Genomics/Proteomics Core | Proteomics and Metabolomics Facility | Chemistry Store Room, Electronics Shop and Glass Shop | Regional NMR Center | Molecular Dynamics PhosphorImager | Fluorescence Microscopy/Image Analysis Center | Protein Purification and Characterization Facilities | Irradiation Resources Facility | Microscope Imaging Network | BSL-3 Facilities | Histotechnology Laboratory | Veterinary Teaching Hospital | Animal Care | Information Technology
BSL-2, BSL-3 and ABSL-3 Laboratories
MRL research is supported by approximately 20,000 sq ft of BSL-2 laboratory space and 10,000 sq ft of BSL3 and ABSL3 laboratory space and is performed in facilities on CSU’s Main Campus (Microbiology Building and Pathology Building) and state-of-the-art facilities on the Foothills Research Campus (the Infectious Disease Annex, the Regional Biocontainment Laboratory, and the Research Innovation Center). In addition to the equipment available in each Faculty’s laboratory, the MRL shares numerous pieces of equipment, including HPLCs, FPLCs, ELISA Plate readers, Lyophilizers, Gas Chromatographs, French presses, Centrifuges and Ultracentrifuges, Spectrophotometers, Video Systems, Vacuum Pumps, Rotavapors, Scintillation Counters, Real-Time PCR, Thermocycler, X-ray developers, Cold room, Warm rooms, Incubators, Environmental Shakers, Biosafety Cabinets, Microscopes, Autoclaves, MilliQ water systems, Ice Machines, glasswashing and drying equipment, etc.
The Genomics and Proteomics Core within the Infectious Disease Research Center (IDRC) at the CSU Foothills Research Campus is a fee for service facility that offers NexGen sequencing. ABI 3130xL Genetic Analyzer is also available to process sequencing samples during dcr2 mRNA analyses. Capillary gel electrophoresis (ABI 3730 DNA analyzer) used in screening of dcr2 knockout mutants is available as part of the Core facilities. The Genomics and Proteomics Core and is fully staffed to assist in sample preparation, sequencing and data analysis and contains state-of-the-art hardware and software including
- Genomics: Affymetrix BioAnalyzer 2100, with GenePix 4000B, Nanodrop 1000, and Biorad IQ5 Multiplex PCR System, and ABI SoLID high throughput sequencer
- Proteomics: Agilent 6520 QTOF, with 1200 series nano and capillary pumps, Nanospray Chip cube, Dual source ESI Multimode source (concurrent esiapci) and Agilent LCC hemstation 1200 series pump, Ternary gradient capability, UVVis detection, and Fraction collector
The Core Software capabilities include
- Genomics: Affymetrix GCOS and EC Software, BiaCore Evaluation Console, Acuity 5.0, GeneExpression Software, Gen5 expression and intensity analysis software AB Primer Express, probe/primer design software, BioRad QuantityOne-chemiluminescence evaluation program
- Proteomics: Agilent Masshunter Workstation, SpectrumMill Proteomics, Workbench, Agilent Chemstation
- Bioinformatics: ArrayTrack Statistical Analysis “R”/ Bioconductor, GeneGo, Ingenuity, MetaCore, Mesa Analytics Next Generation Gene Sequence Analysis, Computer-Aided Drug Design Services.
The Proteomics and Metabolomics Facility (PMF) is operated as a division of the Vice President for Research office at CSU.
PMF provides DNA synthesis, sequencing and mass spectrometry services with computer and software packages to facilitate analysis. PMF labs include:
- Thermo-Finnigan LTQ ES-MS-MS system comprised of an LTQ electrospray ion-trap MS-MS with an Agilent 1200 nanospray HPLC unit and an Agilent 1100 uPS autosampler
- Bruker Daltonics MALDI-TOF/TOF mass spectrometer
- Offline analytical HPLC system with UV and fluorescence detector and fraction collector, Agilent 1200
- Waters micro Q-TOF mass spectrometer with a capillary Waters Aquity UPLC unit
- Waters micro TOF mass spectrometer with a capillary Waters Aquity UPLC unit
- Agilent GC-MS; Perkin Elmer GC-FID
- Applied Biosystems 3130xl Genetic Analyzer
- Bio-Rad iQ5 ICycler (controlled by a HP PC)
- 1 dimensional agarose and SDS-PAGE gel electrophoresis and 2 dimensional SDS-PAGE gel electrophoresis apparatus
- Waters Xevo QQQ-MS with either a chip-cube or nanoLC interface.
