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University of Nebraska Medical Center
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Policies

Core Facility Resource Grant Insert 

The UNMC Biosafety Level 3 Core Facility provides a safe and secure resource for qualified researchers, to better understand Biosafety Level 3 Core Facility organisms and the associated infectious diseases for the improvement health outcomes. There are five well-equipped working suites available to authorized Principal Investigators and their associated staff on a first-come, first-served basis. This facility has many valuable features to meet the needs of the researcher. In addition, on-line scheduling via the UNMC Research Support System (RSS) is used to reserve working suites, facilitating the coordination of shared space and the monitoring of researcher usage and needs. 

The UNMC Biosafety Level 3 Core Facility is 1,392 square feet and located on the main UNMC campus. There are pass-through lockers and autoclaves, five well-equipped working suites, a biosecure corridor with ultra-low freezers and storage units, a donning/dressing anteroom, a doffing/exit room, personal lockers, and an additional secure room to ensure that autoclaved items are sterile. Each of the five working suites and the biosecure corridor have a preprogrammed phone that automatically dials the University of Nebraska Police and Public Safety Department (UNPPSD). The biosecure corridor has an emergency exit, eye wash station, overhead shower, hands-free sink, and a portable transfer device for an unresponsive individual. The doffing/exit room has a hands-free sink and a shower. There are air pressure and fire monitor/alarm systems, along with emergency backup lighting and emergency electrical outlets. Many features contribute to the biosafety and biosecurity of this facility and the researchers needs. 

Working Suites

Working suite B is equipped with a Zeiss LSM 900 Confocal Microscope that contains an Airyscan 2 Super Resolution Detector and four diode lasers, along with a dedicated air table and computer. This confocal microscope provides fast, high-quality resolution, and gentle imaging for multiplexing and live cell imaging. Additional features on this microscope and the associated software include the following.

  • 2 GaAsP High Sensitivity Detectors
  • Airyscan 2 Super Resolution Detector
  • 4 Laser Line System for 405 nm, 488 nm, 561 nm, and 639 nm
  • White light LED light source with DAPI, GFP, Cy3, and Cy5 filtersets for widefield imaging
  • Four Objectives: a Plan Apo 10x/0.16 Air WD 2.0 mm, a Plan Apo 20x/0.8 Air WD 0.55 mm, a Plan Apo 40x/1.3 Oil WD 0.2 mm, and a Plan Apo 63x/1.2 Oil WD 0.19 mm
  • Motorized XY Stage
  • Z piezo insert for fast acquisition of z-stacks
  • Incubation with controlled temperature, humidity, and CO2 for live-cell imaging
  • Zen Software
  • Acquisition Workstation
  • jDCV module for improved spatial resolution of Airyscan 2 data
  • Axio Cam 702 CMOS monochrome camera for widefield imaging

Each of the five working suites in the UNMC Biosafety Level 3 Core Facility are well-equipped with the instrumentation listed below for standard molecular microbiology and tissue culture procedures. In addition, each working suite has storage cabinets, ample benchtop surfaces, shelving, two carts, autoclavable tubs/containers, a clock, three non-cloth laboratory chairs, a stepping stool, and a spill kit with extra personal protective equipment (PPE). 

  • Annually Certified Thermo Scientific Class A2 or Baker Class A2 Biological Safety Cabinet 
  • Two Stacked Thermo Scientific Heracell VIOS 160i CO2 Humidified Incubator Chambers (165 L per electropolished stainless steel chamber)
  • Nor-Lake Manual Defrost Countertop/Stackable -20°C Freezer 
  • Nor-Lake Undercounter Refrigerator 
  • Thermo Scientific Sorvall Refrigerated Legend X1R Tabletop Centrifuge (maximum RCF: 25,000 to 25,999 x g) with 4 x 400 milliliter TX-400 Rotor, Microplate M-20 Rotor, and associated accessories (i.e., safety covers) 
  • Thermo Scientific Sorvall Refrigerated Legend Micro 21 Microcentrifuge with several rotors and associated safety lids 
  • Fisherbrand Analog Vortex Mixer 
  • Corning Minicentrifuge 
  • 5 Liter and 10 Liter Dual General Purpose Water Baths with 12 Liters of thermal beads 
  • Fisherbrand Research Grade Inverted Microscope with C-mount Digital Camera and associated software 
  • Dell Computer with Wi-Fi access 
  • Canon DR-C230 Scanner 

Biosecure Corridor

The biosecure corridor that is adjacent to the working suites has shared equipment and emergency items that includes two-pass through autoclaves, storage cabinets for extra supplies, a large foot-operated/hands free sink, an emergency eyewash and shower, a spill kit, a fire extinguisher, a portable transfer device for an unresponsive individual, and materials for sharp item cleanup, along with the following instrumentation. 

