Author: orandall

American alligators (Alligator mississippiensis) are managed quite differently than most other fish and wildlife species in the United States. As reptiles, they do not fall within the ‘fur and feathers’ category traditional to state wildlife management, which typically receives the bulk of attention, management, and funding. Despite harvest in aquatic habitats, they are also not considered a fishery and are not managed as such. The unique nature of their status has resulted in comparatively less research and management, contributing to significant uncertainties which can hamper decision making. Such challenges are only exacerbated by paradoxical social views of alligators. They are simultaneously considered a nuisance animal with the capacity to threaten human safety, a species of conservation focus due to previous listing under the Endangered Species Act, and a desired hunted species. In some locations, alligators are a flagship species, integral to the identity and tourism of places like Everglades National Park. Such tradeoffs understandably make decision making difficult, which is only compounded by the lack of information and resources dedicated to alligator management and study. Further research into the status and uncertainties of alligator populations falls squarely within the goal of the State and Tribal Wildlife Grants (SWG) Program—to ensure common species remain common and to prevent species from falling through the cracks. Monitoring and understanding alligator populations is crucial to maintain healthy populations, but also because of their status as an indicator of ecosystem health. Living in a variety of wetland habitats, alligators are both apex predators and ecosystem engineers. Alligator populations are particularly sensitive to environmental changes and overharvesting, making them valuable indicators of ecosystem conditions and the effectiveness of management interventions. Studying these populations, however, presents several challenges. Alligators’ long life spans, which can exceed 60 years in the wild, mean that many individuals will outlive a typical research program, thus limiting our understanding of population dynamics over their lifetimes. Given the benefits of alligators to the ecosystem, hunters’ desire for alligator harvest in Georgia, and the SWG goal to prevent species from becoming endangered, research to gain a better understanding of alligator population size and dynamics is needed to enable Georgia DNR to make harvest management decisions that balance hunter satisfaction and population sustainability. The complex social views and unclear management status of alligators, combined with a long-life history and challenges of field studies, has led to significant uncertainties regarding alligator populations in the Southeast. Improved understanding of alligator populations will support better decision-making on harvest management to prevent overexploitation, while also considering the public desire for tags. The objective of this work is to estimate alligator population size and structure with simulations of various harvest quotas in the state of Georgia. Multiple types of data, collected by Georgia Department of Natural Resources (DNR) over decades, will be synthesized into an integrated population model. The model will be customizable to the type and amount of uncertainty based on available data and information from species experts. Additionally, we will simulate the population under varying harvest levels to test the sensitivity of population to harvest to inform Georgia DNR’s alligator tag allocations. Building on the population model, the second objective is to identify key areas of uncertainty in our knowledge of Georgia alligator populations (e.g., age, location, movement) through value of information analysis (VoI). Such identification will help inform the allocation of research efforts to reduce uncertainty and inform optimal decisions for harvest management. The third objective is to develop an optimal monitoring plan for alligator populations considering limited agency resources. This objective will focus on creating an achievable monitoring plan to inform management decisions for alligators in Georgia under the constraints of limited agency funding and personnel. The plan will integrate the results of the first two objectives to guide monitoring recommendations, while also capturing the limitations associated with on the ground monitoring activities. This research is expected to significantly improve the understanding of alligator populations in Georgia, providing valuable insights for effective harvest management and informed decision-making. By integrating decades of data into an integrated population model (IPM), we will estimate population size and structure and quantify the uncertainty surrounding these estimates. Simulations of varying harvest levels will help inform more accurate harvest quotas, while a value of information (VoI) analysis will guide DNR in prioritizing research efforts to reduce the most critical uncertainties. This work will enhance the ability to balance the need for sustainable harvest management with public demand for alligator tags, ultimately contributing to more informed, evidence-based conservation strategies. Furthermore, the findings will be directly applicable to DNR’s ongoing research program, with recommendations tailored to optimize resource allocation and improve future population monitoring efforts. Broadly, this work will serve as an example of effective estimation for data deficient species and science-driven research guidance.

