming and helpful when I was starting out, which made the decision easy. All of the labs I worked with had things I really liked about them; it just came down to what was the best fit.”

WHAT IS THE CURRENT FOCUS OF YOUR RESEARCH? “My research focuses on the consequences of genome doubling in human cells, which is significant for understanding the development of cancer. It has been known for a long time that cancer cells have an abnormal, often near-double, number of chromosomes – the structural units that contain the cells’ genes. What the consequences are, in terms of disease progression, is debated and not entirely clear. I have been working to understand the cellular changes that take place alongside these changes in chromosome copy number. Ultimately, by better understanding the link between chromosomes and the properties of the cell, we may be able to develop more targeted therapy for patients.”

interest and ability. I also checked the websites of those professors to decide which one I thought would be a better fit for me.” WHAT IS THE CURRENT FOCUS OF YOUR RESEARCH? Her current research is focused on harmful algal blooms and how they influence the surrounding environment and human health. 19


BIOTRANS | CURRENT STUDENTS

HYUNGGON PARK 3RD YEAR PH.D. STUDENT IN JONATHAN BOREYKO’S LAB CO-ADVISOR: DAVID SCHMALE Hyunggon received his B.S. in mechanical engineering from Sungkyunkwan University in 2015, and his M.S. in mechanical engineering from the University of Southern California in 2017. His current research focuses on the raindrop impact on sporeladen surfaces. He says that “this project is a good topic for the BIOTRANS program because we are looking at problems in nature from two different perspectives – the physical and biological.”

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WHAT WAS THE ROTATION PROCESS LIKE? “First-year students in the BIOTRANS program are expected to participate in a series of seven week laboratory rotations. Rotations take place in the labs of participating BIOTRANS faculty during the fall and spring semesters of the first year. I started my first rotation with Dr. Sunghwan (“Sunny”) Jung and Dr. David Schmale because, at the time, they were writing a USDA grant proposal called “Liberation and Dispersal of Wheat Pathogens by Rain Splash and Jumping-Droplet Condensation.” This is a great topic for me; we are at the intersection of biology and fluid mechanics.

After Dr. Jung left for Cornell University, I changed my advisor to Dr. Jonathan Boreyko, who is also a fluid mechanist and part of the USDA proposal. For the third rotation I worked with cell detection with Dr. Jing Chen.” HOW DID YOU KNOW WHICH LAB TO CHOOSE? “When I was an undergraduate student, I really liked my fluid mechanics course. So, I decided to study fluid mechanics when I went to graduate school. But the project I did for my master’s was a little boring – it was just classical fluid mechanics. So, that’s why I wanted to do more interesting and cool stuff, which happens to be in nature. This work really motivated me to study, so I searched for this kind of lab. Originally, I was in Sunghwan Jung’s bio-inspired fluid mechanics lab. And I am currently in a nature-inspired fluid-dynamics interface lab with Jonathan Boreyko. By the end of my Ph.D. program, I want to see more biological situations, not only disease transport, but other interesting situations from a physical point of view. David Schmale, who is an expert in disease transport, and Jonathan Boreyko, who is an expert in fluid mechanics, are the perfect combination of advisors, to help me do more biological systems work.”

WHAT IS THE CURRENT FOCUS OF YOUR RESEARCH? “Overall, what we are looking at is how disease spreads through raindrop impact. In my first project, my advisors and I were interested in how spores are liberated from the surface and how it can be transported to other plants. There are two different ways that disease can be transported, one of which is through dry spores, which are generated through raindrop impact. And the second one involves spores that are captured by satellite droplets. Inside of these satellite droplets, there are lots of spores, and so if this droplet lands on another healthy plant, it spreads disease. Liberation is the first part of disease transport. And then the second part is the landing part, which is my current project. To mimic this small droplet generation, I used a mesh to see how small droplets will land on a healthy leaf surface. There are two different leaf directions: a longitudinal direction and a transverse direction. The longitudinal direction means that the droplet moves along the leaf’s direction. And the transverse one is when the droplet moves across the leaf’s direction. So I am trying to see how the droplets move, depending on the leaf direction.”

