Students
Carolyn Adamski
Carolyn Adamski is a senior at The College of St. Scholastica in Duluth, MN. She will soon be graduating with a Bachelor of Science in Biochemistry and plans to pursue a Ph.D. in a related field. Her past research was conducted at the University of California, San Francisco where she looked at the neuronal pathway mediating satiation. At the University of Washington she works with the Schnapp Lab researching the role of the urokinase receptor-associated protein in lung injury and repair. Outside the lab, Carolyn enjoys sunshine, traveling, spending time with family, people watching, and music. Her greatest aspiration in life is to directly help others through her research.
Sofia Annis
Sofia Annis is a rising junior at Smith College in Northhampton, Massachusetts. She is majoring in Biology and Italian Language and Literature. This summer, she is doing research with Dr. Akey of the Genome Sciences department. Her project involves using computational techniques to analyze dog genomic sequences. The goal of the project is to discover links between genotype and phenotype. Next year, she will be studying abroad in Florence, Italy and is looking forward to an international experience and fine Italian coffee. When she’s home, Sofia enjoys photography, reading, and playing with her 200+ rabbits.
James Athappily
James Athappilly is a junior at the University of Washington. Currently, he is pursuing degrees in Computer Engineering and Business. James’ greatest aspiration is to use technology to help expand our current understanding of the human body. This summer he is working in Herbert Sauro’s lab to create a simulation tool that will help researchers and teachers better understand cellular networks. After his undergraduate studies, James plans to earn an MD/PhD and continue using technology to further the limits of science. During his free time, James loves to learn, bike, run, and spend time with his family and friends.
Stephanie Bachar
Stephanie Bachar is a rising junior at the Massachusetts Institute of Technology (MIT) majoring in Biological Engineering. This summer she is working in Lih Lin’s lab in Electrical Engineering. She is assisting in the development of low intensity optical tweezers which use the gradient forces of laser light to trap, move and rotate mesoscopic objects, such as cells. At MIT she is involved in yeast prion and heat-shock protein research at the Whitehead Institute for Biomedical Research and she is the co-chair of the Educational Students Program which offers unique educational opportunities to students in the Boston area. After graduation she hopes to pursue bioengineering as it pertains to international development initiatives.
Rachel Baker
Rachel Baker is a rising senior at Loyola University, Chicago majoring in Molecular Biology and minoring in Classical Studies. In the Amgen program, she is working with Dr. Merrill B. Hille on zebra fish development and studies the protein p120 catenin. She hopes to attend graduate school for Molecular Biology in the future. In her spare time, Rachel enjoys reading, putzing around the Internet, piano, and hiking.
Nathan Cermak
Nate is a fifth year student at the University of Washington, majoring in biochemistry, applied and computational mathematical sciences and sociology. He plans to apply for MD/PhD programs which will allow him to research health from a variety of perspectives- biologically, socially, and statistically. He is a Seattle native and enjoys research, talking, arguing, biking, petting cats, listening to minimally-produced music, tinkering with computers, drinking coffee, riding ferries, and reading e.e. cummings, Philip K. Dick, Ray Bradbury and Kurt Vonnegut.
Trinidad Cisneros
Trinidad Cisneros is a rising senior at California State University Los Angeles majoring in Biology. This summer, he is using molecular biology techniques to study the roles of regulatory proteins involved in early zebrafish development. He is working in the Hille Laboratory subcloning various mutant classes of CDC42, a protein encoded gene that is responsible for cell migration and other signaling pathways. Prior to pursuing a degree in Biology, he spent several years working in social service agencies with various populations, from foster youth to families experiencing homelessness. He intends to continue to help others by pursuing an MD/PhD program after graduation. In his free time, he enjoys painting, drinking coffee, playing soccer, bird watching, writing poetry, hiking and volunteering.
Edward Dale
Edward is a senior at Knox College and is double majoring in Chemistry and Biochemistry. This summer, his research is in Dustin Maly’s lab working on the synthesis of small molecule inhibitors of kinases. This will lead to applications in drug development and the characterization of kinases that are unusually active in afflicted cells. In his free time, he enjoys the outdoors, playing tennis and soccer, and spending quality time with friends. At Knox he runs the Chemistry Club and organizes chemistry demonstrations at local elementary schools. In the future, Edward hopes to pursue a PhD, but is uncertain of the specific area at this time.
