Additional file 1: of Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

Phylogenetic analysis of gene families involved in starch metabolism. Tree calculation was based on a global alignment with free end gaps, BLOSUM62 cost matrix and Jukes-Cantor genetic distance model. The tree was built by the Geneious 5.5.6 Tree Builder module employing a neighbour-joining method. a) alpha-amylases, b) beta-amylases, c) phosphoglucomutases, d) starch synthases, e) sucrose synthases, f) glucose-6-phosphate-phosphate translocators, g) starch branching enzymes, h) ADP-glucose pyrophosphorylases, i) isoamylases. The scale bar at the bottom represents the average substitutions per amino acid site. (PDF 110 kb

Additional file 2: of Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

Valid microarray identifiers for starch genes in the POCI 4x44k and 8x60k platforms. (XLS 46 kb

What led Tel Aviv to become a leading entrepreneurial ecosystem?

“How has Tel Aviv become a leading entrepreneurial ecosystem? ” This thesis investigates the factors behind the growing success of Tel Aviv as an entrepreneurial scene. The economic capital of Israel has become one of the most important clusters of innovation in the World (Engel & del-Palacio, 2011). By analysing these factors with key entrepreneurial actors, the hopes were to find new qualitative evidence to back up the statistics. The aim of the thesis was to use qualitative interviews with chosen entrepreneurs and investors to give insights in Tel Aviv and how it has become a flourishing ecosystem. This has in turn enhanced the previous research on Knowledge-Intensive entrepreneurship by adding a singular case study. Analysing the Tel Aviv ecosystem allowed me to find ten different factors of its success. These can potentially be used as inspiration points for stimulating clusters of innovation around the World.MSc in Knowledge-based Entrepreneurshi

XopB suppresses the flg22-mediated ROS burst <i>A</i>. <i>thaliana</i>.

<p>ROS production (RLU, relative luminescence units) was measured in wild type (black line) and transgenic <i>A</i>. <i>thaliana</i> lines 10 (light grey line) and 12 (dark grey line) upon stimulation with 1 μM flg22. All leaf discs were incubated in 0.2% EtOH for 18 h to induce <i>xopB</i> expression. Values are means +/- SE of 8 independent samples. Statistically significant differences were determined using two-tailed t-test assuming normal distribution. Statistically significance between wild type and the transgenic lines are indicated by asterisks (p<0.05). The experiment was repeated three times with similar results.</p

Deletion of <i>xopB</i> in <i>Xcv</i> leads to higher accumulation of ROS in pepper leaves.

<p>Leaves of pepper plants were infiltrated either with <i>Xcv</i> wild type (<i>Xcv</i> WT), a <i>xopB</i> deletion strain (<i>Xcv</i> ΔxopB) or a <i>xopB</i> deletion strain complemented by <i>xopB</i> (<i>Xcv</i> Δ<i>xopB</i> + <i>xopB</i>) at a concentration of 10⁹ cfu ml^-1. All strains harbour the pBBR1-MCS5 vector. As a control, leaves were infiltrated with 10 mM MgCl₂. Two leaves of two pepper plants were infiltrated using a needle-less syringe. Three days post infection six 4 cm² leaf discs were taken and stained for ROS using DAB solution. After chlorophyll clearance six randomly chosen microscopic images per leaf disc were documented. <b>A)</b> A representative image for each scenario is shown. <b>B)</b> Pixel intensities of microscopic images were determined by means of the ImageJ software. Values shown are means +/- SE of 18 images and were presented relative to the mean value of pepper plants infiltrated with <i>Xcv</i> wild type strain which was set to one. Statistically significant differences to <i>Xcv</i> wild type-infected leaves are indicated by asterisks (***p<0.001).</p

XopB inhibits flg22-triggered callose deposition in transgenic <i>A</i>. <i>thaliana</i> plants.

<p><i>A</i>. <i>thaliana</i> wild type and transgenic plants (line 10 and 12) were watered with 10 ml 1% EtOH 18 h before treatment with 1 μM flg22 or deionized water. For each treatment two leaves of three independent plants were infiltrated. After additional 18 h leaves were bleached with ethanol and subsequently stained with aniline blue. Four to six randomly chosen microscopic images per leaf were documented and the number of callose deposits per mm² was counted. Numbers of callose depositions +/- SE are given below the images and are the means of at least 25 values.</p

Impact of <i>xopB</i> on symptom development, SA content and expression of <i>PR</i> genes during <i>Xcv</i> infection of pepper leaves.

<p>Leaves of five week old susceptible pepper plants were inoculated with <i>Xcv</i> wild type (<i>Xcv</i> WT), <i>Xcv</i> Δ<i>xopB</i>, or a <i>xopB</i> deletion strain complemented with <i>xopB</i> (<i>Xcv</i> Δ<i>xopB</i> + <i>xopB</i>) under control of its own promotor at a concentration of 10⁹ cfu ml^-1. All strains harbour the plasmid pRBB1-MCS5. As control, leaves were infiltrated with 10 mM MgCl₂. <b>A)</b> Formation of disease symptoms in infected pepper leaves. Only the lower halves of the leaves were infiltrated. Pictures were taken 5 days post infection (dpi). Similar results were observed at least three times. <b>B)</b> Levels of free (free SA) and conjugated SA (SAG) in leaves, before, 1 and 3 days after infection with the <i>Xcv</i> strains indicated. Values represent the means +/- SE of four different samples. Statistically significant differences to <i>Xcv</i> wild type-infected leaves were determined using two-tailed t-test and are indicated by asterisks (***p<0.001; *p<0.05). The experiment was repeated with similar results. <b>C)</b> Transcript levels of <i>CaPR1b1</i> and <i>CaPRQ</i> were quantified by qPCR from samples taken 3dpi with the different <i>Xcv</i> strains. Values were normalized to <i>CaEF1alpha</i> and displayed relative to the expression level of <i>Xcv</i> wild type-infected leaves which were set to one. Values are means +/- SD of three independent samples each from a pool of two plants. Significant differences to <i>Xcv</i> wild type-infected leaves were calculated using t-test and are indicated by asterisks (***p<0.001; *p<0.05). Similar results were obtained in three independent experiments.</p

