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The Amgen Scholars Program

2014 Amgen Faculty

Click on the names below to learn more about the 2014 UW Amgen Faculty. Please note this is the Final List of 2014 participating faculty.

* indicates newly added faculty

Jesse Bloom * - Virology, Biology (Evolutionary & Computational)

Website: http://research.fhcrc.org/bloom/en.html

Description: Influenza poses a continuing challenge to human health because it rapidly evolves to escape from immunity. Our lab seeks to better understand this evolution. We use a combination of experimental, computational, and sequencing-based approaches to investigate how influenza changes to escape recognition from both the adaptive and innate arms of the immune system. This work provides an opportunity to study evolutionary biology in the context of a medically important pathogen.

Requirements: We welcome students with interests in either experimental or computational biology or (preferably) both!

Elhanan Borenstein - Genome Sciences

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

Description: We humans are mostly microbes. Microbial communities populate numerous sites in the human anatomy, harboring thousands of microbial species and over 100 trillion microbial cells. This complex ensemble of microorganisms, collectively known as the human microbiome, has a tremendous impact on our health and plays an essential role in numerous diseases. Owing to recent advances in sequencing technologies and metagenomics, studies of the microbiome are now starting to map these communities and to characterize the composition of species found across the human body. Our lab is focused on computational analysis of these data and on addressing fundamental questions concerning the assembly, function, and impact of the microbiome. Specifically, we are using computational systems biology, network analysis, and in-silico modeling to study the microbiome. Multiple exciting projects are available, including analysis of species interaction networks from the human microbiome project, metagenome-wide metabolic modeling, and method development for computational metagenomics.

Requirements: Some computational background and programming experience are required (e.g., working knowledge of perl, python, or Matlab).

Andrew (AJ) Boydston - Organic Chemistry

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 all introductory organic chemistry courses (237-239, or honors track) and any associated laboratory courses.

Matt Bush - Bioanalytical & Biophysical Chemistry

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

Description: Most proteins, particularly those that accomplish complicated tasks, form assemblies with other proteins and molecules that are critical for their function. Our research focuses on developing new mass spectrometry and ion mobility spectrometry technologies to understand the structures and assembly of biomolecular machines and biotherapeutics, especially those that are heterogeneous, dynamic, and interact with complex chemical matrixes. Opportunities are available for projects focused on (1) development of new analytical instrumentation, (2) elucidating the mechanism of ionization for large protein complexes, and (3) investigating the structures of protein complexes related to human health. Specific projects with these areas can be developed based on your interests and prior experience.

James Carothers - Chemical Engineering & Bioengineering

Website: http://carothersresearch.com/

Description: Through the careful application of genetic engineering, synthetic biological systems can be constructed to solve real world problems. In our work, we combine computational modeling, in vitro selection and genetic assembly to construct RNA-based genetic control systems in microbes and cultured mammalian cells. Our aim is to enable better understanding of biological principles and to help meet demands for renewable chemicals and materials for human health. Opportunities are available in the general areas of 1) computational design and analysis of metabolic circuits engineered to produce renewable plastics and 2) engineering complex RNA programs for cell-based therapeutics. Specific projects will be developed based on your background and interests.

Requirements: Experience in any of the following areas would be helpful:

  • Programming (e.g., Unix/Linux shell, Python, Perl, C)
  • Computational modeling and statistical analysis (e.g., kinetics, sensitivity analysis, R)
  • in vitro selection/SELEX (RNA aptamers, ribozymes)
  • Genetic assembly (using Gibson, CPEC, etc.)
  • Metabolic engineering (pathway construction and optimization)
  • Mammalian tissue culture (gene expression and imaging)

