Genomics and Bioinformatics Archives | University of Central ��ӽ紫ý News

Academic Upbringing in Siberia Inspires New Computer Science Professor’s Career

Marisa Ramiccio ’11 — Fri, 14 Nov 2025 14:30:52 +0000

Deep in the pine forest of Siberia lies a unique scientific community that was envisioned as the New Atlantis of science. At its peak, the town was home to more than 65,000 scientists who worked at 35 research institutes dedicated to molecular biology, chemistry, physics and cybernetics. Neighbors and friends would gather at the local cafes or courtyards, not only to exchange pleasantries, but also to discuss the latest discoveries and to debate new scientific trends.

While this sounds like the setting for a sci-fi novel, it’s actually the hometown of Assistant Professor Kirill Medvedev, a new faculty member in the . Medvedev grew up in Akademgorodok, which literally translates to “Academic Town,” a place that sparked his interest in bioinformatics and inspired his career.

“The constant exposure to open, curiosity-driven inquiry made the language of science feel as natural as the Siberian forest around us,” Medvedev says. “My passion for bioinformatics and computational biology was ignited by a fascination with three-dimensional protein structures. I realized that computational approaches are indispensable for decoding life’s molecular machines, and it set me on the path toward research in the field of computational structural biology and bioinformatics.”

Medvedev’s work focuses on the classification and analysis of large-scale biomedical data sets that span the molecular, cellular and tissue levels. With that expertise, he is teaching a Discrete Mathematics course at ��ӽ紫ý this fall. He says he hopes to instill both practical and technical knowledge in his students.

“I hope to share with my students not only the course knowledge but also my experience of being a scientist.”

“I believe that integrity is the defining characteristic of a scientist,” he says.

Medvedev’s work focuses on the classification and analysis of large-scale biomedical data sets that span the molecular, cellular and tissue levels. Within the past decade, he developed the DrugDomain database, which lists the domain features of human proteins that are targets for small molecules and drugs. He augmented the DrugDomain database with artificial intelligence‑powered protein structure prediction, creating a first‑of‑its‑kind resource that maps thousands of post‑translational modifications to their drug targets across the human proteome. He also uses computational modeling to analyze variations within cancer types and employs deep learning methods to identify cancer subtypes.

The opportunity to collaborate with the next generation of scientists, as well as established colleagues, is what Medvedev says drew him to ��ӽ紫ý.

“I was interested in the University of Central ��ӽ紫ý because it’s such a dynamic and fast-growing research hub — one that actively promotes collaboration among researchers.”

“Today, truly groundbreaking science cannot be done by one person, or even one lab, but only through collaboration among multidisciplinary teams,” Medvedev says.

Medvedev earned his doctoral degree in mathematical biology and bioinformatics from the Institute of Cytology and Genetics in 2015. Following that, he’s worked with Professor Nick Grishin at the University of Texas Southwestern Medical Center as a postdoctoral researcher.

Doctoral students with strong computational skills who are interested in working with Medvedev can contact him by email. Basic understanding of molecular or structural biology or biochemistry is beneficial but not required.

Biology Researchers Lead Technology-Driven Seagrass Restoration Projects in ��ӽ紫ý

Ana Hidalgo — Wed, 17 Sep 2025 13:30:37 +0000

Seagrass meadows are rapidly vanishing across the world, threatening animal species that rely on this vital coastal ecosystem for survival.

Two ��ӽ紫ý biology graduate students are leading projects developing innovative solutions for conserving seagrass species in ��ӽ紫ý, with support from Pegasus Professor of Biology Linda Walters and Assistant Professor of Biology and Genomics and Bioinformatics faculty cluster member Robert Fitak. Their projects are among eight selected for funding through the Seagrass Restoration Technology Development Initiative.

The initiative was created in 2023 by the ��ӽ紫ý Legislature and governor through the ��ӽ紫ý Department of Environmental Protection, with Mote Marine Laboratory and Aquarium leading the effort. It aims to support restoration technologies and approaches that address seagrass loss and its widespread ecological and economic impacts on communities across ��ӽ紫ý.

“Seagrasses around the globe, including in ��ӽ紫ý’s Indian River Lagoon, have been decimated in recent decades,” says Walters, who is also director of ��ӽ紫ý’s Coastal and Estuarine Ecology Lab (CEELAB). “The effects rippled through the ecosystem and are tragically evidenced by the large number of manatees that died of starvation when no seagrass was present.”

Luciana Banquero (front) and collaborators from Brevard Zoo monitor an experimental seagrass planting area in the Banana River, collecting data on seagrass and macroalgae abundance. (Photo courtesy of Luciana Banquero)

In partnership with Brevard Zoo, ��ӽ紫ý Institute of Technology, ��ӽ紫ý’s Aquatic Biogeochemistry lab led by biology professor Lisa Chambers and under Walters’ guidance, ��ӽ紫ý biology student Luciana Banquero ’22 is examining how sediment quality, nutrient levels, and interspecies competition influence the success of shoal grass (Halodule wrightii) restoration.

“With colleagues at the ��ӽ紫ý Institute of Technology and the University of Lausanne, this project is sequencing genomic DNA of seagrass-associated microbes, comparing how these communities differ between nursery-grown shoal grass and the natural population in the Indian River Lagoon,” Banquero says.

Banquero, who is in her second year on the project, says seagrass meadows provide essential habitat and food for countless marine species and are critical not just in ��ӽ紫ý but wherever seagrass is found.

“By combining field trials and laboratory experiments, I aim to identify the conditions that promote seagrass establishment and long-term survival, improve restoration outcomes, and better understand how planted seagrass interacts with other macroalgal communities,” Banquero says. “Additionally, my collaborators are contributing samples to Mote Marine Laboratory’s seagrass genetic library, which will be used to study seagrass resilience and diversity at the molecular level.”

Her research, inspired by recent algal bloom events in ��ӽ紫ý, analyzes the sediment quality at shoal grass planting sites in Brevard County’s Indian River Lagoon and Banana River.

