Website: http://www.gs.washington.edu/faculty/akey.htm

Description: Our laboratory is broadly interested in understanding the evolutionary history of human populations. Important events in human history, such as changes in population size or adaptation to new environments, impart signatures on patterns of DNA sequence variation. The research project would focus on analyzing patterns of genetic variation that have been collected in geographically diverse human populations, to better understand human evolutionary history. There is considerable flexibility in developing a specific research project, which will be tailored to the interests and background of the student. Specific examples include, but are not limited to, studying patterns of evolution in regulatory regions of the human genome, investigating how different populations are related to one another, and comparing patterns of polymorphism and divergence at specific candidate genes between humans and non-human primates.

Requirements: There are no specific requirements, although some familiarity with (or interest in learning) basic computer programming would be helpful.

Website: http://depts.washington.edu/wmatkins/lab.html

Description: Two exciting projects are available. Both projects relate to the structure and function of enzymes that metabolize drugs and form the basis for drug-drug interactions that confound prediction of drug clearance. The first project aims to understand the effects of simultaneous binding of multiple drugs at the active site of cytochrome P450s (CYPs), wherein the direct molecular interaction between these drugs within the active site alters their redox properties, and hence their relative reactivity. To explore this, electrochemistry will be attempted to measure the oxidation potential (energy required to remove an electron) of cytochrome P450-bound acetaminophen (Tylenol) in the presence and absence of ‘effector’ drugs. The student will contribute by measuring binding affinities of drugs for CYPs using optical spectroscopy. The second project involves protein engineering of glutathione S-transferases (GSTs) in order to control their stereoselectivity towards hydroxynonenal (HNE), a product of oxidative stress that likely has a causal role in many diseases including Alzheimer’s, atheroschlerosis, cataracts, and asthma. GSTs provide the major route of HNE metabolism. HNE is formed as a racemate, but the individual enantiomers appear to have different biological effects. Understanding the stereochemical selectivity, and manipulating it via protein engineering, could provide new therapeutic strategies for controlling these diseases. The student will perform site-directed mutagenesis.

Requirements: Introductory chemistry course with lab

Website: http://www.bassuklab.org/

Description: The proliferation of urothelial cells of the lower urinary tract are controlled by positive and negative regulators. One example of a negative regulator is the matricellular protein SPARC, which is found in cell nuclei during cell quiescence in a form that is bound to DNA. One example of a positive regulator is the paracrine growth factor FGF-10, which is found in cell nuclei when the cell is actively synthesizing DNA and progressing through the cell cycle.

One goal of this project is to identify which genes SPARC binds to and to determine the extent that such genic interaction is relevant to the overall process of shutting down the urothelial cell cycle.

Another goal of this project is to identify which genes FGF-10 binds to and to determine if such genic interaction is what triggers renewed DNA synthesis and progression through the urothelial cell cycle.

Data obtained from this project will provide a state-of-the art training vehicle to Amgen Scholars and lead to a better understanding of how urothelial cell proliferation is regulated in health and disease.

Requirements: The opportunity in my lab requires working knowledge of use of antibodies in western and immunoprecipitations, how secondary antibodies work, use of imaging equipment, and gel electrophoresis of nucleic acids.

Website: http://depts.washington.edu/daglab/

Description: We perform molecular dynamics computer simulations of proteins involved in amyloid diseases. One disease we focus on transmissible spongiform encephalopathie, including mad cow disease. We are working to characterize the conformational/structural changes associated with pathology and in designing therapeutic and diagnostic agents against these diseases based on the computer models.

