Transcriptome Analysis of Tomato Flower Pedicel Tissues Reveals Abscission Zone-Specific Modulation of Key Meristem Activity Genes

<div><p>Tomato flower abscises at the anatomically distinct abscission zone that separates the pedicel into basal and apical portions. During abscission, cell separation occurs only at the abscission zone indicating distinctive molecular regulation in its cells. We conducted a transcriptome analysis of tomato pedicel tissues during ethylene promoted abscission. We found that the abscission zone was the most active site with the largest set of differentially expressed genes when compared with basal and apical portions. Gene Ontology analyses revealed enriched transcription regulation and hydrolase activities in the abscission zone. We also demonstrate coordinated responses of hormone and cell wall related genes. Besides, a number of ESTs representing homologs of key Arabidopsis shoot apical meristem activity genes were found to be preferentially expressed in the abscission zone, including <em>WUSCHEL</em> (<em>WUS</em>), <em>KNAT6</em>, <em>LATERAL ORGAN BOUNDARIES DOMAIN PROTEIN 1</em>(<em>LBD1</em>), and <em>BELL</em>-like homeodomain protein 1 (<em>BLH1</em>), as well as tomato axillary meristem genes <em>BLIND</em> (<em>Bl</em>) and <em>LATERAL SUPPRESSOR</em> (<em>Ls</em>). More interestingly, the homologs of <em>WUS</em> and the potential functional partner <em>OVATE FAMILIY PROTEIN</em> (<em>OFP</em>) were subsequently down regulated during abscission while <em>Bl</em> and <em>AGL12</em> were continuously and specifically induced in the abscission zone. The expression patterns of meristem activity genes corroborate the idea that cells of the abscission zone confer meristem-like nature and coincide with the course of abscission and post-abscission cell differentiation. Our data therefore propose a possible regulatory scheme in tomato involving meristem genes that may be required not only for the abscission zone development, but also for abscission.</p> </div

Induction of transcription factor genes during abscission.

<p>(A) <i>Blind</i> is specifically expressed in the abscission zone and is further induced significantly during the course of abscission. (B-E) <i>De novo</i> significant induction of four transcription factors.</p

Enriched GO terms among genes differentially expressed in abscission zone after 3 h ethylene treatment.

<p>A Cytoscape view of enriched GO terms in BinGO where categories in GoSlimPlants (Maere <i>et al</i>., 2005) were used to simplify the analysis. The color bar shows the statistical significance, with enrichment significance level <i>P</i><0.05, and the false discovery rate <i>FDR</i> <0.05. The size of the node is proportional to the number of genes in the GO category. The pin-like symbols indicate enriched GO terms specifically in the abscission zone relative to the basal portion and the apical portion.</p

DataSheet_1_CytoSorb in patients with coronavirus disease 2019: A rapid evidence review and meta-analysis.pdf

BackgroundAfter its approval by the European Union in 2011, CytoSorb therapy has been applied to control cytokine storm and lower the increased levels of cytokines and other inflammatory mediators in blood. However, the efficiency of this CytoSorb treatment in patients with coronavirus disease (COVID-19) still remains unclear. To elucidate the Cytosorb efficiency, we conducted a systematic review and single-arm proportion meta-analysis to combine all evidence available in the published literature to date, so that this comprehensive knowledge can guide clinical decision-making and future research.MethodsThe literature published within the period 1 December 2019 to 31 December 2021 and stored in the Cochrane Library, Embase, PubMed, and International Clinical Trials Registry Platform (ICTRP) was searched for all relevant studies including the cases where COVID-19 patients were treated with CytoSorb. We performed random-effects meta-analyses by R software (3.6.1) and used the Joanna Briggs Institute checklist to assess the risk of bias. Both categorical and continuous variables were presented with 95% confidence intervals (CIs) as pooled proportions for categorical variables and pooled means for continuous outcomes.ResultsWe included 14 studies with 241 COVID-19 patients treated with CytoSorb hemadsorption. Our findings reveal that for COVID-19 patients receiving CytoSorb treatment, the combined in-hospital mortality was 42.1% (95% CI 29.5–54.6%, I2 = 74%). The pooled incidence of adjunctive extracorporeal membrane oxygenation (ECMO) support was 73.2%. Both the C-reactive protein (CRP) and interleukin-6 (IL-6) levels decreased after CytoSorb treatment. The pooled mean of the CRP level decreased from 147.55 (95% CI 91.14–203.96) to 92.36 mg/L (95% CI 46.74–137.98), while that of IL-6 decreased from 339.49 (95% CI 164.35–514.63) to 168.83 pg/mL (95% CI 82.22–255.45).ConclusionsThe majority of the COVID-19 patients treated with CytoSorb received ECMO support. In-hospital mortality was 42.1% for the COVID-19 patients who had CytoSorb treatment. Both CRP and IL-6 levels decreased after Cytosorb treatment.</p

