CBSE Research Facilities

Research projects at CBSE benefit from the many excellent research facilities available at UCSC. See buildings.

Facilities Supported by CBSE and QB3

CBSE computing clusters and web servers are used principally for genome browser assembly and genome analysis and comparison. Two large parallel processing systems called the Swarm and the PitaKluster—banks of quadcore Intel Xeon processors or dual AMD Opteron processors, respectively—run on the Rocks Linux operating system. The web servers feed the UCSC Genome Browser and other key genomic tools to researchers throughout the world.

Microarray facility is used for large-scale analysis of alternative splicing and comparative genomics.

Embryonic stem cell and transgenic facility is used for training in conjunction with the UCSC stem cell training program and for faculty-driven research. It features a laboratory for embryonic stem cell growth and manipulation, a state-of-the-art transgenic facility, and a staff with expertise in experimental design, protocol development, and data analysis.

UCSC CIRM shared stem cell facility (SSCF) is an advanced stem cell laboratory for research and training in manipulation techniques and the production of transgenic organisms is used in conjunction with the UCSC stem cell training program and for faculty-driven research in the Institute for the Biology of Stem Cells (IBSC). It features a laboratory for embryonic stem cell growth and manipulation, a state-of-the-art transgenic facility, and a staff with expertise in experimental design, protocol development, and data analysis.

IBSC flow cytometry facility offers multicolor cell analysis by a BD FACS LSRII cell analyzer and single-cell sorting by a BD Biosciences FACS Aria cell sorter. The facility offers assistance with experimental design and protocol development, including fully assisted cell sorting and analysis. The facility is available for use by any interested researcher for stem cell research as well as other life sciences research. This core facility is supported by the California Institute for Regenerative Medicine (CIRM) and the California Institute for Quantitative Biosciences (QB3).

UCSC chemical screening center allows researchers to perform up to 30,000 experiments per day as they test chemical compounds for usefulness in fighting disease or understanding fundamental aspects of a cell's life. The screening center houses liquid handling robotics, detectors, imaging equipment, and compound libraries.

The UCSC genome technology center allows researchers to sequence DNA using next-generation high-throughput instrumentation: sequencers, bioanalyzers, a NanoString instrument, and a microarray printer and scanner. The facility can be used for whole-genome resequencing, targeted resequencing, gene expression analysis, and microRNA discovery. These capabilities are useful for research in areas such as genomics, bioinformatics, and environmental biology. The research of the center focuses on both generating high-quality data for the scientific community and improving next generation platform technology.

Mass spectrometry facility enables the discovery of new molecular structures directly relevant to understanding and treating diseases, the discovery, design, and manipulation of biologically relevant molecules, and the development of new techniques to probe the behavior of macromolecules central to fundamental biological functions. The facility houses two mass spectrometers: a Thermo Finnigan LC/MS/MS (LTQ) and an Ettan MALDI-TOF. This equipment is capable of determining the molecular weight of both small molecules and peptides, identifying proteins, and characterizing protein modifications.

UCSC life sciences microscopy center provides cutting-edge imaging techniques for advanced biomedical research. A core facility for light and electron microscopy, the facility is supported by the California Institute for Regenerative Medicine (CIRM) and the California Institute for Quantitative Biosciences (QB3). The center serves the biological research community at UCSC and provides personalized assistance on various aspects of imaging, from experimental design to training on the shared microscopes and image analysis.

Facilities Available to CBSE Affiliates at UCSC

Electron microscopy and digital imaging facility houses two transmission electron microscopes (TEM) and a scanning electron microscope. One TEM, a JEOL 1200 EX equipped with a 4pi x-ray analyzer and a Gatan Bioscan digital camera, is used for general room temperature applications. The other is a state of the art JEOL 1230 equipped with a Gatan cryostage and transfer device, a Gatan Ultrascan digital camera, and a Gatan 626 video camera. The lab's ISI WB-6 scanning electron microscope is a conventional, tungsten filament instrument equipped with a 4pi x-ray analyzer and digital imaging system.

Electron spin resonance facility houses two instruments used to examine the structure and properties of metal-containing inorganic complexes, peptides, proteins, enzymes, nanoparticles, and biological membranes. The Bruker ELEXSYS 580 X-band spectrometer operates in either continuous-wave or pulsed mode. It features variable temperature control and is capable of excitation at two frequencies, thus enabling double electron-electron resonance (DEER) for measuring long distances between paramagnetic probles. The high-sensitivity Bruker EMX is useful for the limited sample sizes often encountered in biological studies.

Macromolecular X-ray crystallography facility houses high-throughput crystallization robotics, a state-of-the-art rotating anode/imaging plate X-ray crystallography data collection suite, a cryosystem, and computer workstations and software for crystallographic computations, molecular visualization, and model building. UCSC scientists have used the facility to investigate the structure of the ribosome, catalytic RNA ("ribozymes"), the spliceosome, and protein structures relevant to cell cycle regulation. This facility dovetails with the Lawrence Berkeley National Laboratory's Advanced Light Source synchrotron radiation facility.

Molecular ecology and evolutionary genetics facility provides molecular technologies for analyzing the structure and dynamics of genetic diversity found in animal, plant, and microbial populations. The facility houses a DNA sequence analyzer, a DNA fragment analyzer, and other equipment for high-throughput specimen analysis.

The nanofabrication facility in the W.M. Keck Center for Nanoscale Optofluidics houses an FEI Quanta 3D FEG DualBeam—a focused ion beam combined with a scanning electron microscope—for fabrication, imaging, and characterization of nanoscale optofluidic devices. Researchers have access to the shared microfabrication cleanroom facility in Baskin Engineering and to state-of-the art research facilities in center members’ labs.

Nanosecond time-resolved laser spectroscopy laboratory contains several systems capable of measuring different time-resolved spectra from the far ultraviolet to the near infrared regions. These facilities support a wide variety of research, including photochemical and photobiological studies, examination of functional and folding mechanisms of peptides and proteins, and investigation of fast electron and proton transfer in proteins involved in mitochondrial and bacterial respiration.

Nuclear magnetic resonance facility, used to examine molecular structure and folding in studies involving structure and biochemical mechanisms of cancer, anticancer therapies, and environmental toxins. It houses four different high-resolution NMR spectrometers: two 3-channel Varian Unity+ 500’s with indirect and direct detection probes; a state-of-the-art Varian INOVA 600 system with broadband inverse detection capabilities and a cold probe; and a Bruker AC250.