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Fletcher-Hoppe C, Yeh YC, Raut Y, Weissman JL, Fuhrman JA. Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California. ISME Commun 2023; 3:63. [PMID: 37355737 PMCID: PMC10290647 DOI: 10.1038/s43705-023-00268-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/05/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Biological nitrogen fixation, the conversion of N2 gas into a bioavailable form, is vital to sustaining marine primary production. Studies have shifted beyond traditionally studied tropical diazotrophs. Candidatus Atelocyanobacterium thalassa (or UCYN-A) has emerged as a focal point due to its streamlined metabolism, intimate partnership with a haptophyte host, and broad distribution. Here, we explore the environmental parameters that govern UCYN-A's presence at the San Pedro Ocean Time-series (SPOT), its host specificity, and statistically significant interactions with non-host eukaryotes from 2008-2018. 16S and 18S rRNA gene sequences were amplified by "universal primers" from monthly samples and resolved into Amplicon Sequence Variants, allowing us to observe multiple UCYN-A symbioses. UCYN-A1 relative abundances increased following the 2015-2016 El Niño event. This "open ocean ecotype" was present when coastal upwelling declined, and Ekman transport brought tropical waters into the region. Network analyses reveal all strains of UCYN-A co-occur with dinoflagellates including Lepidodinium, a potential predator, and parasitic Syndiniales. UCYN-A2 appeared to pair with multiple hosts and was not tightly coupled to its predominant host, while UCYN-A1 maintained a strong host-symbiont relationship. These biological relationships are particularly important to study in the context of climate change, which will alter UCYN-A distribution at regional and global scales.
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Affiliation(s)
- Colette Fletcher-Hoppe
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - Yi-Chun Yeh
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Department of Global Ecology, Carnegie Institution for Science, Stanford University, Stanford, CA, USA
| | - Yubin Raut
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
| | - J L Weissman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA
- Schmid College of Science and Technology, Chapman University, Orange, CA, USA
| | - Jed A Fuhrman
- Marine & Environmental Biology, Department of Biological Sciences, University of Southern California (USC), Los Angeles, CA, USA.
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Levy KD, Blake K, Fletcher-Hoppe C, Franciosi J, Goto D, Hicks JK, Holmes AM, Kanuri SH, Madden EB, Musty MD, Orlando L, Pratt VM, Ramos M, Wu R, Ginsburg GS. Correction: Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genet Med 2021; 23:2020. [PMID: 33288881 PMCID: PMC8486650 DOI: 10.1038/s41436-020-01054-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Kenneth D Levy
- Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Kathryn Blake
- Nemours Children's Specialty Care, Jacksonville, FL, USA
| | - Colette Fletcher-Hoppe
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | - James Franciosi
- Nemours Children's Hospital University of Central Florida College of Medicine, Orlando, FL, USA
| | - Daisuke Goto
- University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - James K Hicks
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Ann M Holmes
- Department of Health Policy and Management, IU Fairbanks School of Public Health, IUPUI, Indianapolis, IN, USA
| | | | - Ebony B Madden
- National Human Genome Research Institute, Bethesda, MD, USA
| | - Michael D Musty
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Lori Orlando
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | | | - Michelle Ramos
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryanne Wu
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine, Durham, NC, USA
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Levy KD, Blake K, Fletcher-Hoppe C, Franciosi J, Goto D, Hicks JK, Holmes AM, Kanuri SH, Madden EB, Musty MD, Orlando L, Pratt VM, Ramos M, Wu R, Ginsburg GS. Opportunities to implement a sustainable genomic medicine program: lessons learned from the IGNITE Network. Genet Med 2018; 21:743-747. [PMID: 29997387 PMCID: PMC6330142 DOI: 10.1038/s41436-018-0080-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/25/2018] [Indexed: 02/07/2023] Open
Abstract
Purpose While there is growing scientific evidence for and significant advances in the use of genomic technologies in medicine, there is a significant lag in the clinical adoption and sustainability of genomic medicine. Here we describe the findings from the National Human Genome Research Institute’s (NHGRI) Implementing GeNomics In pracTicE (IGNITE) Network in identifying key constructs, opportunities, and challenges associated with driving sustainability of genomic medicine in clinical practice. Methods Network members and affiliates were surveyed to identify key drivers associated with implementing and sustaining a genomic medicine program. Tallied results were used to develop and weigh key constructs/drivers required to support sustainability of genomic medicine programs. Results The top three driver–stakeholder dyads were (1) genomic training for providers, (2) genomic clinical decision support (CDS) tools embedded in the electronic health record (EHR), and (3) third party reimbursement for genomic testing. Conclusion Priorities may differ depending on healthcare systems when comparing the current state of key drivers versus projected needs for supporting genomic medicine sustainability. Thus we provide gap-filling guidance based on IGNITE members’ experiences. Although results are limited to findings from the IGNITE network, their implementation, scientific, and clinical experience may be used as a road map by others considering implementing genomic medicine programs.
