All posts by: Sarah Hansen, M.S. '15

UMBC researchers build next-gen satellite tech to examine Earth’s atmosphere

The first Hyper-Angular Rainbow Polarimeter (HARP) was a nano-satellite about as big as a loaf of bread. Developed by Vanderlei Martins, professor of physics, and his team of scientists and engineers at UMBC’s Earth and Space Institute, the HARP cubesat launched to the International Space Station in November 2019 and was released into orbit in February 2020. HARP spent over two years collecting first-of-its-kind data on Earth’s atmosphere, and finally deorbited in April 2022.

But that was just the beginning. Soon, HARP2 will be part of NASA’s Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission. And the HARP team is preparing now to compete for a spot on the future NASA Atmosphere Observing System (AOS) mission as MegaHARP.

From the HARP cubesat, “We have data now on clouds. We have data over the ocean. We have data over land surfaces in a way that we never had before,” Martins says. The instrument was so impressive that the American Institute of Aeronautics and Astronautics named it SmallSat Mission of the Year in August 2021. “Now,” Martins says, “we are using HARP data to develop algorithms and methodologies that we will use for these other missions.”

Proving it works

On its 27-month flight, HARP’s unique sensors collected new kinds of information about clouds and tiny particles in Earth’s atmosphere, such as wildfire smoke, desert dust, and human-generated pollutants. These particles, collectively known as aerosols, have many effects on the global climate and the health of organisms. The data may inform refined climate models or strategies to reduce the effects of air pollution.

HARP also broke ground in the way it collects data. HARP captures images, but “it’s not a camera that takes pictures. It’s something a lot more sophisticated,” Martins explains. “It’s taking thousands of these pictures and recombining them in a way that becomes a multi-dimensional scientific data set.”

A single composite image generated by HARP can contain the information from up to 1,000 original images. Each image and its information are extractable from the composite, which allows researchers to look at many different parameters depending on their goals.

“The HARP cubesat allowed us to prove that the idea we had of how to create the composite images worked,” Martins says.

an image of part of the Earth's surface, with horizontal stripes and patches of bright colors — The stripes on this image HARP collected of the Mediterranean represent the many wavelengths of light, from near infrared to blue, that HARP’s sensors can detect. The HARP team combined hundreds of images like these to create smooth depictions of areas all around the world. (courtesy of Vanderlei Martins)

Opening the path

HARP’s physical design is also innovative. A single instrument with no moving parts houses the sensors and algorithms used to process all the different data types. That’s a big benefit for any instrument facing the harsh environment of space.

“For us, HARP was a pathfinder,” Martins says. “It was funded as a technology demonstration. So we launched HARP to demonstrate that this technology is possible, and to open the path for other missions that are coming after that.”

HARP2 is already taking advantage of lessons learned from HARP. It will fly on NASA’s PACE mission in 2024, but the team must deliver their instrument to the Goddard Space Flight Center this October.

“HARP2 is basically an advanced copy of the instrument payload in the HARP cubesat,” Martins says. Everything from calibration systems to the raw materials has undergone improvements.

Plus, due to greater availability of technical resources on the larger PACE mission compared to the original cubesat, Martins explains, “HARP2 in five hours will collect as much data as HARP cubesat collected in two years.”

two researchers in all-white, full-body protective gear hold the HARP cubesat inside a "clean room" laboratory. — Researchers work on the HARP cubesat in a clean room. (Marlayna Demond/UMBC)

Launching satellites and careers

Since its inception, HARP has also lived up to UMBC’s mission to educate students and support the regional economy and workforce. Undergraduate and graduate students played key roles in the research, design, and construction phases for HARP and now HARP2.

“Relationships with federal agencies like NASA, all the work that we do with private companies around us, plus the training of students, who then go on to lead the same field they were working in, all fit very well the goals of our public research university,” Martins says.

Through HARP, HARP2, and early preparation for MegaHARP, every iteration of the project has prepared students for successful careers, proven new technologies, and generated new knowledge about the world. But, as an educator, perhaps the most rewarding part for Martins is seeing his students grow, find success, and then reach back to help others.

“We are seeing with HARP a full cycle. Students were involved in the inception of the idea for HARP from the beginning,” he says. “And today, students who were there working on HARP at the beginning are now in positions at NASA supporting the next generation.”

UMBC’s Viswanathan uses the Moon’s craters to track its shifting poles over 4.25 billion years

A new study published in Planetary Science Journal has determined how the Moon’s poles have shifted over more than 4 billion years, a phenomenon known as “true polar wander.” To trace the poles over time, the research team examined the combined effects of more than 5,000 craters on the Moon’s surface.

Each impact, and the subsequent crater, changed the distribution of mass on the Moon slightly. To rebalance, the Moon would have rotated just a little, without its axis moving in space. As a result, the axis would pass through the Moon at slightly different locations—the new poles.

“All this cratering is like a record” of the Moon’s history, says Vishnu Viswanathan, assistant research scientist with UMBC’s Center for Space Sciences and Technology (CSST), a university partnership with NASA’s Goddard Space Flight Center. Viswanathan co-led the study with David Smith, a research scientist at the Massachusetts Institute of Technology.

Water on the Moon?

Professional photo of South Asian person with short, black hair, wearing gold — Vishnu Viswanathan (Image courtesy of Viswanathan)

The study found that over approximately 4.25 billion years, the Moon’s poles wandered 10 degrees in latitude, or 186 miles, from the influence of cratering. Over the past 3.8 billion years, the poles have not wandered more than 2 degrees, or 37 miles. Such a moderate amount of polar wander would have created relatively stable conditions in the Moon’s polar regions over an extended period. That stability likely contributed to favorable conditions for resources such as frozen water.

Scientists have detected ice in colder, shadowed regions near the Moon’s poles. However, its amount and age is unknown. If the poles had moved substantially and frequently over time, any ice would repeatedly be exposed to sunlight and likely lost to sublimation—the process of a solid converting directly to a gas, like dry ice on Earth. With greater stability of the poles over billions of years, there would be more time for water to accumulate near the Moon’s present-day poles.

Stepping back in time

To calculate each crater’s effect on the location of the Moon’s poles, the research team relied heavily on a map of the Moon’s gravitational field, which defines the force of gravity at each point on the Moon’s surface. Sander Goossens, a former UMBC CSST scientist and a co-author on the new paper, developed the map previously using data from NASA’s GRAIL mission, which flew over the surface of the Moon in 2012.

The two GRAIL satellites measured anomalies in the distribution of mass on the Moon (such as craters), to a resolution of a few kilometers. The satellites’ detection is comparable to the way that a driver can feel the rise and fall as they pass over speed humps or potholes, Viswanathan explains.

Using Goossens’s map, Viswanathan and his team figured out a way to mathematically remove each crater’s individual effect, or signature, on the Moon’s gravitational field. The team started by sequentially removing 185 large craters whose ages are known, partly based on samples collected from NASA’s Apollo Moon missions. At each step going backward in time, they recalculated the presumed location of the Moon’s poles, creating a history of the poles’ location as they moved through time—the polar wander.

For the rest of the craters, most of them small, the research team removed their signatures from the gravity field and randomly distributed them through time. The team’s model is designed so more impacts occur in the early history of the Moon, because it’s understood that impacts were more frequent during that period. By running this simulation again and again, they were able to estimate the path of the Moon’s poles based on its cratering history.

