16 research outputs found

    Is Mathematics the Theory of Instantiated Structural Universals?

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    This paper rejects metaphysical realism about structural universals as a basis for mathematical realism about numbers, and argues that one construal of structural universals via non-well-founded sets should be resisted by the mathematical realist

    Isolation of the <i>Bdtar2l<sup>hypo</sup></i> mutant and characterization of macroscopic phenotypes.

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    <p>(<i>A</i>) Four-day-old tissue culture grown seedlings of wild type (accession Bd21), an unrelated control transformant (control) (the unrelated transformant line was included in all our assays to control for any tissue culture regeneration effects) and the transgenic line segregating the <i>Bdtar2l<sup>hypo</sup></i> mutation. (<i>B</i>) Seminal root length quantification of the different genotypes at 4 days after germination (dag). (<i>C</i>) Schematic presentation of the <i>BdTAR2L</i> gene and the location of the T-DNA insertion in the <i>Bdtar2l<sup>hypo</sup></i> mutant. (<i>D–E</i>) Relative expression level of <i>BdTAR2L</i> in different genotypes at 4 dag as determined by qPCR and normalized with respect to the housekeeping gene, <i>BdUBC18</i>. (<i>F</i>) Root elongation in wild type, control and homozygous <i>Bdtar2l<sup>hypo</sup></i> mutants, assayed at 4 dag. (<i>G–H</i>) Quantification of seedling phenotypes at 4 dag. (<i>I</i>) Leaf number at 18 dag. (<i>J–L</i>) Different size parameters of the 5<sup>th</sup> leaf of plants, assayed at 18 dag. (<i>M</i>) Representative image of adult plants at 18 dag. Size bars are 1 cm; differences as compared to wild type are not significant unless indicated otherwise; error bars indicate standard error; * = p<0.05; ** = p<0.01; *** = p<0.001.</p

    Phenotypes of the <i>Bdtar2l<sup>qnull</sup></i> mutant in comparison to its wild type background, Bd21-3.

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    <p>(<i>A</i>) Relative expression level of <i>BdTAR2L</i> in different genotypes at 4 dag as determined by qPCR and normalized with respect to the housekeeping gene, <i>BdUBC18</i>. (<i>B–C</i>) Root elongation in wild type and <i>Bdtar2l<sup>qnull</sup></i> mutants, assayed at 4 dag. (<i>D</i>) Representative Nomarski optics images of mature root portions. Arrowheads point out top and bottom of individual cells in a cortex layer; (<i>E</i>) Quantification of mature cortex cell length at 4 dag. (<i>F</i>) Representative microscopy images of root hairs at 4 dag. (<i>G</i>) Representative light microscopy images of transverse sections across the mature root. (<i>H–I</i>) Quantification of total transverse area and stele area in sections from mature roots. (<i>J</i>) Relative seminal root length in <i>Bdtar2l<sup>qnull</sup></i> mutants during root growth progression. (<i>K</i>) Progressive breakdown of root meristem as indicated by shrinkage of the meristematic zone. (<i>L</i>) Seedling shoot length at 4 dag. (<i>M</i>) Adult shoots. Size bars are 1 cm (<i>B, M</i>) or 100 µm (<i>D,F,G</i>); differences as compared to wild type or mock are not significant unless indicated otherwise; error bars indicate standard error; * = p<0.05; *** = p<0.001.</p

    A schematic overview of the regulation of tryptophan-dependent auxin (indole-3-acetic acid) biosynthesis via indole-3-pyruvic acid (IPA) by ethylene action in Arabidopsis (<i>A</i>) and Brachypodium (<i>B</i>).

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    <p>A schematic overview of the regulation of tryptophan-dependent auxin (indole-3-acetic acid) biosynthesis via indole-3-pyruvic acid (IPA) by ethylene action in Arabidopsis (<i>A</i>) and Brachypodium (<i>B</i>).</p

    Auxin homeostasis in <i>Bdtar2l<sup>hypo</sup></i> roots and its relation to the ethylene pathway.

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    <p>(<i>A</i>) Free auxin (IAA) content in wild type and <i>Bdtar2l<sup>hypo</sup></i> root segments at 4 dag. The root tip comprised the terminal 8 mm of the roots, the elongated parts all above this. (<i>B</i>) Expression levels of the homologs of various genes encoding rate limiting enzymes in alternative auxin biosynthesis pathways in wild type and <i>Bdtar2l<sup>hypo</sup></i> roots at 4 dag. (<i>C</i>) Expression levels of <i>YUCCA</i> homologs in wild type and <i>Bdtar2l<sup>hypo</sup></i> roots at 4 dag. (<i>D</i>) Expression levels of <i>BdTAR1L</i> and <i>BdTAR2L</i> in wild type at 3 dag and after 3 h of ACC treatment. (<i>E</i>) Expression levels of <i>YUCCA</i> homologs in wild type at 3 dag and after 3 h of ACC treatment. All expression levels were determined by qPCR and normalized with respect to the housekeeping gene, <i>BdUBC18</i>; differences as compared to wild type or mock are not significant unless indicated otherwise; error bars indicate standard error; * = p<0.05; ** = p<0.01; *** = p<0.001.</p

    Effect of L-kynerunine (L-kyn) treatment on root elongation of different genotypes.

