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6 Publications

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    02/29/24 | Recommendations for accelerating open preprint peer review to improve the culture of science
    Avissar-Whiting M, Belliard F, Bertozzi SM, Brand A, Brown K, Clément-Stoneham G, Dawson S, Dey G, Ecer D, Edmunds SC, Farley A, Fischer TD, Franko M, Fraser JS, Funk K, Ganier C, Harrison M, Hatch A, Hazlett H, Hindle S, Hook DW, Hurst P, Kamoun S, Kiley R, Lacy MM, LaFlamme M, Lawrence R, Lemberger T, Leptin M, Lumb E, MacCallum CJ, Marcum CS, Marinello G, Mendonça A, Monaco S, Neves K, Pattinson D, Polka JK, Puebla I, Rittman M, Royle SJ, Saderi D, Sever R, Shearer K, Spiro JE, Stern B, Taraborelli D, Vale R, Vasquez CG, Waltman L, Watt FM, Weinberg ZY, Williams M
    PLOS Biology. 2024-02-29;22(2):e3002502. doi: 10.1371/journal.pbio.300250210.1371/journal.pbio.3002502.g001

    Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.

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    01/24/24 | Mechanical stretch regulates macropinocytosis in Hydra vulgaris.
    Skokan TD, Hobmayer B, McKinley KL, Vale RD
    Molecular Biology of the Cell. 2024 Jan 24:mbcE22020065. doi: 10.1091/mbc.E22-02-0065

    Cells rely on a diverse array of engulfment processes to sense, exploit, and adapt to their environments. Among these, macropinocytosis enables indiscriminate and rapid uptake of large volumes of fluid and membrane, rendering it a highly versatile engulfment strategy. Much of the molecular machinery required for macropinocytosis has been well established, yet how this process is regulated in the context of organs and organisms remains poorly understood. Here, we report the discovery of extensive macropinocytosis in the outer epithelium of the cnidarian . Exploiting 's relatively simple body plan, we developed approaches to visualize macropinocytosis over extended periods of time, revealing constitutive engulfment across the entire body axis. We show that the direct application of planar stretch leads to calcium influx and the inhibition of macropinocytosis. Finally, we establish a role for stretch-activated channels in inhibiting this process. Together, our approaches provide a platform for the mechanistic dissection of constitutive macropinocytosis in physiological contexts and highlight a potential role for macropinocytosis in responding to cell surface tension. [Media: see text] [Media: see text] [Media: see text] [Media: see text].

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    01/11/24 | Bridging gaps in traditional research training with iBiology Courses.
    Schnoes AM, Green NH, Nguyen TA, Vale RD, Goodwin SS, Behrman SL
    PLoS Biology. 2024 Jan 11;22(1):e3002458. doi: 10.1371/journal.pbio.3002458

    iBiology Courses provide trainees with just-in-time learning resources to become effective researchers. These courses can help scientists build core research skills, plan their research projects and careers, and learn from scientists with diverse backgrounds.

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    03/01/23 | In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes.
    Chen Z, Greenan GA, Shiozaki M, Liu Y, Skinner WM, Zhao X, Zhao S, Yan R, Yu Z, Lishko PV, Agard DA, Vale RD
    Nature Structural & Molecular Biology. 2023 Mar 01;30(3):360-9. doi: 10.1038/s41594-022-00861-0

    The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis of this difference is unclear. Here, we perform in situ cryo-electron tomography of mouse and human sperm, providing the highest-resolution structural information to date. Our subtomogram averages reveal mammalian sperm-specific protein complexes within the microtubules, the radial spokes and nexin-dynein regulatory complexes. The locations and structures of these complexes suggest potential roles in enhancing the mechanical strength of mammalian sperm axonemes and regulating dynein-based axonemal bending. Intriguingly, we find that each of the nine outer microtubule doublets is decorated with a distinct combination of sperm-specific complexes. We propose that this asymmetric distribution of proteins differentially regulates the sliding of each microtubule doublet and may underlie the asymmetric beating of mammalian sperm.

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    11/09/23 | De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography
    Zhen Chen , Momoko Shiozaki , Kelsey M. Haas , Shumei Zhao , Caiying Guo , Benjamin J. Polacco , Zhiheng Yu , Nevan J. Krogan , Robyn M. Kaake , Ronald D. Vale , David A. Agard
    Cell. 2023 Nov 09;186(23):5041-5053.e19. doi: 10.1016/j.cell.2023.09.017

    Understanding molecular mechanisms of cellular pathways requires knowledge of the identities of participating proteins, their cellular localization and their 3D structures. Contemporary workflows typically require multiple techniques to identify target proteins, track their localization using fluorescence microscopy, followed by in vitro structure determination. To identify mammal-specific sperm proteins and understand their functions, we developed a visual proteomics workflow to directly address these challenges. Our in situ cryo-electron tomography and subtomogram averaging provided 6.0 Å resolution reconstructions of axonemal microtubules and their associated proteins. The well-resolved secondary and tertiary structures allowed us to computationally match, in an unbiased manner, novel densities in our 3D reconstruction maps with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105 and SPACA9 as novel microtubule inner proteins that form an extensive network crosslinking the lumen of microtubule and existing proteins. Additional biochemical and mass spectrometry analyses helped validate potential candidates. The novel axonemal sperm structures identified by this approach form an extensive interaction network within the lumen of microtubules, suggesting they have a role in the mechanical and elastic properties of the microtubule filaments required for the vigorous beating motions of flagella.

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    05/16/22 | In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes
    Zhen Chen , Garrett A. Greenan , Momoko Shiozaki , Yanxin Liu , Will M. Skinner , Xiaowei Zhao , Shumei Zhao , Rui Yan , Caiying Guo , Zhiheng Yu , Polina V. Lishko , David A. Agard , Ronald D. Vale
    bioRxiv. 2022 May 16:. doi: 10.1101/2022.05.15.492011

    The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis of this difference is unclear. Here, we perform in situ cryo-electron tomography of mouse and human sperm axonemes, providing the highest resolution structural information to date. Our subtomogram averages reveal mammalian sperm- specific protein complexes within the outer microtubule doublets, the radial spokes and nexin-dynein regulatory complexes. The locations and structures of these complexes suggest potential roles in enhancing the mechanical strength of mammalian sperm axonemes and regulating dynein-based axonemal bending. Intriguingly, we find that each of the nine outer microtubule doublets is decorated with a distinct combination of sperm- specific complexes. We propose that this asymmetric distribution of proteins differentially regulates the sliding of each microtubule doublet and may underlie the asymmetric beating of mammalian sperm.

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