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Overview

Our faculty pursue a wide range of research interests in virtually every subdiscipline of the biological sciences. For discussion purposes, this work can be loosely sorted into four categories: 1) Botanical Sciences, 2) Computational and Quantitative Biology and Bioinformatics, 3) Ecology, Evolutionary Biology, and Conservation Biology, 4) Integrative Organismal Biology, and 5) Molecular and Cellular Biology and Biochemistry. Learn about individual faculty members’ interests, projects, and publications through our faculty directory, which can by filtered by research specialty.

 

Botanical Sciences

  • Cherry lab: We study wetland plant ecology, focusing on the roles that vascular plants play in key ecological processes and wetland function. Our lab utilizes field and greenhouses experiments to examine the effects of environmental changes on plant community composition, growth and productivity, resource allocation, and litter quality and quantity. We also examine plant-mediated feedbacks to elevation maintenance and coastal resilience in tidal marsh ecosystems.
  • Ciesla lab: We use self-designed bioassays, for example cellular membrane affinity chromatography columns (CMAC) or cell membrane coated nanoparticles to discover new drug leads from complex natural matrices for example plant extracts. Our group focuses on identification of natural compounds (for example phytochemicals) promoting healthspan by mimicking the effects of fasting and endurance exercise.
  • Lopez-Bautista lab: We are interested in the diversity, systematics and evolutionary relationships of Seaweeds and Tropical Terrestrial Algae. Our lab integrate field studies, laboratory analyses and computer algorithms in order to study algae with a polyphasic approach. We are currently generating phylogenomic information with bioinformatic pipelines to better understand the architecture and evolution of the algal chloroplast genome.
  • McKain lab: We study the systematics and genome evolution of flowering plants with a focus on the impact of polyploidy on 1) genome restructuring, 2) gene expression and network evolution, and 3) species diversification.
  • Ramonell lab: We are interested in understanding the molecular mechanisms controlling plant defense against fungi and insects. Using the model plant Arabidopsis, the powdery mildew fungus and aphids as experimental organisms, we employ techniques in genetics, biochemistry, genomics and molecular biology to tease apart the plant signal transduction pathways involved in defending against these pests.
  • Starr lab: We study terrestrial ecosystems and how vascular plants contribute to the sequestration and release of greenhouse gases. Our lab use a variety of plant physiological ecology and land-atmosphere techniquest to address how humans are altering the world’s biogeochemical cycles.

Computational and Quantitative Biology and Bioinformatics

  • Becker lab: We use (i) computational tools in spatial GIScience to understand connectivity and dispersal of animal populations and (ii) bioinformatic tools to study diversity and function of host microbiomes.
  • Earley lab: We use quantitative genetics and multivariate statistical modeling to explore the evolution of behavioral phenotypes like aggression-boldness-activity “syndromes” and performance traits like terrestrial jumping behavior.
  • Ferguson lab: We develop and use statistical models and simulation models to investigate questions related to the ecology and management of fish and wildlife populations and communities. We also use decision analysis methods that combine empirical data and information from stakeholders to evaluate methods to manage natural resources.
  • Fierst lab: We use computational and bioinformatic analyses to study genome evolution. We also use mathematical and computational modeling to explore evolutionary theory and develop machine learning methods to identify and remove contaminants in sequencing data.
  • Jenny lab: We use genomic and transcriptomic data to investigate molecular mechanisms related to acquired tolerance and adaptation to environmental stressors such as environmental pollutants or climate change.
  • Kocot lab: We use transcriptome and genome data and bioinformatic tools (including our own novel software) to study deep metazoan (animal) phylogeny, comparative and evolutionary genomics, and the gene regulatory networks and expression patterns underlying complex traits and processes, especially biomineralization.
  • Lozier lab: We use genome-scale data to address questions about population genetics and phylogeography of wild populations. We employ computational methods to analyze high throughput sequencing data to understand how landscape factors influence genetic diversity, gene flow, and divergence, as well as to resolve how abiotic pressures shape adaptive variation at different levels of biological organization.
  • McKain lab: We use whole genomic, whole transcriptomic, sequence capture, and genome skimming data to understand the relationships of various lineages of flowering plant and the evolution of their genome. We focus on changes that incorporate polyploidy in the adaptation to drought and xeric environments. As part of this research, we develop novel software to facilitate characterization of paralogous genes during the course of polyploid genome diploidization.
  • Reed lab: We use quantitative genetics and genetic mapping to identify the genetic factors that interact with the environment to produce metabolic traits.  We also use novel analytical approaches to construct models of metabolism using large metabolomic datasets integrated with genomic and bioinformatic information.
  • Staudhammer lab: We use advanced statistical modeling techniques to promote better conservation and management in forestry and natural resources. Our lab focuses on mixed effects models, design and analysis of experimental data, quantifying size and structure distributional differences in natural systems, and quantifying model uncertainties.