Rocky Eastman
Rocky is a senior at the University of Washington, where he is pursuing degrees in Molecular, Cellular and Developmental Biology and Philosophy. Rocky has worked with Dr. James Bassuk at the Seattle Children’s Research Institute since January 2008, where he studies diseases of the lower urinary tract. Currently, he is working to engineer urethral tissue in vitro for use in surgical hypospadias repair. He has also studied the progression of proliferative lesions in the lower urinary tract. Outside the lab, you’re likely to find him hanging out with his friends, attending Mariners games, enjoying the outdoors, or studying. After graduation next spring, he plans on attending either medical or graduate school, where he hopes to continue working in pediatric research.
Christina Elias
Christina Elias is a rising junior majoring in Chemical and Biomolecular Engineering at The Ohio State University. This summer, Christina is working in Lilo Pozzo’s lab studying interaction between denatured proteins and surfactants for applications in gel electrophoresis. She enjoys running, intramural sports, reading and exploring new places.
Eric Evangelista
Eric is a rising senior at the University of Washington, majoring in Chemistry and planning to pursue a future career in the medical field. He was born in the Philippines, moved to Canada when he was eight, and moved to Washington when he was 18. This summer, Eric is working in Dr. Rheem Totah’s lab in the UW Medicinal Chemistry Department where he will be working with cardiomyocytes, trying to get the cells to express the CYP 2J2 gene and then determining how various drugs will affect its expression. In his spare time, Eric likes to read, volunteer at the hospital, hang out with friends, play video games, and attempt things like playing the piano, cooking, dancing and drawing.
Emily Fawcett
Emily is a rising senior at Saint Mary’s College of Maryland. She is majoring in Biology with a focus in Molecular Biology, and is minoring in Environmental Studies. This summer she is working in the Merz Lab studying the effects of point mutations in a region of the protein Vps11 on the function of membrane trafficking in yeast. Her previous research experience includes an REU at Arkansas State University determining the utility of elevating endogenous levels of ascorbate in tobacco producing recomninant protein, and independent research at SMCM determining the bacterial composition in organic soil and the guts of bacterial-feeding nematodes. She spends her free time kayaking and sailing on the beautiful Chesapeake Bay, as well as serving as President of the SMCM chapter of the Beta Beta Beta Biological Honor Society. In the future, Emily hopes to continue to graduate school and obtain her PhD in Molecular Biology.
Ellie Frett
Ellie Frett is a rising senior at the University of Iowa in Iowa City. She will graduate in the spring of 2010 with a major in Biomedical Engineering and has plans to pursue Physiology at the graduate level. At her home institution, she has performed research under the instruction of Dr. Kevin Campbell for 2.5 years and will finish off her undergraduate career in his lab. This summer she is working under Dr. Brian Kennedy, helping to determine the role of lamin A in disease. In her free time, Ellie enjoys spending time outdoors, reading and running.
Natalie Grattan
Natalie Grattan, a rising senior at Lawrence University, in Appleton Wisconson, is pursuing a major in Biochemistry and a minor in Music. This summer, Natalie is working in the Wilson Lab studying the immune invasion techniques of Yersinia pestis and Bordatella pertussis, the bacteria that cause the plague and whooping cough respectively. More specifically, she will use flow cytometry and enzyme-linked immunosorbent assays (ELISA) to measure the cytokine response in splenocytes from mice with humanized TLR-4/MD-2 receptors in order to ascertain the importance of variant LPS structures in the stimulation of the immune response by these bacteria. After she graduates, Natalie hopes to combine her love of immunology with a year studying public health abroad, and to eventually work as a medical researcher studying infectious disease epidemiology. When she’s not playing with bacteria, Natalie enjoys hiking, reading, playing violin, and spending time with her friends and family.
