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  1. The co-occurrence of uranyl and arsenate in contaminated water caused by natural processes and mining is a concern for impacted communities, including in Native American lands in the U.S. Southwest. We investigated the simultaneous removal of aqueous uranyl and arsenate after the reaction with limestone and precipitated hydroxyapatite (HAp, Ca10(PO4)6(OH)2). In benchtop experiments with an initial pH of 3.0 and initial concentrations of 1 mM U and As, uranyl and arsenate coprecipitated in the presence of 1 g L−1 limestone. However, related experiments initiated under circumneutral pH conditions showed that uranyl and arsenate remained soluble. Upon addition of 1 mM PO43− and 3 mM Ca2+ in solution (initial concentration of 0.05 mM U and As) resulted in the rapid removal of over 97% of U via Ca−U−P precipitation. In experiments with 2 mM PO4 3− and 10 mM Ca2+ at pH rising from 7.0 to 11.0, aqueous concentrations of As decreased (between 30 and 98%) circa pH 9. HAp precipitation in solids was confirmed by powder X-ray diffraction and scanning electron microscopy/energy dispersive X-ray. Electron microprobe analysis indicated U was coprecipitated with Ca and P, while As was mainly immobilized through HAp adsorption. The results indicate that natural materials, such as HAp and limestone, can effectively remove uranyl and arsenate mixtures. 
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  6. Abstract Background

    Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregularities in histone PTMs can lead to a variety of different diseases including various forms of cancer. Histone modifications are analyzed using high resolution mass spectrometry, which generate large amounts of data that requires sophisticated bioinformatics tools for analysis and visualization. PTMViz is designed for downstream differential abundance analysis and visualization of both protein and/or histone modifications.


    PTMViz provides users with data tables and visualization plots of significantly differentiated proteins and histone PTMs between two sample groups. All the data is packaged into interactive data tables and graphs using the Shiny platform to help the user explore the results in a fast and efficient manner to assess if changes in the system are due to protein abundance changes or epigenetic changes. In the example data provided, we identified several proteins differentially regulated in the dopaminergic pathway between mice treated with methamphetamine compared to a saline control. We also identified histone post-translational modifications including histone H3K9me, H3K27me3, H4K16ac, and that were regulated due to drug exposure.


    Histone modifications play an integral role in the regulation of gene expression. PTMViz provides an interactive platform for analyzing proteins and histone post-translational modifications from mass spectrometry data in order to quickly identify differentially expressed proteins and PTMs.

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