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    <p>(<i>A</i>) Representative images of 4-day-old seedlings, transferred onto media with indicated L-kyn concentration at 2 dag. (<i>B</i>) Quantification of root length after 2 days of indicated L-kyn treatment. (<i>C</i>) Representative Nomarski optics images of mature root portions formed during indicated L-kyn treatment. Arrowheads point out top and bottom of individual cells in the 3<sup>rd</sup> cortex layer; (<i>D</i>) Quantification of mature cortex cell length after 2 days of indicated L-kyn treatment. (<i>E–F</i>) Relative root elongation of indicated mutants and their respective wild type backgrounds after 2 days of indicated 5-methyl-tryptophan treatment. Size bars are 1 cm (<i>A</i>) or 100 µm (<i>C</i>); differences as compared to wild type or mock are not significant unless indicated otherwise; error bars indicate standard error; * = p<0.05; ** = p<0.01; *** = p<0.001.</p

    Sankar_et_al_data_file_4

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    Archive of tables (tab-delimited) of the normalized data used in machine learning for the Ler sections from data file 2, combined with the cell type assignment

    Phenotypic analysis of the <i>zwg</i> mutant.

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    <p>(A) Comparison of adult wild type Sav-0 plant (left) and <i>zwg</i> mutant (right). (B–D) Comparison of wild type (B) and <i>zwg</i> (C) flowers from different perspectives, note increased organ number and shorter organs in <i>zwg</i>. (E–G) Comparison of wild type and <i>zwg</i> siliques. (H) Comparison of flowering time measured as age or rosette leaf number. (I) Comparison of primary root length in tissue culture at 9 days after germination (dag). (J) Comparison of cell number per cell diameter measured at, above or below the 1<sup>st</sup> internode. (K–M) Comparison of transverse stem sections taken below the first internode. (N–O) Gene ontology (GO) classification of genes down-regulated (N) or up-regulated (O) in <i>zwg</i> as compared to wild type, expressed as normalized frequency. Size bars are 1 cm (A), 1 mm (B–G) and 100 µm (K–M).</p

    Analysis of random-primed RNA sequencing of wild-type and <i>vip3<sup>zwg</sup></i> mRNAs.

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    <p>(A) Distribution of the 5′ to 3′ coverage index (i.e. number of reads mapping into the 20% 5′-most region divided by number of reads mapping into the 20% 3′-most region of a transcript) in wild type and <i>vip3<sup>zwg</sup></i>. The box plots indicate maximum, minimum, median and quartile values, as well as the average (wider horizontal bar). Out of range maximum values were added numerically. (B) Relative read abundance in 1% bins cumulated for the 10% of most highly expressed transcripts (n = 2’437). (C) Distribution of the 5′ to 3′ coverage index (box plots, left y axis) and the ratios of median and average between wild type and <i>vip3<sup>zwg</sup></i> (diamonds, right y axis) in nuclear (n = 5’617), chloroplast (n = 34) and prime exosome target (n = 68) genes. Maximum values were added numerically. (D) Distribution of the averages and medians of the 5′ to 3′ coverage index and their wild type to <i>vip3<sup>zwg</sup></i> ratio in random sets drawn from the nuclear or prime exosome target sets. (E) Wild type to <i>vip3<sup>zwg</sup></i> ratio of the 5′ to 3′ end ratios for selected genes as determined by qPCR analyses of three independent RNA samples for each genotype. A value >1 indicates stabilized transcript in <i>vip3<sup>zwg</sup></i>. The respective 5′ to 3′ coverage ratios from the RNA sequencing are given in brackets above. (F) Relative expression levels of <i>FLC</i> in wild type, <i>vip3<sup>zwg</sup></i> and <i>Atski2</i>. n.s.: not significant; *: p<0.05; **: p<0.01; ***: p<0.001.</p

    Isolation and characterization of the <i>zwg</i> locus.

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    <p>(A) Representation of the final mapping interval for <i>zwg</i>, including position of markers and the <i>VIP3</i> polymorphism. (B) Illustration of the 7 bp deletion in the <i>vip3<sup>zwg</sup></i> coding sequence. (C) Conceptual translation of the <i>VIP3</i> wild type and <i>zwg</i> C-terminus. (D) Immunoblot analysis of transgenic GFP-VIP3 or GFP control lines, probed with anti-GFP antibody. Different independent lines are shown, GFP-VIP3 migrates below 75 kDa marker as expected. (E–G) Subcellular localization of GFP-VIP3 fusion protein in nucleus and cytoplasm of differentiated (E) or meristematic (F) root cells, and epidermal leaf cells (G). (H) Gel filtration analysis of GFP-VIP3, fractions pooled for subsequent co-immunoprecipitation of GFP-VIP3 are indicated by bars. (I) VIP3 and AtSKI3 (At1g76630) peptides identified in MALDI-TOF of co-immunoprecipitates obtained from the smallest set of fractions (H). (J) Number of peptides from Paf1c and SKI complex components identified in MALDI-TOF of co-immunoprecipitates obtained from total protein extract of GFP-VIP3 plants. Size bars are 10 µm (E–G).</p
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