Facility personnel offer consultation and expertise in experimental design and data analysis in the areas of Proteomics and Metabolomics. In addition, the facility offers routine services and operation of an Enzyme Freezer program. This facility is housed in the Microbiology Building.
Chemistry Store Room: sells chemicals, glassware, etc. Electronics Shop and Glass Shop: provide services or supplies on a fee or unit cost basis. Regional NMR Center: a NSF Regional Instrumentation Facility with Nicolet wide-bore NT-150, wide-bore NT-200, and NT-400 (400 MHz protons) instruments; and Bruker 600 MHz, 500 MHz, and 350 MHz instruments for routine NMR analysis. The Regional NMR Center has recently made it a policy to give biological samples top priority for the 500 MHz NMR instrument. The Chemistry Department also has Fisons/VG Auto-Spec-5000 high mass resolution MS, and a Fisons/VG Quattro-SQ high mass quadruple MS with Electro-spray interface. The NMR and FAB-MS samples are run with a nominal service fee as charged by the Department of Chemistry.
Molecular Dynamics PhosphorImager and a cooled CCD camera: Networked to a workstation on the 2nd floor of the Microbiology Building.
Fluorescence Microscopy/Image Analysis Center: located in a building adjacent to the Department of Microbiology, it contains two inverted Nikon Diaphot epifluorescence microscopes equipped with stage incubators. One unit has a scanning stage with autofocus, a dual wavelength excitation monochromator, a filter wheel and a chilled Photometrics PXL camera. Filters are available for observations of most common fluorophores.
State-of-the-art Protein Purification and Characterization Facilities, including a Macromolecular X-ray Facility, are available in the Biochemistry and Molecular Biology Department on CSU’s main campus. CSU is a paying member of a consortium that operates a beam line at the Advanced Light Source in Berkeley. Beamline *4.2.2*, also known as the Molecular Biology Consortium (MBC) beamline has already been used to determine several structures. The X-ray facilities are open to all appropriately trained CSU faculty, staff and students
The Molecular and Radiation Biology Building houses a 6000 Ci 137Cs Irradiator (Model 81, Shepard and Associates) that is used for g-irradiation of virulent micro-organisms, including Mycobacterium spp.
The MRL shares State-of-the-art imaging facilities and core infrastructure “The Microscope Imaging Network (http://www.natsci.colostate.edu/min/) funded in part through a core infrastructure grant from the Office of the Vice President for Research. Each instrument has its own supervisor and training mechanism. The Network presently includes:
- Zeiss Laser Scanning Axiovert Confocal Microscope (LSM510 meta) in room W210 A/Z has a META multi-spectral analyzer and a dual laser scanning system. Wavelengths available are 458, 488, 514, 543 and 633nm. It does not have a stage incubator and is used primarily for fixed samples unless the operator provides an incubation chamber. Zeiss imaging software is used to capture and process images.
- Zeiss Laser Scanning Axiovert Confocal Microscope (LSM510 meta) in room 5 at IDA, Foothills Campus also has a META multi-spectral analyzer and a dual laser scanning system. Wavelengths available are 405, 458, 488, 514, 543 and 633nm. This instrument has a stage incubator for live cell imaging and Zeiss imaging software to capture and process images.
