This story originally published on April 21, 2015 in observance of the COPH’s 30^th anniversary celebration.

Three Distinguished USF Health Professors in the Department of Global Health at the USF College of Public Health – Drs. Tom Unnasch, John Adams and Dennis Kyle – are ranked among the university’s best externally-funded investigators in terms of research dollars, and two are in the top five. A major focus of their research is malaria.

A fourth Global Health professor, Dr. Michael White, published a groundbreaking study just last month that may revolutionize the global fight against malaria.

Unnasch, the department chair, said much of Global Health’s research funding comes from external grants from the National Institutes of Health, primarily the National Institute of Allergy and Infectious Diseases.

The Bill and Melinda Gates Foundation has come through with what he called “a substantial portfolio of funding”: a $4.5-million grant to Adams this year for developing new drugs and researching new genetic targets for malaria.

Kyle and Adams also have established collaborations with the Draper Laboratory to conduct research with artificial livers to study malaria in livers, which also is funded by the Gates Foundation, Unnasch said.

The combination of expertise and generous funding has helped put the department on the global cutting edge and in the thick of international connections that will help keep it there.

“The department is becoming quite well-known now as a research institution for malaria and other vector-borne diseases,” Unnasch said. “We have lots of good collaborations with people in Thailand at Mahidol University, and a lot of collaborations with people in Africa. There’s also quite a bit of contact between our department and people in the mosquito control field here in the state of Florida.”

Unnasch said those include regular work with the Florida Mosquito Control Association (of which Unnasch is on the board of directors), the Department of Health Laboratories, the Florida Department of Health, and various research projects with mosquito control in Hillsborough, Pasco, Manatee, Volusia and St. Johns counties, as well as with the Florida Keys Mosquito Control District in Monroe County.

For mosquito researchers, Unnasch said, the reason is obvious. For everyone else, it might be alarming.

“Florida’s the best place in the country if you want to do research on mosquito-transmitted diseases,” he said. “There are four arthropod-borne viruses, or arbovirus, infections that occur in the United States, and three out of the four are endemic to Florida. That’s why Florida spends $75-100 million a year on mosquito control. Only California spends more.”

Last month, the College of Public Health made headlines as Dr. Michael White, a professor in the College of Public Health’s Department of Global Health and the Morsani College of Medicine’s Department of Molecular Medicine, led a team of researchers that became the first to uncover part of the mysterious process by which malaria-related parasites spread at explosive and deadly rates inside humans and other animals.

As drug-resistant malaria threatens to become a major public health crisis, the findings could potentially lead to a powerful new treatment for malaria-caused illnesses that kill more than 600,000 people a year.

In a study published online March 3 in the high-impact journal PLOS Biology, the USF researchers and their colleagues at the University of Georgia discovered how these ancient parasites manage to replicate their chromosomes up to thousands of times before spinning off into daughter cells with perfect similitude – all the while avoiding cell death.

Malaria caused about 207 million cases and 627,000 deaths in 2012, according to the Centers for Disease Control and Prevention.  About 3.2 billion people, or nearly half the world’s population, are at risk of malaria, according to the World Health Organization.

White said that this study, which he called the first for a USF Health laboratory in publishing original research in PLOS Biology, will help get more potential treatments in the pipeline.

“The more we understand their vulnerability,” he said of the parasites, “the better chance we can keep that pipeline full.”

With the collective efforts and expertise of Drs. Adams, Kyle, Unnasch and White, the USF College of Public Health will remain on the front lines of the fight against one of the world’s most daunting health threats.

Related stories:
USF-led study sheds light on how malaria parasites grow exponentially
New antimalarial drug with novel mechanism of action
Dr. Dennis Kyle receives NIH award to understand extreme drug resistance in malaria
Dr. John Adams leads workshop for Gates Foundation scientists conducting malaria research

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Schistosomiasis is a parasitic disease caused by snail-transmitted flatworms.

According to the Centers for Disease Control and Prevention, the disease—which can cause scarring and inflammation of the liver, intestines and bladder, leading to anemia, malnutrition and learning difficulties, particularly in children—affects some 200 million people worldwide.

The disease is most often seen in parts of Africa, South America, the Caribbean and Asia where people use contaminated freshwater for bathing, drinking and cooking.