Ecology, Evolutionary Biology, and Conservation Biology

  • Atkinson lab: We study the determinants of species occupancy within communities and how species traits, particularly stoichiometric traits and thermal preferences, influence ecosystem structure and function within aquatic systems. To do this, we employ a  combination of field observational and mesocosm studies to understand how organismal rates and biodiversity interact to maintain ecosystem processes.
  • Benstead lab: We study ecological interactions among three fundamental drivers of community structure and ecosystem function – temperature, nutrient availability and energy input – that are also changing rapidly because of human activity. A major goal of our research program is to integrate the metabolic theory of ecology, and its emphasis on temperature and body size, with the explicit multiple-element approach to resource limitation that is central to the field of ecological stoichiometry. While our research leverages the unique characteristics of stream ecosystems, we concentrate on broad questions that are relevant to all ecosystem types.
  • Becker lab: We build spatial models and conduct both field and laboratory experiments to understand the biotic and abiotic mechanisms underlying the distribution of wildlife from local to global scales, with the overarching goal of diagnosing patterns of biodiversity threats and loss. Our lab is actively engaged in applying research findings to the management of endangered and threatened species, and we attempt to make applied conservation biology results available to decision-makers.
  • Cherry lab: Our research aims to understand the mechanisms by which tidal marshes can keep pace with sea-level rise through biological feedbacks to marsh surface elevation. In particular, we examine how simultaneously changing external forcing factors, such as elevated CO2, sea-level rise, nutrient enrichment, storm sedimentation, or fire, affect marsh processes that regulate organic matter accumulation, vertical accretion, or the capacity for upslope migration. We combine greenhouse and field studies to (1) identify biophysical processes regulating marsh surface elevations; (2) examine impacts of disturbance or restoration on marsh structure and function; and (3) help develop models that inform adaptive management and restoration strategies.
  • Earley lab: We examine the evolution of multivariate phenotypes using a combination of field sampling, phenotyping, and quantitative genetics. We also examine the evolution of mixed mating systems (selfing + outcrossing) and sex change across the enormous geographical range of our study organism, the mangrove rivulus fish. We have begun to integrate GIS-based spatial analyses with population genetics to determine barriers to gene flow in fragmented mangrove ecosystems.
  • Ferguson lab: We study the ecology and management of fish and wildlife populations and communities including disease ecology of salmon, land use and wildlife occupancy patterns, and endangered species conservation.
  • Fierst lab: We are broadly interested in fundamental questions in evolutionary genetics. Current projects include the evolution of genetic networks, the influence of sex on genetic and genomic evolution, mating system transitions, and the evolution of novelty in microbial metabolism.
  • Howeth lab: We address both basic and applied questions in ecology, with a focus on community ecology, spatial ecology, and invasion biology. The basic research aims to isolate mechanisms and processes driving species diversity and ecosystem function at multiple spatial scales. The applied research uses these basic, multi-scale frameworks to better understand the ecology of species invasions and consequences of habitat fragmentation. In our work, we employ experimental, observational, and synthetic approaches guided by ecological theory, with an emphasis on studies in aquatic ecosystems.
  • Jenny lab: We use a combination of transcriptomic and genomic data, coupled with physiological data, to develop predictive statistical models that can be used to facilitate conservation and species restoration activities.
  • Kocot lab: We employ traditional tools such as histology, light microscopy, and scanning electron microscopy as well as cutting-edge tools such as high-throughput sequencing and micro-CT scanning to study marine invertebrate biodiversity and systematics.
  • Lopez-Bautista lab: We are interested in the diversity, systematics and evolutionary relationships of Seaweeds and Tropical Terrestrial Algae. Our lab integrate field studies, laboratory analyses and computer algorithms in order to study algae with a polyphasic approach. We are currently generating phylogenomic information with bioinformatic pipelines to better understand the architecture and evolution of the algal chloroplast genome.
  • Lozier lab: We use genome scale data to address questions about population genetics and phylogeography of wild populations, especially in invertebrates. We focus on resolving how spatial and environmental landscape factors at multiple scales influence genetic diversity, gene flow, and divergence, as well as understanding how abiotic pressures shape adaptive variation at different levels of biological organization from DNA sequences and gene expression to whole-organism phenotypes.
  • McKain lab: We study the impact of whole genome duplication on the evolution of genomes in flowering plants from perspectives of genome reorganization, novel phenotype development, and speciation. We focus on adaptation to drought, deserts, origins of succulence, and development of novel photosynthesis pathways.
  • Mortazavi lab: We study coastal biogeochemistry, focusing on the impact of natural and human-induced stressors in near-shore ecosystems. We use a combination of field and lab experiments to study the impact of disturbances such as oil spills, elevated nutrient loading, and sea level rise on ecosystem services such as nitrogen removal and carbon sequestration in estuaries and salt marshes.   
  • Olson lab: This microbial ecology lab focuses on increasing the recoverability of environmental microorganisms, examining the resident microbiomes of various organisms, and investigating the responses to changes in those communities, whether from dysbioses or environmental stressors.  Environments studied include terrestrial, freshwater, and marine.
  • Pienaar lab: We develop models and methods to study evolution and are turning tardigrades and their bryophytic habitats into a model system for understanding the evolution of cryptobiosis – the ability of organisms to withstand extreme conditions such as those found in extra terrestrial habitats.
  • Reed lab: We use phylogenetic and quantitative genetic approaches to elucidate the genetic basis and selective forces shaping adaptive metabolic phenotypes, such at host toxin tolerance in mushroom feeding Drosophila.
  • Sobecky lab: We are a systems microbial biology lab that uses molecular biology, molecular ecology and environmental microbiology methods coupled with field-based approaches to study microbially mediated ecosystem services (carbon, nitrogen) in marine, estuarine, freshwater, soils and salt marshes.
  • Starr lab: Our research focuses on addressing questions associated with global change ecology with an emphasis on ecosystem ecology and atmospheric transport. We are currently focusing our efforts on longleaf pine ecosystems, Everglades marshes and forest, arctic tundra ecosystems and cellulosic biofuels.

