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Microbiology & Cell Science

Microbiology & Cell Science

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:

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

Genomics and Bioinformatics

  • 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. 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. Daniel Czyz

    We utilize C. elegans as a model to study the effect of the human microbiome on protein conformational diseases. Also, we are employing non-traditional approaches to combat antimicrobial resistance

    Protein conformational diseases

    • Deciphering the effect of bacteria on host proteostasis
    • Identifying bacterial genes that influence host proteostasis

    Antimicrobial resistance

    • Host-targeted approaches: modulators of host-mediated bacterial uptake and killing
    • Bacteria-targeted: bacteriophages and silver nanoparticles
  • 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. Mariola J. Edelmann

    Host-Pathogen Interactions and Cell Biology/Immunology in Gram-negative infections. Some research topics include:

    • New mechanisms involved in the regulation of inflammatory responses
    • Elucidating function of exosomes and other extracellular vesicles in infectious diseases
    • Mechanisms of bioactive lipid mediators in the host responses to infection and inflammatory conditions associated with infections
    • Identifying function of deubiquitinases in innate immune responses
    • Development of new drugs against Gram-negative infections
  • Dr. Nemat Keyhani

    Fundamental and applied research in fungal host-pathogen interactions, symbiosis, and insect biological control. Fungal biology and genetics. Genes and proteins involved in insect social behavior. Research topics include:

    • Interactions between Beauveria bassiana, a fungal pathogen of arthropods, their insect hosts, and plant partners with which the fungus forms mutualistic associations.
    • Fungal-beetle symbioses focusing on ambrosia beetles and its symbiotic partner and devastating plant pathogen, Raffaelea lauricola.
    • 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:

    • Preferred parasitic organism: Leishmania spp.,
    • Preferentially infects macrophages in mammalian hosts.
    • Novel approaches to parasite control
    • Studies to elucidate the molecular characteristics of parasitophorous vacuoles (PVs) in which Leishmania parasites reside and replicate
    • Identification and characterization of parasite molecules that are secreted in Extracellular Vesicles (EVs) from infected cells.
    • Evaluation of contributions of EVs from infection in tissue remodeling promoted by infection
    • Evaluation of PI3K/Akt signaling in Leishmania-infected cells.

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. 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:

    • Bacterial responses to microgravity in the human spaceflight environment aboard the International Space Station
    • Growth and adaptation of microbes to extremes of temperature and pressure encountered in extraterrestrial environments
    • RNA polymerase structure/function using rifampicin resistance mutations in rpoB and global phenotype/transcriptome alterations
  • 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

    Plant-bacteria interactions and genetic improvement of citrus via CRISPR/Cas genome editing. Current research topics include:

    • Genetic determinants and the signaling pathway underlying a pathogen (Candidatus Liberibacter asiaticus)-triggered immune disease-citrus Huanglongbing
    • Pathogen-triggered immune diseases
    • Transcriptional activator like effectors of Xanthomonas citri citri and canker susceptibility gene
    • CRISPR/Cas genome editing of citrus
    • Citrus microbiome
    • Citrus Huanglongbing (greening) and canker management
  • 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