“Infected humans pass eggs of the Schistosoma parasite in feces or urine, and in areas that do not have adequate sanitation, those eggs often find their way into local bodies of water,” explained USF College of Public Health doctoral student Caitlin Wolfe, who recently co-authored a study examining how removing vegetation that acts as a habitat for the snails can reduce rates of the disease.

“Once in the water, the microscopic eggs hatch into miracidia that infect the snails,” she added. “The parasites then grow and mature into their next life cycle phase, cercaria, in the snail. Infected snails release the cercaria into the water, and the cercaria swim through the water and infect humans when they use infested bodies of water.”

Wolfe and her coauthors, including the principal investigator Dr. Jason Rohr, a former USF professor of integrative biology who currently teaches at Notre Dame, published their study, “A planetary health innovation for disease, food and water challenges in Africa,” in July in the journal Nature.

Wolfe and her colleagues performed their research in Senegal, where 99% of host snails are captured in the freshwater plant Ceratophyllum demersum. Because of the region’s arid soil, fertilizer is often used on crops, and that fertilizer gets into the water supply during heavy rains and subsequent surface runoff.

“More fertilizer in the water leads to more plants and more algae, which leads to more snails, which leads to more schistosomiasis,” she said.

Wolfe and her study co-authors hypothesized that if they could remove vegetation from the waterways and then compost that vegetation to be used as animal feed (the vegetation is safe for the animals; worms need a human host do their damage), they could reduce rates of schistosomiasis and create better access to waterways while increasing food production.

And, it turns out, they were right.

In the villages where the floating vegetation was removed (by hand), schoolchildren had nearly a 1.5 times lower rate of schistosomiasis, waterways stayed clearer and the composted vegetation-turned-animal feed turned out to be 41 to 179 times cheaper than traditional feed. 

“Thankfully,” said Wolfe, who’s concentrating in global communicable disease, “the findings of this study supported the hypothesis! We’ve known that certain snail species have an affinity for specific plants in specific locations (in northern Senegal, it’s the floating vegetation called ceratophyllum), so the notion of removing the plants that these snails like to feed on is something that has been suggested and discussed previously. But this study was one of the first to demonstrate concrete evidence for this intervention. The hope is that because there are additional benefits beyond just reducing transmission of a parasitic disease—such as increased agricultural output when the vegetation is composted and used as animal feed—there will be enough buy-in at local levels to support this intervention.”

Story by Donna Campisano, USF College of Public Health

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Sara Daniels, a USF College of Public Health MSPH student, recently completed a competitive National Institutes of Health (NIH) summer fellowship program.

Daniels, who is concentrating in both health promotion and behavior and global communicable diseases, was a Graduate Research Fellow with the NIH’s G-SOAR program. The program provides U.S. graduate students with valuable experience exploring the intersection of basic, translational and clinical research at the NIH. Daniels noted that the G-SOAR program has an acceptance rate of about 30% every year.

“I applied for the G-SOAR program because I knew I was interested in working for the NIH at some point in the future,” Daniels said. “I was looking for a summer internship and came across the NIH program, which would allow me to network with other graduate students, scientists and principal investigators working at the NIH doing cutting-edge biomedical research. Additionally, I was looking to practice and learn new lab skills.”

Daniels spent the summer working on COVID-19 research.

“My work focused on a specific enzyme that is part of the replication and transcription process known as NSP 14,” Daniels explained. “The lab where I worked studies iron-sulphur clusters and their role in biological processes. Many of these iron-sulphur clusters have been found in proteins encoded in the SARS-Cov-2 [COVID-19] genome and have been found at sites that were previously incorrectly classified as zinc-binding sites. Unfortunately, because of the time constraints of my fellowship, I could not continue with the process and identify potential iron-sulphur clusters on NSP-14. However, my lab will continue to work on further classifications.”

In addition to her lab work, Daniels attended weekly “Becoming a Resilient Scientist” discussion groups and presented at an NIH summer poster day. The latter, she said, was one of the highlights of her fellowship experience, giving her the opportunity to summarize her research into a poster format and share it with others at the NIH, including scientists and medical professionals working in NIH’s clinical center.

“As a second-year MSPH student getting into more technical courses and lab work, my training at the NIH allowed me to advance my understanding of techniques and apply those skills to cutting-edge research,” Daniels said. “The most significant impact this experience will have on my academic pursuits will be in the laboratory techniques that I learned and refined.”

