The Amgen Scholars Program

Website: http://faculty.washington.edu/ajb1515/

Description: When one considers an energy source for driving a chemical reaction, the first thoughts are usually thermal, photo, or electrical impetus. Much less common is the application of mechanical forces to provide energy to overcome activation barriers along a reaction coordinate. This practice, known as mechanochemistry, involves the use of mechanical energy to influence chemical phenomena, including bond making and breaking events. In this regard a mechanophore may be viewed as a moiety that is sensitive to applied stress, which can be applied either in the solid-state (e.g., via shearing) or in solution (e.g., via ultrasound). Our group focuses on the design and synthesis of specialty mechanophores that can be incorporated into macromolecular architectures and applied as stimulus-responsive materials. From these materials, we target applications in areas ranging from stress-sensors to drug delivery.

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

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

Description: Errors in chromosome segregation lead to aneuploidy, which results in birth defects, cancer or cell death. Accurate chromosome segregation is performed by a large molecular machine called the mitotic spindle. The mitotic spindle contains many smaller machines including the centrosome, the microtubules themselves, the kinetochores where the microtubules attach to the chromosome and a multitude of microtubule motors. The ultimate goal of mitotic spindle assembly is to arrange each chromosome with its sister chromatids attached to opposite poles via microtubule fibers. This ensures that when anaphase occurs, the two sister chromatids are pulled apart and partitioned one into each daughter cell. The kinetochore is a part of the mitotic spindle with a critical task. It attaches the chromsomes to the dynamic microtubule fibers and must do so against ~20 pN of force, much more than is required to drag a chromosome through the cellular milieu. All chromosome segregation depends on this connection. We are studying the kinetochore as a molecular machine. The Amgen Scholar would work with two graduate students who are reconstituting the kinetochore from purified components. The student would learn protein purification and quantitative microscopy techniques and would have their own project as part of this larger endeavor.

Requirements: A biology lab course and introductory biology course would be very helpful. A cell biology or biochemistry course would also be helpful.

Website: http://dunham.gs.washington.edu/

Description: My lab works on genome evolution in yeast, ranging from laboratory evolution over a few weeks up to species-level differences over millions of years. We study these topics on a genome-wide scale using microarray and sequencing technologies as well as classical genetics approaches. Summer opportunities include both experimental and computational possibilities.

Requirements: Some laboratory experience (e.g. a lab course or other research experience) is preferred.

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://depts.washington.edu/hadlab/

Description: Inflammation has an important influence on the outcome of disease and injury in the CNS. Our laboratory studies the molecular regulation of inflammatory behaviors in the context of CNS diseases including Alzheimer's Disease, Stroke, Huntington's Disease and HIV associated neurocognitive disorders. We employ engineered mouse models of human disease as well as autopsy tissue from affected patients in these studies.

Requirements: One year of biology and chemistry coursework. Experience with commonly used equipment in molecular and cellular biology laboratories.

Website: http://www.phys.washington.edu/groups/nanopore/index.shtml

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://sop.washington.edu/pharmaceutics/faculty-a-research/rodney-ho.html

Description: Our research program focuses on drug delivery and targeting for cancer and AIDS. The student will learn how to construct anti-HIV or anti-cancer nanoparticles and evaluate their biochemical and biophysical structure and functions of drugs and carriers in test tubes and cell cultures. They will be a part of the overall goal to improve effectiveness and safety of drugs for treatment of cancer and AIDS.

Requirements: Biology and chemistry with laboratory experience. Biochemistry and molecular biology will be helpful.

Website: http://depts.washington.edu/jgroup/Index.htm

Description: Molecular Understanding, Design and Development of Next-generation Biomaterials
An important challenge in many applications, ranging from biomedical devices to drug delivery carriers, is the prevention of nonspecific biomolecular and microorganism attachment on surfaces. To address this challenge, our goals are twofold. First, we strive to provide a fundamental understanding of nonfouling mechanisms at the molecular level using an integrated experimental and simulation approach. Second, we aim to develop biocompatible and environmentally benign ultra low fouling materials based on the molecular principles we have learned. Over the last few years, we have demonstrated that zwitterionic and mixed charge materials and surfaces are highly resistant to nonspecific protein adsorption, even from complex media such as undiluted blood plasma and serum. Both simulation and experimental results show that the strong hydration of zwitterionic materials is responsible for their excellent nonfouling properties. At present, zwitterionic materials have already been applied to a number of applications, including implantable medical devices, early cancer diagnostics, drug/gene delivery, antimicrobial coatings, and marine coatings. Students will have opportunities to work with 20+ Ph.D. students and postdoctoral research associates on one or more of the following topics from molecular principles to product development.

