College of Liberal Arts and Sciences Chemistry

13396

Global population genetic diversity and phylogenetic analysis of Phytophthora palmivora

The pace of disease emergence has been accelerated by significant climate change and dense global trade, due to their introduction into new areas with susceptible hosts or the spread of new detrimental pathogen genotypes. The Phytophthora palmivora is a pathogen with recent reports of invasions, significantly affecting economical plants in tropics and subtropics. However, its origin and past migration pattern remained unclear and the source areas of newly spreading lineages were still unknown. This information is critical to understand the scheme of current invasions and forecast the future spread, and more generally develop plant breeding programs to control this pathogen. We analyzed a set of worldwide representative isolates of P. palmivora and inferred the Southeastern Asia should be the center of origin of this pathogen. We also demonstrate the impact of human activities on the recent long-distance diffusion of the disease. (Flesh-Kincaid Grade Level: 16.2)

13392

Liberibacter and psyllid derived proteins bind Candidatus L. asiaticus bacteriophage late gene promoter

Candidatus Liberibacter asiaticus (Las) is the causal agent of Huanglongbing, a devastating disease that threatens citrus production worldwide. Las is unculturable in vitro, which has severely hampered research progress. The bacterium carries viruses that are latent in infected citrus and the insect vector, the psyllid. We have characterized genes from these viruses, including the holin, which degrades the bacterial membrane. We constructed a reporter system that carries the regulatory sequences of the holin, which would control when the gene is transcribed, fused to a fluorescent reporter, and moved this construct into L. crescens, the closest culturable relative to Las. Surprisingly, the cells fluoresced, indicating that the holin would be “on”. Crude extracts from the psyllid suppressed the fluorescence. This psyllid derived suppressor was deactivated by protein degrading enzymes, indicating the suppressor was a protein. To prove specific binding of this protein to the regulatory DNA, the protein was mixed with the DNA and run through a gel, a molecular sieve used to separate proteins and DNA by size. Because smaller molecules will move faster through the gel, if the protein bound the DNA fragment, the complex would shift upward. When the protein DNA mixture was applied to the gel adjacent to the free DNA, the complex shifted upward, indicating specific binding. The attempts to culture Las may have failed due to the activity of this gene. The identification of the insect derived suppressor protein, and addition to bacterial media, may allow Las to be cultured. Furthermore, because the activity of this gene alone is sufficient to kill the host cell, the identification of a small molecule that activates this gene may lead to a new disease control scheme. (Flesh-Kincaid Grade Level: 13)

13372

What is the relative importance of different life-history stages in intra- and inter-population responses to disturbance? Tests with a long-lived keystone herbivore in Neotropical savannas

Longevity is an important characteristic of most plant and animal species. Whether an individual from a given species lives for a few days, months or multiple years can be determinant for how it interacts with its surroundings. Thus, understanding the average importance of each life stage to the growth of populations of long-lived species is key to our comprehension of their potential interactions with a changing environment. We usually take into account longevity for large trees or vertebrates, but it can be just as important for insects. For instance, colonies of Atta leaf-cutter ants can live up to 20 years, longer than many plants and large vertebrates. These insects have been reported to favor disturbed habitats such as road vicinities during establishment of their colonies as well as having high adult densities in these habitats. This study aimed to determine 1) the importance of each life phase to the overall abundance of these ants in road habitats and 2) if this pattern is identifiable over multiple populations and locations. We found that populations were growing approximately 80% faster near roads due to the higher success of early life stages, and that this pattern could be identified across multiple populations of two leaf-cutter ant species. These species are fundamental to the ecological functioning of their habitats but can be also major crop pests throughout their domain, and our results highlight the importance of understanding their reproduction and early life performance to regulate their populations more effectively in ecological and agricultural settings. (Flesh-Kincaid Grade Level: 17.5)

