SRE Participants

Our 2016 teacher fellows and their host laboratories

Fellow Lab host
Renae Allen

Union County High School

 

Susan Chabot

Lemon Bay High School

Jorg Bungert, PhD

Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine

The focus of our laboratory is to analyze mechanisms regulating gene expression during erythroid cell differentiation. The beta-globin genes are regulated by a locus control region (LCR). The LCR is composed of several DNase I hypersensitive (HS) sites that together mediate chromatin structure alterations and high-level transcription throughout erythroid development. The human beta-globin gene locus consists of five genes that are expressed in a developmental stage specific manner in erythroid cells. During development the different proteins encoded by the beta-globin gene locus (ε, Aγ, Gγ, δ, and βglobin) dimerize with a-globin subunits to form hemoglobin. The beta-type globin genes are expressed at extremely high levels in erythroid cells which is mediated by the LCR.

Results from our previous work suggest that the individual LCR HS elements interact to generate a higher order structure, referred to as the LCR holocomplex, and that this complex communicates in a stage-specific manner with individual globin genes. We also found that the LCR recruits transcription complexes and proposed that the LCR serves as the primary site of transcription complex recruitment and assembly in the beta-globin gene locus. We use transgenic mice and cell culture to identify and functionally characterize cis-regulatory DNA elements and trans-acting components involved in the regulation of the beta-globin genes. We utilize artificial DNA binding domains to modulate and characterize the function of transcription factor binding sites in the beta-globin gene locus. We also use a variety of molecular techniques, including chromatin immunoprecipitation (ChIP), ChIP-sequencing, shRNA mediated knockdown, and overexpression of dominant negative transcription factors to analyze transcription factor function and globin gene regulation.

Charlynn Campbell

Clay High School

 

Amye Goff

Keystone Heights High School

Chris Vulpe, MD/PhD

Professor
Department of Physiological Sciences
College of Veterinary Medicine

Copper and Iron Metabolism
Copper and iron are vital nutrients with a highly conserved and interwoven metabolism that is required for the growth and development of all organisms. An overall research goal of the laboratory is to further understand copper and iron metabolism in mammals with a focus on 1) characterizing the role of the multi-copper ferroxidases (Fe (II)-> Fe(III) in iron homeostasis and 2) identifying the genetic factors that influence iron status in mammals using “in silico” QTL analysis of inbred mouse strains and collaborations to study genetic determinants of iron deficiency in zebrafish and humans.

Toxicogenomics and Green Chemistry
We are utilizing systematic functional analysis through the use of “barcoding” analysis in the budding yeast Saccharomyces cerevisiae to identify conserved toxicity pathways that may provide insight on toxicant susceptibility in people. We are currently focused on breast cancer carcinogens, mitochondrial toxicants, pesticides and emerging contaminants. Most recently we have started using whole genome CRISPR approaches in a similar approach in mammalian cell lines.

Ecotoxicogenomics
We are developing a novel approach for identifying and understanding the toxicity of xenobiotics in aquatic ecosystems by monitoring changes in global gene expression patterns in aquatic indicator species representative of different trophic levels, including Daphnia magna (a crustacean), and Pimephales promelas (fathead minnow). We are assessing the sensitivity, specificity and utility of an ecotoxicogenomics approach for ecological toxicity assessment in real world environmental settings. Tools we are using include traditional microarray technologies as well as high-throughput sequencing methods.

Candace Roy

Vanguard High School

 

Janet Bisogno

Celebration High School

Andy Berglund, PhD

Professor
Department of Biochemistry and Molecular Biology
College of Medicine

 

The Berglund lab uses a broad range of approaches to study the molecular mechanisms of neurological diseases that are caused by microsatellite repeat expansions. For many of these diseases (myotonic dystrophy, ALS and ataxias), RNA processing (pre-mRNA splicing) pathways are negatively impacted with specific changes in pre-mRNA splicing proposed to lead to symptoms observed in affected individuals. We use biochemical, cellular and genomic assays to understand the mechanisms through which these diseases alter pre-mRNA splicing. The goal of our research is to use the results from these fundamental studies to identify innovative strategies to reduce or correct the improper pre-mRNA splicing that occurs in the disease state. For example, we have recently shown that small molecules can be used to rescue the mis-splicing in cell and mouse models of myotonic dystrophy.