NASTARAN ALINEZHADBALALAMI 4TH YEAR PH.D. STUDENT IN DR. DAVALOS’S LAB CO-ADVISOR: SCOTT VERBRIDGE

with. I talked to four or five PIs. They gave us lab tours and interviewed with us. After that, I finalized my list to include three. I did two rotations in the fall and one in the spring – each one followed by a group presentation. I appreciated the opportunity that I was given to really get an inside view on the labs and how they were managed and operated. Specifically, the interactions between students and PIs, as well as the project itself, and the type of work we had to do. I found it really helpful to choose my Ph.D lab.”

Nastaran Alinezhadbalalami received a M.S. in chemical engineering from Michigan Technological University in 2015, where she studied gene and drug delivery for cancer therapy.

HOW DID YOU KNOW WHICH LAB TO CHOOSE? “My area of interest was translational cancer research, which is the main focus of my current lab. The rotations also helped me gain a better

Currently, she is a Ph.D. student in biomedical engineering with a unique focus in computational tissue engineering.

understanding about the type of work I would be doing in the future, so the rotations helped me decide.”

WHAT WAS THE ROTATION PROCESS LIKE? “We were asked to pick five or six faculty members that we were interested to work

WHAT IS THE CURRENT FOCUS OF YOUR RESEARCH? Over the past year, Nastaran has been working on a

microfluidic device that can separate cancer stem cells using a technique called dielectrophoresis. “Cancer stem cells (CSCs) are a subpopulation of tumor cells that usually resist most standard therapies such as chemotherapy and radiation, and are capable of repropagating the tumor. Isolating CSCs is challenging since there is no known single marker that is differentially expressed in CSCs. The technique that I have been working on, known as dielectrophoresis (DEP), can be used to isolate calls based on their bioelectric properties. In our recently accepted paper, we showed that the glioblastoma cells with more “stem-like” properties can be distinguished from other malignant

glioblastoma cells. Our study shows that DEP can be used to isolate populations of cells that wouldn’t be easily separable with traditional marker-based methods.”


BIOTRANS | CURRENT STUDENTS “I think BIOTRANS is really good in getting me up to speed and being able to communicate across disciplinary boundaries. After doing a proteomics rotation and then a biomechanics lab with biologists and physicists and engineers, I was able to speak different languages – or at least understand them,” said Adjerid.

KHALED ADJERID PH.D. RECENT GRADUATE FROM JAKE SOCHA’S LAB CO-ADVISOR: RAFFAELLA DE VITA Khaled Adjerid received his master’s of science in mechanical engineering in 2011 and Ph.D. in engineering mechanics in 2019, both from Virginia Tech. For Khaled, BIOTRANS has been beneficial.

WHAT WAS THE ROTATION PROCESS LIKE? “It was a little bit bewildering. I came out of a very classical mechanical engineering background. And so, I did a rotation in a proteomics lab with Dr. Lazar, which was something completely different – I had to do sequencing. And then I did a rotation with Dr. De Vita and Dr. Socha where we studied the biomechanics of insects, which was just a little bit closer to what I was doing before.”

B I O T R A N S | FA C U LT Y HOW DID YOU KNOW WHICH LAB YOU WANTED TO CHOOSE? “My comfort zone was obviously the engineering side. But I think that with the courses and rotations, I felt more comfortable doing something bio-inspired and biologically-focused. And so I ended up choosing Dr. Socha’s lab, and then having Dr. De Vita as my co-advisor. There, I was able to choose the traditional tools that I am familiar with in order to characterize phenomena that weren’t well understood in biology. For me, I saw that as the perfect transition into a highly interdisciplinary role.” WHAT IS THE CURRENT FOCUS OF YOUR RESEARCH? “[Insects] are really efficient at moving fluids around their bodies. They have a complex network of tubes, [which] delivers oxygen directly to the tissues. The insects are able to regulate flow inside of a “bag of blood”, and then they use that blood pressure to control the opening and closing of these tubes in order to push air in and out of their bodies. [We measure] this by using high resolution X-ray imaging while the animals are alive. We also use high-resolution electron microscopy to look at the microstructures of the tubes. There are a lot of translational possibilities when we are looking at these things.”

Jonathan Boreyko Jing Chen Daniela Cimini Rafael Davalos

Raffaella De Vita Caroline Jones Chloé Lahondère Iuliana Lazar

Linsey Marr Steve Melville Shane Ross David Schmale

BIOTRANS FACULTY members are located in ten different 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 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.