Daniels’ advice to any students interested in NIH fellowships like the G-SOAR program is “to just take a shot and do it.” She also tells students to research labs early in the process. “The application process can be lengthy,” she said, “but so worth it.”

Story by Donna Campisano, USF College of Public Health

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USF College of Public Health professors Drs. Monica Uddin and Derek Wildman are part of a team of researchers examining how the historical trauma experienced by Alaskan Natives can affect the way genes work, demonstrating the impact of traumas that occurred years or even generations before.

Uddin and Wildman are co-authors of the recently published study, “Association between gene methylation and experiences of historical trauma in Alaska Native peoples.” 

The interdisciplinary, interprofessional work was conducted with researchers from the University of Illinois at Urbana-Champaign, McGill University, Kenai Peninsula College and several Alaskan Native heritage institutes. The work, funded by the National Science Foundation, appears in the International Journal of Equity in Health.

“The indigenous Alaskans hypothesized that this historical trauma may still be playing a role [in their genetic expression and health],” Wildman said. “Dr. Uddin and I were approached by Dr. Malhi from the University of Illinois because of our research experience with epigenetics and trauma. We were happy to join the study.”

According to the Centers for Disease Control and Prevention, “Epigenetics is the study of how behaviors and environment can cause changes that affect the way genes work. Unlike genetic changes, epigenetic changes are reversible and do not change your DNA sequence, but they can change how your body reads a DNA sequence.”

The group gave more than 100 indigenous Alaskans from two different regions in the state surveys about cultural identification, historical loss and trauma (some examples of historical trauma faced by Alaskan Natives have been forced relocation to boarding schools and removal of cultural practices, such as speaking their native languages) and general well-being. They also took blood samples to test for DNA methylation, a chemical modification of DNA that often alters the activity of genes.

What the researchers found was that historical loss and trauma were associated with DNA methylation differences in indigenous Alaskans.

“It is well understood that experienced trauma may have long-lasting effects on health. Epigenetics is one way in which trauma can ‘get under the skin,’” Wildman noted.

Epigenetic changes have been associated with health problems such as heart disease, type 2 diabetes and cancer, among others.

The researchers also found that the greater one identified with their heritage and culture, the greater their well-being.

“By reintegrating older cultural practices, folks in Alaska have strengthened community bonds and built resilience to the lasting effects of historical trauma,” Wildman explained. “This study serves as a model for effective collaboration between communities and researchers in the area of public health. We are interested in exploring whether interventions such as fishing ceremonies and other local cultural practices improve the epigenetic landscape and therefore health.”

Story by Donna Campisano, USF College of Public Health

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Lyme disease affects more than 300,000 people annually in the U.S. How can we predict when and where disease prevalence will be highest? Understanding the dynamics between ticks, mice and their habitats may provide important clues.

Drs. Lynn ‘Marty’ Martin and John Orrock are investigating these complex interactions through a National Ecological Observatory Network (NEON) Assignable Assets project. Their work could help illuminate how habitat quality, climate, and the behavioral choices of wild mice influence the spread of a dangerous pathogen.

Of mice, ticks and Borrelia

Certain species of mice are primary vectors for Lyme disease in the wild. Ticks do not pass the disease to each other; instead, each tick must contract the pathogen through an infected host before passing it on to other animals or humans. For many larval ticks, that first host is an infected mouse. Deer mice (genus Peromyscus), which are widely spread throughout North America, make excellent hosts for the Borrelia bacterium that causes Lyme disease.

Orrock, a professor in the Department of Integrative Biology at the University of Wisconsin–Madison, explains, “The mice are really the key because they are so abundant, and they are often the first meal for larval or nymphal ticks. They are also excellent hosts for Borrelia, which makes them a good repository for the pathogen. Adult ticks love to feed on deer, but deer are not great hosts for Borrelia. So if you want to understand the spread of Borrelia in an ecosystem, the mice are a really great place to start.”

Orrock is interested in how the habitats mice live in impact their behavioral choices and, by extension, their likelihood of encountering Lyme-bearing ticks. He teamed up with Martin, an eco-immunologist at the College of Public Health at the University of South Florida, to develop a NEON Assignable Assets proposal to investigate the dynamics of mouse behavior, immunity and pathogen prevalence at eight NEON terrestrial sites. While the researchers have known each other since their graduate school days, this proposal was born in the midst of the COVID-19 lockdowns through a virtual Research Coordination Network (RCN) supported by the National Science Foundation (NSF). The resulting project was funded through an NSF award.