  • Thermo Scientific -150°C Cryogenic Storage Freezer with racks and storage boxes 
  • Two Thermo Scientific TSX Series Ultra-Low -80°C Freezers with racks and storage boxes 
  • Justrite Flammable Storage Cabinet 
  • Justrite Acid/Corrosive Storage Cabinet 
  • RCA Microwave (1.1 cubic feet, 1,000-watt power output with 10 power levels)
  • Several Backup Powered Air-Purifying Respirator (PAPR) Unit Batteries and Chargers

Services and Requirements

The UNMC Biosafety Level 3 Core Facility staff provides guidance and facility-specific training to Principal Investigators and their associated researchers that are interested in utilizing this facility. Annual testing is implemented to ensure competency in biosafety and biosecurity issues, as per institutional requirements. For additional details, please see the associated website for this facility or contact the Laboratory Director of the UNMC Biosafety Level 3 Core Facility. 

Acknowledgment 

If any manuscripts, presentations, and grants include data generated from the use of the UNMC Biosafety Level 3 (BSL-3) Core Facility, please include the following sentence in the acknowledgement section, which is important for continuation of this resource. 

‘The University of Nebraska Medical Center BSL-3 Core Facility is administrated through the Office of the Vice Chancellor for Research.’

The National Institutes of Health (NIH) provides guidance on acknowledgments. 

Rigor and Reproducibility 

Guide to Rigorous and Reproducible Research Data: 

  1. Consult with the Biosafety Level 3 Core Facility staff members in the planning stage, in order to properly prepare for safe, reliable, and reproducible experiments.
  2. Design all experiments with sufficient controls for rigor and accuracy, as well as have sufficient technical and biological replicates in independent experiments to verify reproducibility.
  3. Consult with a statistician if help is needed to develop a power analysis, in order to ensure that the results will be adequately powered.
  4. Ensure that all of your reagents (e.g., cell lines and antibodies) are fully validated. For antibody validation, always titrate and validate specificity.
  5. Key biological and/or chemical resources (i.e., cell lines, antibodies, specialty chemicals, and other biologics) should be addressed in the application’s authentication plan.
  6. Prepare a detailed protocol and document all steps, including reagents, equipment, and data analysis methods that were used in the experiment. Be sure to document any deviations.
  7. Have a data analysis plan that can be easily followed.
  8. Assure that the individuals performing the experiment are appropriately trained, as well as understand each step and the importance of performing them precisely, in order to ensure rigor.
  9. Use only well-maintained instrumentation and make sure that it is used properly, to prevent breakage and to not compromise an experiment. If in doubt on how to properly operate and maintain an instrument in the UNMC Biosafety Level 3 Core Facility, seek advice and/or obtain training with a Biosafety Level 3 Core Facility staff member.
  10. Store all documentation and data in a safe repository and be sure to backup this information. 

Consider Glenn Begley’s six rules for reproducibility shown below. 

  1. Were the studies blinded?
  2. Were all the results shown?
  3. Were the experiments repeated?
  4. Were the positive and negative controls shown?
  5. Were the reagents validated?
  6. Were the statistical tests appropriate? 

Additional recommendations to ensure rigor and reproducibility are available at the National Institutes of Health (NIH) websites. 

Data Management and Sharing 

Per the National Institutes of Health (NIH), "Regardless of the mechanism used to share data, each dataset will require documentation. Documentation provides information about the methodology and procedures used to collect the data, details about codes, definitions of variables, variable field locations, frequencies, and the like. The precise content of documentation will vary by scientific area, study design, the type of data collected, and characteristics of the dataset." The NIH provides an overview of their scientific data sharing policies, as well as information on the repositories that are available for sharing scientific data. 

Researchers are responsible for the data they collect, which should be immediately and initially transferred to a reliable location such as an appropriate Box or SharePoint account with ideally a backup location. To upload the data to a repository for eventual sharing, the UNMC bioinformatics core may be able to assist. Note that each repository has specific requirements with significant variability across data repositories. Also, the appropriate metadata needs to be populated by the Principal Investigator or associated researcher. 

The UNMC website includes information and resources for UNMC researchers to help prepare, create, and submit a data management and sharing plan with their NIH applications. Consultation with UNMC's Data Services Librarian is also available through the McGoogan Health Sciences Library. Since UNMC has an institutional registration for the DMPTool with UNMC specific templates, use UNMC single sign-on (SSO) to access this tool. 

For additional guidance on data management and sharing, see the Harvard Biomedical Data Management website.