VERMONT INBRE: LEAD INSTITUTION CORE

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. UVM DNA Microarray Facility: Activities/Highlights Services Offered: -Consultation on experimental design in collaboration with the Bioinformatics Core Facility -Gene Expression Profiling -target preparation -eukaryotic and prokaryotic -single and double amplification -Nugen based target preps for low RNA targets, i.e., LCM, cell sorting -Hybridization and scanning -DNA Mapping target preparation -Exon Array target preparation -RNA Integrity assessment -Nucleic Acid quantification -RNA extraction assistance and training -SOP's established for all services offered Scientific or technical changes: -Purchased MP Biomedicals Fast Prep 24 system. Developed and optimized methods to homogenize difficult tissues through addition of novel abrasives allowing minimal to no RNA retention. -Purchased another NanoDrop Spectrophotometer and placed in common equipment room for access to qualified users nights and weekends. -Updated to Expert software on Agilent 2100 Bioanalyzer for precise quantification of low recovery targets and ascertainment of relative index numbers to qualify samples for downstream RNA analysis. -Assessed affect of freeze thaw cycling on RNA and cDNA. Presented study at national meeting (ABRF) -Collaborating with the Bioinformatics Core to streamline online ordering of services, data dissemination, and data archiving Professional Development: Staff attended and participated at the following meetings: -Tim Hunter and Scott Tighe: Affymetrix Core Lab Meeting, New Orleans, Feb, 2008 -Tim Hunter and Scott Tighe: Association of Biomolecular Resource Facilities, Feb. 2008 Salt Lake City, UT -Tim Hunter and Scott Tighe: Northeast Regional Life Sciences Core Directors Meeting, Nov. 2007, Cornell University, Ithaca, NY Facility Promotion: -Hosted Open House, June 15, 2007. Over 150 attendees -Provided Workshop on sample requirements and handling for a successful array experiment -Hosted Technology Seminar, "miRNA Profiling using miSCRIPT", March 14, 2008, Dr. Debbie Consiglio, Senior Technical Specialist, Qiagen -Hosted Technology Seminar, PCR Arrays: Focus on your Pathway with qRT-PCR", Jan. 17, 2007, Dr. Tim Steppe, Application Specialist, SuperArray. Facility Presentations: Invited Speaker: -Tim Hunter, Northeast Regional IDeA States Meeting, Aug., 2007, Burlington, VT, Core Directors Workshop, "Best Practices: Core Operation and Management" -Tim Hunter, Northeast Regional Life Sciences Core Directors, Nov., 2007, Ithaca, NY, Meeting Organizer -Tim Hunter, Northeast Regional Life Sciences Core Directors, Nov., 2007, Ithaca, NY, Moderated roundtable discussion on trends in Real-Time Quantitative PCR -Tim Hunter, Association of Biomolecular Research Facilities, Feb., 2008, Salt Lake City, UT. Session Organizer for Nucleic Acid Research Group Study: "A Comparison of Different Priming Strategies for cDNA Synthesis as Measured by Real-Time RT-qPCR" -Scott Tighe, University of Vermont, VCC DNA Analysis User Educational Seminar Series, Jan., 2008 "Nucleic Acid Extractions: Best Approaches" -Tim Hunter, University of Vermont, Mastering the Maze, March, 2008 "Science in the Community: Reaching out with Outreach" Invited Interview: -Tim Hunter, "Real-Time PCR: Staying Power", J BioTechniques, Vol.44, No.2, Feb., 2008 Meeting presentations (Poster): -Scott Tighe and Tim Hunter, Northeast Regional Life Sciences Core Directors, Nov., 2007, Ithaca, NY, Vermont Genetics Network Microarray Facility -Scott Tighe and Tim Hunter, Association of Biomolecular Research Facilities, Feb., 2008, Salt Lake City, UT, Presented poster "Assessing the Affect of RNA and cDNA Freeze-Thaw Cycling on Gene Expression using Microarray and RT-qPCR" Outcomes: Publications: Lu, C., Pelech, S., Zhang, H., Bond, J., Spach, K., Blankenhorn, E., and Teuscher, C. Pertussis Toxin Induces Angiogenesisin Brain Microvascular Endothelial Cells, J of Neuroscience, 2008, in press Casey, T., Bond, J., Tighe, S., Hunter, T., Lintault, L., Patel, O., Eneman, J., Crocker, A., White, J., Tessitore, J., Stanley, M., Harlow, S., Weaver, D., Muss, H., and Plaut, K., Molecular Signatures Suggest a Major Role for Stromal Cells in Development for Invasive Breast Cancer, Breast Cancer Research and Treatment, 2008, in press Rose, P., Bond, J., Tighe, S., Toth, M., Wellman, T., Brisco de Mantiano, EM., LeWinter, M., and Lounsbury, KM., Genes Overexpressed in Cerebral Arteries Following Salt-Induced Hypersensitive Disease are Regulated by Angiotensin II, JunB, and CREB, AM. J. Phys. Heart and Circ. Phys 294: H1075-H1085, 2008 Finucane, K., McFadden, T., Bond, J., Kennelly, J., and Zhao, FQ., Onset of Lactation of the Bovine Mammary Gland: Gene Expression Profiling Indicates a Strong Inhibition of Gene Expression in Cell Proliferation, Funct Interg Genomics, Jan., 2008 Shukla, A., Lounsbury, K., Barrett, T., Gell, J., Rincon, M., Butnor, K., Taatjes, D., Davis, G., Vacek, P., Nakayama, KI., Nakayama, K., Steele, C., and Mossman, B., Asbestos-Induced Peribronchiolar Cell Proliferation and Cytokine production are Attenuated in Lungs of Protein Kinase C-¿ Knockout Mice, American J of Pathology, vol.170, no.1, 2007 Barlow, C., Barrett, T., Shukla, A., Mossman, B., and Lounsbury, K. Asbestos-Mediated CREB Phosphorylation is Regulated by Protein Kinase A and Extracellular Signal-Regulated Kinases 1/2 , Am J Physiology Lung Cell Mol Physiology 292: L1361-1369, 2007 Pulver-Kaste, RA, Barlow, CA, Penar, PL, Tranmer, B, and Lounsbury, KM. Ca2+-Dependent Transcription Patterns in Human Cerebrovascular Smooth Muscle. AM. J. Phys. Heart and Circ. Phys, H97-H105, 2006 Muthusamy, V, Duraisamy, S, Bradbury, M, Hobbs, C, Curley, DP, Nelson, B, and Bosenberg, M. Epigenetic Silencing of Novel Tumor Supressors in Malignant Melanoma, Cancer Research; 66: (23), 11187-11193, 2006 Grants received from UVM Microarray Facility Generated data: Karen Lounsbury, HL67351-06 NIH, NHLBI Title: Calcium Signaling and Gene Expression in Vascular Smooth Muscle Cells, 2007-2012 Thomas McFadden, Grant# 2007-35206-17983 from the USDA Cooperative State Research, Education, and Extension Service, Title: Unilateral Frequent Milking: A Powerful Model for Identifying Biological Mechanisms Involved in Enhanced Milk Production Efficiency. Grants Pending using UVM Microarray Facility Generated data: Helene Langevin, Grant #RO1-AT001121-06, Agency: NIH NCCAM, score 164 Utilization: -Experimental design consultations with 19 investigators -Completion of 22 microarray projects (396 GeneChips) -Performed 197 RNA assessments: 54 PicoChips and 143 NanoChips It should be noted that a test chip was required for each target preparation until 2005