Eva Top, Ph.D.
Research Focus: Bacterial plasmid evolution
The Top lab investigates the ecology and evolution of bacterial plasmids. Plasmids are mobile genetic elements that are found in most bacteria, where they replicate separately from the chromosome and often confer resistance to multiple antibiotics or encode other host–beneficial traits. Because plasmids readily transfer between different bacteria, they play a major role in the rapid spread of antibiotic resistance in pathogens. To limit the spread of drug resistance among human pathogens, we urgently need to better understand the diversity and evolutionary history of resistance plasmids and the mechanisms by which they evolve to successfully persist in bacterial populations. The Top lab actively engages undergraduates in research all year round. Potential projects REU students could participate in include experimental evolution studies to determine the evolutionary mechanisms by which plasmids adapt to their host, host adapt to plasmids, or plasmids and hosts co–evolve. These types of projects entail traditional bacterial culturing techniques, plasmid DNA extraction methods, PCR amplification and DNA sequencing.
Dr. Top's Websites
Doug Cole, Ph.D.
Research Focus: Molecular biology and adaptations of unicellular protozoans
The Cole lab studies the cell and molecular biology of the photosynthetic unicellular protozoans known as Euglenids. One of the evolutionary projects in the lab compares Euglena mutabilis isolated from pristine lakes and extreme environments (e.g. volcanic or mining sites). Extremophilic E. mutabilis can flourish in acidic environs contaminated with heavy metals. Although the lake E. mutabilis can grow at low pH (pH 3), they are sensitive to heavy metal poisoning. Questions to address include (1) how distantly related are these two strains, (2) does the extremophile possess molecular machinery absent from the lake strain and (3) can the lake strain evolve, in a laboratory setting, to become resistant to the presence of heavy metal ions.
Dr. Cole's Website
Larry Forney, Ph.D.
Research Focus: Prokaryote community diversity and evolution
Research in the Forney lab centers on the diversity and distribution of prokaryotes. Both field and laboratory studies are done to explore the temporal and spatial patterns of community diversity, as well as factors that influence the dynamics of inter– and intra–species competition. In addition, research is done to understand how spatial structure and the resulting environmental gradients influence the tempo and trajectory of adaptive radiations in bacterial species and the maintenance of diversity. Most of these studies are highly interdisciplinary in nature. Undergraduate students in his research group conduct research to understand the structure and composition of microbial communities in the microbiomes of humans and animals, the nature of interspecies interactions in these communities, and to compare the tempo of genetic divergence in bacterial populations grown in well–mixed and spatially structured environments. All of these projects are well suited for summer REU interns.
Dr. Forney's Websites
Peter Fuerst, Ph.D.
Research Focus: Development of the nervous system
The Fuerst lab studies how our neurons are wired into a brain. This process involves a huge number of different neuron cell types being able to find and make connections with the correct target. To study this the Fuerst lab use wild type and transgenic mice and zebrafish that allow them to manipulate the genome to study different genes and to label different parts of the brain using fluorescent proteins, such as the brainbow transgenic mice. They also perform cell culture experiments and live imaging experiments wherein they image living brain tissue under a fluorescent microscope to assay how the brain develops over time. REU student projects could easily build upon a large number of ongoing projects involving work with zebrafish, mice, computer modeling and cell culture.
Dr. Fuerst's Websites
Jill Johnson, PhD.
Research Focus: Regulation of protein folding by the molecular chaperone Hsp90.
The Johnson lab studies the function of the molecular chaperone Hsp90, which is required for the function of hundreds of cellular proteins. Most notably, Hsp90 is required for the function of proteins that promote cancerous cell growth and neurodegenerative diseases, such as Alzheimer’s disease. The Johnson lab uses yeast as a model system to understand how Hsp90 and its team of interacting cochaperones mediate the folding and activity of client proteins. The long-term goal is to develop strategies to alter selectively alter Hsp90 or cochaperone function to combat disease. Potential projects REU students could participate in are studies to learn how fine-tuning of Hsp90 function affects the function of a protein involved in DNA repair or studies to investigate how Hsp90 directly interacts with a client protein using purified proteins.
Dr. Johnson's Websites
Paul Hohenlohe, Ph.D.
