Research in the sciences at Gonzaga University covers a wide range of topics at the cutting edge of science, not just in the traditional definitions of the disciplines, but at the interface of biology, chemistry and physics as well. Below you will find short descriptions of the individual research interests and/or available projects in faculty labs. If you are interested in any of these projects, or even if you simply have questions, please contact the faculty member directly.
For more independent research opportunities, check out our neighbors across the river, the WWAMI Medical Education Program. Research faculty at WWAMI may have openings in their labs for Gonzaga undergraduates. Please see the descriptions of their research below.
If you have any questions, please see Christy Watson or contact the WWAMI faculty directly.
If your research will make use of the Gonzaga Greenhouse, you will find more information here.
Summer 2014 Research Positions
For students interested in applying for a Summer 2014 research position, you must check with the specific laboratory below to make sure there is an open position.
Not all faculty have open research positions!
If you are still interested in applying, fill out the application on the Undergraduate Research Main page.
Scroll down to view more detailed information for all faculty members, or click on a faculty member’s name to go to that specific laboratory.
Elizabeth Addis: mechanisms of life history control
Kirk Anders: eukaryotic genetics using yeast as a model organism
Julie Beckstead: interactions between invasive plant species and seed pathogens
Mia Bertagnolli: signaling molecules involved in cell adhesion, migration and disease
Carla Bonilla: molecular mechanisms of bacterial stress response
Shawn Bowers: bioinformatics and biodiversity data discovery
(Dr. Bowers is a member of the Computer Science Department, and has research interests with biological implications.)
Gary Chang: ecology of predatory and herbivorous insects
Bill Ettinger: regulating photosynthetic carbon fixation
Joey Haydock: reproductive partitioning in the cooperatively breeding acorn woodpecker
Hugh Lefcort: predator/prey relations in aquatic snails (Note: Dr. Lefcort accepts summer students only)
Marianne Poxleitner: evolution of cocaine biosynthesis and genetic enhancement of crops
Nancy Staub: salamander evolutionary biology
Brook Swanson: evolution of complex mechanical systems in animals
Steven Whitfield: disease ecology and global amphibian population decline
Dan Chase: organic synthesis of fluorescent molecules
David Cleary: synthesis and characterization of extended inorganic compounds with applications to chemical sensors, batteries, and catalysis
Matt Cremeens: neuropeptides: neuroscience for the organic chemist
Jeff Cronk: enzymatic and structural studies of β-carbonic anhydrase
Greg Gidofalvi: computational chemistry/electronic structure
Kate Hoffmann: cloning and structural characterization of NIS siderophore synthesis enzymes
Eric Ross: stationary phase development for chromatographic analysis of biomembrane interactions
Jennifer Shepherd: rhodoquinone biosynthesis in parasitic helminths
Joanne Smieja: household water treatments
Stephen Warren: synthesis and development of a diagnostic agent for neurodegenerative diseases and type 2 diabetes
Jeff Watson: mechanism of bacterial HMG-CoA reductase, a target for novel antibiotics
Erik Aver: primordial helium abundance
Kenneth Roberts: sperm maturation, function and fertilization with application to male infertility and contraception
Weihang Chai: cellular and molecular mechanisms behind the growth of cancer cells, especially the mechanism that regulates telomeres
Leventa Kapás: humoral/hormonal regulation of sleep in rodent models
James Krueger: biochemical regulation of sleep
Éva Szentirmai: the links between sleep and metabolism
Jonathan Wisor: neurobiological basis for sleep, biological rhythms, and sleep disorders therapeutics
My research is broadly focused on physiological and evolutionary ecology, and specifically on the evolution of mechanisms that control life history strategies. I broadly use vertebrates (birds, snakes, and turtles) as my study systems because they exhibit a wide range of life strategies that frequently diverge from those of traditional model organisms. Taking a holistic approach, my work combines ecological and hormonal measurements in the field with genetic and hormonal analyses in the laboratory.
For Summer 2014 I will be only accepting new students to work on the following project.
Urbanization of yellow-bellied marmots. Spokane is famous for its marmots. Marmots usually do not live in urban areas, although the prevalence of them is increasing. How can some marmots flourish in urban areas, such as Spokane, while others do not? In other species, both baseline and stress induced levels of glucocorticoids vary between urban and rural individuals. This project will explore whether such variation also occurs in marmots and whether this variation allows marmots to breed successfully in urban areas.
I am interested in genes, chromosomes, and genomes: how they contribute to the traits of an organism, how they are transmitted during cell division, and how they can change from generation to generation. My research makes use of the brewer’s yeast Saccharomyces cerevisiae as a model eukaryotic organism, and more recently I have been exploring the genetic analysis of bacterial viruses called mycobacteriophages. With regard to yeast, my students and I are working to understand how a common mistake in cell division--resulting in an extra chromosome--affects phenotype, genome stability, and ultimately, fitness. We are currently studying the effects of duplicating the small chromosome 6. We discovered that an extra copy of chromosome 6 prevents viability, and that an imbalance in tubulin expression is one significant cause. We suspect that there may be additional gene dose imbalances that interfere with other cell functions when chromosome 6 is duplicated. Our current goal is to discover and characterize the other significant dose imbalances at the molecular level. We use a variety of methods, including recombinant DNA techniques, microbial genetics, and whole-genome microarrays. With regard to bacteriophage genes, whole-genome sequencing can identify the genes present in the phage genome, but the sequence alone rarely indicates what the function of each gene is. We are employing similar recombinant DNA techniques and microbial genetics as our yeast work to discover the functions of newly-identified genes in bacteriophage genomes.
Projects will focus on microbial ecology, plant-pathogen interactions, and invasion biology. I work on an invasive plant, cheatgrass (Bromus tectorum) that has devastated the Intermountain West. My long-term goal is to eliminate this invasive species and provide land managers with tools to restore cheatgrass-infested natural areas to native plant communities. I currently have two ongoing projects.
