Research
Experiences for Undergraduates at
Humboldt State University
Sponsored by
National Science Foundation
The Faculty at Humboldt State University
The program
will be organized and managed by Sean Craig, Matt Johnson and Mark Wilson. All the
faculty have extensive experience directing undergraduate research, and
many have co-authored published papers with undergraduates. Here, we briefly
summarize the research interests and extent of collaborations with undergraduate
students of the potential faculty mentors. We include links to research statements
for all faculty interested in mentoring REU students, but note that several will not be able to take on students this coming summer (2008). This page was updated on March 17, 2008.
Mentor List for summer 2008:
1) Dr. Michael Mesler (Biology)-yes (research description)
2) Dr. Michael Camann (Biology)-not yet known
3) Dr. Patty Siering (Biology)-yes (research description)
4) Dr. Mark Wilson (Biology)-yes (research description)
5) Dr. Jianmin Zhong (Biology)-yes
6) Dr. Karen Reiss (Biology)-yes (research description)
7) Dr. Bruce O'Gara (Biology)-yes (research description)
8) Dr. Sean Craig (Biology)-yes (research description)
9) Dr. P. Dawn Goley (Biology)-not yet known
10) Dr. Andrew Kinziger (Fisheries)- yes (research description)
11) Dr. Sarah Goldthwait (Oceanography)-no (scroll down at link)
12) Dr. Andrew Stubblefield (Forestry & Watershed Management)-not yet known
13) Dr. J.M. Varner (Forestry & Watershed Management)-yes
14) Dr. Matt Johnson (Wildlife)-yes (research description)
15) Dr. Mark Colwell (Wildlife)-yes
16) Dr. Susan Marshall (Rangeland Resources & Wildland Soils)-not yet known
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Impact of logging on plant-pollination interactions. Dr.
Michael Mesler.
Logging activities are expected to have a negative impact on the pollination success of native plant species via reductions in population size, increases in the distance separating populations, invasions by exotic competitors, and changes in the composition of local pollinator communities. Predicting responses to habitat alteration is complex, however, because some native plants and pollinators flourish in disturbed, open sites. Moreover, disturbance-related pollination deficits may be less severe for plants that attract a wide variety of pollinators than for those that rely on specific pollinators. Montane sites near the HSU campus provide a rich array of potential study sites that differ in degree of habitat alteration and in the richness of their plant-pollinator assemblages. Students will investigate the impact of habitat fragmentation and degradation on pollination success of a particular plant species and/or the structure of pollinator communities. Expected learning outcomes include greater familiarity with the basic tools and techniques of pollination ecology, including identification of bees and other pollinators.
Disturbance
and recovery responses of insect and microarthropod communities in old
growth forests. Dr.
Michael A. Camann.
Research in my laboratory is focused on the effects of disturbance and recovery on terrestrial arthropod community composition and organization in late-seral and mid-successional forests. Much of that effort is directed toward better characterization of soil and litter microarthropod assemblages in northwestern forests, including arboreal assemblages in forest canopies. Some current projects underway are: (1) low intensity fire effects upon soil and litter microarthropods, (2) habitat effects upon forest canopy insect and microarthropod associations in old growth redwood forests; (3) the role of canopy lichens and detritivorous microarthropods in old growth redwood forest nutrient dynamics; (4) the effects of anthropogenic disturbance and land use upon benthic macroinvertebrate assemblages in the montane South Fork Trinity River; (5) the ecological role of thatch ants in early successional maritime dune associations; (6) the effects of coarse woody debris in structuring forest soil and litter microarthropod assemblages in the ecologically diverse Klamath ecoregion; (7) the effects of silvicultural herbicide use upon forest soil arthropod community organization; and (8) the contributions of remnant old growth trees toward restoring late seral arthropod associations in regenerating managed forests. Undergraduates in my lab might work on some aspect of one of these projects or they might choose to pursue a related project that more closely matches their own interests. Their experience will likely include learning (or improving) field skills, e.g. site selection, sampling design, and data gathering, laboratory skills such as specimen classification and identification, and data analysis and modeling skills in community ecology.
Microbial diversity
in extreme environments. Dr.
Patty Siering.
