Seventeen projects receive
Bio-X funds
Stanford Transgenic
Facility: The Stanford transgenic facility provides
state-of-the-art services for the construction of
transgenic mice. Transgenic animal technology is crucial
for the evaluation of the function of genes in the
context of developing animals. It has emerged as a key
component in biomedical research, in development of
therapeutic strategies for human and animal diseases and
in drug discovery. Funds provided will upgrade the
facility to allow provision of new services involving
embryonic stem cell manipulation and gene targeting for
the creation of knock-out and knock-in mice.
Principal Investigator:
Michael Cleary (Pathology)
Cognitive Neuroscience
Facility: This facility will meet the needs of a
diverse group of neuroscientists from numerous
departments in the schools of Humanities and Sciences,
Engineering, and Medicine. These investigators have been
brought together in large part because of advances in
technology (fMRI, MEG and EEG). The technology has
stimulated research in a wide variety of areas (magnetic
resonance physics, signal and image processing,
bioengineering, biophysics), in addition to the work in
cognitive neuroscience per se. The new equipment, which
will primarily be housed at the Lucas Center, includes
eye-tracking equipment, a computational imaging lab, an
EEG lab, psychophysiological recording instruments, a
magnetic resonance simulator, and Quantitative
Somatosensory Testing equipment.
Principal Investigator:
John Gabrieli (Psychology)
Stanford Synchrotron
Radiation Laboratory: The aim of this funding is to
significantly enhance a new campus-wide core facility for
macromolecular crystallography. This will be achieved
through procurement of the most advanced 3X3 CCD X-ray
detector system currently available in the world, and
implementing it on the newly constructed
Stanford/Scripps/SSRL crystallography beam line at the
Stanford Synchrotron Radiation Laboratory. Such an
acquisition will provide greatly enhanced scientific
capability and higher operational efficiency for Stanford
researchers interested in solving X-ray crystal
structures of macromolecules.
Principal Investigator:
Keith Hodgson (Chemistry)
Electron Microscopy
Facility: This facility is needed to meet Stanford's
acute and rapidly growing demand for a state-of-the-art
shared electron microscopy (EM) resource. Transmission EM
provides a unique capability to visualize cellular
structures that are below the resolution of light
microscopy, as well as the ultrastructure of viruses,
macromolecular complexes and individual molecules.
Scanning EM allows the direct observation of surface
properties, and is important in biology, materials
science and microfabrication. EM facilities presently
available are antiquated and completely inadequate to
support current needs in research and training. This
funding will facilitate the acquisition of a
state-of-the-art transmission EM, scanning EM and
associated sample preparation equipment.
Principal Investigator:
Harley McAdams (Developmental Biology)
Cell Sciences Imaging
Facility: This facility in the Beckman Center is
being given funds for the capital purchase of a 2-photon
laser scanning microscope to enhance and extend available
technologies for using fluorescent markers to visualize
cells and tissues.
Principal Investigator:
Susan Palmieri (Director, Cell Sciences Imaging Facility)
Fluorescence Activated
Cell Sorting (FACS) Core Facility: Biomedical
research requires an ability to separate and describe
unfolding events in complex surroundings. Since the
mid-1980s, the Stanford Shared FACS Facility (SSFF) has
provided a state-of-the-art flow cytometry facility for
immune system studies, molecular biology research,
pre-clinical research, HIV-1 studies and a host of other
enterprising studies in a variety of fields. This
proposal seeks to expand and upgrade the capabilities of
the SSFF by adding a 9-color, 3-laser high speed cell
sorter and a 6-color, 2-laser non-sorting analyzer, and
upgrading the central data store, data management and
data access system of the facility.
Principal Investigator:
David Parks (Genetics)
Stanford Magnetic
Resonance Laboratory: This core facility provides
nuclear magnetic resonance (NMR) instrumentation and
expertise to the Stanford research community for the
study of molecular structure, especially macromolecular
structure, in solution. The applications of NMR straddle
the fields of chemistry, molecular biology, physics,
engineering and computing. This grant will facilitate the
acquisition of instruments that will establish the
Stanford Magnetic Resonance Laboratory as one of the best
such facilities in the world.
Principal Investigator:
Joseph Puglisi (Structural Biology)
Tissue Bank: The
goal of this new facility, to be developed in the
Department of Pathology, is to create a Stanford resource
for obtaining, classifying, storing, retrieving and
experimenting with human and laboratory animal tissues.
The research supported by such a facility would include
state-of-the-art genetic, proteomic, biochemical,
structural and bioengineering analysis of tissues.
Principal Investigator:
Jan Matthijs van de Rijn (Pathology)
Mass Spectrometry
Facility: The goal of this facility is to provide a
critical expansion of the limited mass spectrometry
facilities at Stanford, allowing broad-based,
high-throughput proteomic and small molecule mass
analysis for a wide range of applications in
macromolecular chemistry, pharmacology and
bioengineering. Mass spectrometry is becoming the most
comprehensive and flexible tool for molecular
characterization of small molecules and macromolecules
including proteins. The acquisition of a Q-TOF mass
spectrometer will allow both proteomic analysis and high
throughput identification of small molecules. Coupling
the development of this core to other modern
instrumentation cores (including multiplate readers and a
basic plate robot) is expected to allow a flexible
facility for high-throughput mass analysis, possibly
coupled with other assays.
