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  • Antarctic glaciology  (3)
  • evolution  (2)
  • Cambridge University Press  (3)
  • Oxford University Press  (2)
  • 2020-2023  (5)
  • 1935-1939
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  • Cambridge University Press  (3)
  • Oxford University Press  (2)
  • Frontiers Media  (2)
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  • 1
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Description: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Description: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Keywords: DNA methylation ; evolution ; development ; reprogramming
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Priscu, J. C., Kalin, J., Winans, J., Campbell, T., Siegfried, M. R., Skidmore, M., Dore, J. E., Leventer, A., Harwood, D. M., Duling, D., Zook, R., Burnett, J., Gibson, D., Krula, E., Mironov, A., McManis, J., Roberts, G., Rosenheim, B. E., Christner, B. C., Kasic, K., Fricker, H. A., Lyons, W. B., Barker, J., Bowling, M., Collins, B., Davis, C., Gagnon, A., Gardner, C., Gustafson, C., Kim, O-S., Li, W., Michaud, A., Patterson, M. O., Tranter, M., Ryan Venturelli, R., Trista Vick-Majors, T., & Elsworth, C. Scientific access into Mercer Subglacial Lake: scientific objectives, drilling operations and initial observations. Annals of Glaciology, 62(85–86), (2021): 340–352, https://doi.org/10.1017/aog.2021.10.
    Description: The Subglacial Antarctic Lakes Scientific Access (SALSA) Project accessed Mercer Subglacial Lake using environmentally clean hot-water drilling to examine interactions among ice, water, sediment, rock, microbes and carbon reservoirs within the lake water column and underlying sediments. A ~0.4 m diameter borehole was melted through 1087 m of ice and maintained over ~10 days, allowing observation of ice properties and collection of water and sediment with various tools. Over this period, SALSA collected: 60 L of lake water and 10 L of deep borehole water; microbes 〉0.2 μm in diameter from in situ filtration of ~100 L of lake water; 10 multicores 0.32–0.49 m long; 1.0 and 1.76 m long gravity cores; three conductivity–temperature–depth profiles of borehole and lake water; five discrete depth current meter measurements in the lake and images of ice, the lake water–ice interface and lake sediments. Temperature and conductivity data showed the hydrodynamic character of water mixing between the borehole and lake after entry. Models simulating melting of the ~6 m thick basal accreted ice layer imply that debris fall-out through the ~15 m water column to the lake sediments from borehole melting had little effect on the stratigraphy of surficial sediment cores.
    Description: This material is based upon work supported by the US National Science Foundation, Section for Antarctic Sciences, Antarctic Integrated System Science program as part of the interdisciplinary (Subglacial Antarctic Lakes Scientific Access (SALSA): Integrated study of carbon cycling in hydrologically-active subglacial environments) project (NSF-OPP 1543537, 1543396, 1543405, 1543453 and 1543441). Ok-Sun Kim was funded by the Korean Polar Research Institute. We are particularly thankful to the SALSA traverse personnel for crucial technical and logistical support. The United States Antarctic Program enabled our fieldwork; the New York Air National Guard and Kenn Borek Air provided air support; UNAVCO provided geodetic instrument support. Hot water drilling activities, including repair and upgrade modifications of the WISSARD hot water drill system, for the SALSA project were supported by a subaward from the Ice Drilling Program of Dartmouth College (NSF-PLR 1327315) to the University of Nebraska-Lincoln. J. Lawrence assisted with manuscript preparation. Finally, we are grateful to C. Dean, the SALSA Project Manager, and R. Ricards, SALSA Project Coordinator at McMurdo Station, for their organizational skills, and B. Huber of Lamont-Doherty Earth Observatory for providing the SBE39 PT sensors and the Nortek Aquadopp current meter and assisting with interpretation of the data. B. Huber also provided helpful input on programing and calibrating the SBE19PlusV2 6112 CTD.
    Keywords: Antarctic glaciology ; Basal ice ; Biogeochemistry ; Glacial sedimentology ; Subglacial lakes
    Repository Name: Woods Hole Open Access Server
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  • 3
    Publication Date: 2022-05-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tison, J.-L., Maksym, T., Fraser, A. D., Corkill, M., Kimura, N., Nosaka, Y., Nomura, D., Vancoppenolle, M., Ackley, S., Stammerjohn, S., Wauthy, S., Van der Linden, F., Carnat, G., Sapart, C., de Jong, J., Fripiat, F., & Delille, B. Physical and biological properties of early winter Antarctic sea ice in the Ross Sea. Annals of Glaciology, 61(83), (2020): 241–259, https://doi.org/10.1017/aog.2020.43.
