Grant Boilerplate Descriptions
Biomolecular NMR Facilities: A dedicated NMR facility for structural biology and metabolomics studies is located in the Cummings Life Sciences Center and directed by Dr. Stephen Meredith. Dr. Joseph Sachleben, an experienced NMR spectroscopist, oversees its daily operation and also responsible for implementation of new experiments, user training and consultation. The facility houses three NMR spectrometers: a Varian INOVA 600 MHz, a 500 MHz Bruker AVANCE III, and a 600 MHz Bruker AVANCE IIIHD. These spectrometers are capable of performing the most demanding solution NMR experiments. All spectrometers are capable of variable temperature operation with a maximum range of -5˚C to 150˚C. A Gilson 215 sample preparation robot and a SamplExpress sample changer provides automated sample preparation and acquisition of spectra on series of samples for epitope and small scale metabolomic analysis. Software packages for data processing and structure calculation are installed on workstations in the facility. In addition, as a member of a Chicago-area NMR consortium (University of Illinois at Chicago, Northwestern University and University of Chicago), University of Chicago investigators have guaranteed access to two high-field machines (800 and 900 MHz) located at the nearby University of Illinois at Chicago.
Biophysics: The Biophysics core is directed by Dr. Ronald Rock and Dr. Elena Solomaha and located in the Gordon Center for Integrative Science. The core provides a complete set of instruments for quantitative characterizion of macromolecules and relevant biological systems. Laser light scattering, fluorometry, CD spectrometry, and spectrophotometry determine absolute properties of macromolecules: weight, size, hydrodynamic radius, composition, polarization, intramolecular distances, and the presence of certain functional groups. These complementary techniques, coupled with thermodynamic and interactional data from bulk techniques such as surface plasmon resonance (SPR) spectroscopy and calorimetry, yield a comprehensive, robust, and reliable portrait of the molecule of interest and its biological activity. The facility also offers instrumentation, such as the multimode plate reader and Seahorse extracellular flux analyzer, for direct measurement of cellular and macromolecular activity. The Biophysics Core Facility instruments:
Extracellular Flux Analyzer: Seahorse ECF, Agilent
Isothermal Titration Calorimetry: ITC 200, Malvern
Circular Dichroism Spectrometer: Jasco J-1500, Jasco
Surface Plasmon Resonance. Biacore 3000, GE; ProteOn XPR36, Bio-Rad
Static/Dynamic Light Scattering: NanoStar, DynoPro, DAWN HELEOS, Wyatt Technology
Fluorescence Spectroscopy: Flurolog-3 Yobin Yvon-Horiba; Synergy Neo HST, BioTek
Luminescence: Synergy Neo HST, BioTek
Spectroscopy: Agilent 8453, Agilent; Synergy Neo HST, BioTek
Molecular Imaging: FX Pro Plus Imager, Bio-Rad; ChemiDoc TM XRS+ System, Bio-Rad
Biostatistics: The Biostatistics Laboratory is affiliated with the Department of Public Health Sciences and is located in Billings Hospital (3rd floor of MARP). The faculty oversight/Scientific Director of the core is Dr. Donald Hedeker and the Technical Director is Dr. Theodore Karrison. The facility provides statistical collaborative support for basic science, animal, and human studies, including early and late phase clinical trials. Investigators may request assistance with study design, protocol development, sample-size determination, preparation of grant proposals, randomization, database development, data analysis and interpretation, and manuscript preparation. The Biostatistics Laboratory is currently staffed with three masters-level biostatisticians, four PhD-level biostatisticians (appointed as Research Associates in the Department of Public Health Science), a Research Professional, and a computer programmer with experience in data management. The Core also operates a “biostatistics clinic,” which is open each Tuesday morning from 9 am to 1 pm for short-term consultations.