Website: http://faculty.washington.edu/dovichi/

Description: This laboratory develops and applies tools for the ultrasensitive characterization of biological molecules. These projects are supported by three NIH grants. These projects have recently supported three undergraduates, and it may be best to describe their work, which provides examples of work available to our students. One project is to develop an automated tryptic digestion system on a microscale. This device will be employed as part of an on-line protein characterization system, which will couple the digester with capillary electrophoresis and MALDI mass spectrometry. The undergraduate working on this project is evaluating reaction conditions using a fluorogenic substrate, which requires use of a fluorescent microtiter plate reader. The second project employs capillary electrophoresis and laser-induced fluorescence to characterize protein expression in single breast cancer cells. This project has resulted in one publication for Joan Bleeker, an undergraduate in my group. The third project studies stochastic gene expression in the bacterium D. radiodurans using a wide suite of bioanalytical tools, including flow cytometry, confocal microscopy, and capillary electrophoresis with laser-induced fluorescence. This project has resulted in three publications for Vanessa Palmer, another undergraduate in my lab.

Requirements: A strong background in chemistry or biochemistry.

Website: http://depts.washington.edu/sfields/

Description: Ubiquitin is a 76 amino acid protein that is an essential signaling molecule in nearly every pathway in eukaryotic cells. Ubiquitin is attached to other proteins only after it has been activated by a cascade of three proteins known as E1, E2 and E3 enzymes. There are many E3 enzymes (called ubiquitin ligases) and they determine the target substrate specificity of this cascade. E3s are critical enzymes: several human diseases, including types of cancer and Parkinson's disease, are caused by mutation of genes that encode E3 enzymes. The goal of this project is to develop a new technology to enable easy and rapid identification of substrates for ubiquitin ligases, from yeast to man.

One way to systematically identify targets for an E3 would be to mutate the enzyme and to mutate ubiquitin so that only the single mutant E3 would be able to transfer the mutant ubiquitin. However, identifying such a mutant combination would be extremely difficult. Evolution has solved this problem for us, because there are several ubiquitin-like proteins that are attached to substrates using enzymes that are very similar to the ubiquitin E1, E2 and E3s. The student will engineer a yeast ubiquitin E3 to enable it to transfer a human ubiquitin-like protein to its substrates. This project will teach molecular biology techniques along with biochemistry, and if all goes well, identification of peptides by using tandem mass spectrometry. The project aims to solve an important biological problem (the elucidation of enzyme-substrate relationships for E3 enzymes) by developing an innovative new technology.

Requirements: Some basic biology coursework.

Website: http://www.npl.washington.edu/nanopore/index.htm

Description: We are working on a new and direct technique for sequencing DNA. In this technique, single-stranded DNA molecules are driven through a biological pore where they produce a measurable obstruction of an ionic current that also flows through the pore. In collaboration with a microbiologist we are mutating a naturally occurring pore protein to make it suitable for this sequencing technology.

Website: http://depts.washington.edu/immunweb/faculty/profiles/hajjar.html

Description: My laboratory has two related interests. The first is the link between Innate to Adaptive Immunity to Infection. We are exploring the specificity and mechanisms by which Toll-like receptors contribute to microbial recognition and activation of innate immunity and, thereafter, of antigen-specific immunity. Ongoing studies seek to determine the biological importance of differences between Toll-like receptors of humans and mice in their ability to recognize variant ligands and in the specific cell types on which they are expressed. These studies and studies of developmental differences in innate immune responses are pursued to gain a more complete understanding of Toll-like receptor-dependent and -independent aspects of antigen-specific immunity to bacterial and viral pathogens and to use this knowledge to develop more effective vaccines.

In turn, we are seeking to determine the mechanisms through which cues provided by the innate immune system induce and sustain robust expression of interferon-gamma and assure the fidelity of Th1 and CD8 T cell function. Our group has helped to define the role of differential DNA methylation, post-translational histone modifications and higher-order chromatin structure in the control of T cell effector functions. We are currently working to determine the importance of these processes in the control of interferon-gamma expression and to identify novel regulatory elements within the extended interferon-gamma locus through which these processes and lineage-restricted transcription factors act.

Requirements: Students should have successfullly completed coursework, including laboratories, in chemistry and biology, and ideally microbiology. Prior research experience would be ideal but is not essential. Students should be comfortable with the use of animals, when appropriate, in biological research.