Champak Chatterjee - Chemistry

Website: http://faculty.washington.edu/champak1/ChampakResearchGroup.html

Description: The Chatterjee lab is interested in understanding how chemical changes to proteins can influence their functions inside cells. We are particularly interested in reversible changes to histone proteins that are associated with the regulation of gene activity. The specific histone modification that we are studying is by a small protein called SUMO (small ubiquitin-like modifier). We are employing the tools of protein chemistry and molecular biology to make synthetic SUMO-modified histones that will be subjected to biophysical and biochemical assays in order to study the effects of SUMO on chromatin function. Specific details of the project will be decided after considering the students background and interest but will be focused on (i) applying synthetic organic chemistry to make modified histone proteins and, (ii) performing biochemical or biophysical assays with synthetically modified histones. Results from these studies will uncover new mechanisms by which histone modifications can regulate gene function. This is important for understanding how cells develop normally and also how diseases such as cancer arise from the incorrect timing of histone modifications.

Requirements: Completion of an introductory organic chemistry course along with associated laboratory courses. A background in biochemistry is helpful but not essential.

Trisha N. Davis - Biochemistry

Website: http://depts.washington.edu/biowww/pages/faculty-Davis.shtml

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 graduate students and research scientists who are reconstituting the kinetochore from purified components. Several projects are possible. The student would learn protein purification and quantitative microscopy techniques or mutagenesis and genetics. The student would have their own project as part of this larger endeavor.

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

Maitreya Dunham - Genome Sciences

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

Description: How do two different species know not to mate with each other? In this summer project, you will help discover new genes that are important for speciation in yeast, using genetics and genomics approaches.

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

Horacio de la Iglesia - Biology

Website: http://depts.washington.edu/hacholab/research.php

Description: Research in our laboratory is guided to understand the neural basis of behavior. Specifically, we are interested in biological timing, which can be studied at different levels of organization, using different approaches and throughout the phylogenetic tree. Virtually all living species have biological clocks that generate and control the daily cyclic variations in physiology and behavior, such us rhythms in locomotor activity, temperature and hormonal secretion. In mammals, the master control of these so-called circadian rhythms is exerted by a biological clock located within the suprachiasmatic nucleus (SCN) of the brain. We use behavioral, physiological and molecular techniques in order to understand how the SCN generates and orchestrates this array of circadian rhythms.

Gwenn Garden - Neurology

Website: http://depts.washington.edu/neurolog/research/garden-lab/research.html

Description: Cellular interactions between neurons and glia have an important influence on the outcome of disease and injury in the CNS. These interactions include alterations in communication between neurons as well as the glial response to injury. Our laboratory studies these cellular interactions in the context of CNS diseases including Alzheimer's Disease, Stroke, Huntington's Disease and related disorders. We employ engineered mouse models of human disease, induced pluripotent stem cells from patients, a variety of primary cell culture models and 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.

Jens Gundlach - Physics

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.

Matt Kaeberlein - Genetics, Biochemistry, Molecular Biology

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 four different model organisms for our research: the budding yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the mouse Mus musculus. Depending on interest and experience, an Amgen Scholar summer student would have the opportunity to work on an aging-related project in one of these model systems. Currently available projects include (1) mechanistic studies aimed at defining the interaction between genotype and the response to dietary restriction, (2) studies of mitochondrial function during aging and the effect of mTOR inhibition on mitochondrial disease, and (3) defining the mechanisms by which hypoxia and the hypoxic response influence lifespan.

Requirements: Enthusiasm and interest in the biology of aging.

Deok-Ho Kim - Bioengineering

Website: http://www.openwetware.org/wiki/Kim

Description:Our research focuses on investigating how the engineered microenvironments direct cell function and tissue regeneration. In particular, we are exploring extracellular matrix (topology, rigidity, dimensionality, etc) regulation of cell fate and function in developmental, physiological and pathological process. Several specific thrusts of the current research program include: microscale cardiovascular tissue engineering, BioMEMS for stem/progenitor cell niche engineering, microengineered platforms for cell-matrix mechanobiology, and mechanical regulation of cancer cell invasion and collective cell migration. Positions are available for development of bioengineered tools (e.g. microfluidic systems and nanofabricated cell culture devices) for cancer biology, stem cell and tissue engineering. Students will be working on micro/nanofabrication, biomaterial synthesis, data analysis, quantitative live cell microscopy and cell culture.

