URAP

Annaliese Beery - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Research in our laboratory is focused on factors that influence affiliative social behavior in two species of voles. This project involves working with a graduate student on scoring behavior in multiple types of behavioral trials, or continuations of other pre-arranged research projects...

Annaliese Beery - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

We maintain breeding colonies of meadow voles and prairie voles for social behavior research. This project builds on basic husbandry (covered by staff) to track lineages, wean new litters and determine pup sexes to maintain the long term health and robustness of our breeding program and provide voles for research...

Mike Boots - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Our research group in the Department of Integrative Biology researches the dynamics of infectious disease evolution and population biology in multiple insect systems, including Lepidopteran hosts (moths and butterflies). We are currently working on two interconnected projects: The first project investigates host heterogeneity by examining how environmental factors (such as...

Mike Boots - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Interactions between infectious diseases and their hosts underpin a vast array of ecological and evolutionary dynamics. These antagonistic biotic interactions may influence processes like why organisms sexually reproduce and migrate and infectious disease evolution is important for many applied problems like antibiotic resistance, disease emergence, and agriculture. Many factors impact...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

We are working on a project to study the adaptation and evolutionary history of hummingbirds and sunbirds. Hummingbirds and sunbirds are two groups of birds that have independently adopted nectar as a major component of their diet and have evolved to be morphologically similar. Our project aims to explore whether...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

My lab is involved with a large collaborative project to study disease transmission within and among species of wild birds. As part of this project, swabs of a variety of bird species are being collected to study their microbial communities (i.e. their microbiome). Lab studies suggest that microbial diversity can...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

Students can assist with several ongoing research projects that investigate geographic variation and species limits in birds and integrate these data with quantification of prevalence of disease vectors such as bird malaria and trypanosome infections...

Rauri Bowie - Professor, Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Nest structures are widespread across animals including insects, fish, amphibians, and most conspicuously, birds. Despite their ubiquity, nests remain one of the most understudied components of avian life history. Some of the most remarkable examples of elaborate nest design are within the passerine weaverbirds (family Ploceidae). Weaverbirds are an Old...

Robert Dudley - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Flying insects are the most diverse and abundant form of animal life in the terrestrial biosphere. However, the origins of insect flight remain obscure given the absence of a transitional fossil record. This project will involve construction of a small robot that mimics the likely morphology of early insects, and...

Moisés Expósito-Alonso - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

The global climate is changing at an unprecedented rate due to human activities, threatening global biodiversity and food security. A fundamental question in evolutionary biology is: What enables or limits species to rapidly evolve and adapt to changing climates? In this project, we will use natural ecotypes of Arabidopsis to...

Seth Finnegan - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

For tens of millions of years large parts of California’s Central Valley were flooded by the ocean, creating an inland sea with a unique ecosystem including now-extinct species of clams, snails, sand dollars, corals, and other groups familiar from modern California beaches. Some of the species that lived in...

Seth Finnegan - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Besides coral, marine reefs are made up of many other strange invertebrates, including the little-known “moss animal”, or bryozoan. These abundant, microscopic filter-feeders grow in colonies and build elaborate domes, lacework, and tree-like structures on the ocean floor, from the intertidal to the abyss, from the poles...

Seth Finnegan - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Death assemblages’ are the actively accumulating shelly remains of organisms living at the bottom of the ocean. Because death assemblages accumulate over 100s to 1,000s of years, they are powerful tools to estimate past biodiversity. By comparing the ecological composition of living communities and death assemblages, we can assess recent...

Mimi Koehl - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

We are studying the biomechanics and biofluiddynamics of how organisms interact with their physical environments. Our interdisciplinary work is at the interface between biology and engineering, so students majoring in biology, engineering, physics, or math have all participated in research in our lab. There are a variety of projects that...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Microbiomes change over time, often with important functional consequences for their hosts. But the ecological drivers of microbiome succession are poorly understood. We are studying the role that microbial interactions play in this process by examining the constituents of the digestive microbiome of the insectivorous California pitcher plant (Darlingtonia californica...