The hot springs, steaming fumaroles, boiling mudpots, and sulfurous vents of Lassen Volcanic National Park (LVNP) represent some of the most extreme life-supporting environments on earth with temperatures from 50°C-115°C, and pH from 0-3. Our overall goal is to investigate the relative contributions of biotic and abiotic processes in geochemical cycling in high temperature, low pH environments. We are also interested in metabolic and genetic adaptations permitting life under these extreme conditions. Toward that end, my laboratory recently began using various chemical, molecular, and culture-based approaches to investigate geochemical, microbial, and functional diversity in several sites within LVNP. With the assistance of collaborators and several undergraduates at HSU, we surveyed geochemical composition and physical parameters of 34 sites within LVNP. We have begun culture-independent analyses of microbial diversity in acidic lake sediments (55°C pH 1.90), a fumarole-charged hotspring (93.5°C pH 1.23), and several geochemically distinct mudpots. With the help of a single undergraduate, we successfully isolated several prokaryotes from various acidic, high temperature features within the park, and we are in the process of identifying and characterizing these isolates. We currently are developing the methodology to use 16S rRNA T-RFLP analyses to investigate how microbial communities vary among low pH hotsprings and mudpots seasonally, and as a function of temperature, pH, and site geochemistry. This method will also be used to follow community succession in enrichment cultures derived from environmental samples. Our work continues to involve several undergraduate and graduate students in all aspects of this project. Current and potential undergraduate projects provide differing levels of emphasis on field work, general microbiology, molecular biology, population genetics (theory and data analyses), analytical chemistry and geochemistry.
Molecular ecology
and evolution of pollutant-degrading microbial communities. Dr.
Mark Wilson.
Students working on this project will learn to apply molecular approaches to study microbial communities involved in pollutant degradation. Continuing projects are focused on the characterization of novel polycyclic aromatic hydrocarbon (PAH) -degrading bacteria, and analysis of natural horizontal genetic transfer among these bacteria. Horizontal transfer of large catabolic plasmids is of fundamental importance in the acclimation of microbial communities to an influx of contaminants, and the lateral transfer of genetic material has played a major role in the evolution of modern microorganisms. New efforts will be focused on the isolation and characterization of PAH-degrading bacteria from marine and estuarine environments.
Systematics
and evolution of fishes. Dr.
Andrew P. Kinziger.
My research program is focused on sculpin fishes (Scorpaeniformes) with an emphasis on the Holarctic genus Cottus and Cottoid species endemic to Lake Baikal in Siberia. These two groups of fish exhibit an impressive array of taxonomic, morphological, ecological and behavioral diversity, however at the present time they are poorly understood. To untangle this enigmatic group my research program has used molecular data (DNA sequences) and morphological data to construct phylogenetic hypotheses, describe new species, identify unique population segments, evaluate hybrid zones and investigate biogeographic questions. Students working under my direction will have access to two excellent resources for pursuing research interests in the above areas. First, students will have an opportunity to work in a fully equipped genetics laboratory complete with an automated DNA analysis system for sequencing and microsatellite analysis. Second, students will have access to the HSU Fish Museum, dissecting microscopes, imaging equipment and software for morphological studies.
Morphological,
genetic and behavioral diversification in Townsends chipmunks. Dr.
Karen Reiss.
The Pacific Northwest harbors four species of chipmunks that are externally indistinguishable from one another. Traditionally, these species have been identified on the basis of genital bone morphology. The four species apparently occupy adjacent regions separated by major river boundaries. One molecular systematic study has shown that they form a monophyletic group and are presumably the products of relatively recent speciation, but the phylogeographic pattern of this divergence is unclear. My work aims to 1) generate a population-level phylogeny of these taxa to elucidate the historical pattern of diversification, 2) clarify species ranges at the headwaters of the putative river barriers, and 3) investigate the mechanisms that maintain species boundaries where they are found to exist. Extensive field work supplemented by museum loans generates specimens. Analyses include geometric morphometric analysis of genital bones, mitochondrial genome sequencing and phylogenetic analysis; sound analysis of alarm call vocalizations, and identification of volatile scent gland secretions. Students that work on this project are expected to devise a focal question of their own, and have the opportunity to become trained in a variety of methods: mammal trapping, recording and analyzing vocalizations, field studies of behavior, museum preparation and curation, traditional and geometric morphometrics, DNA extraction and sequencing, phylogentic analysis, histology, and, with the help of a colleague in Chemistry, mass spectrophotometry.