One project is to learn more about a seed pathogen that kills cheatgrass seeds and is being investigated as a potential biological control. Student-lead projects may include determining whether this pathogen can also kill other related Bromus species and whether strains on a given species are specifically adapted to that host. We also want to figure out how the fungal seed pathogen undergoes sex so we can breed better biocontrol strains.
The other project is just beginning but is very exciting. There are naturally occurring die-offs of cheatgrass in the Western United States. Nobody knows who is causing these die offs. We want to figure out if pathogens are involved and how to use these organisms to eliminate cheatgrass and facilitate restoration to native plant communities.
The research work will involve basic microbiology skills (aseptic techniques, making various types of agars, isolation of fungus, and inoculation experiments) as well as seed germination experiments and collecting samples in the field. Preference will be given to students who have completed BIOL 102 and BIOL 201. Please contact Dr. Beckstead, if you have an interest in working on these projects.
Dr. Bertagnolli is not accepting new students for Summer 2014.
As a cell biologist, I am interested in signaling pathways involved with cell adhesion and migration, and how alterations in these processes lead to disease. For example, many individuals with colon cancer have mutations in the Adenomatous Polyposis Coli (APC) gene, which affects cell adhesion and migration and ultimately results in tumor formation and metastasis. Patients with diabetes have altered signaling pathways that result in tissue injury. Using cells cultured in the lab, we can manipulate the genetic and/or physical environment of the cells to mimic the conditions they would experience in patients with these conditions and then study specific parts of signaling pathways that are altered by these conditions. Undergraduate students who participate in these projects become independent in the research laboratory and are exposed to basic laboratory skills as well as more advanced techniques such as cell culture and sterile technique, microscopy, gel electrophoresis and Western immunoblotting. Students typically take Cell Biology (BIOL 201) prior to working in my lab.
This project will focus on original experiments designed to study signaling molecules involved in pathways that lead to tissue injury in diabetes. Control epithelial cells grown in culture will be compared to those that are given high levels of glucose, similar to the conditions found in diabetic patients. Cell morphology, growth rate and adhesion will be analyzed under these conditions. In addition, the distribution of signaling molecules thought to be involved in diabetic pathways will be compared. Laboratory techniques used in these experiments include growing cells in culture, microscopy (both light microscopy and fluorescence microscopy), and image analysis. In addition, the student will gain significant experience in experimental design and data analysis, and the opportunity to interact with collaborators at the Providence Medical Research Center in Spokane.
I am fascinated by the ability of bacteria to survive in all kinds of environments. My research focuses on studying the response to environmental changes of the soil bacterium, Bacillus subtilis; that allow it to survive stressful conditions. B. subtilis is the model Gram positive organism because of its ease of genetic manipulation, sequenced genome and conservation with other pathogenic bacterial species. Bacteria, pathogenic and nonpathogenic, live in complex environments and must monitor their surroundings for nutrients, noxious chemicals, predators, etc. They accomplish this by using proteins that sense the environment (sensor proteins) and proteins that enact changes in gene expression (transcription factors) that alter the physiology of the cell to accommodate the changing conditions. I am interested in understanding the proteins involved in this bacterium’s stress responses at a molecular level.
Student projects will include testing the role of these sensor proteins and transcription factors using in vivo assays such as 1) bacterial survival after exposure to stress on solid and liquid media and 2) understanding the role of sensors proteins in biofilm formation, a form of stress response, by assaying mutants for their ability to form biofilms. Other projects are molecular in nature and include 3) measuring gene expression of stress responsive genes using RT-PCR of different mutant B. subtilis strains and 4) biochemical characterization of sensor proteins in the presence of stress signal molecules to identify activating and regulatory step
My research and each project below is focused on developing informatics tools and approaches related to ecology and biodiversity data discovery and integration.
In collaboration with UC Davis and Arizona State University, we are developing approaches for describing and reasoning over alignments between biological and phylogenetic taxonomies. We have developed a set of tools (collectively called Euler) for describing mappings between two taxonomies and then determining whether the result "makes sense" (is consistent) and if so, to compute the resulting taxonomy induced by the alignment. Given this, there is still a need for developing meaningful visualizations of the resulting taxonomies, developing approaches for explaining (and visualizing) why an alignment is inconsistent (as well as why the alignment produced a certain result), benchmarking different algorithms/tools for performing the alignment, and optimizing the underlying alignment algorithms. Other topics for potential student projects include looking at standard taxonomy revision techniques ("splitting" and "lumping") as well as specific properties of phylogenetic trees to enhance the alignment approach.
Another area for student projects concerns automating the development of ontologies for annotating ecological data sets. This work is in collaboration with UC Santa Barbara (NCEAS) through a variety of ongoing informatics projects to support ecology data management. Ontologies provide structured and controlled vocabularies for describing data sets and can be used to improve the precision and recall of data discovery queries. As an earlier pilot project, we developed a set of scripts to automatically extract and analyze relevant terms from a corpus of ecology papers. We would like to further analyze the results and extend the approach to find richer relationships between terms (which can further improve precision and recall). For example, it may be possible to use co-occurrence or other standard information retrieval approaches to discover relationships among terms. Another approach would be to look at external sources that already provide some term relationships (such as GBIF or WordNet) to "seed" relationships and discover new ones. A similar project would be to extend the approach to consider a wider range of information sources, including ecology metadata repositories (such as the KNB).
The research work described above will involve computer programming skills, primarily focused on developing and running basic scripts (in Python or R) to carry out experiments and to implement relevant tasks. It is anticipated that students will learn a variety of new skills as part of each of the above projects. Students will also potentially collaborate with computer science students working on related topics.
The landscape of Spokane County is a blend of urban and non-urban habitats. The species that live here can respond in different ways to urbanization. Our research team focuses on understanding the contrasting response of a weed, Dalmatian toadflax, and its biological control agent, an herbivorous weevil, to Spokane's landscape. In short, the weed is more abundant in urban areas while the weevil is more abundant in non-urban areas, and we are trying to explain why.