Eva Schmelz Shima Shahab Jake Socha

Mark Stremler Clément Vinauger

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indirect measurements of wind, estimated from the motion of the drone. Schmale worked closely with one team, and Javier González-Rocha, a Ph.D. student in Aerospace and Ocean Engineering, worked with the other team. Each team worked together to safely operate the drones, record important details of the experiments, and download and curate data off the drones.

B I O T R A N S | F I E L D C A M PA I G N

“This research campaign placed students right in the middle of the action. They had to work and communicate across the fields of engineering and biology. They got to see an engineer and mathematician (Ross) speak about biology and a biologist (Schmale) speak in the language of an engineer. When you are participating in interdisciplinary research, it’s always important to be humble, stay engaged, and ask questions,” said Schmale.

Image, left: Shane Ross and David Schmale brought six undergraduate students from partnering colleges to Virginia Tech and the Blacksburg quarry to conduct drone research. Image, bottom right: Piloting an underwater robot through a dye tracking experiment. Photo credit: Peter Means.

Field campaign exposes students to data and decisions research at the interface of engineering and biology Written by Kristin Rose

DRONE WIND STUDIES, WATER rescue manikins, and underwater robots tracking a fluorescent dye: these were not scenes from a science fiction movie but research that was part of a recent field campaign led by Virginia Tech BIOTRANS investigators Shane Ross and David Schmale. Ross and Schmale brought six undergraduate students from partnering colleges to Virginia Tech to conduct data and decisions research in March during spring break. 24

The students came from Morehouse College in Georgia, an all-male historically Black college and university (HBCU), Bennett College in North Carolina, an all-female HBCU, and Hampden Sydney College in Virginia, an allmale college. “The field campaign was a really valuable experience for the visiting students. They collected data and learned to make decisions from their data. We have submitted grants to continue collaborating with faculty at these three colleges.

We hope to bring more undergraduate students to Virginia Tech for summer research experiences in the area of biological transport,” said Schmale, professor in the School of Plant and Environmental Sciences in the College of Agriculture and Life Sciences. On the cold and windy first day of the research campaign, the students participated in drone wind-monitoring experiments at the Kentland Experimental Aerial Systems (KEAS) laboratory

located at Virginia Tech’s Kentland Farm agricultural research facility. “We explained to the students why it is important to measure the weather and wind with drones. With this technology, we have the potential to monitor the spread of plant diseases and even the spread of wildfires with on-the-spot accuracy,” said Ross, professor in the Department of Aerospace and Ocean Engineering in the College of Engineering. The students were divided into two drone teams, with three students to each team. One team made direct measurements of wind using a unique weather station mounted on top of the drone. The other team made

The students came to the field campaign from diverse scientific and educational backgrounds.

There were three biology students and three engineering students within the group. Trent Malone, Donovan Hardy, and Bryan Bloomfield came from Morehouse College; Milan Tisdale and Arianna Shynett came from Bennett College; and Damian Martinez Pineda came from Hampden Sydney College. “These students chose to spend their spring break participating in this research involving the use of unique sensor-based assets and computational-based assets at Virginia Tech. The students’ work helped them to gain a better understanding of how to best apply their technical skillsets toward addressing complex data science challenges. As a result, students were able to broaden their perspective of possible graduate studies, research opportunities, and career paths post-graduation,” said Eddie C. Red, Chair for the Division of Mathematics and Computational Sciences, Morehouse College.


On the second day of the research campaign, the students conducted field research in a local quarry pond in Blacksburg, Virginia. They used a kayak, drones, underwater robots, and

and used a harmless, fluorescent dye and floating assets to accurately record how the dye plume spread. A drone and underwater robot were used to capture data about the spreading

Ross observed that by the second day, “the students felt much more comfortable with each other and with us. They really came together and worked as a team to do a lot of the hands-on experiments

B I O T R A N S | F I E L D C A M PA I G N pristine Virginia Appalachian forest. On this hike, I was able to speak with Dr. Schmale about his journey through college and how he came to find a field of research he was excited about. Honestly, his story was very motivating because I could relate to his struggles as a college student. It is not very often an inner-city kid like myself is able to connect with a Cornell Ph.D. on a scientific and personal level,” said Bloomfield, a senior physics major at Morehouse College interested in autonomous design and artificial intelligence.

the students to the BIOTRANS graduate program, which offers students education and research opportunities at the interface of biology and engineering. BIOTRANS graduate students investigate dynamic transport processes in multiscale biological systems. A first-year BIOTRANS Ph.D. student, Jin Pan, and a more senior BIOTRANS Ph.D. student, Talia Weiss, presented their research to the visiting undergraduate students. Pan talked about the

Sciences Institute, the BIOTRANS graduate program, a diversity and inclusion grant from the Institute for Critical Technology and Applied Science (ICTAS), and grants from the National Science Foundation (AGS-1520825, DMS1821145, and IIS-1637915). Affiliated faculty from the contributing institutions were Eddie Red from Morehouse College, Kelly Mallari from Bennett College, and Michael Wolyniak from Hampden Sydney College.

