About
The Early Career Award Symposium is a yearly event where the University of Washington honors newer faculty members who have recently won prestigious national awards. These awards come from a limited submission process and do not include the many NIH and NSF grant winners. The honorees who speak at the event are asked to gear their short presentations to a general audience. The symposium and the reception that follows are open to the entire campus. No pre-registration is required.
2009
Speakers
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- Mike MacCoss, Assistant Professor, Genome Sciences
- 2007 Presidential Early Career Award for Scientists and Engineers
- Proteomics Technologies: Efforts to Improve the Speed, Dynamic Range, and Sensitivity of Protein Analysis
- View Project Abstract [...]
Over the last decade, mass spectrometry has become the major analytical tool for the direct characterization of complex protein mixtures. Most mass spectrometry-based proteomics workflows have taken a “shotgun” approach to handling complex protein mixtures. In shotgun proteomics, proteins are first digested into peptides to minimize the biochemical diversity and challenges associated with the measurement of intact proteins. The resulting peptides are usually separated by nanoflow liquid chromatography, ionized and emitted into a tandem mass spectrometer, and subjected to tandem mass spectrometry by data-dependent acquisition. This general approach has become extremely powerful for determining the protein contents of a moderately complicated mixture. However, the ability to compare different samples is complicated and many proteins of specific interest can go undetected in one or more samples that are being compared. Data will be presented that illustrate efforts by our lab to improve the analysis of complex protein mixtures and address current technological limitations.
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- Munira Khalil, Assistant Professor, Chemistry
- Packard Fellowship for Science and Engineering
- Ultrafast Chemical Dynamics: A Molecular Perspective
- View Project Abstract [...]
The absorption of light by chemical and biochemical reagents results in material changes in a few femtoseconds (10-15 s), which is comparable to the timescale of a molecular vibration. These ubiquitous processes are responsible for the elementary steps in photosynthesis, vision and DNA photodamage. Our microscopic understanding of ultrafast chemical dynamics remains limited due to the lack of experimental probes capable of monitoring the complex interplay between nuclear, electronic and solvent degrees of freedom. In this talk, I will describe the experimental approaches my group is developing to gain a molecular understanding of how light energy is transformed into chemical and mechanical motion on the femtosecond timescale.
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- Heather Mefford, Acting Assistant Professor, Pediatrics
- Burroughs-Wellcome / CAMS Award
- Finding the missing pieces: Discovery of novel genomic disorders in pediatrics
- View Project Abstract [...]
Genomic disorders are conditions that result from recurrent deletions or duplications of DNA caused by a process called unequal crossing over. These deletions and duplications tend to occur in selected regions of the human genome, which we have termed “rearrangement hotspots,” and can result in the loss (deletion) or gain (duplication) of genes. Known genomic disorders occur in up to ~1/1000 live births and are often associated with abnormal development and cognition. I have used an assay designed to detect deletions and duplications of rearrangement hotspots in order to discover novel genomic disorders in individuals with birth defects or mental retardation. This approach has led to the identification of several new disorders, including one associated with pediatric renal disease and two associated with a wide range of neurocognitive abnormalities including mental retardation, epilepsy and schizophrenia. Discovery and characterization of these disorders has important consequences for clinical diagnosis, prognosis and genetic counseling.
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- Maya Gupta, Assistant Professor, Electrical Engineering
- 2007 Presidential Early Career Award for Scientists and Engineers
- How to Make Good Guesses
- View Project Abstract [...]
I research principles and methods for making good guesses, and the application of guessing to problems in sonar, color image processing, and artificial intelligence. I will talk about some of the main ideas behind our work, such as the importance of guessing as little as you have to, and the difference between the most-likely answer and the answer that is right-on-average.
Event Poster
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2008
Speakers
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- Rhiju Das PhD, Senior Fellow, Biochemistry
- 2008 Burroughs Wellcome Award at the Scientific Interface
- High resolution prediction of new RNA folds
- View Project Abstract [...]