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Affiliation(s)
- Kenneth D Levy
- Indiana University School of Medicine Indianapolis, Indianapolis, Indiana, USA.
| | - Kathryn Blake
- Nemours Children's Specialty Care Jacksonville, Jacksonville, Florida, USA
| | - Colette Fletcher-Hoppe
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California, USA
| | - James Franciosi
- Nemours Children's Hospital University of Central Florida College of Medicine Orlando, Orlando, Florida, USA
| | - Daisuke Goto
- University of Maryland School of Pharmacy, Baltimore, Maryland, USA
| | - James K Hicks
- H. Lee Moffitt Cancer Center and Research Institute Tampa, Tampa, Florida, USA
| | - Ann M Holmes
- Department of Health Policy and Management, IU Fairbanks School of Public Health, IUPUI, Indianapolis, Indiana, USA
| | - Sri Harsha Kanuri
- Indiana University School of Medicine Indianapolis, Indianapolis, Indiana, USA
| | - Ebony B Madden
- National Human Genome Research Institute Bethesda, Bethesda, Maryland, USA
| | - Michael D Musty
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine Durham, Durham, North Carolina, USA
| | - Lori Orlando
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine Durham, Durham, North Carolina, USA
| | - Victoria M Pratt
- Indiana University School of Medicine Indianapolis, Indianapolis, Indiana, USA
| | - Michelle Ramos
- Icahn School of Medicine at Mount Sinai New York, New York, New York, USA
| | - Ryanne Wu
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine Durham, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics & Precision Medicine, Duke University School of Medicine Durham, Durham, North Carolina, USA
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Wong KM, Langlais K, Tobias GS, Fletcher-Hoppe C, Krasnewich D, Leeds HS, Rodriguez LL, Godynskiy G, Schneider VA, Ramos EM, Sherry ST. The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data. Nucleic Acids Res 2016; 45:D819-D826. [PMID: 27899644 PMCID: PMC5210596 DOI: 10.1093/nar/gkw1139] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 10/28/2016] [Accepted: 10/31/2016] [Indexed: 11/24/2022] Open
Abstract
The database of Genotypes and Phenotypes (dbGaP) Data Browser (https://www.ncbi.nlm.nih.gov/gap/ddb/) was developed in response to requests from the scientific community for a resource that enable view-only access to summary-level information and individual-level genotype and sequence data associated with phenotypic features maintained in the controlled-access tier of dbGaP. Until now, the dbGaP controlled-access environment required investigators to submit a data access request, wait for Data Access Committee review, download each data set and locally examine them for potentially relevant information. Existing unrestricted-access genomic data browsing resources (e.g. http://evs.gs.washington.edu/EVS/, http://exac.broadinstitute.org/) provide only summary statistics or aggregate allele frequencies. The dbGaP Data Browser serves as a third solution, providing researchers with view-only access to a compilation of individual-level data from general research use (GRU) studies through a simplified controlled-access process. The National Institutes of Health (NIH) will continue to improve the Browser in response to user feedback and believes that this tool may decrease unnecessary download requests, while still facilitating responsible genomic data-sharing.
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Affiliation(s)
- Kira M Wong
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Kristofor Langlais
- Office of Science Policy, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA
| | - Geoffrey S Tobias
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Colette Fletcher-Hoppe
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Donna Krasnewich
- National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hilary S Leeds
- Office of Science Policy, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Georgy Godynskiy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Valerie A Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20814, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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