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  • 1
    Publication Date: 2013-04-14
    Description: We report a target enrichment method to map nucleosomes of large genomes at unprecedented coverage and resolution by deeply sequencing locus-specific mononucleosomal DNA enriched via hybridization with bacterial artificial chromosomes. We achieved ~10 000-fold enrichment of specific loci, which enabled sequencing nucleosomes at up to ~500-fold higher coverage than has been reported in a mammalian genome. We demonstrate the advantages of generating high-sequencing coverage for mapping the center of discrete nucleosomes, and we show the use of the method by mapping nucleosomes during T cell differentiation using nuclei from effector T-cells differentiated from clonal, isogenic, naïve, primary murine CD4 and CD8 T lymphocytes. The analysis reveals that discrete nucleosomes exhibit cell type-specific occupancy and positioning depending on differentiation status and transcription. This method is widely applicable to mapping many features of chromatin and discerning its landscape in large genomes at unprecedented resolution.
    Keywords: Chromatin and Epigenetics, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-02-11
    Description: Animal waste from concentrated animal feeding operations (CAFOs) is a significant contributor to nitrate contamination of groundwater. To evaluate the cost-effectiveness of alternative policies for controlling nitrate pollution at both the field and farm level, this article utilizes a structural dynamic model of a representative CAFO. The model accounts for herd management, manure handling systems, crop rotations, water sources, irrigation systems, waste disposal options, and pollutant emissions. Results show that the standard approach of limiting the amount of animal waste that may be applied to fields reduces net farm income by more than 25%, whereas the most cost-effective emission-based policies reduce income only marginally. This motivates greater consideration for nonpoint source pollution control policies that target estimated emissions. Furthermore, price instruments are shown to slightly outperform quantity instruments under conditions that are typical for CAFOs. The results also show that adopting alternative technologies and practices is crucial for cost-effective abatement, and demonstrate the importance of accounting for the spatial heterogeneity of both irrigation water and salinity when designing policy mechanisms for nitrate pollution control.
    Keywords: Q53 - Air Pollution ; Water Pollution ; Noise ; Hazardous Waste ; Solid Waste ; Recycling, Q58 - Government Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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