“Algal bloom events can trigger changes in these macroalgal communities, causing native seaweed (Caulerpa prolifera) to dominate the sediment floor and prevent seagrass growth,” Banquero says. “By studying sediment quality and the conditions in which seagrass is planted, we can better understand the complexity of coastal ecosystems and support successful plantings and conservation of these species.”

According to Banquero, researchers have long suspected a competitive dynamic between Caulerpa algae and shoal grass, suggesting that shoal grass tends to perform poorly when the alga is growing nearby. However, no large-scale empirical studies across multiple sites or controlled laboratory trials have been conducted to challenge those long-held assumptions that have guided conservation efforts. Her research aims to fill that gap.

Walters, who has studied the seaweed genus Caulerpa on and off for more than 20 years, notes that members of this genus can be highly invasive and produce noxious secondary chemicals.

“Interactions occur at many levels — from chemicals released by roots to damage from herbivorous fish or boats — and we need to consider all of these factors to get the full story,” Walters says. “This project will study those interactions and clarify whether Caulerpa is harmful and should be removed or avoided when planting seagrass for restoration.”

Seeds of shoal grass (Halodule wrightii, left) and widgeon grass (Ruppia maritima, right), are two focal species of this restoration initiative. Shoal grass was confirmed in 2023 to reproduce sexually as well as clonally — spreading both by seeds and genetically identical shoots — while widgeon grass produces seeds and flowers most of the year. These findings have important implications for restoration. (Photos courtesy of Carla Perscky [left] and Seagrass Wrack Collection [right])

Complementary to this work, biology graduate student Carla Perscky is leading a project on thermo-priming, a novel technique to enhance thermal tolerance of shoal grass (Halodule wrightii) and widgeon grass (Ruppia maritima). This project was inspired by her discovery of Halodule wrightii seeds during a marine heatwave event and recent research in terrestrial and aquatic plants showing that exposure to sub-lethal stress can enhance future resilience.

In collaboration with Fitak, Mote, the ��ӽ紫ý Fish and Wildlife Conservation Commission (FWC), St. John’s River Water Management District and Bethune-Cookman College, the team will identify heat resilience mechanisms at the molecular level and develop practical guidance for restoration in heat-prone environments.

“Our goal is to understand how rising seawater temperatures cause these plants to decline and identify adaptation mechanisms that can help make them more resilient,” Perscky says.

Graduate student Carla Perscky and her team discovered microscopic seeds and flowers by collecting fragments that wash up along the shoreline in the Indian River Lagoon. (Photo courtesy of P. Sacks)

Her work tests whether exposing seagrass to heat stress in a controlled environment can help plants adapt and pass resilience on to future generations.

“We are using novel technologies, including molecular tools such as transcriptomics, which help identify biomarkers linked to stress memory,” she says. “As well as satellite data from the National Oceanic and Atmospheric Administration (NOAA), combined with on-site field data, to track seawater temperatures and detect marine heatwave trends that inform the experimental design.”

To test their hypothesis, Perscky’s team will conduct aquarium experiments that replicate ocean extremes at Mote’s state-of-the-art facility, where plants will be exposed to artificial marine heatwaves to prime them for survival, while open-source data models analyze decades of environmental trends to predict seagrass survival under future climate conditions.

“Thermal priming is not a new technique,” Perscky says. “It’s been used in crops like corn and in coral reefs. When plants and organisms face a second heat event, they remember the first exposure and adapt.”

Fitak, who specializes in genomics, compared the adaptation process to vaccination.

“You expose a young plant to a mini version of marine heat and its system remembers the trigger,” Fitak says. “As adult plants, they become more tolerant for when the real exposure occurs.”

If successful, the approach could be applied not only in ��ӽ紫ý but to other seagrasses around the world.

“This knowledge could guide how seagrass is planted in nurseries across the state and beyond,” Perscky says. “In places like Mosquito Lagoon and Banana River, where water stays warmer because it’s regulated by wind rather than tide, seagrass planted there could be more tolerant.”

Walters adds more insight on this approach, which is currently undergoing testing on corals with success in some species in some locations.

“If we can restore areas with native, thermally primed seagrass, it should be more resilient to future heat events,” she says. “We are aiming to create ‘super seagrass,’ similar to efforts with ‘super corals’ that can tolerate higher temperatures than they currently do.”

Perscky and Banquero cited the importance of partnerships in making their work possible.

“Seagrass restoration is highly experimental and requires significant resources,” Banquero says. “Collaborating with scientists with different expertise and leveraging their long-term knowledge of ��ӽ紫ý’s coastal ecosystems has enabled me to carry out my project.”

Fitak also noted the multidisciplinary nature of the projects.

“This project is a great example of how science is done in an interdisciplinary way,” he says. “Carla is collaborating with researchers from Mote, FWC, and other agencies, along with Dr. Walters and me, because no one is an expert of everything.”

Beyond environmental impacts, student and community involvement is key to the success of these projects. Banquero has been planting seagrass in macroalgal beds in Brevard County, with local volunteers helping monitor the sites.

“It’s been rewarding to hear their perspectives on why protecting these ecosystems matters and to connect with people directly impacted by our work,” she says.

Similarly, Perscky says partnering with Mote has given students and volunteers hands-on opportunities in seagrass monitoring.

Both projects highlight the challenges facing coastal environments and provide tools to help conserve seagrass beds now and in the future with Fitak emphasizing the importance of community support.

“People love seeing healthy seagrass beds and the biodiversity they support, like manatees,” he says. “Communities want to support restoration, but failed plantings can be discouraging. Our goal is to make restoration effective and resilient so these vital ecosystems thrive.”

While the projects are focused in ��ӽ紫ý, Walters points to the broader significance of the work.

“The outcomes of these projects will not only help improve the health of the Indian River Lagoon, but also build on current knowledge and provide practical methods for restoration practitioners to conserve and protect estuaries around the globe,” she says. “I deeply care about this lagoon, and all our efforts aim to improve restoration and resilience so it remains the magical place we know it is well into the future.”

