Facilities

Biomolecular mass spectrometry:

A research, training, and service facility is housed in the Ekeley Building includes eight mass spectrometers for biomolecular and small molecule research (ABI Voyager DE-STR MALDI-TOF MS, ABI QStar Pulsar qTOF MS, ABI 4000 QTrap MS, ThermoElectron LTQ Orbitrap MS, ThermoElectron LCQ Classic MS, Agilent ion trap MS, HP 5989A electrospray ionization single quadrupole MS, HP5988A gas chromatography MS). The qTOF and ion trap instruments are each outfitted with Agilent Model 1100 capillary HPLC or Eksigent Nano LC-2D HPLC systems with autosamplers. The instruments are housed in the Central Analytical Facility, under the supervision of Dr. Katheryn Resing.

DNA microarray:

A facility to process and read Affymetrix chips is housed in the MCDB addition and operated by Ms. Helen Marshall, under the supervision of Drs. Ken Krauter and Ryan Gill. The facility includes an Agilent G2500A GeneArray scanner with fluidics station, hybridization oven, computer workstation, and an Agilent 2100 bioanalyzer.

Mammalian cell culture:

Several facilities are available in Chemistry and Biochemistry, MCDB, and CBEN. A BL2-plus certified cell culture facility in the Cristol Building shared by all Biochemistry investigators is equipped with four containment hoods, five double door CO2 incubators, an automated liquid nitrogen storage unit, a cytospin centrifuge and an inverted microscope with light and fluorescence sources. The facility is supervised by staff specialist Theresa Nahreini, who trains students in sterile technique and oversees daily operations of media preparation and maintenance of cell lines. Cell culture facilities (BL2 and BL2-plus) in MCDB and CBEN are located adjacent to and maintained by individual laboratories (Han, Leinwand, Lee, McIntosh, Olwin/Martin, Anseth).

NMR:

A facility containing 500 and 600 MHz 4-channel Varian Inova NMR spectrometers and a three channel Varian Inova 500 MHz spectrometer is located in the Cristol Chemistry Building and maintained and operated by Drs. Arthur Pardi and Deborah Wuttke, with staff specialist Richard Shoemaker. Funding to purchase a Varian 800 MHz (PI: Pardi) and a 900 MHz (PI: Wuttke) NMR has recently been awarded. These instruments will be shared by investigators at CU Boulder, UCHSC-Denver, and U. Utah, with the 800 MHz instrument located on the CU Boulder campus and the 900 MHz instrument located at UCHSC-Denver.

Biomolecular X-ray crystallography:

a facility in the Cristol Building houses a Rigaku RU-200 rotating anode generator, equipped with an R-AXIS IV++ image plate system, Osmic confocal mirrors and an X-Stream cryo-cooling devise. An R-AXIS IIC image plate system I smounted on a Rigaku RU-H2R rotating anode generator, and is equipped with MSC (Yale design) focusing mirrors and an X-Stream cryo-cooler. Data collection is interfaced to Silicon Graphics, Onyx2 and a digital Alpha computers for computation, refinement, and data reduction. The X-ray facility is maintained by Dr. Steve Edwards, who trains students and oversees daily operations under the supervision of Drs. Lin Chen, Marcelo Sousa, Robert Batey, and Tom Cech.

Fluorescence microscopy:

Chemistry and Biochemistry, MCDB and CBEN have extensive facilities for microscopic analysis of cellular structure. An electron microscopy suite equipped with two Philips CM10 100 KeV electron microscopes are housed in MCDB. These instruments, together with a Balzers high pressure rapid freezer and ultrahigh vacuum-ultralow temperature freeze fracture apparatus, are supervised by Dr. Thomas Giddings, a state employee well versed in EM methodologies. The department also operates facilities for 3D reconstruction, with a Molecular Dynamics scanning confocal microscope, and Silicon Graphics and MacIntosh G3 computers for analysis. A Zeiss LSM5 Pascal scanning confocal microscope is housed in the CBEN building. Three upright deconvoluting light microscopes are housed in the labs of Han, McIntosh, and Winey. Zeiss Axioplan upright and Leica inverted fluorescence microscopes with digital CCD cameras are located in the Cristol Building and shared by Chemistry and Biochemistry laboratories.

National Research Resource laboratory for three-dimensional electron microscopy:

The facility is located in Porter Biosciences and currently supported by a grant from the NIH National Center for Research Resources under the directorship of the PI, Dr. J. Richard McIntosh. In this lab, methods have been developed for EM tomography of cells, allowing 3-dimensional reconstruction of cells with resolutions of ~6 nm. Methods have also been developed for serial section and immunolabeling at the EM level to localize specific antigens in 3-D within the context of cellular structure. This Resource operates a JEOL 1000 high voltage electron microscope, equipped with a goniometer stage for ambient temperature work and a single axis tilting cold stage. The Facility has recently acquired a 200 and a 300 KeV instrumet from FEI, Inc. Each is equipped with field emission gun, goniometer stage, and CCD camera. The 300 KeV is also equipped with a Gatan Imaging Filter to permit acquistion of images based on energy filtered electrons. Supporting computer facilities for tomographic reconstruction and serial section image processing are also available.

Flow cytometry:

A Cytomation flow cytometer/cell sorter, and a Benton Dickinson FACScan Cytometer with FACScan software for data collection and analysis are located in the Cristol Building, and are maintained by Dr. Xuedong Liu. A second Benton Dickinson FACScan cytometer, located in the Porter Building, is available as a facility instrument and is maintained by Dr. Mark Winey.

DNA sequencing:

A service facility located in the Porter Biosciences Building is equipped with two ABI Prism 377 automated DNA sequencers, and is operated by Dr. Yuming Han and two work study students.

Fluorescence spectroscopy:

A SLM 48000S fluorescence spectrometer equipped for steady state and phase modulation lifetime measurements, with laser (Coherent Innova 306 argon ion laser) and arc lamp (Xe or Hg-Xe) excitation sources, is located in the Cristol Building and maintained by Dr. Joe Falke.

Surface plasmon resonance spectrometry:

A Biacore X spectrometer is located in the Cristol Building and maintained by Dr. Art Pardi.

Transgenic animal facility:

A transgenic animal facility is available in the MCDB department, with a total of 8200 sq. ft. including 2700 sq. ft. of animal holding rooms. The facility contains two procedure rooms for performing animal surgeries and other manipulations, and an embryo microinjection facility shared among several Principal Investigators. The facility is managed as a barrier facility; incoming animals from non-approved vendor sources are quarantined and tested prior to introduction into the facility, and all animals are housed in microisolator cages. A sentinel program with regular serology is used to monitor animal health and screen for pathogen outbreaks. Animal care, embryo microinjection, and some other specialized services (e.g. tissue biopsy for genotyping and certain surgical procedures) are available.

Bioinformatics facility:

A facility for bioinformatics and computational biology is located in Porter Biosiciences. The facility currently includes a 50-CPU Opteron Linux cluster with 4 TB storage, but is in the process of adding another 128 compute cores and a database node with 64 GB RAM with support from the W.M. Keck Bioinformatics Initiative. The cluster makes available standard bioinformatics services such as sequence search and alignment, and also hosts newly-developed software tools for RNA folding, community analysis, and motif analysis. The facility is operated by Dr. Rob Knight.