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Research

The faculty’s research programs span areas of broad interest in the cellular and molecular aspects of bacterial, plant and animal life functions, and include;

  • Genomics and Bioinformatics
  • Host-Microbe Interactions
  • Microbial Ecology
  • Microbial Genetics and Physiology
  • Plant Biology and Plant-Microbe interactions.

Areas of research and the corresponding faculty are listed below. Faculty contact information can be found on the faculty directory.

Genomics and Bioinformatics

Dr. Ana Conesa

Functional Genomics and high throughout sequencing analysis, Integration of multi-omits data, and Systems Biology. Some research topics include:

  • Developing algorithms and software tools to integrate multiple types of sequencing and omics data, such as RNA-seq, ChlP-seq, Methyl-seq, and metabolomics to create & visualize systems biology models
  • Understanding functional aspects of gene expression using genome-wide transcriptome profiling and computational approaches
  • Identify responsive genes in case-control, time course, and multifactorial experiments
  • Assign function to novel genes and transcript isoforms using controlled vocabularies

Dr. Valerie de Crecy-Lagard

Utilizing the power of microbial genetics to make efficient use of currently available genomic information and combining comparative genomics approaches with experimental verification to identify novel enzymes, pathways, and chemistries. Some research topics include:

  • The study of tRNA modification genes and functions
  • The discovery of novel DNA modifications,
  • The study of  B vitamin related enzymes
  • The exploration of novel enzymes in the field of metabolite repair

Dr. Claudio Gonzalez

Functional biology and understanding Enzyme, including assessment of molecular strategies to control citrus greening, discovering new mechanisms to minimize oxidative stress damage, and Protein-Protein interactions. Some research topics include:

  • Studying the biochemistry of hydrolytic enzymes using quick screening methods to demonstrate enzymatic activity toward the hydrolysis of selected substrates
  • Using bioinformatics, structure models, and bio-assays to merge protein biochemistry, structure, and biological function.
  • Family of enzymes in study:
  • Esterases, Phosphatases, Epoxide Hyrdolases, Decarboxylases

Dr. Bryan Kolaczkowski

Finding innovative ways to study the evolution of molecular function, principles and mechanistic study of molecular evolution, and evolution of innate immunity in animals and plants. Some research topics include:

  • Investigating how proteins evolved to protect animals and plants from viral infections using computational biology, statistics, structural modeling, and biochemistry

Dr. Graciela Lorca

Functional genomics of transcription factors, identification of small molecules as modulators of gene expression, the study of protein-protein interactions, and applications that include inhibition of virulence determinants and live vaccine development. Some research topics include:

  • Drug repurposing: discovery of “new” antibiotics – Identifying new targets for old drugs
  • Use of a novel probiotic strain to prevent type 1 diabetes – Analyses of the mechanism of disease mitigation and elucidation of bacterial components or molecules involved
  • Functional genomics – Identification of chemicals that modulate the activity of transcription factors and elucidation of function for uncharacterized genes

Dr. Wilfred Vermerris

Development of renewable fuels and Chemicals from enhanced bioenergy crops through genetic approaches. Some research topics include:

  • Plant breeding to enhance crop yield & improve disease resistance
  • Genetic improvement of sugar yield and biomass composition
  • Lignin-based nanotubes as vehicles for gene therapy
  • Lignin nanotubes made from biorefinery waste are able to penetrate human cells in tissue culture and deliver DNA, and do so with low levels of cytotoxicity

Host-Microbe Interactions

Dr. Kelly Rice

Dr. Rice’s research program focuses on aspects of bacterial physiology and cell communication that contribute to biofilm development of pathogenic Gram-positive bacteria. Some research topics include:

  • Streptococcus mutans, the primary causative agent of dental cavities,
  • Contribution of cid/lrg genes to biofilm development and effects of microgravity on biofilm development and physiology
  • Staphylococcus aureus can infect almost all human tissue, genetic resistance to antibiotics, and can be acquired in healthcare settings
  • Identification of endogenous sources of Nitric Oxide (NO) production, it’s effects on biofilm physiology and cell-signaling, and downstream cellular targets
  • Characterization of a novel NO reductase associated with hospital-acquired and livestock-associated MRSA strains
  • Natronomonas pharaonis – enzymatic characterization of Nitric Oxide Synthase (NOS) and discerning the role of NOS in environmental/oxidative stress adaptation.