Researchers’ Credentials
Fitak is an assistant professor in ��ӽ紫ý’s Department of Biology in the College of Sciences. He received his doctorate in genetics from the University of Arizona and his bachelor’s in molecular genetics from The Ohio State University. Before joining ��ӽ紫ý in 2019, he worked as a postdoctoral researcher at the Institute for Population Genetics in Vienna, Austria, and at Duke University. He is a member of ��ӽ紫ý’s Genomics and Bioinformatics research cluster.

Walters joined ��ӽ紫ý in 1997 and was named Pegasus Professor in 2012. She is part of the coastal cluster and leads CEELAB. CEELAB’s work connects ��ӽ紫ý biology students with firsthand experience, putting classroom learning into practice. Walters has received more than $19.7 million in grant funding, published more than 120 peer-reviewed journal articles and authored 11 children’s story books about marine conservation.

��ӽ紫ý Biologist Continues Unraveling Mystery of Magnetic Bacteria

Eddy Duryea ’13 — Tue, 09 Jul 2024 13:44:40 +0000

The remarkable ability of migratory animals to navigate and recall routes may be attributed to a sensitivity to not just Earth’s magnetic fields, but perhaps an interaction with magnetic bacteria living inside them.

The relationship between these magnetic bacteria and the animals they reside in is not yet fully understood, but Assistant Professor Robert Fitak recently compiled a database of animal DNA that houses hundreds of millions of sequences showing the presence of various types of magnetic bacteria to use as a tool in his pursuit to learn more.

��ӽ紫ý Department of Biology Assistant Professor Robert Fitak has been studying magnetic bacteria and the role they may play in the animals they reside in. (Photo by Antoine Hart)

The database signals a step forward in his research and builds off previous hypotheses and analyses published in 2020 in collaboration with colleagues in the United Kingdom and Israel.

In 2021, Fitak continued poring through databases to categorize which animals may host magnetic bacteria and if there are prevalent patterns.

“The first study we did was look at existing datasets and summarize where we found this bacteria in different animals,” he says. “We searched about 50,000 previous scientific studies. Now, we actually expanded that to studying a worldwide database of genetic information and we’ve been able to summarize where these bacteria are located based on trillions of genetic sequences.”

The database was published earlier this year in Data in Brief, and it borrows information from the publicly available Sequence Read Archive from the National Center for Biotechnology Information.

Fitak focused on organizing DNA sequences originating from across animal species that match known magnetic bacteria to assist he and other researchers to narrow their efforts in examination of both environmental and ecological roles of magnetic bacteria or to identify potential host animals.

An Internal Compass?

Fitak and his colleagues are using the refined data to identify potential host organisms for the magnetic bacteria and to provide greater context for examining the roles they may play in animals – such as for navigation.

“Ultimately, if we have a better understanding of how animals navigate, it’ll be useful for conserving endangered or protected species,” Fitak says. “If we know where they’re going to move and how, it can help us make more accurate management decisions.”

He is interested in seeing if the magnetic bacteria reside in regions within an animal so they may sense them, such as parts of the nervous system. Fitak thinks they could serve as a navigational aid for animals or provide an additional boost for creatures like birds or sea turtles already using the Earth’s magnetic field to navigate long distances.

“It’s almost like a microbial compass and we’re studying how that could work,” Fitak says. “We think the animals already use the Earth’s magnetic field like a compass.”

He also says another potential benefit is that scientists may study how animals sense the magnetic fields and potentially mimic how they’re used in a variety of applications such as drug delivery.

However, there is no conclusive evidence that these animals are using the magnetic bacteria to navigate or not, Fitak says.

“The big summary we have so far from our research is that we don’t yet know that these bacteria are sensing the bacteria for the animal, but we do have evidence that they are living in these animals,” he says. “But what we’ve learned is we can use genetic tags that are signatures for bacteria that makes magnets, and we’ve identified these genetic signatures of these bacteria inside various animals – including humans.”

These kinds of bacteria often live in sediments or muds where there isn’t a lot of oxygen, Fitak says. They assemble microscopic and magnetized iron “chains” to assist in their movement, he says.

It is uncertain how organisms end up with these bacteria inside of them, but it is theorized perhaps through absorption or consumption, Fitak says.

“To date, our results across projects show that these magnetic bacteria seem to be a regular component of many species microbiomes,” he says. “Hopefully our future work will show whether they are just incidentally gathered from the environment, a functional component of magnetic sensing for a host animal, or for some other unknown reason.”

Focusing on Sea Turtles

Fitak and his team of student researchers are focused on examining samples from green and loggerhead sea turtles to further study magnetic bacteria.

“Sea turtles are kind of a model of animal navigation,” he says. “We’ve been testing our hypotheses in sea turtles since they travel to very specific places very accurately.”

Focusing on sea turtles was a natural next step since they are known to possess magnetic bacteria and they rely on the Earth’s magnetic field to migrate, Fitak says. has also been instrumental in obtaining samples of turtles, he says.

Julianna Martin, a Ph.D. student working with Fitak, has helped analyze and collect the nearly 150 sea turtle samples.

“I work in the lab to extract the DNA from the samples and use genomics to identify what bacteria are in the samples and which are the magnet making ones we’re looking for,” she says. “I couldn’t collect the samples without the help of the ��ӽ紫ý Marine Turtle Research Group. It’s been a team effort.”

Martin and scientists with ��ӽ紫ý’s Marine Turtle Research Group gently collect tear samples with soft swabs from nesting females – who enter an almost trance-like state when laying eggs – and juveniles in the Indian River lagoon.

The turtles produce large goopy tears when they are on land to keep their eyes moist, and collecting them takes around 30 seconds, Martin says.

“We started with the tear ducts because they’re associated with nerves that are associated potentially with animals’ magnetic sense,” she says. “It makes sense biologically to look there and it’s easy to collect sea turtle tears.”

Martin says she is pleased with their progress thus far but is hoping their momentum propels their research toward more definitive conclusions.

“This research has been really exciting,” she says. “No one had been looking for them specifically in sea turtles. I’m interested in knowing where they came from and what species of magnet-making bacteria each sea turtle species has. It’s a long way away but for now we’re working on describing, ‘are they there?’ and ‘where do they come from?’”

