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  • Data management  (14)
  • Photosynthesis  (3)
  • 1
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 9944-9949, doi:10.1073/pnas.1509448112.
    Description: Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet utilized few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multi-tiered, hierarchical cascade of acclimation responses with different Fe thresholds. The multi-tiered response included changes in Fe acquisition, storage, and photosynthetic proteins, substitution of flavodoxin for ferredoxin, and modified photophysiology, all while maintaining remarkably stable growth rates over a range of Fe concentrations. Modulation of two distinct ferric uptake regulator (Fur) proteins that coincided with the multi-tiered proteome response was found, implying the coastal strain has different regulatory threshold responses to low Fe availability. Low nitrogen (N) and phosphorus (P) availability in the open ocean may favor the loss of Fe response genes when Fe availability is consistent over time, whereas these genes are retained in dynamic environments where Fe availability fluctuates and N and P are more abundant.
    Description: This work was supported by a National Science Foundation Postdoctoral Research Fellowship in Biology to K.R.M.M. (NSF 1103575), National Science Foundation Oceanography grants OCE-1220484, OCE-0928414, OCE-1233261, OCE- 1155566, OCE-1131387, and OCE-0926092, as well as Gordon and Betty Moore Foundation grants 3782 and 3934.
    Keywords: Iron adaptation ; Synechococcus ; Photosynthesis ; Quantitative proteomics
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 2
    Publication Date: 2022-05-25
    Description: Presented at AGU Fall Meeting, American Geophysical Union, Washington, D.C., 10 – 14 Dec 2018
    Description: Data repositories often transform submissions to improve understanding and reuse of data by researchers other than the original submitter. However, scientific workflows built by the data submitters often depend on the original data format. In some cases, this makes the repository’s final data product less useful to the submitter. As a result, these two workable but different versions of the data provide value to two disparate, non-interoperable research communities around what should be a single dataset. Data repositories could bridge these two communities by exposing provenance explaining the transform from original submission to final product. A subsequent benefit of this provenance would be the transparent value-add of domain repository data curation. To improve its data management process efficiency, the Biological and Chemical Oceanography Data Management Office (BCO-DMO, https://www.bco-dmo.org) has been adopting the data containerization specification defined by the Frictionless Data project (https://frictionlessdata.io). Recently, BCO-DMO has been using the Frictionless Data Package Pipelines Python library (https://github.com/frictionlessdata/datapackage-pipelines) to capture the data curation processing steps that transform original submissions to final data products. Because these processing steps are stored using a declarative language they can be converted to a structured provenance record using the Provenance Ontology (PROV-O, https://www.w3.org/TR/prov-o/). PROV-O abstracts the Frictionless Data elements of BCO-DMO’s workflow for capturing necessary curation provenance and enables interoperability with other external provenance sources and tools. Users who are familiar with PROV-O or the Frictionless Data Pipelines can use either record to reproduce the final data product in a machine-actionable way. While there may still be some curation steps that cannot be easily automated, this process is a step towards end-to-end reproducible transforms throughout the data curation process. In this presentation, BCO-DMO will demonstrate how Frictionless Data Package Pipelines can be used to capture data curation provenance from original submission to final data product exposing the concrete value-add of domain-specific repositories.
    Description: NSF #1435578
    Keywords: Provenance ; Frictionless Data ; Data management
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 3
    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 Inomura, K., Deutsch, C., Wilson, S. T., Masuda, T., Lawrenz, E., Lenka, B., Sobotka, R., Gauglitz, J. M., Saito, M. A., Prášil, O., & Follows, M. J. Quantifying oxygen management and temperature and light dependencies of nitrogen fixation by Crocosphaera watsonii. Msphere, 4(6), (2019): e00531-19, doi: 10.1128/msphere.00531-19.
    Description: Crocosphaera is a major dinitrogen (N2)-fixing microorganism, providing bioavailable nitrogen (N) to marine ecosystems. The N2-fixing enzyme nitrogenase is deactivated by oxygen (O2), which is abundant in marine environments. Using a cellular scale model of Crocosphaera sp. and laboratory data, we quantify the role of three O2 management strategies by Crocosphaera sp.: size adjustment, reduced O2 diffusivity, and respiratory protection. Our model predicts that Crocosphaera cells increase their size under high O2. Using transmission electron microscopy, we show that starch granules and thylakoid membranes are located near the cytoplasmic membranes, forming a barrier for O2. The model indicates a critical role for respiration in protecting the rate of N2 fixation. Moreover, the rise in respiration rates and the decline in ambient O2 with temperature strengthen this mechanism in warmer water, providing a physiological rationale for the observed niche of Crocosphaera at temperatures exceeding 20°C. Our new measurements of the sensitivity to light intensity show that the rate of N2 fixation reaches saturation at a lower light intensity (∼100 μmol m−2 s−1) than photosynthesis and that both are similarly inhibited by light intensities of 〉500 μmol m−2 s−1. This suggests an explanation for the maximum population of Crocosphaera occurring slightly below the ocean surface.
    Description: We thank Stephanie Dutkiewicz and Sallie W. Chisholm for useful discussion, Martin Lukeš for technical assistance for the N2 fixation measurement, and the members of Writing and Communication Center at MIT for their advice on writing. This research was supported by the Japan Student Service Organization (JASSO) (grant L11171020001 to K.I.), the Gordon and Betty Moore Foundation (grant GBMF 3775 to C.D. and grant GBMF 3778 to M.J.F.), the U.S. National Science Foundation (grant OCE-1756524 to S.T.W., grant OCE-1558702 to M.J.F., and grant OCE-PRF 1421196 to J.M.G), the Simons Foundation (Simons Postdoctoral Fellowship in Marine Microbial Ecology award 544338 to K.I., Simons Collaboration on Ocean Processes and Ecology award 329108 to M.J.F., Simons Collaboration on Computational BIOgeochemical Modeling of Marine EcosystemS [CBIOMES] award 549931 to M.J.F.), the Czech Science Foundation (GAČR) (grant 16-15467S to O.P.), and the National Sustainability Programme (NPU) (grant LO1416 Algatech plus to O.P.).
