Category: Notable Grants

Climate-smart (CS) agriculture produces food, fiber, and fuel using less resources, optimizing land-use efficiency, and mitigating pollution of air, water, and soils. Row crops are a major agricultural system in Southeast U.S., covering 4 million acres in FL, GA, and AL. Most of this area (95%) is fallow in the winter after harvesting the summer row crops. There is an opportunity to integrate value-added CS Winter Cropping Systems to generate income and economic development while providing ecosystem services including soil protection from erosion, habitat for pollinators, soil organic carbon sequestration, and reduction of nitrate leaching. Project CHEERS addresses USDA’s priority areas of climate smart agriculture and strengthening bioeconomy. This project will form a hub of diverse stakeholder groups including farmers and various enabling agencies and communities such as Extension professionals, CS commodity industry, federal agencies, and academia to address these objectives: 1. Identify long-term behavioral patterns related to CS Winter Cropping Systems among producers; 2. Analyze farm level economic and environmental trade-offs between current and CS Winter Cropping Systems; 3. Equip multiple stakeholders with decision support platforms to assess farm and regional scale economic and environmental trade-offs between current and CS Winter Cropping Systems; 4. Co-design, co-develop, share, and implement actionable science; 5. Inspire and instruct the next generation. This project will enhance economic outcomes of rural stakeholders, reduce entry barriers for beginning farmers, sustainably intensify agricultural production, and create equitable pathways for the next generation of agricultural professionals to play a vital role in the climate-smart bioeconomy.

Funder: USDA NIFA via the University of Florida

Amount: $1,250,000

PI: Daniel Geller, College of Engineering

Novel technologies for crop improvement are needed to face the global societal and climate change challenges. Apomixis, i.e., asexual reproduction through seeds, is a key enabling technology for plant breeding and seed production. Unfortunately, available apomixis technologies are inefficient and a proof of concept (PoC) is currently limited to maize and rice.

The major goal of the ApoSoy project is to develop robust apomictic breeding and seed production systems for soybean. For this purpose, new genes to engineer the three elements of apomixis (apomeiosis, parthenogenesis and autonomous endosperm) will be identified and evaluated using novel tools in Arabidopsis, Cenchrus spp., tomato and rice. These novel genes and tools can then be used to custom engineer robust apomixis in a broad range of crops. As a PoC, these novel technologies will be introduced into soybean to demonstrate the feasibility of engineering efficient apomixis in a strictly self-fertilizing, dicot crop. Such self-fertilizing dicot crops often have the potential for expression of hybrid vigor when crossed but lack a commercially feasible hybrid production system. In the long-term, apomixis technology will allow (i) clonal seed production, (ii) shorter breeding cycles, (iii) fixation of hybrid vigor, (iv) true seed propagation of vegetative crops, and (v) transgene containment. Moreover, individual elements of apomixis can also be used to facilitate (vi) breeding of Page 1 of 35 ApoSoy – Confidential Application polyploid varieties of diploid crops, (vii) haploid production and reverse breeding, and (viii) artificial seed production.

ApoSoy brings together partners with complementary expertise to develop novel and efficient apomixis technologies and to successfully implement the four-year project, including apomeiosis (Underwood/Ozias-Akins), parthenogenesis (Boutilier/Dresselhaus/Grossniklaus) and autonomous endosperm (Figueiredo/Gehring), as well as a professional project management and communication partner (Rohner).

