Overview of the Molecular Mechanisms Core: During the past five years of the NORC grant period major changes in the Molecular Mechanisms Core have occurred. These changes represent improvements occasioned by the introduction of major technologies in genomic analysis and in bioimaging, cell sorting and traditional histology. To accommodate these changes and to provide more services to more scientists, we have simplified the organization of the leadership to provide more funds for technical personnel who will establish the technologies in each subcore. We monitored Core service usage during this period and based on low levels of use, we eliminated the cell culture service. This allowed us to reallocate resources and to expand the Cell Signaling Service, now named the Cell Biology and Bioimaging Subcore. These changes are described in more detail below. Objectives of the Genomics Subcore: To perform DNA sequencing and fragment analysis service including bi-sulfite sequencing and standard sequencing of a broad range of DNA types To offer quantitative PCR instruments for cost effective shared use with support for experimental design, instrument and software use, and data analysis To offer full microarray analysis service including experiment consultation, RNA quality control, labeling of RNA, hybridization of microarray chips, scanning, and data production To provide next-generation sequencing including consultation for experimental design, grant writing support, library creation service or assistance, instrument run, and data analysis To provide high-throughput robotic pipetting for quantitative PCR and custom pipetting projects To offer instrumentation for western blot analysis including in-cell westerns of tissue cultures To offer the Seahorse XF24 Extracellular Flux Analyzer, an instrument that simultaneously measures the two major energy yielding pathways - aerobic respiration and glycolysis as a shared instrument To provide access to appropriate software analysis solutions for primer and probe design, sequence alignment, and data analysis for microarray and next-generation sequencing To develop new methods and protocols for analysis of gene expression including next-generation sequencing, quantitative PCR, microarray analysis, and DNA sequencing To provide instrumentation and expertise for quality control and accurate quantitation of RNA and DNA templates To reduce nutrition research-related costs by providing centralized genomics services and consultation at a fraction of the cost for commercial services or of maintaining instruments in individual investigators' laboratories. To provide training to principle investigators, research associates, post-doctoral researchers, and students in principles of DNA sequencing, quantitative PCR, RNA and DNA quality analysis, and next-generation sequencing To organize and make available training provided from outside sources To provide on-line and print educational and resource materials to increase institutional knowledge and speed the learning process to enhance the time required from experimental concept to data production and analysis To develop new collaborations for data analysis with Dr. Allison's group at UAB. Objectives Cell Biology and Bioimaging SubCore: To provide training on the proper use of our imaging, histology, and analytical flow instrumentation to any PBRC researcher or their staff at no charge To make high-end imaging, analytical, specimen preparation, and histological instrumentation accessible to the PBRC research community and to ensure the instrumentation is well maintained and operational to the best of our ability To provide consultation services as well as collaborate on specific scientific projects that make heavy use of CBBC equipment when possible To develop new methods or modify current techniques to increase the research potential of our imaging and analytical instrumentation To provide access to the necessary software for data analysis and assistance in its use for specific projects To make specific protocols, instructions for instrument use, links to free software for analysis, and relevant scientific articles relating to our instrumentation easily accessible to all via our web site To develop and offer high speed cell sorting capabilities to PBRC researchers To provide continued support for the development of CBBC staff skills through training via external or internal courses and/or scientific meetings
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