13351

Discovering New Physics with Voronoi Tessellations

Over the last 100 years a dramatic revolution has been happened in our picture of the Universe at smallest scale. We have established experimentally the basic framework of particle physics, the standard Model which in turn can explain the observed phenomenon and matter content of the Universe since the Big Bang. But still, there are few fundamental problems that seek solution. Most importantly, the very high mass value secret of the particles -10,000,000,000,0000 order larger than heaviest particle, mystery of dark matter and dark energy. There are some new physics models that can provide solution to those existing problems very elegant way - Supersymmetry, Extra Dimension. Now our job is to look for those new physics at Hadron Colliders. As being a particle physics phenomenologist I am working on experimental data collected from Large Hadron Collider (CERN) events. My recent work named 'Edge detection on Voronoi tessellation' is based upon computational geometry and new in particle physics sector. This method will allow us to study properties of new particles mass, lifetime and other properties. Our method not only can predict the Supersymmetric particle but also provide a possible way to dark matter search. Our paper illustrates several toy examples and some specific Supersymmetry channels- a nice way to hunt for new physics. We have a made a code based on Python programming language which will be made public. (Flesh-Kincaid Grade Level: 13.3)

13282

A methodological framework to assess the influence of land-use/land cover change on ecosystem services in an urban watershed

This project examined how ecosystem services are affected by land-use/land cover change. Ecosystem services are all of the benefits that society receives from nature. Examples include food and material resources, water purification, shade, and recreation among others. Land-use/land cover change happens when what is on a piece of land, or the way the land is used, changes over time. For example, if a forest is cut down to build a mall, this is a change in land-use/land cover. An abandoned farm that floods over time, turning into a pond, is another example. This project specifically addressed how land-use/land cover change in the urban Tampa Bay area affects carbon storage, another ecosystem service. Trees remove carbon from the atmosphere and store it in their wood. When trees are cut down, this carbon is often released back to the atmosphere as carbon dioxide (CO2). Further, we now have fewer trees to continue removing CO2 from the air. CO2 is the direct cause of global climate change. In urban areas, land-use/land cover change occurs rapidly and this, along with a greater use of fossil fuels, means that urban areas are one of the most significant sources of atmospheric CO2. Understanding the impact of land-use/land cover change in urban areas is as an important piece of a larger puzzle that must be solved for society to deal with global climate change. (Flesh-Kincaid Grade Level: 11.6)

13251

An Analysis of Historical Freeze Events and Determination of Blueberry and Peach Critical Bud Temperatures to Aid Growers in Freeze-related Risk Assessments

Freezing temperatures are the most devastating weather-related source of fruit loss for Florida’s blueberry and peach farmers. Although blueberry and peach cultivation has increased in size and economic importance in Florida, growers still lack basic information critical to their decision-making if the temperature drops below freezing. Farmers have a number of strategies that they can use to protect sensitive flower buds and blossoms if it freezes such as coating the plants with a layer of ice to keep tissue temperatures at 32F. Therefore, in order to provide farmers with more accurate information about the temperature at which these freeze protection strategies are necessary, I am using two different methods to determine the temperatures at which peach and blueberry buds and flowers are killed by freezing. The first method uses a programmable freezer to control the rate of cooling with samples removed at intervals from 0C to -27C. Following this controlled freeze test, buds were dissected to determine whether the tissue was living or dead. The percentage of living buds is then used to calculate the bud mortality rate at a range of temperatures. The second method, measures the temperature differential between the buds and a known constant to determine the temperature at which water freezes within the bud, representing the lethal temperature. Analysis of preliminary results from freezing tests conducted in a programmable cooling unit in January and February 2015 found that cold hardiness decreases as buds progress through their developmental stages, with full bloom and petal fall being the least cold hardy. These results will be coupled with analysis of historical weather patterns classifying freeze temperatures to ultimately be used to create a new weather alert tool to give precise, data-driven recommendations for freeze strategies. (Flesh-Kincaid Grade Level: 17.1)

13241

Performance of two southern highbush blueberry cultivars grafted onto Vaccinium arboretum

