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opennotspecifiedMay 2023View details →

FIGURE. 2 in Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)

FIGURE. 2. Bayesian tree based on the complete cyt-b gene for the Hynobius akiensis sensu lato and related species. Asterisks above branches indicate nodes with bootstrap supports for ML inference (bs)>70 % and Bayesian posterior probability (bpp)>95 %.

opennotspecifiedMay 2023View details →

FIGURE. 1 in Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae)

FIGURE. 1. Map of Chugoku and Shikoku district showing ranges of Hynobius akiensis, H. sumidai, H. geiyoensis, H. utsunomiyaorum, H. setouchi and H. iwami.

opencc-by-4.0Jun 2023View details →

Deconvolved STED nanoscopy images of the nuclear phosphatidylinositol 4,5-bisphosphate and nuclear speckle marker SON together with deconvolved confocal images of DAPI stained nuclei in human formalin-fixed paraffin-embedded skin sections

The collection and analysis of formalin-fixed paraffin-embedded (FFPE) human skin sections was approved by the local ethics-committee at the Department of Pathology, University of Cologne, Germany. Written informed consentwas obtained from all patients in accordance with the Declaration of Helsinki. For biopsy materials from archival paraffin blocks of human skin, an informed consent was obtained from all the subjects and ethical approval obtained from the Ethics Committee at the University of Cologne. Surgically removed human FFPE skin biopsies were sectioned into 4 µm sections. Sections were dewaxed, and indirectly immunofluorescently labeled against nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) using  5 µg/mL rabbit primary polyclonal antibody (Echelon Biosciences Inc. Z-A045, clone 2C11). The primary antibody against nPI(4,5)P2 was recognized by the goat secondary antibody conjugated with Abberrior Star 635P (Abberior 2-0002-007-5). Sections were indirectly immunofluorescently labeled against nuclear speckle marker SON using  1 µg/mL rabbit primary polyclonal antibody (Abcam ab121759). The primary antibody against SON was recognized by the goat secondary antibody conjugated with Abberrior Star 580 (Abberrior ST580-1002). Sections were co-stained by DAPI 1:1000 in PBS for 5 min. Imaging of nPI(4,5)P2-635P channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 7% 633 nm laser; 775 Notch filter; 50% 775 nm STED laser; 30% 3D STED; HyD 639-698 nm, photon-counting mode, gain 100, gating 0.3-10 ns. Imaging of SON-580 channel was performed on Leica TCS SP8 STED 3x inverted DMi8 microscope with pulsed white light laser 470-640 nm 1.5 mW and 775 nm pulse STED laser >1.5 W controlled by Leica Application Suite X software and equipped with HC PL APO CS2 100x/1.40 OIL objective used with Leica Type F immersion oil n=1.518. Unidirectional xyz scanning speed was 400 Hz, line accumulation 8. Pixel size was 20 nm in X and Y. Channel settings: 10% 585 nm laser; 775 Notch filter; 80% 775 nm STED laser, 30% 3D STED; Hybrid detector (HyD) 589-616 nm, photon-counting mode, gain 100, gating 0.4-10 ns. Z-stacks of STED images were deconvolved using Huygens Professional 22.10 software (Scientific Imaging B.V.). Data sets were processed using Workflow Processor. The workflow consisted of selecting images, setting up the microscopy and deconvolution parameters and saving deconvolved images as 8-bit TIFF single files for individual channels (which were later used for the quantitative analyses; see below). Microscopy parameters were optimized and set as follows. Sampling intervals were ≤20 nm in X and Y and  ≤20 nm in Z. Numerical aperture was 1.4; refractive indexes of the lens immersion oil was 1.518 and of the embedding media 1.458; objective quality was good, coverslip position was 0 µm and imaging direction was downward. For nPI(4,5)P2-635P STED channel the backprojected pinhole was 216 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 633 and 651 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 25, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 5.1. For SON-580 STED channel the backprojected pinhole was 195 nm; excitation (ex.) and emission (em.) wavelengths (λ) were 585 and 602 nm, resp., ex. fill factor 2. STED depletion mode was pulsed, saturation factor 20, STED λ = 775, STED immunity factor 10 and STED 3X was 30%. Classic MLE algorithm with stabilization of Z-slices was used and signal-to-noise ratio was 4.

opencc-by-4.0Dec 2022View details →

Mindfulness-Based Intervention effect on the psychophysiological marker of self-regulation in women with endometriosis.