In the afternoon, Ross and González-Rocha worked with the students to analyze data from the campaign back at Virginia Tech in the afternoon. The students uploaded software to their computers and began to interpret their results.

Dye tracking experiment at the quarry pond. Photo credit: Peter Means.

a series of floating objects to track a fluorescent dye in the water. Data from this experiment will help make decisions about the transport and mitigation of hazardous agents in the water, such as chemical/oil spills or harmful algal blooms. The goal of the experiment was to understand how a potential hazardous agent was affected by wind and currents. The students and researchers set up a manikin to help simulate rescue scenarios 26

dye in near real-time. “I greatly enjoyed visiting the quarry pond and being able to experience using different tools and techniques to gather data. The research that took place was fascinating, but it was also incredibly gratifying to be in such a beautiful environment with like-minded individuals who shared the same appreciation for research and the environment,” said Shynett, a visiting student from Bennett College.

themselves. This campaign gave students who are interested in field work the opportunity to see if this is something they would like to pursue in the future; it provided an example of what graduate field research looks like.” On the third day of the campaign, Schmale took the students on a hike to the Cascade Falls in Pembroke, Virginia. “We took a 3.5-mile hike into the

“The students were able to appreciate the huge volume of data that we gathered with all of these different assets. It will take us weeks to analyze all of the data from these field experiments, which will serve as the basis of new peer-reviewed manuscripts and grant proposals,” said Schmale. On the final day of the campaign, the visiting students participated in a recruiting event run by the BIOTRANS Interdisciplinary Graduate Education Program (IGEP). BIOTRANS director, a professor in the of Biomedical and Mechanics,

Jake Socha, Department Engineering introduced

Visiting undergraduate students conducted drone wind experiments at the Kentland Experimental Aerial Systems laboratory with Virginia Tech researchers. From left to right: Javier-Gonzalez Rocha, Regina Hanlon, Damian Martinez Pineda, Shane Ross, Jean-Michel Fahmi, Donovan Hardy, David Schmale, Bryan Bloomfield, Milan Tisdale, Trent Malone, Arianna Shynett. Photo credit: Peter Means

spread and biological transport of aerosolized pathogens and Weiss presented her research on the aerodynamics of how frogs leap and skitter over water. The day concluded with lab tours and meeting other researchers involved in the BIOTRANS program. Funding for the campaign was provided by the Fralin Life

“We just received word that our NSF Harnessing the Data Revolution: Data Science Corps grant proposal for $1.2 million was just funded, so we are excited to expose some of the best and brightest students from our partner institutions to more data and decisions research at the engineering/biology interface,” said Ross. 27


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 Jing Chen Written by Tiffany Trent

WHAT IS THE FOCUS OF YOUR RESEARCH? I study mathematical modeling for biological systems. The type of model I work with focuses on understanding the mechanisms, or how things work, in biological systems. Biological systems typically consist of very complex components. In my lab, we’re trying to understand how

all these complex components connect with each other to generate certain functions in a biological system, e.g., how a cell divides. My task is to piece together often-fragmented data obtained from experiments and put them together in a holistic way. For example, a recently-submitted paper shows how phages and bacteria interact with each other to form specific geometric patterns in the bacterial colony. By understanding how a pattern forms in the lab, we get insight about fundamental deeper questions about the interactions of species between phages and bacteria in the natural world. WHY DID YOU CHOOSE VIRGINIA TECH TO CONTINUE YOUR CAREER? I chose Virginia Tech because the collaborative environment in my home department is very impressive. For my research it is very important to stay in close contact with experimentalists, connecting to real problems and questions in biology. I noticed 28

EDUCATIONAL BACKGROUND: Postdoc, National Heart, Lung and Blood Institute, NIH (Advisor: Jian Liu) - 2016

HONORS & AWARDS: Distinguished Scientist Award, Chinese Students and Scholars Association of NIH, 2016

HOBBIES: Singing, skiing, tennis

Ph.D. in Biophysics, University of California, Berkeley (Advisor: George Oster; Co-advisor: John Neu) - 2010

High Distinction in M.S. in Mathematics in Bioscience, 2004

FAVORITE QUOTE: “All models are wrong, but some are useful.”