Dr. Joe Larkin

Studying the development and treatment of autoimmune diseases. Some research topics include:

  • Tolerance – Immune system activation must be tightly regulated in order to prevent immune responses which could result in autoimmune disease
  • Investigating the contribution of T lymphocyte subsets and functions in maintaining tolerance with an emphasis on regulatory T cells (Tregs)
  • Investigating whether changes in gut flora can modulate the onset of the autoimmune disease type 1 diabetes

Dr. Nemat Keyhani

Fundamental and applied research in host-pathogen interactions and insect biological control, and exploring the contributions of proteins within a framework of the biochemistry and evolution of insect social behavior. Some research topics include:

  • Interactions between Beauveria bassiana, a fungal pathogen of arthropods, their insect hosts, and plant partners with which the fungus forms associations.
  • Chemical communication in insects within a framework of the biochemistry and evolution of insect social behavior.
  • Investigating the molecular basis for diverse interactions and dissecting transcriptional and signaling networks involved in B. Bassiana, an insect pathogen that can grow as a saprophyte and also form intimate associations with plants.
  • Investigating the biochemical, molecular, and evolutionary mechanisms involved in insect chemical communication with a particular interest in social insects

Dr. Peter Kima

Host-Pathogen Interactions and Cell Biology/Immunology. Preferred parasitic organism: Leishmania spp.– preferentially infects macrophages in mammalian hosts. Some research topics include:

  • Novel approaches to parasite control
  • Studies to elucidate the molecular characteristics of parasitophorous vacuoles (PVs) in which Leishmania parasites reside and replicate
  • Identifying parasite molecules that are secreted by intracellular parasites which target host cell functions
  • Macrophage Biology including looking at macrophages in pathogensis and healing of wounds

Microbial Ecology

Dr. Brent Christner

Microbial physiology and ecology, Environmental microbiology, Biogeochemistry, Polar microbiology and Bioprecipitation. Some research topics include:

  • Subglacial Antarctic Lakes Scientific Access (SALSA): Integrated Study of Carbon Cycling in Hydrologically-active Subglacial Environments
  • Research on Airborne Ice Nucleating Species (RAINS)
  • A Transoceanic Aerobiology Biodiversity Study (TABS) to Characterize Microorganisms in Asian and African Dust Plumes Reaching North America
  • ARCHIMEDES (A Really Cool High Impact Method for Exploring Down into Europan Subsurface)
  • Europa Lander Science Definition Team

Dr. Jamie Foster

Environmental Microbiology: examining microbial communities and their surrounding environments to improve our understanding of the molecular mechanisms that microbes use to adapt and respond to changes in the environment. Some research topics include:

  • Examine how microbial biofilms sequester and precipitate carbonate using meta-omics
  • Assess the impact of microgravity on host-microbe interactions and examine the effects of microgravity on the normal developmental interactions between an animal host and a bacterial symbiont
  • Modern marine microbialites represent modern analogues to ancient Earth ecosystems. By studying these communities we can gain an understanding of the origins and evolution of life on Earth

Dr. Willm Martens-Habbena

Microbial Ecology and Biogeochemistry – We combine cutting edge molecular biological, microbiological and biogeochemical methods to understand microbial activities and interactions in natural and engineered systems and their influence on carbon and nutrient cycling. Some research topics include:

  • Novel nitrogen-cycling microorganisms in agricultural soils: Microorganisms are critically important for mineralization and nutrient cycling in nature. However, the vast majority of microorganisms has never been cultured in the lab and remains enigmatic. By combining high-throughput sequencing methods with new cultivation techniques and in situ measurements, we aim to understand the role of novel microorganisms in nutrient cycling and greenhouse gas emissions from agricultural soils.
  • Marine Archaea: The global oceans are responsible for about half the primary production on Earth and sequester significant amounts of CO2. About 20% of the microbial plankton in the oceans belongs to two poorly studied groups of Archaea. We are investigating the physiology of ammonia-oxidizing Thaumarchaeota and their contribution to N2O emissions from the oceans. In a new project we are further starting to investigate marine Euryarchaeota. Despite their global abundance in surface oceans, none of these organisms have been isolated and studied in laboratory culture. We aim to bring these organisms into culture and study their activities in situ in the marine water column.

Dr. Eric Triplett

Microbial diversity and genomics, including identification of the drivers of microbial diversity in a wide range of environments, association of bacteria with autoimmune diseases, therapies for citrus greening disease, and culturing the citrus greening pathogen. Some research topics include:

  • Molecular Microbial Ecology, including plant-microbe interactions and colonization of plants by endophytic bacteria
  • Microbial diversity and ecology including high-throughput DNA sequencing and analysis and culture-independent identification of gut bacteria correlated with diabetes

Microbial Genetics and Physiology

Dr. Qiu-Xing Jiang

Cell Physiology and Molecular Biophysics. Some research topics include:

  • Investigate the mechanism behind the lipid-dependent effects on voltage-gated potassium (Kv) channels and the connectioon to lipid metabolic defects in humans. We discovered strong inhibitory effects of nonphospholipids, such as cholesterol and glycosphingolipids, on Kv channels, and are studying their roles in neurological diseases caused by lipid metabolic defects.
  • Understand the molecular basis of a granin family protein in every step of the regulated secretory pathway, and the importance of these proteins in the impaired secretion in human diseases, such as type 2 diabetes, as well as their importance to the metastasis and survival of human neuroendocrine cancer cells
  • Structural and functional studies of membrane proteins and intracellular RNA-binding complexes and their relation to human diseases including cancers and neuroendocrine defects.