Britt Koskella - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Phage, viruses that infect and kill bacteria, are ubiquitous, yet their impacts on beneficial bacteria that colonize plants are not well understood. Phage are abundant in the soil and therefore soil-dwelling bacteria must hone defenses against phage in order to survive. Likewise, phage must hone their capacity to infect...

Britt Koskella - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

We are building a new system (fire blight of pear trees) to better understand how bacteriophage viruses might impact the ability of a bacterial pathogen (Erwinia amylovora) to colonize and infect pear trees. We are tracking bacteria-phage interactions through time by isolating individual phages from each of 25 diseased...

Britt Koskella - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

In natural systems, microorganisms interact with myriad other microbial populations which influence their evolution and ecology. When associated with a eukaryotic host, these complex microbial communities (known as microbiomes) also interact with and impact their host’s ecology and evolution, nutrient acquisition, and pathogen susceptibility. Despite the microbiome's vast importance on...

Juan Liu - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Lateral line sensory system, or lateral line organ, or simply the lateral line, is a system of sensory organs found in fish and some tetrapods (four-legged vertebrates). The lateral line enables those vertebrates to detect and perceive the hydrodynamic and physical environment they inhabit including movement, vibration, and pressure...

Juan Liu - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Scientific illustration is art in the service of science by drawing, painting, or rendering images of scientific subjects to accurately inform and communicate sciences. Research in fossil fishes (paleoichthyology) is at the junction of paleontology and ichthyology, and therefore, possesses characteristics of both —-- the incomplete nature of fossil preservations and...

Juan Liu - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Our study aims to explore the intricate details of mammalian hearing, with a specific emphasis on the function and evolution of the middle ear, with comparative anatomy with fish hearing apparatus. This critical aspect of auditory anatomy plays a pivotal role in the way mammals perceive and interpret sound. By...

Juan Liu - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Catfishes (Siluriformes) are remarkable among hearing specialist fishes in their possession of the Weberian apparatus, a conductive multi-ossicle chain linking the inner ear and swim bladder that is analogous to the middle ear ossicles of the mammalian tetrapods. Work with laboratory animals has produced considerable insight into the role...

Cynthia Looy - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 3-5 hrs     Location: On Campus

At present, flowering plants (angiosperms) represent ~90% of the land plant species and are dominant in most global biomes. However, the first flowering plant is known from the fossil record around 135 million years ago (mya) during the Early Cretaceous, much more recent compared to the gymnosperms, which first appeared...

Cynthia Looy - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: Off Campus

In many ways, the Earth of the Permian period (298.9-251.9 million years ago) would have looked alien to a modern observer: the Earth’s surface was divided between the supercontinent Pangea and the superocean Panthalassa, strange animals neither mammal nor dinosaur dominated terrestrial faunas, and no flower would bloom for more...

Cynthia Looy - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 3-5 hrs     Location: On Campus

Pollinators are essential components of a healthy ecosystem and provide vital benefits to both plants and animals. The student-run pollinator garden around the Valley Life Science Building (VLSB) supports native arthropods (e.g. insects and spiders) and other wildlife and is an environmental education resource for students. We plan to...

Cynthia Looy - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: Off Campus

Plants are adapted to the physical conditions in their environments, including temperature, precipitation, atmospheric CO2 concentrations, and light level. In cooler and drier habitats, leaves tend to be smaller with condensed venation and toothed margins. While under warmer and wetter conditions, leaves tend to be larger, have ‘drip tips’, and...

Charles Marshall - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

The colonization of land by plants and animals from the oceans was pivotal in our planet’s history, leading to major climate change and the evolution of the great forests, dinosaurs, and our own species. However, the first terrestrial and freshwater aquatic ecosystems are poorly understood due to a spotty fossil...