Repression of meristem activity genes during abscission.

<p>Homologs of <i>WUS</i> (A) and <i>OVATE</i> (B) are specifically repressed in the abscission zone. <i>STM</i> (C) and <i>AS1</i> (D) were repressed in the abscission zone, but also in one or more additional tissues. E–F show the repression of the <i>SPL3</i> homolog and the tomato <i>MC</i> gene, a putative ortholog of the Antirrhinum <i>SQUAMOSA</i> gene.</p

List of abscission zone-specific transcription factors.

1<p>Best Arabidopsis homolog if not functional studied in tomato; See text for tomato gene details.</p

Response of ethylene related genes.

<p>Induction of (A) the ethylene receptor <i>LeETR6</i>, (B) ethylene biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase gene (<i>ACO1</i>), and (C-D) two ERF transcription factors during ethylene-promoted abscission.</p

Transcriptome responses of different tissues of tomato pedicels during ethylene-promoted abscission.

<p>A, The total numbers of genes differentially expressed (fold changes ≥2, 4, 8; <i>p</i><0.05) at 3 h and/or 6 h after ethylene treatment. B, Venn diagram showing the overlapping of differentially expressed genes in the abscission zone and flanking tissues (the basal portion and the apical portion). Lists of genes in each tissue are presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055238#pone.0055238.s005" target="_blank">Tables S3</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055238#pone.0055238.s006" target="_blank">S4</a>,<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0055238#pone.0055238.s007" target="_blank">S5</a>.</p

Coordinated expression of auxin and other hormone related genes.

<p>Note the formation of distal to proximal gradient expression pattern for <i>GH3.3</i> (A), <i>TCP</i> (B), and <i>DWF4</i> (F). <i>GA 20ox-3</i> (C), <i>AOS</i> (D), and <i>ABA 8′-hydoxylase</i> (E) genes were most highly expressed in the abscission zone during abscission.</p

Additional file 1 of Response of microRNAs to cold treatment in the young spikes of common wheat

Table S1. Nucleotide sequences of primers for qRT-PCR of miRNAs and their targets. Table S2. Small RNA statistics and genome mapping information referred to the Chinese Spring genome. Table S3. Expression level of miRNAs in the control and cold-treated libraries. Table S4. Novel miRNA information, including mature, star, and precursor sequences, referred to the Chinese Spring genome. Table S5. Fold change of differentially expressed miRNAs and their targets by qRT-PCR. Table S6. Overlapped miRNAs in response to cold stress among wheat, Brachypodium, Medicago, Populus, and Arabidopsis. Table S7. Predicted targets of conserved miRNAs by the TargetFinder program. Table S8. Predicted targets of novel miRNAs by the TargetFinder program. Table S9. Targets of known miRNAs validated by degradome sequencing in the control and cold stress libraries. Table S10. Targets of novel miRNAs validated by degradome sequencing in the control and cold stress libraries. Table S11. Gene Ontology enrichment, including biological process, molecular function, and cellular components for the target genes of differentially expressed miRNAs after cold stress, referred as Chinese Spring. (ZIP 643 kb