QB3 Core Facilities
A listing of QB3 core research facilities.
The backbone of QB3 consists of shared research facilities: technology centers that promote collaboration and education. The new QB3 buildings and facilities provide scientists with technical know-how and access to state-of-the-art instrumentation, technologies, and materials.
We offer core facilities for nuclear magnetic resonance (NMR), magnetic resonance imaging (MRI), advanced imaging, small-molecule drug screening, functional genomics, and proteomics. Each facility is an intellectual commons, managed by seasoned professionals, principal investigators and mentors, aligned to foster scientific interaction and collaboration.
Access to these resources enables scientists and engineers to develop medical devices, drugs, and therapies that improve lives, as well as technologies to alleviate environmental damage and improve energy production and use.
QB3 research facilities serve six general research areas:
Structure Determination
High-Throughput Screening
Genomics and Proteomics
Informatics
Imaging
Bioengineering
Structure Determination
Beamline 8.3.1 at the Advanced Light Source at LBNL
This facility is owned jointly by David Agard, professor of
biochemistry and biophysics at UCSF; Robert Fletterick, professor of
biochemistry, pharmaceutical chemistry and cellular and molecular
pharmacology at UCSF; Robert Stroud, professor of biochemistry and
biophysics and pharmaceutical chemistry at UCSF; Thomas Alber,
professor of biochemistry and molecular biology at UC Berkeley; and James
Berger, associate professor of biochemistry & molecular biology at
UC Berkeley. This is a national facility that generates bright synchrotron
light for studies in materials science, biology, chemistry, physics,
and environmental sciences. The beamline uses a superconducting bend
magnet in the 6-18 keV range to deliver light through an optical
obstacle course in order to resolve a protein structure.
Central California 900 MHz NMR Spectrometer Facility at UC Berkeley
Directed by Professor David Wemmer, this Stanley Hall facility features
four high-field NMR instruments, including 800 MHz and shielded 900 MHz
systems. The instruments are used to study the structures and dynamics
of both proteins and nucleic acids at the atomic level, and for probing
the formation of biologically important molecular complexes and their
functions.
Macromolecular X-ray Crystallography Facility at UC Santa Cruz
Under Harry Noller, professor of molecular, cell, and developmental biology, and Alice
Vrielink and Bill Scott, professors of chemistry and biochemistry, the facility houses a
state-of-the-art rotating anode/imaging plate X-ray crystallography data collection suite,
a cryosystem, and a collection of computer workstations and software for crystallographic
computations, molecular visualization, and model building. This facility dovetails with the
Lawrence Berkeley National Laboratory's Advanced Light Source synchrotron radiation facility.
Membrane Protein Expression Center at UCSF
Directed by Robert Stroud, professor of biochemistry &
biophysics and pharmaceutical chemistry at UCSF, the Membrane Protein
Expression Center (MPEC) develops and applies the latest innovative
methods that yield structurally and functionally intact membrane
proteins for subsequent drug development, structural, and functional
characterization. The MPEC focuses especially on eukaryotic membrane
proteins since these provide many major drug target proteins. The MPEC
accepts target genes for expression in functional form from client
laboratories, which can introduce a gene choice for expression and then
follow the membrane protein expression progress via a
password-protected Intranet web site.
The Magnetic Resonance Laboratory at UCSF
Directed by Thomas James, professor and chair of pharmaceutical chemistry at UCSF, the facility
includes 600 MHz and 500 MHz spectrometers for high-resolution studies of macromolecules including the
solution structure of proteins, nucleic acids, and their complexes.
Nuclear Magnetic Resonance Facility at UC Santa Cruz
This facility in the department of chemistry and biochemistry is used to examine molecular structure
and folding in studies involving structure and biochemical mechanisms of cancer and anticancer therapies
and environmental toxins. It houses three different high-resolution NMR spectrometers.
QB3/College of Chemistry Mass Spectrometry Facility at UC Berkeley
The
facility features state-of-the-art mass spectrometers. It provides
routine nominal and accurate mass measurements of biological, organic
and inorganic compounds as well as structural elucidation through
tandem mass spectrometry. Mass spectral proteomics analysis, mass
measurement of intact proteins, lipids, oligosaccharides, and
non-covalent protein-protein and protein-ligand complexes are also
available.