Blueberry (Vaccinium spp.) has gained popularity worldwide due, in part, to its health benefits, such as antioxidant properties that help scavenge free radicals. World blueberry production has increased in the last years from 127,000 tons in 1991 to 356,000 tons in 2011. This increase in production is linked to the expansion of the harvested area, which increased from 46,000 ha to 81,000 ha during the same period. However, significant soil amendments are required for blueberry production. The high cost of amendments and the desire to move towards more sustainable production systems are, nowadays, an obstacle to expansion of the industry. In order to reduce soil amendments, new production techniques are required. Grafted plants may be an option, since this technique is widely used in several other fruit crops to improve fruit quality, reduce incidence of diseases, and tolerate specific soil conditions. Due to its wide soil adaptation, Vaccinium arboreum has the potential to be used as a rootstock to improve the expansion of blueberry production to soils with higher pH and low organic matter. This research focused on test two different southern highbush blueberry cultivars, ‘Farthing’ and ‘Meadowlark’, grown on amended or non-amended soil, and own-rooted or grafted onto V. arboreum, to assess their performance in the field. Different parameters were evaluated, i.e: canopy volume, berry yield, and fruit quality (total titratable acidity and total soluble solids). As result, grafted plants had a delay growth and fruit yield when comparing with own-rooted plants in the first years of the experiment, however, in the fourth year, plants reached the same size and yield. No significant differences were found for fruit quality. If these results hold true for the next years, the profitability and sustainability of the blueberry industry will be increased. (Flesh-Kincaid Grade Level: 12.3)

13222

Genome-wide binding sites identification of a GntR transcriptional regulator required for virulence in Xanthomonas citri subsp. citri Citrus canker is a devastating disease affecting citrus industry worldwide. Less mechanisms are known regarding to disease development and regulation. Here, we identified a GntR transcriptional regulator that is essential for citrus canker induction in Xanthomonas citri, the causal agent of citrus canker. Transcription factors are proteins that can bind to certain DNA motif at promotor region and manipulate the gene expression at transcriptional level. We have identified the GntR binding motif and demonstrate that DNA binding is required for canker development. We will keep analyzing the function of GntR down-stream target. (Flesh-Kincaid Grade Level: 12.8)

13205

College of Public Health and Health Professions - Public Health (Ph.D. - Social and Behavioral Sciences)

Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the third leading cause of cancer death, yet less than 60% of Americans between 50-75 years of age receive routine screening. The American College of Gastroenterology and the National Cancer Institute consider colonoscopy to be the most sensitive screening measure for the detection of colorectal polyps and the prevention of CRC. Many studies have tested interventions to increase colonoscopy screening, however the overall effectiveness of these interventions is unknown. Thus, this study was a systematic review and meta-analysis of behavioral-based interventions to increase colonoscopy screening. In order to be included in the review, studies needed to have tested the interventions using a randomized controlled trial design and all participants needed to be at least 50 years of age (i.e., the recommended age for screening). Each study was evaluated for methodological quality using the PEDro scale, which resulted in 14 studies included in the meta-analysis. Interventions were grouped by type: mail-based, phone-based and interactive. Additionally, subgroup analyses were conducted for studies that included high-risk populations for colorectal cancer. Phone-based interventions which served as a reminder system and subsequently allowed patients to ask questions regarding different screening modalities were shown to have a significant overall effect. Additionally, interventions conducted on high risk populations (regardless of the intervention type) were shown to be the most effective regardless of the nature of the intervention. These results suggest that programs aimed at the primary prevention of CRC should focus on those individuals who are at a higher risk. (Flesh-Kincaid Grade Level: 15.5)

13189

College of Agricultural and Life Sciences - Horticultural Sciences

The University of Florida has been breeding blueberries adapted to the southern subtropical climate for over 50 years. Recently, the breeding program has placed an emphasis on breeding blueberries with improved flavor. Flavor is a complex biological reaction in response to a variety of compounds present in blueberry fruit, and this experience can vary greatly from person to person. To understand what makes a blueberry taste good, 19 different blueberry types were tested in flavor panels over the course of three years. The compounds affecting flavor (sugars, acids, and volatile aroma compounds) in these blueberries were also measured. The overall liking of blueberry samples was positively related to favorable blueberry texture, sweetness, and flavor intensity. Overall liking was negatively correlated to sourness of the blueberry sample. The sweetness ratings of blueberry samples correlated positively with measures of sugars, and negatively with measures of blueberry acidity. A complex statistical model was also created to reveal the impacts of a number of volatile aroma compounds on the blueberry flavor experience as well. (Flesh-Kincaid Grade Level: 14.6)