Data used in the paper investigating the Mindfulness-Based Intervention effect on the psychophysiological marker of self-regulation in women with endometriosis.

opennotspecifiedDec 2021View details →

Fig. 3 in Specialised metabolites as chemotaxonomic markers of Coptosapelta diffusa, supporting its delimitation as sisterhood phylogenetic relationships with Rubioideae

Fig. 3. The current most likely phylogenetic backbone of Rubiaceae based on nuclear (a), chloroplast (b) and mitochondrial (c) data sensu Rydin et al., (2017) and Wikstrom et al., 2020

opennotspecifiedJul 2021View details →

Fig. 4 in Phytochemical profiling of several Hypericum species identified using genetic markers

Fig. 4. PCA (A) and HCA (B) analyses of 13 metabolites quantified in the extracts of shoots of ex vitro grown Hypericum plants. The PCA biplot (A) shows grouping of the species (points), and the contribution (loadings) of the variables (metabolites, indicated by the arrows) to the grouping. Each species is represented by three biological replicates (three points per species). The points are colored according to their quality of representation on the factor map, expressed by squared cosine (cos2). The direction and length of the loading vectors show how each metabolite contributes to clustering. An ellipse is drawn around each cluster. The species are clustered according to the branches as depicted at HCA dendrogram (B). Each square in the heatmap dendrogram represents the relative content of a metabolite. The red and blue color represent an increase and a decrease of relative metabolite content, respectively. Different color of metabolites (PCA) or lines under the heatmap (HCA) indicate the metabolite contents in leaves (green) and stems (brown). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedJul 2021View details →

Fig. 3 in Phytochemical profiling of several Hypericum species identified using genetic markers

Fig. 3. PCA (A) and HCA (B) analyses of 13 metabolites quantified in the extracts of shoots of in vitro-grown Hypericum plants. The PCA biplot (A) shows grouping of the species (points), and the contribution (loadings) of the variables (metabolites, indicated by the arrows) to the grouping. Each species is represented by three biological replicates (three points per species). The points are colored according to their quality of representation on the factor map, expressed by squared cosine (cos2). The direction and length of the loading vectors show how each metabolite contributes to clustering. An ellipse is drawn around each cluster. The species are clustered according to the branches as depicted at HCA dendrogram (B). Each square in the heatmap dendrogram represents the relative content of a metabolite. The red and blue color represent an increase and a decrease of relative metabolite content, respectively. Different color of metabolites (PCA) or lines under the heatmap (HCA) indicate the metabolite contents in leaves (green) and stems (brown). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedJul 2021View details →

Fig. 2 in Phytochemical profiling of several Hypericum species identified using genetic markers

Fig. 2. Metaphase chromosomes in root tip squashes of several representatives of the genus Hypericum arranged in ascending order from the lowest to the highest value of the DNA content per chromosome: H. xylosteifolium, 2n =40 (A), H. androsaemum, 2n =40 (B), H. hircinum, 2n =40 (C), H. athoum, 2n =16 (D), H. empetrifolium, 2n =18 (E), H. atomarium, 2n =16 (F), H. monogynum, 2n =42 (G), H. stellatum, 2n =18, 20 (H), H. patulum, 2n =36 (I). Photo: S. Hovancov´a.

Fig. 5 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers

Fig. 5. The amplicons generated using degenerate primer approach. (a) Lane M-DNA ladder, Lane 1–250 bp amplicon generated using MTH –F and MTH-R primer pairs of TH gene (b) Lane M-DNA ladder, Lane 1 and 2–800 bp amplicon using primers deduced from the peptide sequence derived through LCMS/MS.

Fig. 4 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers

Fig. 4. Effect of enzyme inhibitors on L-DOPA production in callus cultures of M. pruriens was estimated using HPTLC. The culture without inhibitor was treated as negative control and cultures with different concentration of the inhibitor were the test samples. (Control-untreated, C = Cimetidine at 1.98 μM and 19.8 μM; Q = Quinidine at 1.46 μM and 14.6 μM; A = L-ascorbic acid at 567 μM and 851 μM; K = Kojic acid at 703 μM and 1055 μM).

Fig. 3 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers

Fig. 3. Effect of substrate concentration on partially purified enzymes. The assay was performed for PPO activity with 50 mM catechol as substrate at pH 6.0 while keeping the temperature for reaction at 30 ◦ C. For TH activity, 30 mM L-tyrosine was the substrate and assay done at pH 7.0 and 25 ◦ C.