Martin and Orrock wanted to investigate two related questions:

• How do habitat and climate factors impact the behavior and immunity of Peromyscus mice?
• What is the prevalence of Lyme disease in Peromyscus populations in different habitats and climate zones?

The NEON program provides an opportunity to investigate both questions on a continental scale. Orrock says, “The infrastructure that NEON already has in place really enables our research—we couldn’t do this anywhere else. NEON built the stage, and we just showed up to play on it.”

Martin adds, “It wouldn’t be possible to do this research in one place. We could start in John’s backyard in Wisconsin, but we really need the scale across multiple locations to answer these questions. Even with a lot of money and a good-sized team, we would not be able to come close to what we are able to do with the NEON program.”

They ultimately selected eight NEON field sites representing a range of habitat types across the eastern and upper Midwestern U.S., including:

• Blandy Experimental Farm (BLAN), Virginia
• Harvard Experimental Forest & Quabbin Watershed (HARV), Massachusetts
• Mountain Lake Biological Station (MLBS), Virginia
• Oak Ridge National Laboratory (ORNL), Tennessee
• Smithsonian Conservation Biology Institute (SCBI), Virginia
• Smithsonian Environmental Research Center (SERC), Maryland
• Steigerwalt-Chequamegon (STEI), Wisconsin
• University of Notre Dame Environmental Research Center (UNDE), Michigan

Building a better mousetrap

To answer their research questions, Orrock and Martin tapped into NEON in several ways.

• Through an Assignable Assets request, Orrock’s team had iButton dataloggers added to small mammal traps at each of the eight sites. Using two temperature dataloggers—one on the outside of the cage and one on the inside—allowed them to log the time that a small mammal entered the trap.
• Martin’s team is analyzing ear punches taken from Peromyscus mice (and other target species) caught in the small mammal traps. The samples are analyzed for the presence of Borrelia and for aspects of the immune response to bacteria.
• Other data collected by the NEON—including meteorological data, plant community composition and other sensor and observational data—provide important context for analyzing the dynamics of mouse behavior and immunity. For example, mouse activity can be correlated with temperature or with other aspects of the habitat.

This experimental design will allow them to explore complex relationships between habitat quality, climate, mouse traits and the prevalence of Lyme disease in Peromyscus mice. One of the hypotheses that they are investigating is that mouse activity is driven by climate and habitat variables, which in turn influences the likelihood that they will encounter an infected tick.

For Lyme disease transmission to take place, both the mouse and the tick must be in the same place at the same time. That means, for example, that temperatures must be suitable for both species. Habitat characteristics such as food availability also impact how active mice are, how far they travel in search of food and how healthy they are.

“We are working across eight NEON sites,” says Martin. “Some of the habitat is fantastic for mice, some not so much. Some are hot, some are cold, some are near human agriculture, some have limited food resources. And so the issue is, how does that habitat heterogeneity percolate through the immunity and behavior of individual mice to influence where and when Lyme disease shows up.”

For example, when food resources are scarce, mice are likely to spend more hours of the day out searching for food, which increases the odds that they will encounter ticks. At the same time, nutrient-deprived mice are less healthy and less able to mount an effective immune response against Lyme disease or other pathogens. All these variables work together in a complex web to influence how the pathogen is spread between ticks and mice and how sick mice get if they are infected. Understanding these dynamics could help researchers better predict Lyme disease hot spots in the future.

Bringing immunology out of the lab and into the wild

One of the exciting things about the study is the opportunity to study immunology in the wild. Most immunology studies take place in highly controlled laboratory conditions using genetically inbred animals. While these studies provide important insights into the pathology of Lyme disease, they don’t tell us much about how it is actually transmitted in the wild.

Martin says, “I’ve been frustrated since I became a scientist with the lack of immunology studies that take place outside. All of immunology has been about keeping things hyper-clean and controlled. Genetically engineered mice are kept in little boxes, they’re fed, the temperature is perfect and the lights come on and off when the researchers want—it’s a quasi-paradise for mice. Is that how the immune system of anything evolved? Of course not. This is an opportunity to learn what actually happens in the natural environment.”