RNA is a fundamental biomolecule whose long chains have captivated biologists for decades. Like its cousin DNA, RNA has a four-letter “alphabet” that can carry information. Indeed in the (now revised) Central Dogma of Molecular Biology, the primary role of RNA was thought to be as a temporary linear message, a copy of DNA to be translated into the proteins that are our cells’ workhorses. But instead of being simple straight lines, many RNA chains are now known to double back on themselves to form complex, intricate folds. Indeed, these RNA sequences can take on unique three-dimensional conformations that allow them to cut and paste themselves and even to carry out chemical reactions on other biological molecules like proteins. This incredible versatility of RNA raises a fundamental “linguistic” question: how does a string of the letters A, G, C, and U code for the “meaning” of an RNA chain – its three-dimensional functional fold? Our research program is tackling this problem in a series of tractable steps. The first stage involves generalizing the fundamental insights that have led to remarkable, high resolution solutions for an analogous and longer standing problem for another biopolymer, proteins. These insights include the use of existing molecular structures to understand which conformations are preferred by small fragments of the RNA chain – something like setting up a “dictionary” for three-letter words. The second stage is to refine these folds to higher resolution. Here again, experience in modeling the “Protein World” is invaluable. In particular, the necessity of keeping track of all the atoms in a protein, rather than using a computationally cheaper but cruder representation, has been a key insight leading to recent high resolution predictions of protein structure from sequence. The final stage is a set of thorough experimental tests of the folding algorithm, with applications to fascinating RNA sequences from viruses like HIV, from bacteria, and from our own cells. To continue the linguistic analogy, one set of tests will involve predicting “synonyms” for existing RNA sequences. The end result will thus be a carefully validated method for translating RNA sequences into their potential folds, hopefully enabling us to fluently read how these important parts of our genomes take life in three dimensions.
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- Dao Nguyen, Post-Doctoral Research Fellow, Microbiology
- 2007 Burroughs Wellcome – Career Award for Medical Scientists
- The sheltered life of bacteria in biofilms: Implications for human infections and therapy
- View Project Abstract [...]
Antibiotics have revolutionized the treatment of infectious diseases and are a cornerstone of modern medicine. Yet, many chronic bacterial infections are very difficult to treat or even incurable with current antibiotic therapies. A devastating example is the respiratory infection caused by the bacterium Pseudomonas aeruginosa in patients with the genetic disease cystic fibrosis. These patients typically become infected with P. aeruginosa early in life, and most remain chronically infected thereafter and eventually die from respiratory failure. A key question is how do these bacteria persist? Bacteria can grow in clusters and form structured communities called biofilms. Biofilms are found both in natural environments and in human hosts, and are now recognized as an important factor in the persistence of chronic bacterial infections. Bacteria living in biofilms are much more resistant to antibiotics and immune defenses than those not living in biofilms, and we do not yet fully understand the mechanism of such resistance. My research is focused on understanding the role of a bacterial stress response called the stringent response in P. aeruginosa biofilm growth and resistance to antibiotic killing. The stringent response regulates many cellular activities that help bacteria survive and adapt to conditions of stress and starvation. My research suggests that the stringent response is involved P. aeruginosa biofilm formation and may be an important mechanism that allows biofilm bacteria to mount their resistance against antibiotics. Further insights on this response will help us identify new therapeutic strategies to effectively eliminate biofilm bacteria.
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- Magdalina Balazinska, Assistant Professor, Computer Science & Engineering
- 2007 Microsoft New Faculty Fellow
- Monitoring the Physical and Digital Worlds
- View Project Abstract [...]