Lisa Huffman
Lisa comes from a wheat farm in Cavendish, Idaho, and is a rising senior at the University of Idaho majoring in Biological Systems Engineering. For the Amgen Scholars Program, she is working in the Regnier lab to help develop myocardial tissue patches to repair the heart after infarction. In her free time, she enjoys reading, the outdoors, running, and being with her family and friends. She intends to pursue a graduate degree in Biomedical Engineering in order to develop new ways to improve the quality of peoples’ lives.
Allison Ikeda
Allison Ikeda is a rising junior at Whitman College in Walla Walla, WA. She is double majoring in Biochemistry, Biophysics, and Molecular Biology, and Economics with a minor in Japanese. She is passionate about exploring how to engineer immune responses and is conducting research under the mentorship of Dr. Hong Shen, Chemical Engineering. Her research examines the interactions between dendritic cells and T cells in the presence of artificial bacterial components to mimic bacterial infection and exposure. This research aids in the development of synthetic nano particles that target cells of the immune system to create a more effective immune response. When not in the lab, Allison enjoys being outdoors, especially running and kayaking in the Seattle and San Juan areas.
Scarlett Johnson
Scarlett is a rising junior at Amherst College and is majoring in Psychology. This is her first extensive research experience; she will spend the summer working with yeast in Dr. Field’s lab in the hopes of isolating and building a library of mRNA molecules with 2′, 3′-cyclic phosphates. Outside of class, Scarlett is a resident counselor, tour guide and student health educator, and she plans to pursue a PhD or MD after graduation. When home in Hawaii, she enjoys running, going to the beach and eating fruit in her backyard.
Elena Latorre
Elena Latorre is a rising senior at University of Puerto Rico, Mayaguez, majoring in Biological Sciences. During the summer, Elena will be working in the Rabinovich Lab, where her research involves the detection of DNA damage and senescence markers in colon tissue from ulcerative colitis (UC) patients, in hopes of someday being able to determine which UC patients will be at high risk of developing high-grade dysplasia or cancer. Her previous research experience includes work in cutaneous leishmaniasis treatment as part of the Photodynamic Therapy Lab in the Wellman Center for Photomedicine, Massachusetts General Hospital. Elena has also done research at her home school where she has worked in the synthesis of nanoparticles aimed towards the prevention of heart attacks. Born in Puerto Rico, she enjoys spending time with family and friends, reading, traveling, and great food. In an effort to help her community, Elena created and developed the “HOPE FOR KIDS” Project, designed to bring financial aid and support to “La Esperanza” Home for Abused Children in San Sebastian, Puerto Rico. In the future, she hopes to become a physician and clinical researcher in order to help improve people’s lives.
Wynton McClary
Wynton McClary is a Biology Pre-med major at Eastern Washington University in Cheney, Washington and will graduate in the spring of 2010. He has a great interest in biochemistry and the health sciences. Currently his research is in Dr. Atkin’s medicinal chemistry lab group and involves the study of glutathoine S-transferases, and important group of proteins involved in removing a wide range of xenobiotics from the body. In order to study these proteins he will be using azatryptophan-labeled nanodiscs which will act as an artificial membrane. The nanodiscs will provide the glutathione S-transferases with a more natural environment to be studied in. He hopes to one day earn either a MD/PhD or MD. Wynton is a certified tutor at his home institution and his interests include playing tennis, hiking along the coast, and playing jazz guitar.
Christopher Mount
Christopher Mount is a rising junior majoring in Bioengineering at the University of Washington. This summer he is conducting drug delivery research in Dr. Suzie Pun’s lab. His primary work focuses on the development of an ampiphilic triblock copolymer micellar drug delivery system. He and his mentor are investigating the potential of this system to enhance the delivery characteristics and in-vitro stability of the near-infrared contrast agent Indocyanine Green. More recently, they have turned their attention to assessing whether micellar encapsulation can enhance the cell-killing properties of chemotherapeutics such as doxorubicin. Beyond the lab, this summer Chris is enjoying the great outdoors of Washington State, particularly fishing and hiking.
