Tim Bushnell, PhD
As the Director of URMC’s Shared Resource Laboratories, Tim Bushnell, PhD, serves as an ambassador for building the bridge between basic science research facilities and clinical scientists in order to drive clinical and translational research at the University of Rochester. The tools housed by the Shared Resource Laboratories give investigators at the University, as well as throughout New York State, the ability to conduct studies geared toward personalized medicine. When speaking of the Labs, Dr. Bushnell paraphrases an old BASF commercial, “We don’t make the science, we help make it better.”
What are Shared Resource Laboratories?
The Shared Resource Laboratories consist of a series of technologies, resources, and staff members that support investigators with their research. High-end tools, including the laser capture microdissection instrument in the Confocal and Conventional Microscopy Core; the Hi-Seq 2500 in the Rochester Genomics Center; and an analytical flow cytometer, image stream, cell sorters, and a CyTOF in the Flow Cytometry Core are used by hundreds of investigators every day.
“The shared resources represent the bridge between the questions that researchers are asking and the end product – be it a paper, be it a patent, be it something that improves the human condition,” Dr. Bushnell said. “We provide that scientific technical expertise because it’s very difficult for one researcher to be an expert in all the different tools.”
The Shared Resource Laboratories are made up of more than 20 facilities which house a variety of state-of-the-art instruments. Several of the more popular facilities include:
Confocal and Conventional Microscopy Core
Contact: Linda Callahan¸PhD
The Confocal and Conventional Microscopy Core assists researchers in attaining high quality imaging data through advanced microscopy instruments. The laser capture microdissection instrument, for instance, allows researchers to outline an individual cell in a sample, remove the cell from the sample using a UV laser, and process the cell for RNA, DNA, or proteomic profiles. The instrument can identify tissue using bright field microscopy or florescence microscopy.
Dr. Linda Callahan, Director of the Confocal and Conventional Microscopy Core, says investigators use the instrument to understand where cells are within affected tissue.
“[We can] dissect out different cell types from different tissues so we know exactly what the profiles are,” she said.
Rochester Genomics Research Center
Contact: John Ashton, PhD
The Rochester Genomics Research Center supports all aspects of genomics research at the University of Rochester, including studies in viral genome, HIV, microbiome, and general RNA expression. The Illumina Hi-Seq 2500 generates millions of sequenced data points that researchers can map to a human reference genome. Comparing this genome to disease-specific mutations and gene abnormalities is effective in the diagnosis and treatment of disease.
“What once took years and millions and millions of dollars to sequence the entire human genome, we can now get down to about five days and [a] cost of only about $1,000,” said Dr. John Ashton, Associate Director of the Genomics Research Center. “This is extremely powerful for research, as well as for personalized medicine.”
The Genomic Research Center collaborates with the Center for Integrated Research Computing on the UR River Campus, using the BlueHive and BlueGene Clusters to conduct data analysis.
Flow Cytometry Core
Contact: Tim Bushnell, PhD
The Flow Cytometry Core is a full-service facility offering a range of top-of-the-line digital flow cytometers, an image stream, cell sorters, and a CyTOF mass cytometer.
The analytical flow cytometer measures the physical and biochemical characteristics of cells both on the surface of cells and intercellularly.
“It’s important in clinical research, it’s important in clinical diagnostic work, it’s important in basic research,” Dr. Bushnell said. “Our tools are geared toward helping investigators identify the unique populations in a single cell suspension, be it from blood or bone marrow or tissue culture or any other sample we can put in a single cell.”
Cells identified by an analytical flow cytometer are represented as dots on a plot. In 1979, University of Rochester investigator Leon Wheeless published a paper that sought to combine the principles of flow cytometry with the ability to image and visualize the entire cell and its processes. The technical limitations of the time prevented the project from moving forward, but in the late 2000’s, Amnis, a company specializing in flow cytometry, made the idea possible when it released the Amnis Image Stream. The University acquired the instrument in 2006.
The technology of the analytical flow cytometer was combined with the technology developed to make inkjet printers to create a cell sorter: a tool that separates and purifies cells based on their surface characteristics. The cells moving through the sorter appear to be a solid stream, but they are actually a series of droplets. The cells can then be returned to the researcher at 99% purity for use in downstream work (culture, genomics, proteomics, etc.).
The Flow Cytometry Core is also home to the CyTOF, an instrument that combines the principles of flow cytometry with a detector from a mass spectrometer. This hybrid tool measures highly dimensional data to screen and characterize detailed intercellular pathways. URMC’s CyTOF was the seventh installed at a research institution in the United States. URMC acquired the instrument through a partnership within the UNYTE Translational Research Network and it is supported by an NIH shared instrumentation grant.
How can researchers access the services?
To schedule an initial consultation, investigators can call or e-mail the directors of the core facilities. During the consultation, the directors describe the correct tools investigators can use for their research, and the best practices for doing their experiments. Researchers are assisted through every step of the process, including sample preparation, utilizing the instruments to analyze the samples, interpreting the data, and then transforming the outcomes into a publishable form.
How much do the services cost?
“We drive the cost as low as possible for each investigator,” Dr. Bushnell says.
Rates for the services, which are subsidized by the University, are calculated based on cost recovery. Since individual resources have different pricing structures, Dr. Bushnell recommends investigators contact the core directors or visit the Shared Resources website.
Where can researchers find more information?
Click here for a video of Dr. Bushnell explaining the purpose of and how to use the Shared Resource Laboratories.