| The Amgen Scholars Program |  |
2007 Amgen Faculty
Amgen applicants will select three projects that they would like to work with that best match their skills and interests and rank them in order of preference.
Click on the faculty's name to see a description of their research.
Prof. Martha M. Bosma - Biology
Website: http://faculty.washington.edu/martibee/
Spontaneous activity in the developing brain is critical to normal circuit development, playing an important role in regulating cell number, axon pathways, and synaptic connections. Our lab uses physiological techniques (imaging of intracellular Ca2+ and patch clamp recording) to determine the roleof a certain class of neurons, the serotonergic raphe neurons, in synchronizing and driving spontaneous activity in the embryonic mouse hindbrain. We have shown that these newly generated raphe neurons are capable of spontaneous electrical events, and pacemake activity in the remainder of the neurons in the developing hindbrain. We are determining the ionic mechanism ofthe spontaneous electrical events, and assessing the role of these mechanisms in wildtype and raphe knockout animals.
It would be great if the students had taken coursework in physiology, neurobiology, and/or development.
Prof. Daniel Chiu - Chemistry
Website: http://depts.washington.edu/chem/people/faculty/chiu.html/
Our lab has been focused on developing new physical methods for probing complex biological processes at the single-cell and single-molecule level. We are applying these new tools to two broad sets of biological questions: (1) Synaptic transmission, and (2) Single-cell cancer biology.
No particular requirements, except that they have taken sufficient numbers of chemistry/biology lab courses.
Prof. Valerie Daggett - Medicinal Chemistry
Website: http://depts.washington.edu/~daglab/
My lab is involved in performing realistic computer simulations of protein dynamics and folding. We are attempting to determine the underlying rules governing protein folding, which has ramifications for biotechnology, genomics, and human health. We also study protein misfolding diseases, in particular prion diSeases---for example mad cow disease. Finally, we have begun a project we are calling dynameomics, which seeks to map the normal protein dynamics and unfolding of all known protein folds. We are constructing a large database and now mining this database to determine the general rules of folding. Individual projects in the lab can focus on protein diease, general protein folding, the development of datamining approaches, and graphical user interfaces to make the resulting data available to the community.
Prof. Norman Dovichi - Chemistry
Website: http://faculty.washington.edu/dovichi/
This laboratory develops and applies tools for the ultrasensitive characterization of biological molecules and are supported by three NIH and one DOE grant. These projects include 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 one publication for Vanessa Palmer, another undergraduate in my lab.
A background in chemistry or biochemistry.
Prof. Jens Gundlach - Physics
Our research is centered around a relatively new technique for analyzing DNA at the single-molecule level. In this technique, single-stranded DNA molecules are driven through a nanometer scale pore where they produce a measurable obstruction of an ionic current that also flows through the pore. We have recently begun a collaboration with a biologist to develop and optimize a new porin for improved analysis of DNA.
Prof. Stephen Hauschka - Biochemistry
Website: http://depts.washington.edu/biowww/faculty/hauschka.html
Students will participate in studies related to how striated muscle genes are regulated during skeletal and cardiac muscle development, or in studies in which muscle gene regulatory components are modified so as to provide improved levels of therapeutic gene expression during the treatment of neuromuscular diseases. Depending upon the specific project, students will learn how to manipulate gene sequences, how to carry out PCR and enzyme reactions, and how to use embryonic or adult muscle cells in tissue culture assays.
Prof. Merrill B. Hille - Biology
Website: http://protist.biology.washington.edu/bio2/people/bio.html?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.
Prof. Rachel Klevit - Biochemistry
Website: http://depts.washington.edu/biowww/faculty/klevit.html
Our goal is to understand the relationship between the three-dimensional structure of proteins and protein-protein complexes and their physiological function. We concentrate on proteins involved in human health and disease, with a focus on breast cancer and heart disease. Undergraduate researchers work with graduate students or post-doctoral fellows in the lab and gain experience in a wide array of approaches and techniques, including: molecular biology (cloning, site-directed mutagenesis, yeast two-hybrid screens, etc.), protein chemistry (purification, enzyme assays, ligand-binding assays, etc.), and structural and biophysical techniques (NMR, CD, MS). Current projects involve the proteins BRCA1(breast cancer protein-1), PDE5 cardiac phosphodiesterase), HSP27 (human heat shock protein), and PhoQ (pathogenic virulence factor).