Website: http://www.biology.washington.edu/index.html?navID=42&parecID=159

The students will study the role of a regulatory protein, p120 catenin, in early zebrafish development. This protein likely regulates the adhesion and motility of cells that form the early embryonic structures. The kinds of molecular biology techniques the students will use are PCR, transformation of bacteria, sterile technique, sub cloning and moving genes to different vectors, in vitro preparation of mRNA, Western Blots. If the student progresses rapidly they will be able to inject their mRNA construct in to zebrafish eggs and see where they go during early development with live or confocal microscopy. Most of our genes have green fluorescent protein markers.

The students should have had a course with some protein signaling or protein structure understanding, for example a 200 or 300 level cell biology class with a chemistry prerequisite or a biochemistry class. The students should be willing to concentrate well in manipulations, since errors are very expensive. Diligence in the preparation of labile mRNA will be required.

Website: http://depts.washington.edu/pceut/faculty_research/faculty_members/ho_rodney.html

Website: http://depts.washington.edu/envhlth/faculty.php?Kavanagh_Terrance

Website: http://depts.washington.edu/biowww/faculty/kennedy.html

Description: A major focus in my research group is to understand the mechanisms which control aging. We use yeast, worms and mice as models organisms for aging research and have identified genes which modulate the aging process. In an intensive research program a summer student would be given a project related to one of these aging genes and conduct experiments to determine the function(s) of that gene that important for the control of aging. Dietary restriction is one intervention that results in life span extension in every model organism tested. Many of the genes we study are important to mediate the downstream effects of dietary restriction and understanding the mechanisms by which dietary restriction extends longevity is a primary goal of our aging research.

Website: http://depts.washington.edu/chem/people/faculty/mkhalil.html

Website: http://www.ee.washington.edu/research/photonicslab/

Description: One of our research directions is "photonics at the interface of engineering and biology/biomedicine." Currently, we are working on two projects along this direction: (1) Using plasmonic tweezers to trap and manipulate biology cells and molecules. (2) Control cellular and neuronal signal transduction using light through the mediation of semiconductor quantum dots.

Website: http://depts.washington.edu/malylab/

Description: Cells are able to integrate an enormous array of environmental information and convert these signals into complex behaviors such as growth, differentiation, and motility. This relay of extracellular stimuli into a phenotypic response involves the transfer of information through complex signal transduction networks that are precisely regulated, both spatially and temporally. Determining how these signal transduction networks are able to turn simple inputs into complex behavior is one of the greatest challenges in modern biology and will provide valuable insight into the cause and treatment of many diseases such as cancer, diabetes, and inflammation. Our group studies how cells sense and respond to their environment, by developing new biochemical and chemical tools that allow a greater quantitative understanding of cellular signaling than is possible with currently available methods. Using the tools of organic synthesis and protein biochemistry we are generating cell permeable small molecules that allow the activation or inactivation of specific signaling enzymes in living cells. While we are interested in studying the function of a number of protein families that are involved in signaling, our initial efforts are focused on enzymes that mediate intracellular phosphorylation (the protein kinases and phosphatases). These studies focus on three main areas: 1) The location-specific function of kinases and phosphatases. 2) The quantitative characterization of specific intracellular phosphorylation events. 3) The conformational plasticity of signaling enzymes.

The specific project within these areas will depend on your interests and prior research experience.

Requirements: Completion of an introductory organic chemistry course (and any associated laboratory courses).