The study began in 2022 and is expected to run through 2024 to gather three full years of data. In the 2022 sampling season, they sent out thousands of iButtons and successfully recorded the capture of more than 1,900 small mammals, nearly 900 of which were Peromyscus mice. Ear punches were taken from 30 mice at each location. Those samples are still undergoing analysis (including RNA sequencing and reverse transcription PCR) to detect the presence of Borrelia or biomarkers of immunity to Lyme disease. Orrock and Martin expect that several scientific publications could result from their work, starting with an investigation of how habitat quality and climate factors influence the behavior and activity level of Peromyscus mice.

Ultimately, a better understanding of the dynamics of disease transmission in the wild could inform public health policy and enable more accurate predictions of where humans are most at risk of encountering Lyme disease. It could also be used to build better models of how climate change and land use will impact the spread of Lyme disease in the future—or even hindcast using NEON data.

Orrock says, “Another benefit of the NEON program that doesn’t exist in most datasets is that capacity to understand change over time, which is even more essential in an era of global climate change. As ecologists, you really can’t infer much about the effects of climate change if all your studies are done over one or two years. With the NEON data, we could potentially go back and hindcast to predict how sick rodents were in the past based upon what we’ve learned in the present—much like stock analysts use hindcasting to test stock selection strategies. Because NEON has deep records of tick loads on mice over many years, we can use our data to hindcast and gain additional insight that would not be possible in any other system.”

Reposted from the NEON Observatory Blog

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Artemisinin combination therapies (ACTs) have greatly decreased deaths caused by Plasmodium falciparum malaria, a mosquito-borne disease that accounts for roughly 90 percent of the world’s malaria mortality.

But Plasmodium falciparum is becoming increasingly resistant to ACTs, making an already dangerous parasite even more threatening.

“Like antibiotic drugs used to treat other microbial infections, antimalarial drugs put evolutionary pressure on the parasite to evolve or to go extinct,” explained Dr. Justin Gibbons, a post-doctoral scholar in the USF College of Public Health’s (COPH) Center for Global Health and Inter-Disciplinary Research. “Random genetic changes occur all the time in these parasites and some of these changes may confer resistance to the drug treatment. The greater the resistance, the more likely these altered parasites can successfully reproduce, and, over time, parasites can become more and more resistant to ACTs until they won’t work anymore.”

Gibbons and his fellow researchers, including those from USF’s Morsani College of Medicine and the University of Glasgow, have identified a mutation in the MRST gene in Plasmodium falciparum that increases its sensitivity to ACT.

Their study, “A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum,” was published in the journal mSphere in May. The first author of the study was Caroline Simmons, who recently graduated the COPH with her PhD.

“Most studies of ACT resistance mechanisms identify broad pathways that are changed, but not the contribution of specific genes,” Gibbons said. “This study identified and characterized a gene that regulates pathways relevant to ACT resistance mechanisms that had not been identified before.”

According to Gibbons, Plasmodium falciparum resists artemisinin treatment by entering a dormant state until the drug has been cleared by the body—and then resumes growth.

“Instead of entering a quiescent state that is artemisinin resistant, the mutant is more sensitive to artemisinin, suggesting the decreased translation during this period is hobbling the normal artemisinin response,” Gibbons said.

Identifying this mutant gene can be a boon to those treating ACT-resistant Plasmodium falciparum.

“This gene can potentially be targeted by drugs that will impair the parasite’s ability to respond to artemisinin,” Gibbons noted, “which could extend the useful life of ACT.”

Story by Donna Campisano, USF College of Public Health

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According to the World Health Organization (WHO), nearly half of the world’s population in 2021 was at risk of malaria, a life-threatening disease most often transmitted to humans via mosquito bites. And while the disease is most prevalent in tropical countries, several cases of locally acquired malaria have recently been reported in the U.S.

While there are treatments for malaria, the main drug, artemisinin, is becoming less and less effective against a particularly deadly malaria-causing parasite called Plasmodium falciparum.

To better understand this drug resistance, a group of researchers, including those from the USF College of Public Health (COPH), set out to examine the genetic changes that occur in parasites treated with antimalarial drugs.

Their research, “Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins,” was published in June in the journal Microbiology Spectrum.

