Digital Commons @ George Fox University: 3-Year Report

A look at the use and content of our institutional repository three years in

Same Titles, Different Formats: Does Print or Electronic Get More Use?

This article examines the use of both print and electronic monographs at George Fox University libraries over a period of thirty-three months for 8,500 titles that were held in both formats. Results indicate that print is more likely to be used than electronic. The implications of the findings, as well as related factors determining future decision making relative to format, are discussed

About Pennington ePress

Pennington ePress is the academic open press of George Fox University Libraries. Our mission is to publish academic works by authors who are affiliated with George Fox University, or who have work in research areas of significant interest to the university. In addition, Pennington ePress includes some public-domain, out-of-print books of relevance and interest to the university or Northwest Yearly Meeting. Public Access: Full texts of works are published online in a public-access format, available free to users worldwide. Analytics: The DigitalCommons is indexed by Google and Google Scholar and provides download statistics and readership maps to authors. Processing Charges: Pennington ePress does not levy any author processing charges. Print-on-demand: Some titles are made available as print-on-demand publications. Current publications available in this printed format will be available at the Pennington ePress storefront at lulu.com. Style: Pennington ePress does not provide editing, design, and composition (typesetting) services. ISBNs: All new works are assigned International Standard Book Numbers for both electronic and printed editions. Cataloging: Catalog records for Pennington ePress are available via OCLC. Readership: Pennington ePress can support projects for any size readership, and can serve as a platform for scholars whose works might not meet the financial requirements for publication by a traditional press. Preservation: Permanent access to materials is ensured through the GFU DigitalCommons. Copyright and Licensing: Works are published under a nonexclusive permission to publish agreement. The electronic works reside in the Digital Commons@George Fox University repository and remain at all times free to readers. Authors retain ownership of copyright, and may publish elsewhere without restrictions or limitation. In retaining copyright, authors are free to superimpose a license on their work in any manner they choose, including assigning a Creative Commons license. Questions are welcome. Please direct them to Alex Rolfe at [email protected]

Ruler Arrays Reveal Haploid Genomic Structural Variation

Despite the known relevance of genomic structural variants to pathogen behavior, cancer, development, and evolution, certain repeat based structural variants may evade detection by existing high-throughput techniques. Here, we present ruler arrays, a technique to detect genomic structural variants including insertions and deletions (indels), duplications, and translocations. A ruler array exploits DNA polymerase’s processivity to detect physical distances between defined genomic sequences regardless of the intervening sequence. The method combines a sample preparation protocol, tiling genomic microarrays, and a new computational analysis. The analysis of ruler array data from two genomic samples enables the identification of structural variation between the samples. In an empirical test between two closely related haploid strains of yeast ruler arrays detected 78% of the structural variants larger than 100 bp.United States. National Institutes of Health (Grant R01GM069676

A multi-parametric flow cytometric assay to analyze DNA–protein interactions

Interactions between DNA and transcription factors (TFs) guide cellular function and development, yet the complexities of gene regulation are still far from being understood. Such understanding is limited by a paucity of techniques with which to probe DNA–protein interactions. We have devised magnetic protein immobilization on enhancer DNA (MagPIE), a simple, rapid, multi-parametric assay using flow cytometric immunofluorescence to reveal interactions among TFs, chromatin structure and DNA. In MagPIE, synthesized DNA is bound to magnetic beads, which are then incubated with nuclear lysate, permitting sequence-specific binding by TFs, histones and methylation by native lysate factors that can be optionally inhibited with small molecules. Lysate protein–DNA binding is monitored by flow cytometric immunofluorescence, which allows for accurate comparative measurement of TF-DNA affinity. Combinatorial fluorescent staining allows simultaneous analysis of sequence-specific TF-DNA interaction and chromatin modification. MagPIE provides a simple and robust method to analyze complex epigenetic interactions in vitro

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

SummaryEukaryotic genomes are packaged into nucleosomes whose position and chemical modification state can profoundly influence regulation of gene expression. We profiled nucleosome modifications across the yeast genome using chromatin immunoprecipitation coupled with DNA microarrays to produce high-resolution genome-wide maps of histone acetylation and methylation. These maps take into account changes in nucleosome occupancy at actively transcribed genes and, in doing so, revise previous assessments of the modifications associated with gene expression. Both acetylation and methylation of histones are associated with transcriptional activity, but the former occurs predominantly at the beginning of genes, whereas the latter can occur throughout transcribed regions. Most notably, specific methylation events are associated with the beginning, middle, and end of actively transcribed genes. These maps provide the foundation for further understanding the roles of chromatin in gene expression and genome maintenance

211 Identifying lupus patient subsets and specific pharmacodynamic changes through immune cell deconvolution of gene expression data in atacicept-treated patients in the APRIL-SLE study

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Prostanoid receptor EP1 and Cox-2 in injured human nerves and a rat model of nerve injury: a time-course study

BACKGROUND: Recent studies show that inflammatory processes may contribute to neuropathic pain. Cyclooxygenase-2 (Cox-2) is an inducible enzyme responsible for production of prostanoids, which may sensitise sensory neurones via the EP1 receptor. We have recently reported that while macrophages infiltrate injured nerves within days of injury, they express increased Cox-2-immunoreactivity (Cox-2-IR) from 2 to 3 weeks after injury. We have now investigated the time course of EP1 and Cox-2 changes in injured human nerves and dorsal root ganglia (DRG), and the chronic constriction nerve injury (CCI) model in the rat. METHODS: Tissue sections were immunostained with specific antibodies to EP1, Cox-2, CD68 (human macrophage marker) or OX42 (rat microglial marker), and neurofilaments (NF), prior to image analysis, from the following: human brachial plexus nerves (21 to 196 days post-injury), painful neuromas (9 days to 12 years post-injury), avulsion injured DRG, control nerves and DRG, and rat CCI model tissues. EP1 and NF-immunoreactive nerve fibres were quantified by image analysis. RESULTS: EP1:NF ratio was significantly increased in human brachial plexus nerve fibres, both proximal and distal to injury, in comparison with uninjured nerves. Sensory neurones in injured human DRG showed a significant acute increase of EP1-IR intensity. While there was a rapid increase in EP1-fibres and CD-68 positive macrophages, Cox-2 increase was apparent later, but was persistent in human painful neuromas for years. A similar time-course of changes was found in the rat CCI model with the above markers, both in the injured nerves and ipsilateral dorsal spinal cord. CONCLUSION: Different stages of infiltration and activation of macrophages may be observed in the peripheral and central nervous system following peripheral nerve injury. EP1 receptor level increase in sensory neurones, and macrophage infiltration, appears to precede increased Cox-2 expression by macrophages. However, other methods for detecting Cox-2 levels and activity are required. EP1 antagonists may show therapeutic effects in acute and chronic neuropathic pain, in addition to inflammatory pain