Cytometry and Antibody Technologies Facility (CAT): This facility is directed by Dr. Anne Sperling. The main facility is located in the Biological Sciences Learning Center and has a satellite facility in the Albert Merritt Billings Hospital. The CAT Facility serves the faculty by providing access to state-of-the-art technology in quantitative analytical approaches to measure molecular and cellular function. The facility is designed to meet the widespread needs for specialized cytometric analysis and continues to respond to the demand for new and improved technology. The CAT facility supports a Helios mass cytometer, which allows for the detection of 40+ parameters on a cell-by-cell basis. Currently the main facility employs 4 standard cytometers, including a custom-built BD LSRII with 3 lasers (405nm, 488nm and 633nm) and 8 detectors, two custom 4 lasers (405nm, 488nm, 561nm, and 640nm), 15 parameter detectors BD LSR-Fortessa (one equipped with a 96 well HTS unit) and a LSR-Fortessa X20 equipped with 5 lasers (UV, 405nm, 488nm, 561nm, and 640nm) and 18 parameter detectors. In addition, the CAT facility has 2 BD FACSAriaII high-speed cell sorters with 4 lasers (405nm, 488nm, 561nm and 640nm) and 15 parameter detectors, as well as a BDFACS Aria Fusion cell sorter equipped with 5 lasers (UV, 405nm, 488nm, 561nm, and 640nm) and 18 parameter detectors. This last instrument, incased in a BSL2 laminar flow hood, is dedicated solely for users processing human patient samples in a translational research setting. All of the cell sorters are equipped with 96-well plate robotic arm attachments, various nozzle tip sizes (70um – 130um) and temperature control (4C – 37C). The satellite facility has 2 benchtop analyzers, a BD Accuri C2 (488 and 640nm laser with 4 parameter detectors) and a custom-built BD LSRII equipped with 4 lasers (405nm, 488nm, 561nm, and 640nm) and 12 parameter detectors. Additionally, the facility has an imaging cytometer, the EMD-Millipore ImageStreamX MkII, which has 4-lasers (405nm, 488nm, 561nm, 640nm) and two 6-channel CCD cameras to collect up to 10-color fluorescence image data from thousands of cells per second. The facility also has a dedicated Luminex bead analyzer from BioRad to perform multiplex cytokine assays. Trained users are provided 24-hour access on any of these instruments with the exception of the Helios mass cytometer, which is operated by the staff of the facility.
Cellular Screening Center: The Cellular Screening Center (CSC) is a high-throughput screening facility that performs small molecule and siRNA screens. We have about 150,000 small molecules and the Dharmacon Human siGENOME siRNA library. The CSC is directed by Dr. Geoffrey Greene and located in the Gordon Center for Integrative Science. Dr. Siquan Chen manages the day-to-day operation of the facility. 80% projects are using 384-well plates and 20% 96-well plates. Eight liquid handlers and four plate readers are implemented in the CSC, each with a defined role in the screening process. Five of these liquid handlers and three of the readers are integrated with a ThermoFisher Scientific F3 robotic arm for around-the-clock screening. The entire setup is monitored by a computerized alert system, which automatically sends e-mail, and text message alerts to CSC staff members if there are any errors during the screen. Two network cameras are installed in the laboratory space for monitoring remotely. CSC staff members perform regular quality control checks on the instruments. The entire laboratory is in a clean room environment and all screens are performed in Class 100 space. The CSC has partnered with the Center for Research Informatics (CRI) at The University of Chicago to maintain CSC databases. All data that is obtained from the four readers are automatically stored at a remote server where it is backed up nightly. The CSC has bioinformatics support to maintain the security of the data, the availability of data, and to aid in data analysis.