Website: http://faculty.washington.edu/merza/

Description: We are a cell biology research group in the Department of Biochemistry at the University of Washington's School of Medicine. Our goal (and that of many other labs) is to understand the fundamental, evolutionarily conserved mechanisms of membrane organization in eukaryotic cells - ultimately in sufficient detail that this aspect of biology will morph into an engineering discipline. We focus on mechanisms of membrane docking, fusion, and repair in living cells and intact organelles. Technologies that we will use include:

• microscale device fabrication (patterned surfaces, supported membranes; with the UW Center for Nanotechnology)
• yeast genetics & high-throughput genomics
• cell-freee biochemical assays
• protein biochemistry
• fluorescence spectroscopy
• ultrasensitive fluorescence microscopy
• structural biology: cryo electron microscopy of (with Tamir Gonen's group)

The specific project depends on your experience, interests and goals. Please visit our web site: http://faculty.washington.edu/merza.

Requirements: We strongly prefer undergraduates who have taken at least one year of General Chemistry with laboratory. Biologists, chemists, engineers, and other interested students are encouraged to apply.

Website: http://faculty.washington.edu/dpozzo/

Description: Electrophoresis, the motion of charged particles due to an externally applied electric field, is routinely used to separate biomolecules (e.g. DNA, Proteins) from complex mixtures (e.g. human plasma). Besides its paramount importance in most biological fields, electrophoretic separations are also used in diagnostic applications and in biosensors. This research aims to improve electrophoretic bio-separations through the use of nano-structured materials that have not been traditionally applied in this area. These materials include new surfactants and surfactant mixtures, structured sieving matrices (e.g. micelle crystals) and/or non-traditional electrolytes. We will make use of fundamental principles in colloid and polymer science to correlate the physics of the system to the overall efficiency of the separation. Leading edge electrophoresis techniques (e.g. microfluidics, capillary electrophoresis) will be used in conjunction with in-situ characterization experiments to probe the structure and conformation of biomolecules during the separation. Students working in this project will also be exposed to a wide variety of cutting-edge experimental techniques including scattering methods and spectroscopy.

Requirements: Interested students must have completed all of the basic Chemistry courses as well as Organic Chemistry and Physics. Basic laboratory experience is also essential. Students from Chemical Engineering Departments are especially encouraged to participate.

Website: http://faculty.washington.edu/spun/

Description: The Pun Lab develops nanoparticles for delivery of genes, siRNA, and molecular imaging agents. Applications for these delivery vehicles include siRNA to the central nervous system, cancer therapy, and tissue engineering. Researchers in our lab learn techniques related to mammalian cell culture, nanoparticle formulation and characterization, and gene transfection assays.

Website: http://www.pathology.washington.edu/Research/labs/Rabinovitch/

Website: http://www.bioeng.washington.edu/regnier/main.html

Description: The goal of our research is to understand the molecular and cellular mechanisms that regulate cardiac and skeletal muscle contraction, and how these mechanisms are disrupted in diseases.  We use the knowledge gained from these experiments to design protein and gene based therapies to improve the performance of diseased muscle and to develop tissue engineered muscle constructs as cell-replacement therapy for myocardial infarct (heart attack) and skeletal muscle injuries. Many research projects are done in collaboration with other laboratories at the University of Washington, at other institutions across the US, and in Italy.
Further information is provided at our website: http://www.bioeng.washington.edu/regnier/main.html

Requirements: Basic Biology and Chemistry courses are essential.  Coursework in Biochemistry, Cell Biology and Physiology would help.

Website: http://depts.washington.edu/taneli/

Website: http://depts.washington.edu/bioe/people/core/sauro/sauro.html

Description: Our group works in the area of synthetic biology, this is where we reengineer cellular networks, usually genetic networks, to carry out new functions. In the long term such functions could include reengineering pathways to generate biofuels or drugs or cells that can act as living sensors to detect harmful compounds. We have a number of projects currently underway, including: a project to develop a computer aided work station to help researchers design and test new cellular networks before they are built into a host organism, we are developing strategies in the lab to prevent evolutionary selection from destroying engineered networks, we are building engineered networks in ecoli such as gene cascades or simple oscillators to test our ability to predict the function of novel networks and assembly methods, we have projects to understanding the propagation of noise through cellular networks using mathematical theory and modeling and using light microscopy to study fluctuations in engineered networks via GFP and other florescence probes, finally we have computer programming projects to develop new software that might be useful to synthetic biology engineers. Synthetic biology is a new exciting field that requires researches to bring different disciplines together, including molecular biology, modeling, engineering etc. We have had many undergraduates come through our lab in the past and many have published papers in reputable journals and have successfully gone on to do PhDs

Requirements: An interest in science and engineering cells. If the student wants to do wet lab work then some experience in basic lab techniques would be useful. If the student wants to do a computational project, the ability to program in at least one computer language is required.

