Services
The Scientific Core for Animal Modeling and Telepathology is designed as a collaborative core that will be coordinated by the Core Leader and administrative staff at the CCM (in concert with the PSW RCE Administrative Core at UC Irvine). The budget provides Core support for faculty, technical staff, and administration, but other costs incurred by current and future projects will be covered on a fee-for-service charge-back basis to the various projects. The Core will facilitate access to a broad array of existing core laboratories and services at UC Davis with already-established fee structures.
Histopathology Laboratory Service
Expertise:The UC Davis Center for Comparative Medicine and Mouse Biology Program has provided international leadership in the area of mouse pathobiology over the past decade. This program manages the UC Davis Mutant Mouse Regional Resource (funded by NIH/NCRR) and in this context Drs. S. Barthold, R. Cardiff, A. Borowsky and S. Griffey contribute to a critical mass of expertise in mouse pathobiology.
Histopathology services:
The Mutant Mouse Pathology Laboratory (MMPL) is a full service research histotechnology and immunohistochemistry (IHC) laboratory. The Laboratory specializes in optimizing IHC for use in mouse tissues. This task is more difficult for mouse tissues than other animal tissue sources because many of the best antibody reagents are monoclonal antibodies developed in mice/mouse cell lines. Standard secondary antibodies against mouse immunoglobulin for IHC detection in mouse tissue is highly prone to background non-specific staining. Two approaches for working around this problem are to (i) use non-mouse primary antibodies and (ii) block endogenous immunoglobulins prior to primary antibody incubation. The MMPL is highly experienced in both techniques and has optimized a comprehensive list of antibodies for IHC specifically on mouse tissues. In addition to mouse tissues, the laboratory is experienced in handling a wide variety of species, including the capacity for using human tissues under IRB approval, usually with patient identifiers removed from the specimens. Additional techniques which have been used in the laboratory include: histochemical detections such as beta-galactosidase detection; organ or whole animal whole mount preparations; In Situ hybridization (ISH) for message RNA detection; laser capture microdissection and tissue array preparations using the Chemicon Semi-automated tissue arrayer. Pathology can be submitted directly to the MMPL via the Pathology request form.
Whole slide imaging
The MMPL uses a novel technology to produce images of an entire histopathological specimen (Whole Slide Imaging - WSI). ScanScope®, (Aperio® Technology) is a new type of digital slide scanner that scans a microscope slide in 3 to 5 minutes capturing 8 to 20 gigabyte images at 50,000 dpi. Images are then compressed (1:20), processed, and stored for presentation (see below). Thus far, we have produced more than 2000 whole slide images using the ScanScope system(http://imagearchive.compmed.ucdavis.edu/). We have co-developed a Flash6-based browser with Zoomify® that compresses and presents the 8 to 20 gigabyte images using a multi-layer wavelet JPEG format with compression ratios reaching 20:1 without significant image degradation.These images can be viewed locally or from a web server (see below). Unlike standard web-based still images, which must be downloaded for viewing within a browser, Zoomify-processed images are viewed directly from the web. Because the images are acquired at their maximal resolution, "lower" magnification views of an image are constructed by the server/viewer at the user's request. This software allows the viewer to move around the slide image at any magnification as if they were sitting at a microscope. The browser by Zoomify (Zoomify.com) has customized "smart client" software that displays and "zooms" all of the existing image formats, in a rapid and user-friendly manner. Using the combination of ScanScope system and Zoomify browser, entire slides are captured and processed (up to 20 gigabytes) in less than 20 minutes. Zoomify also provides "hot spot"-based annotation for the images, thereby allowing better representation and illustration of whole slide images. IP voice-over has now been coupled with the browser in the conferencing module to enable multi-user web-based conferences (see below).