1. Surface modifications and coatings
2. Implantable hydrogels and sensors
3. In vitro and in vivo drug and gene delivery
4. Antimicrobial coatings
5. Organic and polymer synthesis of biopolymers
6. Combinatorial synthesis of peptide-based materials
7. Molecular simulations studies of protein-surface interactions
8. Quantitative structure-property relationship (QSPR) modeling

Website: http://www.kaeberleinlab.org/

Description: The Kaeberlein lab is interested in understanding the basic biology of aging. Projects in the lab have a common theme centered on defining the genetic and environmental factors that influence longevity and healthspan. We use three different model organisms for our research: the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and mice. Depending on interest and experience, an Amgen Scholar summer student would have the opportunity to work on an aging-related project in yeast or C. elegans (or possibly both). Currently available projects include (1) mechanistic studies aimed at defining why specific yeast mutants respond differentially to dietary restriction, (2) characterizing the relationship between mRNA translation and aging, with specific emphasis on the interplay between mitochondrial and cytoplasmic translation, and (3) defining the mechanisms by which the hypoxic response influences aging and healthspan in C. elegans. Opportunities to contribute to our SAGEWEB project (http://www.sageweb.org) are also available for students interested in aging-related bioinformatic/computational studies and/or software development.

Requirements: Enthusiasm and interest in the biology of aging.

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/rtmoon/

Description: Randall Moon studies the highly conserved Wnt signal transduction pathways. Wnts are secreted ligands that activate receptor-mediated pathways that regulate cell proliferation, cell fate, and cell behavior in development, and stem and progenitor cells in adults. His first goal is to identify the roles of Wnt signaling at the level of the organism, with a focus on regenerative processes in adults. His second goal is to elucidate the mechanisms by which Wnts signal. His third goal is to understand how Wnt signaling is linked to diseases, and to identify candidate therapies. The lab uses a wide range of methods, from studying human embryonic stem cells,to genome-wide siRNA screens, to small molecule screens, to proteomics. One current project studies the roles of Wnt signaling in heart regeneration in zebrafish, another project focuses on how beta catenin has different roles in different cancers, and a third project focuses on the roles of Wnt signaling in human embryonic stem cells, and hematopoietic progenitor cells.

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.uwaging.org

Description: The focus of the laboratory research is on the use of experimental animal models to examine the effects of cell signaling and reactive oxygen species (ROS) on lifespan and healthspan.  Transgenic mice that overexpress catalase have been found to be protected against multiple health challenges, including cardiac aging, sarcopenia and some cancers. A mitochondrial antioxidant drug, SS-31, is also being studied in mice, worm and yeast models. The interrelationships of mitochondrial ROS and mitochondrial damage with cell signaling pathways that mediate improved healthspan, including resistance to cardiac hypertrophy and failure, are also studied in the laboratory. As the mTOR pathway is a strong candidate in this linkage, we are using transgenic mice with altered mTOR signaling to explore this relationship. Projects are available in mouse and worm aging and healthspan studies, as well as in proteomic studies of effects of ROS and mTOR on protein translation and turnover.

Requirements: Should have completed some biology coursework and lab experience.

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

Description: In the past decade silicon photonics has revolutionized our ability to manipulate light on the chip-scale, with implications in computation, commincations and biomedical technology. For instance, the silicon nanophotonic microring resonator is a highly sensitive and label-free biosensing technology that has shown promise for detecting bimolecular and whole-cell binding interactions. Our lab aims to study interactions between cell receptors (including carbohydrates antigens) and protein, bacterial and viral binding partners using this silicon photonic platform. This Amgen project will focus on developing methods to engineer a non-fouling and biocompatible interface on our silicon microring resonator devices and assess subsequent interactions using complex samples, including human plasma.