This animation traces the “polar wander” of the Moon’s poles from about 4.25 billion years ago to the present day. (NASA Scientific Visualization Studio)

The Moon’s origin story

Moving forward, the new research may increase understanding of the formation of the Moon and the solar system in general. Information from the study about the shape of the Moon at different time points could help refine understanding of the Moon’s orbital path at those times. Also, shortly after the Moon formed, it was much closer to Earth and spinning faster. The contribution of small craters to the Moon’s shape could help add more detail to our understanding of how it reached its current location.

Viswanathan is excited about NASA’s Artemis mission, which will likely collect more samples from previously unvisited craters near the Moon’s south pole. “More samples from more craters would tell us quite a lot about the Moon’s cratering history,” he says. Knowing accurate ages of the large craters, including the largest, the South Pole-Aitken basin, would help refine the polar wander model. Information about the craters’ composition could increase understanding of resources—such as water—present on the Moon.

The project has also been an opportunity for Viswanathan and his team to grow and gain new expertise. An astronomer and a planetary geodesist who has researched other aspects of the Moon, Viswanathan came to the project with the beginnings of the math needed to track the poles based on the gravitational field. “But I had very little idea of these craters’ names before,” he says. “So it was a nice way to familiarize with them.”

The project, and especially the close collaboration with colleagues, has also served as an anchor for him throughout the pandemic. He shares, “I was so invested in the project for the last nearly three years. This kept me sane.”

UMBC to co-lead new Baltimore Social-Environmental Collaborative with $2.3M grant

American cities face environmental challenges that are exacerbated by climate change, from air and water quality issues to flooding and heat. Low-income neighborhoods and areas that were previously subject to racial redlining often experience these effects more intensely.

A new program supported by the U.S. Department of Energy (DoE) has funded Urban Integrated Field Laboratories in three American cities (including Baltimore) to generate resilience-enhancing solutions to urban climate challenges in collaboration with community organizations. The Baltimore-centered consortium, named the Baltimore Social-Environmental Collaborative (BSEC), will receive $24.5 million through the program. UMBC will receive $2.3 million of this larger grant.

Leading UMBC’s work on the project is Claire Welty, professor of chemical, biochemical, and environmental engineering and director of the Center for Urban Environmental Research and Education (CUERE). Johns Hopkins University leads the overall project, which also includes collaborators at the Pennsylvania State University, Morgan State University, the National Renewable Energy Laboratory, Drexel University, and the University of Virginia.

“This Baltimore Social-Environmental Collaborative is an important program during a critical time for our region, for our state, and for our planet,” says Karl V. Steiner, vice president for research at UMBC. “I am pleased that Baltimore was selected to serve as a representative metropolitan area for the climate challenges faced by many mid-sized industrial cities across the U.S.”

Listening to the community

Welty and UMBC colleagues such as Andrew Miller, professor of geography and environmental systems, bring decades of expertise in environmental monitoring to the project through their individual research and the Baltimore Ecosystem Study (BES). Originally funded as one of only two urban Long-Term Ecological Research (LTER) sites in the U.S., the BES has compiled massive datasets on the Baltimore region’s watershed, ecology, and sociological issues related to the environment for more than 20 years. The new BSEC will bring opportunities to expand this work in fresh directions.

“The exciting thing is leading from the needs of the community. To me, that’s what’s different about this,” Welty says. “What we want to try to do is partner with the communities to come up with solutions to these climate impact problems, and then what we’re bringing to the table are our tools to implement that.”

A researcher standing among greenery and holding a clipboard looking at a sampling station, which looks like an transformer box with the front panel open, with a small solar panel attached to it on a tall pole — Andrew Miller checks on a water sampling station in Catonsville, MD. (Victor Fulda/UMBC)

Welty and Miller bring expertise in understanding patterns of water quality, flood and groundwater modeling, and rainfall patterns and how they are changing. UMBC also brings experience interacting with local agencies, such as the Baltimore City Department of Public Works and Maryland Department of the Environment. Other institutions in the consortium bring complementary expertise, such as overall climate forecasting, an understanding of how climate impacts intersect with issues of public health, and experience building trust with community groups.

“Among us, we think we have tools that can be applied to solve these problems,” Welty says. “We’re not imposing our tools on community groups, though, or telling them what their problems are. They’re telling us, and we’re responding with support and resources.”

Adding nuance

Welty, Miller, and others have spent decades generating models and collecting on-the-ground (and sometimes underground) observations of water quality, flow, and more in the Baltimore region. They will continue that work with the BSEC, and with input from communities, prioritize certain issues or geographic areas.

The BSEC will also fund deployment of new sensors at existing Baltimore Ecosystem Study stream sampling stations in the Gwynns Falls watershed . These stations have a 22-year record of weekly water quality sampling, and the new sensors will add data on other parameters at 15-minute intervals, 24 hours a day, seven days a week. The data will be accessible in near- real time, on only about a one-hour delay.

The BES data is “the best urban water quality data set in the world. This is not meant to replace that, but to add nuance,” Welty says. For example, Baltimore streams have struggled with inundation from road salt in the winter. “You might miss the peak of a salt event with weekly sampling,” Welty says, but finer scale sampling would easily identify it in the data.

two researchers in tall wellington boots stand along the gravelly bank of a stream, which is passing under a bridge. — Claire Welty (left) and Andrew Miller check out one of their study sites in Woodlawn, MD. (Victor Fulda/UMBC)

A giant puzzle to put together

The BSEC is a unique project that brings together wide-ranging expertise to address pressing urban needs. “The guiding objective of the BSEC process is to produce the urban climate science needed to inform community-guided, equitable pathways for climate action,” says Ben Zaitchik, professor of Earth and planetary sciences at Johns Hopkins and the overall project lead. “In doing so, we address a number of fundamental urban science questions from across natural science and social science disciplines.”

UMBC’s Steiner adds, “This partnership with John Hopkins University and other research institutions is building upon our strong and long-term record of environmental research and educational initiatives here at UMBC. It will both challenge and enable us to explore equitable climate solutions.”

While the exact priorities and concerns that local communities will bring to the forefront are unknown, the BSEC group plans to bring their tools to bear in a way that best serves the people of Baltimore. Building coalitions with researchers and community members, learning the communities’ needs, and then finding the best ways to address them “is like a giant puzzle to put together,” Welty says. “It’s going to be exciting to see how it all unfolds.”

New UMBC research finds that viruses may have “eyes and ears” on us

New UMBC-led research in Frontiers in Microbiology suggests that viruses are using information from their environment to “decide” when to sit tight inside their hosts and when to multiply and burst out, killing the host cell. The work has implications for antiviral drug development.

A virus’s ability to sense its environment, including elements produced by its host, adds “another layer of complexity to the viral-host interaction,” says Ivan Erill, professor of biological sciences and senior author on the new paper. Right now, viruses are exploiting that ability to their benefit. But in the future, he says, “we could exploit it to their detriment.”

Not a coincidence

The new study focused on bacteriophages—viruses that infect bacteria, often referred to simply as “phages.” The phages in the study can only infect their hosts when the bacterial cells have special appendages, called pili and flagella, that help the bacteria move and mate. The bacteria produce a protein called CtrA that controls when they generate these appendages. The new paper shows that many appendage-dependent phages have patterns in their DNA where the CtrA protein can attach, called binding sites. A phage having a binding site for a protein produced by its host is unusual, Erill says.

Even more surprising, Erill and the paper’s first author Elia Mascolo, a Ph.D. student in Erill’s lab, found through detailed genomic analysis that these binding sites were not unique to a single phage, or even a single group of phages. Many different types of phages had CtrA binding sites—but they all required their hosts to have pili and/or flagella to infect them. It couldn’t be a coincidence, they decided.