The potential to share the unique discovery of magnetic bacteria aiding animals in navigation is truly wondrous, Fitak says.

“What’s been exciting is just being able to tell people that there are bacteria that exist in this world that make magnets,” he says. “People are awestruck, and it would be incredible if animals were indeed using these magnetic bacteria to navigate.”

Fitak encourages researchers interested in studying magnetic bacteria to .

All sea turtle samples were collected under ��ӽ紫ý MTRG protected species permits (MTP-231, MTP-171, and NMFS 26268)

Researcher’s Credentials

Fitak is an assistant professor in ��ӽ紫ý’s Department of Biology in the College of Sciences. He received his doctorate in genetics from the University of Arizona and his bachelor’s in molecular genetics from The Ohio State University. Before joining ��ӽ紫ý in 2019, he worked as a postdoctoral researcher at the Institute for Population Genetics in Vienna, Austria, and at Duke University. He is a member of ��ӽ紫ý’s Genomics and Bioinformatics research cluster.

Martin is a ��ӽ紫ý biology Ph.D. student who aspires to continue her genetic research at the university. She earned her bachelor’s degree at St. Mary’s College of Maryland and worked at the American Genome Center at the Uniformed Services University.

Stories of Innovation, Discovery Highlight ��ӽ紫ý Research Top 10 News List of 2023

Thu, 07 Dec 2023 21:44:15 +0000

With researchers continuing to understand space and the planetary bodies around it, ��ӽ紫ý’s Top 10 Research News list included the completion of NASA’s OSIRIS-REx mission.

In a first-of-its-kind mission for the United States that spanned over seven years, the unmanned spacecraft mapped and studied the surface of the near-Earth asteroid Bennu, then retrieved a sample for researchers to study the asteroid’s composition.

Topping the list was a story on the world’s first energy-saving paint inspired by butterflies. The plasmonic paint utilizes a nanoscale structural arrangement of colorless materials — aluminum and aluminum oxide — instead of pigments to create colors. The paint can contribute to energy-saving efforts and help reduce environmental impacts.

Other stories included a $12.6 million Defense Advanced Research Projects Agency grant looking to create self-repairing, biological and human-engineered reef-mimicking structures. ��ӽ紫ý is helping design reef structures that will be used to mitigate coastal flooding, erosion and storm damage that threaten civilian and Department of Defense infrastructure and personnel. Another story featured new research on the earliest presence of Homo sapiens in Southeast Asia, pushing back the presence of humans in that part of the world by at least 20,000 years and a human presence in the region for at least 56,000 years.

Here are the Top 10 ��ӽ紫ý Research News Stories of 2023:

1. ��ӽ紫ý Researcher Creates World’s First Energy-saving Paint – Inspired by Butterflies

2. The Long Journey of NASA’S OSIRIS-REx

3. Human Migration Timeline Redrawn by Fresh Fossil Analysis

4. New ��ӽ紫ý-developed Battery Could Prevent Post-hurricane Electric Vehicle Fires

5. ��ӽ紫ý Researchers Are Advancing AI-assisted Drug Discovery

6. ��ӽ紫ý is Designing Self-repairing Oyster Reefs to Protect ��ӽ紫ý’s Coastlines

7. New DOD-funded Project Will Develop Morphing Hypersonic Engine

8. ��ӽ紫ý Researchers Create Bioabsorbable Implants for Better Bone Healing

9. ��ӽ紫ý Team Awarded $2.3M Grant for Innovative Intervention to Prevent Falls

10. Deadly Frog Disease More Prevalent in Central ��ӽ紫ý Than Expected, ��ӽ紫ý Study Finds

The annual top 10 list is based on ��ӽ紫ý Today page views and coverage ��ӽ紫ý research received by global, national, state, and local media. The stories were generated by news releases and pitches from ��ӽ紫ý Communications and Marketing, ��ӽ紫ý’s Office of Research and ��ӽ紫ý’s colleges.

Deadly Frog Disease More Prevalent in Central ��ӽ紫ý Than Expected, ��ӽ紫ý Study Finds

Wed, 13 Sep 2023 16:08:19 +0000

University of Central ��ӽ紫ý researchers have found that an understudied, deadly disease of frogs is more widespread in Central ��ӽ紫ý than previously thought and may become more of a problem in other parts of the U.S. due to environmental impacts.

The findings, recently published in the Journal of Animal Ecology, showed that the pathogen amphibian Perkinsea infected a third of frogs sampled, and its presence was associated with the cooler, wetter conditions typical of a ��ӽ紫ý winter.

��ӽ紫ý gopher frogs, which live in gopher tortoise burrows, had the highest disease prevalence and intensity, which the researchers say is concerning as the threatened species is declining in most of its range.

Perkinsea is part of a unique group of organisms known as protists that don’t fit easily into the categories of plant, animal or fungi. When Perkinsea spores enter a frog, they find their way to the liver and other organs and eat the tissue from the inside out, leading to death.

“We have this pathogen that we basically know nothing about, and this is the first real stab at trying to understand where it’s showing up and why,” says Matthew Atkinson ’23PhD, a lecturer in ��ӽ紫ý’s and the study’s lead author — which he completed during his time as a doctoral student in the same department. “And we can’t do anything for protecting species unless we know what’s actually happening in the first place. So that’s been a big focus with us.”

Frogs are a crucial part of many ecosystem food webs and are also considered indicator species, since their sensitivity to environmental changes can serve as early warning signs of ecosystem disruption.

As northern regions become warmer from environmental impacts, more areas could experience conditions favorable to Perkinsea infections in frogs, the researchers say.

“We observed this really strong relationship between average temperature, where the lower the average temperature, the more infections we saw,” Atkinsons says.

Heavy precipitation, such as that from Hurricane Irma in 2017, was also associated with the disease as was the presence of another deadly frog disease, ranavirus, which is known as the Ebola of frogs.