 

 

Lloyd Alvin Wade

Walton High School

Marco Salemi, PhD

Associate Professor
Department of Pathology, Immunology, and Laboratory Medicine
College of Medicine

 

The last 25 years have witnessed an unprecedented development of molecular evolution, phylogenetic and population genetic methods. On one hand, the advent of PCR technologies has allowed for the generation and rapid accumulation of nucleotide sequence data from many organisms including several eukaryotic species, bacteria, viruses and eventually the full human genome. On the other hand, the increase in computational speed of computer clusters, as well as desktop and laptop computers, has allowed for the implementation of sophisticated algorithms that would not have been computationally feasible just two decades ago.

The discovery of fast-evolving viruses, such as HIV and HCV, poses special challenges to evolutionary theory. The understanding of both inter- and intra-host evolution of these viruses is crucial and has broad applications ranging from molecular epidemiology to drug resistance, pathogenesis and forensics. Molecular evolution of pathogenic viruses includes experimental work to isolate and sequence viral strains from different hosts or from the same host over time, DNA and RNA sequencing techniques, as well as the development and application of phylogenetic and population genetic methods to gain insights on the interplay between viral evolutionary patterns, origin and spread of epidemic outbreaks and pathogenesis.

More recently, our lab has also been investigating the molecular evolution and phylogeography of pathogenic bacteria such as MRSA and V. Cholera. Phylogenomics and phylogeography of bacteria is a new exciting field of research, based on the analysis of genome-wide SNPs, using state-of-the art phylogenetic methods and the Bayesian coalescent framework. Full genome bacterial sequences are obtained with the Illumina technology and analyzed with in-house pipelines implemented in the Galaxy software platform.

Iris Payan

Hollywood Hills High School

 

Donely Santiago

Mandarin High School

Sixue Chen, PhD

Associate Professor
Department of Biology
College of Liberal Arts and Sciences
Director, Proteomics and Mass Spectrometry Core
Interdisciplinary Center for Biotechnology Research

 

My research is focused on the signaling and metabolic mechanisms underlying plant interaction with the environment. My lab research has been particularly focused on three topics: glucosinolate metabolism, guard cell signal transduction, and plant pathogen interaction.

Project 1. Glucosinolate metabolism. Glucosinolates are a group of naturally occurring thioglucosides, present in Brassica plants (e.g., canola and cabbage). Glucosinolate degradation products display diverse biological activities, including defense against insects and herbivores, N/S nutrition and growth regulation. From a human perspective, glucosinolate metabolites account for the distinctive flavors of cabbage and condiments. Some of the metabolites such as isothiocyanates exhibit anticarcinogenic properties. The core glucosinolate pathway has been well studied in Arabidopsis. However, we know little about how the components in different pathways interact to produce plant phenotypes and traits. Nor do we know how different layers of molecular control work together. The lack of such fundamental knowledge is a major reason why plant genetic engineering has been largely unsuccessful. It poses a chronic problem for rational engineering of crops for better quality and defense. Research in this project is focused on characterizing the regulatory and metabolic networks involving glucosinolate metabolism using multidisciplinary approaches. We aim to identify protein and metabolite changes in response to perturbation of glucosinolate metabolism and to integrate the data into glucosinolate networks. The process of networking will generate new testable hypotheses concerning glucosinolate metabolic pathways and related pathways. The ultimate objective is to use the immense biosynthetic potential of plants as an efficient, environmentally friendly and renewable source of fine chemicals and pharmaceuticals.

Project 2. Guard cell signaling networks. Guard cells are highly specialized plant epidermal cells that enclose tiny pores called stomata. Stomatal movements control both uptake of carbon dioxide and loss of water, and thus play important roles in plant growth and acclimation to environmental stresses. The plant hormone abscisic acid (ABA) is a key indicator of drought stress. ABA induces stomatal closure via an intricate intracellular signaling network in guard cells, thereby promoting plant water conservation. It is our central hypothesis that protein redox modification and dynamic changes in key metabolites are critical regulatory mechanisms in ABA signaling. We are testing the hypothesis by pursuing: identification of guard cell proteins whose redox status is altered in response to ABA and determination of their specific redox-sensitive amino acid residues, quantification of ABA-induced changes in metabolites implicated in guard cell signaling, and integration of the new information into a dynamic model of ABA-induced stomatal closure. Accomplishing these objectives is significant because it will reveal novel components of ABA signaling networks and provide knowledge of regulatory mechanisms underlying stomatal movements that will help to develop crops with enhanced stress tolerance and productivity.