The ability to monitor CtrA levels “has been invented multiple times throughout evolution by different phages that infect different bacteria,” Erill says. When distantly related species demonstrate a similar trait, it’s called convergent evolution—and it indicates that the trait is definitely useful.

Grayscale image of an organism with a round portion and curved tail portion. — A delta phage, the first identified in the new study to have binding sites for CtrA. (Transmission Electron Microscope image captured by Tagide deCarvahlo at UMBC’s Keith Porter Imaging Facility)

Timing is everything

Another wrinkle in the story: The first phage in which the research team identified CtrA binding sites infects a particular group of bacteria called Caulobacterales. Caulobacterales are an especially well-studied group of bacteria, because they exist in two forms: a “swarmer” form that swims around freely, and a “stalked” form that attaches to a surface. The swarmers have pili/flagella, and the stalks do not. In these bacteria, CtrA also regulates the cell cycle, determining whether a cell will divide evenly into two more of the same cell type, or divide asymmetrically to produce one swarmer and one stalk cell.

Because the phages can only infect swarmer cells, it’s in their best interest only to burst out of their host when there are many swarmer cells available to infect. Generally, Caulobacterales live in nutrient-poor environments, and they are very spread out. “But when they find a good pocket of microhabitat, they become stalked cells and proliferate,” Erill says, eventually producing large quantities of swarmer cells.

So, “We hypothesize the phages are monitoring CtrA levels, which go up and down during the life cycle of the cells, to figure out when the swarmer cell is becoming a stalk cell and becoming a factory of swarmers,” Erill says, “and at that point, they burst the cell, because there are going to be many swarmers nearby to infect.”

black and white microscope image with two dark ovals attached in the middle. One has a long skinny tail, the other has a thicker, shorter "stalk." — A Caulobacter bacterium divides, producing a stalked cell (right) and a swarmer cell with a flagellum (left). (public domain)

Listening in

Unfortunately, the method to prove this hypothesis is labor-intensive and extremely difficult, so that wasn’t part of this latest paper—although Erill and colleagues hope to tackle that question in the future. However, the research team sees no other plausible explanation for the proliferation of CtrA binding sites on so many different phages, all of which require pili/flagella to infect their hosts. Even more interesting, they note, are the implications for viruses that infect other organisms—even humans.

“Everything that we know about phages, every single evolutionary strategy they have developed, has been shown to translate to viruses that infect plants and animals,” he says. “It’s almost a given. So if phages are listening in on their hosts, the viruses that affect humans are bound to be doing the same.”

There are a few other documented examples of phages monitoring their environment in interesting ways, but none include so many different phages employing the same strategy against so many bacterial hosts.

This new research is the “first broad scope demonstration that phages are listening in on what’s going on in the cell, in this case, in terms of cell development,” Erill says. But more examples are on the way, he predicts. Already, members of his lab have started looking for receptors for other bacterial regulatory molecules in phages, he says—and they’re finding them.

New therapeutic avenues

The key takeaway from this research is that “the virus is using cellular intel to make decisions,” Erill says, “and if it’s happening in bacteria, it’s almost certainly happening in plants and animals, because if it’s an evolutionary strategy that makes sense, evolution will discover it and exploit it.”

For example, to optimize its strategy for survival and replication, an animal virus might want to know what kind of tissue it is in, or how robust the host’s immune response is to its infection. While it might be unsettling to think about all the information viruses could gather and possibly use to make us sicker, these discoveries also open up avenues for new therapies.

“If you are developing an antiviral drug, and you know the virus is listening in on a particular signal, then maybe you can fool the virus,” Erill says. That’s several steps away, however. For now, “We are just starting to realize how actively viruses have eyes on us—how they are monitoring what’s going on around them and making decisions based on that,” Erill says. “It’s fascinating.”

UMBC and University of Maryland School of Medicine receive $13.7M NIH FIRST grant to increase faculty diversity

UMBC and the University of Maryland School of Medicine (UMSOM) have received a five-year, $13.7 million grant from the National Institutes of Health (NIH) to enhance recruitment and training of junior faculty from groups underrepresented in biomedical science. Funding is through the NIH Common Fund Faculty Institutional Recruitment for Sustainable Transformation (FIRST) program, which was founded last year to support efforts to hire groups of diverse, early-career research faculty.

The grant will enable the universities to hire a group of four faculty members at UMBC and six at UMSOM, each of whom will have cross-campus appointments at both institutions.

“Faculty hired under UM-FIRST will advance our teaching and research missions and serve as leaders for institutional change as we pursue our vision of a diverse professoriate,” says William LaCourse, dean of the College of Natural and Mathematical Sciences and professor of chemistry and biochemistry at UMBC. “These faculty and those who follow will also serve as role models for future generations of underrepresented students.”

standing faculty member addresses seated students in a classroom — Dean William LaCourse teaches Chemistry 100 in spring 2022. (Marlayna Demond ’11/UMBC)

Fostering culture change

The grant aims to build self-reinforcing communities of scientists committed to diversity and inclusive excellence through the recruitment of early-career faculty who are competitive for assistant professor positions and have demonstrated commitment to promoting diversity and inclusion. UMSOM and UMBC will measure their progress against clearly defined metrics of institutional culture change, diversity, and inclusion to determine if hiring efforts and other evidence-based strategies are achieving the program’s goals.

The grant “is designed to foster sustainable culture change and promote inclusive excellence by enabling us to hire a diverse cohort of new faculty and to support faculty development, mentoring, and promotion opportunities,” says James Kaper, the lead on the grant and the James and Carolyn Frenkil Distinguished Dean’s Professor, vice dean for Academic Affairs, and chair of microbiology and immunology at UMSOM.

Building on a legacy of inclusion

The NIH FIRST grant builds on UMBC’s highly esteemed Meyerhoff Scholars Program, launched more than 30 years ago, which has led UMBC to become a leading university for developing underrepresented STEM undergraduates. UMBC is now the nation’s number #1 producer of Black undergraduates who go on to complete a PhD in the natural sciences or engineering and #1 for Black undergraduates who complete an M.D./Ph.D.

portrait of Nykia Walker — **Nykia Walker**, a Pre-professoriate Fellow in biological sciences, studies how breast tumors initiate metastasis. (Image courtesy of Nykia Walker)

At the same time that UMBC excels in educating undergraduates, the university is also classified as one of only 146 R1 (“very high research activity”) institutions in the nation.

UMBC’s efforts to promote faculty diversity in STEM include the PROMISE Academy and ADVANCE, which has increased women faculty in STEM by 70 percent at UMBC since 2003.

The College of Natural and Mathematical Sciences’ Pre-professoriate Fellowship offers incoming faculty two-year appointments as research assistant professors, with structured mentoring and other scaffolds for success. Faculty who came to UMBC through this program in biological sciences, physics, and chemistry have already been converted to tenure-track assistant professors.

Unwavering dedication

The recent $10M INCLUDES grant awarded to UMBC further builds a robust, diverse pipeline in STEM at UMBC by supporting postdocs from underrepresented groups, and the PROMISE Allegiance for Graduate Education and the Professoriate (AGEP) program offers professional development and community to all graduate students and postdocs at UMBC and throughout the University System of Maryland.

UMSOM’s efforts to promote a diverse STEM and health-science pipeline include the UMB CURES program for middle and high school students, several internship and summer research programs for college students, and multiple post-graduate training programs that give underrepresented minority scholars direct experience in a laboratory setting.