Principal Investigator:
Tom Wandless (Chemistry)
Microarray Facility: Tools
for capturing the functional state of a collection of
cells have advanced rapidly in the last decade. Prominent
among these are a variety of DNA microarray technologies.
In particular, complementary DNA microarrays have made it
practical to quantify the expression of thousands of
genes in parallel. This mode of analysis has been used to
observe gene expression variation in a variety of human
tumors and other tissue as well as a number of
single-cell organisms and plants. The facility will
provide Stanford researchers easy access to the most
advanced functional genomic technologies at nominal cost.
Researchers will be able to access the facility at a
number of levels.
Principal Investigator:
Michael Fero (Genetics)
Surface Plasmon
Resonance Facility: This new facility will acquire a
Biacore surface plasmon resonance instrument. This
instrument detects and monitors binding between two or
more biomolecules, in real time, without the use of
molecular labels. It records in exquisite detail the
kinetics of binding (i.e., rates of association and
dissociation) between most biomolecules and
macromolecules (small molecules, peptides, proteins,
carbohydrates, RNA, DNA, lipids, vesicles and even whole
cells) in aqueous solutions under physiological
conditions. It also measures the strength of binding
between biomolecules (i.e., affinity constants) and is
often used to search for novel binding partners (i.e., to
search for a unknown receptor for a known ligand). The
instrument is fully automated and performs dozens of
these extremely sensitive measurements in a very short
amount of time (hours) and with minimal quantities of
material; there is no other instrument available that
provides this kind of data with such ease, speed and
versatility.
Principal Investigator:
Michael Rexach (Biological Sciences)
Small Animal Imaging
Laboratory: The mission of the small animal imaging
shared resource is to support the multidisciplinary
research program in molecular and cellular imaging
through application and advancement of technologies for in
vivo biological assessment and imaging in animal
models of human biology and disease. The imaging resource
will provide Stanford scientists and engineers with a
suite of imaging tools for in vivo analyses in
living animal models and further the development of
imaging technologies. Imaging strategies that link in
vivo analyses to the high throughput ex vivo
assays of DNA microarray technologies, advanced confocal
and two-photon microscopy and ultra-flow cytometry will
be advanced for an integrated set of high throughput in
vivo and ex vivo analyses. The results from
these combined imaging modalities will be used to define
the complex relationships between molecular events,
anatomy and function, in both animals and in humans.
Principal Investigator:
Chris Contag (Pediatrics)
Biofilm Laboratory: The
laboratory will combine engineering and biomedical
approaches to study biofilms. The objectives of this
biofilm laboratory are: a) to use state-of-the-art
optical and genomic tools to elucidate the physiology,
metabolism and genetic interactions of microbes in
biofilms; b) to determine physical-chemical parameters of
biofilms, such as density, packing, shear stress and
chemical gradients; and c) to integrate both approaches
into a comprehensive, quantitative view on biofilms with
capabilities for development of rational conceptual
models and numerical simulation of biofilm structure and
function. A biofilm laboratory facility is crucial for
ongoing biofilm research and will serve as a platform for
a campus-wide research thrust on microbial biofilms.
Principal Investigator:
Alfred Spormann (Civil and Environmental Engineering)
Product Realization
Laboratory (PRL): The PRL is a teaching laboratory on
campus that supports the design and fabrication of
prototype devices. In the past, there has been almost no
biomedical engineering activity in the lab and little
activity from medicine or biology. The funds given will
enhance the PRL to support a new range of medical and
biological applications. The enhancements include the
addition of capabilities to manufacture small-scale
plastic and metal parts. This will leverage an existing
core facility and provide a new resource for future
biomedical applications and engineering education.
Principal Investigator:
David Beach (Mechanical Engineering)
Supercomputer and
Immersive Visualization Facility: Stanford is
establishing a new interdisciplinary program in
biocomputation. This program builds upon the world-class
engineering, medicine and science departments located in
close proximity to each other. Two critical and
inextricable components of a world-class biocomputation
center are supercomputing and advanced visualization. It
is proposed to acquire a large parallel computer (256
processors) and six network-connected "Immersive
Visualization Work-benches" for this facility. The
computer will enable basic and clinical research efforts
ranging from subcellular and cellular level computing to
organ system level computing. The workbenches will
provide unprecedented visualization capabilities in six
locations and will be configured with haptic interfaces
to enable human interactions with computer models in
applications ranging from feeling forces exerted on
single molecules to developing realistic patient models
and environments for surgical training.
Principal Investigator:
Charles Taylor (Surgery)
Parallel Computer
Cluster for Computational Biosciences: The facility
will involve the acquisition of a computer resource,
comprising many hundreds of desktop processors linked
together, for computationally intensive computational
biology at Stanford. Applications include simulation of
biomaterial aging, nanotube biosensors, protein folding
and protein design.
Principal Investigator:
Kyeongjae Cho (Mechanical Engineering)
Bioinformatics
Facility: This existing resource at Stanford has
successfully catered to the bioinformatics needs of more
than 130 laboratories on campus from 37 different
departments with a wide variety of hardware and software
needs. It also provides educational opportunities to help
researchers utilize the software effectively. The current
funding allows expansion of this facility's capabilities
into genomic and functional genomic data analysis, and
enhancement of consulting services currently provided to
assist Stanford researchers with customized needs.
Principal Investigator:
Lee Kozar (System Software Developer/Molecular and
Genetic Medicine) SR
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