Funder: Georgia Department of Natural Resources

Amount: $247,824

PI: Kelly Robinson, Warnell School of Forestry and Natural Resources

Fruit ripening is a highly regulated developmental process. From a human diet perspective, fruit are a reservoir of antioxidants and vitamins. Until recently, a few fruits have served as model systems to investigate mechanisms associated with fruit ripening. However, aspects of ripening physiology and their regulation by transcription factors and hormones are fruit-specific, and show substantial variability across fruits. Blueberry production has increased worldwide due to its popularity as a fruit rich in antioxidants. However, ripening physiology is poorly understood in blueberry. Hence, advances in breeding fruit with high quality and development of tools to manipulate ripening and fruit quality have been limited. In this proposal three aims are presented to advance our understanding of blueberry ripening physiology. In Aim 1, we propose to investigate the spatiotemporal dynamics of ripening using analyses of expression of ripening-related genes, metabolite compositions, and hormone concentrations. In Aim 2, we propose to investigate the role of candidate blueberry ripening-related transcription factors. We will functionally validate their roles by overexpression in tomato and blueberry and identify their targets using ChIP-Sequencing in blueberry. In Aim 3, we propose to fill gaps in our understanding of hormonal regulation of blueberry fruit ripening, primarily that of abscisic acid and auxin, and their interactions with ethylene. Collectively, the proposed work will enhance our understanding of blueberry ripening physiology. This knowledge will help improve blueberry productivity and sustainability, and result in an increase in yield and fruit quality.

Funder: USDA NIFA

Amount: $649,992

PI: Savithri Nambeesan, College of Agricultural and Environmental Sciences

The objectives of this project are to:

1. Investigate the mechanisms of pathogenicity of Eimeria field isolates that cause poultry coccidiosis and assess the bird responses to infections. The team will (1) propagate and harvest pure cultures of Eimeria isolates to obtain high quality DNA for generating full genome sequences of Eimeria parasites; (2) test the ability of divergent isolates to induce coccidiosis in commercial birds and measure the differential responses to individual and mixed infections; and (3) study the influence of host genetics on resistance, susceptibility, and tolerance to field Eimeria isolates, in combination with defined environmental conditions that influence the birds’ microbiome and intestinal integrity leading to pathological status and pre-disposition to secondary infections.

2. Identify and characterize the molecular mechanisms of Clostridium perfringens infections resulting in necrotic enteritis and develop effective vaccines. The team will (1) employ next-generation sequencing to fully characterize the genomes of C. perfringens isolates (collected from field cases in the Southeast and mid-Atlantic regions) causing necrotic enteritis and comparatively analyze those sequences to identify virulence factors that contribute to the development of clinical and subclinical enteritis; this will allow a better understanding of the incidence of necrotic enteritis in the context of coccidiosis in commercial poultry; (2) test the effects of those isolates on the pathological and immunological responses of chickens with divergent genetic backgrounds, which could further delineate the differential responses in commercial chicken breeds to aid in identifying and using species genetics in commercial operations; (3) use the identified virulence factors as targets for designing and developing vaccines (based on already established nanoparticle platforms) as alternative measures to antibiotics for controlling enteritis.

3. Test and determine effective non-drug alternatives to antibiotics for the prevention and treatment of coccidiosis and necrotic enteritis. For Objective 3, there is an impetus to find effective non-drug alternatives, and the team will employ an integrated approach involving applied studies to better understand the mechanistic actions of several alternative candidates on performance, physiological, microbial, immunological, and metabolic responses of the host. In vivo (birds) and in ovo (late-stage embryos) trials will investigate the applications of well-defined probiotics, prebiotics, postbiotics, and phytogenics during coccidiosis and necrotic enteritis to characterize these critical physiological changes that directly impact bird health and performance. Specific measurable variables at the enteric and systemic levels will collectively provide strong host response correlates that can be utilized in translational studies to refine the applications of such effective alternatives in commercial settings.

