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BEST MASTER’S THESISOptimizing Plasticulture Bed Geometries for Enhancing the Sustainability of Vegetable Production
Nathan L. HoltBest Master’s Thesis Agricultural and Biological Engineering
Sanjay ShuklaChair, Supervisory Committee Southwest Florida REC – Immokalee Agricultural and Biological Engineering
BEST DOCTORAL DISSERTATIONMolecular Characterization of Candidate Genes for Quantitative Traits in Populus
Cintia Leite RibeiroBest Doctoral Dissertation Major: Plant Molecular and Cellular Biology Program
Matias KirstChair, Supervisory Committee School of Forest Resources and Conservation
Damian AdamsUnit: School of Forest Resources and Conservation
Title: Assessment of Feasible Forest Water Yield Program Features and Landowner Preferences
Soohyoun AhnUnit: Food Science and Human Nutrition
Title: Detection and Molecular Identification of Viable Shiga Toxin-Producing E.coli (STEC) in Meat by Multiplex DNA Sensor Array System Combined with Nucleic Acid Photo-Labeling
Nikolay BliznyukUnit: Agricultural and Biological Engineering
Title: Novel Methods for Spatio-Temporal Modeling and Inference for Infectious Diseases
Nathan BoydUnit: Horticultural Sciences/ Gulf Coast REC – Balm
Title: Development of Precision Application Technology for Weed Management in Vegetables
John BromfieldUnit: Animal Sciences
Title: Uterine Infection and Immunity: What’s Protecting the Germline from Pathogens?
Samantha BrooksUnit: Animal Sciences
Title: Identification of Heritable Genetic Components Contributing to Cryosurvival in Stallion Sperm
Phillip LancasterUnit: Animal Sciences/ Range Cattle REC – Ona
Title: Metabolic Differences in Growing Heifers and Mature Beef Cows Having Low and High Feed Efficiency
Guodong LiuUnit: Horticultural Sciences
Title: Rapid Identification of Phosphorous-Efficient Genotypes from Tomato Germplasm Banks
Paul MonaghanUnit: Agricultural Education and Communication
Title: Using Social Marketing Research to Understand the Dissemination of Innovations Promoted by Florida Friendly Landscaping Practices
Patricio MunozUnit: Agronomy
Title: Discovering the Molecular Mechanism of 2,4-D Herbicide Resistance
Gulcan OnelUnit: Food and Resource Economics
Title: Creating Sustainable Workforce for Small Fruits and Vegetables Industry in Florida: The Impact of Federal Immigration Programs and Solutions to Labor Shortages
Joshua PattersonUnit: School of Forest Resources and Conservation
Title: Intraspecific Variation in Phenotype and Gamete Compatibility of Caribbean Staghorn Coral Acropora cervicornis
Elizabeth PienaarUnit: Wildlife Ecology and Conservation
Title: Game Ranching in Southern Africa: Can Trophy Hunting Incentivize Conservation and Recovery of Both Game and Non-Game Species on Private Lands?
Paul SarnoskiUnit: Food Sciences and Human Nutrition
Title: Developing Better Processed Tomato Products
Huiping YangUnit: School of Forest Resources and Conservation
Title: Application of Germplasm Cryopreservation for Molluscan Shellfish Aquaculture
2015 UF RESEARCH FOUNDATION PROFESSOR
Michelle D. DanylukCitrus Research and Education Center – Lake Alfred Food Science and Human Nutrition
2015 UF RESEARCH FOUNDATION PROFESSOR
Zhenli HeIndian River Research and Education Center – Ft. Pierce Soil and Water Science
IMPACT ON:
Pest ControlTitle: Effect of Trap Design, Bait Type, and Age on Captures of Drosophila suzukii (Diptera: Drosophilidae) in Berry Crops
Authors: L. E. Iglesias, T. W. Nyoike, and O. E. Liburd
Journal: Journal of Economic Entomology
IMPACT ON:
Air QualityTitle: Reforestation as a Novel Abatement and Compliance Measure for Ground-Level Ozone
Authors: T. Kroeger, F. J. Escobedo, J. L. Hernandez, S. Varela, S. Delphin, J. R. B. Fisher, and J. Waldron
Journal: Proceedings of the National Academy of Sciences of the United States of America (PNAS)
IMPACT ON:
Human HealthTitle: Vitamin B-6 Restriction Reduces the Production of Hydrogen Sulfide and its Biomarkers by the Transsulfuration Pathway in Cultured Human Hepatoma Cells
Authors: B. N. DeRatt, M. A. Ralat, O. Kabil, Y. Y. Chi, R. Banerjee, and J. F. Gregory III
Journal: Journal of Nutrition
IMPACT ON:
Quantifying BiodiversityTitle: Decomposing Biodiversity Data Using the Latent Dirichlet Allocation Model, a Probalisitc Multivariate Statistical Method
Authors: D. Valle, B. Baiser, C. W. Woodall, and R. Chazdon
Journal: Ecology Letters
IMPACT ON:
Virus TransmissionTitle: Transcriptomics of Differential Vector Competence: West Nile Virus Infection in Two Populations of Culex pipiens quinquefasciatus Linked to Ovary Development
Authors: D. Shin, A. Civana, C. Acevedo, and C. T. Smartt
Journal: BMC Genomics
IMPACT ON:
Crop ManagementTitle: Measurement and Modeling of Phosphorous Transport in Shallow Groundwater Environments
Authors: G. S. Hendricks, S. Shukla, T. A. Obreza, and W. G. Harris
Journal: Journal of Contaminant Hydrology
IMPACT ON:
Youth Drug UseTitle: The 4-H Health Rocks! Program in Florida: Outcomes on Youth Tobacco, Alcohol, and Other Substance Abuse Prevention
Authors: M. Kumaran, K. Fogarty, A. Terminello, and W. M. Fung
Journal: Journal of Youth Development
IMPACT ON:
Coral Reef HealthTitle: Members of Native Coral Microbiota Inhibit Glycosidases and Thwart Colonization of Coral Mucus by an Opportunistic Pathogen
Authors: C. J. Krediet, K. B. Ritchie, A. Alagely, and M. Teplitski
Journal: The ISME Journal
IMPACT ON:
Citrus GreeningTitle: Citrus tristeza virus-based RNAi in Citrus Plants Induces Gene Silencing in Diaphorina citri, a Phloem-Sap Sucking Insect Vector of Citrus Greening Disease (Huanglongbing)
Authors: S. Hajeri, N. Killiny, C. El-Mohtar, W. O. Dawson, and S. Gowda
Journal: Journal of Biotechnology
University of Florida UNITED STATES PLANT VARIETY PROTECTION No. 201300199
Drs. Daniel W. Gorbet and Barry L. TillmanSeptember 30, 2013 In recognition of your outstanding contribution in the development of the TUFRunner Brand ‘727’ Peanut
University of FloridaUNITED STATES PLANT VARIETY PROTECTION No. 201200394
Drs. Daniel W. Gorbet and Barry L. TillmanJuly 30, 2013In recognition of your outstanding contributionin the development of the ‘Spain’ Peanut
University of Florida UNITED STATES PLANT PATENT No. PP24,057
Dr. Zhanao DengDecember 3, 2013 In recognition of your outstanding contribution in the development of the Lantana camara plant named ‘UF-T3’
University of Florida UNITED STATES PLANT PATENT No. PP24,043
Dr. Zhanao DengNovember 26, 2013 In recognition of your outstanding contribution in the development of the Lantana camara plant named ‘UF-T4’
University of Florida UNITED STATES PLANT PATENT No. PP24,432
Drs. Zhanao Deng and Brent K. HarbaughMay 6, 2014 In recognition of your outstanding contribution in the development of the Caladium plant named ‘UF-172’
University of Florida UNITED STATES PLANT PATENT No. PP24,327
Drs. Zhanao Deng and Brent K. HarbaughMarch 18, 2014 In recognition of your outstanding contribution in the development of the Caladium plant named ‘UF-48-5’
University of Florida UNITED STATES PLANT PATENT No. PP24,431
Drs. Zhanao Deng and
Brent K. HarbaughMay 6, 2014
In recognition of your outstanding contribution in the development of the Caladium plant named‘UF-18-49’
University of Florida UNITED STATES PLANT PATENT No. PP24,422
Dr. Rosanna FreyreMay 6, 2014
In recognition of your outstanding contribution in the development of the Ruellia plant named ‘R10-102’
University of Florida UNITED STATES PLANT PATENT No. PP24,441
Dr. Donald L. RockwoodMay 13, 2014
In recognition of your outstanding contribution in the development of the Eucalyptus tree named ‘G5’
University of Florida UNITED STATES PLANT VARIETY PROTECTION No. 201000002
Dr. Kenneth H. QuesenberryFebruary 6, 2013