    Description: This work presents the results of physical and biological investigations at 27 biogeochemical stations of early winter sea ice in the Ross Sea during the 2017 PIPERS cruise. Only two similar cruises occurred in the past, in 1995 and 1998. The year 2017 was a specific year, in that ice growth in the Central Ross Sea was considerably delayed, compared to previous years. These conditions resulted in lower ice thicknesses and Chl-a burdens, as compared to those observed during the previous cruises. It also resulted in a different structure of the sympagic algal community, unusually dominated by Phaeocystis rather than diatoms. Compared to autumn-winter sea ice in the Weddell Sea (AWECS cruise), the 2017 Ross Sea pack ice displayed similar thickness distribution, but much lower snow cover and therefore nearly no flooding conditions. It is shown that contrasted dynamics of autumnal-winter sea-ice growth between the Weddell Sea and the Ross Sea impacted the development of the sympagic community. Mean/median ice Chl-a concentrations were 3–5 times lower at PIPERS, and the community status there appeared to be more mature (decaying?), based on Phaeopigments/Chl-a ratios. These contrasts are discussed in the light of temporal and spatial differences between the two cruises.
    Description: S. Stammerjohn was supported by the PIPERS and LTER Programs of the U.S. National Science Foundation, ANT-1341606 (S. Stammerjohn and J. Cassano, U Colorado) and ANT-0823101 (H. Ducklow, LDEO/Columbia University), respectively. Steve Ackley (UTSA) was supported by the PIPERS program of the U.S. National Science Foundation ANT-1341717 and by NASA Grant 80NSSC19M0194 to the Center for Adv. Meas. in Extreme Environments at UTSA.Ted Maksym (WHOI) was supported by the PIPERS program of the U.S. National Science Foundation ANT-1341513. This research was supported by the Belgian F.R.S-FNRS (project ISOGGAP and IODIne, contract T.0268.16 and J.0262.17, respectively). Fanny Van der Linden, Sarah Wauthy, Gauthier Carnat, Célia Sapart and Bruno Delille are PhD students, postdoctoral researchers and research associate, respectively, of the Belgian F.R.S.-FNRS. This work was also supported by the Australian Government's Cooperative Research Centre program through the Antarctic Climate & Ecosystems Cooperative Research Centre, and by the Australian Research Council's Special Research Initiative for Antarctic Gateway Partnership (Project ID SR140300001). Daiki Nomura was supported by grants from the Japan Society for the Promotion of Science (#17H04715) and the National Institute for Polar Research through Project Research KP-303 (ROBOTICA) and #28-14.
    Keywords: Antarctic glaciology ; biogeochemistry ; sea ice
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Description: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Description: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Keywords: sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
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  • 5
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baker, M. G., Aster, R. C., Anthony, R. E., Chaput, J., Wiens, D. A., Nyblade, A., Bromirski, P. D., Gerstoft, P., & Stephen, R. A. Seasonal and spatial variations in the ocean-coupled ambient wavefield of the Ross Ice Shelf. Journal of Glaciology, 65(254), (2019): 912-925, doi:10.1017/jog.2019.64.
    Description: The Ross Ice Shelf (RIS) is host to a broadband, multimode seismic wavefield that is excited in response to atmospheric, oceanic and solid Earth source processes. A 34-station broadband seismographic network installed on the RIS from late 2014 through early 2017 produced continuous vibrational observations of Earth's largest ice shelf at both floating and grounded locations. We characterize temporal and spatial variations in broadband ambient wavefield power, with a focus on period bands associated with primary (10–20 s) and secondary (5–10 s) microseism signals, and an oceanic source process near the ice front (0.4–4.0 s). Horizontal component signals on floating stations overwhelmingly reflect oceanic excitations year-round due to near-complete isolation from solid Earth shear waves. The spectrum at all periods is shown to be strongly modulated by the concentration of sea ice near the ice shelf front. Contiguous and extensive sea ice damps ocean wave coupling sufficiently so that wintertime background levels can approach or surpass those of land-sited stations in Antarctica.
    Description: This research was supported by NSF grants PLR-1142518, 1141916, 1142126, 1246151 and 1246416. JC was additionally supported by Yates funds in the Colorado State University Department of Mathematics. PDB also received support from the California Department of Parks and Recreation, Division of Boating and Waterways under contract 11-106-107. We thank Reinhard Flick and Patrick Shore for their support during field work, Tom Bolmer in locating stations and preparing maps, and the US Antarctic Program for logistical support. The seismic instruments were provided by the Incorporated Research Institutions for Seismology (IRIS) through the PASSCAL Instrument Center at New Mexico Tech. Data collected are available through the IRIS Data Management Center under RIS and DRIS network code XH. The PSD-PDFs presented in this study were processed with the IRIS Noise Tool Kit (Bahavar and others, 2013). The facilities of the IRIS Consortium are supported by the National Science Foundation under Cooperative Agreement EAR-1261681 and the DOE National Nuclear Security Administration. The authors appreciate the support of the University of Wisconsin-Madison Automatic Weather Station Program for the data set, data display and information; funded under NSF grant number ANT-1543305. The Ross Ice Shelf profiles were generated using the Antarctic Mapping Tools (Greene and others, 2017). Regional maps were generated with the Generic Mapping Tools (Wessel and Smith, 1998). Topography and bathymetry data for all maps in this study were sourced from the National Geophysical Data Center ETOPO1 Global Relief Model (doi:10.7289/V5C8276M). We thank two anonymous reviewers for suggestions on the scope and organization of this paper.
    Keywords: Antarctic glaciology ; Ice shelves ; Seismology
    Repository Name: Woods Hole Open Access Server
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