During Fall 2013, our research will proceed in two directions. First, we will analyze data collected in the field this past summer. The other direction will be in developing a theoretical model of weevil and toadflax populations that focuses on connecting larger-scale patterns to events in individual habitat patches. Ideally, prospective students should brainstorm some of their own hypothetical explanations for the patterns in weed and weevil abundance, and then visit me in person to discuss how a model might influence their ideas.
Several different lines of evidence suggest that changes in calcium concentration in the chloroplast may have a role in regulating photosynthetic carbon fixation (dark reactions). To test this theory, Dr. Ettinger is in the process of measuring the levels of calcium inside different compartments of the plant chloroplast. Many different ion selective electrodes or fluorescent metal binding dyes lack the ability to effectively discriminate between calcium and magnesium ions. The calcium sensitive biolumenescent protein aequorin has been routinely used to measure calcium in biological systems. The protein emits photons in proportion to the calcium activity in solution. A recombinant DNA vector (pMAQ6) has been developed that directs the expression of aequorin in the plant chloroplast stroma. Dr. Ettinger and his students are transforming common wall cress Arabidopsis thaliana with pMAQ6 with the hopes of measuring calcium concentrations in the chloroplast stroma, and is developing other vectors to direct the expression of aequorin and direct its alternate localization to the thylakoid lumen and the plant cytosol. This research requires skills developed in quantitative analysis (CHEM310, or CHEM240), and genetics and evolution (BIOL202) or molecular biology.
My students will be working on our project to measure Ca2+ concentrations in living plant chloroplasts. We are using calcium-sensitive proteins as in-vivo probes of calcium concentrations. One such probe, Aequorin is a bioluminescent protein that luminesces in direct proportion to the amount of calcium present in solution. My collaborator, Carl Johnson, previously created an RBCS:aequorin construct to study calcium concentrations in the chloroplast stroma. Last summer my students modified Dr. Johnson’s vector to create two thylakoid-localized versions of Aequorin; one with an OE23 transit peptide, and the other with an OE17 transit peptide. The OE23:Aequorin and OE17:Aequorin chimeric genes have been successfully transformed into Arabidopsis thaliana plants. We have performed subcellular localization studies on the transgenic plants and have demonstrated that the plant transformed with the OE23:Aequorin construct is expressing Aequorin and localizing the protein to the thylakoid. We need to do further studies to assess the localization of the OE17:Aequorin protein product. Furthermore, many of the localization studies have been performed on Tobacco plants. We greatly desire to create transgenic tobacco plants using our vectors. This would enable us to perform much more comparative studies.
Another Calcium-sensitive protein probe we are working on is YC3.6, which is calcium-sensitive fluorescent protein. We have designed vectors that should express YC3.6 in plant cells and target the protein selectively to the chloroplast stroma using a transit peptide from the small subunit of Rubisco (RBCS), or to the thylakoid lumen using the transit peptides from either OE17 or OE23. The RBCS:YC3.6 construct was recently created and we are attempting to transform Arabidopsis thaliana plants with that construct. My students will also be working on cloning the YC3.6 gene into an E.coli expression vector. Overexpressing YC3.6 in E. coli will allow us to purify significant amounts of YC3.6 to be used in the study of the pH and oxygen sensitivity of the protein.
The general goal of the project has been to explicitly test hypothesis concerning reproductive partitioning in the cooperatively breeding acorn woodpecker, which have been under study at Hastings Natural History Reservation in central coastal California since 1971. What is cooperative breeding and what is reproductive partitioning? Cooperative breeding refers to social species in which the parents as well as other individuals in the social group provide care for offspring (termed alloparental care). Reproductive partitioning refers to distribution of parentage in social groups in which more then one breeder of each sex competes to breed. In most cooperatively breeding birds, social groups only contain a breeding pair and their offspring that do not breed, at least in part due to incest avoidance, so reproductive partitioning is not an issue. Acorn woodpeckers are unusual among cooperatively breeding birds in that social groups can consist of up to seven males that are unrelated to up to three females within a single social group, in addition to their offspring that are also group members. Thus, reproductive partitioning, which can range from egalitarian with each individual obtaining about equal reproductive success to high skew where a single individual of each sex monopolizes breeding, becomes an important component of each individual’s fitness. Several hypotheses have been proposed that make predictions for the amount of skew, based on factors including within sex relatedness, competitive ability and probability of successfully dispersing to another group. The goals off my students have involved collecting parentage information to test a specific one of these hypotheses.
A critical question to understanding the fitness costs and benefits of sociality in acorn woodpeckers is to obtain parentage information on reproductive partitioning within groups that contain at least two potential breeders within a sex. Because group structure varies considerably (number of potential breeders, age structure, genetic relatedness, and genealogical relationship), information on many groups is required to build a complete picture.
Previous work with students from Gonzaga University has produced the development and optimization of microsatellite primers to determine parentage as well as individual genotypes for 800 individuals (on up to 12 loci). My students have worked on relatively small sets of groups that are similar in structure (e.g. 2 potentially cobreeding males and a single female breeder) addressing specific hypotheses. Despite the wealth of data produced thus far, more data is needed, especially in complex social groups (see project 2 below). In addition, I hope to begin development of a new technique that will allow for the determination of mating success among cobreeding males by detection of sperm in the perivitelline layer of eggs (see project 1 below).