The Cellular and Tissue-Based Processing cGMP facility is located in the Kovler Laboratory building. The faculty director is Amittha Wickrema, Ph.D. Diane Ostrega, M.S. M.B.A, has served as the Technical Director since the facility’s inception in 2001 and has over 30 years experience in clinical and basic research. The facility employs two additional staff members, an Asst. QC/QA Manager, and a Cleanroom Technician. The mission of the facility is to provide a laboratory environment as well as resources and consultative services for preparing cellular and biological products suitable for infusion into patients. The facility is FDA registered and follows regulations set forth by 21CFR Part 1271, which outlines requirements for preparing human cells, tissues and tissue based products for treating patients. The facility provides positive and negative pressure clean rooms, Biological Safety Cabinets, instrumentation for cell isolation, peptide vitalization, cryopreservation and assay and endotoxin analysis.
The Advanced Electron Microscopy Core Facility at The University of Chicago occupies over 2000 sq. ft in the Gordon Center for Integrative Sciences (GCIS). The cornerstones of the facility are the Cryo-EM dedicated FEI Talos 200kV xFEG electron microscope (which has a Falcon II direct detection camera), and the FEI Tecnai F30 300kV FEG (s)TEM Electron Microscope. Both of these scopes are supported by the FEI Tecnai Spirit 120kV LaB6 routine, Cryo-EM capable, electron microscope. The facility also contains a RMC high-pressure freezer, a FEI vitrobot, 2 Leica freeze-substitution devices, an Edwards evaporator, 2 Leica ultramicrotomes, a Fishione dual-axis high tilt holder for tomography, 2 Gatan Cryo-holders, Gatan plasma cleaner, computer workstations, ancillary laboratory equipment such as light microscopes, wet lab bench space, a CO2 incubator, fume hoods, and general consumables related to electron microscopy. Facility Director Jotham Austin, PhD and Yimei Chen oversee the daily operations of the core. The core provides preparation and imaging services, and training for transmission electron microscopy. All basic, “classic” TEM sample preparation and imaging can be provided including, but not limited to: chemical fixation; tissue embedding; sectioning; immunogold-labeling; negative staining; and imaging. We also offer advanced techniques, such as single particle analysis workflows, from negative stain analysis thru to automated Cryo-EM data acquisitions. Correlative Light/Electron Microscopy (CLEM), which allows users to correlate fluorescently-tagged proteins to high resolution TEM structure studies. 3D electron tomography and STEM 3D electron tomography, both of which can provide accurate three-dimensional reconstructions with 5 – 7 nm resolution.
The Genomics Core Facility is located in the Knapp Center for Biomedical Discovery and directed by Dr. Yoav Gilad, Professor in the Department of Human Genetics. In addition to Dr. Gilad the core has a dedicated staff of 11 people including 4 PhD level scientists. The major services provided are Next Generation DNA Sequencing, DNA microarrays and Sanger DNA Sequencing. A Fluidigm C1 Single-Cell Autoprep system is available for specific single cell applications.
- Next Generation Sequencing: The Facility utilizes Illumina NextSeq500, HiSEQ 2500 and HiSEQ 4000 instruments to perform DNA sequencing (whole genome, ChIP, other) and RNA sequencing services.
- Microarray Analysis: The Facility owns and operates Illumina HiScan, Affymetrix Gene Chip, and Axon 4000B microarray scanners.
- Sanger DNA Sequencing and Genotyping: The Facility operates two Applied Biosystems 3730XL and one 3130XL genetic analyzers for small and high throughput users.
Other services offered include technical consultations, nucleic acid purification, sample processing and library construction. Plate and micro-volume readers are provided for client use.
The Genomics Core is supported by the Cancer Center Support Grant (P30 CA014599).
