8th annual awards ceremony - research.ifas.ufl.edu · cintia leite ribeiro best doctoral...

8th Annual

AWARDS CEREMONY

2015UF/IFASFLORIDA AGRICULTURAL EXPERIMENT STATION

UF/IFAS Awards of Excellence for

GRADUATE RESEARCH

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

2015 UF/IFASEarly Career Scientist

SEED FUNDING

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/IFAS RICHARD L. JONES

NEW FACULTY RESEARCH AWARDEE

UF/IFAS RICHARD L. JONESNEW FACULTY RESEARCH AWARDEE

Dr. Jianping WangAssistant ProfessorAgronomy

2015 UNIVERSITY OF FLORIDA

RESEARCH FOUNDATION PROFESSORS

2015 UF RESEARCH FOUNDATION PROFESSOR

Michelle D. DanylukCitrus Research and Education Center – Lake Alfred Food Science and Human Nutrition


Robert J. Fletcher, Jr.Wildlife Ecology and Conservation


Bin GaoAgricultural and Biological Engineering


Zhenli HeIndian River Research and Education Center – Ft. Pierce Soil and Water Science


Gary F. PeterSchool of Forest Resources and Conservation


José Eduardo P. SantosAnimal Sciences

UF/IFASHigh Impact

RESEARCH PUBLICATIONS

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

UF/IFAS

PLANT PATENTS

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’


Dr. Zhanao DengNovember 26, 2013 In recognition of your outstanding contribution in the development of the Lantana camara plant named ‘UF-T4’


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’


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’


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’


Dr. Rosanna FreyreMay 6, 2014

In recognition of your outstanding contribution in the development of the Ruellia plant named ‘R10-102’


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

UF/IFAS

UTILITY PATENTS

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

Antimicrobial Peptides and Uses Thereof

Zhijian Li and Dennis Gray

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

UF/IFAS

SPECIAL RECOGNITION

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

8th Annual

AWARDS CEREMONY


1,220REFEREED JOURNAL PUBLICATIONS IN 2014

65

UniversityofFloridaGainesville,FL

[email protected]

UniversityofFloridaGainesville,[email protected]

UniversityofFloridaGainesville,FL

[email protected]

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 downregulated 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

8th Annual

AWARDS CEREMONY


8th annual awards ceremony - research.ifas.ufl.edu · cintia leite ribeiro best doctoral...

Documents