In recognition of your outstanding contribution in the development of the Ocoee ‘UFWC5’ White Clover
UTILITY PATENTS
Increased Stress Tolerance, Yield and Quality Via Glutaredoxin Overexpression
Balasubramani Rathinasabapathi and Sabarinath Sundaram
UTILITY PATENTS
Increased Stress Tolerance and Enhanced Yield in Plants
Balasubramani Rathinasabapathi and Walid Fouad
UTILITY PATENTS
Viral-Based Transient-Expression Vector System for Trees
William Dawson, Svetlana Folimonova and Alexey Folimonova
UTILITY PATENTS
Method and Apparatus for Measuring Gas Transmission Rate of Semi-Barrier Materials
Bruce Welt and Ayman Abdellatief
UTILITY PATENTS
Materials and Methods for Synthesis of a Flavor and Aroma Volatile in Plants
Harry Klee and Denise Tieman
UTILITY PATENTS
Recombinant Host Cells and Medial for Ethanol Production
Brent Wood, Lonnie Ingram, Lorraine Yomano and Sean York
UTILITY PATENTS
Re-Engineering Bacteria for Ethanol Production
Lorraine Yomano, Sean York, Shengde Zhou, Keelnatham Shanmugam and Lonnie Ingram
UTILITY PATENTS
Materials and Methods for Efficient Succinate and Malate Production
Kaemwich Jantama, Mark Haupt, Xueli Zhang, Jonathan Moore, Keelnatham Shanmugam and Lonnie Ingram
UTILITY PATENTS
Semiochemical Reservoir to Attract Subterranean Termites Tunneling in Soil
Nan-Yao Su
UTILITY PATENTS
Method of Inhibition of Enzymatic Browning in Food Using Hypotaurine and Equivalents
Kurt Schulbach and Maurice Marshall
NATIONAL ACADEMY OF SCIENCES
Linda M. BartoshukProfessor Food Science and Human Nutrition Member since 2003
Lonnie O. IngramDistinguished Professor Microbiology and Cell Science Member since 2001
Robert J. CousinsEminent Scholar Food Science and Human Nutrition Member since 2000
James W. JonesDistinguished Professor Agricultural and Biological Engineering Member since 2012
Harry J. KleeEminent Scholar Horticultural Sciences Member since 2012
NATIONAL ACADEMY OF SCIENCES
AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCES (AAAS) FELLOWS
Andrew D. HansonEminent Scholar Horticultural Sciences
Robert J. CousinsEminent Scholar Food Science and Human Nutrition
2015 RESEARCH PROFESSOR EMERITUS
Barry J. BreckeProfessor Emeritus West Florida REC Milton and JayAgronomy
1,220REFEREED JOURNAL PUBLICATIONS IN 2014
65
UniversityofFloridaGainesville,FL
UniversityofFloridaGainesville,[email protected]
UniversityofFloridaGainesville,FL
PolkCountyExtensionUniversityofFlorida
Bartow,[email protected]
LETTER Decomposing biodiversity data using the Latent Dirichlet
Allocation model, a probabilistic multivariate statistical
method
Denis Valle,1* Benjamin Baiser,2
Christopher W. Woodall3 and
Robin Chazdon4
AbstractWe propose a novel multivariate method to analyse biodiversity data based on the Latent Dirich-let Allocation (LDA) model. LDA, a probabilistic model, reduces assemblages to sets of distinctcomponent communities. It produces easily interpretable results, can represent abrupt and gradualchanges in composition, accommodates missing data and allows for coherent estimates of uncer-tainty. We illustrate our method using tree data for the eastern United States and from a tropicalsuccessional chronosequence. The model is able to detect pervasive declines in the oak communityin Minnesota and Indiana, potentially due to fire suppression, increased growing season precipita-tion and herbivory. The chronosequence analysis is able to delineate clear successional trends inspecies composition, while also revealing that site-specific factors significantly impact these succes-sional trajectories. The proposed method provides a means to decompose and track the dynamicsof species assemblages along temporal and spatial gradients, including effects of global changeand forest disturbances.
KeywordsBiodiversity data, cluster analysis, community ecology, Latent Dirichlet Allocation, multivariatestatistics, text-mining.