Funder: USDA ARS

Amount: $728,944

PI: Todd Applegate, College of Agricultural and Environmental Sciences

Global forests are increasingly at risk from multiple, synergistic stressors, threatening both timber production and ecosystem services. While trade-offs between productivity and resilience are well-documented, studies investigating belowground stress response mechanisms are limited, particularly for long-lived tree species. Furthermore, the genetic basis of these traits and the degree to which genetic co-associations may constrain adaptation and limit genomic selection in tree breeding programs is unknown. The goal of this project is to assess productivity-resilience tradeoffs under the combined effects of drought, fire, and pathogen stress across southern yellow pine species. We address these knowledge gaps with the following objectives. (1) Assess coordinated, whole tree productivity and functional trait responses to multiple stressors (drought, brown spot needle blight, and fire). (2) Identify genetic associations with stress response mechanisms, and test for evolutionary constraints between productivity and resilience traits using genetic co-association networks. (3) Develop multi-trait genomic prediction models to identify optimal targets for genomic selection and tree breeding programs. (4) Work with pine breeding cooperative partners to develop performance rating sheets to assist landowners, forestry and restoration practitioners in selecting seed stock that meets their goals along the productivity-resilience spectrum. This project is directly aligned with the program priorities of improving the sustainable management of forests under the threats of climate change, pathogens, and increased environmental pressures. Findings will provide critical information to optimize seed selection, enhance the success of forest restoration, and support tree breeding programs in improving forest sustainability in a rapidly changing world.

Funder: USDA NIFA

Amount: $749,038

PI: Helen Bothwell, Warnell School of Forestry and Natural Resources

The Penn School for Culture and Community is in the first instance a partnership between the Penn Center National Historic Landmark District and the University of Georgia’s Willson Center for Humanities & Arts. This partnership has led to a series of other collaborations, with other institutions, communities, and foundations. These have intersected in turn with a growing national and international interest in the Penn Center and in the island of St. Helena, including the recognition of the Penn Center as one of only four places nationally in the new UNESCO network of global sites of the memory of enslavement and the transatlantic slave trade. Along with Atlanta’s “Sweet Auburn” (Auburn Avenue) National Historic Landmark District, Penn Center is also one of only two National Historic Landmark Districts in the entire country that center the history and heritage of African American communities. Uniquely as a project connected to the diasporic power of Gullah Geechee communities, all our programming is tied to this singularly important space and the history and legacies that have emanated from it since its founding in 1862 as one of the first schools in the South by and for formerly enslaved Black communities. What began four years ago as a project to create student residencies to conduct research, engage in hands-on workshops and community service, and learn in place at the Penn Center has become a model and a movement. Our focus on critically (re)examining the complex histories of slavery, Reconstruction, and Gullah Geechee culture is not just important, it’s crucial for renewing democracy. We have learned a great deal together about the culture, history, art, architecture, music, foodways, conservation, and literature of coastal and island Gullah Geechee communities and about the relationships between these Gullah Geechee communities and the mainland. Our proposal for a second phase of funding is focused on institutionalizing our evolving relationships, which are now national and international in scope, into a defined program that other institutions, communities, and foundations can access and contribute to sustainably and equitably. This work grows organically. During the past three years of these residencies, in addition to attracting humanities, arts, media, and social sciences students and faculty from our official partner colleges and universities, including HBCUs in South Carolina, North Carolina, and Georgia, we have welcomed two hundred and fifty students from eighteen higher learning institutions. Many of these students and faculty are now engaging in ongoing initiatives outside of the spring residency week. For instance, Architecture and Design students from the Georgia Institute of Technology are assisting Penn Center in modeling and mapping projects to develop sustainability planning, while University of Georgia Art, Public History, and African American Studies students have participated in independent study projects on St. Helena Island, such as creating a digital inventory and co-composing exhibition booklets connected to the holdings of Penn Center’s York W. Bailey Museum and Penn Center’s archives in the University of North Carolina at Chapel Hill’s Southern Historical Collection. The dynamic collaborations between Penn Center and these wide-ranging programs have established a foundation for cultivating diverse, interdisciplinary, and cross-institutional projects in future years. By modeling the next phase of the student residencies on the idea of a school, we are responding to and advancing Penn Center’s original, unbroken mission to focus on education, civic engagement, the protection of land and water, and the preservation of Gullah Geechee history and culture. The Penn School for Culture and Community is modeled on Penn Center’s ongoing and unwavering emphasis, as it enters its 163rd year, on framing education as a process that is multigenerational, multidisciplinary, cross-institutional, and joy-filled. It is in keeping with this spirit that we have begun to call students who attend each residency ‘Penn Scholars’ (which the students love). This naming will instill them with a sense of purpose and achievement, as well as connect them directly to former graduates of the nineteenth and twentieth centuries who were addressed as such by the teachers and staff during the eighty-six years that Penn Center was known as Penn School. Our proposed naming therefore speaks to our commitment to sustainability and continuity, in that we will undertake to build a sense of the students as being Penn Center alumni with lifelong contributions to make to this place, especially since so many of them have returned voluntarily after their first spring residency to work on capstone research, thesis, or service projects at other times during the calendar year.