Xiaosong Li - Computational Science, Chemistry and Materials Science

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

Description: Research in the Li group focuses on developing and applying computational methods and theories for studying properties and reactions that take place in large systems, such as polymers, biomolecules, and clusters. Students will have a unique opportunity to participate in interdisciplinary research subjects.

Requirements: Interest and motivation in computational research.

Lutz Maibaum - Chemistry

Website: http://depts.washington.edu/bpsd/faculty/lmaibaum

Description: Our research group is interested in the physical and chemical properties of lipid bilayers and their interactions with other biomolecules. Our goal is to understand biological phenomena involving the cell membrane, and to use this knowledge to help design novel materials with desirable properties. Our approach is based on computational and mathematical modeling of these enormously complex systems.
There are several opportunities for Amgen scholars in our group. We would love some help with the following problems, but we are certainly flexible and will design a project based on a scholar's interests:

1. How does the chemical composition in one leaflet of a lipid bilayer affect the composition in the opposing leaflet? Very little is currently known about this important questions, which will play a crucial role in our understanding how composition inhomogeneities in cell membranes occur.

2. How do lipid bilayers interact with strongly charged peptides? Many proteins that interact with cell membranes show an increase in charged amino acid content. We are trying to obtain a general understanding of these interactions, in particular the role of the membrane composition.

Requirements: An interest and aptitude in using computers to solve mathematical problems. Not required, but very helpful, will be the knowledge of at least one computer programming language, and the completion of at least one upper division physical chemistry course.

Dustin Maly - Chemistry

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).

Dana Miller * - Biochemistry

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

Description: Animals are constantly interacting with the environment, matching cellular biochemistry with current conditions and available resources. The inability to rapidly sense and respond when conditions change can be fatal. The focus of our lab is to understand fundamental strategies that animals use to survive in an ever-changing environment, and leverage this knowledge to improve the survival of people that are challenged by injury, disease, and even aging. One focus of our research is to determine how early experiences alter the response to environmental stresses later in life. This is a common strategy, where animals “predict” future changes in the environment based on prior experiences, a phenomenon referred to as “stress memory”. We have discovered that exposure to the toxic gas hydrogen sulfide establishes an epigenetic stress memory in the molecular genetic model organism C. elegans. We are currently using molecular genetic and biochemical approaches to delineate the mechanistic basis of how the response to sulfide activates the chromatin remodeling factors that mediate this epigenetic effect, to define how the formation of the stress memory changes the structure and accessibility of DNA at the promoters of genes, and to figure out how the ability to form and maintain the epigenetic memory of sulfide exposure changes with age. An Amgen scholar in our lab would work closely with graduate students performing experiments using cutting edge molecular techniques to reveal new mechanistic features of epigenetic changes that allow for modulation of fundamental stress response pathways in animals.

Requirements: Introductory-level biology and chemistry courses are highly recommended; lots of enthusiasm and curiosity are essential.

Shao-En Ong - Pharmacology

Website: http://www.quantbiology.org

Description: Proteins are the workhorses of the cell. Using mass spectrometry-based quantitative proteomics, our lab focuses on developing novel techniques to study proteins involved in a variety of cellular processes, including proliferation, differentiation, and signaling. Two current projects in the lab are 1) identifying regulatory proteins such as transcription factor complexes and their role in controlling cell fate, and 2) examining kinases and their interaction partners in different functional states (e.g., active vs. inactive). These tools have widespread implications for cancer biology, regenerative medicine and drug discovery. Our research takes a multidisciplinary approach, combining experimental and computational analyses to provide a systems-view of the cell. The focus of the project will be designed to suit the prior experience and specific interests of the candidate.

