skip to main content

Title: Vision, challenges and opportunities for a Plant Cell Atlas
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.  more » « less
Award ID(s):
1916797 2052590 1905869 1916804
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more » ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; « less
Date Published:
Journal Name:
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally. Community discussions focused on topics such as data analysis tools and annotation standards; computational expertise and cyber‐infrastructure; modes of community organization and engagement; methods for ensuring a broad reach in the PCA community; recruitment, training, and nurturing of new talent; and the overall impact of the PCA initiative. These targeted discussions facilitated dialogue among the participants to gauge whether PCA might be a vehicle for formulating a data synthesis center. The conversations also explored how online tools can be leveraged to help broaden the reach of the PCA (i.e., online contests, virtual networking, and social media stakeholder engagement) and decrease costs of conducting research (e.g., virtual REU opportunities). Major recommendations for the future of the PCA included establishing standards, creating dashboards for easy and intuitive access to data, and engaging with a broad community of stakeholders. The discussions also identified the following as being essential to the PCA's success: identifying homologous cell‐type markers and their biocuration, publishing datasets and computational pipelines, utilizing online tools for communication (such as Slack), and user‐friendly data visualization and data sharing. In conclusion, the development of a data synthesis center will help the PCA community achieve these goals by providing a centralized repository for existing and new data, a platform for sharing tools, and new analytical approaches through collaborative, multidisciplinary efforts. A data synthesis center will help the PCA reach milestones, such as community‐supported data evaluation metrics, accelerating plant research necessary for human and environmental health.

    more » « less
  2. Abstract  
    more » « less
  3. Sustainability, including environmental and social sustainability, has been identified across all sectors, from government to industry to academia, as a critical area for action. Sustainability goals and actions, by necessity, require input from many fields, but engineers play a potentially outsized role due to the structures and products they build, and the associated choices they make. The Engineering for One Planet (EOP) initiative aims to address this challenge by ensuring all future engineers, no matter their discipline, are equipped with the skills, knowledge, understanding, and mindsets to design, build, and create in sustainable ways. Much has been achieved to date by the EOP initiative, through a process of multi-stakeholder engagement, in both understanding and piloting solutions to realize the EOP vision. However, in order to achieve the far reaching systemic changes desired, a roadmap for a Collective Impact-informed, cross-sector, collaborative initiative was developed. This roadmap leverages the approaches yielded from the recent National Science Foundation (NSF)-funded EOP Scaling for Impact Workshop, the lessons learned and results achieved from the initiative to date, and key considerations drawn from a Collective Impact approach that centers equity. This roadmap calls for stakeholders—including academia, industry, accrediting and professional organizations, community organizations, non-profits, funders, and those communities most impacted by the negative impacts of environmental and social sustainability challenges— to move beyond singular programmatic interventions, and instead work to collaboratively understand and construct coordinated solutions, to integrating sustainability into engineering education and the engineering profession. The roadmap’s call to action invites collaborators to join this initiative and engage with the roadmap as a starting point for their work together; the roadmap provides immediate action steps, and invites collaborators to further shape the roadmap into a collective, achievable plan for systems change, that they, their institutions/organizations, and other cross-sector collaborators can embrace. For systems change is never complete and the solutions not finite; it is only through ongoing, collective action that we can fully understand, and learn how to address the lack of sustainability in engineering as the complex, social problem it is. 
    more » « less
  4. Abstract

    Carbon dioxide (CO2) quantification is critical for assessing city‐level carbon emissions and sustainable urban development. While urban vegetation has the potential to provide environmental benefits, such as heat and carbon mitigation, the CO2exchange from biogenic sectors and its impact from the environmental perturbations are often overlooked. It is also challenging to simulate the plant functions in the complex urban terrain. This study presents a processed‐based modeling approach to assess the biogenic carbon fluxes from the vegetated areas over the Chicago Metropolitan Area (CMA) using the Weather Research and Forecast—Urban Biogenic Carbon exchange model. We investigate the change of CO2sink power in CMA under heatwaves and irrigation. The results indicate that the vegetation plays a significant role in the city's carbon portfolio and the landscaping management has the potential to reduce carbon emissions significantly. Furthermore, based on the competing mechanisms in the biogenic carbon balance identified in this study, we develop a novel Environmental Benefit Score metrics framework to identify the vulnerability and mitigation measures associated with nature‐based solutions (NbS) within CMA. By using the generalized portable framework and our science‐policy confluence analysis presented in this study, global cities can maximize the effectiveness of NbS and accelerate carbon neutrality.

    more » « less
  5. The research data repository of the Environmental Data Initiative (EDI) is building on over 30 years of data curation research and experience in the National Science Foundation-funded US Long-Term Ecological Research (LTER) Network. It provides mature functionalities, well established workflows, and now publishes all ‘long-tail’ environmental data. High quality scientific metadata are enforced through automatic checks against community developed rules and the Ecological Metadata Language (EML) standard. Although the EDI repository is far along in making its data findable, accessible, interoperable, and reusable (FAIR), representatives from EDI and the LTER are developing best practices for the edge cases in environmental data publishing. One of these is the vast amount of imagery taken in the context of ecological research, ranging from wildlife camera traps to plankton imaging systems to aerial photography. Many images are used in biodiversity research for community analyses (e.g., individual counts, species cover, biovolume, productivity), while others are taken to study animal behavior and landscape-level change. Some examples from the LTER Network include: using photos of a heron colony to measure provisioning rates for chicks (Clarkson and Erwin 2018) or identifying changes in plant cover and functional type through time (Peters et al. 2020). Multi-spectral images are employed to identify prairie species. Underwater photo quads are used to monitor changes in benthic biodiversity (Edmunds 2015). Sosik et al. (2020) used a continuous Imaging FlowCytobot to identify and measure phyto- and microzooplankton. Cameras at McMurdo Dry Valleys assess snow and ice cover on Antarctic lakes allowing estimation of primary production (Myers 2019). It has been standard practice to publish numerical data extracted from images in EDI; however, the supporting imagery generally has not been made publicly available. Our goal in developing best practices for documenting and archiving these images is for them to be discovered and re-used. Our examples demonstrate several issues. The research questions, and hence, the image subjects are variable. Images frequently come in logical sets of time series. The size of such sets can be large and only some images may be contributed to a dedicated specialized repository. Finally, these images are taken in a larger monitoring context where many other environmental data are collected at the same time and location. Currently, a typical approach to publishing image data in EDI are packages containing compressed (ZIP or tar) files with the images, a directory manifest with additional image-specific metadata, and a package-level EML metadata file. Images in the compressed archive may be organized within directories with filenames corresponding to treatments, locations, time periods, individuals, or other grouping attributes. Additionally, the directory manifest table has columns for each attribute. Package-level metadata include standard coverage elements (e.g., date, time, location) and sampling methods. This approach of archiving logical ‘sets’ of images reduces the effort of providing metadata for each image when most information would be repeated, but at the expense of not making every image individually searchable. The latter may be overcome if the provided manifest contains standard metadata that would allow searching and automatic integration with other images. 
    more » « less