Like many of these other initiatives, “The true strength of UM-FIRST,” LaCourse says, “ is in the unwavering dedication of the leadership, faculty, and staff of these two institutions to inclusive excellence and social justice.”

Students in UMBC’s ICARE program connect scientific research with community

Bats as biomonitors, community connections to the zero-waste movement, and oyster aquaculture are just a few of the topics that students in UMBC’s Interdisciplinary Consortium for Applied Research in the Environment (ICARE) master’s program are exploring through Baltimore-centered community-engaged research. As the first cohort in the program heads into their second and final year, they are excited about their work and looking ahead to becoming the next generation of environmental science leaders.

“B” is for bat

Chris Blume, M.S. ’23, geography and environmental systems, has studied bobcats, bees, and birds. So when he came to ICARE, he jokes, “I had to choose another ‘b’ animal.” Jokes aside, in his undergraduate and working experience, Blume found that “the social aspect was missing” in conservation science, which often focused on wildlife. “And that’s what drew me to ICARE, because it seemed like there was a focus on the community.”

In his project, Blume is using bats as biomonitors to detect levels of heavy metals in different neighborhoods across Baltimore. “Because of their biology and their ecology, they make great biomonitors in rural environments,” he says, “but I wanted to see how that works in urban places.”

Chris Blume climbs a ladder to inspect his bat boxes attached to a light pole about 15 feet off the ground.. — Bat boxes are most successful when they get ample direct sunlight and are about 15 – 20 feet off the ground.

Chris Blume outdoors, holding a wooden bat box about the size of his torso — Bat boxes are most successful when they get ample direct sunlight and are about 15 – 20 feet off the ground.

How can bats provide information about heavy metals? Through their guano (poop). “I have literally a fridge with a bunch of guano,” he says, waiting for analysis later this fall. In addition to the guano analysis, Blume is giving away bat boxes to local residents and offering evening “bat walks” to teach local Baltimoreans about these important native critters. He’s also created citizen science opportunities by posting acoustic recordings of bat calls on a public website, where anyone can listen and help identify which bat species show up where.

In the future, Blume wants to pursue a Ph.D. and continue his bat research, as well as continue to create citizen science and community engagement opportunities.

Building the bridge

Natalia Figueredo, M.S. ’23, geography and environmental systems, has always been community-oriented, influenced by her early childhood in Bolivia and her teenage years in Queens, New York. In New York, she noticed that “there were all these big projects going on in communities, and the community didn’t ask for them,” she says. She wanted to do something different.

After working with the Ironbound Community Corporation in Ironbound, New Jersey, she became passionate about doing inclusive research for mutual benefit, and ICARE was a perfect fit to advance her career. “What interested me about this program,” she says, “is that it was trying to build that bridge between scientific research and community engagement.”

Figueredo’s research project focuses on engaging South Baltimore residents in the zero-waste movement, in the context of recent battles over a nearby trash incinerator. She is also working closely with partners at the Global Alliance for Incinerator Alternatives (GAIA) and the South Baltimore Community Land Trust, in addition to her faculty mentor Maggie Holland, associate professor of geography and environmental systems.

several people walking down a street in Baltimore — Natalia Figueredo (second from left) meets with members of the South Baltimore Community Land Trust. (Courtesy of Figueredo)

Figueredo is surveying residents from across the city about their waste management practices and access to the zero-waste movement. She’s also interviewing South Baltimore community leaders and conducting focus groups with neighborhood residents. Figueredo hopes to find out whether they feel supported in pursuing zero-waste goals and to learn what local knowledge and practices already exist related to the movement—whether or not the residents identify them as such.

Research always comes with bumps in the road, but overall Figueredo has had a rewarding experience so far. She wanted to choose a graduate program where people would champion and support her, she says—“and that’s definitely how I feel with the ICARE team.”

Putting research into practice

Darryl Acker-Carter, M.S. ’23, marine, estuarine, and environmental science, is studying a new method of oyster aquaculture with partners at the company Solar Oysters. Traditionally, oysters have been cultivated in wire baskets at the water’s surface. A new system, called the Solar Oyster Production System (SOPS), uses a solar-powered ladder structure to rotate the baskets through the entire water column. The goal is to produce healthier, more-uniform oysters in less space. At the end of the growing season this fall, Acker-Carter will compare oyster size, survival rate, and meat-to-shell ratio of oysters in the experimental rotating ladders, non-rotating ladders, and traditional surface-only baskets at a site in Curtis Bay, in south Baltimore.

Acker-Carter has been interested in oysters for several years. “I like social science, but I also like the biological side of things, and I saw that nexus through oysters,” he says. To some, how to best cultivate oysters may seem like a purely scientific question, but “when you actually get down to, ‘Let’s make some change,’ it’s all social science,” Acker-Carter says, “because it’s all managing people and their perspective about how to harvest oysters and their relationships to natural resources.”

The ICARE program has helped Acker-Carter see how research fits into community engagement. “I used to think research was very isolated,” he says, “but in ICARE, you’re putting that research into practice. You can create benefit in the community by doing the research, and giving people access to that data.”

Darryl Acker Carter smiling and holding out a small blue crab in his palm while on a boat — Darryl Acker-Carter holds a very small blue crab on a boat.

five people around trays containing oysters, one is dumping a bucketful of oysters onto the tray — Darryl Acker-Carter holds a very small blue crab on a boat.

Committed to community

For program leader Tamra Mendelson, professor of biological sciences, ICARE is exceeding expectations. “I am thrilled with how the program is going,” she says. “The students themselves are so strong. They are motivated. They are engaged. They are very sharp, and they’ve bonded as a cohort, which makes us really happy. I do think that’s a huge secret to success—having students feel like they are part of a network of peers supporting each other.”

The community partners have also been critical for the program’s success. One session led by Stephen Freeland, director of the individualized study program at UMBC, brought students and partners together for a brainstorming session across projects and topic areas, embodying the program’s commitment to bridging science and community. “Just bringing everyone to the table, literally, and helping everyone see that their voice is equally important in solving these environmental problems and doing the research was really powerful,” Mendelson says.

Mendelson shares that she and her fellow faculty have also been developing their community-engagement skills in working alongside their students. “I’m amazed at how important relationships are, and trust,” Mendelson says. “Building relationships with members of the community has been much more interesting and complicated than I expected. It’s work. But it’s good work.”

That community engagement piece makes ICARE different from other environmental science programs, explains Kevin Omland, professor of biological sciences. “We’re definitely tackling different issues in different places than lots of environmental science has, even 10 or 20 years ago,” he says, “so it’s really satisfying to see that coming into place.”

“ICARE fulfills so many of the stated missions and goals of UMBC—to connect with community, to address the climate crisis, to increase diversity and inclusion,” Mendelson says. She looks forward to working with the second cohort of ICARE students, who started this fall, preparing them for successful careers in environmental science and leading local change.

Viruses may be ‘watching’ you – some microbes lie in wait until their hosts unknowingly give them the signal to start multiplying and kill them

Ivan Erill, Professor of Biological Sciences, UMBC

After more than two years of the COVID-19 pandemic, you might picture a virus as a nasty spiked ball – a mindless killer that gets into a cell and hijacks its machinery to create a gazillion copies of itself before bursting out. For many viruses, including the coronavirus that causes COVID-19, the “mindless killer” epithet is essentially true.

But there’s more to virus biology than meets the eye.