Phillip Poonka
Phillip is a rising junior in the UW Bioengineering Program. He is currently interested in the regulation of cells and tissue engineering. This summer, he hopes to get a better direction for his area of specialization by working with genetically modified cardiomyocytes in the HAMM Lab. Phillip’s personal interests include playing and listening to the piano and practicing Taekwondo. Phillip did not regret declining several study abroad offers to participate in the Amgen Scholars Program and he feels very blessed to participate in such a rewarding program, especially after spending the previous summer in unrelated positions like a medical interpreter, graphic designer, marketing intern, manager, cook, barista, and server.
Suzanne Rohrback
Suzanne Rohrback is a rising junior at Kenyon College in Gambier, OH, majoring in biochemistry. This summer, she is exploring the field of toxicololgy in Dr. Kavanagh’s lab, where she will be studying how exposure to diesel exhaust affects endothelial cells (for example, their ability to heal), and looking for possible compensatory mechanisms which may counteract the damage caused by this pollutant. Suzanne works in two labs while at Kenyon, studying the distribution of serotonin throughout the central nervous system of the Vanessa butterfly in one, and the expression and properties of the protein SCP, which is involved in muscle relaxation, in the other. After growing up in Redmond, WA, she is happy to return to the Pacific Northwest and to explore Seattle for the summer. In her time away from science, Suzanne likes to indulge her artistic side by knitting, dancing and playing the piano. She plans to pursue a PhD in neurochemistry and/or pharmacology.
Michelle Sansky
Michelle is a rising junior at Syracuse University where she is currently completing a B.S. in Biology with a minor in Policy Studies. through the Amgen Scholars Program, she is completing Human Embryonic Stem Cell research in the Ruohola-Baker Biochemistry Lab. Over the past year, Michelle has been working on a research project involving cancer chemotherapeutic drug development at Syracuse University alongside her mentor, Dr. Thomas Fondy. During her junior year, she was able to enhance her school’s pre-health program by founding a student organization consisting of over two-hundred undergraduates. The organization, Shadows of Health, provides students with education and experience in the health field by coordinating lectures and shadowing opportunities between students and local health-professionals. A fundraising branch of Shadows of Health has recently been established to support the Duk Lost Boys Clinic of Southern Sudan. Apart from science and health-care, Michelle enjoys cooking, antiquing, drinking coffee, and reading.
Kristin Santroch
Kristin Santroch is a rising senior at Whitworth University where she is majoring in chemistry. This summer she will be working in the Khalil lab synthesizing and characterizing inorganic and organic model compounds to better understand electron transfer reactions in enzymes. After graduation, Kristin plans to either pursue a PhD in chemistry or go to dental school. In her spare time, Kristin enjoys spending time with friends and family, running, eating strawberry pie, and enjoying the beauty of the Pacific Northwest.
Ian Silverman
Ian was born and raised in Albany, NY. He is currently a senior at Binghamton University, majoring in Biochemistry and working in a Microbiology lab where he studies dispersion in Pseudomonas aerugionsa Biofilms. As an Amgen Scholar he is conducting research in biophysics, specifically working to develop a new method for sequencing DNA. By electrophoretically driving ssDNA through a small hole (nanopore) in a lipid membrane and measuring the changes in ionic current through that pore, one can theoretically determine the exact sequence of the DNA. After graduation, Ian intends to go to graduate school and ultimately pursue a career in biotechnology. When not in lab, he enjoys sailing, golfing, hiking, and playing the guitar with his band.
Rita Sodt
Rita Sodt is a senior at the University of Washington majoring in Computer Science with a minor in Spanish. Her research interest is in computational biology and currently she works with Dr. Kristin Swanson in the Department of Pathology on a mathematical model that quantifies the growth of gliomas (a highly invasive type of brain tumor). She is writing a program to simulate the anisotropic growth of gliomas in a 3D visual brain. After graduating she plans to pursue graduate school in Computer Science with a focus on computational and mathematical biology. In her free time she likes to play frisbee and do outdoor activities including hiking and camping in the Northwest.