Funder: Foundation for Food & Agriculture Research

Amount: $659,080

PI: Peggy Ozias-Akins, College of Agricultural and Environmental Sciences

Compound floods (CFs), a combination of hydrologic and coastal flood processes, are a worldwide phenomenon that affects coastal communities within a tropical cyclone’s (TC) path and low-lying urbanized landscapes prone to high tides and extreme rainfall events. CF assessments and their modeling tools have become widely available in recent years (mid-2010s) but have failed to understand the physical interaction between flood drivers, which can lead to better coupling techniques and modeling outputs, such as flood mitigation solutions (FMS). Furthermore, local knowledge (LK) and citizen science have been traditionally overlooked as only inputs in the FMS planning phase and not throughout the entire design process, resulting in a less salient solution for the community. Thus, there is a clear disconnection between CF modeling approaches, LK, and FMS. The overall objective of this project is to integrate and improve current flood modeling techniques with LK concepts to improve the interaction of flood drivers during CF events and include LK as an input variable. At the completion of the proposed research, we will develop a one-of-a-kind modeling framework capable of assessing CF holistically. Moreover, we will produce an adaptable methods handbook to guide future endeavors to include LK and citizen science in any flood modeling framework and co-develop FMS with stakeholders and community members. These outcomes are expected to have an important positive impact on the general flood science community and provide direct and immediate support to the impacted communities in an equitable manner.

Funder: NSF

Amount: $999,732

PI: Felix Santiago Collazo, College of Engineering

This is a standard proposal (SP) to the ECDRE program. We propose to develop a dynamic risk model and climate suitability model based on existing climate data and current observational/experimental data to be generated through these research objectives: (1) document the distribution of HLB and ACP in cold-hardy citrus growing regions of south Georgia, north Florida and east-central California, (2) evaluate preference of ACP to cold-hardy citrus cultivars, (3) determine the titer of CLas in trees following exposure to cold and freezing events, and (4) tolerance and acclimatization in ACP populations to cold and determine underlying mechanisms in the insect’s body to these adaptations. The proposal addresses three priority areas stated by the Citrus Disease Subcommittee (CDS) and ECDRE program: (#2) regional management or eradication of ACP, (#3) predictive models of psyllids movement and dispersal, early detection of HLB, and (#9) greater understanding of the ecology and interactions of the citrus production system and HLB disease complex. Citrus production acreage in areas with cool winter temperatures is increasing and the sustainability of cold-hardy citrus production in parts of California, Florida and Georgia. The lack of scientific studies on the effect of cold on both CLas and ACP populations leaves cold-hardy citrus production in US at risk and must be addressed. Our proposed objectives will provide basic information on the influence of cold on vector and pathogen biology, which would help in developing region-specific risk models to help in decision-making process for effective sampling, surveillance and future expansion of groves.

Funder: USDA NIFA

Amount: $1,121,019

PI: Apurba Barman, College of Agricultural and Environmental Sciences

The bacterial cell envelope is a multi-layered structure that performs a variety of critical functions such as providing protection from physical and chemical insults, including antibiotics. The cell envelope is essential to viability but how cell envelope biogenesis is regulated is poorly understood. Gram-negative bacteria are characterized by a cell envelope with three layers: an inner membrane composed of glycerophospholipids (GPLs), a cell wall made up of peptidoglycan (PG), and an asymmetric outer membrane in which the inner leaflet is comprised of GPLs and the outer leaflet is enriched in lipopolysaccharide (LPS). The biosynthetic pathways responsible for the production of LPS, PG, and GPLs rely on shared precursor pools. Specifically, LPS and GPLs both require acyl-acyl carrier proteins and LPS and PG both require UDP-N-acetylglucosamine. Thus, although it is important that enough LPS, PG, and GPLs are produced to support growth, it is critical that each biosynthetic pathway is tightly controlled to prevent runaway flux that could deplete the shared precursor and indirectly inhibit the production of another essential cell envelope component. Despite the importance of balanced cell envelope biosynthesis, little is known about the regulatory systems that control cell envelope biogenesis outside of classical model systems. Work in my laboratory is focused on identifying and characterizing the various processes that regulate cell envelope biosynthesis in Gram-negative bacteria, with a particular focus on the opportunistic pathogen Pseudomonas aeruginosa. I previously found that, in P. aeruginosa, the LPS and PG biosynthetic pathways are coordinated through a regulatory interaction between their committed enzymes, LpxC and MurA, respectively. Genetically uncoupling LPS and PG biogenesis resulted in measurable phenotypic changes such as loss of viability and alterations to cellular morphology, highlighting the importance of maintaining balanced cell envelope biosynthesis. Current studies in my laboratory have identified additional factors that appear to influence the equilibrium between LPS and PG production, indicating that the regulation of these pathways is multi-faceted. Over the next five years, my group will seek to further clarify the regulation of cell envelope biogenesis in P. aeruginosa using a combination of genetics, biochemistry, cell biology. The goals of this proposal are to (i) dissect the molecular basis of LPS and PG coordination along with the physiological consequences of uncoupling the two pathways, (ii) characterize two novel regulators of cell envelope biogenesis, and (iii) define the array of factors that control LPS, PG, and GPL production in P. aeruginosa. In addition to laying the groundwork for future therapeutic development in an organism infamous for antibiotic resistance, this work has the potential to provide insight into fundamental principles that govern bacterial physiology and cell envelope biosynthesis.

