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opennotspecifiedJan 2023View details →

Fig. 4 in Diurnal accumulation of K -dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.)

Fig. 4. Analysis of circadian regulation of asparaginase protein. Plants were exposed to a 16 h light and 8 h dark cycle followed by exposure to continuous light. Leaves were sampled at the indicated times and asparaginase detected by immunoblotting.

opennotspecifiedJan 2023View details →

Fig. 1 in Diurnal accumulation of K -dependent L-asparaginase in leaf of common bean (Phaseolus vulgaris L.)

Fig. 1. RNA-Seq expression profile of PvASPG1 and PvASPG2. Expression value is given as Z-score (Severin et al., 2010). Samples are grouped by tissue. Data are from O'Rourke et al. (2014) (see Supplementary Table S1).

opencc-by-4.0Aug 2023View details →

Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density.

Raw data files concerning the publication, Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density Julia Eckert, Benoit Ladoux, Rene-Marc Mege, Luca Giomi and Thomas Schmidt Nature Communications (2023) 14:5762. doi: https://doi.org/10.1038/s41467-023-41449-6 Abstract: Changes in tissue geometry during developmental processes are associated with collective migration of cells. Recent experimental and numerical results suggest that these changes could leverage on the coexistence of nematic and hexatic orientational order at different length scales. How this multiscale organization is affected by the material properties of the cells and their substrate is presently unknown. In this study, we address these questions in monolayers of Madin-Darby canine kidney cells having various cell densities and molecular repertoires. At small length scales, confluent monolayers are characterized by a prominent hexatic order, independent of the presence of E-cadherin, monolayer density, and underlying substrate stiffness. However, all three properties affect the meso-scale tissue organization. The length scale at which hexatic order transits to nematic order, the ”hexanematic” crossover scale, strongly depends on cell-cell adhesions and correlates with monolayer density. Our study demonstrates how epithelial organization is affected by mechanical properties, and provides a robust description of tissue organization during developmental processes.   Data description: WT.zip  - zipped raw image data and extracted vertices of experiments on wild-type cells KO.zip  - zipped raw image data and extracted vertices of experiments on eCad KO-cells FigureData.zip  - zipped data referring to each of the figures in the paper   Software: The software to analyze the data presented here is found on GitHub, [https://github.com/hexanematic/orientation tracker]

opencc-by-4.0Apr 2024View details →

Phylogenetic Effect on Tree Radial Growth Depends on Drought and Tree Sizes

This dataset is the calculated Blomberg's K values from tree growth rates.

Fig. 5 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 5. Analysis of 2D Scores Plot by Partial Least Squares Discriminant Analysis (PLS-DA) of characterized flavonoids in soybean leaves from the C9 and WT genotypes, infected (I) or noninfected (NI) by P. s. pv. tomato 36 h after inoculation. Points represent replicates analyzed, whereas ellipses indicate 95% confidence region.

Fig. 9 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 9. Expression analysis of target genes performed by qRT-PCR involved in plant bacterial interactions from BiP-overexpressing (C9) and wild-type (WT) soybean plants infected (I) or noninfected (NI) with P. syringae pv. tomato. The expression levels were obtained using the 2-ΔCT method. Bars (mean SE; ± n = 4) with the same capital letters indicate no significant difference between control and inoculated treatments and those followed by the same lowercase letters indicate no significant difference among genotypes within the same treatment (Student's test: P <0.05).

Fig. 8 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 8. Relative abundance of the flavonoid derivatives from BiP-overexpressing (C9) and wild-type (WT) soybean plants infected (I) or noninfected (NI) with P. syringae pv. tomato. Bars (mean ± SE; n = 4) with the same capital letters indicate no significant difference between control and inoculated treatments and those followed by the same lowercase letters indicate no significant difference among genotypes within the same treatment (Student's test: P <0.05).

Fig. 4 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 4. Absolute concentrations of phytohormones (A) and of flavonoid aglycones (B) by UHPLC/MS QqQ. The data represent the mean ± standard error. Bars (mean ± SE; n = 4) with the same capital letters indicate no significant difference between control and inoculated treatments and those followed by the same lowercase letters indicate no significant difference among genotypes within the same treatment (Student's test: P <0.05).

Fig. 3 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 3. Clustering analysis by Heat Map method of the characterized metabolites by GC/MS in soybean leaves from the WT and C9 genotypes, infected (I) or noninfected (NI) by P. syringae pv. tomato 36 h after inoculation. Differences in the abundance of the metabolites are indicate in response to treatments.

Fig. 6 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 6. Clustering analysis by Heat Map method of the characterized flavonoids by LC QqQ in soybean leaves from the WT and C9 genotypes, infected (I) or noninfected (NI) by P. syringae pv. tomato 36 h after inoculation. This shows the differences in the abundance of the flavonoids analyzed by LC-MS in response to bacterial infection. Differences in the abundances of the detected flavonoids are indicate in response to treatments. Green color represents a decrease, and red color an increase.

