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      Proteome analysis of Aspergillus flavus isolate-specific responses to oxidative stress in relationship to aflatoxin production capability

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          Abstract

          Aspergillus flavus is an opportunistic pathogen of plants such as maize and peanut under conducive conditions such as drought stress resulting in significant aflatoxin production. Drought-associated oxidative stress also exacerbates aflatoxin production by A. flavus. The objectives of this study were to use proteomics to provide insights into the pathogen responses to H 2O 2-derived oxidative stress, and to identify potential biomarkers and targets for host resistance breeding. Three isolates, AF13, NRRL3357, and K54A with high, moderate, and no aflatoxin production, were cultured in medium supplemented with varying levels of H 2O 2, and examined using an iTRAQ (Isobaric Tags for Relative and Absolute Quantification) approach. Overall, 1,173 proteins were identified and 220 were differentially expressed (DEPs). Observed DEPs encompassed metabolic pathways including antioxidants, carbohydrates, pathogenicity, and secondary metabolism. Increased lytic enzyme, secondary metabolite, and developmental pathway expression in AF13 was correlated with oxidative stress tolerance, likely assisting in plant infection and microbial competition. Elevated expression of energy and cellular component production in NRRL3357 and K54A implies a focus on oxidative damage remediation. These trends explain isolate-to-isolate variation in oxidative stress tolerance and provide insights into mechanisms relevant to host plant interactions under drought stress allowing for more targeted efforts in host resistance research.

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          LXXIII.—Oxidation of tartaric acid in presence of iron

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            A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

            (2013)
            Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. Availability: http://samtools.sourceforge.net. Contact: hengli@broadinstitute.org.
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              The return of metabolism: biochemistry and physiology of the pentose phosphate pathway

              The pentose phosphate pathway (PPP) is a fundamental component of cellular metabolism. The PPP is important to maintain carbon homoeostasis, to provide precursors for nucleotide and amino acid biosynthesis, to provide reducing molecules for anabolism, and to defeat oxidative stress. The PPP shares reactions with the Entner–Doudoroff pathway and Calvin cycle and divides into an oxidative and non-oxidative branch. The oxidative branch is highly active in most eukaryotes and converts glucose 6-phosphate into carbon dioxide, ribulose 5-phosphate and NADPH. The latter function is critical to maintain redox balance under stress situations, when cells proliferate rapidly, in ageing, and for the ‘Warburg effect’ of cancer cells. The non-oxidative branch instead is virtually ubiquitous, and metabolizes the glycolytic intermediates fructose 6-phosphate and glyceraldehyde 3-phosphate as well as sedoheptulose sugars, yielding ribose 5-phosphate for the synthesis of nucleic acids and sugar phosphate precursors for the synthesis of amino acids. Whereas the oxidative PPP is considered unidirectional, the non-oxidative branch can supply glycolysis with intermediates derived from ribose 5-phosphate and vice versa, depending on the biochemical demand. These functions require dynamic regulation of the PPP pathway that is achieved through hierarchical interactions between transcriptome, proteome and metabolome. Consequently, the biochemistry and regulation of this pathway, while still unresolved in many cases, are archetypal for the dynamics of the metabolic network of the cell. In this comprehensive article we review seminal work that led to the discovery and description of the pathway that date back now for 80 years, and address recent results about genetic and metabolic mechanisms that regulate its activity. These biochemical principles are discussed in the context of PPP deficiencies causing metabolic disease and the role of this pathway in biotechnology, bacterial and parasite infections, neurons, stem cell potency and cancer metabolism.
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                Author and article information

                Contributors
                baozhu.guo@ars.usda.gov
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                21 February 2018
                21 February 2018
                2018
                : 8
                : 3430
                Affiliations
                [1 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Department of Plant Pathology, , University of Georgia, ; Tifton, GA USA
                [2 ]ISNI 0000 0004 0404 0958, GRID grid.463419.d, USDA-ARS Crop Protection and Management Research Unit, ; Tifton, GA USA
                [3 ]ISNI 0000 0000 9323 1772, GRID grid.419337.b, Center of Excellence in Genomics & Systems Biology, International Crop Research Institute for the Semi-Arid Tropics (ICRISAT), ; Patancheru, Telangana India
                [4 ]ISNI 0000 0004 1936 8091, GRID grid.15276.37, Department of Biology, Genetics Institute, , Interdisciplinary Center for Biotechnology Research, University of Florida, ; Gainesville, FL USA
                [5 ]GRID grid.410625.4, College of Biology and Environmental Science, , Nanjing Forestry University, ; Nanjing, China
                [6 ]ISNI 0000 0004 1760 2876, GRID grid.256111.0, College of Plant Protection, , Fujian Agriculture and Forestry University, ; Fuzhou, Fujian China
                [7 ]ISNI 0000 0001 0662 7451, GRID grid.64337.35, Department of Plant Pathology and Crop Physiology, , Louisiana State University, ; Baton Rouge, LA USA
                [8 ]ISNI 0000 0004 1936 738X, GRID grid.213876.9, Department of Crop and Soil Sciences, , University of Georgia, ; Tifton, GA USA
                Author information
                http://orcid.org/0000-0002-2343-6566
                http://orcid.org/0000-0002-4562-9131
                Article
                21653
                10.1038/s41598-018-21653-x
                5821837
                29467403
                6c2df0e1-3405-4cdd-a1dd-501373e26b1f
                © The Author(s) 2018

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 October 2017
                : 3 February 2018
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