Grant Abstracts 2010   Colorado State University Randy A. Bartels, Stuart Tobet Fort Collins, CO $1,000,000 2010 The research team of Randy Bartels and Stuart Tobet at Colorado State University proposes to develop and build a new imaging technology that will allow a direct view of the complex world of molecular communication within and between cells. Achieving the project’s goal requires a new approach to forming images of the spatio-temporal concentration of biomolecules and increases the sensitivity of unlabeled molecular detection in optical microscopy by up to six orders of magnitude. They propose to observe changes in molecule concentrations at up to picomolar levels. This sensitivity will use a new approach to capturing vibrational Raman spectral information using properties of ultrafast laser pulses interacting with coherent quantum Raman-active molecular vibrations. Images formed from this ultra sensitive Doppler shifted Raman detection will be combined with multimodal nonlinear microscope images to simultaneously capture morphology, cell translation and molecular signaling. A new view of molecular signaling leading to changes in cell mobility and cell differentiation may be revealed by this new technology.   Fred Hutchinson Cancer Research Center Harlan S. Robins, Christopher S. Carlson Seattle, WA $1,000,000 2010 FHCRC researchers led by Harlan Robins and Christopher Carlson propose to develop advanced DNA sequencing methods to measure past and present pathogenic exposure in humans. By sequencing tens of millions of antibody genes per person – over 100 times more genes than we can sequence with existing technology – they aim to identify rearrangements that are shared by individuals with the same disease. A catalogue of unique B cell DNA signatures corresponding to distinct pathogen exposures and disease states would comprise a library of associations that can be quickly and inexpensively accessed by clinicians to diagnose and predict risk of future diseases. Eventually, such a repository could be used to screen for novel correlations between environmental exposures and existing or emerging diseases.   University of California, Irvine Enrico Gratton, J. Lawrence Marsh, Michelle Digman Irvine, CA $1,000,000 2010 UCI scientists Enrico Gratton, Lawrence Marsh and Michelle Digman will develop optical microscopy technology capable of imaging biologically relevant events in live animals across cellular and subcellular scales, and in 3D at significant tissue depths. They will use their unique feedback based imaging methodology that has the capability to capture weak signals at the speeds necessary to detect fast biochemical reactions (~ms), and at the resolution needed to allow visualization of critical biomolecular events (~20nm) while still retaining the ability to image across lateral distances (~cm) and at a significant depth (up to 3mm) into the tissue. For this project, they demonstrated the principles of feedback imaging in 3D and imaging in strongly scattering media. Their aim is to show that that these technologies can work together for live animal tissues in an upright microscopy configuration. The project’s biological focus is on cell migration in tissues, a fundamentally more complicated problem than cell migration in 2D. Cell migration is important in cancer metastasis, wound healing, tissue regeneration, stem cell proliferation and developmental biology. The resolution, speed, sensitivity and depth necessary to visualize and characterize the molecular dynamics at the basis of 3D migration have not yet been achieved. This proposed development will advance our knowledge of fundamental biological processes.   University of California, Los Angeles Mayank Mehta, Katsushi Arisaka, Bahram Jalali Los Angeles, CA $1,000,000 2010 While Einstein revealed the nature of physical space, the nature of mental representation of space is not well understood. The UCLA team lead by Mayank Mehta will address this question at the interface of physics and neurobiology using novel experimental tools and mathematical theories. They hypothesize that mental space is defined by a sequence of neuronal events, or neural ensemble activity patterns. To test this hypothesis, they will focus on a brain region called the hippocampus which is known to be involved in spatial perception and shows spatially selective activity. The team will measure the influence of behavior on hippocampal ensemble activity, including its rhythmicity and the precise spike timing of neurons using whole cell patch clamp, multi-electrode devices and two-photon microscopy. The sequence of neural events measured during natural navigation will be manipulated by a virtual reality system. The emergence of long-term spatial memories will be investigated by determining the influence of calcium influx on hippocampal synaptic plasticity that could permanently encode the sequence of events using distinct neural activity patterns and oscillations. The results could provide a new theory of how a mental representation of space is generated from environmental stimuli, behavior and brain’s internal dynamics.   