Funder: Andrew W. Mellon Foundation

Amount: $1 million

PI: Nicholas Allen, Franklin College of Arts and Sciences, Department of English; Willson Center for Humanities & Arts

This proposal spans three years with combined efforts from three universities representing three states in the Eastern region (University of Georgia, Auburn University, and Clemson University). This proposal addresses USDA Strategic Plan priority areas by providing opportunities for American agriculture producers to be competitive in the marketplace, provide a safe, nutritious food product, and expand economic development in rural America. The addition of alfalfa in the Southern region meets USDA Science and Research Strategy Priority of cultivating a resilient ecosystem. Further, this proposal supports the development of improved alfalfa forage and seed production systems by aligning with priority areas 1, 2, and 3, specifically in that it will increase alfalfa forage production (30%), improve alfalfa forage systems to optimize economic returns to alfalfa producers and end-users (livestock producers)(30%), and support marketing as a livestock feed in the region represented (30%). An additional outcome of this work will be the ability to quantify and estimate carbon sequestration benefits when annual crop acreage is transitioned to alfalfa as perennial cover-crop option addressing priority 6 (10%). Specifically, the research and Extension approaches described 1) will quantify performance expectations of growing beef animals utilizing alfalfa as a primary feed source, 2) evaluate economic benefits using alfalfa in the region, and 3) expand education efforts of alfalfa integration in the South to intensify system resilience and sustainable forage production and expand knowledge base beyond field technicians to point of sale contacts in the region.

Funder: USDA NIFA 

Amount: $750,024 

PI: Jennifer Tucker, College of Agricultural and Environmental Sciences 

Climate change is causing unpredictable and severe winter weather, which can devastate wheat crops in major growing regions like Europe, North America, and China. Sudden cold snaps or warm spells during winter can reduce wheat yields by up to 50%, posing a major challenge for farmers and food production worldwide. Wheat, like many staple crops, has a complex genome with multiple copies of each gene, which can sometimes help plants adapt to stress but also complicates breeding efforts. Traditional methods for improving wheat’s cold tolerance rely on field tests, but as cold events become less predictable, this approach is becoming unreliable. To address this, we are using cutting-edge tools to uncover hidden genetic traits that could improve wheat’s ability to survive cold temperatures. Our project will take a closer look at how individual cells in wheat respond to cold, focusing on understanding how specific genes are activated or silenced. By combining advanced single-cell genomics and artificial intelligence (AI) models, we aim to pinpoint the genetic “switches” that help wheat tolerate freezing temperatures. In collaboration with a leading European wheat breeding company, we will test these findings in controlled environments and real-world fields. The ultimate goal is to identify new genetic markers that can quickly be used in breeding programs to develop wheat varieties that are more resilient to extreme cold. Beyond wheat, our research will create a framework for improving other important crops with complex genomes, helping agriculture adapt to the challenges of a changing climate and ensuring more stable food production for the future.

