Boilerplate document for grant preparation

Updated August 2014

The Biological Sciences Division (BSD) of the University of Chicago has a strong commitment to shared research facilities (cores) housing state-of-the-art technologies available to all research faculty, staff and students on campus. Each core facility is managed by a full-time professional Technical Director with oversight by a Faculty Director. The Technical Director and his/her staff oversee the day-to-day operation and also provide user training.

The BSD recognizes that core facilities are extremely valuable partners in our research efforts and require continued and significant investment. Two Divisional entities exemplify our commitment: 1) an active standing faculty committee (the Research Resources Oversight Committee) which serves as an institutional “board of directors” and meets monthly to advise the Dean on institutional investment of financial and space resources in the facilities, implement his recommendations, and review facility operations and 2) a centralized administrative support unit within the BSD Office of the Dean (the Office of Shared Research Facilities) which serves as the home department for the facilities. This operation is funded entirely by Divisional resources ($716,000 for FY15) and provides operational management support, highly efficient fiscal management, HR support, grant support, and coordinated strategic planning for the facilities. In addition to these Divisional units, a Faculty Oversight Committee that addresses user satisfaction and requests for development of new services oversees each facility. The oversight structure provides expert supervision and responsiveness to faculty needs for services and innovations.

Many of the existing BSD Cores were established with Divisional resources and continue to be underwritten with BSD funds. From FY05-FY14, $30 million of institution funds have been identified for investment in Shared Research Facilities. The funding has provided for new equipment, operational support for newly developed cores, dedicated information systems for data management and administrative support for the facilities. In addition to financial resources, the BSD has developed a strategic space plan to house shared resources. This continued investment in the facilities will ensure the facilities will remain at the forefront of the technologies they offer.

Major Core Research Facilities

Animal Resource Center: https://animalresources.uchicago.edu The University of Chicago Animal Resources Center (ARC) has a PHS assurance with OLAW and is a USDA registered research facility. AAALAC International has accredited the animal care program since 2002.There are 5 full time veterinarians, including the Attending Veterinarian, Dr. George Langan, who support the animal care and use program at The University of Chicago. All the veterinarians are board certified by the American College of Laboratory Animal Medicine. In addition, there are eight veterinarian technicians who along with the veterinarians are responsible for the veterinary care for all animals at the University.

The ARC is approximately 140,000 sq ft of animal housing and procedural space in eight facilities. There are facilities designed to accommodate both large and small animal species, but the majority of the facilities are dedicated to housing barrier mice, approximately 20,000 cages at any given time. Barrier mice are housed in positively pressurized individually ventilated cage racks and changed in biological safety cabinets. Caging and bedding are autoclaved prior to use and cages are provided with irradiated food and acidified water. There are specialized areas for research involving surgical, behavioral and biohazardous (ABSL 2) studies and an off campus location for ABSL3 studies.

Animal care technicians (ACT) are responsible for providing daily husbandry and observing animals for signs of illness or abnormal behavior. Each animal is observed at least once a day. The procedure for reporting and recording animals that appear to be ill or behaving in an abnormal manner varies with the species and severity of the problem. In an emergency situation (regardless of species), the ACT immediately notifies the clinical veterinarian, the husbandry supervisor and/or the veterinary technician for the facility by paging or phone call. The animal is attended to and information is entered in the medical record for USDA covered species or an AHOD (Animal Health Observation Document) is produced for rodents or exotic species.

If a sick rodent is found during routine health observation, the ACT completes the AHOD to identify the animal and list their observations. A veterinary technician, special services technician or facility supervisor and the health problem evaluated collects the AHODs. Follow-up by the clinical veterinarian occurs as necessary. Information regarding resolution, treatment and monitoring is noted on the AHOD form and a plan for treatment is indicated.

If a large animal species is found with a health problem during routine health observations, the ACT notifies either the veterinary technicians or clinical veterinarian directly or by pager or phone. The veterinary technicians and/or the clinical veterinarian evaluate the animal and develop a treatment plan.

All animal facilities are staffed 7 days a week with the regular animal care staff. An on-call husbandry supervisor oversees the weekend and holiday husbandry staff. A veterinary technician is present all day on weekends, and for abbreviated hours during holidays, to provide treatment and care to large animal species. A husbandry supervisor and veterinarian are on-call at all times. Signs are posted in each facility alerting investigative staff how to contact a veterinarian and husbandry supervisor in the event of an emergency.

The most current ARC text for grant writing purposes can be found at: https://animalresources.uchicago.edu/page/grants-help.

Bioinformatics: http://cri.uchicago.edu/?page_id=1185 The bioinformatics core in the Center fro Research Informatics is directed by Dr. Samual Volchenboum. Technical director Dr. Jorge Andrade manages the daily operations of the core and it ten PhD level bioinformaticians. The core has access to a number of computing resources including:

·  High Performance Computing (HPC) Cluster

o  2304 standard cores (2.2 GHz AMD Opteron 6274)

o  80 high-memory cores (2.25 GHz Intel Xeon E7-4860)

·  Storage: 1.1 PB Isilon cluster with space to be provisioned for labshares and individuals

·  Large Memory Linux Supercomputer

o  Memory: 1 terabyte of RAM

o  Processor: Intel® Xeon® CPU E7-8870 @ 2.40GHz x 8 – 160 cores

o  Storage: 40T of shared storage space

·  Backup and Restore System: Tivoli Storage Manager (TSM)

The Bioinformatics Core offers services and expertise designed to allow BSD investigators to take full advantage of available high-throughput technologies. The aim of the Core is to provide the following services:

·  Bioinformatics analysis of high-throughput biological data using well-defined analysis pipelines

·  Direct consulting with bioinformaticians in the Core for specific/custom-made analysis or pipelines

·  Training in the use of publicly and commercially available bioinformatics software and tools, enabling investigators to develop bioinformatics expertise within their laboratories

·  Grant writing assistance, so that the bioinformatics components of a grant are fully developed and integrated with the investigator’s research, thereby increasing the investigator’s competitiveness for external funding

Biomolecular NMR Facilities: http://nmr.bsd.uchicago.edu A dedicated NMR facility for structural biology and metabolomics studies is located in the Cummings Life Sciences Center and directed by Dr. Shohei Koide. 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: http://biophy.uchicago.edu The Biophysics core is directed by Dr. Ronald Rock 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.