M.S. in Mathematics in Bioscience, Technical University of Munich Munich, Germany - 2004 B.S. in Biology, Fudan University, Shanghai, China - 2002

Scholarship for Excellent Foreign Students from Bavarian Ministry of Science, Research and Arts, Fall 2003 and Spring 2003 First Class People’s Scholarship from Fudan University, Shanghai, China, 2001

FAVORITE THING TO DO AROUND BLACKSBURG: Roaming around and taking scenic photos

FAVORITE TYPE OF MUSIC OR ARTIST: Any piece I can sing. FAVORITE BOOK OR BOOK SERIES: The Three-Body Problem, The Count of Monte Cristo

Second Class People’s Scholarship from Fudan University, Shanghai, China, 1999-2000

when I interviewed here that the experimentalists truly valued my modeling research. Virginia Tech also provides great mentoring opportunities for junior faculty; John Tyson and Daniela Cimini have really helped me in that regard. In fact, I’m currently working on a collaboration with Dr. Cimini related to chromosome oscillation. WHAT DO YOU ENJOY ABOUT BEING AN AFFILIATED FACULTY MEMBER WITH THE BIOTRANS PROGRAM? BIOTRANS is a great experience. What impresses me most about BIOTRANS is the many activities organized by the program—seminars, happy hours, etc.—that are designed to enhance communication between students and faculty. The program’s rotation mechanism is extremely useful for students because they can get ideas about what they’re interested in.

WHAT ADVICE DO YOU HAVE FOR PROSPECTIVE GRADUATE STUDENTS? Passion and interest are very important; these will carry you through career troughs. Seldom is it the case that research has no difficulties, but the passion and interest will serve as the inner drive to help you pull through. Research and coursework are very different, and you must learn to set your own agenda in research. It’s very helpful to break down long-term goals into small pieces so you’re not overwhelmed. On the other hand, be sure to be flexible with your plans, because you don’t know what you’re going to encounter. WHAT HAS BEEN YOUR MOST MEMORABLE EXPERIENCE SINCE JOINING VIRGINIA TECH OR MOVING TO BLACKSBURG? I met my husband in my first month at Virginia Tech. Virginia is for lovers! Image, previous page: Jing Chen. Image, this page: From left to right: Sean McMahon, Jing Chen, Xiaochu Li, Yirui Chen, Xiangyu Yao, Kelly Graff, and29 Dilara Long. Image courtesy of the Chen lab.


BIOTRANS | ALUMNI CORNER

After BIOTRANS Adwoa Baah-Dwomoh, Ph.D. Written by Kendall Daniels

engineering and mechanics, both from the College of Engineering. She says that both of her advisors were and continue to be excellent mentors, who helped her both academically and personally. For Adwoa, Virginia Tech is a not-so-unfamiliar place. She completed her Bachelor’s degree in materials science and

ADWOA BAAH-DWOMOH received her Ph.D. from Virginia Tech in May 2018. This year, she was the recipient of a Distinguished Alumni Award given by the Mid-Atlantic Prep & IMSD Research Symposium (MAPRS). When she was a student at BIOTRANS, the program was called MultiSTEPS, which was an acronym for MultiScale Transport in Environmental and Physiological Systems. There, she studied the biomechanics of soft tissues – specifically the mechanical properties of pelvic supportive ligaments - with the ultimate goal of aiding the treatment of pelvic floor disorders. During her time at BIOTRANS, she was co-advised by Raffaella De Vita, professor of biomedical engineering and mechanics, and Rafael Davalos, the L. Preston Wade Professor of biomedical 30