Research Focus: Genomic architecture of evolving populations
Research in the Hohenlohe lab focuses on basic questions in evolutionary genetics and genomics. His lab applies Restriction–site Associated DNA sequencing (RADseq), a technique well–suited for natural populations of non–model systems, to population genomic studies in a wide range of taxa. Much of this work has applications in conservation biology; for instance, his major ongoing projects examine the genomics of hybridization and introgression in threatened trout species, and the genomics of selection in Tasmanian devils threatened by devil facial tumor disease. Because the ability of many researchers to produce population genomic datasets has outstripped our ability to interpret them, his lab also focuses on testing basic hypotheses and developing novel analytical tools for population genomics. Toward this end Holenlohe’s group combines experimental evolution with whole–genome sequencing in polymorphic laboratory populations of yeast. Undergraduate students in Holenlohe’s lab are currently involved in all of these projects, including both the molecular biology lab work and bioinformatic analysis of RADseq data. REU students could easily join any of the on–going projects. The yeast work in particular provides unique opportunities for relatively small–scale, self–contained genomic evolution experiments ideally suited for REU students.
Dr. Hohenlohe's Websites
Craig McGowan, Ph.D.
Research Focus: Locomotor biomechanics and motor control
Research in the McGowan lab seeks to understand the relationships between the musculoskeletal morphology of terrestrial vertebrate animals (including humans) and the biomechanics and neural control of locomotor performance. We address questions geared towards understanding the in-vivo dynamics of individual muscles, the influence of musculoskeletal architecture on muscle function, and the links between limb morphology, whole animal locomotor performance and habitat utilization. Animals live in complex habitats and in addition to steady speed locomotion they must perform a variety of non-steady locomotor tasks. For example, the ability to change speed quickly, turn or jump can have direct implications for evolutionary success. The mechanical demands of such tasks can differ greatly and the musculoskeletal system must be able to meet these demands. We ask research questions such as: How do individual muscles contribute to different locomotor tasks? How is mechanical output modulated in limbs with different morphologies? How do habitat use and musculoskeletal specialization influence how animals modulate performance? Our research program addresses these types of questions by examining muscle function on multiple levels from fascicle strain and tendon force, to joint mechanics, limb mechanics and ultimately whole animal performance in an ecologically and evolutionarily relevant framework.
Dr. McGowan's Websites
Tanya Miura, Ph.D.
Research Focus: Viral pathogenesis and evolution
Respiratory viruses from many different families co-circulate in human populations and cause a wide range of disease severities, from the common cold to bronchiolitis or pneumonia. Clinical studies frequently detect more than one virus in patients with respiratory symptoms. However, it is not clear how unrelated viruses interact within shared host cells or with the host's immune system to determine disease severity. The Miura lab is studying how two unrelated respiratory viruses affect each other’s ability to infect and replicate within cells, alter host immune responses, and cause disease, using cell culture models of respiratory epithelial cells and infection in mice. These changes are expected to influence the rate and outcomes of viral evolution, as they alter the selective pressures on replicating viruses. Viral co-infection is also being studied in fruit flies to understand the dynamics of co-circulating viruses within a population of hosts. These studies will provide critical information about the interactions between respiratory viruses and their hosts that influence viral replication, transmission, evolution, and disease outcomes.
Dr. Miura's Websites
Scott Nuismer, Ph.D.
Research Focus: Coevolutionary genetics
Research in the Nuismer lab focuses on the ecology and evolution of species interactions. The overall aim of his research team is to better understand how coevolution shapes patterns of biodiversity and the geographic distributions of interacting species. Some of the key questions being addressed include: Can interactions between species drive the evolution of assortative mating and potentially speciation? How do interactions between host and parasites alter patterns of gene expression? Do interactions with parasites mediate phenotypic divergence? Work in the Nuismer lab addresses these issues through a combination of mathematical modeling and empirical studies. Projects will be geared towards REU students with a foundation in mathematical or modeling skills and will place them in a research environment with other undergraduate researchers and graduate students.
Dr. Nuismer's Websites
Christine Parent, Ph.D.
Research Focus: Adaptive radiation; Intraspecific competition in diversification
Research in the Parent lab centers on the evolutionary process of diversification in lineages exposed to novel environment. Adaptive radiation, defined by ecological diversification in a rapidly multiplying lineage, is possibly the single most important source of biological diversity in the living world. The variation is the result of evolution in novel and geographically fragmented environment, and is the focus of the research conducted in Dr. Parent’s lab. The general approach of her lab is to (1) observe present– day patterns of biodiversity to infer past evolutionary processes, and (2) test those processes with manipulative experiments in laboratory populations. The Parent lab uses field observations, comparative analyses, laboratory experiments, molecular phylogenetics, and integrates them with theoretical modeling. REU students in the Parent lab could work on projects involving experimental evolution (using Tribolium beetles or fruit flies), molecular phylogenetics, morphometrics, and/or comparative analyses.