Successful completion of General Chemistry, Organic Chemistry, and 1 year of Biology are required. Students that have taken a course in Biochemistry and/or Physical chemistry are given preference.
Prof. Lih Y. Lin - Electrical Engineering
Website: http://www.ee.washington.edu/research/photonicslab/
Working on manipulating biological cells or nanoparticles using the opto-plasmonic tweezers we are currently building.
Working with graduate students on characterization of various nanoscale quantum dot photonic devices.
Prerequisites: Understanding fundamental optical principles and photonic devices, understanding basic quantum mechanics.
Prof. Rene Overney - Chemical Engineering
Website: http://www.cheme.washington.edu/people/faculty/overney.htm
§ Nanocomposites and Local Properties
While in materials, such as ceramics, metals and oxides, size limitations are noticeable only below 10nm (quantum-well effects), it was found that in polymer systems interfacial effects can be noticeable over a distance of tens to hundreds of nanometers. One of the great challenges to date is to obtain material and transport property information on that scale. Current analysis methods are generally still only probing macroscopic properties. This applies particularly for material and transport properties of nanocomposite materials. Organic-inorganic nano-composites are promising materials with unique material and transport properties. They have tremendous potential for applications in areas such as catalysis, fuel cells, microelectronics, organic batteries, optics and gas separation systems. This summer UG research program will familiarize students with nanocomposite materials and their potential in generating unique properties, such as reversed selectivity in membranes, fuel cells and organic batteries. Students will be involved in material engineering, and be introduced to a wide variety of contrast enhancing scanning probe methods to explore the heterogeneous nature of these materials.
§ Nanomechanical Prescreening Analysis of Cancerous Cells
The simplicity of scanning force microscopy (SFM) that operates on the nanoscale in real space has facilitated mankind's access to analyzing material properties, assembling nanoscale structures, and utilizing nano-scaled device functionalities. The working principle of SFM is very simple and comparable to a scanning phonograph needle, and is well suited as a nano-mechanical sensor. During this UG summer project the students will be involved in nanoscale measurements of viscoelastic properties and adhesion of cells and tissue materials. The general objective of this study in which this UG summer project is situated is to develop a mechanical prescreening procedure to detect the onset of pathological cell growth that leads to cancer. The research project involves besides sample preparation, nano-mechanical SFM studies, literature research on tissue materials, also in the participation of the development of a statistical ensemble screening method involving SFM.
§ Nanocontrol of the Molecular Mobility in Electronic Organic Photonic Materials
In general, the pursuit for highly efficient electronic organic materials is limited by the molecular mobility and its control. In photonic organic material devices, where the wide bandwidth of light is used for ultra-fast information exchange, the material's molecular mobility is crucial for highly efficient devices. This project is addressing one of the most important properties of photonic materials, the electro-optical activity, which is a measure of the strength of the non-linear dipole field. The UG students working in this project will learn about the effect of intermolecular and intramolecular constraints on properties of organic photonic materials, and how to utilize them in a complex molecular architecture to maximize desired material and transport properties. This project introduces the students to a wide variety of organic electronic materials from liquid crystals to polymers. The project entails state-of-the-art material property analysis such as scanning probe techniques.
Prof. Suzie Hwang Pun - Bioengineering
Website: http://faculty.washington.edu/spun/
The Pun Lab focuses on the development of non-viral gene delivery vehicles. Applications for these materials include siRNA delivery to the central nervous system, tumor-specific gene delivery and tissue engineering. Research in this area would involve learning cell biology, molecular biology, and bioconjugate chemistry techniques to prepare and test delivery vehicles in cultured cells.
Prof. Alexander Rudensky - Immunology
Website: http://pilgrim.immunol.washington.edu/members.html
Our research is focused on understanding the molecular mechanisms governing the development and function of CD4 T lymphocytes and their role in T cell mediated immunity. CD4 T cells recognize foreign and self protein antigens in the form of relatively short peptide fragments associated with MHC class II molecules displayed on the surface of antigen-presenting cells and play a central role in regulation of adaptive immune responses to infection and the maintenance of tolerance to self.