engineering in the College of Engineering at Virginia Tech before she received her Master’s degree in materials science and engineering from the University of Florida. Currently, she is a biomaterial research engineer at W.L Gore and Associates. We spoke with Adwoa to learn more about her experience since she graduated from the BIOTRANS program. LOOKING BACK, HOW HAVE THINGS TURNED OUT SINCE COMPLETING YOUR PH.D.? BIOTRANS introduced me to a lot of faculty that I would not have necessarily been exposed to otherwise. I feel like BIOTRANS gave me a broader education in general, which was very helpful in helping me land my current position at Gore. One of the things that my company liked about me was that I had a lot of research experience in a lot of different areas. BIOTRANS helped me become more well-rounded. WHAT DO YOU DO NOW AT YOUR COMPANY? My official title is

a Research Technologist, but I am essentially a Biomaterials Research Engineer. One thing that primarily falls into my purview is synthesizing, developing, and characterizing polymer materials for implantable medical devices. At its core, Gore is a materials engineering company and all of our materials technology is

based off of one main material, polytetrafluoroethylene (PTFE). I mainly focus on materials for medical devices, but we have our hands in all kinds of other things, ranging from industrial filtration systems, aircraft materials, to fabrics and textiles, with our most well-known product being the GORE-TEX material. The duties that I am specifically responsible for include: thinking up materials for implantable medical devices, applying in-vitro, in-vivo, and ex-vivo techniques to assess material interactions with biological systems, and influencing material selection decisions for new medical device product development. HOW DO YOU SEE YOUR BIOTRANS EXPERIENCE PLAY OUT AS A RESEARCH ENGINEER? Back when BIOTRANS was MultiSTEPS, I remember its mission being that it looks at the interface of engineering and biology and so I feel like that was very true in my graduate education. I liked how the faculty were doing their research on multi-

length scales. Some people were looking at the nanometer scale and some people were looking at stuff that was miles long in terms of length-scale. When I first heard of a biomaterials engineer, I only thought of somebody who works in the medical field. BIOTRANS helped me think of biomaterials and biology as a whole, instead of only thinking about it in terms of medical-related applications. CAN YOU GIVE AN EXAMPLE OF SOMETHING FROM YOUR BIOTRANS RESEARCH THAT PLAYS OUT IN YOUR WORK NOW AS A RESEARCH ENGINEER? When I was with Dr. De Vita, we did a lot of mechanical testing of materials. At my current position, I have to have a real understanding of mechanical

WHAT ADVICE WOULD YOU GIVE TO POTENTIAL STUDENTS WHO ARE CONSIDERING THE BIOTRANS PROGRAM? Talk to all of the faculty. Joining BIOTRANS was how I actually found out about Dr. De Vita. Previously, I didn’t know that she was a faculty member whom I could work with. She was an amazing advisor and she continues to be an amazing mentor. She is my friend now and I still speak with her to this day. I can confidently say that the connections that you make [through BIOTRANS] can go farther than just academic achievement. BIOTRANS tries to foster that kind of good mentoring relationship between the student and the professor, which can sometimes be lacking

WHAT IS YOUR FAVORITE PART OF YOUR CURRENT JOB? There is a preconceived notion that if somebody goes into academia, they have the freedom to do whatever research that they want to do; whereas, if you go into the industry, you are beholden to only do very specific things. I can’t speak for all industries, but at Gore, in my current position, there is a general focused area that I have to play in. But at the same time, I have the freedom to research whatever I want. It’s like an academic setting in the sense that I can do whatever research that I want – if I can convince people that it’s important. At Gore, they really encourage free thinking and thinking about the cutting-edge. Since I am in a

Images, left to right: Medical device development at W.L. Gore and Associates, GORE-TEX material, electrical engineering at W.L. Gore and Associates. Images courtesy W.L. Gore and Associates.

properties of materials, what tests would be good to use, and what characterization techniques need to be used. I can confidently say that my training with regards to mechanical properties is something that I use daily, specifically for biomaterials characterization.

at a graduate level. BIOTRANS does an amazing job at picking faculty who want to not only advise their students, but faculty that truly care for their students and their success academically, professionally, and personally.

research scientist position, they really encourage us to think of the next frontier in the space that we can play in.

31


Fralin Life Sciences Institute Steger Hall 1015 Life Science Circle Blacksburg, VA 24061

fralin.vt.edu

Virginia Tech BIOTRANS researchers and visiting students at the Kentland Experimental Aerial Systems laboratory. Photo credit: Peter Means.

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BIOTRANS, 2019  

Editor: Kristin Rose Volume 4

BIOTRANS, 2019  

Editor: Kristin Rose Volume 4

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