Areas of research and the corresponding faculty are listed below. Faculty's direct contact information can be found on the faculty directory.
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:
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Host Microbe Interactions
Daniel Czyz Lab
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
Sarah Doore Lab
The Doore lab is interested in viruses of bacteria—known as bacteriophage or phage—and how they interact with their bacterial hosts. We investigate this at three stages of the infection process: 1) host attachment, when the phage identifies a suitable host cell; 2) middle infection, when the phage genes are expressed; and 3) late infection, when new phage particles are assembled and released upon death of the host. We use a specific type of virus, known as Moogleviruses, to investigate these processes in the human pathogen Shigella flexneri. Approaches include classical genetics, next-generation sequencing, experimental evolution, and cryo-electron microscopy. In addition to S. flexneri-infecting Moogleviruses, we are interested in determining the abundance and diversity of this phage group in other non-model bacteria, including Cronobacter sakazakii and Serratia marcescens.
Mariola Ferraro Lab
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
Claudio Gonzalez Lab
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
Melissa Jones Lab
The Jones Lab is interested in investigating the relationship between human noroviruses and commensal bacteria. Specifically, how viral interactions impact the bacteria that make-up the intestinal microbiome and how alterations in bacterial gene and protein expression ultimately impact viral infection of host cells. The goal of understanding the molecular nature of this bacterial-viral relationship is to use this knowledge to determine molecular mechanisms of viral infection, develop improved norovirus capture and detection methodologies and investigate novel ways to prevent viral transmission or infection.
Peter Kima Lab
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.
Joseph Larkin III Lab
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
Graciela Lorca Lab
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
Kelly Rice Lab
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:
- Contribution of cid/lrg genes to Streptococcus mutans biofilm development and stress resistance.
- Effects of simulated microgravity on S. mutans biofilm development and physiology.
- Identification of endogenous sources of Nitric Oxide (NO) production by Staphylococcus aureus, and its effects cell physiology and downstream cellular targets.
- Exploration of antimicrobial effects of lignin on bacterial pathogens.
- Determination of simulated microgravity and spaceflight effects on S. aureus quorum sensing and biofilm formation.
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Microbial Ecology
Marc G. Chevrette Lab
Microbes are the best chemists in the world and their metabolites are the language of microbial interactions. Microbially produced secondary metabolites influence many aspects of microbiome ecology and are an important source of antibiotics and other medicines.
Our research focuses on the ecology and evolution of the genes that encode secondary metabolism and how microbial metabolites shape microbiome interaction networks. We deploy both computational and experimental approaches to describe the eco-evo dynamics of bacteria and the genes that assemble their secondary metabolites.
Brent Christner Lab
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
Jamie Foster Lab
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
Willm Martens-Habbena Lab
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.
Luiz Roesch Lab
The Roesch Lab uses molecular analysis to test fundamental hypotheses in microbial ecology. Our focus is the Human Microbiome, but we are also interested in Space Biology and in developing user-friendly analytic tools to find microbial biomarkers of health and disease.
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Microbial Physiology
The Averesch Lab
Metabolic Engineering for Space and Earth, leveraging Systems and Synthetic Biology – modification of biochemical pathways for construction of microbial cell factories with new-to-nature functions to:
- Discover advanced bio-polyesters
- Optimize resource efficiency
- Understand life's limits
The Maupin-Furlow Lab
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
The Xin Wang Lab
We are interested in the designing principles of cells and their synthetic biology applications. Our research interests include:
- Photosynthesis
- Cyanobacteria
- Synthetic Biology
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Plant Molecular Biology & Microbe Interactions
Jessie Fernandez Lab
My research interest is based on understanding how plant pathogens grow inside the host cell, suppress, or evade host defenses and cause disease. To investigate this, we use a fungal model organism known as Magnaporthe oryzae, the causal agent of rice blast disease. During early stages of infection, M. oryzae initiates the timely secretion of a repertoire of small proteins into rice cells to suppress or evade host pathogen surveillance. The identification and molecular mechanisms of these proteins are unknown but could provide targets for the development of novel anti-blast strategies. The initial goal of my research program is to dissect the functions of the secreted proteins during rice blast infection and study their role in pathogenicity or fungal development. Our lab will incorporate a multifaceted approach that employs the use of different scientific disciplines such as biochemistry, genetics, cell biology, microscopy, molecular biology, and general microbiology.
Zhonglin Mou Lab
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
Nian Wang Lab
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
The Vermerris Lab
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
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Genomics, Bioinformatics, and Artificial Intelligence
Valerie de Crecy-Lagard Lab
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
Raquel Dias Lab
The Dias lab develops and applies cutting-edge Artificial Intelligence (AI) methods to examine important research questions across multiple fields of biological sciences and biomedical research.
Our research interests include: 1) improving interpretability and accuracy of AI models for bioinformaticians, 2) modelling effects of genetic and non-genetic factors on autoimmune and infectious diseases 3) developing AI techniques to integrate microbial and host ‘omics’ data for disease prediction and prevention.
Eric W. Triplett Lab
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
Meixia Zhao Lab
Our research laboratory uses a combination of computational and functional genomic, genetic and epigenetic approaches to study the mechanisms underlying genome evolution, transposon silencing, and epigenetic regulation of meiotic recombination and plant-microorganism interactions using maize and soybean as model systems.
- Stem Education Research and Professional Development