Charles Marshall - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

This research seeks to understand the factors responsible for species dispersal. Specifically, we are interested in dispersals during an event known as the Great American Biotic Interchange (GABI). GABI was a large-scale exchange of taxa between North and South America via the emergence of the Isthmus of Panama. These...

Michael Nachman - Professor, Museum of Vertebrate Zoology, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Within ~500 years, house mice (Mus musculus domesticus) have expanded into a wide variety of habitats across North and South America. House mice can be found from the tropics to the arctic, and populations inhabiting these different environments have adapted to different thermal regimes. This project will focus on the...

Michael Nachman - Professor, Museum of Vertebrate Zoology, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Within ~500 years, house mice (Mus musculus domesticus) have expanded into a wide variety of habitats across North and South America. House mice can be found from the tropics to the arctic, and populations inhabiting these different environments have adapted to different thermal regimes. Mice from cold regions are larger...

Daniel Okamoto - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Climate change is dramatically altering the oceans. These changes include increases in sea surface temperature, pH, dissolved oxygen, and primary productivity. We use experiments and field data to assess how these changes affect the physiology, growth, reproduction, and behavior of marine animals. We have numerous samples from past experiments and...

Victor Ortega Jimenez - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Marangoni effect is used by water striders (Veliidae) and rove beetles (Staphylinidae) to induce an ultrafast escape response against inter- or intra-specific predators. However, it is unclear if the surfactants secreted by these insects, that reduce surface tension of water, can also affect predator’s locomotion during the chasing...

Michael Shapira - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Toxins play important roles in inter-species interactions, and the ability to overcome them can open new niches. The potential of animal genomes to facilitate such adaptations is limited; instead, toxin resistance in animals is often provided by gut bacteria. Human activity and industry has dramatically increased the prevalence of...

Michael Shapira - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Animal microbiotas are increasingly recognized as essential for host health. The gut microbiota is the richest, and was shown to contribute to diverse host functions. Perturbations in microbiota composition are associated with human disease, raising interest in manipulating the microbiota to promote healthier living or treat pathology. However, current understanding...

Michael Shapira - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 12 or more hours     Location: On Campus

Aging involves a multi-system physiological deterioration. In addition to affected tissues, and likely as a consequence, aging also affects the gut microbiota, an extensive microbial community which contributes to diverse host functions. Imbalances in microbiota composition, or dysbiosis, are often associated with pathology, and recent reports indicate that aging...

Ellen Simms - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Introduced plants can become invasive when they escape the insect and microbial enemies that control native plant populations. Legumes benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. We have found that three invasive leguminous plant species (French broom, Spanish broom, and Scotch...

Ellen Simms - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: Off Campus

Until recently there was still the idea that when it comes to the microbial world, since it is so small, everything must be everywhere. Much current research is showing this claim does not hold water. Few things are truly everywhere and most things, even on the micro scale, have very...

Ellen Simms - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

Bacteriophages (phages, for short) are viruses that attack and kill bacteria. Phages tend to be host specific (specialize on particular bacteria), which allows them to influence bacterial community composition. Legumes are plants that benefit from symbiotic relationships with nitrogen-fixing bacteria called rhizobia, which colonize nodules in legume roots. Rhizobia...

Ellen Simms - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

High temperature is an abiotic stress that impedes the growth and productivity of all crops irrespective of their heat tolerance. High temperature affects the development of both vegetative and reproductive structures. It arrests cell proliferation arrest, increases vacuolization, causes over-development of chloroplasts, certain abnormalities in other organelles, and comprehensively...

Rebecca Tarvin - Professor , Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

Evolutionary transitions underlying phenotypic change are difficult to study because they often occur over millions of years. However, the fruit fly has a short generation time and a small genome that is well annotated and cheap to sequence. We used a large-scale experimental evolution approach to evolve toxin-sequestering...