Requirements: Prior research experience strongly recommended.

Alex Paredez - Molecular and Cellular Biology

Website: http://www.biology.washington.edu/users/aparedez

Description: Giardia is an important parasite that affects a wide variety of animal hosts, including over 100 million (mostly impoverished) people each year. Treatment options are limited; therefore, the WHO has recognized giardiasis as a neglected disease. In addition to Giardia being a major parasite, this organism stands out as one of the most evolutionary divergent eukaryotes (from animals) that can be manipulated in the laboratory. While the majority of microtubule cytoskeleton components can be identified in the Giardia genome, none of the core set of homologous actin-binding proteins (e.g.: nucleators, motors, bundling, and severing proteins), can be found in Giardia. Yet, the Giardia actin cytoskeleton still has complex organization and is regulated by G-protein signaling. Moreover, the Giardia actin cytoskeleton has a conserved role in cellular organization, trafficking, and cytokinesis (novel mechanism without contractile ring or midbody). Importantly the giardial actin cytoskeleton is both essential and highly divergent from that of humans; therefore, it represents an important potential target for treating this neglected disease and an opportunity to gain insight into evolution of the cytoskeleton. Several projects are available depending on a particular student's interest.

Requirements: An interest in cellular mechanisms, microscopy, and a sense of humor.

Jim Pfaendtner - Chemical Engineering

Website: http://prg.washington.edu/

Description: The student joining this project will work on understanding the role of solvents and interfaces in controlling the mechanism of lipase family enzymes. Some enzymes such as lipases maintain activity in a variety of novel solvents such as ionic liquids or organic solvents. The underlying molecular scale reasons for this are unknown and therefore prevent us from rationally designing new solvents and processes. The student working on this project will learn molecular and multiscale modeling methods to study the atomic scale transformations that lead to solvent-induced conformational change in several lipase family enzymes. The PI and grad student working on this project will train the Amgen Scholar to perform molecular simulations on a supercomputer and carry out an extended study of enzyme structure and dynamics.

Requirements: Students should have general understanding of basic concepts from physical chemistry and thermodynamics. No prior computational modeling experience is necessary for this project.

Suzie Pun - Bioengineering

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

Description: The Pun Lab develops delivery vehicles for therapeutic proteins, peptides and nucleic acids. Applications for these delivery vehicles include siRNA to the central nervous system, cancer therapy, and immunomodulation. Researchers in our lab learn techniques related to polymer and peptide synthesis, mammalian cell culture, nanoparticle formulation and characterization, and gene transfection assays.

Peter Rabinovitch - Experimental Pathology

Website: http://www.pathology.washington.edu/research/labs/rabinovitch/

Description: Aging is single greatest risk factor for many human diseases; however, the biological process of aging is often overlooked as a causative mechanism of disease. The Rabinovitch laboratory has focused on two disease processes in which to study the contribution of aging mechanisms.  Studies of cardiac aging, hypertrophy and failure primarily utilize mouse models, while studies of ulcerative colitis utilize human biopsies and resection specimens. In either of these areas, the Amgen Scholar would learn of the mechanisms of aging that contribute to disease and the use of cutting-edge molecular and genomic research technologies.

Cardiac aging. We use mouse models to examine the effects of cell signaling and reactive oxygen species (ROS) on cardiac aging.  Transgenic mice that overexpress catalase have been found to be protected against multiple health challenges, including cardiac aging. A mitochondrial antioxidant drug, SS-31, appears to provide similar protection. The interrelationships of mitochondrial ROS and mitochondrial damage with cell signaling pathways that mediate improved healthspan, including resistance to cardiac hypertrophy and failure, are studied. As the mTOR pathway is a strong candidate in this linkage, we are using transgenic mice with altered mTOR signaling to explore this relationship. Global proteomic and genomic approaches are also used to study the effects of ROS and mTOR on protein translation and turnover.