Proximate mechanisms of sperm competition and skew. The eventual goal will be to determine potential proximate mechanisms by which skew is maintained and paternity determined by genotyping sperm present on the perivitelline membrane of eggs. The idea behind this relatively new technique is to identify the sperm trapped between the ovum’s perivitelline layers as an allelic record of sperm competition close to the time and place of fertilization. It involves the relatively simple procedures of collecting eggs either prior to or immediately after the start of incubation and removing the perivitelline membrane. The technical hurdles involve eliminating the maternal and/or embryonic DNA attached to the membrane that, due to their higher concentration, can potentially confound PCR amplification of the sperm DNA, and matching the remaining DNA to potential sires. In collaboration with Dr. Bart Kempenaers of the Max Planck Institute, I hope to have a student working on refining this technique and overcoming the technical hurdles mentioned above. In the case of acorn woodpeckers, the application of this technique over the next few years offers the opportunity to infer information about the mating history of females that, because copulations are almost never seen, cannot be obtained observationally. This will be particularly valuable in the following contexts: (a) Is sperm from both males in groups with 2 cobreeder males (and a single breeder female) generally present at fertilization, even though almost two-thirds of nests are sired by a single male? If not, then it would suggest that females copulate with only a single male for each clutch, in which case it is plausible that males could adjust their behavior according to copulatory access (e.g. for degree of effort in feeding nestlings) If sperm from both males is generally present, the question remains as to why one of the males is generally so much more successful at gaining paternity and has implications for breeders not knowing actual paternity; (b) Do sperm present differ between sequential nests involving the same coalition of males? If so, this would suggest that females copulate with a different male for each clutch, offering a mechanistic explanation for the observed switching of paternity between successive clutches; (c) In large, complex groups containing 2 joint-nesting females and/or 4+ cobreeder males this technique will be especially informative, particularly when such coalitions include younger sons that appear not to achieve their fair share of paternity (based on previously collected data). d) Do sperm present differ in sequential nests involving the same coalition of males and breeder females? If so, this would suggest that females are not consistent with what males they copulate with, again offering a mechanistic explanation for the observed switching of paternity between successive clutches.
Reproductive partitioning in complex groups.The other students working in my lab will continue to investigate the patterns of reproductive bias in large male coalitions (one student) and among complex social groups containing joint-nesting females and large male coalitions (a second student). While only 12% of groups between 2004 and 2008 involved 3 or more cobreeder males, 27% of breeder males lived in coalitions of 3 or more and are thus important to estimating the direct and indirect fitness benefits of cobreeding. Similarly only 15% of groups contain joint-nesting females, but 23% of breeder females live in coalitions. Preliminary data from the complex social groups suggest that nests produced by joint-nesting females are more likely to be multiply-sired than nests of single females and that there is no difference in the frequency of multiple paternity between nests with small vs. large coalitions of cobreeder males. Both of these patterns will be addressed in these student projects.
Please note that Dr. Lefcort accepts applications for summer research positions only.
This research comes about due to the threat of high levels of carbon dioxide that humans are releasing. Carbon dioxide in water is converted to carbonic acid. Sea water that is more acidic lowers calcium and aragonite saturation states which make it harder for organisms to calcify their shells and skeletons. Most attention has been directed at marine creatures where a 0.1 increase in ocean water acidity since the industrial revolution has been noted. Although this value appears small, the change has occurred 10 times faster than at any time in the last 50 million years.
While much attention has been given to marine systems, CO2 may also affect freshwater aquatic systems. Lake acidification gained attention during periods of worry in the 1980’s over acid rain but few studies have explored the effects of CO2 on aquatic systems.
My lab studies the ecological and behavioral effects of heavy metal pollution on populations of Physella columbiana and Lymnaea palustris aquatic pulmonate snails. I am looking for two students to explore how atmospheric CO2 increases may affect snail ecology. In partial collaboration with Dr. Cleary (Chemistry), my students and I will bubble CO2 into pond water and then look at the effects of acidic water on snail anti-predatory behavior.
Although most of the work will be in the laboratory the students need to be prepared to work outside to gathering snails from the field.
I currently have two projects underway in my lab. The first is a plant genetic engineering project to confer aphid resistance to roses. The second is a bioinformatics projects to sequence and annotate Erythroxylum chloroplasts.
The first project is important because aphids are a major pest of many important food crops as well as ornamental plants. This research will focus on transforming a miniature rose species with the enzyme b-Farnesyl Synthase (EBF). EBF is responsible for making the sesquiterpene Farnesene that acts as an aphid deterrent as well as a kariomone to attract parasitic wasps that lay eggs in aphids, thereby destroying them.
Miniature roses grown in tissue culture will be transformed using a strain of Agrobacterium tumefaciens previously engineered to contain the EBF gene. Rose plants will be regenerated from the transformed tissue in culture. A series of plant growth regulators will initiate shoot and root growth until viable rose plants are obtained. These plants can then be grown in a growth chamber or greenhouse. After transformants have been established they will be evaluated for the EBF gene using traditional molecular biology techniques. The transformed roses’ ability to deter aphids will be evaluated in studies conducted in growth chambers.
The second project will use Bioinformatics and Phylogenetics to better understand the evolutionary histories of the genus Erythroxylum. There are over 200 different species of Erythroxylum. Two species, E. coca, and E. novogranatense (commonly called “coca”) have been cultivated for thousands of years and cocaine, an alkaloid, isolated from the leaves. However, the wild species do not produce cocaine. This leads to interesting questions about the evolutionary relationships between the cultivated and wild species. Current studies using morphological, chemical, and molecular data to create phylogenies are underway. Unfortunately, DNA sequences commonly used to collect the necessary molecular information are problematic.
Sequencing an entire Erythroxylum chloroplast (or mitochondrial) genome will greatly enhance the information available to create accurate phylogenies. This project will begin by isolating DNA from Erythroxylum chloroplasts. The DNA will be sequenced using Solexa 454, or Ion Torrent sequencing technology. This sequence will be annotated using common bioinformatics programs. Once an Erythroxylum reference genome has been established alternative methods will be used to sequence multiple chloroplast genomes from previously isolated DNA. Differences among these sequences will be used to create more accurate phylogenies describing the evolutionary relationships of the genus.
Dr. Staub is currently on sabbatical, and not accepting new students.