Ecology Letters (2014)
INTRODUCTION
Multivariate analyses in community ecology were initiallyapplied to vegetation data (Williams & Lambert 1959; Whit-taker 1967) and since have been applied to a broad range ofecological communities from benthic invertebrates (Clarke1993) to microbes (Ramette 2007). While the multivariatetoolbox that community ecologists have utilised includes abreadth of analyses (Gauch 1982; McCune et al. 2002;Borcard et al. 2011; Legendre & Legendre 2012), these toolsdo not always conform to the conceptual models that eco-logists use. For instance, a common conceptual model for var-iation in species abundance posits that a particular set ofspecies might be gradually replaced by another set of speciesalong an environmental gradient, resulting in an intermediatetransition area with a mixed composition (i.e. not dominatedby any given community). Unfortunately, the multivariateclustering methods commonly employed to identify these setsof species (e.g. hierarchical or k-means cluster analysis) arebest suited for abrupt changes in species compositions and failto adequately represent the gradual transitions describedabove.For the first time, we propose the use of a probabilistic
model called Latent Dirichlet Allocation (LDA) for biodiver-sity data. More specifically, when we refer to biodiversity
data, we mean a matrix with the abundance of each species ateach site. This method generates biologically interpretableresults because it decomposes each sampling unit into distinctcomponent communities; and characterises each of thesecomponent communities in terms of the relative abundance ofspecies. Furthermore, the model adequately represents theuncertainty associated with its estimates and properly handlesmissing data. LDA was originally proposed in 2003 for appli-cations involving text-mining (Blei et al. 2003) but over timethis model has become a key tool for the machine learningcommunity, being applied to a wide range of problems suchas fraud detection (Xing & Girolami 2007), digital imageanalysis (Vaduva et al. 2013) and bioinformatics (Liu et al.2010).We start by providing a succinct description of LDA. Then,
we illustrate its use with simulated data and contrast the infer-ence provided by our method with that from standard cluster-ing tools used for the analysis of biodiversity data. Finally, weapply LDA to two real-world applications: spatial and tempo-ral patterns in temperate forest species composition andinferred temporal patterns in secondary Neotropical forestsuccession. These applications illustrate the fresh insights thatcan be gained through the use of LDA. We conclude with adiscussion of the limitations of this method and suggestions oftopics for future research.
1School of Forest Resources and Conservation, University of Florida,
136 Newins-Ziegler Hall, Gainesville, FL, 32611, USA2Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler
Hall, Gainesville, FL, 32611, USA
3United States Forest Service, Northern Research Station, 1992 Folwell
Avenue, St. Paul, MN, 55108, USA4Department of Ecology and Evolutionary Biology, University of Connecticut,
75 N. Eagleville Road Unit 3043, Storrs, CT, 06269-3043, USA
*Correspondence: E-mail: [email protected]
© 2014 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.This is an open access article under the terms of the Creative Commons Attribution License, which permits use,
distribution and reproduction in any medium, provided the original work is properly cited.
Ecology Letters, (2014) doi: 10.1111/ele.12380
RESEARCH ARTICLE Open Access
Transcriptomics of differential vector competence:West Nile virus infection in two populations ofCulex pipiens quinquefasciatus linked to ovarydevelopmentDongyoung Shin, Ayse Civana, Carolina Acevedo and Chelsea T Smartt*
Abstract
Background: Understanding mechanisms that contribute to viral dissemination in mosquito vectors will contributeto our ability to interfere with the transmission of viral pathogens that impact public health. The expression ofgenes in two Culex pipiens quinquefasciatus populations from Florida with known differences in vector competenceto West Nile virus (WNV) were compared using high throughput sequencing.
Results: A total of 15,176 transcripts were combined for comparison of expression differences between the twopopulations and 118 transcripts were differentially expressed (p < 0.05). The fold change in expression of thedifferentially expressed genes ranged from -7.5 – 6.13. The more competent population for WNV (Gainesville) overexpressed 77 genes and down regulated 44 genes, compared with the less competent population for WNV (VeroBeach). Also, splicing analysis identified 3 transcripts with significantly different splice forms between the twopopulations. The functional analysis showed that the largest proportion of transcripts was included in the catalyticactivity and transporter activity groups except for those in the unknown group. Interestingly, the up- regulatedgene set contained most of the catalytic activity function and the down- regulated gene set had a notableproportion of transcripts with transporter activity function. Immune response category was shown in only the downregulated gene set, although those represent a relatively small portion of the function. Several different vitellogeningenes were expressed differentially. Based on the RNAseq data analysis, ovary development was compared acrossthe populations and following WNV infection. There were significant differences among the compared groups.
Conclusions: This study suggests that ovary development is correlated to vector competence in two Culexpopulations in Florida. Both populations control energy allocations to reproduction as a response to WNV. Thisresult provides novel insight into the defense mechanism used by Culex spp. mosquitoes against WNV.
Keywords: Culex pipiens quinquefasciatus, West Nile virus (WNV), High throughput RNA sequencing, Vectorcompetence
* Correspondence: [email protected] Medical Entomology Laboratory, University of Florida, 200 9th St. S.E.,Vero Beach, FL 32962, USA
© 2014 Shin et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the CreativeCommons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, andreproduction in any medium, provided the original work is properly credited. The Creative Commons Public DomainDedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article,unless otherwise stated.
Shin et al. BMC Genomics 2014, 15:513http://www.biomedcentral.com/1471-2164/15/513