Core Facilities

Administrative Core Facility

This Core facility is the administrative structure of the Liver Research Center. The activities include all scientific and administrative supervisory functions of the Center and its administrative leadership, including the organization and supervision of Core facilities, the planning and scheduling of the enrichment program and the review and oversight of individual pilot feasibility projects. All fiscal records and accounts for the Core’s Pilot Projects are fully computerized and analysis sheets are distributed electronically to principal investigators on a monthly basis. The Core provides administrative support for the Executive Committee (Drs. Boyer, Cheng, Flavell, Garcia-Tsao, Gorelick, Groszmann, Nathanson and Strazzabosco) as well as organizing and facilitating Liver Center seminars including visiting speakers and annual meetings of the External Advisory Board. Questions about this core should be directed to the Center Director, Dr. James Boyer (785-5279), Center Coordinator, Ann Thompson (785-5279) or Center Administrator, JoAnn Sullivan (785-5526).

Cellular and Molecular Physiology Core Facility

This Core facility is the “work horse” of this Center and is organized to provide technical expertise, equipment and personnel to Liver Center Investigators who wish to work with: a) Isolated cell preparations including: hepatocytes, cholangiocytes, endothelial cells, stellate cells, portal fibroblasts and hepatic lymphocytes, primarily from rat and mouse. Recently human hepatocytes have also been obtained. b) Cell culture facilities for short and long term cultures and cell lines. c) Isolated liver perfusion preparations for studies utilizing the whole organ. d) Gene expression using Quantitative real time PCR machine or e) Altering gene expression in these cells and tissues using siRNA transfection and adenovirus infection technologies. f) The Center also provides access to Animal Models of Disease: Expertise is available for the use of rat and mouse animal models of Cholestatic liver disease (bile duct ligation, estrogen administration, LPS administration) and fibrosis and cirrhosis (bile duct ligation, CCL4 and Phenobarbital administration, Schistosomiasis). By centralizing these procedures in a Core facility, investigators are assured of a high degree of quality control and preparations can often be used simultaneously by more then one investigator.

1. Cell and Isolation and Organ Perfusion Component
   This facility isolates hepatocytes and non-parenchymal liver cells, including bile duct cells, Kupffer cells, Ito cells and endothelial cells from rats and mice, maintains rodent and human hepatocytes in short term collagen sandwich cultures and maintains long-term cultures of cell lines including HepG2, WIF2B, COS-7, and SKHep1 cells. The facility also performs isolated liver perfusions, including normal, cirrhotic and cholestatic livers. To use this facility, Liver Center investigators should contact Kathy Harry (x5-3151) for isolated cell preparations or for perfused liver preparations. New investigators should first contact the Core's Director, Dr. Boyer (x5-5279).
2. Molecular Biology Component
   This component includes a) A Quantitative measurements of mRNA by real time RT-PCR (ABI 7500 real time thermal cycler). b) A Fotodyne Imaging Workstation: This new instrument uses a CCD camera to photograph gels and blots in either transmitted white and UV light or reflected white light modes. Interested individuals should contact Dr. Boyer (x5-5279). c) BioTek Synergy 2 Multi-Detection Microplate Reader: This newly acquired equipment provides fluorescence intensity, time resolved fluorescence, fluorescence polarization, glow and flash luminescence, UV-Vis absorbance, FRET, TR-FRET, BRET, area scanning, and spectral scanning. d) Interfering RNA (siRNA transfections) and 3.4.4 Adenovirus infection. e) Generation of pooled RNA and protein samples from well characterized experimental models and controls. f) Access to the Keck Biotechnology Resource Laboratory: The Keck Biotechnology Resource Laboratory provides state-of-the-art biotechnology resources throughout the University. Molecular Sequencing and primer construction are common facilities available to all Yale faculty. The Keck facilities also include advanced biostatistical resources, microarray facilities, and a dedicated proteomics core that are cost-shared with this Center.

Morphology Core Facility

The Morphology Core Facility provides instrumentation and technical expertise for the preparation, acquisition and analysis of images of cells and tissues at both the light and electron microscopic level. Given the cost of such instrumentation and the high level of technical expertise required to perform these investigational techniques, this Core was established to ensure the availability of these techniques for Center members. In recognition of the broad usefulness of this Core facility, the School of Medicine has partnered with the Liver Center by making ongoing, major investments to ensure that the facility remains state-of-the-art.

