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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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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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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The USF College of Public Health’s Genomics Program and the Center for Global Health and Infectious Diseases Research (GHIDR) recently hosted a Digital Spatial Genomics Symposium, in collaboration with biotech companies Nanostring and Illumina.

More than 100 attendees participated in the one-day symposium held in February, with a majority being USF faculty and students. Representatives from other institutions, such as Moffitt Cancer Center and Shriners Hospital for Children, also attended.

The symposium showcased the NanoString GeoMx Digital Spatial Profiler (DSP). This cutting-edge technology has numerous applications, including the ability to identify and analyze specific genes and proteins associated with diseases such as Alzheimer’s disease, infectious diseases and cancer.

By understanding how these markers are expressed and distributed within tissues, researchers can develop better diagnostic tools and therapies for patients. The GeoMx DSP instrument is housed in the Byrd Institute Spatial Biology Core, which provides researchers with access to the NanoString Digital Spatial Profiler as a shared resource.

According to Dr. John Adams, director of the USF Genomics Program and co-director of GHIDR, the NanoString GeoMx DSP is particularly noteworthy for its ability to perform whole transcriptome and protein assays, which provide a comprehensive view of gene expression and protein distribution in a given sample.

However, to fully utilize this technology, a follow-up sequencing step is required using the Illumina instrument. This additional step is necessary to identify the specific probe and map it to its corresponding gene. The USF Genomics Sequencing Core and Byrd Institute Spatial Biology Core work together to provide comprehensive service support, enabling researchers to take full advantage of this advanced technology.

Adams emphasized that the USF Genomics Program Core Facilities have all the necessary instrumentation for next-generation sequencing (NGS) applications, including the Illumina NextSeq2000 and 10x Genomics Chromium Controller for high-throughput sequencing and single-cell analysis. The availability of the GeoMx DSP and the associated sequencing capabilities represents a significant step forward in the university’s efforts to support innovative research in the field of genomics.

The symposium featured presentations from renowned researchers who have utilized digital spatial genomics profiling to analyze tissue and gain insights into the development of Alzheimer’s disease and cancer.

Dr. Gopal Thinakaran, CEO of the Byrd Alzheimer’s Center and Research Institute at USF, presented his research on Alzheimer’s tau pathogenesis. He emphasized the sensitivity and versatility of the GeoMx technology, which enables the detection of genes with varying levels of expression in different tissue types, including challenging samples.

 Dr. Kenneth Tsai, pathology research vice chair of Moffitt Cancer Center, presented his research on the tumor immune landscape of Merkel cell carcinoma and its relevance to immunotherapy. He showcased how digital spatial technology has enabled a breakthrough in visualizing cancer development, opening new treatment possibilities.

Representatives from Nanostring and Illumina also introduced the latest DSP technologies and key applications to discover more about accessing the full richness of spatial biological complexity.

The symposium included breakout sessions in the afternoon, covering sample preparation for the GeoMx Digital Spatial Profiler and its data analysis connection within the workflow to visualize tissue structures.

The USF researchers have been encouraged to utilize the GeoMx Digital Spatial Profiler and Next-Gen sequencing by Nanostring and Illumina. As part of this encouragement, they offered the GeoMx Whole Transcriptome Atlas Grants, which cover the cost of reagents, including four slides worth of Whole Transcriptome Reagents for GeoMx from Nanostring, which costs $10,000, and the initial sequencing cost of reagents from Illumina, which costs $5,000.

During the symposium, two grant winners were announced: Drs. Paula Bickford and Lianchun Wang.

Bickford’s project focuses on studying the role of aging in response to therapeutic stem cell-derived exosomes following traumatic brain injury. Wang’s project aims to investigate the roles of microglial heparan sulfate in brain homeostasis and Alzheimer’s disease. Both emphasized the importance of the NanoString GeoMx DSP, which allows for spatial profiling of gene expression in tissues, providing a high-resolution view of the molecular landscape of diseases such as Alzheimer’s.

The Genomics Program Sequencing and Computational Cores have supported 26 grant proposals with letters of support, and 11 of these proposals, amounting to $16 million in grant funding, have been successfully funded. These grants focus on various fields, including Alzheimer’s disease, infectious diseases, cancer and other areas utilizing digital spatial, single-cell multiomics and other next-generation sequencing technologies.

 Dr. Min Zhang, the USF Genomics Program sequencing core director and one of the organizers of the event, highlighted the importance of genomics cores in providing hands-on training, consultation and assistance to USF researchers. This support includes help with grant proposals, experimental design and data analysis to achieve research goals. In fact, demonstrating the in-house capability of cutting-edge technologies is crucial for success in grant proposals.