“Artemisinin works by causing damage to the parasite through a process involving a substance called heme, which is released when the parasite digests hemoglobin,” explained lead author Camilla Valente Pires, a postdoctoral scholar at the COPH’s Center for Global Health and Inter-Disciplinary Research who works in the lab of Dr. John Adams.  Adams is a malaria expert and a co-author of the paper. “However, the specific genetic changes that lead to resistance to artemisinin are complex and not yet fully understood,” Pires added. “That’s why, in this study, we took a systematic approach to study the genes responsible for how the malaria parasite responds to the oxidative stress caused by antimalarial drugs.”

The researchers, who, in addition to the team from the COPH, included scientists from USF’s Morsani College of Medicine, the University of Notre Dame, the University of Glasgow and the University of Cambridge, tested a group of genetically modified malaria parasites using a drug called dihydroartemisinin (DHA), which is similar to artemisinin, and another drug called bortezomib (BTZ), which blocks a specific process in the parasite. This allowed the scientists to create profiles of how the genes in the parasites interacted with the drugs. 

By comparing the response of the genetically modified parasites to the drugs, the researchers said they could better understand the parasite’s response—or lack of it—to artemisinin.

“We found that lipid metabolism and the export of proteins played important roles in how the parasites reacted to the drugs,” Pires said. “Surprisingly, we discovered that specific factors involved in protein export were significant differences between how DHA and BTZ worked.”

Pires said that by understanding these factors, scientists can gain insights into how the drugs work and how the parasite interacts with them.

“In the future, additional studies can build upon our findings and confirm the specific ways in which these factors interact,” Pires stated. “This will help us deepen our understanding of how the parasite responds to artemisinin and aid in the development of effective combinations of drugs for treating malaria.”

Story by Donna Campisano, USF College of Public Health

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Dr. Vania Assis, a postdoctoral scholar working at the USF College of Public Health’s (COPH) Center for Global Health Inter-Disciplinary Research, recently guest edited an issue of the scientific journal Philosophical Transactions of the Royal Society B.

 The issue focused on amphibian immunity.

“Amphibians are a group of animals that include frogs, toads, salamanders, newts and caecilians,” said Assis, who works with COPH Professor Lynn “Marty” Martin in the Martin Lab. “They are known for their unique ability to live both on land and in water. Amphibians are considered bioindicators of environmental health. This means that their well-being and the presence of diseases in their populations can serve as warning signs for potential threats to human health. By monitoring the health of amphibians, we can detect early signs of environmental degradation or disease outbreaks that might have broader implications for human populations.”

Philosophical Transactions of the Royal Society B publishes high-quality themed issues on topics of current importance within the life sciences. Each issue is guest edited by leading authorities with research, reviews and commentary from prominent researchers.

Assis, who specializes in native anurans (for example, toads and frogs) from Brazil as well as the invasive cane toads here in Florida, saw a need to dedicate a themed issue to amphibians that would include research on their eco-immunology (the causes and consequences of immune variation). To cover various aspects like endocrine-immune interactions, stress and disease, she partnered with Drs. Stefanny C.M. Titon (University of Sao Paulo) and Jacques Robert (University of Rochester) to create a publication exploring the physiological responses and conservation needs of amphibians.

“To become a guest editor, you must be a leading research authority and submit a proposal. If your proposal is selected, you can invite the authors and take care of the editorial process with the help of the journal’s editorial team,” said Assis, who was responsible for editing five manuscripts. “Being a guest editor has allowed me to contribute to the scientific community by promoting necessary research and fostering discussion of critical concern. I am grateful for the opportunity to contribute to the field and support the recognition of amphibians as a significant group needing conservation efforts.”

This marks the third time Assis has been a guest editor. In 2022, she edited an issue of Integrative and Comparative Biology and in 2020 took on an issue of the Journal of Experimental Zoology – Part A, a publication she’s been on the editorial board of since 2019.

“I thoroughly enjoy organizing issues and symposiums, as it allows me to bring attention to deserving research and raise awareness about the conservation needs of vulnerable species,” Assis said.

Story by Donna Campisano, USF College of Public Health

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When Stephanie Carraway relocated to Tampa from Florida’s East Coast 12 years ago, she took a job as a secretary in the infection prevention department at Moffitt Cancer Center.

“My time there proved to be highly influential,” said Carraway, a native of Islamorada, Fla., and a 2006 graduate of Florida State University. “I became deeply inspired by the department, prompting me to pursue a specialization in infection prevention.”