Funder: USDA NIFA 

Amount: $800,000 

PI: Robert Schmitz, Franklin College of Arts and Sciences, Department of Genetics 

Cultivated peanut has an exceptionally narrow genetic base. This imposes limitations on the improvements that can be made by breeding with peanuts of pure pedigree, in particular with regard to pest and disease resistance. Here we propose to continue the work of incorporation of new pest and disease resistances from wild species into agronomically elite peanut lines from the Southeast of the USA. The work is based on advanced progeny from complex crosses between elite lines and wild species. We propose to use the advanced genetic tools that have been developed in the wake of the peanut genome project. The tracking of wild chromosome segments greatly aids in overcoming linkage drag and provides the foundation of knowledge needed for the development of dedicated, small-scale, parallel marker assays to aid selection in breeding programs. Targets of the proposed work are new, very strong sources of resistance to late leaf spot, early leaf spot, rust, and root-knot nematode.

Funder: Mars, Incorporated 

Amount: $1,187,502 

PI: David Bertioli, College of Agricultural and Environmental Sciences 

Plants supply essential nutrients, fibers, and pharmaceuticals vital for human survival, and raw materials for numerous industries, including bioenergy, which supports jobs and drives economic development. Glycosyltransferases (GTs) catalyze the formation of glycosidic linkages to produce complex carbohydrates, which are highly abundant in all plants. This project will use high-throughput (HTP) biochemical, biophysical, and computational biology approaches to study carbohydrate metabolic processes in Sorghum bicolor, a platform energy crop. The integrated biochemical and biophysical data will enable the development of data-driven artificial intelligence and machine learning (AI/ML) computational tools to expand and accelerate functional prediction of plant gene products, efficiently linking genome sequence with gene function. The proposed research using S. bicolor as a model will provide functional information that can be extrapolated to decipher beneficial multigene traits across diverse plant species. The resulting foundational knowledge will drive innovation in the emerging bioeconomy, support US economic resilience, and advance initiatives focused on increased energy security.

Funder: U.S. Department of Energy 

Amount: $1,915,000 

PI: Breeanna Urbanowicz, Franklin College of Arts and Sciences, Department of Biochemistry and Molecular Biology 

Campylobacter jejuni is a major cause of bacterial-induced diarrhea worldwide. Infection leads to high rates of morbidity and mortality in low-and-middle income countries (LMICs), particularly in young children where up to 85% of infants are C. jejuni stool positive by one year of age. Also, post-infectious complications such as GuillainBarré syndrome, irritable bowel syndrome, reactive arthritis, and environmental enteric dysfunction (EED) are increasingly reported. EED is a subclinical chronic disorder resulting from improper nutrient absorption, intestinal injury and prolonged inflammation that leads to growth stunting, impaired cognitive development, and further complications. In parallel, campylobacters continue to show increasing rates of fluoroquinolone resistance, particularly ciprofloxacin, and are thus high priority pathogens for new antimicrobial development. Through genomics studies examining Campylobacter infection profiles in seven sites in sub-Saharan African and South Asia, we discovered that exclusively breastfed infants showed a significantly higher abundance of C. jejuni in their stools compared to non-breastfed infants, and that breastfed infants were predominantly colonized with asaccharolytic (non-carbohydrate metabolizing) strains of C. jejuni while infection with fucose-metabolizing campylobacters was less frequent. While examining the mechanism behind this selection, we discovered that human breastmilk is unexpectedly toxic to C. jejuni. This finding was confirmed using 5 different isolates and 5 independent breastmilk donor samples. Through directed evolution studies, we isolated C. jejuni strains resistant to breastmilk and demonstrated that the milk bioactive agents were derived from proteins and lipids. This study will investigate how components of human breastmilk can suppress the survival of C. jejuni, and in turn will explore how C. jejuni can develop resistance to those components. The specific aims of this project are to identify the bactericidal lipids and antimicrobial peptides within a pooled collection of human breastmilk, then characterize the mechanisms by which C. jejuni can become resistant to these components, and subsequently test how the identified C. jejuni mutations and toxic milk components impact bacterial colonization in a mouse model of C. jejuni-induced EED. Completion of these aims will fill major gaps in our understanding of EED development and how breastmilk components influence C. jejuni colonization. This study may also identify novel treatments to prevent colonization with this pathogen to reduce the burden of disease and mortality.

Funder: NIH 

Amount: $2,731,162 

PI: Christine Szymanski, Franklin College of Arts and Sciences, Department of Microbiology