Advances in miniaturization and wireless networking have made it possible to deploy specialized devices capable of sensing the physical world and communicating information about that world: e.g., environmental sensors, miniature tags for object tracking, and location-sensing devices. Similarly, we now have powerful sensors to collect information about the digital world: e.g., network monitors and server monitors. With these advances, we are headed toward a new world, where millions of heterogeneous sensors will produce Petabytes of data. This data will be "streaming-in" in real-time from geographically distributed locations. Handling such data raises many important challenges. First, we need techniques to process and query the sensor data in real-time. Second, we need methods to archive and access historical sensor data. Third, sensor data is often dirty and ambiguous due to sensor errors and limitations in the sensing technology. We need techniques to handle such inaccuracies. Fourth, in addition to addressing each challenge in isolation, we need systems that can properly handle all three aspects (live, historical, and dirty) of the sensor data at the same time. In this talk, we will motivate the need for new data management systems that can help us make the best of the data streams produced by both physical and digital sensors. We will present the above challenges in more detail and will outline our solutions for addressing them.
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- Tadayoshi Kohno, Assistant Professor, Computer Science & Engineering
- 2008 Sloan Fellowship
- Privacy-Respecting Digital Forensics
- View Project Abstract [...]
Criminal activity is rampant on the Internet. Traditionally, investigators and law enforcement officers have had to rely on mostly ad hoc digital forensic trails to catch the perpetrators of these crimes. These traditional forensic trails, while helpful, are generally limited in that: (1) they are weak and forgeable and (2) they do not respect the privacy of normal Internet citizens in the common cases when there are no criminal incidents to investigate. These limitations beg the question: Can we create computer systems that inherently provide strongly un-forgeable yet privacy-respecting forensics evidence? I will touch on two research directions focused on meeting these goals. The first direction is to create a new Internet with built-in forensic trails that are both significantly stronger and more privacy-respecting than the forensic trails we have today. The second targets creating strong, privacy-respecting methods for recovering stolen laptops and other mobile devices.
Event Poster
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2007
Speakers
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- Clark Lombardi, Assistant Professor, Law
- 2006 Carnegie Foundation Scholar
- Muslim Judges and the Emergence of a New Islamic Law
- View Project Abstract [...]
The general public, policy makers and even some important contemporary scholars often assume that “Islamic law” is a fairly stable body of norms that were articulated in detail by great sages of the past, and can only be applied to modern circumstances by classically trained religious scholars. This assumption is implicit in many academic, policy and media discussions of Islamic law. It also informs many of the policies that NGO’s and the U.S. government pursue in the Muslim world. My research suggests that that many Muslims themselves do not agree with these propositions. Thus, what Muslim judges are applying as “Islamic law” is quite different from what many people assume. Studying Muslim legal systems in depth and going to the court cases themselves, I have shown that constitutional definitions of Islamic law and judicial interpretation of Islamic law is quite different in different countries. Amidst the diversity, the following patterns emerge: (i) in many cases, constitutions leave interpretation largely, and often entirely, in the hands of judges who are trained in secular law rather than classical Islamic law; (ii) their interpretive methodology does not draw heavily on the classical tradition, and (iii) their interpretations diverge from those of contemporary classically trained scholars and are, in many cases, quite liberal and (iv) Islamist sections of the public have not challenged novel judicial interpretations as illegitimate and, indeed, have recognized them as binding. I have been exploring what changes in Islamic society led people to accept the authority of judges to interpret Islamic law in the creative ways they do. Finally, I ask what it means that common Western assumptions about “Islamic law” seem inconsistent with the actual experience of Islamic law in Muslim countries. I ask whether Western attempts to deal with global Islamization or to promote the rule of law in Muslim countries are inappropriate because they are based on false assumptions about Islamic law.
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- David Marcinek, Research Assistant Professor, Radiology
- 2006 Ellison Foundation New Scholar in Aging
- Problems at the Power Plant: Inefficient Mitochondria in Aged Skeletal Muscle
- View Project Abstract [...]