Image Computing, Analysis and Repository Core (ICAR): ICAR provides computing, data storage, and consulting services for facilitating the integration of imaging technologies with cancer and biomedical research in the UC Comprehensive Cancer Center. Usage of the core's instruments is free to all researchers, while consultations may involve chargeback depending on time and complexity. ICAR also collaborates with the Human Imaging Research Office's Bio-Medical Imaging Repository (BMIR) and the BSD Center for Research Informatics in the development of methods for the curation and querying of large scale human and animal imaging databases. The Core's instruments include the Scientific Image Reconstruction and Analysis Facility (SIRAF), a computing cluster acquired via an NIH Shared Instrument Grant optimized for image processing and visualization, and the Animal Imaging Repository (AIR), which provides network file sharing services for animal researchers. Chun-Wai Chan (MS, Astronomy and Astrophysics) oversees their operation and provides consultation related to high performance computing and storage. Dr. Hsiu-Ming Tsai (Ph.D. Optical Engineering) oversees the Image Analysis and Programming sub-core and provides consultation for advanced image processing methods. The faculty director for ICAR is Dr. Charles Pelizzari (Dept. of Radiation Oncology). Space for housing the instruments and personnel offices is provided by the Dept. of Radiology in the Franklin McLean Institute.
Integrated Light Microscopy: The Integrated Light Microscopy Facility (ILMF) functions as a supervised, user-based Core providing state-of-the-art microscopy imaging capabilities to all University investigators. The primary mission of the Facility is to provide a valuable, unique service to the University community by furnishing high-quality microscopy instrumentation, user training, image analysis tools, and expert assistance. The ILMF is directed by Dr. Benjamin Glick and managed by three full-time technical directors. Together Dr. Vytas Bindokas, Dr. Christine Labno and Ms. Shirley Bond have a combined 65 years of microscopy experience with specialties in live cell imaging, physiologic measurements, clinical immunopathology, and immunostaining (including antibody generation and testing) as well as extensive experience in image processing and analysis. The main location is a custom-designed space in the Knapp Center for Biomedical Discovery (KCBD) room 1250, and houses twelve microscopes, including two with superresolution capability (the new Leica Ground State Depletion superresolution/TIRF microscope and the Leica SP5 II STED-CW superresolution confocal). Other systems in the KCBD location include the Leica SP8 spectral confocal with white-light laser, the Olympus FV1000 laser scanning confocal, two Olympus DSU spinning disk confocal systems, a stereomicroscope and five bright-field and fluorescence light microscopes. The facility can accommodate live cell imaging in multiple formats, including the Zeiss Lightsheet Z1 SPIM system, The 3-I Lattice Lightsheet system, the Olympus VivaView incubator microscope, three systems with full-wrap incubation chambers and three stage-top incubation systems. Two high-resolution digital slide scanners are run as a drop-off service. These scanners yield digital slides containing detail equivalent to 100x magnification for color histology and multi-color fluorescence materials. The Abbott 129 satellite location houses four microscopes including a Leica SP5 2-photon laser scanning confocal, a 3-I Marianas laser spinning disk confocal, a Leitz upright scope, and an Axiovert 135 fluorescence/DIC microscope. The facility offers high-end analysis software (MetaMorph, Imaris, Huygens Pro, ImageJ, etc), free temporary networked data storage, and workstations for data analyses and presentation. Details and policies can be found on the Core website.
Microsurgery: The Animal Microsurgery Center (Core) in the Department of Surgery is directed by Dr. Anita Chong. The core provides microsurgical services to the researchers in other Departments at University of Chicago, as well as non-University of Chicago investigators. The Core has all essential surgical equipment, including four surgical microscopes, microsurgical tools, anesthesia machine, ventilator, and sutures for surgery and microsurgery in rodents. Current mouse and rat surgical models include: abdominal and cervical heart, kidney, pancreas, small bowel, liver, skin and islet transplantations; kidney, liver and heart Ischemic model; bariatric surgical procedures, including gastric banding, VSG, RYGB, DJB, BPD; Cardiovascular and metabolic models including MI, aorta hypertension, A&V catheterizations; Cancer and immunological models including Barrett’s esophagus and tumor implantation; General procedures: IV injection, thymectomy, splenectomy, nephrectomy, catheterization, blood glucose tests and diabetic models. Dr. Dengping Yin, the Core technical director has over 20 years experience with rodent microsurgery and can develop surgical techniques and approaches according to the requirements of individual investigators; and train laboratory and clinical research personnel in surgical procedures in the rodents.