MOESM1 of Developing a high-throughput phenotyping method for oxidative stress tolerance in barley roots

Additional file 1: Fig. S1. Flowchart of viability staining and fluorescence image acquisition. a Preparation of root sample for viability staining. (From left to right panel) Surfaced sterilized seeds were germinated in a large Petri dish with wet filter paper for 1 day. Uniformly germinated seeds were then chosen and placed in paper rolls before placing it in a beaker with growth media for another 3 days. Isolated root segments were placed in a micro Petri dish containing 5 µg/ml FDA for 5 min and then transferred to another micro Petri dish containing 3 µg/ml PI for 10 min; Stained root segments were washed with distilled water and positioned on a glass slide and covered with a cover slip. b The prepared slide was placed on a fluorescent microscope mechanical stage under the fluorescent light and root fluorescent image was acquired by the LAS V3.8 software

Additional file 1 of A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences

Additional file 1: Supplementary file 1. Hordeumvulgare P1B ATPase coding sequences

Table_1_Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile.DOCX

Arabidopsis is used as a model species in numerous physiological and genetic studies. Most of them employ parafilm-wrapped sterile culture. Here we demonstrate that this method is prone to potential artifacts and can lead to erroneous conclusions. We compared the effect of different sealing methods including air-permeable paper tape and traditional parafilm on Arabidopsis seedling growth, root development and gene expression network. Although seedlings grown in Petri dishes after 1 week sealed with paper tape showed a similar growth phenotype to that of parafilm-sealed seedlings, more than 700 differentially expressed genes (DEG) were found, including stress and nutrition-responsive genes. In addition, more H2O2 was accumulated in the tissues of parafilm-sealed plants. After 14 days of growth, paper tape-sealed plants grew much better than parafilm-sealed ones and accumulated higher chlorophyll content, with 490 DEGs found. After 3 weeks of growth, paper tape-sealed plants had higher chlorophyll and better growth compared to parafilm-sealed ones; and only 10 DEGs were found at this stage. Thus, the obvious phenotype observed at the latter stage was a result of differential gene expression at earlier time points, mostly of defense, abiotic stress, nutrition, and phytohormone-responsive genes. More O2 content was detected inside paper tape-sealed Petri dishes at early growth stage (7 days), and distinct difference in the CO2 content was observed between parafilm-sealed and paper tape-sealed Petri dishes. Furthermore, the carbon source also influenced seedlings growth with different sealing methods. In conclusion, conventional sealing using parafilm was not the optimal choice, most likely because of the limited gas exchange and a consequent stress caused to plants.</p

Effect of salinity on the sap osmolality in 6-week-old salt-stressed and control wheat

Means ±SE (=6).<p><b>Copyright information:</b></p><p>Taken from "A root's ability to retain K correlates with salt tolerance in wheat"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2697-2706.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2486465.</p><p></p

Assignment of phenomenological coefficients to their realizing transporters.

<p>Assignment of phenomenological coefficients to their realizing transporters.</p

A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast <i>Saccharomyces cerevisiae</i>

<div><p>Cationic and heavy metal toxicity is involved in a substantial number of diseases in mammals and crop plants. Therefore, the understanding of tightly regulated transporter activities, as well as conceiving the interplay of regulatory mechanisms, is of substantial interest. A generalized thermodynamic description is developed for the complex interplay of the plasma membrane ion transporters, membrane potential and the consumption of energy for maintaining and restoring specific intracellular cation concentrations. This concept is applied to the homeostasis of cation concentrations in the yeast cells of <i>S</i>. <i>cerevisiae</i>. The thermodynamic approach allows to model passive ion fluxes driven by the electrochemical potential differences, but also primary or secondary active transport processes driven by the inter- play of different ions (symport, antiport) or by ATP consumption (ATPases). The model—confronted with experimental data—reproduces the experimentally observed potassium and proton fluxes induced by the external stimuli KCl and glucose. The estimated phenomenological constants combine kinetic parameters and transport coefficients. These are in good agreement with the biological understanding of the transporters thus providing a better understanding of the control exerted by the coupled fluxes. The model predicts the flux of additional ion species, like e.g. chloride, as a potential candidate for counterbalancing positive charges. Furthermore, the effect of a second KCl stimulus is simulated, predicting a reduced cellular response for cells that were first exposed to a high KCl stimulus compared to cells pretreated with a mild KCl stimulus. By describing the generalized forces that are responsible for a given flow, the model provides information and suggestions for new experiments. Furthermore, it can be extended to other systems such as e.g. <i>Candida albicans</i>, or selected plant cells.</p></div

(A) The effects of 80 mM NaCl application on membrane potential in the mature zone of 6-d-old Baart 46 seedlings

(B) Steady-state membrane depolarization 60 min after salt application measured in all four cultivars. Mean ±SE (=6).<p><b>Copyright information:</b></p><p>Taken from "A root's ability to retain K correlates with salt tolerance in wheat"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2697-2706.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2486465.</p><p></p

Sketch of the system and the model-relevant key elements.

<p>Sketch of the system and the model-relevant key elements.</p

Image_2_Plants Grown in Parafilm-Wrapped Petri Dishes Are Stressed and Possess Altered Gene Expression Profile.tif

Arabidopsis is used as a model species in numerous physiological and genetic studies. Most of them employ parafilm-wrapped sterile culture. Here we demonstrate that this method is prone to potential artifacts and can lead to erroneous conclusions. We compared the effect of different sealing methods including air-permeable paper tape and traditional parafilm on Arabidopsis seedling growth, root development and gene expression network. Although seedlings grown in Petri dishes after 1 week sealed with paper tape showed a similar growth phenotype to that of parafilm-sealed seedlings, more than 700 differentially expressed genes (DEG) were found, including stress and nutrition-responsive genes. In addition, more H2O2 was accumulated in the tissues of parafilm-sealed plants. After 14 days of growth, paper tape-sealed plants grew much better than parafilm-sealed ones and accumulated higher chlorophyll content, with 490 DEGs found. After 3 weeks of growth, paper tape-sealed plants had higher chlorophyll and better growth compared to parafilm-sealed ones; and only 10 DEGs were found at this stage. Thus, the obvious phenotype observed at the latter stage was a result of differential gene expression at earlier time points, mostly of defense, abiotic stress, nutrition, and phytohormone-responsive genes. More O2 content was detected inside paper tape-sealed Petri dishes at early growth stage (7 days), and distinct difference in the CO2 content was observed between parafilm-sealed and paper tape-sealed Petri dishes. Furthermore, the carbon source also influenced seedlings growth with different sealing methods. In conclusion, conventional sealing using parafilm was not the optimal choice, most likely because of the limited gas exchange and a consequent stress caused to plants.</p

Effect of four weeks of 150 mM NaCl on the sap Na concentration of the flag leaf of salt-treated plants

Means ±SE (=6). The Na content in the control plants was negligible.<p><b>Copyright information:</b></p><p>Taken from "A root's ability to retain K correlates with salt tolerance in wheat"</p><p></p><p>Journal of Experimental Botany 2008;59(10):2697-2706.</p><p>Published online 20 May 2008</p><p>PMCID:PMC2486465.</p><p></p