Integrative Organismal Biology

  • Atkinson lab: We use freshwater mussel and amphibian communities as model systems to understand how organismal process rates and thermal preferences influence ecosystem function and structure and determine community assembly. We are also investigating how gut microbial communities influence the organismal functional effect traits.
  • Becker lab: We investigate mechanisms of host-pathogen dynamics and host-microbiome interactions, including detailed mechanistic studies of diversity-disease relationships, using tropical and temperate amphibians and their symbiotic microbial communities as our study system.
  • Caldwell lab: We investigate the molecular mechanisms of organismal regulation and metabolic response to protein stressors implicated in human neurological diseases including Parkinson’s, Alzheimer’s, and related disorders.  Our focus is on discovery of gene targets for therapeutic development and drug discovery, as well as environmental contributors to neurodegeneration using the nematode model system, C. elegans.
  • Chtarbanova lab: We use the fruit fly Drosophila as an in vivo model to investigate how the process of age-dependent chronic inflammation (inflammaging) impacts nervous system integrity and function and affects neurodegenerative diseases. We also investigate the molecular mechanisms by which aging alters the organismal ability to fight infections.
  • Correll lab: We use genetically-modified animal models to investigate the pathogenesis of cardiac hypertrophy and heart failure at both the whole organ and single-cell levels.
  • Earley lab: We investigate the neurobiological, hormonal, genetic and physiological mechanisms underlying the expression of diverse phenotypes, mostly those that arise through environment-genotype interactions. We manipulate the social and physical environments (including salinity, temperature, and exposure to pollutants) and examine phenotypic endpoints including behavior, life history, and sex.
  • Hatoum-Aslan lab: We study host-pathogen interactions between microorganisms–bacteria and their viruses (phages)–with a focus on the defensive and offensive molecular weaponry that they use against each other.
  • Jenny lab: We are interested in understanding the cellular response to stress, with a strong focus in toxicant exposure that usually leads to chronic oxidative stress and inflammation, to elucidate mechanisms that play a role in determining the difference between tolerance to the stress and the development of disease endpoints.  Using the zebrafish model, we can measure changes from the cellular and molecular level (e.g., changes in gene or protein expression) to the organismal level (e.g., changes in physiology or cognitive function).
  • McKain lab: We are interested in the adaptation of flowering plants to extreme drought through the development of novel anatomy (e.g. succulence) and physiology (e.g. water storage). Using a genomic approach, we look at changes in gene expression as a means to the development of novel phenotypes across time. Our focus is in the subfamily Agavoideae, which includes the genus Agave, a group of desert plants from North America. We also look at comparative genomics between agaves and aloes as two lineages that have adapted to the deserts of North America and Africa.
  • Olson lab: This microbial ecology lab examines host-pathogen interactions in marine invertebrates to better understand disease transmission, prevalence, and etiology.
  • Ramonell lab: We are interested in understanding the molecular mechanisms controlling plant defense against fungi and insects. Using the model plant Arabidopsis, the powdery mildew fungus and aphids as experimental organisms, we employ techniques in genetics, biochemistry, genomics and molecular biology to tease apart the plant signal transduction pathways involved in defending against these pests.
  • Reed lab: We use the fruit fly, Drosophila, to model the relationships between environmental factors like diet and exercise, and genes in shaping metabolic phenotypes like obesity and type 2 diabetes.
  • Sobecky lab: We are a systems microbial biology lab that investigates the role of mobile genetic elements and horizontal gene transfer  in microbial adaptation and evolution.