Take HIV, the virus that causes AIDS. HIV is a retrovirus that does not go directly on a killing spree when it enters a cell. Instead, it integrates itself into your chromosomes and chills, waiting for the right moment to command the cell to make copies of it and burst out to infect other immune cells and eventually cause AIDS.

Exactly what moment HIV is waiting for is still an area of active study. But research on other viruses has long hinted that these pathogens can be quite “thoughtful” about killing. Of course, viruses cannot think the way you and I do. But, as it turns out, evolution has endowed them with some pretty elaborate decision-making mechanisms. Some viruses, for instance, will choose to leave the cell they have been residing in if they detect DNA damage. Not even viruses, it appears, like to stay in a sinking ship.

My laboratory has been studying the molecular biology of bacteriophages, or phages for short, the viruses that infect bacteria, for over two decades. Recently, my colleagues and I have shown that phages can listen for key cellular signals to help them in their decision-making. Even worse, they can use the cell’s own “ears” to do the listening for them.

Escaping DNA damage

If the enemy of your enemy is your friend, phages are certainly your friends. Phages control bacterial populations in nature, and clinicians are increasingly using them to treat bacterial infections that do not respond to antibiotics.

The best studied phage, lambda, works a bit like HIV. Upon entering the bacterial cell, lambda decides whether to replicate and kill the cell outright, like most viruses do, or to integrate itself into the cell’s chromosome, as HIV does. If the latter, lambda harmlessly replicates with its host each time the bacteria divides. This video shows a lambda phage infecting E. coli.

This video shows a lambda phage infecting E. coli.

But, like HIV, lambda is not just sitting idle. It uses a special protein called CI like a stethoscope to listen for signs of DNA damage within the bacterial cell. If the bacterium’s DNA gets compromised, that’s bad news for the lambda phage nested within it. Damaged DNA leads straight to evolution’s landfill because it’s useless for the phage that needs it to reproduce. So lambda turns on its replication genes, makes copies of itself and bursts out of the cell to look for more undamaged cells to infect.

Tapping the cell’s communication system

Some phages, instead of gathering intel with their own proteins, tap the infected cell’s very own DNA damage sensor: LexA.

Proteins like CI and LexA are transcription factors that turn genes on and off by binding to specific genetic patterns within the DNA instruction book that is the chromosome. Some phages like Coliphage 186 have figured out that they don’t need their own viral CI protein if they have a short DNA sequence in their chromosomes that bacterial LexA can bind to. Upon detecting DNA damage, LexA will activate the phage’s replicate-and-kill genes, essentially double-crossing the cell into committing suicide while allowing the phage to escape.

Scientists first reported CI’s role in phage decision-making in the 1980s and Coliphage 186’s counterintelligence trick in the late 1990s. Since then, there have been a few other reports of phages tapping bacterial communication systems. One example is phage phi29, which exploits its host’s transcription factor to detect when the bacterium is getting ready to generate a spore, or a kind of bacterial egg capable of surviving extreme environments. Phi29 instructs the cell to package its DNA into the spore, killing the budding bacteria once the spore germinates.

https://youtu.be/MkUgkDLp2iE

Transcription factors turn genes on and off.

In our recently published research, my colleagues and I show that several groups of phages have independently evolved the ability to tap into yet another bacterial communication system: the CtrA protein. CtrA integrates multiple internal and external signals to set in motion different developmental processes in bacteria. Key among these is the production of bacterial appendages called flagella and pili. Turns out, these phages attach themselves to the pili and flagella of bacteria in order to infect them.

Our leading hypothesis is that phages use CtrA to guesstimate when there will be enough bacteria nearby sporting pili and flagella that they can readily infect. A pretty smart trick for a “mindless killer.”

These are not the only phages that make elaborate decisions – all without the benefit of even having a brain. Some phages that infect Bacillus bacteria produce a small molecule each time they infect a cell. The phages can sense this molecule and use it to count the number of phage infections taking place around them. Like alien invaders, this count helps decide when they should switch on their replicate-and-kill genes, killing only when hosts are relatively abundant. This way, the phages make sure that they never run out of hosts to infect and guarantee their own long-term survival.

Countering viral counterintelligence

You may be wondering why you should care about the counterintelligence ops run by bacterial viruses. While bacteria are very different from people, the viruses that infect them are not that different from the viruses that infect humans. Pretty much every single trick played by phages has later been shown to be used by human viruses. If a phage can tap bacterial communication lines, why wouldn’t a human virus tap yours?

So far, researchers don’t know what human viruses could be listening for if they hijack these lines, but plenty of options come to mind. I believe that, like phages, human viruses could potentially be able to count their numbers to strategize, detect cell growth and tissue formation and even monitor immune responses. For now, these possibilities are only speculation, but scientific investigation is underway.

Having viruses listening to your cells’ private conversations is not the rosiest of pictures, but it’s not without a silver lining. As intelligence agencies all around the world know well, counterintelligence works only when it’s covert. Once detected, the system can very easily be exploited to feed misinformation to your enemy. Similarly, I believe that future antiviral therapies may be able to combine conventional artillery, like antivirals that prevent viral replication, with information warfare trickery, such as making the virus believe the cell it is in belongs to a different tissue.

But, hush, don’t tell anybody. Viruses could be listening!

* * * * * *

Ivan Erill, Professor of Biological Sciences, University of Maryland, Baltimore County

This article is republished from The Conversation under a Creative Commons license. Read the original article.

UMBC-led Baltimore Ecosystem Study receives federal support for critical environmental monitoring

The U.S. Forest Service (USFS) has allocated $500,000 to carry forward the landmark Baltimore Ecosystem Study (BES), led by UMBC in close collaboration with area partners.

The BES has been collecting data for more than 20 years on the Baltimore region’s watersheds, ecology, and social issues related to the environment. From 1998 to 2018, the BES was one of just two urban Long-Term Ecological Research (LTER) sites funded by the National Science Foundation (NSF) in the United States. The groundbreaking project helped generate momentum for the now-thriving field of urban ecology.

Headquartered at UMBC’s Technology Research Center, BES has engaged UMBC researchers in fields as diverse as ecology, art, and environmental engineering. Dozens of researchers from other institutions have conducted experiments and made insightful discoveries about urban ecology through the study. Even more have analyzed the data produced by BES researchers—which is entirely public—for their own work.

Long-term partnership

As NSF’s funding priorities shifted in 2019, the agency did not renew funding for the BES, despite the program’s impact. Since then, BES leaders at UMBC and dedicated external colleagues have found ways to keep the core data-collection systems going to provide uninterrupted information to researchers around the world.

The team advocated for UMBC to be “a center of gravity to continue studying Baltimore’s ecosystem,” as a nexus for a strong existing network of scientists with a broad range of expertise, says Chris Swan, professor of geography and environmental systems and director of the BES.

The U.S. Forest Service made sense as a leader to help carry the work forward, as the agency “has always been a strong partner all through the Baltimore Ecosystem Study,” says Claire Welty, professor of chemical, biochemical, and environmental engineering. The new allocation from USFS will ensure that this partnership—and the important work of the BES—continues.

man inspects plants growing outside a greenhouse — Chris Swan, director of the Baltimore Ecosystem Study. (Marlayna Demond ’11/UMBC)

Connections with public impact

With support from UMBC administrators—particularly Karl V. Steiner, vice president for research—Swan, Welty, and others have worked hard to find new funding sources for BES projects. In addition to the U.S. Forest Service allocation, NSF awarded Peter Groffman, a long-time collaborator at the City University of New York, $600,000 to continue collection of long-term stream chemistry data in the Baltimore area. The funding, awarded in September 2021, is part of the NSF’s Long Term Research in Environmental Biology Program.

