CALIFORNIA INSTITUTE OF TECHNOLOGY
BECKMAN INSTITUTE
P I L O T P R O G R A M
The Beckman Institute has inaugurated a new pilot program designed to foster the establishment of future Resource Centers that
are presently in earlier stages of development. The purpose of this new program is to increase the BI's flexibility and
responsiveness to new directions and innovations from the Caltech community. More information for prospective pilot program
investigators may be found on the Call for Proposals page.
We are pleased to announce the establishment of three new pilot projects, approved by the Beckman Institute Executive Committee in spring 2005, along with the four projects approved in December 2003. The Principal Investigators, project titles, and brief descriptions of each are listed below. For
more information contact the PIs at the e-mail addresses given.
Rapid, Systematic Identification of Genomic Regulatory Elements Controlling
Region- and Neuron-Subtype-Specific Gene Expression in Mammalian Brain
David J. Anderson, PI
wuwei@its.caltech.edu
This proposal aims to try to develop new, high-throughput methods for identifying DNA regulatory elements that control gene
expression in highly specific regions and cell types in the brain. The identification of such elements is a critical first step in
applying molecular genetic methods to the functional mapping of brain circuits for innate and learned behaviors. Traditional
approaches to this problem, which involve the creation and analysis of multiple transgenic mice for each candidate regulatory
element investigated, are too slow, expensive and labor-intensive to permit the level of fine-structure mapping that is needed to
achieve this objective. We therefore propose to develop and validate simpler and more rapid methods, utilizing short-term
cultures of brain slices and electroporation techniques, to overcome these obstacles. If successful, this approach could be scaled
up to permit a comprehensive and systematic mapping of brain region- and cell type-specific enhancer elements. A collection of
such elements would provide a valuable resource for the entire Neuroscience community, that could be applied not only to better
understanding brain functional architecture, but also how drugs and genetic variants affect behavior.
Automated High-Throughput Behavior Capture and Screening
Alan Barr, PI
barr@gg.caltech.edu
The purpose of this BI Pilot Project is to develop new technology and a prototype system for screening complex organismal phenotypes related to animal motion and behavior modes that are dominated by motion. The basic strategy is to develop new hardware and software modules whose combination autonomously tracks and processes the motion and behavior of individuals within controlled environments. We want to make it as easy to rigorously capture, quantify, and screen behavior for key organisms as it is to run a gel or amplify a sequence of DNA.
The system can be thought of as a set of image-capture and automated model-making tools based on a new type of time-dependent geometric models, called "generative" models. The new technology will permit the high-throughput quantification of traits that manifest as a change in body motion, orientation, or shape. In the Pilot Project, we will focus on developing a minimalist proof-of-concept prototype of the generative modeling and feature extraction approach, as these are key to the viability of the longer term project.
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Figure 1: Conceptual block
diagram of automated Behavior Capture system.
In the Pilot Project, we will focus on the generative modeling and feature extraction components. The new technology developed in this Pilot Project will enable future studies that require high throughput and advanced behavioral screening. Our new technology will be of use not only to labs studying nematodes, mice, zebra fish, and fruit flies, but will be useful to other biologists using comparative methods and those mapping developmental or behavioral traits across phylogenetic trees.
Development of Cryoelectron Tomography as a General Method to Image Complex Biochemical Reactions
Grant Jensen, PI
jensen@caltech.edu
Nearly all molecular biologists today are studying complex biochemical reactions that depend on dynamic assemblies of multiple
proteins and other macromolecules. Cryoelectron tomography is a rapidly developing technique that theoretically could allow us
to directly visualize in three-dimensions the positions, shapes, and even gross conformational changes of the various
macromolecular players involved in these myriad reactions. Briefly, cryoelectron tomography involves imaging a frozen-hydrated
biological sample in a transmission electron microscope multiple times while incrementally tilting it about one or two axis, and then
reconstructing its 3-D structure computationally. This pilot project will combine, test, and improve state-of-the-art new
cryoTEM instrumentation, protocols, and image processing strategies in a pioneering effort to directly image a complex
biochemical reaction in-vitro.
Hybridization Chain Reaction
Niles A. Pierce, PI
niles@caltech.edu
The Hybridization Chain Reaction (HCR) BI Pilot Program will develop amplifiers for applications in molecular sensing and imaging. HCR mechanisms
are based on metastable nucleic acid strands that do not hybridize into complexes until the introduction of a target nucleic acid fragment triggers self-assembly.
During the first year, the Pilot Program will focus on the refinement of basic HCR mechanisms and begin to explore generalizations that include aptamer triggers
(for detecting non-nucleic acid targets), nonlinear schemes (for increased sensitivity), colorimetric readout mechanisms (for readout by the human eye) and in situ multiplexing (for biological imaging applications).
Coupled Flow Cytometry and Isotope-ratio Mass Spectrometry
Alex L. Sessions, PI
als@gps.caltech.edu
Isotope tracers such as 3H and 14C are frequently used for tracking organic molecules such as drugs or metabolites through complex biological processes. In theory, these radioisotopes could also be measured in specific types of cells that were isolated by flow cytometry, allowing us to directly investigate subsets of cells. For example, we might examine drug uptake by white blood cells in a multicellular organism, or butyrate metabolism in a specific bacterium isolated from sediments. Unfortunately, flow cytometry creates aerosol particles, making the introduction of radioisotopes unsafe. Delivery of large doses of radioactivity is also incompatible with many human experiments. The goal of this project is therefore to develop methodology and instrumentation for measuring the stable (
13C) isotope content of small collections of cells sorted by flow cytometry. This technology should open a range of new experimental approaches involving the use of
13C tracers in biological systems.
Novel Protein Technologies
David A. Tirrell, PI
tirrell@caltech.edu
The Novel Protein Technologies BI Pilot Project will combine organic, biological and materials chemistry to develop, evaluate, and make widely available a new set of tools for the engineering of natural and artificial proteins. The focal point will be new technologies for the synthesis and application of proteins and protein-like macromolecules that are built - at least in part - from artificial amino acids. If successful, the long-term objective will be to establish a BI Resource Center that will effect a fundamental change in the way scientists and engineers think about proteins and about the control of protein structure and function.
Spin-Polarized Molecules for Structural and Systems Biology
Daniel P. Weitekamp, PI
weitekamp@caltech.edu
Nuclear magnetic resonance (NMR) is the most widely used and incisive method of molecular spectroscopy, despite being the least sensitive. Nearly all NMR spectroscopy and magnetic resonance imaging (MRI) relies on detecting the weak ordering (polarization) of the nuclear spin magnetic moments that results from equilibration in the applied magnetic field. If instead, the spins could be nearly fully polarized, signal enhancement in excess of 10,000 would result. Such enhanced signals have been achieved using several nonequilibrium methods, which however are not yet widely available. The principal goal of the pilot program is to develop efficient, general, scalable and accessible procedures enabling the wide use of such hyperpolarized molecules in NMR and MRI studies, both
in vitro and
in vivo. This entails creating nonequilibrium spin order in favorable atoms and molecules, transferring spin order to target molecules of interest and, within seconds, placing these molecules into the environment of biological interest. In addition, new spectroscopic strategies will make timely use of the spin order, for example in multidimensional NMR and MRI. The methodological developments under the pilot program will accelerate the acquisition of biological information, such as molecular structures, binding affinities, and metabolic rates.
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