Changes in the TCA cycle intermediates and expression of related genes.

<p>Three inner boxplots represent levels of (I) citric acid, (II) 2-oxoglutaric acid (III) succinic acid and (IV) fumaric acids measured in cells of <i>T. pseudonana</i> grown in different conditions: nitrogen limitation (Nitro), lowered iron concentration (Iron), salt addition (Salt), carbonate addition (Carbo). Values on the plots represent median values (horizontal line) of normalized peak intensity divided by median for the control samples. Outer boxplots represent relative expression of TCA-enzymes genes. Values on the plots represent median values (horizontal line) of expression divided by median for the control samples. Asterisks below a treatments name mark a statistical significant change with p-value <0.05 * or p-value < 0.01 ** in Tukey’s Test. The round arrow indicates the direction of the TCA cycle.</p

Heat-map of metabolic changes in<i>Thalassiosira pseudonana</i> treated in four conditions for 24 hours.

<p>Pearson correlation was used to cluster the results. Intensity of colours represents log₂-transformed ratios of measured mean (n=5) analyte’s intensity to its respective mean value in the control conditions. Analytes, which could not be measured in more than 3 samples, were marked grey. Asterisks mark t-test P-value, where “**” marks P < 0.01 and “*” marks P < 0.05. Note, this is one heat-map, which has been presented in two blocks of data.</p

Heat-map visualization and cluster tree representations of amino acid contents and genotypes

Data were obtained from experiments where plants were starved of sulphate for 10 d. The heat-map was generated by using log base 2-transformed fold changes. The given data represent the ratio of the determined amino acids for control and starved plants. Each amino acid is represented by a single column and each genotype by a single row. Red indicates decreased relative metabolite content whereas blue indicates increased relative contents of amino acids compared with the wild-type. Separated heat-map visualization of amino acid contents in control and mutant plants are presented in in available at online and the respective diagrams in Fig. S2.<p><b>Copyright information:</b></p><p>Taken from "Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2831-2846.</p><p>Published online Jan 2008</p><p>PMCID:PMC2486478.</p><p></p

Contents of cysteine (upper row), γ-glutamylcysteine (GEC; middle row), and glutathione (GSH; lower row) are shown for plants overexpressing , , and , respectively, or down-regulated with respect to

Plants were grown for 10 weeks on soil before thiol extraction. knock-downs are represented by cross-hatched columns, overexpressing lines by white columns, and wild-type (WT) and empty-vector control lines (EV) by black columns. Values are the mean ±SD of three independent experiments. Asterisks indicate that the difference between the wild-type plants and the manipulated transgenic plants was significant using -tests ( ≤0.05).<p><b>Copyright information:</b></p><p>Taken from "Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2831-2846.</p><p>Published online Jan 2008</p><p>PMCID:PMC2486478.</p><p></p

Heat map generated from amino acid measurements reflecting log base 2-transformed and normalized amino acid levels and its similarity among themselves and the genotypes

The top colour bar indicates the relative log base 2-fold changes ranging between reduced relative (red) and increased relative (blue) contents of amino acids with respect to the wild-type.<p><b>Copyright information:</b></p><p>Taken from "Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2831-2846.</p><p>Published online Jan 2008</p><p>PMCID:PMC2486478.</p><p></p

Phenotype of mature knock-down plants, a sketch depicting the location of the T-DNA insertions, and quantification of gene expression in mutant plants

(A) Wild-type plants (left in each picture) and three mutant plants (right) at 10 weeks. Each of three individually selected homozygote mutant plants is presented. The plants were grown at the same time. (B) Identification of T-DNA insertion. Boxes in black represent exons, lines represent non-coding regions, and boxes in grey indicate T-DNA insertions. (C) q-RT-PCR analysis of plants derived from the knock-down screen. RNA was extracted from 28-d-old soil-grown plants. Ratios to controls are shown.<p><b>Copyright information:</b></p><p>Taken from "Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2831-2846.</p><p>Published online Jan 2008</p><p>PMCID:PMC2486478.</p><p></p

Expression analysis of , , and , respectively, in overexpressing lines from 28-d-old soil-grown plants with northern blot hybridization and q-RT-PCR, respectively

(A) Wild-type and empty-vector plants served as controls. RNA from 10 plants per treatment was extracted and 10 μg total RNA was subjected to northern blot analysis. Gene-specific probes were radioactively labelled and hybridized as described in Materials and methods. Equal loading in each track is demonstrated by comparing the amount of the 28S rRNA. Transcript sizes are given in brackets. (B) Quantification of gene expression in transgenic plants overexpressing , , and , respectively. Gene expression was assessed by q-RT-PCR as described in Materials and methods. The data represent the average relative to the gene expression in control plants.<p><b>Copyright information:</b></p><p>Taken from "Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2831-2846.</p><p>Published online Jan 2008</p><p>PMCID:PMC2486478.</p><p></p