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      Fast and reliable molecular methods to detect fungal pathogens in woody plants

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          Abstract

          Plant diseases caused by pathogenic microorganisms represent a serious threat to plant productivity, food security, and natural ecosystems. An effective framework for early warning and rapid response is a crucial element to mitigate or prevent the impacts of biological invasions of plant pathogens. For these reasons, detection tools play an important role in monitoring plant health, surveillance, and quantitative pathogen risk assessment, thus improving best practices to mitigate and prevent microbial threats. The need to reduce the time of diagnosis has prompted plant pathologists to move towards more sensitive and rapid methods such as molecular techniques. Considering prevention to be the best strategy to protect plants from diseases, this review focuses on fast and reliable molecular methods to detect the presence of woody plant pathogens at early stage of disease development before symptoms occur in the host. A harmonized pool of novel technical, methodological, and conceptual solutions is needed to prevent entry and establishment of new diseases in a country and mitigate the impact of both invasive and indigenous organisms to agricultural and forest ecosystem biodiversity and productivity.

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          Most cited references119

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          AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

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            Five potential consequences of climate change for invasive species.

            Scientific and societal unknowns make it difficult to predict how global environmental changes such as climate change and biological invasions will affect ecological systems. In the long term, these changes may have interacting effects and compound the uncertainty associated with each individual driver. Nonetheless, invasive species are likely to respond in ways that should be qualitatively predictable, and some of these responses will be distinct from those of native counterparts. We used the stages of invasion known as the "invasion pathway" to identify 5 nonexclusive consequences of climate change for invasive species: (1) altered transport and introduction mechanisms, (2) establishment of new invasive species, (3) altered impact of existing invasive species, (4) altered distribution of existing invasive species, and (5) altered effectiveness of control strategies. We then used these consequences to identify testable hypotheses about the responses of invasive species to climate change and provide suggestions for invasive-species management plans. The 5 consequences also emphasize the need for enhanced environmental monitoring and expanded coordination among entities involved in invasive-species management.
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              MIQE précis: Practical implementation of minimum standard guidelines for fluorescence-based quantitative real-time PCR experiments

              The conclusions of thousands of peer-reviewed publications rely on data obtained using fluorescence-based quantitative real-time PCR technology. However, the inadequate reporting of experimental detail, combined with the frequent use of flawed protocols is leading to the publication of papers that may not be technically appropriate. We take the view that this problem requires the delineation of a more transparent and comprehensive reporting policy from scientific journals. This editorial aims to provide practical guidance for the incorporation of absolute minimum standards encompassing the key assay parameters for accurate design, documentation and reporting of qPCR experiments (MIQE précis) and guidance on the publication of pure 'reference gene' articles.
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                Author and article information

                Contributors
                nicola.luchi@ipsp.cnr.it
                Journal
                Appl Microbiol Biotechnol
                Appl. Microbiol. Biotechnol
                Applied Microbiology and Biotechnology
                Springer Berlin Heidelberg (Berlin/Heidelberg )
                0175-7598
                1432-0614
                31 January 2020
                31 January 2020
                2020
                : 104
                : 6
                : 2453-2468
                Affiliations
                [1 ]GRID grid.503048.a, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), ; Via Madonna del Piano, 10, I-50019 Sesto Fiorentino (Firenze), Italy
                [2 ]ANSES Plant Health Laboratory, Unit of Mycology, Domaine de Pixérécourt, 54220 Malzéville, France
                Author information
                https://orcid.org/0000-0003-3119-7574
                https://orcid.org/0000-0001-9359-5098
                https://orcid.org/0000-0002-7955-9207
                Article
                10395
                10.1007/s00253-020-10395-4
                7044139
                32006049
                9edc6f22-16ad-4119-aba9-791a223bca7e
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 23 October 2019
                : 10 January 2020
                : 19 January 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100010661, Horizon 2020 Framework Programme;
                Award ID: 771271
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001665, Agence Nationale de la Recherche;
                Award ID: ANR-11-LABX-0002-01
                Award Recipient :
                Categories
                Mini-Review
                Custom metadata
                © Springer-Verlag GmbH Germany, part of Springer Nature 2020

                Biotechnology
                early detection,dna-based techniques,fungal pathogens,invasive species,plant biosecurity,surveillance

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