- Zeiss Axioplan 2: Located in room 216W A/Z, the Zeiss Axioplan 2 imaging microscope is an upright modular transmitted light and incident light polarizing and fluorescence microscope with a pyramid design and an Infinity Color-corrected Optical System. It has available 5 objectives: 4x, 10x, 20x, 40x and 100x with capability for phase contrast, differential interference contrast (20x, 40x and 100x objectives) and fluorescence microscopy. Filter cubes are loaded for FITC/GFP, TRITC/Cy3 and dual channel fluorescence. The stage is motorized in z and the new Axiovision Release 4.7 software can control the stage, filter sets, and AxioCam camera to provide Z-stack and multi-channel digital image capture capabilities. More information is at: http://www.cvmbs.colostate.edu/bms/axioplan_facil.htm
- Olympus Spinning Disk Microscope with DIC optics and Mosaic Photoablation/ Photoactivation/Photoconversion system, dual view split chip acquisition for simultaneous recording of images at two wavelengths, heated stage, and widefield Xenon light source with spherical aberration correction. Laser lines available for the CSU22 spinning disk are 440, 473, 561 and 660 nm. A 325 mW argon 488 nm laser is available for photoablation studies through the mosaic illumination system (thousands of mirrors to illuminate small selected regions across the image simultaneously) and can be replaced with a mercury lamp for photoactivation or photoconversion studies. The sensitive cascade II 1kX1K camera can operate in a sensitive enhanced (non-linear) mode or in a linear mode. This microscope is designed for live-cell imaging work, especially long-term (hrs to days) studies during which phototoxicity and photobleaching must be minimized. Images are captured utilizing Slidebook software.
- Nikon inverted epifluorescence microscopes (three) with video cameras for digital imaging are available within the Fluorescence Microscopy/Image Analysis Center in room 224 MRB. Filter cubes for all common fluors (DAPI, Fluorescein, Rhodamine, Texas Red, Cy 3, Cy5) are available and are interchangeable between microscopes. One microscope has DIC optics, an optional phase oil-immersion condenser, and a stage incubator and filter wheel for live cell studies (ratio imaging included) and one has a color camera for imaging stained sections. A specialized light source for darkfield illumination of slides is available and is especially useful for counting silver grains on emulsion treated samples. All microscopes utilize Metamorph software for image capture and analysis.
- JEOL 2000 Transmission Electron Microscope in W11 A/Z is a 200 kev microscope capable of imaging intermediate thickness sections but normally operated in a lower voltage mode. An EM preparation laboratory with an ultramicrotome is available to trained facility users. This instrument does not have a digital camera and groups should either provide their own film or arrange for film costs with the facility supervisor.
The Infectious Disease Research Center (IDRC), located at the CSU Foothills campus, is a 25,000 sq. ft. [BSL-2, BSL-3 and ABSL-3] facility with 9,100 sq. ft dedicated to BSL3 containment area. MRL laboratories have shared use of the Bulk Culture and Immunology BSL-3 Suites. The Bulk Culture Suite which is dedicated to TB research is approximately 3,000 sq ft and is utilized for the large-scale growth and manipulation of virulent M. tuberculosis including MDR-M. tb strains. This bulk culture/molecular biology suite contains all the equipment for culture manipulation (biosafety cabinets, 37°C warm rooms, 32°C and 39°C incubators, centrifuges, electroporator, pass-through autoclave, cold room).
The Immunology Suite in which cell and animal infections are carried out is equipped with a Calibar Flow Cytometer with a Macintosh computer loaded with Cell Quest software. Other equipment includes a real-time PCR detection system, a microplate fluorometer with PlateReader™ software, a Cytomation Mo-Flo MLS 2000 multi-laser cell sorter, a Beckman Coulter Z1 series particle counter, a Microplate ELISA reader, a ELISA microplate washer, a Leica Cryostat/Microtome for sectioning infected tissues for immuno-histochemical staining and microscopic analysis, and an Olympus BH2 microscope with RFCA reflected light fluorescence module with a Polaroid digital camera attachment. The Immunology suite also contains two Class II bio-safety cabinets for tissue culture, two CO2 incubators. Equipment within this laboratory includes: a Becton Dickinson FACSCalibur flow cytometer, The BDTM LSR II flow cytometer have the ability to detect up to 13 colors per sample. The BDTM LSR II flow cytometer is equipped with four lasers, in addition to a sophisticated BDTM High Throughput sampler that allow rapid collection of samples directly from a 96 well plates and the latest BD FACSDive sowftware, a PE Biosystems ABI Prizm 7700 real-time PCR detection system, a BD FACS Aria III Cell Sorter is equipped with four lasers.