Funder: NIH

Amount: $1,806,485

PI: Katherine Hummels, Franklin College of Arts and Sciences, Department of Microbiology

Neuroinflammation is a key aspect of Parkinson’s Disease (PD) pathology. Extracellular alpha-synuclein (aSyn) aggregates influence immune responses in both the central nervous system (CNS) and periphery. The preformed fibril (PFF) aSyn rodent model of PD effectively mimics many PD features, including dopaminergic cell loss, behavioral deficits, and widespread α-synuclein inclusions. In the PFF α-syn model, PFF α-syn seeds promote endogenous aSyn recruitment, leading to synuclein propagation and neurodegeneration. Neuroinflammation has been confirmed in rats and mice post-PFF α-syn injection, though conflicting reports raise questions about its presence in mice. The study aimed to identify variables affecting inflammatory phenotypes in PFF aSyn mice, including endotoxin (LPS) in aSyn preparation, species-specific aSyn characteristics, and animal facility conditions. In the original study, we found that inflammatory phenotypes were more pronounced in mice with endotoxin-removed PFF aSyn. Species-matched mouse PFF aSyn induced inflammatory phenotypes in non-transgenic wild-type mice. Consistency in inflammatory phenotypes was observed across different facilities, depending on previous results. This supplementary study aimed to further explore inflammatory responses and validate findings, including the role of peripheral immune cells in brain regions with p-aSyn pathology and gliosis. The study’s completion will establish quality control guidelines and profiles of inflammatory factors in PFF aSyn mice.

Funder: Michael J. Fox Foundation

Amount: $259,169

PI: Jae Kyung Lee, College of Veterinary Medicine

Brain tumors are the leading cause of cancer-related deaths among children. Recent studies have identified new subtypes of brain tumors, including high-grade glioma with G34R/V mutations in the histone variant H3.3 (HGG-G34). This subtype primarily affects the cerebral hemispheres of adolescents and young adults. In addition to the histone mutation, HGG-G34 often exhibits mutations in both ATRX and TP53. However, the precise pathogenic mechanism of HGG-G34 remains poorly understood. Currently, there are no established therapeutic approaches tailored to this subtype, and patients continue to face a dismal prognosis. Therefore, there is an urgent clinical need to elucidate the cellular and molecular mechanisms underlying the development of HGG-G34 and to identify new therapeutic targets. To address these knowledge gaps, we have developed a new human embryonic stem cell-based model that allows us to introduce various combinations of mutations into a defined cell population. Using this mode, we have demonstrated that the three core mutations (H3.3G34R, ATRX, and TP53) specifically transform interneuronal progenitors of the ventral forebrain, shedding light on the cellular origin of HGG-G34. We also discovered that H3.3G34R and ATRX mutations cooperatively enhance the expression of DMRTA2, a forebrain-specific transcription factor, which is crucial for the high proliferation of HGG-G34 cells. Additionally, our data indicate that the majority of HGG-G34 cells exhibits characteristics of radial glial (RG) cell, a type of neural/glial progenitor cell that only exists in the developing brain. These findings collectively indicate a dysregulation in developmental programs in HGG-G34. However, the precise molecular mechanisms underlying tumorigenesis, including the transcriptional targets of DMRTA2, the exact role of ATRX mutation, and the maintenance of RG-like state, are still unclear. Additionally, the clinical relevance of RG-like cells in malignant brain tumors has not been fully studied. In this proposal, we aim to unravel the transcriptional targets of DMRTA2 by employing ChIP-seq and assess their involvement in tumorigenesis by loss-of-function experiments (Aim 1). Additionally, we will investigate the interplay between H3.3G34R and ATRX mutations by examining the impact of ATRX mutation on the expression, function, and distribution of DMRTA2 (Aim 2). Furthermore, we will examine the maintenance mechanisms and clinical relevance of RG-like cells through mouse xenograft models and analysis of clinical samples obtained from human patients (Aim 3). Our innovative HGG-G34 model, scientific expertise, and strong local collaborations uniquely position us to achieve these aims. The outcomes of this project are expected to provide novel insights into the tumor biology of HGG-G34 and serve as a foundation for our long-term goal of developing personalized treatment and diagnostic approaches for patients suffering from this devastating disease.

