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. Vermont Genetics Network Bioinformatics Core (BC) Highlights September 2005 June 30, 2006 For each of the three BC Aims we reprint the aim and then summarize highlights.
AIM 1 Provide bioinformatics services that make investigators more competitive for research funding. Services include experimental design as well as data management and analysis. These services will include support for experimental programs involving oligonucleotide microarrays, LC-Mass spectrometry, and protein structure/function. More generally, the BC supports development of custom databases. Highlights Support for oligonucleotide arrays (Affymetrix GeneChips) continues to be productive (Table) and to occupy Dr. Anjanette Watson full time. Highlights include two peer-reviewed publications from support activities since September 2005, support for an NIH R01 at Middlebury College, two studies (a total of 82 GeneChips) on human biopsies, strong support for bovine researchers (four projects) in the College of Agriculture and Life Sciences at UVM, support for experiment design, including analysis of sources of variation and power calculations based on publicly available data. We provided designs for 9 projects that have not yet begun. Project Area Organism Source Chips Project Status Cardiovascular Disease Human Cell culture 8 Peer reviewed publication Milk production Mouse Mammary surgery 8 Peer reviewed manuscript Dental caries Strep. Mutans WT/KO culture 15 Manuscripts in preparation. Milk production Cow Mammary biopsy 8 Manuscript in preparation Cardiovascular Disease Rat Brain surgery 6 Manuscript in preparation Immune Response Mouse Primary Culture 6 Inferences validated by RTQ-PCR. Muscle atrophy Human Muscle biopsy 15 RTQ-PCR Validation of inferences in progress Milk production Cow Mammary biopsy 8 Validation in process Breast Cancer Human Breast biopsy 67 Analysis in process: Significant inferences based on permutation test. Connective Tissue Remodeling Mouse Plexus surgery 6 Analysis in progress Brain function Mouse Brain surgery 8 Analysis in process Radiation Damage Human Cell culture 4 Outreach/Educ Yeast Culture 20 Completed modules at 4 colleges TOTAL 6 179 2 peer-reviewed manuscripts Table: Affymetrix GeneChip studies processed by the BC during Sep 2005 June 2006.
AIM 2 Provide laboratory/lecture modules to Baccalaureate Institutions (BPI). The BC played a role in the highly successful VGN oligonucleotide microarray outreach module, a BioQuest BEDROCK bioinformatics workshop, and guest lectures on NCBI resources. In collaboration with the Outreach Core we will deliver laboratory/lecture modules involving gene expression, proteomics, and bioinformatics. Microarray outreach activities are described in the Outreach Core progress report. In addition: Dr. William Barnes, on sabbatical with the VGN from Clarion University in Pennsylvania, developed a bioinformatics outreach module and is in the process of gathering feedback at UVM. VGN staff, Dr. Anjanette Watson and Bryan Fleming, hosted a three day NCBI workshop. The VGN ERIS resource (see Aim 3) was used to announce the workshop statewide and attendance was at capacity (80 people on the first day and 40 on the two subsequent days). Attendees represented Norwich University, Green Mountain College, and the Rat Genome Database, as well as 11 departments/units (4 colleges) at UVM.
AIM 3 Support the development of administrative infrastructure for electronic networks (Figure 2). With BRIN funding the BC developed infrastructure that allows organizations to monitor changing needs, interests, and progress of participants, to collect usage data, to target information to participants, and to match advisors with prot g s. This support is based on member profiles . Such infrastructure is already in use; proposed activities would allow us to share it with both other Vermont organizations and with other INBRE awardees. The VGN initiated construction of a database of Vermont Experts in Science and Technology, which has since grown in scope to become the VGN ERIS Project. ERIS resources have been used to make 11 statewide announcements and to capture the publications and keyword indexing of 25 UVM scientists. Briefly, the idea underlying ERIS is to take advantage of publicly available information in public personnel directories, bibliographic citation databases, grant award databases, and calendars to provide information about people s expertise and interests, research projects, publications, and events. This information will be exchanged through statewide email announcements, a web page, and robots that automatically notify participants of new entries.
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