Dr. Parent's Websites
Barrie D. Robison, Ph.D.
Research Focus: Behavioral evolution; Game based simulations of evolution
The Robinson lab conducts empirical research on the patterns and processes of adaptation to captivity, typically focusing on the evolution of tameness related behaviors in fish. The Robinson lab combines high throughput video based behavioral measurements with genomic analyses to identify the genes and physiological pathways that facilitate or constrain adaptation to the captive environment, and drive the apparent convergence of multiple domesticated populations to a “tame” phenotype.
A second, but related, axis of research involves the creation of a playable simulation of evolutionary biology. In collaboration with Dr. Terry Soule’s lab in the department of Computer Science, the Robinson lab have created EvolveTD, a “tower defense” style video game in which the attackers adapt to the environment and player defenses according to realistic models of quantitative trait evolution. Ultimately, the Robinson lab seeks to create a fun, engaging video game that can be used to teach the concepts of genetics and evolutionary biology, and to conduct agent based simulation research.
Dr. Robison's Websites
Paul Rowley, Ph.D.
Research Focus: Characterization of antifungal “killer toxins” produced by yeasts
Yeasts used for brewing and baking have the ability to secrete proteins called “killer toxins” that are lethal to disease-causing fungi. One unique feature of killer toxins is that they are often encoded upon double-stranded RNA (dsRNA) molecules that are replicated by viruses in the yeast cytoplasm. Despite the advantages of killer toxin production, different killer toxins vary in their ability to inhibit the growth of certain strains and species of yeasts. The current research focus of the Rowley lab is to better understand the diversity, specificity, and potency of killer toxins and use this information to design potent antifungal drugs against pathogenic fungi. Undergraduate students in the Rowley lab are involved in (1) the discovery of novel viral dsRNAs that encode killer toxins, (2) the determination of the genetic sequence of dsRNAs by next generation sequencing, and (3) the assaying of purified killer toxins against pathogenic fungi in vitro and in vivo.
Dr. Rowley's Websites
Deborah Stenkamp, Ph.D.
Research Focus: Development of the vertebrate retina
The Stenkamp lab studies how the specific neuronal and glial types of the vertebrate retina are generated and differentiated during development, and how they are regenerated after retinal damage. We use the zebrafish as our primary animal model, because teleost fish such as zebrafish develop as many as nine spectrally distinct types of retinal photoreceptors, and have the capacity for functional retinal regeneration. Our experiments involve developmental and genetic manipulations and the use of live and static imaging, and molecular analyses including RNA-seq. REU students would join projects that investigate the differential expression and evolution of tandemly-replicated visual pigment genes in teleost fish and primates. In many cases these tandem replications are very recent evolutionary events. REU students may also participate in collaborative projects with the Fuerst lab in which we investigate retinal structure and regenerative capacity in the gar, a fish that did not experience the genome-wide gene duplication event of teleosts and has a genome structure more similar to mammals.
Dr. Stenkamp's Websites
David Tank, Ph.D.
Research Focus: Molecular plant systematics; Phylogenetics
The Tank lab is broadly interested in the investigation of the patterns and processes that shape plant biodiversity. In general, research of the Tank lab is focused on the use of molecular methods to reconstruct phylogenetic relationships in plants and the application of phylogenetic methods to understand plant evolution. The evolutionary causes and consequences of processes such as hybridization, polyploidy, pollination biology, biogeography, rapid diversification, and niche evolution can only be understood in light of a robust phylogenetic hypothesis, and these hypotheses are a necessary component of modern taxonomic treatments and classification systems. Research in the Tank lab is directed at multiple levels of plant phylogeny and current projects range from comparative phylogeography of the Pacific Northwest inland rainforest communities, to the study of species boundaries and diversification among very closely related species, to patterns of diversification among some of the major lineages comprising the plant tree of life. In addition, successful applicants would also have the opportunity to take Dr. Tank’s Advanced Field Botany course — an intensive, two–week field course taught out of the University of Idaho McCall Field Campus.