Biostatistics: http://health.bsd.uchicago.edu/Biostatistics-Laboratory. The Biostatistics Laboratory, is closely associated with the Department of Health Studies and is located in the Billings Hospital (3rd floor of MARP). The faculty oversight/Scientific Director of the core is Dr. Ronald Thisted 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 four masters-level biostatisticians, four PhD-level biostatisticians (appointed as Research Associates in the Department of Health Studies), and two bachelors-level computer programmers with experience in database design and 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.

Brain Research Imaging Center: http://3tmri.bsd.uchicago.edu The Brain Research Imaging Center (BRIC), located in the AMB, Q-300 suite of the Medical Complex, houses a research-dedicated Philips Achieva Quasar Dual 16 Channel 3T MRI scanner. The BRIC is co-directed by Dr. Gregory Karczmar (Radiology) and Dr. Jean Decety (Psychology). The 3T facility delivers cutting-edge whole-body imaging and spectroscopy with real time control of RF transmission, gradient switching, data acquisition and triggering. The 3T facility has the necessary auxiliary equipment for brain functional MRI (fMRI), including the devices for presenting visual and auditory stimuli to people undergoing fMRI scans and the devices for recording their behavioral and physiological responses. The 3T facility plays an important role in the work of a number of departments and crosses University Divisional boundaries with impact on both the Biological and Social Sciences. Associated with the 3T facility is an excellent group of researchers working to develop magnetic resonance imaging methods and apply them to the whole University research community.

Cellular Screening Cener: http://www.igsb.anl.gov/services/csc/ The Cellular Screening Center (CSC) is a high-throughput screening facility performssmall molecule and siRNA screens. It is directed by Dr. Geoffrey Greene and located in the Gordon Center for Integrative Science. The technology and expertise in all aspects of screening are an invaluable resource for high-throughput screening. Eight liquid handlers and three plate readers are implemented in the CSC, each with a defined role in the screening process. Five of these liquid handlers and all 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. Two network cameras are installed in the laboratory space for monitoring to aid in remote troubleshooting. Critical instrumentation is maintained by original manufacturer service engineers with preventative maintenance completed annually or semi-annually as directed by the manufacturer. CSC staff members perform regular quality control checks on the instruments. The entire laboratory is a clean room and all screens are performed in Class 100 space. All of the instrumentation is run by three well trained staff members. Dr. Siquan Chen, Scientific Director of the CSC, brings over thirteen years of assay development and high throughput screening experience. Mr. Samuel Bettis, Technical Director of the CSC, has worked for over twelve years in both industry and academia in high-throughput screening laboratories. He is responsible for the build, setup, and operation of the CSC. During the past eight years running the CSC he has overseen the success of dozens of high-throughput screens. The CSC has partnered with the Center for Research Informatics (CRI) at The University of Chicago to maintain CSC databases and integrate that information with the screening data. All of the data that is obtained from the three readers are automatically stored at a remote location where it is backed up nightly. This data is secure with each end user able to access their data through the CRI databases. The CSC has bioinformatic support to maintain the security of the data, the availability of data, and to aid in data analysis.

Cellular & Tissue-based Processing cGMP: http://osrf.bsd.uchicago.edu/facilities.php# 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.

Electron Microscopy http://tomocryo.uchicago.edu/ The Advanced Electron Microscopy Core Facility occupies over 2000 sq. ft in the Sub-Basement of the Gordon Center for Integrative Sciences (GCIS) and is directed by Dr. Benjamin Glick. The centerpiece of the facility is the FEI Tecnai F30 300kV Electron Microscope, and is supported by the recently added Tecnai Spirit 120kV routine Electron Microscope. The facility also operates a Bal-Tec high-pressure freezer, 2 freeze-substitution devices, an evaporator, 2 ultramicrotomes, a Fishione dual-axis high tilt tomography holder, 2 cryo-holders, 1 beta-tilt holder, pumping station, several 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 for transmission electron microscopy. All basic TEM sample preparation and imaging can be provided including, but not limited to: chemical fixation; tissue embedding; sectioning; immunogold-labeling; negative staining; and imaging. A special strength of the facility is that samples can be prepared by high-pressure freezing that allows rapid cryo-fixation of samples, eliminating the artifacts associated with traditional chemical fixation. These samples can then be imaged traditionally (60-100nm sections), but the samples can be processed (300nm sections) for accurate three-dimensional reconstructions with 5–7 nm resolution. This method is proving to be indispensable for understanding how molecular structures are linked to cellular architecture and function. Furthermore, our facility has the ability to perform elemental analysis using X-ray energy-dispersive spectrometry. Cutting edge technologies that are being integrated into the facilities routine services include, Correlative Light Electron Microscopy (CLEM), which allows users to correlate fluorescently tagged proteins to high resolution TEM structure. The second technique is Scanning Transmission Electron Microscopy (STEM) tomography. STEM-tomography would allow user to create 3D reconstructions with 5-7nm resolution with a sample thickness of 1-2 microns.