CBSE Research Facilities

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

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.

Flow cytometry facility houses a state-of-the-art high-speed cell sorting and analysis system, FACSAria. Its four-laser system allows simultaneous detection of up to 14 parameters. Up to four cell populations can be sorted simultaneously at high purity and deposited in bulk or as single cells into a range of standard test tubes, multiwell plates, or slides, allowing convenient and flexible analysis of purified cells. The facility also provides licensed FlowJo software for data analysis and display. This facility is part of the CIRM-funded Shared Stem Cell Facility.

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.

Facilities Available to CBSE Affiliates at UCSC

UCSC life sciences microscopy center provides cutting-edge imaging techniques for advanced biomedical research. It has a Leica SP5 X confocal microscope, a Leica DM5500 B wide-field microscope, and a Zeiss live imaging microscope. A PerkinElmer Volocity spinning disk confocal and a Zeiss LSM5 spot scanning Confocal are maintained at different locations, but available for shared use. Biomedical researchers at UCSC have access to a variety of other light microscopy resources maintained by individual faculty members. These include a Leica SP3 confocal microscope in the Sullivan lab, a Prairie Technologies Ultima-IV two-photon microscope in the Zuo lab, and a Delta Vision wide-field fluorescent microscope with iterative deconvolution technology in the Bhalla lab.

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 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.

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.

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 for a wide variety of research applications. 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.

Buildings

Biomedical Sciences Building

Biomedical Sciences Building, under construction, is designed to promote interdisciplinary interactions and will house faculty from the Departments of Molecular, Cell, and Developmental Biology, Chemistry and Biochemistry, Biomolecular Engineering, and Microbiology and Environmental Toxicology. The building will provide approximately 92,000 square feet of state-of-the-art laboratory space and facilities.

Engineering 2 Building. Photo: Jim MacKenzie

Engineering 2 Building and Jack Baskin Engineering Auditorium were completed in fall 2004. Built in part with support from CBSE and QB3, it provides 96,000 square feet of teaching, research, and office space and an interactive learning center. It also provides office and laboratory space for faculty in biomolecular engineering, computer science, computer engineering, electrical engineering, and for visiting bioinformatics researchers.

This building, designed by Los Angeles architects Anshen + Allen, received a merit award for design from the American Institute of Architects, Los Angeles Chapter in November 2004. The award jury praised the use of different materials to emphasize the building's different functions.

MORE… about the design award

Physical Sciences Building. Photo: Jim MacKenzie

Physical Sciences Building, completed in Spring 2006, is designed to foster interaction among researchers exploring human and environmental health. Completed in part with support from CBSE and QB3, this five-story building has 132,000 assignable square feet of space for laboratories and classrooms in chemistry, environmental toxicology, and biomolecular engineering. It features state-of-the-art lab, classroom, and support facilities to serve a diverse group of scientists.

Sinsheimer Laboratories. Photo: Don Kenny

Sinsheimer Laboratories houses research conducted by CBSE faculty affiliates in molecular, cell, and developmental biology and chemistry, including the stem cell training laboratory and the microarray facility. Its 98,000 square feet are designed around an open, central stairwell and atrium to maximize contact between faculty, students, and research staff.

Other CBSE research takes place in Thimann Labs, which is home to some of the chemistry and biochemistry research, and the Jack Baskin Engineering Building.