Overall, the NanoString DSP and single-cell technologies represent a significant step forward in understanding complex diseases, such as cancer and Alzheimer’s disease. By providing a detailed view of the molecular landscape of cells within tissues, researchers can develop more effective diagnostic tools and therapies. As such, this technology is an important area of research with the potential to improve public health outcomes.

Story by Desiree Lara Norat and Min Zhang, USF College of Public Health

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The USF College of Public Health’s Genomics Program and the Center for Global Health and Infectious Diseases Research hosted, along with biotech companies 10x Genomics, Illumina and Miltenyi Biotec, a symposium on new technologies and applications pertaining to single-cell genomics.

“The USF Genomics Program sequencing and computational cores provide trainings and services for single-cell analysis,” Dr. John Adams, director of the USF Genomics Program and co-director of the Center for Global Health and Infectious Diseases Research, said. “The goal of the program is to provide advanced support in cutting-edge genomic technologies and applications for USF researchers. The RNAseq [a technique that measures gene expression] workshops are offered three times a year and have trained 236 researchers in 74 groups from nine USF colleges. About 35 percent of participants are faculty and staff, 65 percent are students and post-docs.”

As the name implies, single-cell genomics examines the inner workings and individuality of a single cell, rather than a group of cells.  Single-cell analysis helps identify new and/or rare cell types, increasing scientists’ understanding of the complexity of cell samples.

The one-day symposium, held in August at USF’s new Research Park building, had 160 attendees. About 60 percent of the audience was made up of USF researchers (faculty and students). Forty percent came from other institutions, such as Moffitt Cancer Center, the University of Florida, Florida State University, Florida A&M University, AdventHealth, Johns Hopkins All Children’s Hospital and others. 

Presentations covered a wide range of topics, including using single-cell analysis to discover more about metabolism, diabetes and cancer. Leading researchers came from USF, the University of Florida, Moffitt Cancer Center, Florida State University and Johns Hopkins All Children’s Hospital and shared their latest discoveries and uses of various single-cell approaches in their research.

Dr. Ji Li, a professor in the department of surgery within USF’s Health Heart Institute at the Morsani College of Medicine, presented “Signal Transduction of Activated Protein C in Aging.” The presentation highlighted how single cells can regulate age-related conditions such as heart disease.

“This symposium brought insights and updates on a wide range of topics, including new technologies and applications introducing the power of single-cell multiomics analysis and spatial technology and single-cell sample preparation and analysis,” explained Dr. Min Zhang, the USF Genomics Program sequencing core director and one of the organizers of the event. “Single-cell technology allows us to analyze genetic information on a cell-by-cell basis through the use of microscopic fluid lines to capture single cells and prepare barcoded, next-generation sequencing (NGS) cDNA libraries. Entirely new layers of genetic data can be obtained.”

According to Zhang, single-cell technology is a boon not only for understanding biology but also for improving human health.

“This symposium showed us wonderful examples of how we can bring the science to the bench,” she said. “It gave us some considerations to think about when choosing which single-cell products to use for our research projects. By taking full advantage of the power of single-cell multiomics, we can address important modern concerns such as profiling the adaptive immune system to do things like track flu or COVID-19-related immune cells and understand their cellular state.”

Story by Donna Campisano, USF College of Public Health

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Want to be part of the next generation of scientists that tackle real-world problems like climate change, pandemics and disease prevention?

The USF College of Public Health (COPH) genomics program is offering a new micro-certificate that provides professionals with a foundational understanding of the field of genomics and precision medicine through the COPH’s Lifelong Learning Academy which addresses workforce development beyond the degree programs.

This June, the program is rolling out the first of the two core courses, Public Health Lab Bioinformatics; and next year they hope to offer the second core course, Applied Genomics.

“The genomics micro-certificates are part of a comprehensive effort by the USF genomics program to support advanced workforce training. Our continuing education training in genomics data science is designed to provide high-value research skills to current public health professionals,” said Dr. John Adams, distinguished university and USF Health professor.

This continuing education training is ideal for public health laboratory and hospital personnel to increase their genomics knowledge base for career advancement. The program provides training in NextGen sequencing and bioinformatics workflows to prepare professionals to fill gaps in the workforce. Participants will strengthen their knowledge base in genomics to successfully integrate new technologies into their laboratories.

