The Gladstone Histology and Light Microscopy Core is open to Gladstone, UCSF and the greater Bay Area science community. We provide excellent service, collaboration and support for many histological techniques, light microscopy and advanced imaging, image processing and quantitation.

Provides access and training on two FACS Calibur benchtop cytometers, one FACS Canto II multi-laser digital cytometer, one FACS Aria II cell sorter, one FACS Aria III cell sorter, and one Sony SH800 cell sorter. These systems are primarily used for the rapid analysis and sorting of single-cell suspensions. To analyze the light scatter and fluorescence characteristics of a cell population, one of the benchtop machines is appropriate. For more complex assays requiring more than four differentiating markers, then the high-end multi-laser Canto II system would work well. To rapidly retrieve or sort a particular sub-group of cells from a mixed sample, then a cell sorter would be required.

Core performs standard-of-care and advanced molecular testing for patients with cancer, and to provides special expertise in solid tumors. Services include targeted gene sequencing, microsatellite instability testing, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS). CCGL is staffed with board-certified surgical pathologists and board-certified molecular pathologists who can properly evaluate the quality of samples submitted for testing as well as make correlations between the pathologic diagnosis of a tumor and the molecular findings in the tumor.

Core includes instrumentation for structural biology with focus on cryo-electron microscopy. Used for imaging ranging from atomic resolution to whole cells, with emphasis on linking structural and dynamics information with biological functions.

The DEM Flow Cytometry Core offers instruments and training in flow cytometer operation and techniques. The core offers two BD LSRII analyzers with up to 17-color capacity, as well as a FACS ARIAII for fluorescent cell sorting. Both the analyzers and sorter are within BSL2 (or above) lab space to allow for analysis and sorting of infected human samples.

The Nikon Imaging Center at UCSF is equipped with several advanced microscopes. We have two super-resolution microscopes, three confocal microscopes, and three widefield systems. One of our super-resolution systems is a Nikon N-STORM microscope which is capable of PALM, STORM, and other variants of single molecule switching and localization microscopy. It is capable of 3-color imaging with up to 20 nm resolution in XY and 50 nm resolution in Z. This system is also capable of high-speed TIRF microscopy with frame rates > 100fps. The other super-resolution system is a Nikon N-SIM structured illumination microscope, which can produce images with ~100 nm resolution in XY and 350 nm in Z. This microscope can acquire four color images and can acquire a super-resolution image in ~2 seconds, so it can be used for live cell imaging.
Our confocal microscopes include a Nikon C1si laser-scanning confocal, capable of 3-color imaging and spectral imaging, and two 4-color spinning disk confocals optimized for video rate data acquisition from live cells. One of the spinning disk confocals is a CSU-W1 equipped with an sCMOS camera for imaging of large fields of view; the other is a CSU-22 with an EMCCD for imaging dim samples. One of our widefield microscopes is optimized for multi-day time-lapse imaging of live cells and one is optimized for five-color imaging (DAPI / FITC / Cy3 / Cy5 / Cy7). Our third widefield microscope is optimized for high speed multicolor Z-stack acquisition. This high speed microscope uses an Andor Zyla camera and is capable of acquiring 5.5 megapixel images at 100 fps, and can acquire multicolor and Z-stack images at this frame rate. This camera can also acquire smaller fields of view at higher frame rates (>1000 fps). It can also rapidly acquire large fields of view by image stitching and acquire data from multiwell plates rapidly. It is also equipped with photoactivation and photobleaching lasers for FRAP and photoactivation experiments. We also have color (RGB) image acquisition capabilities.
We have also developed a light sheet “Ultramicroscope” that allows imaging of cleared tissue samples up to 2 cm on a side, and has 1x, 2x, and 5x objectives, along with an 8x optical zoom system, allowing imaging resolutions from 20 m to 0.5m. Illumination is provided by a four line laser launch, with 405 nm, 488 nm, 561 nm, and 640 nm excitation. We have successfully imaged a number of cleared tissues with this microscope, including cleared mouse embryos, brains, spinal cords, and bone.
We have a full suite of image analysis tools available for data analysis, including Nikon Elements, Metamorph, Huygens, ImageJ/Fiji, Cellprofiler, and Matlab, and high power workstations (up to 8 cores, 128 GB RAM) for data analysis.

The Parnassus Flow CoLab assists investigators whose research requires molecular marker characterization of cells in suspension as well as the isolation of cells based on those markers. Advanced cell sorting and cytometric analyses by Flow or Mass Cytometry are conducted within the Core.

We provide services involved in generating new research models. These range from traditional ES cell targeting and transgenesis, to new genome-editing techniques such as CRISPR and TALEN. A full range of services is available, from training, consultation, and construct design, to targeting, genotyping, and post-targeting QC such as Southern blots to confirm single integrations.