Tumor Microenvironment Network (TMEN) »  TMEN Research »  Cores »  Quantitative Core

 Quantitative Core

Johnathon Lakins, PhD

Investigator, Leader of Quantitative Core 

Quantative Core Picture

Introduction to the Quantitative Core:

The primary goal of the Quantitative Core is, firstly, to provide specialized equipment for the measurement of the mechanical properties of cells and the cellular microenvironment.  Secondly, the Core aims to offer centralized expertise in the experimental approaches to studying the cellular responses to mechanical inputs, ranging from the molecular level at the cell extracellular matrix interface to cell- and tissue- level biochemical responses in 2-D and 3-D synthetic and natural organotypic cultures. This expertise will include consultation and training for both Core personnel and industry specialists in the use of Core equipment and analysis of experimental results. Core expertise will also entail the development of new approaches and extend existing experimental and computational capabilities in response to the unique problems posed by new pilot projects.  The decision to organize this Core around the UCSF Department of Surgery Center for Bioengineering and Tissue Regeneration is a recognition of the wealth of expertise and specialized instrumentation in this area of study available within the Center and the need to make this more readily  accessible to investigators with intersecting research interests. A Core website describing objectives, equipment, capabilities, protocols, and useful links, as well as an online training component, will aid in disseminating information on Core services. 

The organizational structure and interaction of the Quantitative Core with the rest of the UCSF TMEN Brain Cancer Center and other core facilities at UCSF is shown in the adjacent flow diagram. An Executive Committee will work closely with the Core Director, Valerie Weaver, PhD, to set priorities and requests for pilot projects. The daily operation of the Core will be overseen by the Core Manager, Johnathon Lakins, PhD. Dr. Lakins will also serve as the primary interface with other centralized cores at UCSF and in the Bay Area for projects deemed to require additional or complementary equipment and expertise. The Quantitative Core will build upon the already extensive collaborations that the Center for Bioengineering and Tissue Regeneration has developed with the Nano Fabrication Core, Biological Imaging Development Center (BIDC), and Nikon Imaging Center (NIC) at UCSF, and the Integrative Cancer Biology Program (ICBP) at Lawrence Berkeley National Laboratory (LBNL).

In addition to equipment for molecular biology and protein biochemistry, the Quantitative Core facility has one room equipped with a chemical fume hood for biomaterials synthesis and development and two rooms dedicated to quantitative imaging. Specialized equipment includes an AR 2000ex rheometer; two inverted widefield epiflourescent microscopes; an Olympus IX81 with Spot Color Camera; a computer (NIS Elements)-controlled, air table-rmounted Nikon TE2000-U with heated environmental chamber, CO2 control, automated stage, and Roper Cool Snap cooled CCD camera for Traction Force Microscopy and live cell imaging; an Asylum Atomic Force BioScope II with transmission and epifluorescence optics and attached nanoindentor mechanically isolated on a Herzan TS-140  antivibration table, which is located in an acoustic isolation hood for cell, tissue, and biomaterial high-resolution rheological mapping; and a Tissue Growth Technologies compression force bioreactor for applying static and dynamic compressive forces to tissue constructs. Arriving in December 2011 will be an Andor spinning disc confocal microscope configured for live cell imaging and in the Spring 2012 this will be augmented with a Mosaic system for high spatiotemporal spot illumination for photoconversion and ablation experiments. Core participants will also have unrestricted access to a Zeiss Laser Scanning Confocal Microscope. Moreover, within the Biological Imaging Development Core (BIDC),, there is a custom-built 4-channel, 2-photon microscope configured for live and fixed sample deep imaging to which Core members will have access. The Core also jointly owns an Objet30 3-D Printer.

For computation, the Quantitative Core has multiple PC computer stations with standard commercial communication and image and word processing software. All PC stations have dedicated storage space and are networked to the UCSF Department of Surgery server, as well as to a high-capacity (8 Terabyte) storage system from Drobo Robotics, Inc., that is shared only within the Core. In addition, the Core has a Dell precision T5400 configured as an offline high-speed data intensive analysis workstation with dual quad core Intel Xeon processors (X5450, 3 GHz), 8 Gb RAM, 15K SAS drives in RAID 0 configuration, and NVIDIA FX1700 3D graphics card. The Dell precision T5400 is also equipped with commercially available software, highly optimized math libraries for science and engineering applications in Windows and Linux environments, and custom-built application specific analysis software. The latter includes the LIBTRC-2.0 software for calculation of force vector fields from traction force microscopy images; and Core-developed software for the rapid extraction of elastic moduli from AFM force-distance indentation curves and computation of fluorophore height information from scanning angle-fluorescent interference contrast microscopy images. All major equipment is under control of a dedicated PC running the appropriate instrument specific software.

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