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  1. Book ; Online ; E-Book: Assessments and Conservation of Biological Diversity from Coral Reefs to the Deep Sea

    Lopez, Jose Victor

    Uncovering Buried Treasures and the Value of the Benthos

    2024  

    Author's details Jose Victor Lopez
    Keywords Aquatic ecology ; Biodiversity ; Conservation biology ; Ecology ; Marine sciences ; Oceanography
    Subject code 577.7
    Language English
    Size 1 online resource (264 pages)
    Edition First edition.
    Publisher Nikki P. Levy
    Publishing place Kidlington, England
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 0-12-824113-6 ; 9780128241127 ; 978-0-12-824113-4 ; 0128241128
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Change and stasis of distinct sediment microbiomes across Port Everglades Inlet (PEI) and the adjacent coral reefs.

    Krausfeldt, Lauren E / Lopez, Jose Victor / Bilodeau, Catherine Margaret / Won Lee, Hyo / Casali, Shelby L

    PeerJ

    2023  Volume 11, Page(s) e14288

    Abstract: Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port ... ...

    Abstract Deep water ports are human built coastal structures that by definition welcome ship traffic and disturbance. Evidence is accumulating that enhanced port activities such as dredging or deepening have negatively affected nearby natural habitats. Port Everglades Inlet (PEI) is a large active South Florida cargo port for over two million people and lies adjacent to coral reefs, dwindling mangroves, and recreational beaches. In this study, the microbial communities of PEI and adjacent reef sediments were characterized to serve as indicators for change due to dredging and assess anthropogenic influence on these sensitive ecosystems by sequencing the V4 region of 16S rRNA ahead of a large-scale port deepening event. For the first time, this study established baseline bacterial community characterizations and their patterns of diversity prior to and after a maintenance dredging event. PEI samples were collected for two consecutive years 2020 (Phase I, before maintenance dredging) and 2021 (Phase II, after maintenance dredging) from PEI sediments and adjacent coral reef sediments. In spite of their proximity and tidal connections through the PEI, reef and PEI sediment microbial communities were distinct. Changes in microbial diversity within the intracoastal waterway (ICW), a route for community exchange or transfers, were the greatest after maintenance dredging occurred. Microbial diversity in reef sediments also changed after dredging, indicating potential influence from resuspended sediments due to an associated increase in trace metals and decrease in cyanobacterial diversity. Sediments were identified as a possible source of human and coral pathogens, although dredging did not affect the relative abundances of these indicator microorganisms. This study highlighted the utility and relative ease of applying current molecular ecology methods to address macroscale questions with environmental management ramifications.
    MeSH term(s) Animals ; Humans ; Coral Reefs ; RNA, Ribosomal, 16S/genetics ; Bays ; Anthozoa/genetics ; Microbiota/genetics ; Bacteria/genetics
    Chemical Substances RNA, Ribosomal, 16S
    Language English
    Publishing date 2023-01-13
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.14288
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: ddPCR Reveals SARS-CoV-2 Variants in Florida Wastewater

    Gering, Eben / Colbert, Jacob / Schmedes, Sarah / Duncan, George / Lopez, Jose Victor / Motes, Jessy / Weiss, James / Azarian, Taj / Tekin, Omer / Blanton, Jason

    medRxiv

    Abstract: Wastewater was screened for the presence of functionally significant mutations in SARS-CoV-2 associated with emerging variants of concern (VOC) by ddPCR, and results accorded with sequencing of clinical samples from the same region. We propose that PCR- ... ...

    Abstract Wastewater was screened for the presence of functionally significant mutations in SARS-CoV-2 associated with emerging variants of concern (VOC) by ddPCR, and results accorded with sequencing of clinical samples from the same region. We propose that PCR-based screening of wastewater can provide a powerful tool for rapid and inexpensive screening of large population segments for VOC-associated mutations and can hone complementary sampling and sequencing of direct (human) test material to track emerging VOC.
    Keywords covid19
    Language English
    Publishing date 2021-04-13
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.04.08.21255119
    Database COVID19

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  4. Article ; Online: Standards recommendations for the earth biogenome project

    Lawniczak, Mara K.N. / Durbin, Richard / Flicek, Paul / Lindblad-Toh, Kerstin / Wei, Xiaofeng / Archibald, John M. / Baker, William J. / Belov, Katherine / Blaxter, Mark L. / Bonet, Tomas Marques / Childers, Anna K. / Davey, Robert P. / Di Palma, Federica / Fang, Qi / Wilfried, Haerty / Hall, Neil / Hoff, Katharina J. / Howe, Kerstin / Jarvis, Erich D. /
    Johnson, Warren E. / Johnson, Rebecca N. / Liu, Xin / Lopez, Jose Victor / Myers, Eugene W. / Pettersson, Olga Vinnere / Poelchau, Monica F. / Pruitt, Kim D. / Rhie, Arang / Castilla-Rubio, Juan Carlos / Sahu, Sunil Kumar / Salmon, Nicholas A. / Soltis, Pamela S. / Swarbreck, David / Thibaud-Nissen, Francoise / Wang, Sibo / Wegrzyn, Jill L. / Zhang, Guojie / Zhang, He / Lewin, Harris A. / Richards, Stephen

    Proceedings of the National Academy of Sciences of the United States of America. 2022 Jan. 25, v. 119, no. 4

    2022  

    Abstract: A global international initiative such as the Earth BioGenome Project (EBP) requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress towards its goals. Towards this end the EBP initiated five ... ...

    Abstract A global international initiative such as the Earth BioGenome Project (EBP) requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress towards its goals. Towards this end the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing; Sequencing and Assembly; Annotation; Analysis; and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website (earthbiogenome.org), with the recognition that opportunities, technologies and challenges may improve or change in the future requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the standards process, and areas where additional challenges will need to be met.
    Keywords Internet ; area ; committees ; metagenomics ; sampling ; volunteerism ; volunteers ; wills ; United States
    Language English
    Dates of publication 2022-0125
    Document type Article ; Online
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2115639118
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  5. Article ; Online: Standards recommendations for the Earth BioGenome Project.

    Lawniczak, Mara K N / Durbin, Richard / Flicek, Paul / Lindblad-Toh, Kerstin / Wei, Xiaofeng / Archibald, John M / Baker, William J / Belov, Katherine / Blaxter, Mark L / Marques Bonet, Tomas / Childers, Anna K / Coddington, Jonathan A / Crandall, Keith A / Crawford, Andrew J / Davey, Robert P / Di Palma, Federica / Fang, Qi / Haerty, Wilfried / Hall, Neil /
    Hoff, Katharina J / Howe, Kerstin / Jarvis, Erich D / Johnson, Warren E / Johnson, Rebecca N / Kersey, Paul J / Liu, Xin / Lopez, Jose Victor / Myers, Eugene W / Pettersson, Olga Vinnere / Phillippy, Adam M / Poelchau, Monica F / Pruitt, Kim D / Rhie, Arang / Castilla-Rubio, Juan Carlos / Sahu, Sunil Kumar / Salmon, Nicholas A / Soltis, Pamela S / Swarbreck, David / Thibaud-Nissen, Françoise / Wang, Sibo / Wegrzyn, Jill L / Zhang, Guojie / Zhang, He / Lewin, Harris A / Richards, Stephen

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 4

    Abstract: A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five ... ...

    Abstract A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.
    MeSH term(s) Animals ; Base Sequence/genetics ; Biodiversity ; Eukaryota/genetics ; Genomics/methods ; Genomics/standards ; Humans ; Reference Standards ; Reference Values ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/standards
    Language English
    Publishing date 2022-01-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2115639118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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