Funder: National Institutes of Health

Amount: $1,676,104

PI: Kosuke Funato, Franklin College of Arts and Sciences, Department of Biochemistry and Molecular Biology

The increasing rise in antibiotic resistance and the diminished discovery of new antimicrobials threatens global healthcare. Of particular concern are Gram-negative pathogens, as these organisms are intrinsically resistant to multiple classes of antibiotics and the discovery of novel drugs targeting these bacteria has remained challenging. The innate resistance of these organisms is provided primarily by their outer membrane (OM), a defining feature of Gram negatives that encapsulates their peptidoglycan layer. Unlike the inner membrane (IM) that is composed solely of glycerophospholipids (GPLs), the OM is asymmetrical with GPLs found in the inner leaflet and lipopolysaccharide (LPS) localized to the outer leaflet. This unique membrane organization affords protection from large polar molecules, as well as lipophilic compounds, creating an impervious barrier. Remarkably, the high-priority Gram-negative pathogen Acinetobacter baumannii can completely inactivate LPS biosynthesis as an alternative mechanism of resistance to the “last-resort” polymyxin antibiotics. The primary objective of this application is to investigate the mechanisms required for maintenance of the cell envelope of A. baumannii, regardless of LPS status. While the benefit of an asymmetric OM relative to a GPL bilayer is apparent due to the impermeable barrier it provides, the lack of LPS essentiality in A. baumannii can be used as a tool to explore novel mechanisms of OM stability in both the presence and absence of LPS. For Aim 1, we will investigate the role of surface lipoproteins that are induced during envelope stress and that are prominent during LPS-deficiency. We will also investigate how these proteins are transported across the OM. Aim 2 focuses on the characterization of two glycosyltransferases required for the tandem transfer of sugars during LPS synthesis, a unique mechanism in the assembly of a bacterial glycoconjugate. Finally, in Aim 3, we will characterize a novel OM cardiolipin synthase and how it impacts OM integrity. An OM cardiolipin synthase challenges current dogma that dictates all major GPLs are synthesized at the cytoplasmic face of the IM. Completion of the Aims will provide novel insights into cell envelope biogenesis and promote the development of novel therapeutics targeting Gram-negative pathogens.