QB3 Macrolab at UC Berkeley
Directed by Professor James Berger and managed by Scott Gradia, this
Stanley Hall facility offers automated liguid-handling services to
enable high-throughput analysis in several key areas. Services are
available in 1) cloning and mutagenesis, 2) protein expression and
purification, and 3) protein crystallization reagents and other useful
consumables.
High-Throughput Screening
The Small Molecule Discovery Center (SMDC) at UCSF
The SMDC provides University of
California scientists with access to innovative discovery
technologies, including high-throughput and fragment-based screening
and "hit-to-lead" medicinal chemistry. The center is under the
direction of UCSF's Jim Wells, Harry W. and Diana Hind Professor
in Pharmaceutical Sciences, and Adam Renslo, Associate Director and
Adjunct Assistant Professor of Pharmaceutical Chemistry. The SMDC
occupies a custom-built facility on the fifth floor of Byers Hall on
the UCSF Mission Bay campus.
Chemical Screening Center at UC Santa Cruz
UC Santa Cruz's Chemical Screening Center houses high-throughput
screening (HTS) robotics that are used to search for biologically
active compounds and siRNA targeted toward a variety of biological
systems. Investigators can test up to 30,000 chemical compounds per day
for biological function and/or usefulness in fighting diseases, such as
cancer, malaria, Parkinson's disease or cholera. The Screening Center houses liquid handling robotics, detectors,
imaging equipment, and compound libraries, including a growing
collection of unique marine natural products. A detailed list of
equipment and compound libraries may be found at http://chemscreen.ucsc.edu/equipment-list
.
Genomics and Proteomics
Microarray Facility at UC Santa Cruz
Established by Manuel Ares, professor of molecular, cell, and developmental biology at UC Santa Cruz,
and managed by microarray technology specialist Lily Shiue, this resource facilitates large-scale analysis
of alternative splicing and comparative genomics.
Proteomics Facility at UC Santa Cruz
Designed to perform large-scale comparisons in protein expression, this facility houses an Amersham
Ettan proteomics lab with differential gel electrophoresis technology. It is collaboratively operated by
chemistry and biochemistry professors Ted Holman and Tony Fink and environmental toxicology professor Don
Smith.
The UCSF Core Facility for Genomics and Proteomics in the Center for Advanced Technology at UCSF
This facility was established by Joe DeRisi, assistant professor of biochemistry & biophysics at
UCSF, Erin O'Shea, professor and vice chair of biochemistry & biophysics at UCSF, and Jonathan Weissman,
professor of cellular & molecular pharmacology. The facility is fully equipped to whole genome approaches,
in particular expression profiling.
Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
Faculty Advisors: Michael Eisen, Associate Professor of Genetics and
Development, and Rachel Brem, Assistant Professor of Genetics and
Development. Managed by Leath Tonkin. Established by a generous
gift of the Vincent J. Coates Foundation. The facility in Stanley Hall
is equipped with a Solexa 1G Genome Analyzer to exploit massively
paralleled sequencing for genome sequencing, ChIP sequencing, small RNA
discovery, and expression profiling.
Vincent J. Coates Proteomics/Mass Spectrometry Laboratory at UC Berkeley
The proteomics / mass spectrometry laboratory (P/MSL) offers full
services in protein identification and characterization. These
services include protein identification from complex samples through
MudPIT analysis, post-translational modification analysis, and
identification of proteins from gel bands.
Functional Genomics Laboratory at UC Berkeley
The FGL mission is to conduct state-of-the-art research in functional genomics, with a focus on using DNA microarray technologies, and to make these technologies available to both campus and off-campus users (recharge rates vary depending on affiliation). Complementing the high-throughput DNA sequencing capabilities of the Vincent J. Coates Genomic Sequencing Laboratory, the FGL specializes in the fabrication, use, and analysis of DNA microarrays for large-scale gene expression profiling and genetic profiling, and provides full core lab services for Affymetrix GeneChip arrays and Agilent DNA microarrays. FGL scientists are actively involved in the development of new techniques for microarray-based experimentation and statistical approaches for analyzing complex datasets. Research support services include hands-on training and consultation from the unit's Director and highly trained staff; software, computational facilities, and databases for gene expression data analysis; prefabricated DNA microarrays; a full complement of robotics technologies for the fabrication of custom microarrays; and Agilent Bioanalyzer sample analysis.
