29 research outputs found

    Summit County conservation inventory: volume I, a natural heritage assessment, 1997 final report

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    Prepared for: Summit County Open Space and Trails Dept., Summit County Planning Dept.December 1997.Includes bibliographical references

    Manual / Issue 13 / Storage

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    Manual, a journal about art and its making. Storage. Manual 13 opens with an introduction by Fred Wilson, who confides, “You can look at all the opulence on display in a museum and begin to understand that something nefarious might be behind it. Storage, for me, is where the action is.” Museums usually make choices for viewers, their curators presenting what they think most important within a category. They can be so good at doing this that visitors sometimes don’t realize there’s anything else to see: they don’t realize the nature of the decisions behind an exhibition, and they accept that the elites have made a judgment about which shoe is the shoe to see. Visitors can learn about what’s great, but they don’t necessarily consider the process of discernment. –– Fred Wilson The RISD Museum’s thirteenth issue of Manual unpacks the idea and reality of storage—objects museums don’t put on view, works made as containers of various sorts, and more metaphorical considerations about how meanings and narratives are stored. This issue serves as a companion to the Raid the Icebox Now series of exhibitions on view at the RISD Museum through November 2020, in which nine contemporary artists and design collectives use the museum and its collections as a site for critical creative production and presentation. Raid the Icebox Now marks the 50th anniversary of Raid the Icebox 1 with Andy Warhol, held in 1970 at the RISD Museum. Softcover, 120 pages. Published Fall/Winter 2019 by the RISD Museum. Manual 13 (Storage) contributors include: Christina Alderman, Issac M. Alderman, A.H. Jerriod Avant, Hannah Carlson, Wai Yee Chiong, John Dunnigan, Maria Morris Hambourg, David Hartt, Elaine Tyler May, Claire McCardell, Denise Murrell, Ingrid Schaffner, Holly Shaffer, Tanya Sheehan, John W. Smith, Mimi Smith, Sassan Tabatabai, Allen Wexler, and Fred Wilson.https://digitalcommons.risd.edu/risdmuseum_journals/1039/thumbnail.jp

    Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis

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    Background: The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome.Methods: To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls.Results: Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation.Conclusion: A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics

    Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

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    Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

    Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

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    We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

    Finishing the euchromatic sequence of the human genome

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    The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

    Using directional OCT to analyze photoreceptor visibility over AMD-related drusen

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    Investigators have reported reduced visibility of the cone photoreceptors overlying drusen using adaptive optics (AO) imaging techniques. Two hypotheses have been proposed to explain this phenomenon. First, the disease-related deformation of the photoreceptor outer segment (OS) may reduce its ability to act as a wave guide, thus decreasing the cell's familiar reflectance pattern. Second, drusen could disorient the photoreceptors away from the eye's pupil, reducing the amount of light reflected back out the pupil. In this work, we use directional OCT (dOCT) images of drusen in AMD patients to measure the respective contributions of these deforming and disorienting factors

    Ecosystem Services and Disservices Are Bundled in Simple and Diverse Cover Cropping Systems

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    Agroecosystems are increasingly expected to provide multiple ecosystem services. We tested whether and how cover crop selection (identity and number of species) affects provisioning of multiple services (multifunctionality). In a 3-yr study of 10 cover crop treatments and eight ecosystem services, certain services consistently co-occurred. One such service “bundle” included cover crop biomass production, weed suppression, and nitrogen retention. Another set of bundled services included cash crop production, nitrogen supply, and profitability. We also identified trade-offs: as some services increased, other disservices arose, limiting multifunctionality. However, functionally diverse mixtures ameliorated disservices associated with certain monocultures, thereby increasing cover crop multifunctionality
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