Salamanders communicate via pheromones. My research focuses on understanding the structure, function, and evolution of pheromone-producing glands. Salamanders are known for their moist glandular skin, yet little is known about which glands actually produce pheromones other than the well-studied courtship glands on the male chin (known as the mental gland). While pheromones from the mental gland have been well studied, little is know about the pheromones that females produce or about the pheromones that males produce from non-mental glands sources. Interestingly, males of some species lack the pheromone-producing mental gland that is supposedly so important for courtship. Do they produce pheromones from other glands? Do they have pheromone genes?
1) To identify pheromone producing glands in plethodontid salamanders we are starting a new project to first check the species’ genome for pheromone genes. Ideally we would like to be able to do this with formalin-fixed specimens, so we don’t have to use fresh tissue from living animals. Using primers for pheromone genes in Plethodon shermani, we will use the polymerase chain reaction (PCR) and gel electrophoresis to identify pheromone genes in other species. PCR products will be sequenced and compared to known pheromone genes. Sequence results from this study will be used to build specific probes for in-situ hybridization projects to identity specific pheromone-producing glands.
2) in situ hybridization studies: We design pheromone (PRF, PMF, SPF) specific mRNA probes to use with in situ hybridization to detect which glands, of the many in salamander skin, are actually producing pheromone mRNA in both males and females. Several questions can be addressed using this approach: 1) Where are courtship pheromones produced in males that lack specialized courtship glands? 2) Which glands in the post-cloacal region produce pheromones?
The Swanson Lab studies how complex mechanical systems evolve in animals. Specific current projects include: a study of the swimming performance costs of sexually selected male ornamentation in sword-tail fish, a study of the microstructure and impressive material properties in crustaceans, and a study of the effects of heavy metal pollution on fish feeding and swimming performance. Research students are involved in experimental design, data collection (in the field and in the lab), data analysis and presentations.
Amphibian populations on several continents have been decimated by the emerging infectious disease chytridiomycosis, and as a result it has been estimated that more than 100 species of amphibians worldwide may have been driven extinct by declines associated with this disease. Chytridiomycosis is caused by the chytrid fungal pathogen Batrachochytrium dendrobatidis (Bd), which infects skin tissues of adult frogs. Few mitigation strategies exist to prevent these disease-associated extinctions, but in the last few years research has identified symbiotic cutaneous bacteria living on the the skin of frogs that can inhibit the growth of Bd, and these symbiotic bacteria are now viewed as a leading mitigation strategy for preventing further Bd-associated extinctions. I am seeking students that can help to assess inhibition of this fungal pathogen via symbiotic bacteria collected from amphibian populations in Costa Rica. Research for Spring 2014 will likely involve standard microbiological techniques working with fungal and bacterial cultures. The ultimate goal of this research is to develop biocontrol programs via bacterial probiotics that may lead to large-scale conservation solutions to global amphibian declines.
Highly efficient and tunable organic fluorescent molecules are a growing area of chemical interest as there is significant push for their incorporation into a variety of materials applications such as organic light-emitting diodes, molecular and ionic sensors, and stains for biological markers. One notable example is the 4,4-fluoro-4-bora-3a,4a,diaza-s-indacene core, better known as BODIPY. BODIPYs exhibit remarkable qualities such as intense UV-absorbing and emitting capabilities, high quantum yields, and general insensitivity to a variety of chemical environments. However, the main disadvantage associated with BODIPYs is that they typically absorb and emit between 500-530 nm and possess generally low Stokes shifts of 15-20 nm (600-800 cm-1). Strategies to combat this issue typically involve the installation of secondary and tertiary fluorophore units with different absorption and emission wavelengths. While somewhat successful, such molecules are complex and often require long synthetic routes. An alternative solution to this issue involves a desymmetrization of the BODIPY core to create more energetically discrete ground and excited states. This project aims to expand the scope of fluorescent molecules that exhibit optoelectronic properties akin to BODIPYs but with enhanced Stokes shifts and near-infrared emitting capabilities.
Students working on this project will have the opportunity to learn the following techniques: organic and organometallic synthesis, air-free chemical manipulation via a Schlenk line and/or Glovebox, TLC and column chromatography, 1H and 13C NMR spectroscopy, UV-visible spectroscopy, fluorometry, and mass spectrometry.
Students who are interested should contact Dr. Chase.
Click here to download a description of Dr. Cleary's research interests.
Contact Dr. Cleary
Dr. Cremeens will be on sabbatical during the 2014-2015 academic year, and is not accepting new research students until Fall 2015.
Like serotonin, neuropeptides are signaling molecules within the brain and gastrointestinal tract. Problems with signaling often cause health problems. Despite the prevalence of neuropeptides within the brain and their importance, they are often poorly characterized under physiological conditions. Our research aims to provide key structural characteristics of neuropeptides under physiological conditions for the sake of aiding the rational design of therapeutics.
Neuropeptides are found within neural tissue and bind to transmembrane G-protein coupled receptors (GPCRs). A given neuropeptide may interact with multiple receptors, each inducing unique effects within the nervous system. That they function as ligands to GPCRs, despite their often unstructured or only partially structured nature, is impressive. Whether or not the partially structured site displays a recognition motif is an open question. Directly identifying the functionally important characteristics of a given neuropeptide has been difficult because under physiological conditions they are primarily unstructured, which makes it rather challenging to obtain structural information for rationally designing therapeutics.
This research will target neuropeptides where a fundamental structural question relates to the cis-trans isomerization of an amino acid (proline). For example, under physiological conditions, endomorphin structural characteristics are unknown, and cis-trans proline isomerization might play an important role in receptor binding. Site-specific carbon-deuterium (C-D) labeled neuropeptides will be synthesized by solid-phase peptide synthesis and undergo spectroscopic characterization (IR, circular dichroism, and NMR). The insights gained from these studies will help unravel the complex nature of neuropeptide structure and specificity, which would ideally translate into more facile design of highly selective agonists and antagonists.