The new funding from NSF and USFS “is designed to keep the core going,” Swan says. “It will fund our quarterly and annual science meetings. It will support some of the co-PI summer salaries, technician salaries, field equipment and vehicle usage, some student support, and a little bit of travel.”

The quarterly meetings, in particular, are a key benefit the BES offers to the community. “Policymakers come to our quarterly meetings to listen and ask questions about the latest science,” Welty says. “They view the meetings as an important resource.” Attendees include staff from the Maryland Department of the Environment, Baltimore City Public Works, and more.

These important public connections, and the understanding that BES data have a real public impact, motivate Swan, Welty, and others to ensure BES continues for years into the future. “We’re going to keep going because we are a strong network of experts with so much to contribute,” Swan says. “We do science, but we also reach into the community, and NGOs, and policy—and we do that well.”

flat body of water backed by a variety of large downtown buildings — Baltimore Harbor is connected to Chesapeake Bay, the largest estuary in the United States and an area of intense research interest. (Rebecca Schley/CC BY-NC-ND 2.0)

Serving up the data

In addition to collecting data and hosting quarterly meetings, UMBC support has allowed the BES to keep its website up and running. This is where researchers, policymakers, and other interested parties can access the data from any study conducted as part of BES—from water quality to the results of re-greening efforts. The website is incredibly important, Swan says, “because one of the main things we do is serve up the data we collect to the public.”

Educational materials for K-12 teachers on related topics are available on the website. BES leaders also send out regular communications to a listserv of more than 500 researchers. Communications include content from the quarterly meetings and occasionally additional updates, such as relevant research papers and conferences.

Undergraduate and graduate students also benefit from access to BES data, Welty explains. Open access allows them to “discover things we haven’t yet begun to imagine from all this soil, water, and vegetation data collected for over two decades.”

A network, not a place

Swan and Welty are quick to point out that even though the BES meetings take place at UMBC, and the university hosts the website, BES itself is not a place. “We are a huge network of people, and anyone who wants to join, who’s doing socio-environmental research on Baltimore, can,” Swan says.

He notes that other organizations that have lost major NSF funding have found ways to continue their work fruitfully—and the BES plans to do the same. With champions at UMBC and on Capitol Hill, including U.S. Senator Chris Van Hollen of Maryland, the program’s future looks bright.

Steiner is thrilled to see new funding arriving to keep this important work going. “As a public R1 research university, we are committed to ensuring our work has a strong public impact,” he says. “We highly appreciate the support of our elected officials, and the partnership of researchers across the region, to fulfill this mission.”

UMBC’s Chris Swan awarded NSF funding for U.S.-Brazil partnership on stream biodiversity

A new collaboration between scientists in the U.S. and Brazil hopes to increase our ability to predict how biological communities may change in a warming world. The researchers will investigate differences in biodiversity in tropical and temperate streams to better understand the differences between organisms in these ecosystems. The National Science Foundation has supported the project with a three-year, $500,000 seed award.

Biodiversity is under threat from shifts in temperature, weather patterns, and habitat availability worldwide, says Chris Swan, co-lead on the project and professor of geography and environmental systems at UMBC. “Scientists like myself study what regulates the number of species that you see and the combination of species that you see, and why they occur the way that they do,” Swan says. “Those patterns are changing due to global change.”

The new study will focus on functional diversity, a concept that looks at species’ traits and the roles they fill in the ecosystem, rather than just the number of different species present. For example, in a forest, there might be a large number of bird species, but if they all eat seeds, there’s low functional diversity. Functional diversity would be higher if, among the same number of species, some ate seeds, others ate insects, and others ate small rodents.

“What is the functional response in terms of biodiversity to this global change? That’s what we’re studying,” Swan says. The results could help scientists make predictions about how species in temperate climates might adapt to rising temperatures.

man stands in front of milkweed and other native plants, trees in background — Chris Swan stands near native plantings. (Marlayna Demond ’11/UMBC)

Big questions, small organisms

The study will include researchers from UMBC, Virginia Tech, and University of California-Riverside in the U.S., and São Paulo State University and São Carlos State in Brazil. Streams near São Paulo, Brazil, and Blacksburg, Virginia, will represent tropical and temperate climates, respectively. The team will collect data from each stream monthly for a year.

They’ll manually measure the number of invertebrate species and how many of each species are present. Invertebrates they are likely to find include a wide variety of insects, worms, and crustaceans (such as crayfish). The team will also record traits of each individual, like its size and whether it was collected from the streambed, swimming in the water channel, or flying in the air above the stream.

On top of data on all the organisms, the researchers will also record information about the stream environment, like acidity, temperature, and the presence of nutrients like nitrogen, plus the streambed material (rock or sand, for example), the stream’s sun exposure, and more.

They will intentionally include large and small streams, too. The size of the stream “has practical implications,” Swan says, because in addition to small streams making up 60 percent of all river miles, “if you change a landscape, say by development, you are more likely to flatten a small stream than a large stream. So they are disproportionately under threat.”

a narrow stream runs through a forest — Small streams make up 60 percent of all river miles. (Tobias Wrzal/public domain)

Tropical trend

Some differences between species in tropical versus temperate streams are known. For example, tropical organisms tend to be smaller and have shorter life cycles. Their populations also tend to be smaller. This means local populations disappear through random effects more often in tropical ecosystems, creating space for other species to fill their functional roles.

The new study will produce a much larger data set than previously existed, to further clarify some of these differences between temperate and tropical stream ecosystems and possibly discover new ones.

One of the collaborators, Kurt Anderson at UC-Riverside, focuses on modeling ecological data. The team will “use the parameters that we estimate from the field data to tune his models,” Swan says, “so we can make predictions and test our hypotheses about what could happen in the future.” One hypothesis might be that as the world warms, organisms in temperate streams could start to take on traits more common in the tropics.

Biodiversity is the key to success

Beyond the research, the collaboration also presents unique opportunities for international education. The U.S. and Brazilian faculty leads will offer a joint online course for graduate and advanced undergraduate students, where they will read and analyze academic papers related to the study. “We realized that learning, teaching, and discussion styles are not the same in the two countries,” Swan says, so this class will give students and faculty alike the chance to navigate new ways of interacting along with discovering new science.

One core point Swan will emphasize with his students is the importance of biodiversity on a global scale. In ecology, the presence of a wide variety of organism types and the functions that they perform is called the “portfolio effect.” Just like a diverse financial portfolio, a diverse biological “portfolio” of species is less likely to suffer heavy losses across the board as conditions change—something is bound to adapt and survive. Also, “if you have more species, then you have more niches filled,” Swan says, “so resources are being used more efficiently.”

“Variety in life is the whole kit and caboodle,” Swan says. “If you didn’t have variety, nothing would be able to adapt. There would be no adaptation to change.”

With ample biodiversity, though, adaptation to change is much more likely. But what that looks like—which species will adapt successfully or will be most at risk—is still unknown. Starting with tiny organisms in streams, Swan and colleagues are working to help figure that out.