Those who enroll in the micro-certificate program must complete two core courses and one elective course. Students will be able to choose one of the following as their elective course: Fundamentals of Genetics, Experimental Design of Meta-omics, Cancer Genomics/Drug Discovery/Targeted Therapeutics, and Emerging Technologies.

All courses are online learning and are self-paced. Each course consists of short online-videos readings, exercises and knowledge checks. Participants will spend approximately 15 hours in each course, depending on their familiarity with the topic, to finish within six weeks.

“Genomics is at the forefront of public health, especially as relates to emerging diseases (I’m sure we can all think of a few of those!),” said Dr. Monica Uddin, professor of psychiatric genomics. “By completing the program, we hope that students gain not only practical training in next generation sequencing and bioinformatic workflows, but also a deeper understanding of genomics from a public health perspective.”

The micro-certificate is the first of its kind at the COPH.

“There’s been a big push for public health workforce development due to emerging public health issues, such as COVID-19. This has created a need in the industry for competency-based short-cycle programs in public health. Short-cycle programs or micro-certificates allow professionals to obtain the knowledge necessary to upskill in a specialized area quickly,” said Dr. Ann Joyce, associate director of continuing education.

The genomics program is also looking to create a future pipeline with these micro-certificates for those that want to continue their education and earn a full certificate and/or grad certificate.

“Micro-certificates broaden the field of professional development, which provides a more complete higher education ecosystem. The goal is to provide lifelong learning experiences for our alumni and community partners. We’re not just saying goodbye to graduates once they complete their degree, micro-certificates allow them to come back and enhance their degrees and obtain continuing education credits,” Joyce said. “These micro-certificates also allow students to control their career trajectory and earn stackable credits. We’re hoping to target other areas in public health, and I’m excited about what we are doing for lifelong continuing education.”

The program will run from June 20 through July 15, 2022. For more information and to enroll, click here.

Story by Caitlin Keough, USF College of Public Health

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A team of researchers led by Dr. John Adams from the USF College of Public Health (COPH) have recently published an article looking at the pathways some deadly malaria-causing parasites use to survive not just human fever—the body’s natural defense against pathogens—but also the drugs designed to attack them.

The article, “The apicoplast link to fever-survival and artemisinin-resistance in the malaria parasite,” was published in the journal Nature Communications in July. The study’s three lead authors are the COPH’s Drs. Min Zhang, Chengqi Wang and Jenna Oberstaller, all of whom work in the college’s Center for Global Health and Infectious Disease Research and USF genomics program.

Malaria is still the most devastating parasitic disease of humans, with over 200 million cases each year. Resistance to frontline antimalarial drugs, such as artemisinin, is rising—threatening to undo decades of progress against the disease.

“There are no other drugs poised to replace artemisinin, and it’s critical we continue to study parasite biology to find weaknesses we can exploit to develop new interventions,” Dr. Oberstaller emphasized. “Ideal targets would be parasite-specific, as they would provide fewer worries about off-target effects on humans. We focused on studying how parasites survive human fever because the ability to survive such harsh conditions is a fairly unique talent—which we hypothesized to involve unique parasite pathways essential for parasite survival that could be promising targets for intervention.”

The research employed the use of a genome-editing technique called piggyBac-transposon mutagenesis that the team previously used to uncover genes essential for malaria parasite survival in ideal conditions.

“This technology was also successfully applied here to study parasite growth in response to human febrile temperatures,” Dr. Zhang said. “More than 200 piggyBac-mutant parasites were identified with differential responses to increased temperature, allowing us to determine which genes drive parasite survival of fever.”

Unexpectedly, the researchers discovered that malaria parasites use ancient pathways co-opted from plants to survive human fever—and further, they are now repurposing the same pathways to evolve resistance to front-line antimalarial drugs. A small parasite organelle derived from algae, called the apicoplast, is the key to surviving both the heat and artemisinin derivatives.

“We noticed similarities between processes driving parasite fever-response and the mechanism of drug resistance to artemisinin—which made us investigate the connection further. We discovered that parasite genes with plant orthologs [genes in two different species that evolved from the same ancestral gene] tend to increase their expression level in response to fever conditions, and many of those same genes are also increased in drug-resistant parasites taken from clinical patients,” Drs. Wang and Oberstaller said. “This leads us to speculate that these ancestral genes enable parasite survival of extreme temperatures and artemisinins.”

The research will help scientists develop multiple antimalarial drugs that target multiple, unrelated pathways.

“Knowing not only how a drug works, but also which pathway(s) it targets, enables us to develop the smartest types of intervention,” Dr. Oberstaller explained. “This will lead to better combination therapies to combat emerging resistance.”