The carbonic anhydrases (CAs) catalyze a reaction of fundamental biochemical and physiological importance, the interconversion of carbon dioxide and bicarbonate ion
All CAs are zinc-dependent enzymes and a well-established mechanistic paradigm requires the coordination of substrate to the catalytic zinc ion (Zn2+). The structures determined for the b class carbonic anhydrases (β-CAs), common in plants and bacteria, generally fall into two distinct subclasses based on the observed coordination of zinc. One subclass of β-CAs coordinate Zn2+ tetrahedrally with four protein-derived ligands, and in this configuration access of substrate to the zinc coordination sphere is apparently blocked. The ability of substrate to coordinate to zinc is observed in the other structural subclass. The available evidence supports the hypothesis that the blocked configuration, as seen for example in ECCA, a β-CA from Escherichia coli, represents an inactive conformation of the enzyme, and that all such β-CAs can undergo a transition to an active conformation. In addition, a unique, non-catalytic binding mode for the substrate bicarbonate was discovered in ECCA that appears to stabilize the blocked, inactive form of the enzyme and seems to represent a regulatory mechanism.
This project specifically aims to characterize the allosteric bicarbonate site that is likely shared by many eubacterial β-CAs, including a number of pathogens (e.g., Mycobacterium tuberculosis, Salmonella typhimurium). The structural and functional effects of its disruption by targeted mutagenesis are to be investigated by the primary method of X-ray crystallography, supported by kinetic measurements. In view of its potential as a site for therapeutic intervention, the characterization of the allosteric site will be furthered, in collaboration with Stephen Warren and coworkers, by a virtual screen for potential non-substrate ligands and subsequent determination by crystallography of the structures of the binary complexes. Finally, the relationship between allosteric bicarbonate binding and the hypothesized structural transition in ECCA will be probed by testing the effects of mutations designed to shift the conformational equilibrium, The two observed structural subclasses serve as an explicit two-state model for regulation.
This project will be attractive to students with interest in biochemistry, particularly protein structure and enzymology. It integrates a textbook example of an extremely fast enzyme with allosteric regulation of enzyme activity. The project also emphasizes computational methods, including molecular graphics, modeling, and informatic methods of drug discovery.
A second project that is getting underway is a systems biology investigation of the effects of β-CA knockouts or attenuation of enzyme activity on metabolic flux and expression profiles in prokaryotic cells. The substrates of carbonic anhydrase are hubs in a metabolic network, and limitation of the rate of CO2/HCO3- interconversion is likely to have significant effects on a number of cellular systems. Existing methods of metabolic modeling, such as flux balance analysis, will be applied to these systems to predict the effects of loss of CA activity, and eventual comparison with systems data obtained for wild-type and knockout strains. The development of inhibitors, the goal of the first project, will in principle allow titration of CA activity, in order to examine the effects of varying levels of CA activity on the systems properties of the affected cells. This project will be mainly computational and curational in its early stages, and will be blended with experimental data as progress permits.
With recent advances in the computational resources available to chemists, computational methods that describe the motion of the electrons in atoms and molecules (aka electronic structure methods) have become an increasingly useful tool for understanding/interpreting molecular properties as well as the energetics and dynamics of reactions. Nonetheless, to establish electronic structure theory as a truly predictive tool in chemistry, the development of more accurate and cost-effective methods is desirable. Research in our group aims to address this goal on two fronts. Recently, we have been able to reduce the computational cost of existing models (without a significant loss in accuracy) by developing a systematic procedure for the construction of natural orbitals. In conjunction with collaborators at Argonne National Laboratory, we are also actively pursuing the development of the Graphically Contracted Function approach for electronic structure theory; this method, although still in its infancy, has the potential to significantly improve the cost-effectiveness and accuracy of current state-of-the-art computational models.
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Bacterial pathogens must scavenge iron from their host for growth and proliferation during infection. They have evolved several strategies to do this, one being the biosynthesis and excretion of small, high-affinity iron chelators known as siderophores. Two general pathways for siderophore biosynthesis exist: the well-characterized nonribosomal peptide synthetase (NRPS)-dependent pathway and the NRPS-independent siderophore (NIS) pathway, which relies on a different family of understudied and novel synthetases. NIS synthesis enzymes fall into at least four distinct families (A, A’, B, and C,) based on substrate specificity, and are associated with some of the most virulent and persistent bacterial infections (staph, anthrax, plague) We are initially interested in contributing new structural information for this understudied family of enzymes, as the only two examples of structurally characterized NIS synthetases revealed a novel-binding fold and unique enzyme chemistry. Further structural information, both within types A and C, and new structures of types B and A’, as well as clear information about the secondary substrate binding pocket, and higher oligomerization state, are the primary goals for our work.
Since NIS sythetases fall into four types, we have identified a member of each type, and are pursuing structural characterization as well as developing functional assays. Beginning with two identified siderophore synthesis pathways, we will structurally characterize the type A enzyme DesD from Streptomyces coelicolor (a benign soil bacteria which has been the source of a majority of known natural product antibiotics.) We are also studying the vibrioferrin synthesis pathway out of Vibrio haemolyticus (shellfish food poisoning) by studying PvsB (type B) and PvsD (type A) and Francisella tularensis type A’ protein FslA (which causes the veterinary infection of tularensemia).
Currently several projects in the lab have been optimized for overexpression and purification, and we have begun crystallization trials. Future work for the year will include co-crystallization with substrates or substrate mimics, and the development of functional assays to allow us to quantify the behavior in solution. All of these studies are designed to provide novel structure/function information for uncharacterized subtypes of NIS synthetases, which we intend to use to begin a long-term program exploring not only possible therapeutics for bacterial infection, but also to the better understanding of new enzyme chemistries.
Our research involves developing materials and methodologies for chromatographic analysis of adsorption, binding, and partition events at lipid bilayers. Such interactions can, among other things, influence a drug’s activity and toxicity, affect the activity of membrane proteins, and determine the bioaccumulation of environmental chemicals. Furthermore, lipid bilayers are integral components in many biosensing and liposome-based delivery strategies and the characterization of solute adsorption behavior is crucial to the development and application of these technologies.