Recharge system for histopathology and slide imaging services
The laboratory has established a recharge price structure within the University of California. This system is reviewed and updated annually. The recharge structure allows research groups to pay for both technical services and expert professional consultation as needed for the project goals. The recharge structure includes all aspects of histopathology, whole slide imaging, and patholoogy informatics support. Additionally, recharge pricing for new assay development, and for training of outside personnel in the MMPL, are established. The Laboratory employs a full time experienced laboratory manager and two full time employees. Additional technical expertise is available through part time employees of the laboratory with expertise in specialized aspects of histopatholoigic analysis.
Multiplex microbead detection systems
An important capability of the Animal Modeling and Telepathology Core is the multiplex microbead assay system, based on the flow cytometer and software of Luminex (Austin, TX). This system enables simultaneous detection of multiple analytes in an efficient, sensitive, and specific fashion. Previously, the Core has used the Luminex technology to detect antibodies to multiple infectious agents in a single serum sample (mice and nonhuman primates). A major current focus of the multiplex studies in the Core has been directed at the analysis of nonhuman primate immunomodulators (cytokines, chemokines) for assessing host responses to infectious pathogens. Several commercial vendors (Millipore-Linco, BioRad, InVitrogen-BioSource) provide multiplex panels for sensitive detection of numerous mouse and human cytokines and chemokines. In anticipation of the need to measure these immunomodulators in studies in nonhuman primates infected with various pathogens, the Core has tested the cross-reactivity of the commercial panels for detection of cytokines and chemokines of rhesus macaques at the California Primate Center. Accordingly, the Core now has the capability to analyze multiple immunomodulators of innate and adaptive immunity in pathogenesis and vaccine studies of various infection pathogens in macaques.UC Davis Mouse Biology Program
The UC Davis Mouse Biology Program (MBP) is a center of excellence that is based at the CCM to support scientists at UC Davis as well as the nation, with growing international linkages. This Program provides investigators with molecular construct design and strategy, construct preparation, microinjection, assisted reproduction techniques, cryopreservation, infectious disease diagnostics and surveillance, genotyping, comprehensive immunologic, physiologic, and pathologic phenotyping, bioinformatics support, and colony management and distribution. The UC Davis MBP hosts one of three NIH/NCRR-supported Mutant Mouse Regional Resource Centers, and participates in the NCI-sponsored Mouse Models of Human Cancer Consortium. Expertise and capabilities of the MBP insure immediate access of RCE investigators to a well-coordinated nationwide distribution network with international linkage for sharing of mouse models and related resources, and provision of genetically- and microbially-defined mouse models. Accordingly, the MBP can assist RCE and non-RCE investigators by creating virtually any type of genetic alteration in any desired strain of mouse, but can also provide investigators with access to a large and rapidly growing archive of existing mutant mouse lines. A particular strength of the CCM and the MBP is their combined expertise in comparative (veterinary and medical) pathology of genetically altered mice and infectious disease.The Mutant Mouse Pathology Laboratory (directed by CCM member R. D. Cardiff, MD, PhD) receives referrals from all over the world (over 200 scientists in 8 different countries, with over 1,000 accessions per year, and an archive of 11,000 cases representing over 200 mutations). CCM hosts several faculty members who span both medical (Drs. Cardiff, Borowsky and Galvez) and veterinary (Drs. Barthold and Griffey) pathology with specific expertise in the laboratory mouse. Dr. Cardiff is a renowned cancer biologist with expertise in transgenic mouse pathology. He serves as Chair of the Standing Committee for Pathology and Laboratory Medicine of the NCI Mouse Models of Human Cancer Consortium. Dr. Barthold, in addition to his interest in infectious disease research, is also an internationally-recognized authority on biology and pathology of laboratory mice. This unique blend of medical and veterinary perspectives, fostered by the CCM, is critical to accurate phenotypic interpretation and validation of phenotype as models for human disease. Expertise in mouse pathology is difficult to find, but the CCM and UC Davis MBP offers nearly 100 years of collective mouse pathology experience through its pathology group, with nearly equal experience in experimental pathology of murine infectious disease models. The laboratory, directed by Dr. Borowsky, has a technical staff composed of three experienced technicians and offers services in routine histology, morphometrics, special stains, immunohistochemistry and in-situ hybridization. In addition, Dr. Galvez serves as the Director of the Department of Pathology Electron Microscope and Digital Imaging Laboratory, so that its specialized equipment is readily available to the RCE.
