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  1. Article: Characterization of microbiomic and geochemical compositions across the photosynthetic fringe.

    Weeks, Katelyn / Trembath-Reichert, Elizabeth / Boyer, Grayson / Fecteau, Kristopher / Howells, Alta / De Martini, Francesca / Gile, Gillian H / Shock, Everett L

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1176606

    Abstract: Hot spring outflow channels provide geochemical gradients that are reflected in microbial community compositions. In many hot spring outflows, there is a distinct visual demarcation as the community transitions from predominantly chemotrophs to having ... ...

    Abstract Hot spring outflow channels provide geochemical gradients that are reflected in microbial community compositions. In many hot spring outflows, there is a distinct visual demarcation as the community transitions from predominantly chemotrophs to having visible pigments from phototrophs. It has been hypothesized that this transition to phototrophy, known as the photosynthetic fringe, is a result of the pH, temperature, and/or sulfide concentration gradients in the hot spring outflows. Here, we explicitly evaluated the predictive capability of geochemistry in determining the location of the photosynthetic fringe in hot spring outflows. A total of 46 samples were taken from 12 hot spring outflows in Yellowstone National Park that spanned pH values from 1.9 to 9.0 and temperatures from 28.9 to 92.2°C. Sampling locations were selected to be equidistant in geochemical space above and below the photosynthetic fringe based on linear discriminant analysis. Although pH, temperature, and total sulfide concentrations have all previously been cited as determining factors for microbial community composition, total sulfide did not correlate with microbial community composition with statistical significance in non-metric multidimensional scaling. In contrast, pH, temperature, ammonia, dissolved organic carbon, dissolved inorganic carbon, and dissolved oxygen did correlate with the microbial community composition with statistical significance. Additionally, there was observed statistical significance between beta diversity and the relative position to the photosynthetic fringe with sites above the photosynthetic fringe being significantly different from those at or below the photosynthetic fringe according to canonical correspondence analysis. However, in combination, the geochemical parameters considered in this study only accounted for 35% of the variation in microbial community composition determined by redundancy analysis. In co-occurrence network analyses, each clique correlated with either pH and/or temperature, whereas sulfide concentrations only correlated with individual nodes. These results indicate that there is a complex interplay between geochemical variables and the position of the photosynthetic fringe that cannot be fully explained by statistical correlations with the individual geochemical variables included in this study.
    Language English
    Publishing date 2023-04-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1176606
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Polyethylene Glycol Impacts Conformation and Dynamics of

    Liebau, Jessica / Laatsch, Bethany F / Rusnak, Joshua / Gunderson, Keegan / Finke, Brianna / Bargender, Kassandra / Narkiewicz-Jodko, Alex / Weeks, Katelyn / Williams, Murphi T / Shulgina, Irina / Musier-Forsyth, Karin / Bhattacharyya, Sudeep / Hati, Sanchita

    Biochemistry

    2024  

    Abstract: Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular ... ...

    Abstract Polyethylene glycol (PEG) is a flexible, nontoxic polymer commonly used in biological and medical research, and it is generally regarded as biologically inert. PEG molecules of variable sizes are also used as crowding agents to mimic intracellular environments. A recent study with PEG crowders revealed decreased catalytic activity of
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase.

    Hu, Quin H / Williams, Murphi T / Shulgina, Irina / Fossum, Carl J / Weeks, Katelyn M / Adams, Lauren M / Reinhardt, Clorice R / Musier-Forsyth, Karin / Hati, Sanchita / Bhattacharyya, Sudeep

    ACS catalysis

    2020  Volume 10, Issue 17, Page(s) 10229–10242

    Abstract: Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from " ... ...

    Abstract Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by
    Language English
    Publishing date 2020-08-14
    Publishing country United States
    Document type Journal Article
    ISSN 2155-5435
    ISSN 2155-5435
    DOI 10.1021/acscatal.0c02381
    Database MEDical Literature Analysis and Retrieval System OnLINE

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