Findings from this new research can help with conservation efforts moving forward, says Anna Savage, study senior author and an associate professor in ��ӽ紫ý’s Department of Biology.

“While this is only a starting point for managing and protecting species, it tells us where and when to focus, so that in the future we could do things like avoid releasing head-started frogs of threatened and managed species into the wild at times of year when they are more likely to suffer from disease,” Savage says. “Gopher frogs are the most threatened and most susceptible species we know of to date, so those are the species that could benefit the most.”

How the Work Was Performed

For the study, the researchers sampled more than 1200 frogs from 20 wetland locations across the Central ��ӽ紫ý peninsula from August 2017-19. Data collected during sampling included average pH, presence of standing water, number of frog species, and fish and crayfish prevalence.

Their sampling methods were non-destructive, as only a small sample of tissue from the toe or tail was removed.

In the lab, the researchers extracted DNA from their samples using a Quantitative Polymerase Chain Reaction, or qPCR, protocol developed at ��ӽ紫ý. The innovative method allows for researchers to quantify pathogen presence and intensity without euthanasia.

How People Can Protect Frogs

Savage has several suggestions for what people can do to help protect frogs.

“One thing that everyone can do is be careful not to spread animals and pathogens around,” she says. “If you like to boat, fish or hike, be aware that all of the major frog diseases can survive on your nets, shoes and boots for days, and you could be spreading spores from one location to the next if you don’t decontaminate your gear in between sites. All it takes is rinsing things in a weak solution of household bleach or leaving items out to dry in the sun for at least a few days before traveling somewhere new.”

“You can also write to your local representatives and let them know that conserving natural areas and preventing more development of state lands is the main thing that is causing species to decline,” she says. “Diseases are a major problem, but losing habitat and connectivity among frog populations is an even bigger problem that, when combined with disease, can cause us to lose populations entirely.”

Researcher Credentials

Atkinson received his doctoral degree in integrative biology from ��ӽ紫ý and joined ��ӽ紫ý’s Department of Biology, part of ��ӽ紫ý’s College of Sciences, in 2023.

Savage received her doctoral degree in ecology and evolutionary biology from Cornell University. She is a member of ��ӽ紫ý’s Genomics and Bioinformatics Cluster and joined ��ӽ紫ý’s Department of Biology in 2015.

Monitoring Genetic Mutations Will Be Important for ��ӽ紫ý Panther Management

Mon, 22 Aug 2022 14:05:50 +0000

The introduction of Texas pumas to ��ӽ紫ý in the 1990s as part of a genetic rescue may have helped save ��ӽ紫ý panthers from extinction, but it also brought some harmful mutations with it along the way.

In a new study led by ��ӽ紫ý, researchers show that nearly half of the harmful mutations found in recent ��ӽ紫ý panthers came from the introduced Texas pumas, as well as from Central American pumas that were released into Everglades National Park in the 1950s and 1960s.

The findings, published recently in the Journal of Heredity, point to the importance of monitoring ��ӽ紫ý panther population genetics as well as the need to genetically screen any future introductions.

The ��ӽ紫ý panther’s population reached a dangerously low number of only 30 panthers in the 1970s and 1980s, which led to inbreeding and producing offspring with genetic problems, including heart defects, sexual defects such as cryptorchidism, and other diseases.

Genetic rescue efforts implemented in the 1990s brought pumas from Texas to ��ӽ紫ý to breed with panthers in the Sunshine State. The process is known as genetic admixture.

The efforts appeared to help, with the ��ӽ紫ý panther population rebounding to between 120 and 230 adults, according to estimates from the ��ӽ紫ý Fish and Wildlife Conservation Commission, and reports of greater genetic variation now present in the population.

However, the new findings show this genetic influx had both good and bad mutations with it.

“There’s a genetic signal that harmful mutations from different source populations were introduced into the ��ӽ紫ý panther population,” says the study’s lead author Alexander Ochoa, a postdoctoral scholar in ��ӽ紫ý’s Department of Biology and Genomics and Bioinformatics research cluster.

“Although there’s still no evidence of these mutations emerging at the phenotypic level, we want to monitor the genetic health of the ��ӽ紫ý panther because things could also go south pretty quickly, especially if their population remains small,” Ochoa says.

He says if researchers find an indication that the current fitness of the population is declining, then perhaps wildlife managers should consider future introductions and genetic rescue programs for ��ӽ紫ý panthers.

“And if that’s the case, with the information we have in hand, we may be able to assess the genetic health of potential source populations, and pinpoint and select individuals that are best suited for these introductions,” Ochoa says. “Ideally, we would want to select individuals that carry smaller amounts of harmful, or deleterious, mutations for introductions.”

Surprising Discovery

An interesting discovery from the new research was the Central American roots of some of the deleterious genetic material.

Central American pumas were introduced to the ��ӽ紫ý population, specifically to Everglades National Park, during poorly documented releases of captive pumas during the 1950s and 1960s.

As a result, ��ӽ紫ý panthers from Everglades National Park in South ��ӽ紫ý contain genetic ancestry from Central America, and like the introduction of pumas from Texas, brought good and bad mutations to the population.

The study found that 16% of the deleterious mutations present in ��ӽ紫ý panthers are of exclusive Central American origin, whereas 33% of these mutations are of exclusive Texas origin. Another 4% of these deleterious mutations are of shared Central American and Texas origin.

For the study, researchers used whole-genome sequences to identify and compare levels of mutation load of panthers from ��ӽ紫ý with no Texas or Central American ancestry (non-admixed); Everglades National Park panthers with Central American ancestry; Texas pumas; and panthers that had a mix of ��ӽ紫ý and Texas ancestry.

They looked at proportions of harmful mutations and genotypes carrying these mutations.

The researchers found that, although genetic admixture increased ��ӽ紫ý panther fitness by offsetting the expression of existing harmful mutations, admixed ��ӽ紫ý panthers have now become carriers of many new harmful mutations.