Jeffrey Staples
Jeff Staples is a rising senior at Brigham Young University. He will finish with a BS in Bioinformatics and minors in Computer Science and Ballroom Dance. Crayfish phylogenetics was his first research area; however, his real passion is using computational power to research human ailments, such as coronary artery disease, obesity, and mad cow disease. Jeff completed a successful research internship during the summer of 2008 with Harvard/MIT’s Bioinformatics and Integrative Genomics undergraduate research program. He has also received two individual research grants and is a 2009 Goldwater Scholar. Aside from research, Jeff is a sports enthusiast with an emphasis in soccer.
Michelle Wang
Michelle is a rising senior at the University of Washington majoring in Chemistry. She is planning on pursuing Pharm D/PhD Program for her future career. She has been working in Professor Chiu’s laboratory on microfluidics droplet releasing projects for the past year. In the Amgen Scholars Program, she is working in Dr. Ho’s laboratory on developing better contrast agent delivery cancer cells. She enjoys playing sports and spending her time with her family and friends.
Mallika Yavatkar
Mallika Yavatkar is a rising junior at Scripps College pursuing a Bachelor’s degree in Molecular Biology with a minor in Hispanic Studies. This summer she is working in Dr. Maly’s Laboratory at the University of Washington on engineering a synthetic construct to study protein function in cells. Her focus is primarily on selectively regulating the Pim-1 kinase by exploiting the relationship between the anti-apoptotic protein, Bcl-XL and the pro-apoptotic protein, BAD. Previously at the Oregon Health Sciences University Casey Eye Institute, she conducted research directed at understanding the mechanisms of uveitis and the design and testing of therapies that specifically inhibit these mechanisms. Outside of the lab, she has numerous interests including reading, painting, playing her trumpet, and traveling.
Faculty
Joshua Akey – Genetics/Genomics
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.
William M. Atkins – Medicinal Chemistry
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
James Bassuk – Program in Human Urothelial Biology
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.
Valerie Daggett – Bioengineering
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.
Norm Dovichi – Chemistry
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.
Stan Fields – Genome Sciences and Medicine
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.
Jens Gundlach – Physics
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.
Lynn Hajjar – Immunology
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.
Merrill B. Hille – Biology
Website: http://www.biology.washington.edu/index.html?navID=42&parecID=159
Description: 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.
Requirements: 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.
Rodney Ho – Pharmaceutics
Website: http://depts.washington.edu/pceut/faculty_research/faculty_members/ho_rodney.html
Terrance Kavanagh – Environmental and Occupational Health Sciences
Website: http://depts.washington.edu/envhlth/faculty.php?Kavanagh_Terrance
Brian Kennedy – Biochemistry, Molecular Biology
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.
Munira Khalil – Chemistry
Website: http://depts.washington.edu/chem/people/faculty/mkhalil.html
Lih Y. Lin – Electrical Engineering
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.
Dustin Maly – Biochemistry
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.
Requirements: The specific project within these areas will depend on your interests and prior research experience. Completion of an introductory organic chemistry course (and any associated laboratory courses).
Alex Merz – Cell Biology
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)
Requirements: The specific project depends on your experience, interests and goals. Please visit our web site: http://faculty.washington.edu/merza. 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.
Lilo Pozzo – Chemical Engineering
Website: https://www.cheme.washington.edu/facresearch/faculty/lpozzo.html
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.
Suzie Hwang Pun – Bioengineering
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.
Peter Rabinovitch – Pathology
Website: http://www.pathology.washington.edu/Research/labs/Rabinovitch/
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.
Requirements: Basic Biology and Chemistry courses are essential. Coursework in Biochemistry, Cell Biology and Physiology would help.
Hannele Ruohola-Baker – Biochemistry
Website: http://depts.washington.edu/taneli/
Herbert Sauro – Bioengineering
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.
Lynn Schnapp – Pulmonary and Critical Care Medicine
Website: http://depts.washington.edu/pulmcc/faculty/schnapp.htm
Description: Mechanisms of Acute Lung Injury and Repair
Requirements: 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.
Hong Shen – Chemical Engineering
Website: http://www.cheme.washington.edu/people/faculty/shen.htm
Description: 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.
Kristin Swanson – Pathology, Mathematics, Applied Mathematics, Neural Pathology
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.
Rheem A. Totah – Medicinal Chemistry/Drug Metabolism
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