University of California, Riverside Susan Wessler, Peter Atkinson, Jason Stajich Riverside, CA $1,000,000 2010 While draft genome sequences are available for the three mosquito species that are the subject of this proposal: Anopheles gambiae, Aedes aegypti and Culex quinquefasciatus, active transposable elements (TEs) for efficient genetic analysis are not. Class 2 TEs isolated from other organisms are quickly inactivated when introduced into mosquitoes. The UCR team led by Susan Wessler, Peter Atkinson and Jason Stajich, will address this bottleneck through a novel strategy to exploit mosquito genome sequences to identify new mosquito TEs that may have superior mobility properties. They will focus their strategy in part on one type of TE called MITEs that were discovered in the laboratory of Dr. Wessler. As the most abundant component of the three mosquito genomes, MITEs have evolved mechanisms to evade genome surveillance and spread through populations. This project has five Aims. Aim 1 will use newly developed computer pipelines to annotate and characterize all class 2 TEs and their family relationships and identify candidate active TEs. Aim 2 will determine the small RNA profiles of the annotated TEs to find TEs that have evaded host surveillance. Aims 3 and 4 will test the mobility of candidate TEs by exploiting high throughput yeast and mosquito cell assays. In Aim 5, they will analyze a diversity panel of mosquito strains to detect TEs in the act of amplifying. The researchers seek to develop these new active mosquito TEs as incisive genetic tools which will directly increase the ability of researchers to identify mosquito genes responsible for the transmission of deadly human pathogens.   University of California, San Francisco Michael Fischbach, Pieter Dorrestein, David Relman, Justin Sonnenburg San Francisco, CA $1,000,000 2010 This multi-institutional team led by Michael Fischbach at UCSF has observed that antibiotic production is widespread among human gut bacteria. They propose to identify antibiotics produced by gut bacteria and characterize their role in modulating the composition of the gut microbiome. Antibiotic-mediated interactions could explain two intriguing observations from early data from the Human Microbiome Project: that the composition of the gut microbial community differs dramatically between people, and that even within individuals, the gut community consists of a stable ‘core community’ and a dynamic ‘auxiliary community’. This project will focus on 1) Functionally characterizing antibiotic production by gut microbes, 2) Using a new mass spec technology to create a molecular map of the gut community, and 3) Integrating these data into a quantitative network model of interspecies interactions in the gut community. These results may enable the team to begin modeling the dynamics of synthetic gut communities, and they will form a basis for studying how changes in host genetics (e.g., polymorphisms in innate immunity genes) and the environment (e.g., changes in diet) perturb the composition of the gut community.   University of Oregon William Cresko, Hui Zong Eugene, OR $1,000,000 2010 The team of William Cresko and Hui Zong at the University of Oregon propose to combine innovative cell labeling and genome sequencing technologies with analytical tools from evolutionary biology to identify causative genetic changes during cancer development. They will use a mouse glioma model developed by Dr. Zong’s lab to generate sporadic tumorigenic cells and unequivocally label them with Green Fluorescent Protein (GFP), thus revealing close interactions between cells that will become tumors and their normal neighboring neurons. These cells will be precisely collected at distinct tumorigenic phases using a Laser Capture Microdissection system. Next Generation Sequencing approaches developed in Dr. Cresko’s lab will be used for genomic and transcriptomic analysis of these cells, and the specific mutations causing tumor formation will be determined using multivariate evolutionary genetic analyses. This work may help identify causal genetic changes across the tumorigenic process, starting from the earliest stages of tumor formation, revealing the critical supporting roles of normal neurons to glioma cells and possibly leading to new methods for early detection and treatments of glioma and other tumors.   University of Washington Eberhard Fetz, Jeffrey Ojemann, Brian Otis, Babak Parviz Seattle, WA $1,000,000 2010 The brain is the world’s most powerful autonomous computer, whose operations remain to be understood and whose functions can be rescued when impaired. The computational capabilities of biological neural networks and silicon computers are complementary and could operate synergistically if directly connected. Recent advances in low-power electronic and biocompatible microfabrication technology will allow the team led by Eberhard Fetz to develop implantable computer systems that interact continuously with the brain. The project will develop and deploy autonomous recurrent brain-computer interfaces (R-BCI) that implement novel interactions between brain sites. By operating continuously, the R-BCI will allow the brain to learn to exploit these new resources to optimize its function. This novel paradigm opens many fundamentally new research directions, depending on the site of recording and stimulation, and the programmable transform between recorded activity and stimulation. The R-BCI also has numerous clinical applications for bridging damaged biological pathways and for strengthening weak neural connections. This project will also create a powerful new multi channel “Keck Active Electrode Array” with integrated electronics to implement minimally invasive recording and stimulation of large numbers of brain sites.