Funder: National Institutes of Health

Amount: $2,696,610

PI: Michael Trent, College of Veterinary Medicine

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This project seeks to answer the question how much fresh (low salinity) water is carried from the Arctic Ocean along the East Greenland Coast into the North Atlantic Ocean and how much this transport may vary as more of the Greenland and Arctic ice sheets melt. For this purpose, an array of six moorings is to be deployed on the Northeast Greenland Shelf to make continuous measurements of temperature, salinity, and current velocities. An exciting new feature of this array includes a variable ballast buoy at the top of one of the moorings, the one closest to the coast, that allows measurements to be made all the way to the ocean surface when the region is ice free, but that prohibits collision of the instruments with sea-ice or icebergs in winter by keeping the mooring line below the ice then. The mooring observations are to be complemented by a modeling study that estimates how the East Greenland Coastal Current evolves over longer time scales. A collaboration with European partners who have a similar mooring array in deeper waters further offshore allows to examine the spatial extent of the current system. Together these efforts will fill a critical gap in our understanding of Arctic-Subarctic exchange, and results will be applicable to a range of scientific fields beyond physical oceanography including climate science, marine biogeochemistry, and fisheries management, among others. The oceanic circulation of the high-latitude North Atlantic is a critical component of our climate system and is potentially sensitive to the release of fresh, surface waters from the Greenland Ice Sheet and the Arctic Ocean. A large gap exists in our monitoring of this freshwater input on the Northeast Greenland Shelf (NEGS). This gap will be filled by measuring the southward-flowing East Greenland Coastal Current (EGCC) on the NEGS for the first time with continuous, direct measurements over an entire year. Based on existing data from summer shipboard sections and satellites, it is hypothesized that the freshwater transport in the EGCC is as strong as the freshwater transport of the better known East Greenland Current (EGC) further offshore at the shelf break. If true, the EGCC would be a major contributor to the total freshwater budget of the Arctic and a key player in Arctic-Subarctic exchange. In addition to the mooring array, it will be analyzed how these data fit into the larger scale NEGS circulation using model simulations, reanalysis products, and satellite data. The new ice-avoiding buoy technology that is to be developed as part of this project has the potential to be widely applicable to a range of environments and is significantly more cost-effective than other similar products. Results from this project will: (1) quantify the volume, heat, and freshwater transports of the EGCC on the NEGS, (2) compare these transports to those of the EGC measured by European partners, (3) identify the physical drivers of transport variability in the EGCC, and (4) assess the long-term variability of the EGCC and its role in the Arctic freshwater budget.

Funder: National Science Foundation

Amount: $3,376,389

PI: Nicholas Foukal, Franklin College of Arts and Sciences, Department of Marine Sciences

Bordetella pertussis (Bp), the causative agent of “whooping cough,” is the most important vaccine-preventable disease and an NIH and CDC high priority. The incidence rates of pertussis have increased over recent years, corresponding to the switch from the whole cell pertussis vaccine (wP) priming and acellular pertussis vaccine (aP) boosting vaccination in the early 2000s, to the current aP-only vaccination. Women given the safer but less effective aP vaccines are a rapidly increasing proportion of birthing mothers, creating a complex transition that we poorly understand and that may have particular risks to the most highly sensitive population, newborns. To protect neonates during the months before they can be fully vaccinated the CDC recommends a cocooning strategy, vaccinating all their potential contacts, creating local “herd immunity” to prevent exposure. This strategy is based on the dated and inaccurate belief that aP vaccines that protect against disease also prevent infection/transmission. In fact, there is growing evidence that aP vaccinated individuals, despite significant antiBp antibody titers, can still be colonized and can transmit Bp to close contacts, including their babies. Another approach, maternal vaccination where antibodies to Bp are transferred via placenta and colostrum/milk to the newborn, although the actual protective effect of antibody transfer is unknown. In fact, the efficacy of maternally transferred antibodies in protecting against colonization or disease has not been determined clinically. Such a clinical study would be challenging and costly and has not been attempted. The experimental evidence indicates that antibodies alone do little to prevent disease. Therefore, we are effectively in the middle of a nationwide test of the differential effects of wP-primed and aP-primed vaccination of mothers on the protection conferred to their offspring without a complete understanding of the likely impact. To address this urgent knowledge gap, we recently developed a novel mouse neonatal experimental infection system that more accurately models the unique features of the human neonatal immune system, enabling us to probe vaccine-induced protection against Bp transferred from mother to offspring. Our exciting preliminary data demonstrate that both the wP and aP maternal vaccinations confer substantial protection to the offspring’s lungs. These results demonstrate that we can measure the profound effects of maternal vaccination on the protection of pups. This approach allows us the specific means to examine the mechanisms of differentially conferred protection, as proposed below. Here we will utilize a combination of innovative immunological techniques to address the central hypothesis that transferred maternal antibodies contribute to protection in neonates via mechanisms we can distinguish using tools unique to the mouse model.

Funder: National Institutes of Health 

Amount: $393,345 

PI: Eric Harvill, College of Veterinary Medicine