The Core has two confocal microscopes, plus a combined confocal and two-photon microscope (see below). Both of our conventional confocal microscopes are Zeiss LSM 510 laser scanning microscopes. Both have three fluorescence detection channels, and one also has a meta-detector. The Core maintains four epifluorescence microscopes, a fluorescence dissecting microscope, and two spectrometers for fluorescence measurements in cell populations. Two-photon microscopy: This component consists of a Zeiss LSM 510 NLO combined confocal and two-photon microscope, plus a SpectraPhysics MaiTai titanium: sapphire laser for two-photon excitation. An Electron microscopic facility includes a Tecnai 12 Biotwin and a Phillips 410 electron microscope. Routine transmitted electron microscopy techniques are available by request. The Core maintains three microscopes for video microscopy, two of which also are used for epifluorescence work for imaging single cells. The facility also co-sponsors a short course on confocal microscopy which is offered periodically for interested users. Interested investigators should contact Dr. Michael Nathanson or Mr. Al Mennone (x5-7312) for access to the confocal microscope, EM or other light microscopic equipment.

Clinical Translational Core

The overarching goal of the Clinical Core is to facilitate translational and patient-oriented research. The Clinical Translational Core aims to develop an infrastructure for patient-oriented research by streamlining regulatory compliance, attaining high-quality samples linked to large clinical phenotypic information through integration of diverse databases and, innovative application of statistical tools. The following specific resources represent the foundation of the Clinical Translational Core of the Liver Center:

• A Clinical Core Research Coordinator with particular expertise in effectively addressing NIH, IRB and HIPAA policies and reporting requirements concerning confidentiality, inclusion of women, children and ethnic/minority participation in clinical studies, data and safety monitoring requirements; and to ensure the protection of human research participants. In addition to being in charge of ensuring that all regulatory requirements for Liver Center protocols are met, the coordinator trains Liver Center staff and/or study coordinators on the requirements and best practices so that compliance can be maintained. This ensures that all Liver Center clinical studies follow local and federal guidelines.
• Liver Center Clinical Registry that consists of 1) Patient Databases, that include a prospective database of patients attending the outpatient liver clinics at Yale and the CT-VA Healthcare System (that is referred to as the Patient Registry of the Clinical Core or PaRCC). Patients in the PaRCC have given specific consent to be contacted for possible participation in future clinical studies and most of them have also consented to provide samples for the serum and tissue bank (SaRCC). Other liver disease-specific databases available to Center members include those of patients with compensated and decompensated cirrhosis, acute-on-chronic liver failure, hepatitis C, hepatocellular carcinoma (HCC), autoimmune liver disease and inherited metabolic liver diseases (Gaucher and Wilson disease). 2) The Serum and Tissue Bank that is referred to as the Sample Registry of the Clinical Core (or SaRCC) and currently consists of frozen samples of serum and EDTA plasma (for DNA) obtained from patients included in the PaRCC. It also consists of liver biopsy slides and paraffin blocks stored at the Pathology Departments of both Yale and the VA. Both the PaRCC and the SaRCC are linked and maintained by the Clinical Core Research Coordinator with the objective of providing Center members with data regarding numbers of patients with specific diagnoses seen at the Center in a defined period of time to assess the feasibility of a specific study, contact patients for participation in a study and provide serum/tissue samples for use in research. The Clinical Core has also established collaboration with the Yale Center for Clinical Investigations (YCCI) through its Biorepository Core that is responsible for the processing, storing and tracking of blood and tissue samples through the Clinical Core, as well as maintaining the database for the samples in storage.
• A Biostatistician that provides assistance to basic researchers with clinical study design, particularly for small pilot projects that are the initial step in the translational process. For established clinical investigators using the clinical component, this resource provides consultation for clinical study/trial development particularly in establishing sample size calculations and advice regarding the most appropriate study design. Furthermore, biostatistical analysis of patients already in liver disease-specific databases continue to provide new insights into the natural history of these heterogeneous disorders.

Investigators interested in using the Clinical Translation Core services should contact the program coordinator, Michele Antisdel at 932-5711, ext 2228 or michele.antisdel@yale.edu.