Habitat ecology
of coastal wildlife. Dr.
Matt Johnson.
My lab addresses ecological questions concerning the habitat ecology of wildlife near the coast - that is, the ecological processes wildlife follow to select habitats, how human land use affects their conservation, and how vegetation management influences wildlife populations. Currently, we are working in coastal grasslands and forests, examining how logging and grazing affect wildlife such as raptors, small mammals, bats, and songbirds. Students will generate hypotheses focusing on wildlife responses to habitats, and then test deduced predictions by collecting data on wildlife in the field. Such an understanding will help illustrate some of the complexities of the relationships between wildlife, habitat, and conservation.
Effects of environmental toxicants on behavior and neural function.
Dr.
Bruce O'Gara.
The oligochaete worm, Lumbriculus variegatus, is a widely distributed and common constituent of freshwater, benthic environments. Aquatic oligochaetes are important members of aquatic communities where they serve in such diverse roles as aiding in the decomposition of organic matter and as food for higher trophic levels. Lumbriculus normally positions itself so that its head is buried in the substrate and its tail is extended into the water column. Thus, these animals are susceptible to the effects of environmental toxicants that are present in either the sediments or the water column. Research in my laboratory has shown that exposure of Lumbriculus to low concentrations of copper disrupts the performance of several stereotyped locomotory behaviors and reduces the conduction velocity of neuronal action potentials mediating escape behaviors. Student projects would examine the effects of additional toxicants on motor behaviors, the electrophysiological correlates of escape behaviors, and alterations in the physiology of the circulatory system. In conducting behavior studies, students would videotape touch-evoked behaviors such as helical swimming, body position reversal and crawling. The performance of these behaviors would then be evaluated via frame-by-frame analysis of video tape recordings. Electrophysiological analysis of escape behaviors involves the recording of action potentials from giant axons via a noninvasive methodology that does not harm the worm and allows repeated testing of individuals as they undergo exposure to a toxicant. Data collected in these neurophysiology experiments are recorded and analyzed on a computer-based data acquisition system. In the near future, we hope to have an automated system up and running that will allow the monitoring of worm heart rate during exposure to toxicants (we presently perform a manual analysis of heart rate). Students participating in each of these studies will be involved in the design, data collection, analysis, and interpretation of experimental results.
Population and community ecology of benthic marine invertebrates.
Dr.
Sean Craig.
Many colonial/clonal marine organisms exhibit an extraordinarily diverse array of life-history strategies, some of which appear to contradict evolutionary theory. For example, an entire class of bryozoans (class Stenolaemata) reproduce sexually via polyembryony: the production of a single zygote which divides up to several hundred times to produce a clone of offspring. The cloned genotype is a unique, unproven genetic combination, rather than a copy of the mother successful genotype. This strategy is similar to xeroxing a single lottery ticket hundreds of times in order to win, and appears to make little sense. Understanding this strategy may throw light on the evolution of sex. With colleagues in the United Kingdom and South Africa, I have developed polymorphic microsatellite loci that confirm polyembryony in an intertidal bryozoan. These tools are available to (1) type bryozoan colonies in the field to identify clonal diversity and the degree of larval dispersal, and (2) determine the fitness of copied genotypes, relative to novel genotypes, grown in the laboratory or field. Students in my lab could study this, and other enigmatic strategies (such as fusion of colonial marine sea squirts, bryozoans, or hydroids to form genetic chimaeras, which I have worked on in the past) using molecular-genetic tools. In addition, I have several undergraduates in my lab investigating the pattern of succession on artificial fouling panels deployed below floating docks in Humboldt Bay. We have 2 years of data that suggests there is no climax state in these communities, and the pattern of succession appears to be highly seasonal. There are a large number of introduced species (approximately 35% of the fauna on our experimental panels), and many are dominant space competitors. This system is highly amenable to manipulative experiments, and future REU students could easily develop projects manipulating species diversity, density, or spatial position to determine their effects on succession and invisibility of these communities by exotic species.