Project 3. Plant pathogen interaction. The study of pathogen response and defense in crop species is of essential importance as the applications are directly related to agricultural production. Pseudomonas syringae pv tomato (Pst DC3000) causes speck disease in tomato (Solanum Lycopersicum), a crop growing in large quantities in Florida and having both nutritional and economical value. The goal of this project is to take what is known about pathogen host interactions and observe in greater detail mechanisms that plants utilize in response to pathogen infection at the posttranscriptional levels, including protein expression, redox and phosphorylation/dephosphorylation switches. Understanding changes in protein expression as well as redox and phospho-switches will provide important insights into how plant response and resistance to pathogens are occurring. Further investigation into unique/novel proteins and regulations will advance our knowledge of plant defense against pathogens, and allow researchers to use biotechnology to prevent future bacterial speck disease outbreaks.

Interestingly, as we gain more and more knowledge, the above projects have become interconnected with each other. Glucosinolate metabolism plays a role in pathogen defense and affects stomatal movement, which serves as the first line of defense against pathogen invasion. In addition to hypothesis generation projects, another major part of my research program has been hypothesis driven, i.e., characterizing molecular, biochemical and physiological functions of specific genes and proteins identified by proteomics and metabolomics approaches. One of the projects has been focused on understanding the key steps in the methionine chain-elongation pathway, which directly connects methionine (primary) metabolism to glucosinolate (spealized) metabolism. Our integration of hypothesis generation and hypothesis driven research will ultimately lead to a holistic view of cellular networks and processes in plants and will create important stepping stones towards potential biotechnological applications in enhanced yield, bioenergy and defense.

Hermione Joseph

 

Wendy Vidor

Matanzas High School

Matias Kirst, PhD

Professor
School of Natural Resources and Conservation
College of Agriculture and Life Science

Matias Kirst joined the School of Forest Resources and Conservation in 2005 as an Assistant Professor in Quantitative Genetics. In addition to his affiliation to the SFRC, he is also a member of the Plant Molecular and Cellular Biology Program (PMCB) and the University of Florida Genetics Institute (UFGI). His group in Quantitative Genomics Research is part of the Forest Genomics Laboratory. Research is focused in three areas: (1) Fundamental Genomic Research in the genetic regulation of gene expression and gene expression networks; (2) Applied Genomic Research for the discovery of genes, metabolic and regulatory networks that control variation in wood quality, growth and other important traits for the forestry and agronomic industry; and (3) Technology and genomic tool development.

Jennifer Broo

Saint Ursula High School

Marco Salemi, PhD

Dan Hahn, PhD

Jessica Mahoney

Edgewater High School

Dan Hahn, PhD

Associate Professor
Department of Entomology and Nematology
Institute of Food and Agricultural Sciences

 

I am broadly interested in the proximate physiological and biochemical mechanisms that underly the diversification of life histories. I take a comparative approach to life history physiology by studying physiological traits in closely-related species with divergent life histories and by studying life history plasticity within species. Life histories are essentially a series of resource allocation events. Intermediary metabolism is the underlying biochemical process by which resources are allocated to different pools within an organism including growth, maintenance, and reproduction. Therefore, understanding how the timing and magnitude of resource allocation evolve requires an understanding of modifications to intermediary metabolism.

In addition to the metabolic basis of life history evolution, I am also broadly interested in how insects interact with their environment and physiological mechansims of environmental stress resistance.

Kathy Savage

Oviedo High School

Valerie de Crecy-Lagard, PhD

Professor
Department of Cell Biology and Microbiology
Institute of Food and Agricultural Sciences

General area: Comparative genomic. Bacterial genetics. Experimental evolution. Genetic Code.

The main focus of Dr. de Crecy-Lagard’s laboratory is to utilize the power of microbial genetics to make efficient use of the avalanche of genomic information now available. By combining comparative genomics approaches with experimental verification, new enzymes, pathways and chemistries that had previously evaded identification are revealed.

We have identified several new tRNA modification families that are now under study. By using a new model organism, the naturally transformable bacterium Acinetobacter ADP1, very simple protocols for genetic manipulation have been developed and are now being used to test predictions, build selection strains, and perform pathway engineering. Finally, the use of experimental evolution protocols to adapt bacteria to new metabolic constraints is being explored.