UMBC’s Chengpeng Chen receives $1.7M NIH grant to develop human liver model

It can take more than 10 years and a billion dollars to get one new drug approved, and less than 10 percent of drugs succeed in clinical trials. Part of the problem is that common techniques used to study drug candidates, such as simple cell cultures and mouse models, don’t accurately represent how a drug will behave in the human body, says Chengpeng Chen, assistant professor of chemistry and biochemistry.

portrait of Chengpeng Chen — Chengpeng Chen (Marlayna Demond ’11/UMBC)

The low success rate motivated Chen to pursue development of more realistic models of human organs, starting with the liver. The hope is that researchers will one day use these models early in the drug development process to rule out drug candidates that are doomed to fail later on. That way, companies can quickly divert resources to projects with more promise. A new five-year, $1.7 million grant from the National Institute for General Medical Science will support Chen’s interdisciplinary work.

Chen learned about the concept of “organs-on-a-chip” during his postdoctoral research. These 2D, usually plastic devices use tiny amounts of liquid in tiny tubes to imitate organ function. He was hooked on the idea of creating miniature, realistic models of human systems. In addition to supporting drug development studies, such systems can increase understanding of many diseases, without the ethical issues that accompany using animal or human subjects.

Recreating the liver—in miniature

Chen’s first goal is to perfect his liver model, which goes a step beyond an organ-on-a-chip. Instead of a 2D mimic in plastic tubes, “We’re mimicking everything—the cell types, the architecture, and also the 3D microenvironment of the cells,” he says. Ultimately, he hopes to expand to other organs, but the liver is an important place to start, he says. The liver is involved in the metabolism of many drugs, and liver diseases are common.

Other models have recreated single cell types in the liver, but if successful, Chen’s will be the first to include all four major cell types interacting with each other the way they do inside the body.

“We can recreate the architecture of the real tissue, so when we put the cell types together, we think they will show total liver function,” Chen says. “But if we want to study them separately, we can separate them easily.”

While this might sound like the beginning of a quest to grow artificial organs for transplant, “We’re not there yet,” Chen says. He and his group will create “miniaturized liver functional units” that represent all the functionality of the liver on a tiny scale, mainly for biomedical research purposes. While a complete liver contains about 500 billion cells, each model will have approximately 2 million cells and be about the size of a typical thumbtack.

The goal is to create a model that researchers anywhere can replicate. “We want to make this technology standardized and modular,” Chen says, “so that anyone can build the model like Legos.”

two seated researchers, one standing, discussing a figure on a computer screen — Curtis Jones (right), discusses experimental results with fellow chemistry Ph.D. student John Terrell (center) as Chengpeng Chen looks on. (Marlayna Demond ’11/UMBC)

Metabolism monitoring

Once Chen’s team optimizes the model, Chen is interested in looking at how the extracellular matrix—the material in between cells that binds them together and helps shuttle material from cell to cell—influences activity inside the cell, and how it changes during the course of disease.

student uses a mass pipetting tool to conduct research — G.K. Monia Kabandana conducts research in the Chen laboratory. (Marlayna Demond ’11/UMBC)

A disease known as liver fibrosis induces changes in the extracellular matrix (ECM), stiffening and thickening the liver. Some researchers have looked at how the ECM affects various functions within liver cells, but not at how it may drive metabolic processes. That’s what Chen’s team will look at first with the new model, which should give more comprehensive results than looking at single cell types alone.

They’ll investigate how ECM changes affect essential metabolic pathways like energy production, construction of lipids and amino acids, and oxidative stress. Then they’ll conduct an untargeted sweep of all metabolites in the cell, measuring whether and how they are affected by ECM changes.

Shared facilities on campus administered by the College of Natural and Mathematical Sciences, such as the Keith Porter Imaging Facility and Molecular Characterization and Analysis Complex, will make the work possible.

Fighting fatal diseases

In the long term, “the ultimate biological goal is to find new therapies for fibrosis diseases,” Chen says. “New knowledge is needed. We’re starting with the liver in this project, because liver fibrosis is one of the most prevalent fibroses. And it’s fatal.”

Liver fibrosis is similar to cardiovascular diseases where tissue thickens, Chen explains. Earlier, “We initiated blood vessel studies, because in cardiovascular diseases, the blood vessels are stiffer. It’s called sclerosis, but it is very similar to fibrosis,” he says. “They both have extracellular matrix microstructure changes.”

There are other diseases that involve ECM changes, too. “If we can figure out how those changes cause disease,” Chen says, “it’s not just a fundamental science question, but also has biomedical applications.”

Chengpeng Chen (right) and his four graduate students: Tao Zhang, G.K. Monia Kabandana, John Terrell, and Curtis Jones.

Interdisciplinary effort

Some may be surprised that Chen is in the chemistry and biochemistry department, given the biological and even engineering nature of his work. Chen is part of a new generation of scientists that doesn’t hesitate to forge connections across disciplines.

“I really don’t see a boundary for chemistry work,” Chen says. With the new grant, he plans to add at least two new graduate students to the group, who will receive training in a wide range of techniques and disciplines.

Whether developing technologies to generate new models, measuring biological functions in tissues, or studying the roles of individual metabolites in chemical pathways, Chen’s work puts him at the frontier of scientific research and in position to have a significant public impact.

UMBC’s Jeffrey Gardner receives $1.3M from NIH to discover new treatments for fungal disease

Like bacteria, fungi can cause disease inside your body and on your skin, or even grow on medical equipment like catheter tubing and wound dressings. Many fungal diseases are treatable with antifungal medications, but drug resistance is a growing problem. With a new four-year, $1.3 million grant from NIH, Jeffrey Gardner and his students will be looking for new ways to target disease-causing fungi.

Typically, drugs that treat fungal disease prevent the fungus from making its cell wall, which either kills the fungus outright or weakens it enough that the immune system can finish it off. But that method is highly susceptible to developing resistance.

“But what if you had an external attack on the fungus? What if there were enzymes that actively degraded the fungal cell wall, which is not going to generate resistance easily?” asks Gardner, associate professor of biological sciences. “Our goal is to find enzymes that effectively break down the fungal cell wall, that can be used as a treatment in parallel with cell wall synthesis blockers, or on their own.”

Homing in on the right enzyme

With the new support from NIH, Gardner’s lab will investigate hundreds of bacterial enzymes to figure out which best target Aspergillus fungus, a group of common disease-causing mold species. Previous work from other groups has found particular bacterial species that slow down fungal growth. Gardner’s team will start by looking at every gene and protein in these bacteria to figure out “which genes are turned on, and which proteins are made, while the bacteria are degrading and eating the fungus,” he explains.

Gardner expects that should whittle down the candidate list from about 4,000 genes to a few hundred. “How do we figure out which ones of those couple hundred actually matter? That’s where our genetic system comes in,” he says. The team will generate bacterial strains that lack a functional version of each of the candidate genes and see which strains are less efficient at eating the fungus.

That process should further narrow the list of genes to a few dozen, Gardner says. Then, they’ll produce strains that are missing different combinations of the candidate genes. When they find a combination that can’t survive at all on fungus alone, they’ll be confident the genes knocked out in that strain are the ones necessary to eat the fungus. Finally, they’ll run biochemistry experiments to determine the function and mechanism of each enzyme.

several dozen thin, white, glossy filaments on a black substrate, each with a small round, fuzzy black tip — Filaments of Aspergillus fungus (Giles Chapelain/CC BY-NC-ND)

From one to a billion

This kind of brute-force methodology, involving hundreds of unique strains of bacteria, highlights the advantages of working with species that multiply incredibly fast. “That’s the power of microbiology—you can go from a single cell to an overnight culture with a billion cells,” Gardner says. “You can do many, many experiments at a scale and at a speed that really isn’t possible with, say, a fly or a mouse system.”