In general, high performance affinity chromatography (HPAC) techniques seek to relate the retention of a substance on a packed column to the strength of its specific interaction between the stationary and mobile phases of the column. In principle, this approach to characterizing bioaffinity interactions can offer a number of analytical advantages over other techniques; however it does require the establishment of stable and immobilized biological “films” or “layers” on micro-particulate materials to serve as the stationary phases. The lack of such materials has been a significant impediment to the application of HPAC to biomembrane interactions.
Recent work in our lab has produced materials and methods for assembling lipid bilayers on nanometer-scale silica colloids which we are now using to create lipid bilayer-based stationary phases for liquid chromatography. Preliminary results with the materials are very promising, particularly with respect to evaluating weak and moderate affinity interactions such as those between metal ions and ionophore receptors and channels. Low affinity interactions are particularly difficult to analyze by other techniques and thus the development of materials and methodology that can reliably do so may have particularly broad impact in the field.
Ongoing development of the lipid-silica materials and their application in studies of membrane interactions are the current foci of our research. Projects are available that pertain to the biophysical characterization of lipid bilayers supported within porous silica particles, developing thin organic films for the purpose of affecting lipid-particle interactions, assembling and characterizing new capillary chromatography instrumentation configurations with new pumps and detectors, and chromatographically analyzing molecular interactions with lipid bilayers.
Dr. Shepherd’s research seeks to elucidate the biosynthetic pathway of rhodoquinone (RQ, 1 in Figure 1) which will later be used as a target for the development of new anti-parasitic drugs. RQ is an essential electron carrier used in the anaerobic energy metabolism of species such as the parasitic helminths, the free-living nematode Caenorhabditis elegans (C. elegans), and the purple non-sulfur bacterium, Rhodospirillum rubrum (R. rubrum). RQ is not synthesized or used in humans and other mammals with a primarily aerobic energy metabolism. However, RQ is structurally similar to ubiquinone (coenzyme Q or Q, 2 in Figure 1), an important lipid component involved in electron transport in the aerobic respiratory chain, and the biosynthetic pathways of RQ and Q are proposed to be similar. The biosynthesis of Q has been well-characterized in both prokaryotic and eukaryotic species.
It has recently been shown by Dr. Shepherd’s laboratory that catabolism of Q is required for RQ biosynthesis in R. rubrum. A mutant strain (F11) of R. rubrum has also been identified which can synthesize Q, but not RQ, and therefore cannot grow anaerobically. After sequencing the whole genome of F11, and a spontaneous revertant (RF111), we identified a new gene, rquA, which is the first known gene required for RQ biosynthesis. We are currently working on the expression, purification and characterization of the gene product (RquA). Using bioinformatics and RNA sequencing data, we have also identified four new candidate genes that may be involved in RQ biosynthesis in R. rubrum. We are in the process of preparing gene knock-out mutants to determine the necessity of these genes for RQ biosynthesis. In addition, we have begun work with the C. elegans worm model using RNAi gene knock-downs to identify further candidates required in the RQ biosynthetic pathway. Characterization and regulation of unique enzymes in the RQ biosynthetic pathway will provide a novel target for antihelminthic drug discovery.
Figure 1. Schematic representation of potential ways RquA acts in the biosynthesis of RQ. Pathway A represents the methylation of DMeQ to form a pool of Q reserved for the biosynthesis of RQ. Pathway B represents a complex in which RquA acts in conjunction with other enzymes to act as an amidotransferase to substitute Q’s methoxy group with an amino group on RQ
According to the most recent assessment by the World Health Organization, 884 million people around the world lack access to “improved water supply” and more than 2.5 billion lack access to “improved sanitation”. The health consequences of inadequate access to improved water and sanitation include an estimated 4 billion cases of diarrhea and 1.6 million deaths each year, mostly among young children in developing countries. My projects involve the development and optimization of sustainable, household water treatments for the removal of biological pathogens and naturally occurring inorganic contaminants such as arsenic and fluoride.
I am looking for a student to determine whether or not charred cow bone will effectively remove fluoride ions from natural waters.
The world, especially the industrialized world, is facing 2 emerging epidemics. These epidemics will create significant medical needs that will negatively impact health care systems and the economies of the world if a proactive approach is not taken towards new solutions. One of these emerging epidemics is Type 2 Diabetes which is impacting a growing percent of our population. The other epidemic is the result of the steady increase in the average age of the population world wide (which is projected to continue) coupled to the exponential link between increasing age and the incidence of neurodegenerative disease. Biochemical changes in the metabolism of cell types involved in both of these diseases have been noted.
Lactate has been considered a dead-end waste product of anaerobic metabolism since the 1930's. However, new evidence has emerged showing that lactate is an important energy source that is shuttled between cells and throughout the body. Lactate is being shown to play an important role in muscle and brain metabolism, with the associated implications for diseases in which these tissues form an important component. Muscle metabolism and its alteration have large implications in Type 2 Diabetes. Biochemical changes in the metabolism of the heart muscle are also implicated in congestive heart failure.
In brain metabolism, glucose has traditionally been thought to be the exclusive energy source. However, new hypotheses are emerging that the preferred energy substrate for neurons is not glucose but may instead be lactate. This has wide implications for the study of brain function and diseases as monitored by energy usage. For example, in Alzheimer's disease it has been reported that metabolic deficits often precede the appearance of first symptoms. A probe that could monitor the Krebs cycle could give early indication of decrease in neuronal metabolic activity and neuronal death. This could be an invaluable research tool and diagnostic for neurodegenerative diseases including Alzheimer's and Parkinson's disease.