MRL investigators also have shared use of a necropsy room which houses two class II bio-safety cabinets linked directly to class I bio-safety cabinets via an access door for the manipulation of infected tissues. Adjacent to this room is a dedicated area that houses 2 Glas-Col aerosol generating devices for exposure of experimental animals. Included in the IDRC is up to 8,000 sq ft of space for housing rodents under BSL3 and BSL2 containment. This facility has holding rooms for up to 2,000 mice and is equipped with Thoren racks, and HEPA-filtered cage changing stations. The IDRC facility also contains common rooms and facilities such as media prep and glassware washing rooms, a central office space with desks and computers, and locker and shower rooms. All procedures in the BSL-3 facility strictly adhere to CSU Biosafety Committee guidelines as well as those guidelines outlined in a Biosafety Procedure and Practice Manual.
The Histotechnology Laboratory is located in the Veterinary Teaching Hospital (VTH) Building of the CSU main campus. The facility is part of the Colorado State Veterinary Diagnostic Laboratory, fully accredited by the American Association of Veterinary Laboratory Diagnosticians. The facility provides routine histopathology processing equipment including dedicated fume hood trimming stations, a Shandon Hypercenter Plus 1 automated tissue processor, a Technicon Duo tissue processor, a Tissue Tek dispensing console, a Shandon Hypercenter wax station, a Lipshaw paraffin dispenser, 4 Leica 2035 rotary retracting microtomes, a Shandon AutoShart 5 microtome knife sharpener, a Shandon Varistain 24-3 automated staining unit, a Sakura coverslipping unit, and automated block and slide labeling systems (TBS). For frozen section work, 2 Tissue Tek Cryo consoles and a Slee cryostat are available. A DuPont MT-3 ultramicrotome and glass knife maker augment a college electron microscopy facility including 2 transmissions and 1 scanning units. For immunohistochemistry, dedicated fume hood workstations surround a new $80,000 Ventana NexES automated immunohistochemistry stainer.
The CSU Veterinary Teaching Hospital is a nationally recognized veterinary hospital. The hospital admits all animal species, including more than 20,000 dogs and 3,500 cats per year. The clinicians at the CSU VTH are specialists and serve as experts in their field. The VTH, a leader in veterinary medicine, provides care to patients and at the same time provides access to cutting edge technologies and services to faculty, researchers and veterinary students. It is a full-service hospital catering to all specialties with services such as neurosurgery, endoscopy, diagnostic aids, MRI’s, CT’s and ultrasounds.
The CSU animal care program is monitored through a single, central Institutional Animal Care and Use Committee (IACUC) that reports directly to the Vice-President for Research. The Painter Center is the primary, centralized animal facility located on the main campus managed by Laboratory Animal Resources (LAR). All aspects of animal-based research are supported by the Painter Center, including those requiring Animal Biosafety Level 2 and 3 capabilities. Investigators from 12 departments on campus, including MRL investigators, are served by this facility. A state-of-the-art ABSL-3 animal laboratory is housed in the Painter Center for Animal Care close to the Microbiology Building. Animals are housed under hygienic and humane conditions in quarters that are accredited by the American Association of Laboratory Animal Sciences. The ABSL-3 laboratory is an isolated multi‑room suite of 692 sq ft. The Infectious Disease Research Center (IDRC) is located on the Foothills Research campus, 4 miles from Main campus. The IDRC is composed of a series of several interconnected and one stand alone building. Within these facilities there are multiple isolated suites housing animals in ABSL-2 and ABSL-3 conditions, one of them dedicated to TB research (see BSL-3 Facilities).
All facilities and labs are fully wired for information technology and all offices and laboratories contain multiple computers to provide the hardware and software necessary to do state-of-the-art science. Colorado State University fully supports the computers in these facilities with multiple full-time personnel.