    Keywords: Crocosphaera ; Carbon ; Cell flux model ; Daily cycle ; Iron ; Light ; Nitrogen ; Nitrogen fixation ; Oxygen ; Photosynthesis ; Temperature
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-10-21
    Description: Presented at 2022 OCB Summer Workshop, Woods Hole, MA, 20 - 23, June 2022
    Description: An unparalleled data catalog of well-documented, interoperable oceanographic data and information, openly accessible to all end-users through an intuitive web-based interface for the purposes of advancing marine research, education, and policy. Conference Website: https://web.whoi.edu/ocb-workshop/
    Description: NSF #1924618
    Keywords: Data management
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 5
    Publication Date: 2022-10-21
    Description: Presented at Ocean Sciences, San Diego, 16-21, February 2020
    Description: BCO-DMO curates earth science data where models become increasingly important. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of chemical and biological properties within the ocean ecosystem. We feel the time is at hand for the scientific community to begin a concerted and holistic approach to the curation of code and software.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 6
    Publication Date: 2022-10-21
    Description: Presented at Ocean Sciences, San Diego, 16-21, February 2020
    Description: Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine biological, chemical, physical, and biogeochemical data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster will introduce the repository and describe some of the strategic enhancements coming to BCO-DMO, and presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input can help BCO-DMO improve its service to the research community.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 7
    Publication Date: 2022-10-21
    Description: Presented at AGU Fall Meeting 10 – 14 December 2018, Washington, D.C.
    Description: The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is a publicly accessible earth science data repository created to curate, publicly serve (publish), and archive digital data and information from biological, chemical and biogeochemical research conducted in coastal, marine, great lakes and laboratory environments. The BCO-DMO repository works closely with investigators funded through the NSF OCE Division’s Biological and Chemical Sections and Antarctic Organisms & Ecosystems. The office provides services that span the full data life cycle, from data management planning support and DOI creation, to archiving with appropriate national facilities. Recently, more and more of the projects submitted to BCO-DMO represent modeling efforts which further increase our knowledge of the chemical and biological properties within the ocean ecosystem. But, as a repository traditionally focused on observational data as a primary research output, what roles should domain-specific data repositories play in this field? Recognizing code as a first class research product, how should repositories support the discovery, access and reuse of code and software used in hypothesis driven research? We feel the time is at hand for the community to begin a concerted and holistic approach to the curation of code and software. Such strategy development should begin with asking what is the appropriate output to curate? What is the minimum metadata required for re-use? How should code be stored and accessed? Should repositories support or facilitate peer reviewing code? The answers to these questions will better inform domain-specific repositories on how to better manage code as a first class research asset in order to support the scientific community. This presentation will explore these topics, inviting discussion from the audience to advance a collective strategy.
    Description: NSF #1435578
    Keywords: Data management ; Provenance ; Data repository ; Worfklow ; Modeling Conference Name: AGU 2018 Conference Location: Washington, D.C
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-10-21
    Description: Presented at OCB Summer Workshop, June 24-27 2019, Woods Hole MA.
    Description: Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine ecosystem data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. This poster describes some of the existing infrastructure and strategic enhancements at BCO-DMO in support of the F.A.I.R principles.
    Keywords: Data management ; F.A.I.R data ; Open science ; Open data
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 9
    Publication Date: 2022-10-21
    Description: Presented at OCB Summer Workshop, June 24-27 2019, Woods Hole MA.
    Description: Oceanographic data, when well-documented and stewarded toward preservation, have the potential to accelerate new science and facilitate our understanding of complex natural systems. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the NSF to document and manage marine ecosystem data, ensuring their discovery and access, and facilitating their reuse. The task of curating and providing access to research data is a collaborative process, with associated actors and critical activities occurring throughout the data’s life cycle. BCO-DMO supports all phases of the data life cycle and works closely with investigators to ensure open access of well-documented project data and information. Supporting this curation process is a flexible cyberinfrastructure that provides the means for data submission, discovery, and access; ultimately enabling reuse. Based upon community feedback, this infrastructure is undergoing evaluation and improvement to better meet oceanographic research needs. This poster presents an opportunity for you to provide feedback on enhancements yet to come. We invite you to think about your own research workflow of searching and accessing new data for research, and to provide your feedback through the poster’s interactive sections. Your input will help BCO-DMO improve its service to the research community.
    Description: Award(s): NSF #1435578
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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  • 10
    Publication Date: 2022-10-21
    Description: Presented at Fall AGU (ESIP Data Helpdesk), New Orleans, 11-17, December 2021
    Description: BCO-DMO curates a database of research-ready data spanning the full range of marine ecosystem related measurements including in-situ and remotely sensed observations, experimental and model results, and synthesis products. We work closely with investigators to publish data and information from research projects supported by the National Science Foundation (NSF), as well as those supported by state, private, and other funding sources. BCO-DMO supports all phases of the data life cycle and ensures open access of well-curated project data and information. We employ F.A.I.R. Principles that comprise a set of values intended to guide data producers and publishers in establishing good data management practices that will enable effective reuse.
    Description: Award(s): NSF #1924618
    Keywords: Data management ; Open science ; Survey ; Research needs
    Repository Name: Woods Hole Open Access Server
    Type: Presentation
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