The California National Primate Research Center at UC Davis
The California National Primate Research Center (CNPRC) is a unique scientific resource for investigators conducting basic and applied research on non-human primate models of human disease. With more than 40 years of experience in primate research and husbandry, the CNPRC offers specialized facilities, highly trained professionals and support staff and comprehensive diagnostic and laboratory services. The AAALAC-accredited CNPRC is part of a national network of eight primate centers sponsored by the NIH/NCRR. Co-located with the CCM on 300 acres at UC Davis, the CNPRC houses approximately 5,000 monkeys. The majority of the monkeys are rhesus macaques (Macaca mulatta), with small populations of South American titi monkeys (Callicebus moloch) and cynomolgus monkeys (Macaca fascicularis). The Center's facilities include animal quarters (including ABSL-2 containment for non-human primates), nurseries, animal hospitals, a computer facility, a seminar hall, conference rooms, offices, research service cores, and research laboratories. As with the exceptional depth of expertise in mouse biology at CCM, the CNPRC has strong diagnostic and experimental pathology support for research using non-human primate models. The Morphology Core of the CNPRC provides gross and microscopic pathology support, electron microscopy support, imaging, photomicroscopy, etc. Telepathology expertise in the CCM is currently being linked to the CNPRC. The CNPRC is currently renovating and updating a ABSL-3 containment facility for housing infected monkeys.Research at the CNPRC is broad-based, but areas of particular relevance to the RCE are infectious disease, immunology and respiratory disease. Notably, the Center is currently accommodating NIH-sponsored research in a number of infectious diseases, including SIV/HIV, measles virus, respiratory syncytial virus, influenza virus, cytomegalovirus, herpesviruses, Helicobacter spp., Borrelia burgdorferi, and Salmonella. These efforts have stimulated the development of primate-related core service support, including the Immunology Service Core, which provides rhesus-specific analysis of humoral and cellular immune responses. This core processes blood, mucosal and lymphoid tissue for analysis, and can quantitatively assess humoral immune responses through ELISA for IgM, IgG, IgA or IgE, and perform antigen-specific assays. The core performs lymphocyte proliferative assays, using standard mitogens as well as specific antigens of interest. The laboratory also performs cytotoxic T cell assays through customized transformation or infection of appropriate target cells with the agent of interest. For example, assays are available for SIV, SHIV (HIV env), measles, HSV-2 and CMV. In addition, the core has developed cytokine/chemokine ELISPOT assays for cells secreting IL-2, IL-4, IL-6, IFN gamma, MIP1 beta, TNF beta (lymphotoxin) and RANTES. These assays can quantify specific cytokine-secreting cells in a lymphocyte preparation by limiting dilution. These assays are intended to supplement direct cytokine measurements that can be performed with using commercially available kits for human cytokines. Like the CCM, the CNPRC is engaged in development of new assays that serve the needs of scientists utilizing the primate resource, including ELISAs for antigen-specific IgA responses in dilute samples of mucosal secretions and low-level serum antibodies, mixed lymphocyte reaction (MLR) assays for MHC-typed monkeys for adoptive immunotherapy protocols, and DNA microarrays for characterizing T-cell responses in nonhuman primates.