A specific aim of this research is to develop a probe that monitors lactate's function as an energy substrate while minimizing the number of assumptions and measurements needed to account for the other activities of the molecule and its metabolites. The goal is to monitor some of lactate's functions, but not all of them. To this end lactate analogs have been selected and will be synthesized and evaluated based on their potential for being trapped in the Krebs cycle where it is likely that rate and/or amount of accumulation can be correlated to the rate of activity for the cycle, thus providing a diagnostic indicator for many diseases where energy usage is altered. While currently there is no direct way to monitor aerobic metabolism in vivo at the cellular level,these analogs have this potential when developed as Positron Emission Tomography probes. This is timely and critical research that could advance our understanding of the diagnosis and treatment of energy dependent diseases.
I am looking for a motivated independent student to evaluate lactate analogs for their lactate dehydrogenase activity.
The Watson lab studies the structure and function of the enzyme HMG-CoA reductase (HMGR). In humans, this enzyme is the key regulatory point for the biosynthesis of cholesterol and is the target for statin drugs. Bacteria also use this enzyme, and in some pathogenic bacteria such as methicillin-resistant Staphylococcus aureus (MRSA), it is vital for the survival of the pathogen. Emerging evidence from our lab suggests that there is another class of bacteria that use HMGR in an unknown fashion. We have recently cloned, expressed and purified the HMGR from a member of this new class, the opportunistic lung pathogen Burkholderia cenocepacia, which causes, among other things, fatal infections in late-stage cystic fibrosis patients. This organism is naturally resistant to nearly all antibiotics currently available; understanding the function of this enzyme in the life cycle of the pathogen could provide new ways to attack it. We have begun studies to knock out the gene for HMGR B. cenocepacia to explore the enzyme's physiological role.
I am seeking up to two students to focus on structural and functional characterization of this newly discovered form of HMGR. Primary projects include enzyme kinetics, fluorescence and/or circular dichroism spectroscopy, and characterization of stereospecificity in the enzyme reaction. All students will learn basic biochemistry lab techniques such as protein expression, purification and characterization. While typically students will have completed CHEM 331 and BIOL 201 prior to working in the lab, exceptions can be made.
My research is on the Primordial Helium Abundance. The focus is on determining the amount of helium produced in the very early universe (3 minutes after the Big Bang) by analyzing the spectral emissions of dwarf galaxies.
In addition to an introduction to Astrophysics and Cosmology, the research involves widely applicable skills such as computer programming, statistical analysis, and model evaluation. Beyond an eagerness to learn, no prior experience in any of those areas is required.
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Research in my lab focuses on the role of the epididymis in sperm maturation and function. Sperm are produced in the testis but gain the ability to fertilize an egg as they transit the epididymis. As sperm transit the epididymis they acquire proteins necessary for normal function from the epididymal fluid, which is a secretory product of the epididymal epithelium. The purpose of our research is to understand this maturation process.Our current main focus in on the role of CRISP1, an epididymal protein acquired by the sperm, in the regulation of sperm functions such as the acrosome reaction. Likewise, the role of CRISP4, a second CRISP protein produced in the epididymis and related to Crisp-1, is also under investigation. Experiments are also being performed to determine how the two isoforms of the CRISP1 protein (Proteins D and E) become attached to the sperm plasma membrane. This work has implications for clinical conditions of sperm dysfunction leading to male infertility.
My lab is also interested in the protein composition of sperm and the origin of sperm proteins. In collaboration with colleagues at Pacific Northwest National Lab, we have undertaken a total proteomic analysis of human sperm to determine the proteins required for sperm maturation. We are also using signal-trap cloning to identify and catalog cDNAs from the mouse epididymal epithelium encoding secretory proteins that become part of the sperm proteome.
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For information on research in the Chai lab, please visit her homepage at WSU.
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We are interested in understanding the relationship between the regulation of sleep and metabolism. We study the role of metabolism- and feeding-related humoral and neuronal signals in the regulation of biological clocks, sleep-wake activity and arousal. Also, we investigate the effects of clocks and sleep, and the impairments thereof, on metabolism, eating and thermoregulation. We use integrative approach, in vivo rodent models, with simultaneous measurements of the amount and intensity of sleep, oxygen uptake, carbon dioxide production, food intake, body temperature, locomotor and wheel running activities supplemented by blood sampling for hormone measurements.
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My laboratory is concerned with the biochemical regulation of sleep. We described the somnogenic actions of many cytokines and showed that interleukin-1 (IL1) and tumor necrosis factor (TNF) are involved in physiological sleep regulation. Our second interest deals with sleep and infectious diseases. Bacterial, protozoan, fungal and viral infectious agents greatly alter sleep. In the case of bacteria we worked out the molecular steps responsible. Currently we are focusing our efforts on the mechanisms involved in influenza virus – induced sleep. In this case, viral double-stranded RNA, released from infected cells, seems responsible for initiating the sleep cascade. Very recently we showed that in mice challenged intranasally with influenza virus, the virus is found within hours in the olfactory bulb where it enhances brain production of cytokines. A third interest of my laboratory is with sleep function and the brain organization of sleep. In short, we hypothesized that neuronal assemblies are the organizational level at which sleep is initiated and that local sleep at this level is dependent upon prior activity within the local network. Thus, we showed that extracellular ATP, released by active glia and neurons enhances expression of TNF and IL1 that in turn drive increases in NREMS locally. TNF expression by neurons is enhanced in the somatosensory cortex if afferent input induced by whisker twitching is increased. Further, individual cortical columns such as somatosensory barrels alternate between functional states, one of which is usually associated with organism sleep and that the sleep-like functional state is induced by TNF. In collaboration with Drs. Sandip Roy, (Engineering) and Hans Van Dongen (Sleep and Performance Research Center) this view of sleep is being mathematically modeled.
The focus of my research is how sleep, metabolism and body temperature regulation are related. In the laboratory, we work with laboratory animals, with rats and mice. A student who is interested in this type of research can participate at many levels, from doing surgeries on animals through data collection, to data analysis.
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