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      Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics

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          Abstract

          <p class="first" id="d4426420e235">Mitochondria host vital cellular functions, including oxidative phosphorylation and co-factor biosynthesis, which are reflected in their proteome. At the cellular level plant mitochondria are organized into hundreds of discrete functional entities, which undergo dynamic fission and fusion. It is the individual organelle that operates in the living cell, yet biochemical and physiological assessments have exclusively focused on the characteristics of large populations of mitochondria. Here, we explore the protein composition of an individual average plant mitochondrion to deduce principles of functional and structural organisation. We perform proteomics on purified mitochondria from cultured heterotrophic Arabidopsis cells with intensity-based absolute quantification and scale the dataset to the single organelle based on criteria that are justified by experimental evidence and theoretical considerations. We estimate that a total of 1.4 million protein molecules make up a single Arabidopsis mitochondrion on average. Copy numbers of the individual proteins span five orders of magnitude, ranging from &gt;40 000 for Voltage-Dependent Anion Channel 1 to sub-stoichiometric copy numbers, i.e. less than a single copy per single mitochondrion, for several pentatricopeptide repeat proteins that modify mitochondrial transcripts. For our analysis, we consider the physical and chemical constraints of the single organelle and discuss prominent features of mitochondrial architecture, protein biogenesis, oxidative phosphorylation, metabolism, antioxidant defence, genome maintenance, gene expression, and dynamics. While assessing the limitations of our considerations, we exemplify how our understanding of biochemical function and structural organization of plant mitochondria can be connected in order to obtain global and specific insights into how organelles work. </p>

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          The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

          The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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            Chlorophyll fluorescence analysis: a guide to good practice and understanding some new applications.

            Chlorophyll fluorescence is a non-invasive measurement of photosystem II (PSII) activity and is a commonly used technique in plant physiology. The sensitivity of PSII activity to abiotic and biotic factors has made this a key technique not only for understanding the photosynthetic mechanisms but also as a broader indicator of how plants respond to environmental change. This, along with low cost and ease of collecting data, has resulted in the appearance of a large array of instrument types for measurement and calculated parameters which can be bewildering for the new user. Moreover, its accessibility can lead to misuse and misinterpretation when the underlying photosynthetic processes are not fully appreciated. This review is timely because it sits at a point of renewed interest in chlorophyll fluorescence where fast measurements of photosynthetic performance are now required for crop improvement purposes. Here we help the researcher make choices in terms of protocols using the equipment and expertise available, especially for field measurements. We start with a basic overview of the principles of fluorescence analysis and provide advice on best practice for taking pulse amplitude-modulated measurements. We also discuss a number of emerging techniques for contemporary crop and ecology research, where we see continual development and application of analytical techniques to meet the new challenges that have arisen in recent years. We end the review by briefly discussing the emerging area of monitoring fluorescence, chlorophyll fluorescence imaging, field phenotyping, and remote sensing of crops for yield and biomass enhancement.
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              Free Radicals in Biology and Medicine

              Free Radicals in Biology and Medicine has become a classic text in the field of free radical and antioxidant research. Now in its fifth edition, the book has been comprehensively rewritten and updated whilst maintaining the clarity of its predecessors. Two new chapters discuss 'in vivo' and 'dietary' antioxidants, the first emphasising the role of peroxiredoxins and integrated defence mechanisms which allow useful roles for ROS, and the second containing new information on the role of fruits, vegetables, and vitamins in health and disease. This new edition also contains expanded coverage of the mechanisms of oxidative damage to lipids, DNA, and proteins (and the repair of such damage), and the roles played by reactive species in signal transduction, cell survival, death, human reproduction, defence mechanisms of animals and plants against pathogens, and other important biological events. The methodologies available to measure reactive species and oxidative damage (and their potential pitfalls) have been fully updated, as have the topics of phagocyte ROS production, NADPH oxidase enzymes, and toxicology. There is a detailed and critical evaluation of the role of free radicals and other reactive species in human diseases, especially cancer, cardiovascular, chronic inflammatory and neurodegenerative diseases. New aspects of ageing are discussed in the context of the free radical theory of ageing. This book is recommended as a comprehensive introduction to the field for students, educators, clinicians, and researchers. It will also be an invaluable companion to all those interested in the role of free radicals in the life and biomedical sciences.
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                Author and article information

                Journal
                The Plant Journal
                Plant J
                Wiley
                0960-7412
                1365-313X
                November 07 2019
                January 2020
                November 03 2019
                January 2020
                : 101
                : 2
                : 420-441
                Affiliations
                [1 ]Institut für Biologie und Biotechnologie der Pflanzen (IBBP) Westfälische Wilhelms‐Universität Schlossplatz 7‐8 48143 Münster Germany
                [2 ]Institut für Nutzpflanzenforschung und Ressourcenschutz (INRES) Rheinische Friedrich‐Wilhelms‐Universität Bonn Friedrich‐Ebert‐Allee 144 53113 Bonn Germany
                [3 ]Institut für Pflanzengenetik Leibniz Universität Hannover Herrenhäuser Str. 2 30419 Hannover Germany
                [4 ]Department Biologie I ‐ Botanik Ludwig‐Maximilians‐Universität München Grosshadernerstr. 2‐4 82152 Planegg‐Martinsried Germany
                [5 ]Institut für Zelluläre und Molekulare Botanik (IZMB) Rheinische Friedrich‐Wilhelms‐Universität Bonn Kirschallee 1 53115 Bonn Germany
                [6 ]Institut für Biologie Martin‐Luther‐Universität Halle‐Wittenberg Weinbergweg 10 06120 Halle/Saale Germany
                [7 ]Institute of Developmental and Molecular Biology of Plants, and Cluster of Excellence on Plant Sciences (CEPLAS) Heinrich Heine University Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany
                Article
                10.1111/tpj.14534
                31520498
                8bd0892f-a3e8-451f-bce8-35c3d641a328
                © 2020

                http://creativecommons.org/licenses/by/4.0/

                http://doi.wiley.com/10.1002/tdm_license_1.1

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