I would like students to have taken an undergraduate immunology class, a class in molecular/cell biology, and a class in genetics. Previous lab experience is a plus.
Prof. Hong Shen - Chemical Engineering
Website: http://www.cheme.washington.edu/people/faculty/shen.htm
The students will be working on developing nanoparticle-based delivery systems to modulate both innate and adaptive immunity. One student will be working on optimizing formulation of nanoparticles to target the intracellular signaling pathway for the generation of safe and effective antiviral innate immunity. Another student will be working on optimizing formulations of nanoparticles to target antigen presentation pathway for the generation anti-tumor adaptive immunity.
Some background in biology will be a plus, but it is not required.
Prof. Carol Sibley - Genome Sciences
Website: http://www.gs.washington.edu/labs/sibley/index.htm
My lab studies drug resistance in malaria parasites. We use both molecular biology methods- PCR and sequence analysis- and yeast genetics to identify and study genes associated with parasite genes responsible for resistance to several commonly used antimalarai drugs. Our work involves close collaboration with colleagues in Africa- principally Kenya and Tanzania- and Southeast Asia- mainly Thailand and Indonesia. This combination of lab based studies with a clear connection to an important real world problem catches studnet interest, and has been a very effective way to demonstrate the utility and excitement of science.
Prof. Kristin Swanson - Pathology
Website: http://www.amath.washington.edu/~swanson/
Our lab is interested in linking clinical imaging modalities through mathematical modeling of the biological process underlying the imaging. Specifically, we are interested in predicting future behavior of primary brain tumors (gliomas) from current imaging observations. We make comparisons of our mathematical model predictions with clinical imaging observations as well as microscopy of operative and autopsy tissue.
Completion of the following courses preferred but not necessary:
AMATH 301 Scientific Computing
AMATH 352, MATH 308/9 Linear Algebra
Prof. Willie Swanson - Genome Sciences
Website: http://www.gs.washington.edu/labs/swanson/
The overall interest of my laboratory group involves identifying genes that have potential to be involved in speciation. Studies of adaptive evolution have revealed multiple classes of reproductive proteins under positive selection, including those involved in gamete-recognition, seminal fluid factors and proteins in the reproductive tract. The student(s) that I sponsor will be involved in a study of mouse reproductive proteins which may be good candidates for genes involved in reproductive isolation and, consequently, speciation. This project will provide hands-on training and experience in the high-throughput proteomic techniques necessary to identify proteins in prostate and seminal fluid for this study. In addition, the student will learn to use bioinformatic techniques to cull prostate protein and gene sequences from the Prostate Expression Databases (PEDB) for use in identifying prostate contributions to seminal fluid by matching the database sequences to the protein sequences we derive in the laboratory. Throughout the student's experience here, emphasis will be placed on the importance of clearly defining scientific questions and on relating data obtained from laboratory work to information available in the current body of scientific literature.
Prof. Christopher B. Wilson - Immunology
Website: http://depts.washington.edu/immunweb/faculty/profiles/wilson.html
My laboratory has two related interests, and it would be possible to have a student working in each area over the summer. The first emphasis are studies addressing 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, other primates 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.
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.
Prof. Paul Yager - Bioengineering
Website: http://faculty.washington.edu/yagerp/
We are developing microfluidics-based analytical techniques for molecules of biomedical interest. Ongoing projects focus on the use of optical detection methods, including fluorescence, optical absorbance, and surface plasmon resonance imaging. Projects are funded by NIH and the Bill and Melinda Gates Foundation.
Prof. Xiao-Hua Andrew Zhou - Biostatistics
Website: http://faculty.washington.edu/~azhou/
We are planning to have one undergraduate student to engage in
- statistical research with an application to clinical studies in Alzheimer’s disease
- statistical research with an application to depression and other mentalhealth studies
- statistical genetics
- bioinformatics
Junior and senior undergraduates with at least one-year of calculus, linear algebra, multivariate calculus, and other math or statistics courses. GPA is least 3.0