The culmination of the project will be “identifying the enzymes, knowing what they’re doing, how they’re doing it, and how well they’re doing it,” Gardner says.

The power of microbes

As a microbial researcher who cares about “interesting bits of biology that have no medical relevance at all,” Gardner says he never imagined he would receive an NIH grant to pursue work with clear biomedical implications. But as his research at UMBC over the last decade has progressed, he’s realized his work can transcend typical disciplinary boundaries. “I think that’s the exciting part, and the power of microbial systems, that you have that latitude,” Gardner says.

His first major grant from the Department of Energy focused on bacteria’s role in biofuel production. A second project funded by the National Science Foundation looks at how bacteria contribute to the carbon cycle by breaking down dead matter on the forest floor. And now, with funding from NIH, his group will look at how bacteria can help fight fungal disease.

“If you can find an interesting bug, with some interesting physiology, the types of questions can really span major different areas,” Gardner says.

The techniques often remain the same, though. “Our wheelhouse is genetics, systems biology, and physiology,” Gardner says. In the new project, “We’re leveraging an established pipeline to work on a problem that is a step away from what we have traditionally done. We’ve got lots of tools and tricks for working with the bacteria.”

The wide range of methods used in Gardner’s lab means that his group offers great training opportunities for students. With the new grant, Gardner is looking forward to adding two new Ph.D. students and several undergraduate researchers to his team.

Jeffrey Gardner and Cassandra Nelson, Ph.D. ’17, biological sciences, in the Gardner laboratory. (Marlayna Demond ’11/UMBC)

Essential support

Gardner knows, from personal experience, the importance of research training and mentorship along a scientist’s full career path, including in his time at UMBC. Before applying for this current grant, he took advantage of a program offered by UMBC’s College of Natural and Mathematical Sciences specifically for people seeking major NIH grants. The program, orchestrated by Phyllis Robinson, professor of biological sciences, included workshops, critique partners, and mentoring. “That was absolutely essential for my success,” Gardner says.

Moving forward, if the project goes well and Gardner is able to secure a second round of funding in a few years, he says the next questions will be, “How do we engineer the enzymes to be more potent? How do we make them do their job of killing fungi better?” The lab could even ask which combination of enzymes would target a specific fungus most effectively, or provide the broadest protection against many fungal species.

But for now, they’ll focus on nailing down the basics, he says. “We need to find out who’s there and what they’re doing first.”

UMBC’s Leamon defines “solar clock” that can precisely predict solar cycle events years in advance

Ever since humans could first observe sunspots about 400 years ago, we’ve been using them to try to define the solar cycle. Approximately every 11 years, solar activity such as sunspots and solar flares ebbs and flows, causing changes to weather patterns on Earth and occasionally threatening telecommunications. Predicting these changes reliably could help everyone from farmers to the military.

Traditionally, scientists have used the concept of a “solar minimum,” when solar activity is reduced, to mark the beginning of each cycle. But the “solar minimum” framework is somewhat arbitrary and imprecise, explains Robert Leamon, research scientist at the Partnership for Heliophysics and Space Environment Research (PHaSER), a UMBC partnership with NASA.

Leamon led new research showing that a “solar clock” based on the sun’s magnetic field, rather than the presence or absence of sunspots, can precisely describe and predict many key changes throughout the solar cycle. The new framework offers a significant improvement over the traditional sunspot method, because it can predict surges in dangerous solar flares or changing weather trends years in advance.

Specifically, the new research, published in Frontiers in Astronomy and Space Sciences, shows that the solar cycle operates as a distinct sequence of events. Notable, and sometimes abrupt, changes occur at each one-fifth of a cycle. That’s true regardless of the exact length of a given cycle, which can vary by several months to a year. In a nod to music enthusiasts, Leamon and colleagues call it a “circle of fifths.”

portrait of Robert Leamon — Robert Leamon (courtesy of Robert Leamon)

Finding the landmarks

The new paper by Leamon, Scott McIntosh, at the National Center for Atmospheric Research (NCAR), and Alan Title, at the Lockheed Martin Advanced Technology Center, builds on work by Leamon, McIntosh, and Daniel Marsh, also at NCAR, published in 2020. That paper demonstrated the existence of a solar cycle phenomenon the research team dubbed “the terminator.”

The sun’s magnetic field changes direction each solar cycle, but there is overlap between consecutive cycles. The sun’s magnetic field is sometimes called the polar field, because it either points to one of the sun’s poles or the other. A terminator marks when the previous cycle’s polar field has completely disappeared from the sun’s surface, and is quickly followed by a dramatic rise in solar activity.

The new paper points to additional landmarks along the journey through a full solar cycle from terminator to terminator. These landmarks are clearer and more consistent than using sunspots as a guide to cycle length. For example, “The max number of sunspots doesn’t quite align with when the polar field reverses, but the polar field reversal happens at exactly one-fifth of the cycle going from terminator to terminator,” Leamon says.

At two-fifths of a cycle, dark areas called “polar coronal holes” re-form at the sun’s poles. At three-fifths of a cycle, the last X-flare, a class of very large and potentially dangerous solar flares, occurs. At four-fifths, sunspots are at a minimum—but this landmark is less consistent. And then the sun passes through another terminator, after which solar activity rapidly picks up again. Other phenomena, such as UV emissions, also line up nicely on the fifths.

bronze ball with swirling eddies on the surface; one area is black by contrast — The dark area represents a coronal hole on the sun’s surface. The new solar clock framework can predict formation and dissolution of coronal holes. (NASA/SDO)

Symptoms and causes

The team picked out patterns in data collected daily by two ground-based observatories. The Dominion Radio Astrophysical Observatory in Penticton, Canada has measured solar radio flux, which serves as a useful proxy for solar activity, daily since 1947. The Wilcox Solar Observatory at Stanford University has collected daily measurements of magnetic fields on the sun’s surface since 1975.

Once the team noticed the changes that occur at exactly one-fifth of a cycle, they asked, “How many different solar things can we look at? And then we realized they all overlap on this same set of fifths,” Leamon says. Different parameters shift at different points on the cycle, but “everything is tied to these five landmarks.”

This new theory of a solar clock changes the focus from sunspots to shifts in magnetic field. “It’s almost like symptoms and causes,” Leamon says. While sunspots are an important symptom, the magnetic field is the underlying cause driving the solar cycle.

The longest threads

This shift in framework improves researchers’ ability to predict events in the solar cycle more precisely and further in advance, which gives people like satellite operators time to make preparations as needed based on predicted solar activity. Once observatories detect an initial polar field reversal, the precise length of the first fifth of the cycle is set. That means the timing of the other fifths (and their associated events) is a simple matter of multiplication.

The new framework also puts tighter bounds on the period within the cycle when severe flares are expected, which is useful information for people on Earth. Rather than a gradual shift from minimum to maximum activity, the period from terminator to about three-fifths of a cycle seems to be the peak period for flares, with a rapid drop-off after that point until the next terminator. The current cycle began after a terminator in December 2021, and the new framework predicts the last major flares should occur in mid-2027.

Leamon points to a quote by physicist Richard Feynman to explain the value of a theory like this one, that accounts for many variables within a system. “Nature uses only the longest threads to weave her patterns, so that each small piece of her fabric reveals the organization of the entire tapestry,” Feynman said. Leamon and colleagues’ new theory is an example of one of these long threads—precisely predicting many aspects of the solar cycle with a single, simple parameter, and making it easier for humans to be ready for changes driven by the sun.