Informatics
Resource for Biocomputing, Visualization, and
Informatics at UCSF
This facility was established by Tom Ferrin, professor of pharmaceutical chemistry and biopharmaceutical
sciences at UCSF. This facility provides access to state-of-the-art computer graphics hardware and software
for research on biomolecular structures and interactions. It houses the Computer Graphics Laboratory, an
NIH National Center for Research Resources Biomedical Technology
Research Center for the integrated analysis of biological sequence, structure, and functional information.
The other major components of the Center include the
Babbitt Laboratory and the Sequence Analysis and Consulting Service (SACS).
Imaging
Electron Spin Resonance Facility at UC Santa Cruz
Managed by Glenn Millhauser, professor of chemistry and biochemistry, the facility houses a Bruker
ESP 380 X-band spectrometer that operates in either continuous-wave or pulsed mode at variable temperatures
and a high-sensitivity Bruker ExexSys 500 for limited sample sizes needed for many biological studies.
Non-core facility available by special arrangement only.
Margaret Hart Surbeck Laboratory of Advanced Imaging at UCSF
Established by Sarah Nelson, professor and chair of the division of bioengineering at UCSF, the facility
will have a 3 Tesla and a 7 Tesla magnets for high-field MRI and magnetic resonance
spectroscopy to study the physical and metabolic details of human tissues.
UCSF Nikon Imaging Center
The UCSF Nikon Imaging Center (NIC) is a core facility for light
microscopy developed in partnership with Nikon Instruments Inc.,
Technical Instruments, and several other providers of microscopy
instrumentation. Opened in September 2006, the facility serves QB3 and
UCSF. The NIC will provide investigators access to cutting edge
microscopy resources with a particular emphasis on developing novel
imaging solutions to systems biology challenges; promote
cross-discipline collaborations, training, and courses; and foster
collaborations with biopharmaceutical companies.
W.M. Keck Advanced Microscopy Laboratory at UCSF
Being established by David Agard, director of QB3 at UCSF, HHMI investigator, and professor of biochemistry
and biophysics at UCSF, and John Sedat, professor of biochemistry and biophysics at UCSF, this facility specializes
in developing improved light microscopes and high-resolution cryo-electron tomography and single particle methods.
Non-core facility available by special arrangement only.
Bioengineering
Biomedical Micro and Nanotechnology Core (BMNC) at UCSF
Operated by Tejal Desai, UCSF professor of physiology and
bioengineering, with partial sponsorship from the Sandler Foundation
and QB3, this facility houses technologies needed to 1) link soft
biomolecular structures to hard material surfaces for biosensors, array
technologies, and new medical devices, and 2) topographically and
chemically pattern hard and soft substrates for microfluidics, cell
patterning, targeted delivery, and tissue engineering. Core equipment
in the clean room includes equipment for photolithography, wet chemical
etching, polymer spin coating, and reactive ion etching. In addition,
the facility has a Nano eNabler™ molecular printer and an atomic force
microscopy system with nanolithography capabilities for developing and
characterizing micro and nanoscale organic and inorganic surfaces.
Located on the second floor of Byers Hall, the facility serves as a
resource for those interested in developing new micro/nanotechnology
platforms for their research.
Biomolecular Nanotechnology Center at UC Berkeley
Directed by UC Berkeley professors Luke Lee, Dorian Liepmann, and
Richard Mathies, the Biomolecular Nanotechnology Center (BNC) is a
11,500 sq ft class 1,000/10,000 cleanroom facility located in Stanley
Hall. Once it is fully equipped, the BNC will feature a full range of
lithography, deposition, etching, metrology, and microscopy equipment
as well as facilities for performing biological experiments. The center
focuses on microfluidic processing of glass and polymer materials.
Experimentation on proteins, nucleic acids, cells, and tissues is encouraged. In addition to a state-of-the-art research lab, the center
also features a teaching lab for hands-on training of both
undergraduate and graduate students.
Nanosecond Time-Resolved Laser Spectroscopy Laboratory at UC Santa Cruz
The department of chemistry and biochemistry contains several systems capable of measuring different time-resolved
spectra from the far ultraviolet to the near infrared regions for a wide variety of research applications. Non-core
facility available by special arrangement only.
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