Gene expression stability of 13 candidate genes in sugarcane as predicted by geNorm.

<p>Average expression stability (M) following stepwise exclusion of the least stable gene across all the samples within an experimental set. The least stable gene is on the left, and the most stable on the right. The name <i>eIF-4a</i> in the figure stands for <i>eIF-4α. ACT</i> stands for “β-actin” and <i>TUB</i> stands for “β-tubulin”.</p

Correlation coefficients based on the visualizing reference genes ranked by geNorm, Normfinder and deltaCt.

<p>The p-value indicated by asterisks (***<0.0001; **<0.05).</p

Thirteen reference genes surveyed in this work with their amplification and expression characteristics in <i>Saccharum officinarum.</i>

<p>Mean Ct values and RNA concentration were used for calculating slopes and correlation coefficients (R²). According to the formula [E = (10^(−1/slope)−1)×100%, qPCR efficiencies (E) were calculated based on the standard curves. Mean Ct value (mean), Standard deviation (SD) and Covariance (CV) were calculated by Microsoft Excel 2003 and the Ct values from all of the samples were used. The sequence numbers were obtained from <a href="http://www.ncbi.nlm.nih.gov/nucest/?term=sugarcane" target="_blank">www.ncbi.nlm.nih.gov/nucest/?term=sugarcane</a>.</p

Expression stability of 13 reference genes in <i>Saccharum officinarum</i> as calculated by Normfinder.

<p>*β-actin,</p><p>**β-tubulin.</p

Expression levels and variation of 13 reference genes across four experimental sets in <i>Saccharum officinarum.</i>

<p>Mean Ct value (Mean), Standard deviation (SD) and Covariance (CV) were calculated by Microsoft Excel 2003. 1^st set: leaf, leaf sheath, stem epidermis,stem pith and bud from “ROC”20, “ROC”22, FN40, liucheng03-182 and YC05-179; 2^nd set: ABA, MeJA and SA, treated-samples from “ROC”20, FN40, Liucheng03-182 and YC05-179; 3^rd set: H₂O₂, NaCl, PEG, CuCl₂ and CdCl₂ treated-samples from “ROC”20, FN40, liucheng03-182 and YC05-179; 4^th set: 2ⁿset+3^rd set.</p

Additional file 2: of Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system

Figure S2. Melting curves of S. scitamineum candidate PCR reference genes. (TIF 10506 kb

Isolation of a Novel Peroxisomal Catalase Gene from Sugarcane, Which Is Responsive to Biotic and Abiotic Stresses

<div><p>Catalase is an iron porphyrin enzyme, which serves as an efficient scavenger of reactive oxygen species (ROS) to avoid oxidative damage. In sugarcane, the enzymatic activity of catalase in a variety (Yacheng05–179) resistant to the smut pathogen <i>Sporisorium scitamineum</i> was always higher than that of the susceptible variety (Liucheng03–182), suggesting that catalase activity may have a positive correlation with smut resistance in sugarcane. To understand the function of catalase at the molecular level, a cDNA sequence of <i>ScCAT1</i> (GenBank Accession No. KF664183), was isolated from sugarcane infected by <i>S. scitamineum</i>. <i>ScCAT1</i> was predicted to encode 492 amino acid residues, and its deduced amino acid sequence shared a high degree of homology with other plant catalases. Enhanced growth of ScCAT1 in recombinant <i>Escherichia coli</i> Rosetta cells under the stresses of CuCl₂, CdCl₂ and NaCl indicated its high tolerance. Q-PCR results showed that <i>ScCAT1</i> was expressed at relatively high levels in the bud, whereas expression was moderate in stem epidermis and stem pith. Different kinds of stresses, including <i>S. scitamineum</i> challenge, plant hormones (SA, MeJA and ABA) treatments, oxidative (H₂O₂) stress, heavy metal (CuCl₂) and hyper-osmotic (PEG and NaCl) stresses, triggered a significant induction of <i>ScCAT1</i>. The ScCAT1 protein appeared to localize in plasma membrane and cytoplasm. Furthermore, histochemical assays using DAB and trypan blue staining, as well as conductivity measurement, indicated that <i>ScCAT1</i> may confer the sugarcane immunity. In conclusion, the positive response of <i>ScCAT1</i> to biotic and abiotic stresses suggests that <i>ScCAT1</i> is involved in protection of sugarcane against reactive oxidant-related environmental stimuli.</p></div

Additional file 1: of MALAT1 promoted invasiveness of gastric adenocarcinoma

Cancer-related target gene expression by MALAT1 silencing. To analyze the relation among cancer-related target genes by siMALAT1, NanoString nCounter gene expression analysis was carried out. (XLSX 42 kb

Additional file 1: of Identification and evaluation of PCR reference genes for host and pathogen in sugarcane-Sporisorium scitamineum interaction system

Figure S1. Melting curves of sugarcane candidate PCR reference genes. (TIF 3140 kb

Q-PCR analysis of the <i>ScCAT1</i> expression patterns in Yacheng05–179 plantlets with abiotic elicitors.

<p>Data are normalized to the <i>GAPDH</i> expression level. (<b>A</b>) The relative expression of <i>ScCAT1</i> under the stresses of 5 mM SA, 10 mM H₂O₂, 25 µM MeJA and 100 µM ABA. (<b>B</b>) The relative expression of <i>ScCAT1</i> under 25% PEG stress. (<b>C</b>) The relative expression of <i>ScCAT1</i> under 250 mM NaCl stress. (<b>D</b>) The relative expression of <i>ScCAT1</i> under 100 µM CuCl₂ stress. All data points are means±SE (n = 3). SA: salicylic acid; H₂O₂: hydrogen peroxide; MeJA: methyl jasmonate; ABA: abscisic acid; PEG: polyethylene glycol; NaCl: sodium chloride; CuCl_2: copper chloride.</p