UC Davis Center for Vector Borne Diseases
The mission of the University of California Center for Vector Borne Diseases is to advance the study of endemic/enzootic and emerging vector borne diseases through cooperative research, service and training. The Center arose when the Arbovirus Research Unit moved from the School of Public Health at Berkeley to the Veterinary School at Davis, and was expanded to include faculty with interests in vector borne diseases from the Veterinary School, Medical School, College of Agricultural and Environmental Sciences, external University of California campuses, and agencies such as the California Department of Health Services. Many Category A-C agents are maintained and transmitted in nature by a variety of blood-feeding arthropods. To fully understand the biology, transmission, pathology and disease threat posed by vector-borne microbes, it is often necessary to carry out experiments that utilize vector exposure. Blood-feeding arthropods are often difficult to colonize and maintain.The Scientific Core for Animal Modeling can coordinate access to such arthropod colonies for RCE research. Currently available colonies of vector arthropods at UC Davis include Ixodes pacificus, Ixodes scapularis (tick vectors of Borrelia, Anaplasma, Babesia, Bartonella, et al.), Pediculus capitus, Pediculus humanus (louse vectors of Rickettsia prowazekii), Ctenocephalides felis (flea vector of Bartonella, Rickettsia typhi, Yersinia pestis, Francisella tularensis), Lutzomyia longipalpis (sand fly vector of Leishmania, Borrelia), Phlebotomus papatasi (sand fly vector of Leismania), and several species of mosquito, including Anopheles gambiae (vector of Plasmodium spp.), Aedes aegypti and Aedes albopictus (vectors of hemorrhagic fever viruses), Ochlerotalus dorsalis (vector of WEE and SLE viruses), Culiseta melanura (vector of EEE and WN viruses), Culex p. pipiens, Culex p. quinque, and Culex tarsalis (vectors of WN, SLE, EEE, WEE, and/or Rift Valley Fever viruses). In addition, faculty in the Center for Vector Borne Diseases have animal use permits to maintain, for experimental purposes, breeding and non-breeding colonies of wild species of rodents and birds which are natural or surrogate hosts for several different human pathogenic viruses and bacteria.
Telepathology
The Animal and Modeling and Telepathology Core continues to strengthen and expand its capabilities and web applications for telepathology. Capabilities for whole slide imaging: We have added functionality to better link our services as well as better serve our clients though the web site. During the past year, Aperio Technologies whole slide images were fully integrated into our collaborative telepathology server, allowing us to easily serve whole slide images based on both Zoomify as well as Aperio. We have continued to strengthen our commitment to bring true Z-plane focus ability to our telepathology clients, and have several pilot projects aimed to explore the limitations of Z-plane focus within a whole slide image. Standardization of fixation for histopathology analysis: We have developed image standardization by focusing on the variable which can greatly affect image quality. Specifically, a microwave based fixation protocol has been tested to achieve standardized and shortened fixation times. A large study will be done to evaluate the effect of microwave energy in fixation across multiple tissues, as well as its use as a post-fixative. Expansion of server space: During the last year, our network capabilities were expanded by adding an additional terabyte of dedicated drive space. This significantly expands telepathology capabilities.Our information retreval system for pathology laboratory information is being developed as an online resource for collaborators and clients. In addition to being our own information system online, we have worked very closely with the caBIG community (NCI), specifically with the pre-clinical trials group caELMIR project. caELMIR (http://caelmir.compmed.ucdavis.edu) is an electronic laboratory management information retrieval system, which will be available to the scientific community shortly. The caELMIR system enables easy storage and recording of all of experimental data in a single distributed database and thus enhances the ability to share experimental data, while still maintaining a high level of security for sensitive or unpublished data. Web tool for comprehensive online collaboration and conferencing: In addition to the well established whole slide image collaborative tool, we have recently added the ability to conduct real-time virtual meeting using Adobe's Breeze communication platform. By utilizing the conference capabilities of this platform, our users are able to conduct remote conferences with voice and video as well as share desktop application. These new capabilities not only enable sharing and discussion of pathology via whole slide images, but also any other type of scientific media can now be viewed in a collaborative conference allowing for a much richer scientific exchange.