Molecular and Cellular Biology and Biochemistry

  • Caldwell lab: We utilize quantitative behavioral analysis, molecular biology, genomic, genetic, biochemical, and fluorescent imaging methods to investigate and define genetic and epigenetic factors underlying human neurological diseases including Parkinson’s, Alzheimer’s, ALS, epilepsy, and dystonia using the nematode model system, C. elegans.
  • Hatoum-Aslan lab: Our research uses molecular, genetic, and biochemistry approaches to understand how bacterial immune systems work and the mechanisms that their viruses (phages) use to counter them.
  • Correll lab: Our lab utilizes molecular biology, biochemical, and biophysical approaches to understand how alterations in unfolded protein response signaling and calcium handling dynamics effect transcriptional changes that drive the development and progression of heart disease.
  • Chtarbanova lab: Our lab employs genetic, biochemical, molecular and cell biology techniques to study the changes of innate immune activation and function in the aging organism and how they relate to infection and neurodegenerative disease.
  • Ciesla lab: Our lab uses innovative drug discovery approaches in identification of new drug leads with possible application in the prevention and treatment of aging-associated diseases. The main focus is on the the evolutionary conserved adaptive stress cellular signaling pathways and ectopic olfactory and taste receptors.
  • Becker lab: We use molecular tools to (i) understand mechanisms of pathogen hybridization and the evolution of virulence, (ii) perform retrospective pathogen sampling of museum-preserved specimens, and (iii) quantify the effect of host MHC diversity on host-pathogen dynamics.
  • Duffy lab: We use molecular, genetic, and biochemical approaches to study host-pathogen interactions between viruses and the cells they infect.
  • Ramonell lab: Our laboratory is focused on understanding the molecular mechanisms controlling plant defense against fungi and insects. We use techniques in genetics, biochemistry, genomics and molecular biology to investigate plant innate immunity and its associated signal transduction pathways.
  • Jenny lab: We use molecular, genetic and biochemical approaches to study to the mechanisms by which environmental stressors may result in developmental toxicity, or contribute to the development or progression of disease pathologies at later stages in life.  This is primarily accomplished through the use of the zebrafish in vivo model and various human cell lines for human health related research.
  • Olson lab: This microbial ecology lab explores the diversity of metabolites produced by microorganisms and tries to identify methods to increase their production in the laboratory.
  • Sobecky lab: We are a systems microbial biology lab that uses microbial genetics, molecular biology, molecular ecology and environmental microbiology-based methods and approaches to study microbial mechanisms and cellular adaptations to human-induced and natural disturbances in marine, estuarine, freshwater, soils and salt marsh ecosystems.