Fig. 2 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers

Fig. 2. Effect of pH on the activity of partially purified enzymes from Mucuna pruriens. The assay was performed using 50 mM catechol and 30 mM L-tyrosine as substrates for the PPO and TH enzyme activity, respectively. Four different buffers with their optimal buffering capacity in the pH range of 3–10 were used in separate assays.

Fig. 7 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers

Fig. 7. Homology modelling and secondary structure prediction of PPO enzyme from Mucuna pruriens (a) Predicted secondary structure of PPO (b) Phyre2 protein model for PPO with 3D model dimensions (in Å) (X:49.941 Y:64.463 Z:57.979). Image colored by rainbow N → C terminus (c) Three dimensional SWISS protein model for PPO enzyme with two active copper binding ligands (copper ions bridging oxygen moiety is illustrated as small yellow spheres highlighted in the box), conserved histidine residues and metal complex interactions (in dotted lines). Chain A for Ligand 1: H.183, H.204, H.213, F.367, H.371; metal interactions: A:H.183, A:H.204, A:H.213. Chain A for Ligand 2: H.337, H.341, F.367, H.370, H.371; metal interactions: A:H.337, A:H.341, A:H.371). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6. The 1800 in L-DOPA synthesis in Mucuna pruriens (L.) DC. is regulated by polyphenol oxidase and not CYP 450/tyrosine hydroxylase: An analysis of metabolic pathway using biochemical and molecular markers

Fig. 6. The 1800 bp amplicon of full-length PPO cDNA obtained after deducing the 5′and 3′ ends through RACE analysis. Lane 1- 1 Kb DNA marker, Lane 2 and 3 the amplicon in duplicate after amplification using gene specific primers.

Fig. 4 in Characterisation of Thai strawberry (Fragaria × ananassa Duch.) cultivars with RAPD markers and metabolite profiling techniques

Fig. 4. Metabolite pathway display shows significant difference between Praratchatan No.80 and Akihime at 25Daa. Changes of metabolites are displayed as ratio>1 (blue), <1 (red), no change (grey) and not detected (white). Analysis comprised six biological replicates per cultivar. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Characterisation of Thai strawberry (Fragaria × ananassa Duch.) cultivars with RAPD markers and metabolite profiling techniques

Fig. 5. PCA analysis of volatile analysis of Akihime and Praratchatan No.80. Freeze-dried tissue was analysed by SPME-GC-MS. Samples and metabolites are displayed as score plot (A) and loading plot (B). Six biological replicates are displayed individually.

Fig. 3 in Characterisation of Thai strawberry (Fragaria × ananassa Duch.) cultivars with RAPD markers and metabolite profiling techniques

Fig. 3. Heatmap of metabolites detected in strawberry fruits of Praratchatan No.80 and Akihime. Metabolites were analysed by GC-MS and LC-MS from polar extracts and by GC-MS from non-polar extracts. Ripening stages are displayed as 7, 10, 13, 16, 19, 22, 25, 28Daa. Only significant compounds, as determined by twoway ANOVA analysis, are displayed. Biological replicates are displayed individually. A more detailed version of this figure is available as Supplementary Fig. 3.

Fig. 2 in Characterisation of Thai strawberry (Fragaria × ananassa Duch.) cultivars with RAPD markers and metabolite profiling techniques

Fig. 2. Stages of fruit development from flower (FL) to overripe fruit of strawberry cultivar Akihime (A) and Praratchatan No.80 (B). Stages are labelled as days after anthesis (Daa). PCA analysis of metabolite composition of Praratchatan No.80 (circles) and Akihime (squares) at eight different fruit ripening stages (C). Metabolites of polar and non-polar extracts were analysed by GC-MS and LC-MS. Data includes 134 identified metabolites including primary and specialised metabolism. Analysis comprised six biological replicates, which are displayed individually.

Fig. 1 in Characterisation of Thai strawberry (Fragaria × ananassa Duch.) cultivars with RAPD markers and metabolite profiling techniques

Fig. 1. Dendrograms of six strawberry varieties based on their genetic (A) and metabolic (B) similarities. The genetic information is based on the degree of band sharing of 228 polymorphic alleles. The metabolic data comprises 129 metabolites identified in polar and non-polar leaf extracts by GC-MS. (C) Representative leaf of six strawberry cultivars.