Story by Donna Campisano, USF College of Public Health

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The pandemic could not divert USF’s top faculty researchers from making big discoveries that shape our understanding of the past, present and future.

One USF researcher brings dinosaurs to life through augmented reality while a colleague explores the origins of life through planetary chemistry. Another faculty member’s research sounded early alarms about people turning to alcohol amid the stress and fear of the COVID-19 pandemic, while her colleague is the co-founder of the new Center for Justice Research & Policy at USF. And in USF’s Department of Physics, a professor’s discovery holds the potential to revolutionize the Internet of Things.

These are just a few of the faculty research achievements newly recognized with USF’s Outstanding Research Achievement Awards. Despite the COVID-19 pandemic’s interruptions to campus life in 2020, this year’s awards recognize 22 faculty members—the largest group to date—for their achievements that defied the disruption caused by the last year’s shutdown.

“The University of South Florida’s reputation as a top urban-based research university is fueled by our innovative faculty and researchers,” said USF President Rhea Law. “I congratulate each of the outstanding awardees for such a productive year in their work to change lives and shape the future.”

The largest internal recognition of its kind at USF, the annual nominations are submitted by deans, department chairs, center and institute directors, and associate deans of research. The nominations are reviewed by members of the USF Research Council. Each faculty member receives $2,000 with the award and recognition at an event later in the fall.

Awardees include USF College of Public Health’s Dr. John Adams and Dr. Lynn Martin.

John H. Adams, PhD, FAAAS, FASTMH

Distinguished USF Health Professor and Distinguished University Professor, Center for Global Health Infectious Disease Research and USF Genomics Program

Dr. Adams is an international expert in malaria research. His research focuses on host‐parasite interactions and improving the understanding of infection and pathogenesis in malaria. His group is actively engaged in vaccine and drug discovery projects. In 2020, he received a National Institutes of Health grant to accelerate vaccine development for vivax malaria, the most prevalent type of malaria outside of the African continent. The project builds upon his group’s successful development of a greatly improved liver culture system for the early infective stages of human malaria parasites. As the lead investigator on the grant, Dr. Adams brought together an international consortium from six institutions to prepare a vaccine for clinical trial. He also the lead investigator for an NIH 2020 exploratory grant to collaborate with researchers in Thailand to evaluate the pharmacogenomics of an antimalarial drug.

“The rapid development of safe, effective mRNA vaccines was an amazing accomplishment and highlights the importance of ongoing investment in biomedical research. Although perceived as a new technology, the mRNA vaccine approach has been in development for some time and many research groups were able to quickly pivot to apply the technology for SARS-CoV-2 vaccine development. Indeed, our NIH U01 project will be able to leverage some of the successful mechanics of vaccines for our vivax malaria vaccine in development,” Dr. Adams said. “This award mainly reflects the achievement of my research team. My team members are a great group of dedicated scientists and it is too bad these are given only as awards to individuals.”

Lynn B. Martin, PhD

Professor, Global Health and Infectious Disease Research

Dr. Martin is an internationally-renowned expert in disease ecology and invasive species. In 2020, he was awarded a $1.5 million, four-year National Science Foundation grant to fund an international project on the molecular genetics of one of the world’s most invasive species, the house sparrow. The research will take him, postdocs and students to Senegal, Vietnam, Norway, Spain, Australia, and New Zealand to study how the sparrows became one of the most broadly distributed animals in the world. He also submitted several other large grant proposals in 2020 which are still pending decisions. In 2020, he and his trainees and collaborators published 10 papers in high-profile journals including American Naturalist, eLife, Proceedings of the Royal Society B, and Bioscience. Two of those publications were invited (eLife and Bioscience), and all but two papers included a student or postdoc from his lab. Dr. Martin is also the co-creator and co-host of the popular podcast, Big Biology.

“COVID has helped me appreciate how privileged I am to work in a place where my job is to provide solutions for important problems. As my own research involves diseases that spillover from wildlife, like SARS-COV2, this pandemic has motivated me to work harder to find ways to predict and prevent the next one,” Dr. Martin said. “I’m really excited to receive this award, but science like the kind done in my lab is a group effort.  This award wouldn’t have been possible without the excellent work of so many colleagues and especially students.”

Story reposted from USF Research and Innovation Newsroom.

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The USF College of Public Health (COPH) recently signed an agreement with the Faculty of Tropical Medicine at Mahidol University in Thailand.