Aging and Genomic Instability in Ulcerative colitis. Aging, telomeres and mitochondrial function appear to interact with genomic instability as mechanisms behind the increased cancer risk in ulcerative colitis. Confocal microscopy and immunohistochemistry are used to study these processes in UC colon biopsies and resection specimens.

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

Michael Regnier - Bioengineering; Physiology & Biophysics

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.

Hannele Ruohola-Baker - Biochemistry, Institute for Stem Cells and Regenerative Medicine

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.

Wendy Thomas - Bioengineering

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

Description: The Thomas lab studies the mechanical regulation of adhesive proteins, and applies this knowledge to develop new technologies. We study adhesive proteins that are involved in thrombosis (blood clots), or in bacterial infections. We also design novel biological adhesives and adhesive proteins for biotech applications including diagnostics, drug delivery and microrobotics.

Requirements: The background needed depends on the project within the lab. For some projects, we prefer freshman biology and chemistry. For other projects, we prefer other skills such as programming, advanced math (eg. differential equations or transport math), or CAD skills.

Rheem A. Totah - Medicinal Chemistry

Website: http://sop.washington.edu/medchem/faculty-a-research/rheem-totah.html

Description: Our lab is interested in investigating cytochrome P450 enzymes expressed in extra-hepatic tissue and are involved both in drug and also endogenous substrate metabolism. One project focuses on CYP2J2 and its role in drug induced cardiac toxicity. Adult cardiomyocytes will be 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 role of CYP2C8 mediated metabolites of arachidonic acid on angiogenesis in different cell types. CYP2C8 is polymorphic and we want to determine how this genetic variation affects enzyme activity. 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

Judit Villen - Genome Sciences

Website: http://faculty.washington.edu/jvillen/lab/

Description: My lab is interested in how signaling networks shape the cellular proteome and function, and how the structure and activity of these networks is altered upon disease onset and progression. To learn about these questions, we develop and apply mass spectrometry-based approaches that involve quantitative measurements on nearly complete proteomes.  Our team is very interdisciplinary with a background ranging from chemistry and biology to engineering and computer sciences. Opportunities for summer students include experimental and computational options. Specific projects can be assigned based on background and interests.

Requirements: Previous research experience is preferable.

Bo Zhang - Bioanalytical Chemistry, Electrochemistry

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

Description: Our group research is focused on developing new electrochemical methods to solve important challenges in electron transfer, neurochemistry, and electrocatalysis. We currently have two projects available for incoming Amgen students. The first project studies electron-transfer and electrocatalysis at single metal/semiconductor nanoparticles using nanoelectrodes. The second project develops and uses electrochemical arrays to image neuronal secretion from single cells and cells in a network. Students with strong motivation and interest in analytical chemistry and physical chemistry are welcome to participate in our research.

Requirements: A strong background and motivation in chemistry.

Ying Zheng - Bioengineering

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

Description: Our research interest is to understand and engineer the fundamental structure and functions in living tissue and organ systems of our human body from nanometer, micrometer to centimeter scale. Our research topics include vascular growth and remodeling, blood-endothelium interactions, and the development of the organ specific system (i.e. heart, kidney and bone marrow). Our research utilize a variety of engineering tools (e.g. microfabrication, biomaterial synthesis and molding), imaging tools (e.g, fluorescence microscopy, confocal microscopy, and scanning and transmission electron microscopy), and biological technologies (e.g. flow cytometry, ELISA, cell culture, genomics and proteomics etc) work with engineered vascularized tissue and human blood samples. Students with strong motivation and interest in tissue engineering, biomaterials, and regenerative medicine are welcome to participate in our research.

Requirements: The requirements depend on projects in the lab. At least one aspect of the following is needed: basic biology and chemistry courses and lab skills, or imaging analysis skills with programming, or CAD/solidworks design skills.