In 2013, Carraway enrolled in classes at USF to acquire a graduate certificate in infection control, which sparked an even broader interest in public health. In 2015, she received her MPH from USF’s College of Public Health with a specialization in infection control.

Carraway said what she loves about the work is her ability to have a direct impact on an individual’s health and well-being.

“Our primary objective revolves around ensuring the well-being of both patients and staff, shielding them from the risks associated with communicable diseases and infections that they might be vulnerable to during their hospital stay,” Carraway said. “It is truly gratifying to witness the positive impact my team can make by introducing projects or processes that enhance the health outcomes of our patients and the safety of our staff.”

Carraway credits her COPH training with helping her climb to the top.

“The invaluable knowledge I gained at USF has played a pivotal role in shaping my current position,” she stated. “My experience at USF has enabled me to successfully transition into the role of an infection preventionist, significantly expanding my responsibilities within my organization. I started as a secretary and today, I stand as director of infection prevention at a prominent comprehensive cancer center, a testament to the transformative power of education and personal growth.”

Infection control’s ever-changing nature keeps Carraway on her toes.

“I am dedicated to the education of health care personnel and the general public regarding infectious diseases and effective measures to contain their spread,” she said. “Through this outreach, I aim to foster awareness and empower individuals with knowledge on limiting the transmission of infectious diseases. I firmly believe that in this role, the learning process never ceases. There is an endless array of knowledge and skills to acquire, and I relish the opportunity to face and overcome such challenges.”

Carraway said one of her greatest professional accomplishments is being selected as a fellow of the Association for Professionals in Infection Control and Epidemiology (APIC). Fellows of the APIC must demonstrate exceptional expertise and leadership in the field of infection control and epidemiology, including publishing in peer-reviewed journals and exhibiting proficiency in at least three of the four domains of infection prevention (for example, operations and performance improvement, professional stewardship, etc.).

“Receiving the title of APIC fellow is an accomplishment that I am immensely proud of. It highlights my dedication to infection prevention and control, as well as my commitment to advancing the field through leadership and scholarly contributions,” Carraway said.

Carraway intends on staying put at Moffitt, at least for the time being.

“I love working at Moffitt. I feel like I have truly found my passion and I love what I do,” she said. “I am not sure what the future holds for my career, but I am along for the ride!”

Alumni Fast Five:

What did you dream of becoming when you were young?

I was always inspired by doctors and thought medicine was super cool!

Where would we find you on the weekend?

You will most likely find me spending time with my family. My weekends are when I get to have fun with my 5-year-old daughter and my husband. I look forward to different activities and watching my daughter grow and play! There is no other place I would rather be.

What is the last book you read?

I am currently pursuing my MBA, so the only books I have read lately are about finance!

What superpower would you like to have?

I would love to be able to heal people. You know…place your hand on a broken arm and fix it. There would be no better feeling!

What’s your all-time favorite movie?

This is tough, and I am not sure I could pick just one. I really loved “Mrs. Doubtfire” growing up and that’s in my top 10!

Story by Donna Campisano, USF College of Public Health

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In collaboration with Pacific Biosciences (PacBio), the USF College of Public Health’s Genomics Program  and Sequencing Core recently hosted a Genomics Symposium entitled “Long Read Single Molecule Sequencing: A New Era in Genomics.”

Pacific Biosciences, commonly known as PacBio, is a biotechnology company that develops and manufactures cutting-edge systems for gene sequencing, a process that allows scientists to determine what genetic information is carried in a particular segment of DNA.

The PacBio Discoveries Roadshow provided the audience with a valuable opportunity to explore tools that have the potential to fuel the next breakthroughs in understanding genetic diseases, identifying novel genetic variations and exploring the complexities of the human genome, revealing functional elements and accelerating disease research. These tools can also offer advancements in areas such as microbiome research, environmental genomics and understanding symbiotic relationships.

This year’s roadshow includes stops in North America, Europe, South America and Asia with over 40 events on the schedule from March to May. Scientists were again able to come together, listen to talks from local researchers using PacBio sequencing technologies and hear about the new PacBio products and applications.

On Tuesday, May 16, PacBio’s Discoveries Roadshow brought them to Tampa, where over 70 people came together in the USF Research Park Building to hear about the latest updates in PacBio sequencing technologies. Emily Reynolds, territory account manager at PacBio, stated that USF Research Park in Tampa was an ideal location to host this research conference event.