“I was expecting that the genetic rescue program was in general beneficial to ��ӽ紫ý panthers,” Ochoa says. “But at the same time one of the unexpected findings was that a reasonable amount of novel harmful mutations from different source populations were also introduced into the ��ӽ紫ý panther population. And we need to monitor these mutations in current ��ӽ紫ý panthers because that’s something that ��ӽ紫ý panthers did not have before.”

Next Steps

Assistant Professor of Biology and study co-author Robert Fitak helped lead the research. He says the ��ӽ紫ý panther has been a generally positive conservation success story, and that it now can also serve as a model to inform genetic rescues in other species.

“We know that in the future many more species are going to become endangered, suffer from severe inbreeding, and have to be managed by conservation actions such as genetic rescue,” Fitak says. “Our results will help us understand what the potential negative genetic consequences of these actions will be, or what we need to be prepared for.”

For ��ӽ紫ý panthers, Fitak says next steps should include sequencing entire genomes of more individuals to explore the distribution of harmful genetic traits in the population.

“Until recently, most studies of wildlife genomes have focused on their adaptations, in other words, those traits that are beneficial and specific to the species,” Fitak says. “Now, we are flipping the question around and asking what about the bad, or ‘deleterious,’ traits?”

“We know that the genetic mixing has overall been a success for ��ӽ紫ý panthers, but we need to be aware of any deleterious genetic stowaways that are tagging along for the ride,” he says.

Study co-authors were Dave Onorato with the ��ӽ紫ý Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute; Melody Roelke-Parker with Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc.; and Melanie Culver with the University of Arizona.

The work was supported by ��ӽ紫ý’s .

Ochoa received his doctoral degree in natural resources from the University of Arizona and joined ��ӽ紫ý in 2020.

Fitak received his doctorate in genetics from the University of Arizona and his bachelor’s in molecular genetics from The Ohio State University. Before joining ��ӽ紫ý in 2019, he worked as a postdoctoral researcher at the Institute for Population Genetics in Vienna, Austria, and at Duke University. He is a member of ��ӽ紫ý’s Genomics and Bioinformatics research cluster.

Study title: Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered ��ӽ紫ý Panthers

3 ��ӽ紫ý Colleges Receive $4.5M for Infectious Disease, Travel Health Research Initiative

Susan Vernon-Devlin — Wed, 20 Jul 2022 16:38:10 +0000

University of Central ��ӽ紫ý’s , and have received $4.5 million dollars in funding for a research initiative aimed at mitigating the damage caused to hospitality, travel, and small businesses by health crises, like the COVID-19 pandemic.

The funding for the collaborative research project comes from the ��ӽ紫ý Strategic Investment Program, supporting ��ӽ紫ý President Alexander N. Cartwright’s vision that ��ӽ紫ý will become a “University for the Future” as a top public institution and the world’s leading public metropolitan research university

The Infectious Disease and Travel Health Initiative has three major areas of focus:

To provide an advance warning system through its data collection methods.
To bring travelers and those who serve them closer to science, bridging the gap between basic science and behavioral science.
To create a resource for small to medium-sized businesses in tourist areas to help them manage future health crisis situations that may arise.

The primary investigator on the initiative, Professor Robertico Croes, focuses his research on tourism economics, human development, poverty, and tourism management with a special interest in small and developing economies.

Croes says the Infectious Disease and Travel Health initiative is critical given travelling’s economic impact on the world and its ability to alleviate poverty and elevate human development.

“We began this project in the early days of the pandemic,” Croes says. “Health crises like this are not an anomaly, they are becoming more and more frequent. Sometimes they are isolated to one area of the globe, but as we saw with COVID, they can devastate entire segments of the economy and small businesses often can’t recover as they don’t have the resources that large corporations have in order to mitigate a crisis.”

Griffith Parks, a collaborator on the initiative and professor and director of the at ��ӽ紫ý’s College of Medicine, says he is enthusiastic about the project.

“We are thrilled to have the support from the university on this important and unique initiative,” Parks says. “We aspire to build an initiative that will draw in faculty and students from other colleges, not just the three currently involved, such as nursing and health professions, who have an interest in population health, travel and tourism and in infectious diseases. Most importantly, a goal of the initiative is to have a strong impact on our Central ��ӽ紫ý communities by creating connections that will help to improve and support the health of our tourism workforce and industries.”

Pandemics can have devastating consequences for regions where tourism and travel are the economic lifeblood. According to Visit ��ӽ紫ý it’s estimated the local economy in Central ��ӽ紫ý took a $40 billion hit from lower rates of travel during the height of the COVID-19 pandemic.

Taj Azarian, an assistant professor at the Burnett School of Biomedical Sciences who investigates the emergence and spread of bacterial infectious diseases is collaborating on the project.

“��ӽ紫ý is a major tourist destination, as well as an international corridor to the United States. Further, its recent history has been marked by several notable public health events, as such, ��ӽ紫ý is an ideal location to focus translational infectious disease research.” Said Azarian. “Here, or initiative will serve to strengthen business continuity, improve health and safety of travelers, and establish a sentinel network for early detection of emerging threats.”

Rosen College Associate Dean and Professor Alan Fyall, a collaborator on the initiative, says the work could have a global impact.

“The pandemic has woken the world up to the fragility and vulnerability of the global tourism industry,” Fyall says. “The time is thus ripe to bring together an internationally recognized and highly experienced interdisciplinary team to develop new science-based solutions and strategies to build future economic and social strength for Central ��ӽ紫ý and beyond.”

The initiative’s collaborators also includesReseResea Kenneth Alexander, chief of the Division of Infectious Diseases at Nemours Children’s Hospital, ��ӽ紫ý, who says this is crucial work for future generations.

“It is important that Nemours Children’s Hospital joins in this initiative with ��ӽ紫ý for two reasons,” Alexander says. “First, many of our tourist guests here in ��ӽ紫ý are children. Second, many in our tourism labor force are raising families. Therefore, the health of children is central to the success of our tourism industry.”

The Infectious Disease and Travel Health Initiative research project received funding in the Academic Excellence Category of the ��ӽ紫ý Strategic Investment Program. The funding will help in hiring research faculty who can secure additional funding for the project; establishing new courses and a Travel & Health track of study within the Master of Public Health degree program; and developing partnerships within the hospitality, healthcare, and science industries. Current ��ӽ紫ý faculty from several disciplines are engaged with the initiative.