Expression of <i>xopB</i> in Arabidopsis alters expression of ROS-responsive and ROS-producing enzymes.

<p><i>A</i>. <i>thaliana</i> wild type (WT), <i>xopB</i>-expressing lines 10, 12 and <i>fls2</i> mutant plants were watered with 10 ml 1% EtOH. After 18 h leaves were infiltrated with 1 μM flg22 or deionized water as a control. Samples were taken after 30min. Total RNA was isolated and reverse transcribed into cDNA. Transcript accumulation of <i>AtOXI1</i>, <i>AtRBOHD</i>, <i>AtPRX33</i>, and <i>AtPRX34</i> was measured by qPCR. Expression of <i>AtTUB4</i> was used to normalize the expression of each sample. Expression levels are shown relative to the water-treated wild type. Values are means +/- SD of three independent replicates. Statistical differences (p<0.05) were determined (a) between water-treated wild type and the transgenic or fls2 plants and (b) between water- and the flg22-treated plants, respectively, using two-tailed t-test assuming normal distribution. Similar results were obtained in two independent experiments.</p

The <i>Xanthomonas campestris</i> pv. <i>vesicatoria</i> Type-3 Effector XopB Inhibits Plant Defence Responses by Interfering with ROS Production

<div><p>The bacterial pathogen <i>Xanthomonas campestris</i> pv. <i>vesicatoria</i> 85–10 (<i>Xcv</i>) translocates about 30 type-3 effector proteins (T3Es) into pepper plants (<i>Capsicum annuum</i>) to suppress plant immune responses. Among them is XopB which interferes with PTI, ETI and sugar-mediated defence responses, but the underlying molecular mechanisms and direct targets are unknown so far. Here, we examined the XopB-mediated suppression of plant defence responses in more detail. Infection of susceptible pepper plants with <i>Xcv</i> lacking x<i>opB</i> resulted in delayed symptom development compared to <i>Xcv</i> wild type infection concomitant with an increased formation of salicylic acid (SA) and expression of pathogenesis-related (<i>PR)</i> genes. Expression of <i>xopB</i> in <i>Arabidopsis thaliana</i> promoted the growth of the virulent <i>Pseudomonas syringae</i> pv. <i>tomato (Pst)</i> DC3000 strain. This was paralleled by a decreased SA-pool and a lower induction of SA-dependent <i>PR</i> gene expression. The expression pattern of early flg22-responsive marker genes indicated that MAPK signalling was not altered in the presence of XopB. However, XopB inhibited the flg22-triggered burst of reactive oxygen species (ROS). Consequently, the transcript accumulation of <i>AtOXI1</i>, a ROS-dependent marker gene, was reduced in <i>xopB</i>-expressing Arabidopsis plants as well as callose deposition. The lower ROS production correlated with a low level of basal and flg22-triggered expression of apoplastic peroxidases and the NADPH oxidase <i>RBOHD</i>. Conversely, deletion of <i>xopB</i> in <i>Xcv</i> caused a higher production of ROS in leaves of susceptible pepper plants. Together our results demonstrate that XopB modulates ROS responses and might thereby compromise plant defence.</p></div

Inducible expression of <i>xopB</i> in transgenic <i>A</i>. <i>thaliana</i> plants causes severe phenotypic changes.

<p>Arabidopsis wild type and two independent <i>xopB</i>-expressing transgenic plants (EtOH::<i>xopB</i>, lines 10 and 12) were analysed. Expression of <i>xopB</i> was induced by watering ca. five week old plants with 10 ml 1% (v/v) EtOH. <b>A)</b> Analysis of <i>xopB</i>-specific transcript accumulation by RT-PCR in the transgenic lines 10 and 12 before and 4 h, 24 h and 48 h after ethanol application. As reference, <i>Actin</i>-specific mRNA levels are shown. The binary plasmid (Plasmid) which was used for <i>A</i>. <i>thaliana</i> transformation was included as positive control, genomic DNA (gDNA) from wild type to exclude contamination with genomic DNA and water (H₂O) as negative control. <b>B)</b> Analysis of XopB protein accumulation upon induction of <i>xopB</i> expression in the transgenic lines (10, 12) by western blotting with a XopB-specific antibody at time points described in (A). The amido black stained RubisCO-band is shown as loading control. <b>C)</b> Phenotypic changes in transgenic Arabidopsis plants caused by <i>xopB</i> expression compared to wild type. Shown are three plants each before watering plants with ethanol (0dpi) and 3, 4 or 7 dpi.</p