13178

College of Agricultural and Life Sciences - Horticultural Sciences

Brassica carinata, also known as Ethiopian mustard, is increasingly being sought after as an non-edible and economic crop in North America due to its high seed oil content and favorable fatty acid profile for use as a jet biofuel. They produce a a chemical called glucosinolates (GSL) in which an enzyme breaksdown into a more toxic form (mainly isothiocyanate, ITC) to function as a defensive mechanism and protect the plant against herbivory and disease. GSL content as well as enzyme activity affects the persistence of these compounds after the plant residue is tilled into the soil. Studies have shown that certain soil-borne diseases are being suppressed long after the active compounds are no longer detected suggesting the importance of enriching for certain microbial and fungal communities as a means for crop protection. The types and quantities of GSL vary with Brassica species, plant organ, growth stage, and soil environment. Although, there are many studies involving GSL from Brassica species, little information exist for B. carinata and how it affects the soil microbial and fungal communities. In this study, we examined GSL production of B. carinata in the leaves, stem, roots, and seeds at different growth stages and using different soil types. In addition, we also look at the enzyme activity in B. carinata and in the soil environment. GSL and ITC affected the microbial community in the rhizosphere of B. carinata as well as at various times after soil incorporation of plant residue. To decrease the persistence of GSL/ITC in soils that lack enzymatic activity, we evaluated the potential use of Pseudomonas putida, commonly used for bioremediation. The results of this study will help to mitigate the use of synthetic pesticides, maintain a healthy soil environment and ultimately reduce the need for non-renewable petroleum based fuel. (Flesh-Kincaid Grade Level: 13.8)

13164

College of Agricultural and Life Sciences - Agronomy

13163

Efficacy of a 1,3-Dichloropropene and Chloropicrin Mixture Used with Totally Impermeable Film for Nutsedge Control

Because of the ban on the use of Methyl Bromide, a widely used fumigant in plasticulture vegetable production, the need for alternative fumigants is especially high. Fumigants are used in conjunction with plastic films to hold the fumigant in the ground. Totally impermeable film holds fumigant in the ground longer, leading to lower fumigant rates, better control of recalcitrant weeds, and lower production costs. My research focuses on using a mixture of 1,3-dichloropropene and chloropicrin in conjunction with totally impermeable film and virtually impermeable film (standard film) for the control of nutsedge species. Initial results show that using TIF increases the retention of fumigant compared to VIF. Implementing TIF with 224 kg/ha of 1,3-D:Pic significantly improved nutsedge control compared to a higher rate of 280 kg/ha with VIF. (Flesh-Kincaid Grade Level: 13.5)

13162

House Sparrow Declines in North Central Florida

"House Sparrows are native to Europe, and were once considered very invasive in North America. A few decades after their introduction to North America, the House Sparrow colonized much of the continent, and in very large numbers. Now, the House Sparrow has been practically extirpated from our farms and rural lands, unsurprisingly, as our farmers have gotten better at storing and harvesting grains. However, the House Sparrow is not doing well in our urban areas and we don't know why. North American researchers have given little attention to their declines on our continent, especially compared to European research (where the House Sparrow is native).

The objectives of this study were to (i) understand how House Sparrows are currently distributed in residential and commercial areas, (ii) determine what habitat characteristics affect where House Sparrows are and (iii) determine if the presence of other birds in urban areas is associated with the presence of House Sparrows. This study confirmed that House Sparrows are no longer present in the backyards of Gainesville, FL and that they are no longer a common sight in urban areas (near our restaurants, shopping malls, etc). House Sparrow decline in urban areas may be a precursor sign to the health of our cities/ (Flesh-Kincaid Grade Level: 15.7)"

13159

College of Agricultural and Life Sciences - Plant Pathology

Strawberry is a specialty crop with a high value in Florida market. However, strawberries can be affected by diseases in the field that can decrease its production and the grower’s economic profit. One of the most important diseases of strawberries is gray mold, caused by Botrytis cinerea, a fungus with a wide host range. This fungus produces its reproduction structures (spores) rapidly and is controlled with a large amount of fungicide sprays that can lead to fungal resistance. The common test used to determine resistance to fungicide evaluates the spore germination; however, this test is time and space consuming, and its measurements are subjective. Our objective was to adapt a resazurin-based assay to evaluate B. cinerea sensitivity to two fungicides. Resazurin is a non-toxic dye that indicates the activity of the cell by a chemical reaction of reduction that changes the color of the dye from blue to pink. Our findings suggest that this rapid and reliable technique can be used on a large scale to assess the sensitivity of B. cinerea to fungicides, giving the growers a faster report for disease management. (Flesh-Kincaid Grade Level: 13.6)