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  1. Free, publicly-accessible full text available June 13, 2023
  2. 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 rolemore »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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  3. Peptide nucleic acid (PNA) is a unique synthetic nucleic acid analog that has been adopted for use in many biological applications. These applications rely upon the robust Franklin–Watson–Crick base pairing provided by PNA, particularly at lower ionic strengths. However, our understanding of the relationship between the kinetics of PNA:DNA hybridization and ionic strength is incomplete. Here we measured the kinetics of association and dissociation of PNA with DNA across a range of ionic strengths and temperatures at single-molecule resolution using total internal reflection fluorescence imaging. Unlike DNA:DNA duplexes, PNA:DNA duplexes are more stable at lower ionic strength, and we demonstrate that this is due to a higher association rate. While the dissociation rate of PNA:DNA duplexes is largely insensitive to ionic strength, it is significantly lower than that of DNA:DNA duplexes having the same number and sequence of base pairing interactions. The temperature dependence of PNA:DNA kinetic rate constants indicate a significant enthalpy barrier to duplex dissociation, and to a lesser extent, duplex formation. This investigation into the kinetics of PNA:DNA hybridization provides a framework towards better understanding and design of PNA sequences for future applications.
  4. The crystal chemistry of carnotite (prototype formula: K2(UO2)2(VO4)2·3H2O) occurring in mine wastes collected from Northeastern Arizona was investigated by integrating spectroscopy, electron microscopy, and x-ray diffraction analyses. Raman spectroscopy confirms that the uranyl vanadate phase present in the mine waste is carnotite, rather than the rarer polymorph vandermeerscheite. X-ray diffraction patterns of the carnotite occurring in these mine wastes are in agreement with those reported in the literature for a synthetic analog. Carbon detected in this carnotite was identified as organic carbon inclusions using transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) analyses. After excluding C and correcting for K-drift from the electron microprobe analyses, the composition of the carnotite was determined as 8.64% K2O, 0.26% CaO, 61.43% UO3, 20.26% V2O5, 0.38% Fe2O3, and 8.23% H2O. The empirical formula, (K1.66Ca0.043Al(OH)2+0.145 Fe(OH)2+0.044)((U0.97)O2)2((V1.005)O4)2·4H2O of the studied carnotite, with an atomic ratio 1.9:2:2 for K:U:V, is similar to the that of carnotite (K2(UO2)2(VO4)2·3H2O) reported in the literature. Lattice spacing data determined using selected area electron diffraction (SAED)-TEM suggests: (1) complete amorphization of the carnotite within 120 s of exposure to the electron beam and (2) good agreement of the measured d-spacings for carnotite in the literature. Small differences between the measuredmore »and literature d-spacing values are likely due to the varying degree of hydration between natural and synthetic materials. Such information about the crystal chemistry of carnotite in mine wastes is important for an improved understanding of the occurrence and reactivity of U, V, and other elements in the environment.« less