“The interdisciplinary nature of the project and the involvement of engineering and nanoscience will have a tremendous impact on combatting future infectious disease and travel health,” says Sudipta Seal, chair of the in the College of Engineering and Computer Science and co-principal investigator on the grant.

Seal’s statement was echoed by project collaborator Jane Gibson, a professor of pathology at ��ӽ紫ý’s College of Medicine.

“We are excited to harness the collective expertise at ��ӽ紫ý to support the health and well-being of our tourist industry colleagues, visitors and community,” Gibson says.

The Infectious Disease and Travel Health Initiative is ongoing with work on the initiative starting this summer.

New Genetic Clues Could be Key to Saving Sea Turtles from Mysterious Disease

Thu, 07 Apr 2022 11:40:12 +0000

University of Central ��ӽ紫ý researchers have discovered an abundance of new gene variants in the immune system of sea turtles, which could be key to one day saving the ancient marine animals from a major disease — fibropapillomatosis.

The discovery, which is detailed in a recent study in the journal Royal Society Open Science, sheds light on the role the gene variants, known as MHC class I alleles, play in potentially protecting sea turtles from the disease.

This is the first time researchers have studied variation in MHC genes in green sea turtles. MHC proteins act as a gatekeeper of an adaptive immune system. If they recognize a pathogen threat, then the immune system responds specifically to it.

Fibropapillomatosis, or FP, causes sea turtles to develop tumors on their bodies, which can limit their mobility and also their health by interfering with their ability to catch and eat prey.

Researchers are still working to uncover the causes of FP, which could include environmental contamination. They are also trying to figure out why some sea turtles, such as loggerheads, are rarely observed with FP, while others, such as green sea turtles are often afflicted.

About half of the green sea turtles observed in the Indian River Lagoon have FP, researchers say.

Central ��ӽ紫ý’s Atlantic coastline hosts about one-third of all green turtle nests in the state, and sea turtle health is important because the animals contribute to healthy oceans and coastlines by grazing and maintaining sea grass beds.

All sea turtles are categorized as threatened or endangered because of threats from pollution, coastal development and fishing, in addition to infectious diseases.

Better understanding the role genes play in protecting sea turtles can inform intervention strategies, such as captive breeding using turtles who have genetic defense against FP, says study co-author Anna Savage, an associate professor with ��ӽ紫ý’s Department of Biology and a member of ��ӽ紫ý’s Genomics and Bioinformatics research cluster.

“Just the baseline knowledge of how much variation is out there and is it relating to any certain phenotypes is really valuable, just for looking at how things change into the future,” Savage says. “But then also, if and when we do find really strong relationships between particular genetic variants and disease susceptibility, that’s a possible management tool if you need to intervene for the population to have a chance, if you know which of these MHC alleles are really important for surviving disease threats.”

The study’s lead author, Katherine Martin, a doctoral student in ��ӽ紫ý’s Department of Biology, spearheaded the research in which MHC class I genes were sequenced from 268 green sea turtles and 88 loggerhead sea turtles.

Katherine Martin, a doctoral student in ��ӽ紫ý’s Department of Biology, loads the next-generation sequencer that enabled the study.

The samples came from ��ӽ紫ý’s Marine Turtle Research Group’s database of more than 30,000 Indian River Lagoon sea turtle records dating back to the early 1980s.

The researchers found 116 new-to-science alleles, some of which seemed to be associated either with the development of FP but also potentially the regression of tumors.

However, the researchers say even with all the new alleles discovered, they are still going to need more sampling to get a full picture of what role MHC alleles play in protecting sea turtles.

“We kind of have limited time to figure out what’s under the hood of their immune system,” Martin says. “And so I think studies like this show that there’s still a lot to learn about these organisms.”

The researchers’ next steps include expansion of sampling of green sea turtles and loggerheads as well as sampling and analyzing genetic information from other sea turtle species.

The work was funded by the ��ӽ紫ý Sea Turtle License Plate Program and builds on previous studies, including research that looked at leeches as a possible vector that transmits FP to sea turtles.

The study also included co-author Kate Mansfield, director of ��ӽ紫ý’s Marine Turtle Research Group. Mansfield is an associate professor in ��ӽ紫ý’s Department of Biology and a member of ��ӽ紫ý’s Sustainable Coastal Systems research cluster.

��ӽ紫ý Expert Will Help Track COVID Spread, Reinfection and Vaccine Breakthroughs

Wed, 16 Jun 2021 15:15:23 +0000

A University of Central ��ӽ紫ý infectious-disease epidemiologist is working with The Rockefeller Foundation and the University of ��ӽ紫ý on a new collaboration to strengthen the ongoing response to SARS-CoV-2.

The work could affect approaches to control the virus, such as isolation strategies and vaccine development, and establish infrastructure to respond to future emerging infectious diseases.

The project is funded by philanthropic organization The Rockefeller Foundation as part of to strengthen global capabilities to detect and respond to pandemic threats.

��ӽ紫ý will receive the funds in partnership with UF to become part of a U.S. Regional Accelerators for Genomic Surveillance program that will provide strategic, coordination, and operational support toward improved and diversified regional surveillance efforts across a network of institutions. These institutions include the Broad Institute of MIT and Harvard, Louisiana State University Health Shreveport, and University of Wisconsin-Madison.

��ӽ紫ý and UF together will receive $340,000 for the project.

The work at ��ӽ紫ý will be led by Taj Azarian, an assistant professor and infectious-disease epidemiologist in the . Azarian will work closely with Marco Salemi, the project’s lead at UF and a member of UF’s Emerging Pathogens Institute.

The ��ӽ紫ý experts and their labs will work to establish a network of public, private, and industry partners that will strive to increase the representativeness of SARS-CoV-2 monitoring around the state, Azarian says.