Dr. Julie Maupin-Furlow

Microbial biochemistry and physiology in extremophiles and Archaea, and mechanisms of post-translational modification and Ubiquitin-proteasome systems. Some research topics include:

  • Microbial extremophiles for advancing bioenergy, health and astrobiology
  • Microbial extremophiles from the Dead Sea as model systems
  • Energy-dependent proteolytic systems for protein quality control and cell function

Dr. Wayne Nicholson

Astrobiology, including planetary protection, interplanetary transport of spores, and survival/growth/evolution in space and on Mars. Some research topics include:

  • Microbiology of the human spaceflight environment including mutations to multiple antibiotic resistance on ISS and bacterial stress responses to the spaceflight environment
  • RNA Polymerase Structure/Function including Rifampicin resistance mutations in rpoB and global phenotype/transcriptome alterations

Dr. Chris Reisch

Microbial Physiology and Synthetic Biology – Studying the physiology and metabolism of bacteria using novel tools for genome editing and transcriptional control of gene expression. Some research topics include:

  • Developing synthetic biology tools that function in diverse bacteria, including the Alpha-, Beta-, and Gamma-Proteobacteria.
  • Organic Sulfur Metabolism in Marine Bacteria – Marine bacteria are primary drivers of the global sulfur cycle, however, the pathways used for many parts of this cycle are unknown. We are interested in identifying the biochemistry, molecular biology, and regulation of these pathways in model marine bacteria.    ‚Äč

Dr. Tony Romeo

Molecular genetics and regulation, including global regulatory circuitry, regulatory RNAs & RNA binding proteins, translation & transcription control, and bacterial virulence, biofilm formation, metabolism, motility. Some research topics include:

  • Studying regulatory mechanisms by which microbes sense changes in the environment and respond by modifying their behavior and metabolism
  • Global regulatory systems that coordinate expression of numerous genes throughout the bacterial genome
  • Novel global regulatory system in Csr systems, based on an mRNA binding protein, CsrA, and noncoding regulatory RNAs that sequester and antagonize CsrA

Plant Biology and Plant-Microbe Interactions

Dr. Nian Wang

Molecular Genetics and functional genomics of plant-bacteria interactions and methods to control citrus bacterial diseases. Some research topics include:

  • Virulence mechanism of Candidates Liberibacter asiaticus (Las) and control of HLB by nullifying the virulence mechanism of Las
  • Virulence factors and effectors of Xanthomonas axonodopis pv. citri
  • Screening of antimicrobial small molecules against Las
  • Bacterial diversity associated with citrus

Dr. Zhonglin Mou

Genetic, molecular, biochemical, and genomic approaches to investigate the fundamental aspects of plant defense responses. Some research topics include:

  • Investigating signal transduction pathways and their activation mechanisms using the model plant Arabidopsis.
  • Epigenetic regulation of plant immunity by the Elongator complex
  • Regulation of plant immunity by extracellular pyridine nucleotides
  • Regulation of SA accumulation during pathogen infection
  • Engineering SAR in crop plants

Dr. William Gurley

Optical sensing for early detection of Citrus Greening, develop screen for disease resistance, and studying changes in gene expression in bacteria and plants during early stages of transfer of the Liberibacter from the psyllid to the plant phloem cells. Some research topics include:

  • Transcription in plants: mechanisms of gene activation and repression
  • Identifying protein binding partners that control many aspects of development and environmental responsiveness
  • General transcription factors from plants
  • Cloning & characterization of TFIIB & subunits of Mediator
  • Heat Shock and mechanisms of Gene activation in response to abiotic stress such as those resulting from exposure to high temperature

ETOH Pilot Plant Dedication

For more information on departmental research interests, or to contact the research faculty, please visit the Department Faculty Directory or visit the department Google Scholar Page.

Florida Center for Renewable Chemicals and Fuels (FCRC)

FCRC was established in January 2002 with the primary goal of facilitating research and graduate education throughout the State University System in the multi-disciplinary areas of renewable chemicals and fuels. The Center provides a vehicle to solve new technological challenges, serves as a forum to foster productive interactions among faculty and students, assists faculty in the development of competitive research grants, and increases the visibility of this important activity at the state and national levels.

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