Website: http://depts.washington.edu/pulmcc/faculty/schnapp.htm

Description: Mechanisms of Acute Lung Injury and Repair

Our lab is focused on the processes that govern acute lung injury and its resolution. In particular, we are interested in why lung injury resolves under certain circumstances (i.e. Adult Respiratory Distress Syndrome) and progresses to end-stage fibrosis in other circumstances (i.e. Idiopathic Pulmonary Fibrosis). To answer these questions, we use different models of lung injury in transgenic mice to examine select pathways in injury and fibrosis. To complement these studies, we are analyzing samples from patients with acute lung injury and other lung diseases using cutting-edge methodologies in proteomics to identify new pathways in lung injury.

Website: http://www.cheme.washington.edu/people/faculty/shen.htm

Our laboratory focuses on developing technologies to probe and intervene the immune and nervous system.

1. Engineering immune cells for the development of single-cell based biosensors;
2. Developing molecular probes for monitoring chemical reactions of intracellular compartments;
3. Developing modular delivery systems for mediating functions of immune cells and nerve cells.

Website: http://www.amath.washington.edu/~swanson/

Description: The Swanson research lab is located in the University Medical Center, and focuses on mathematical modeling and the analysis of quantifiable data obtained through medical imaging such as MRI, PET, and CT. With our convenient location in the UMC, we are in a unique position to compare model results and predictions with data obtained from real patients receiving care at the University. Student researchers necessarily learn aspects of neuro anatomy, tumor evolution and biology, medical imaging, computational and data processing methods. Individualized projects are chosen to best meet the student's interests and abilities, while at the same time serving the overarching goals of the lab.

The lab's current focus includes, but is not limited to, the modeling of brain tumor growth, evolution and response to therapy, and comparisons of information obtained from superficially disparate imaging modalities such as MR and PET. This modeling effort provides many interesting avenues for student research: from data acquisition and processing to investigation and development of new mathematical models of tumor processes.

Our lab is truly interdisciplinary: with over a dozen members with backgrounds ranging from biology to applied mathematics and computer programming, we are able to determine suitable research projects for just about anyone with a scientific background. A vast majority of our lab members are pre-med, providing a stimulating environment with many resources for information and opportunities.

Students are supervised daily by the lab manager, with at least once weekly lab meetings involving progress reports to Dr. Swanson.

Requirements: The student should be have a strong interest and background in either mathematics or medical imaging, and be in good academic standing. Student should have intermediate to advanced computer experience and be comfortable spending extended periods of time at a computer. A strong candidate will have a background in mathematics, including a full calculus sequence, differential equations and linear algebra. Preference will be given to students with experience in any of the following computer programming languages: MATLAB, C++, FORTRAN, PHP, SQL.

Website:http://depts.washington.edu/medchem/faculty/Totah.html

Description: Work in our lab focuses on cytochrome P450 enzymes that are involved in drug metabolism as well as the metabolism of essential fatty acids such as the ω3 and ω6 fatty acids.  We are looking at modulation of fatty acid metabolism in extrahepatic tissues and potential toxicity caused by different drug substrates.  The student will be investigating the mode of inhibition of fatty acid metabolism by measuring inhibitory kinetic constants and identifying metabolites that are formed from various fatty acids using liquid chromatography coupled with mass spectrometry. 

Requirements: Chemistry and Chemistry Lab