Talks included representatives from PacBio discussing innovations in applications and instrumentation, as well as three scientific talks from local southeast researchers.

PacBio’s revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads, offering the most comprehensive view of genomes, transcriptomes (transcriptomes represent the complete set of RNA molecules transcribed from the genome) and epigenomes (the collection of modifications and factors that modify gene expression within a genome).

With HiFi reads, which provide an accuracy of 99.9 percent and up to 25 kb length sequencing, PacBio is the only sequencing technology that allows for the accurate detection of various types of variants, from single nucleotides to structural variants, which can uncover complex genomic structures, identify structural variations and provide a more comprehensive understanding of genomes.

Most single-cell experiments are done with short reads, which only capture the ends of molecules due to fragmentation. Sequencing fragments limit expression information to the gene level, missing important isoform diversity that could be important for disease or biological function. 

Dr. John Adams, director of the USF Genomics Program and co-director of the Center for Global Health and Infectious Diseases Research, presented his research on the functional analysis of gametocyte development in human malaria parasites (gametocytes differentiate into male and female gametes, crucial for malaria transmission).

His talk focused on the utilization of long-read single-cell RNA sequencing to characterize the full-length Plasmodium transcripts from the malaria parasite. This approach, empowered by PacBio MAS-Seq (Multiplexed Arrays Sequencing method) for single cell isoform sequencing along with 10x single-cell barcode and UMI information, enables the identification of stage-specific differentially expressed isoforms (different forms of the same proteins).

Dr. Chengqi Wang, a research assistant professor in the USF Genomics Program and a computational expert in genomics data analysis and the single-cell isoform analysis field, highlighted the significance of mRNA isoforms (mRNA are molecules that carry the genetic information cells need to make proteins).

“Many genes of the mutant parasite can generate multiple isoforms, and mRNA isoforms can be considered as variations of a recipe to prepare different proteins,” Wang stated.

Dr. Michael Kladde, professor of biochemistry and molecular biology at the University of Florida, presented a novel, cost-effective and multiplexed method for achieving high levels of on-target sequencing, allowing for the detection of genetic and epigenetic heterogeneity.

His talk, titled “Precision, flap endonuclease-mediated targeted profiling of genetic and epigenetic heterogeneity on single DNA molecules,” emphasized the utilization of PacBio HiFi long reads at high coverages. This methodology has been instrumental in revealing epigenetic mechanistic insights in cancer, sepsis and other disease conditions. Epigenetic mechanisms can alter the way a gene is expressed.

The keynote speaker, Dr. Jeremy Schmutz, faculty investigator at the Hudson Alpha Institute for Biotechnology AL, showcased the remarkable world of HiFi genomics in their research over the past three years. They have successfully applied PacBio HiFi sequencing to address challenging issues in genome sequencing, including human de novo disease identification (a human de novo disease is a disease not present in either parent but present in their child) and sequencing complex plant genomes. Dr. Schmutz presented early data results from the newest PacBio sequencing platform, Revio.

The Revio long-read sequencing system holds great potential for enabling large-scale research projects with enhanced efficiency. Consequently, researchers will be able to undertake ambitious endeavors more swiftly and cost effectively, while attaining a more comprehensive and precise understanding of structural variations, epigenetic profiles and single nucleotide variants.

Dr. Min Zhang, the USF Genomics Program sequencing core director and one of the organizers of the event, emphasized the capabilities of the PacBio Revio long-read sequencing system and the MAS-Seq for single-cell isoform sequencing.

“The PacBio HiFi read technology overcomes the limitations of short-read sequencing, allowing scientists to delve deeper into unraveling complex biological systems by employing long-read single-cell sequencing,” Zhang said. Researchers can now gain a more comprehensive understanding of genetic diversity, specifically in terms of cell type-specific isoform diversity and the role of isoforms in diseases and biological processes such as cancer or Alzheimer’s.

Moreover, PacBio’s tools provide invaluable assistance in deciphering disease mechanisms, identifying disease-associated variants and uncovering novel drug targets. These advancements have the potential to significantly improve diagnostics, therapies and personalized medicine approaches.

Story by Donna Campisano and Dr. Min Zhang, USF College of Public Health, Genomics Program

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