Research Facilities Supported by QB3 at UCSC
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 facilitates large-scale analysis of alternative splicing and comparative genomics.
UCSC CIRM shared stem cell facility (SSCF) is an advanced stem cell laboratory for research and training in stem cell manipulation techniques 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 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.
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.
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.
UCSC life sciences microscopy center provides cutting-edge imaging techniques for advanced biomedical research. A core facility for light and electron microscopy, 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.
Nuclear magnetic resonance 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.
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.
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.
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. Non-core facility available by special arrangement only.
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. Non-core facility available by special arrangement only.