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      Bryo-Activities: A Review on How Bryophytes Are Contributing to the Arsenal of Natural Bioactive Compounds against Fungi

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          Abstract

          Usually regarded as less evolved than their more recently diverged vascular sisters, which currently dominate vegetation landscape, bryophytes seem having nothing to envy to the defensive arsenal of other plants, since they had acquired a suite of chemical traits that allowed them to adapt and persist on land. In fact, these closest modern relatives of the ancestors to the earliest terrestrial plants proved to be marvelous chemists, as they traditionally were a popular remedy among tribal people all over the world, that exploit their pharmacological properties to cure the most different diseases. The phytochemistry of bryophytes exhibits a stunning assortment of biologically active compounds such as lipids, proteins, steroids, organic acids, alcohols, aliphatic and aromatic compounds, polyphenols, terpenoids, acetogenins and phenylquinones, thus it is not surprising that substances obtained from various species belonging to such ancestral plants are widely employed as antitumor, antipyretic, insecticidal and antimicrobial. This review explores in particular the antifungal potential of the three Bryophyta divisions—mosses (Musci), hornworts (Anthocerotae) and liverworts (Hepaticae)—to be used as a sources of interesting bioactive constituents for both pharmaceutical and agricultural areas, providing an updated overview of the latest relevant insights.

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          MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

          Efficient analysis of very large amounts of raw data for peptide identification and protein quantification is a principal challenge in mass spectrometry (MS)-based proteomics. Here we describe MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data. Using correlation analysis and graph theory, MaxQuant detects peaks, isotope clusters and stable amino acid isotope-labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space. By integrating multiple mass measurements and correcting for linear and nonlinear mass offsets, we achieve mass accuracy in the p.p.b. range, a sixfold increase over standard techniques. We increase the proportion of identified fragmentation spectra to 73% for SILAC peptide pairs via unambiguous assignment of isotope and missed-cleavage state and individual mass precision. MaxQuant automatically quantifies several hundred thousand peptides per SILAC-proteome experiment and allows statistically robust identification and quantification of >4,000 proteins in mammalian cell lysates.
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            Phytozome: a comparative platform for green plant genomics

            The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.
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              MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

              Background Mass spectrometry (MS) coupled with online separation methods is commonly applied for differential and quantitative profiling of biological samples in metabolomic as well as proteomic research. Such approaches are used for systems biology, functional genomics, and biomarker discovery, among others. An ongoing challenge of these molecular profiling approaches, however, is the development of better data processing methods. Here we introduce a new generation of a popular open-source data processing toolbox, MZmine 2. Results A key concept of the MZmine 2 software design is the strict separation of core functionality and data processing modules, with emphasis on easy usability and support for high-resolution spectra processing. Data processing modules take advantage of embedded visualization tools, allowing for immediate previews of parameter settings. Newly introduced functionality includes the identification of peaks using online databases, MSn data support, improved isotope pattern support, scatter plot visualization, and a new method for peak list alignment based on the random sample consensus (RANSAC) algorithm. The performance of the RANSAC alignment was evaluated using synthetic datasets as well as actual experimental data, and the results were compared to those obtained using other alignment algorithms. Conclusions MZmine 2 is freely available under a GNU GPL license and can be obtained from the project website at: http://mzmine.sourceforge.net/. The current version of MZmine 2 is suitable for processing large batches of data and has been applied to both targeted and non-targeted metabolomic analyses.
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                Author and article information

                Journal
                Plants (Basel)
                Plants (Basel)
                plants
                Plants
                MDPI
                2223-7747
                21 January 2021
                February 2021
                : 10
                : 2
                : 203
                Affiliations
                [1 ]Department of Biotechnology, University of Verona, Cà Vignal 1, Strada Le Grazie 15, 37134 Verona (VR), Italy; mauro.commisso@ 123456univr.it
                [2 ]Department of Chemistry and Biology, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano (SA), Italy; fguarino@ 123456unisa.it
                [3 ]Department of Medicine and Surgery, Respiratory Disease and Lung Function Unit, University of Parma, Via Gramsci 14, 43125 Parma (PR), Italy; laura.marchi@ 123456unipr.it
                [4 ]Department of Biology, Ecology and Earth Sciences, University of Calabria, Via Ponte P. Bucci 6b, Arcavacata di Rende, 87036 Cosenza (CS), Italy; antonella.muto@ 123456unical.it
                [5 ]Laboratory of Plant Biology and Plant Proteomics (Lab.Bio.Pro.Ve), Department of Chemistry and Chemical Technologies, University of Calabria, Ponte P. Bucci 12 C, Arcavacata di Rende, 87036 Cosenza (CS), Italy; amalia.piro@ 123456unical.it
                [6 ]Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco delle Scienze 11/A, 43124 Parma (PR), Italy
                Author notes
                [†]

                All authors equally contributed to the manuscript.

                Author information
                https://orcid.org/0000-0001-6474-8577
                https://orcid.org/0000-0001-8536-4257
                https://orcid.org/0000-0002-6296-621X
                https://orcid.org/0000-0002-3937-251X
                Article
                plants-10-00203
                10.3390/plants10020203
                7911284
                33494524
                115e00fd-c043-4af6-a0eb-04522dcdb224
                © 2021 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 23 December 2020
                : 15 January 2021
                Categories
                Review

                bryophytes,plants bioactive compounds from early-diverged land,natural antifungals,plant extracts,mosses,liverworts,hornworts

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