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      Spatial specificity of auxin responses coordinates wood formation

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          Abstract

          Spatial organization of signalling events of the phytohormone auxin is fundamental for maintaining a dynamic transition from plant stem cells to differentiated descendants. The cambium, the stem cell niche mediating wood formation, fundamentally depends on auxin signalling but its exact role and spatial organization is obscure. Here we show that, while auxin signalling levels increase in differentiating cambium descendants, a moderate level of signalling in cambial stem cells is essential for cambium activity. We identify the auxin-dependent transcription factor ARF5/MONOPTEROS to cell-autonomously restrict the number of stem cells by directly attenuating the activity of the stem cell-promoting WOX4 gene. In contrast, ARF3 and ARF4 function as cambium activators in a redundant fashion from outside of WOX4-expressing cells. Our results reveal an influence of auxin signalling on distinct cambium features by specific signalling components and allow the conceptual integration of plant stem cell systems with distinct anatomies.

          Abstract

          Auxin activity controls plant stem cell function. Here the authors show that in the cambium, moderate auxin activity restricts cambial stem cell number via ARF5-dependent repression of the stem‐cell‐promoting factor WOX4, while ARF3 and ARF4 promote cambial activity outside of the WOX4‐expression domain.

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          Differential expression analysis for sequence count data

          High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.
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            NCBI GEO: archive for functional genomics data sets—update

            The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository for high-throughput microarray and next-generation sequence functional genomic data sets submitted by the research community. The resource supports archiving of raw data, processed data and metadata which are indexed, cross-linked and searchable. All data are freely available for download in a variety of formats. GEO also provides several web-based tools and strategies to assist users to query, analyse and visualize data. This article reports current status and recent database developments, including the release of GEO2R, an R-based web application that helps users analyse GEO data.
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              Floral dip: a simplified method forAgrobacterium-mediated transformation ofArabidopsis thaliana

              The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration. In the present study, this method was evaluated and a substantially modified transformation method was developed. The labor-intensive vacuum infiltration process was eliminated in favor of simple dipping of developing floral tissues into a solution containing Agrobacterium tumefaciens, 5% sucrose and 500 microliters per litre of surfactant Silwet L-77. Sucrose and surfactant were critical to the success of the floral dip method. Plants inoculated when numerous immature floral buds and few siliques were present produced transformed progeny at the highest rate. Plant tissue culture media, the hormone benzylamino purine and pH adjustment were unnecessary, and Agrobacterium could be applied to plants at a range of cell densities. Repeated application of Agrobacterium improved transformation rates and overall yield of transformants approximately twofold. Covering plants for 1 day to retain humidity after inoculation also raised transformation rates twofold. Multiple ecotypes were transformable by this method. The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.
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                Author and article information

                Contributors
                thomas.greb@cos.uni-heidelberg.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                28 February 2018
                28 February 2018
                2018
                : 9
                : 875
                Affiliations
                [1 ]GRID grid.473822.8, Gregor Mendel Institute (GMI), Austrian Academy of Sciences, , Vienna Biocenter (VBC), ; Dr. Bohr-Gasse 3, 1030 Vienna, Austria
                [2 ]ISNI 0000 0001 2190 4373, GRID grid.7700.0, Centre for Organismal Studies (COS), , Heidelberg University, ; Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
                [3 ]ISNI 0000000121896553, GRID grid.4605.7, Novosibirsk State University, ; 2 Pirogova Street, Novosibirsk, 630090 Russian Federation
                [4 ]GRID grid.418953.2, Institute of Cytology and Genetics, ; 10 Lavrentyeva Avenue, Novosibirsk, 630090 Russian Federation
                [5 ]ISNI 0000 0001 0791 5666, GRID grid.4818.5, Department of Agrotechnology and Food Sciences, Subdivision Biochemistry, , Wageningen University and Research Center, ; Stippeneng 4, 6708WE Wageningen, The Netherlands
                [6 ]ISNI 0000 0004 1770 5832, GRID grid.157927.f, Present Address: Instituto de Biología Molecular y Celular de Plantas (IBMCP-CSIC), , Universidad Politecnica de Valencia, ; Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
                Author information
                http://orcid.org/0000-0002-6176-646X
                Article
                3256
                10.1038/s41467-018-03256-2
                5830446
                29491423
                27dd8648-7d95-4a38-bc5c-9153e339de35
                © 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
                : 9 May 2017
                : 31 January 2018
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