Mitochondria play a key role in integrating cellular energetics and the control of cell survival. As a result they are a critical element in aging and many degenerative diseases. Our research focuses on identifying aspects of in vivo mitochondrial dysfunction that contribute to degenerative pathologies with the goal of linking these functional deficits to the biochemical and molecular changes responsible for these dysfunctions. We believe that an integrated study of mitochondrial energetics in the living organism is required for a mechanistic understanding of mitochondrial dysfunction in aging and disease. To that end, we have developed novel methods to directly measure mitochondrial function in vivo. Optical and magnetic resonance spectroscopies provide independent measures of O2 and ATP fluxes in the intact animal. By independently measuring these fluxes we determine several parameters of mitochondrial energetics in skeletal muscle, including the coupling of ATP production to oxygen consumption. We have found that mitochondria in mouse skeletal muscle become less efficient with age, which results in a reduction in the ATP produced per oxygen consumed. This reduced efficiency can lead to an energetic stress on the cell and may impact cell survival.
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- David Ginger, Assistant Professor, Chemistry
- 2006 Research Corp Cottrell Scholars Award
- Novel Imaging Tools for Nanostructured Plastic Solar Cells
- View Project Abstract [...]
New materials offer the promise of making large area solar cells from inexpensive, easily manufactured materials such as plastics. However, the operation of these novel photovoltaics depends on details of the mixing between electron donating and electron accepting materials on length scales too small to probe with conventional techniques. While it is understood that this nanoscale film structure is critical to the performance of polymer photovoltaics we lack a detailed understanding of this relationship. This talk will describe new microscopy techniques developed in our lab at the University of Washington in order to image the properties and performance of nanostructured polymer solar cells with resolution as fine as 20 nanometers. Our results suggest that there is still room to improve these devices.
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- Charles Asbury, Assistant Professor, Physiology and Biophysics
- 2006 Packard Fellowship and 2006 Searle Scholar Award
- How are Chromosomes Separated During Cell liision? Biophysics at the Kinetochore-Microtubule Interface
- View Project Abstract [...]
An exquisite molecular machine, the mitotic spindle, organizes and separates chromosomes in dividing cells, thereby ensuring equal partitioning of the genetic material. Our overall goal is to reconstitute spindle functions using pure components and apply new tools for manipulating and tracking molecules to uncover how this machine operates. Elucidating the molecular basis for kinetochore function is essential for understanding cancer progression because chromosome loss, which occurs frequently in cancer, can result from mutations that weaken kinetochore-MT attachments. This work also brings us closer to a complete understanding of one of nature’s most fascinating molecular machines. Chromosome movements are linked to depolymerization and growth of microtubule (MT) filaments, the tips of which transmit tension to specialized sites on each chromosome, called kinetochores. Recent work suggests that a component of kinetochores in yeast, Dam1, contributes directly to kinetochore-MT attachment, force production, and regulation of attached MTs, perhaps by forming a ring encircling the MT. To test these hypotheses, we developed an in vitro (cell free) motility assay where Dam1-coated beads attach the tips of individual MTs. Like kinetochores, the beads remain tip-bound and undergo assembly- and disassembly-driven movement. This reconstitution of movement allows us to apply advanced optical trapping techniques to assess quantitatively the potential for Dam1 to contribute to attachment, force production, and MT regulation, and to test key predictions of the ring hypothesis.
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- Suzie Pun, Assistant Professor, Bioengineering
- 2006 Presidential Award in Science and Engineering
- Synthetic Gene Delivery Systems for Non-liiding Cells
- View Project Abstract [...]
Gene therapy offers the possibility of treating diseases by intervening with the readout of the genetic code in affected cells. Synthetic vehicles are attractive materials that can be used to accomplish gene delivery but are usually limited in their applications due to poor delivery efficiencies in non-dividing cells. One of the objectives of our research is understand the barriers to synthetic gene delivery and to develop materials that can overcome transport limitations in order to accomplish rapid intracellular delivery to cell nuclei. In this talk, I will discuss our progress toward designing vehicles with improved cell-specific uptake and intracellular trafficking.
Event Poster
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Contact
Questions or comments can be addressed to: research@u.washington.edu