“The birthplace of artemisinin resistance”

As part of the agreement, Thai faculty and students exploring RNA-sequencing and drug discovery will have the opportunity to come to COPH for training. RNA is a molecule similar to DNA; RNA sequencing is a technique used to reveal the presence and quantity of RNA in a sample.

This new partnership will provide COPH students from the USF genomics program with an opportunity to travel to Thailand for an international field experience in drug discovery.

“This partnership with Mahidol University was created to better understand malaria drug resistance in Southeast Asia, the birthplace of artemisinin [an anti-malaria drug] resistance,” noted Dr. John Adams, a Distinguished University Professor specializing in malaria research who helped negotiate the agreement. “We hope this partnership will endure for many years to come.”

Background

The agreement stems from a series of previous collaborations between the COPH’s Adams’ Lab and Mahidol’s Dr. Kesinee Chotivanichthe.

In 2018, the Adams’ Lab published a paper titled “Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis.” The lab was able to insert point mutations (changes to a single nucleotide) within the whole genome of Plasmodium falciparum (one of the species of parasites that causes malaria). This made it possible to screen a wide range of P. falciparum mutants against drugs known to cause resistance in natural infections in order to understand the reason for resistance.

Testing theories

The next step is to test hypotheses on patient isolates exhibiting drug resistance. That’s where the partnership with Mahidol becomes particularly important.

“Resistance to anti-malarial drugs can develop in a region and spread throughout the world,” Adams said. “Dr. Chotivanichthe is studying malaria drug resistance in Thai patients and can provide P. falciparum patient isolates that are able to be screened in the Adams’ Lab. The comparison of known and unknown mutations will help us learn more about drug resistance. By better understanding how this takes place, we can suggest more effective parasite drug targets and also, one day, predict the potential for drug resistance.”

Story by Donna Campisano, USF College of Public Health

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Jyotsna Chawla, an infectious disease researcher working in the USF College of Public Health’s (COPH) Adams Lab, is lead author of the journal article “Targeting Gametocytes of the Malaria Parasite Plasmodium falciparum in a Functional Genomics Era: Next Steps.” She is currently investigating sexual stages of the deadly malaria parasite for her doctoral thesis project.

The article, published in March in the journal Pathogens, was co-authored by fellow COPHers Drs. Jenna Oberstaller, a postdoctoral scholar, and John Adams, a malaria expert, Distinguished USF Health Professor and director of the college’s genomics program.

What was studied

Malaria is a life-threatening disease transmitted to people through the bite of infected female Anopheles mosquitoes. The World Health Organization reported that in 2018, Plasmodium falciparum accounted for 99.7 percent of estimated malaria cases in the WHO African Region, 50 percent of cases in the WHO South-East Asia Region, 71 percent of cases in the Eastern Mediterranean and 65 percent in the Western Pacific.

“When a mosquito bites an individual, the infective forms of the parasite ride in with the saliva and quickly migrate to the liver where they remain dormant for a few days,” explained Chawla, a doctoral candidate in molecular medicine at the Morsani College of Medicine. “Following incubation, thousands of parasites enter the bloodstream where they undergo multiple rounds of division in the red blood cells, exponentially increasing the number of parasites in our body, making us feel very sick. However, not all parasites are asexually dividing and being cleared with antimalarial drugs—these are the non-replicating forms called gametocytes. Gametocytes are picked up during a blood meal and thus provide the crucial link for human-to-vector transmission.”

Chawla’s journal article focused on interrupting Plasmodium falciparum transmission—and, thus, malaria—by targeting gametocytes.

“Weaknesses in parasite biology can be exploited to develop new therapies, but this calls for better tools and techniques,” Chawla said. “Previous work in the Adams Lab achieved a much-needed breakthrough—they used transposons (or what we call jumping DNA elements) to randomly insert itself in the parasite genome, which generated about 38,000 mutants. In my study, I proposed to use the Plasmodium mutants to uncover gametocyte biology of the malaria parasite.”

Implications

Chawla says her research is important because blocking transmission is a critical aspect of the malaria elimination strategy. “It would be ideal to have a multiunit vaccine that targets different stages of the parasite including transmission,” she said. “To get there we must fill the knowledge gaps in the biology of the malaria life cycle.”

“We were able to identify sexual-stage genes and are now working on validating our findings,” Chawla added. “Next, we are gearing to perform a first-ever whole genome sexual-stage screen in Plasmodium falciparum, a study that will scan 5,000 mutants simultaneously. Through these attempts, we anticipate gaining insight into the key pathways and processes essential for sexual development and transmission that can be targeted in the deadly malaria parasite.”

Story by Donna Campisano, USF College of Public Health

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