Fig. 7 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 7. Schematic overview of flavonoid biosynthesis pathway reconstructed using the characterized compounds from soybean leaves. Each colored square box is indicative of the abundance levels of the metabolites involved in the flavonoid biosynthesis and identified for each WT and C9 genotypes, infected (I) or noninfected (NI) by P. syringae pv. tomato. The main flavonoids of pathway are sketched by continuous line while compounds not detected, but intermediate of the pathway, are sketched by dashed line. Compounds marked by blue asterisk were more abundant in the inoculated C9 genotype while compounds marked by red asterisk were more abundant in the inoculated WT genotype.

Fig. 2 in BiP-overexpressing soybean plants display accelerated hypersensitivity response (HR) affecting the SA-dependent sphingolipid and flavonoid pathways

Fig. 2. Analysis of the metabolic profiles of the C9 and WT genotypes in soybean leaves from the WT and C9 genotypes infected (I) or noninfected (NI) by P. syringae pv tomato 36 h after inoculation. In (A) 2D Scores Plot generated by Partial Least Squares Discriminant Analysis (PLS-DA) of all the metabolites. Points represent analyzed replicates, whereas ellipses indicate 95% confidence region. In (B) Major metabolites responsible for discrimination between inoculated and mock inoculated soybean groups identified by VIP score. Green color represents a decrease, and red color an increase.

Fig. 59 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 59. Putative reaction catalyzed by HTH (HOTHEAD). Shown are the successive oxidations of the ω-hydroxyl group to the aldehyde and eventually, to the carboxy-group, leading to an α,ω-dicarboxylic acid. Members of the GMC oxidoreductases typically react readily with dioxygen to produce hydrogen peroxide.

Fig. 57 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 57. Reaction catalyzed by DNA-photolyases. The excited state reduced FAD is generated via activation by an additional antenna chromophore (top). In the case of CRY3 N5,N10-methenyltetrahydrofolate was shown to act as the antenna chromophore (G¨obel et al., 2017). During the repair reaction the reduced FAD returns to the ground state and requires re-activation by the antenna chromophore for the next reaction cycle. While the redox state of the flavin cofactor does not change in the overall reaction, intermediate transfer or electrons is critical for the reaction mechanism (see text).

Fig. 56 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 56. The oxidation of glycolate catalyzed by glycolate oxidase. Glycolate, the shortest substrate of the family of 2-hydroxy acid oxidases, is oxidized to glyoxylate in the peroxisomes. The members of the family feature different chain-length specificities (see text for further details). The reduced FMN is reoxidized by dioxygen yielding hydrogen peroxide.

Fig. 58 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 58. Flavoenzymes involved in the generation of ROS in A. thaliana. A total of 68 flavin-dependent enzymes were found to be involved in the formation of ROS in A. thaliana, either as hydrogen peroxide or superoxide radical (dark blue, taken from Table 1). Out of these 68, 48 enzymes were predicted to be present in a single cellular compartment, 19 were in at least two and one enzyme was predicted in at least three cellular compartments. The enzymes are ubiquitously distributed across the different cellular compartments (AP, apoplast = 19; PX, peroxisome = 15; PM, plasma membrane = 12; M, mitochondria = 11; Cyto, cytosol = 12; CP, chloroplast = 10; N, nucleus = 4; G, Golgi and EX, extracellular region = 2 and ER, endoplasmic reticulum = 1 enzyme). The predicted ROS producing flavoproteins from Table 5 are shown in light blue. Out of 18, 13 enzymes were predicted to be present in a single cellular compartment and 5 were predicted to be present at least in two. (PM = 2; M = 1; Cyto = 2; CP = 10; N = 3; EX = 2, EMS, endomembrane system = 1 and ER = 2). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 53 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 53. Mechanism of action of quiescin sulfhydryl oxidase. The enzyme possesses two pairs of cysteines (see text) of which only the proximal pair is shown in the figure. In the resting state, the two proximal cysteines form an intramolecular disulfide that is reduced via interaction with the reduced dithiol of the thioredoxin domain. The reduced proximal dithiol then reduces the FAD, which is reoxidized by dioxygen.

Fig. 54 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 54. Mechanism of Erv and Ero as partners for protein disulfide isomerase. In contrast to quiescin sulfhydryl oxidase, Erv and Ero do not interact directly with client proteins but serve to keep protein disulfide isomerase in an active oxidized state in order to allow for the proper generation of disulfide bonds in client proteins. Reduced Erv and Ero are reoxidized by dioxygen giving rise to the production of hydrogen peroxide.

Fig. 52 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 52. Reaction of glutathione reductase with its cognate substrate glutathione. Glutathione reductase is primed by reduction at the expense of NADPH generating the reduced FAD, which subsequently reduces the internal disulfide bond. Next, oxidized glutathione (GSSG) is cleaved to two molecules of (reduced) glutathione (GSH) by a dithiol-disulfide exchange reaction. For a detailed mechanistic discussion see Miller (2013).

Fig. 51 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana

Fig. 51. Proposed reaction mechanism of lysine-specific histone demethylase. The oxidation of a methylated lysine residue (typically in position 4 of histone 3) is shown. Initially, oxidation of the substrate generates reduced FAD, which is re-oxidized by dioxygen leading to the production of hydrogen peroxide. The intermediate imine is hydrolyzed by water to produce the final products, the demethylated lysine side chain and formaldehyde (see also reaction of sarcosine oxidase).