Requirements: To ensure a successful research experience, students should have a basic familiarity with general/organic chemistry and introductory biology (protein structure, basic cell biology).

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/

Description: My laboratory works on stem cell biology utilizing two systems, Drosophila germ line stem cells and human embryonic stem cells.  In both cases we have shown that microRNAs play an important role in stemness.  Our goals now include defining the key microRNA targets and their function in stem cells and their differentiating progeny.  Further, we seek to understand the regulation and importance of the stem cell specific hypoxic metabolism.  The goal is to understand whether the key stemness character observed in normal stem cells is also observed in pathological stem cells, so called cancer stem cells. 

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: amath.washington.edu/~etsb

Description: COMPUTATIONAL DYNAMICS OF BRAIN FUNCTION

We work on the dynamics of neurons, structured neural networks, and large neural populations. The goal is to help uncover mechanisms that enable these systems to encode, propagate, and make decisions about sensory inputs. I enjoy the highly collaborative work with cognitive neuroscientists, with electrophysiologists, and with psychiatrists and neurologists that this requires. Achieving this goal also requires generalizing mechanisms uncovered in these and other studies to develop the mathematical theory of spiking neural networks. The shared aim is a theoretical framework which describes and connects the neural dynamics occurring on different spatial and temporal scales, ranging from single neurons and small circuits to populations.

Website: http://www.pathology.washington.edu/research/labs/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 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: Our lab is interested in investigating cytochrome P450 enzymes that are involved in drug metabolism and have a known endogenous function. Several research opportunities exist to study the biochemical role of these enzymes. One project focuses on CYP2J2 and its role in drug induced cardiac toxicity. Stem cell derived adult cardiomyocytes are treated with various drugs and the change in RNA and protein expression is measured. Also the effect of drugs on the activity of CYP2J2 is assessed using LC-MS. A second project investigates the pharmacogenetic nature of CYP2C8. This enzyme is polymorphically expressed in various ethnic groups which results in a variable pharmacological response to drugs metabolized by this enzyme. We are currently investigating the mechanism behind the variable activity of the main variants of this enzyme. We utilize molecular biology to engineer the different variants, UV spectroscopy and LC-MS to assess the changes in activity.

Requirements: Intro to Chemistry and intro to Biochemistry

Website: http://depts.washington.edu/micro/faculty/traxler.htm

Description: We would like to have a student work on a genetic analysis of genes that are involved with exchange of DNA between bacteria by conjugation. Specifically, we are interested in the similarity of conjugation systems that act in the standard lab bacterium E. coli and in bacterial pathogens like Agrobacterium tumefaciens and Burkholderia cenocepacia (which can infect plants and cystic fibrosis patients, respectively). We want to compare proteins that are important in these different organisms to determine how similar their transfer systems are.

Requirements: Basic understanding of biology and chemistry required (advanced high school or introductory college); helpful knowledge and skills include basic understanding of genetics and molecular biology.

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

Description: Our research group develops and uses functionalized micro- and nanomaterials as tools for studying the biological trafficking of pathogens involved in disease and for developing new technologies that benefit human health. We focus currently on three major research areas: (1) Employing synthetic and protein engineered viral mimics to study pathogen-host interactions during sexual transmission of HIV, (2) Designing drug delivery systems to mucosal tissue for the purpose of developing topical microbicides and stimulating mucosal immunity, and (3) Developing diagnostics for infectious disease and cancer.

Requirements: Molecular biology, biochemistry, organic chemistry

Website: http://faculty.washington.edu/zhangb/index.html

Description: Our research is focused on fundamental and applied aspects of electrochemistry and biochemistry utilizing materials in the 1-100nm range. Two projects are available for undergraduate students. The first project studies electron-transfer and energy conversion at individual metal/semiconductor nanoparticles. A molecular-scale nanoelectrode is used to address individual nanoparticles and characterize their electrochemical properties. The second project is focused on the analysis of individual biopolymer molecules (e.g., DNA, RNA) using of a graphene nanopore field-effect transistor type sensor. Both of the projects involve the development and application of novel nanomaterials and nanotools. Therefore, students with a strong motivation and interest in nanotechnology, analytical chemistry, and physical chemistry are welcome to participate in our research.

Requirements: A strong background and motivation in chemistry.