Rebecca Tarvin - Professor , Integrative Biology, Museum of Vertebrate Zoology

Status: Full- no new appr needed     Weekly Hours: 6-8 hrs     Location: On Campus

The Tarvin Lab studies how and why poison frogs don’t poison themselves. We aim to measure the effect of toxin consumption on frog health and chemical defenses through toxin feeding experiments paired with phenotypic assays (health monitoring, jumping challenges) and genomic assessment (RNA and DNA sequencing...

Rebecca Tarvin - Professor , Integrative Biology, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 9-11 hrs     Location: On Campus

Amphibians -- frogs, salamanders, and caecilians -- exhibit a stunning variety of chemical defenses, ranging from antimicrobial peptides to antipredator neurotoxins and biological glues. Amphibian glues are the least-studied of these defenses. Additionally, the methods used to measure amphibian stickiness are not standardized, with some researchers gluing together beer cans to...

Rebecca Tarvin - Professor , Integrative Biology, Museum of Vertebrate Zoology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Amphibians -- frogs, salamanders, and caecilians -- exhibit a stunning variety of chemical defenses, ranging from antimicrobial peptides to antipredator neurotoxins and biological glues! These defenses generally co-occur with physiological, morphological, and behavioral adaptations that sometimes exhibit convergence with distantly related taxa. However, research into amphibian chemical defense has been far...

Jack Tseng - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Bone crushing dogs were a diverse and successful subfamily of canids that thrived throughout North America for nearly 30 million years. As bone crushing dogs evolved they show convergent features with hyaenas in their cranial anatomy (i.e. a large sagittal crest and domed forehead to dissipate stress). While the skull...

Jack Tseng - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 3-5 hrs     Location: On Campus

With over 260 recognized extant species, the order Carnivora is one of the most diverse mammalian groups today, with a history tracing back approximately 60 million years. Crown carnivorans are divided into two suborders: Feliformia (cats, genets, hyenas, mongooses, etc.) and Caniformia (dogs, bears, raccoons, weasels, skunks, seals, etc.). Despite...

Jack Tseng - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Studying vertebral measurements and trabeculae's shape and orientation can provide a more comprehensive understanding of how rodent groups adapted to their specific environments and lifestyles. Quantifying the gross morphological variation of each rodent group through vertebral measurements can provide information about weight-bearing capacity, stability, strength, mobility, and flexibility. Additionally...

Jack Tseng - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: 6-8 hrs     Location: On Campus

Human actions and infrastructure are impacting biodiversity in real time, rapidly changing environments, modifying ecological interactions, and introducing new selection pressures that living organisms have never before encountered. To develop effective, targeted conservation strategies, we need to understand how anthropogenic actions, infrastructure, and management decisions influence evolution. One of the...

Jose Pablo Vazquez-Medina - Professor, Integrative Biology

Status: Current Term Now Closed     Weekly Hours: to be negotiated     Location: On Campus

Oxidative damage to mitochondria has been implicated in the pathogenesis of diabetes, stroke, nonalcoholic fatty liver disease (NAFLD), and many other metabolic syndrome disorders. Recent work shows that deletion of the antioxidant protein peroxiredoxin 6 (PRDX6) dysregulates mitochondrial function. PRDX6 is a multi-functional enzyme that expresses at least 2...

Jose Pablo Vazquez-Medina - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: 9-11 hrs     Location: On Campus

This project seeks to characterize cells isolated from the blubber of northern elephant seal pups during the post-weaning fasting period. Elephant seal pups nurse from their mothers for ~1 month, after which they are abruptly weaned and carry out a terrestrial post-weaning fast for several months prior to...

Jose Pablo Vazquez-Medina - Professor, Integrative Biology

Status: Full- no new appr needed     Weekly Hours: to be negotiated     Location: On Campus

The focus of this project is to develop tissue culture models to answer mechanistic questions that are relevant to physiological responses during diving and under stress conditions in sea turtles. This project will examine sea turtles’ adaptations to hypoxia by characterizing gene expression and reactive oxygen species generation under differential...