They will do this by genome sequencing SARS-CoV-2 isolates from positive SARS-CoV-2 test samples taken from around ��ӽ紫ý — with individuals’ identities redacted.

Azarian says particular interest will be placed on monitoring cases of reinfection or vaccinated cases who become sick with COVID-19. These viral isolates will be prioritized for genome sequencing, which will allow the experts to identify new variants and understand how the virus is spreading in the community, he says.

“So, let’s say someone had COVID-19 early, like last summer, and then they get tested and they’re infected again,” Azarian says. “We’re interested in tracking that and looking at the viral genomes to see how different they are from the virus that was circulating earlier when they were infected.”

“We also want to monitor cases of vaccine breakthrough,” he says. “For example, someone received a vaccine and got sick weeks later with COVID.”

“Another priority is monitoring the populations that are either unvaccinated or undervaccinated,” he says.

Knowing this information can help with vaccination and community-level control efforts, Azarian says.

“Overall, we are trying to stay one step ahead of the virus,” Azarian says.

He says the selection of ��ӽ紫ý to work on the project was made possible by the concentrated expertise of the Genomics and Bioinformatics cluster at ��ӽ紫ý, the collaboration with the Salemi Laboratory, and also his recent work on rapid, onsite COVID-19 detection and viral sequencing on campus through a Higher Education Emergency Relief Fund II award.

“One of the things that we do in my laboratory is apply genome sequencing of pathogens to understand how they spread and transmit in the community,” he says.

“Getting funding through the university to start up our genomic surveillance on campus and do everything in-house provided a good springboard to show that we have the resources to be able to help increase the regional and national capacity to do genomic surveillance.”

Azarian received his doctorate in epidemiology from the University of ��ӽ紫ý and completed a postdoctoral fellowship at Harvard’s T.H. Chan School for Public Health in the Center for Communicable Disease Dynamics. He was recruited to ��ӽ紫ý through the Genomics and Bioinformatics Cluster initiative and joined ��ӽ紫ý’s Burnett School of Biomedical Sciences, part of ��ӽ紫ý’s , in 2018.

New ��ӽ紫ý Study Examines Leeches for Role in Major Disease of Sea Turtles in ��ӽ紫ý

Thu, 18 Feb 2021 15:30:19 +0000

University of Central ��ӽ紫ý researchers are homing in on the cause of a major disease of sea turtles, with some of their latest findings implicating saltwater leeches as a possible factor.

The disease, known as fibropapillomatosis, or FP, causes sea turtles to develop tumors on their bodies, which can limit their mobility and also their health by interfering with their ability to catch and eat prey.

FP causes sea turtles to develop tumors on their bodies, which can limit their health and mobility. Photo credit: Jake Kelley. Permit: MTP-231 and NMFS #19508

While the cause of FP isn’t known, saltwater leeches have been suspected to play a role due to their frequent presence on areas of sea turtles where FP tumors often develop, such as on their eyes, mouths and flippers.

The results, which were published recently in the journal , are the first evidence of a significant association between leeches and the disease in sea turtles, according to the researchers.

“��ӽ紫ý is one of the areas most heavily impacted by FP,” says Anna Savage, an associate professor in ��ӽ紫ý’s and study co-author. “Over the past three decades, approximately half of the green turtle juveniles encountered in the Indian River Lagoon have FP tumors, which is one of the highest rates documented,” she says.

Sea turtle health is important because the ancient marine reptiles contribute to healthy oceans and coastlines by grazing and maintaining sea grass beds.

All sea turtles are categorized as threatened or endangered because of threats from pollution, coastal development and fishing, in addition to infectious diseases.

Central ��ӽ紫ý’s Atlantic coastline hosts about one-third of all green turtle nests in the state and is one of the most important nesting areas in the world for loggerheads.

Knowing if leeches play a role in the disease transmission can help researchers better understand and predict its spread, as well as inform conservation actions, such as leech removal in sea turtle rehabilitation centers.

The Process

Leah Rittenburg, a recent undergraduate alumna of ��ӽ紫ý’s Biology Department and the study’s lead author, spearheaded the research and was responsible for the genetic analyses. Photo credit: MTRG. Permit: MTP-231 and NMFS #19508

The study’s lead author and a recent undergraduate alumna of ��ӽ紫ý’s Biology Department, Leah Rittenburg, spearheaded the research and was responsible for the genetic analyses.

To find out a possible connection between leeches and FP, the researchers documented the presence of leeches on green and loggerhead turtles captured from the Indian River Lagoon and also used genetic analyses to determine if leeches collected from the turtles contained chelonid alphaherpesvirus 5, or ChHV5, the virus most likely responsible for disease development in an individual turtle.

“Our historical data, collected by the between 2006 and 2018, revealed that leech parasitism was significantly associated with FP in green turtles but not in loggerhead turtles,” Rittenburg says.

“For the genetic analysis, about one-fifth of the leeches we collected were positive for ChHV5, and one leech species trended towards coming from FP-positive turtles, further supporting the hypothesis that leeches may act as ChHV5 transmitters,” she says.

Saltwater leeches have been suspected to play a role in FP due to their frequent presence on areas of sea turtles where FP tumors often develop. An arrow points to a leech. Photo credit: Chris Long. Permit: MTP-231 and NMFS #19508

Now that the researchers have demonstrated a relationship between FP and leeches, they want to evaluate more specifically if leeches transmit the turtle herpesvirus, which would provide stronger evidence that the virus in an underlying cause of FP.

Study co-authors were Jake R. Kelley, a master’s student in ��ӽ紫ý’s Department of Biology, and Kate L. Mansfield, an associate professor in ��ӽ紫ý’s Department of Biology and director of the ��ӽ紫ý Marine Turtle Research Group.

The research was funded by grants from ��ӽ紫ý’s and by a ��ӽ紫ý Sea Turtle License Plate grant.

Savage received her doctorate in ecology and evolutionary biology from Cornell University. She is a member of ��ӽ紫ý’s Genomics and Bioinformatics Cluster and joined ��ӽ紫ý’s Department of Biology, part of ��ӽ紫ý’s College of Sciences, in 2015.

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