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opennotspecifiedAug 2021View details →

Fig. 1 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging

Fig. 1. DESI-MSI analysis of JA-related compounds in the developing Phaseolus vulgaris seeds. (a) Optical image of the section. (b) Mass spectrum obtained from the section. Ion images of m/z (c) 277.2172, (d) 291.1953, and (e) 293.2117. Three different developing seeds were analyzed, and the results from one are shown as representative data. Scale bar = 2 mm. Compound names are defined in Table 1.

opennotspecifiedAug 2021View details →

Fig. 3 in Unique localization of jasmonic acid-related compounds in developing Phaseolus vulgaris L. (common bean) seeds revealed through desorption electrospray ionization-mass spectrometry imaging

Fig. 3. LC-ESI-MS analysis of JA-related compounds in the extracts from the radicle and seed coat of developing Phaseolus vulgaris seeds. Base peak chromatogram of m/z 277.2173 ±10 ppm for (a) radicle and (b) seed coat, m/z 291.1966 ± 10 ppm for (c) radicle and (d) seed coat, and m/z 293.2122 ± 10 ppm for (e) radicle and seed coat, respectively. Peaks with arrow indicates JA-related compounds: (a) and (b) αLA, (c) and (d) OPDA, and (e) and (f) OPC-8:0. Compound names are defined in Table 1.

Fig. 2 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging

Fig. 2. Comparison of sample pretreatment methods for MALDI-MSI analysis. (A) Intensities of ion peaks corresponding to organic acids, sugars, and alkaloids in the three different sections using airbrush, iMLayer or combined methods for matrix application. Data represent the mean ± SE of intensities of ions at m/z 230.9, 381.0, 264.1 and 367.1 (n = 3), respectively. Photographs of DHB matrix material prepared by different methods: (B) Spray by airbrush, (C) Sublimation by iMLayer, (D) Spray after sublimation. Films and crystals observation were recorded under the light microscope (× 40).

Fig. 5 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging

Fig. 5. Distribution of the main coumarins in diverse tissue parts in the plant of C. lansium. All the MSI were acquired in positive ion mode. The number of pixels in x and y axis was 243 × 248 for the fruit, and 100 × 70 for the stem and 65 × 37 for the leaf parts. The distributions are displayed as heat maps, with the color code between black (low) and red (high). Images were exported from the Shimadzu Imaging software. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging

Fig. 4. Distribution of the main alkaloids in diverse tissue parts in the plant of C. lansium. All the MSI were acquired in positive ion mode. The number of pixels in x and y axis was 243 × 248 for the fruit, and 100 × 70 for the stem and 65 × 37 for the leaf parts. The distributions are displayed as heat maps, with the color code between black (low) and red (high). Images were exported from the Shimadzu Imaging software. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Visualizing the spatial distribution of metabolites in Clausena lansium (Lour.) skeels using matrix-assisted laser desorption/ionization mass spectrometry imaging

Fig. 1. Optical images of different tissue sections of Clausena lansium (Lour.) Skeels plants. (A) Fruit cross section, (B) Part of stem cross section, (C) Leaf cross section (magnification at 40x).

Fig. 6 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 6. Multiple sequence alignment for the catalytic domain of V. betonicifolia protein disulfide isomerases, VbPDI1-2 with previously reported PDIs from Rubiaceae (OaPDI) and Violaceae (GbPDI). The active site residues CGHC are highlighted.

Fig. 4 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 4. Vibe cyclotide/acyclotide properties A. Graphical representation of net acidity, basicity and hydrophobicity of cyclotide/acyclotide* from V. betonicifolia, calculated using a peptide property calculation tool, https://www.peptide2.com/N_peptide_hydrophobicity_hydrophilicity.php (Kyte and Doolittle, 1982; Sims, 2010). B. Sequence alignment highlighting physicochemical similarity. Hydrophobic residues are highlighted in yellow, basic in red and acidic in blue. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 3. Vibe cyclotides identified from small scale extraction of V. betonicifolia. A. Base peak ion (BPI) chromatogram from V. betonicifolia containing deconvoluted masses for (M + H)+ of candidate cyclotides. B. Isotopic mass pattern of native, reduced/alkylated, endoproteinase GluC cleaved cyclotides exemplified by kalata S/ varv A (B), vibe 13 (C) and a new cyclotide present in the extract but absent in the transcriptome (D).

Fig. 2 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 2. Schematic representation of the general organisation of cyclotide precursors and multiple sequence alignment of 28 cyclotide precursor proteins obtained from the de novo transcriptome assembly of V. betonicifolia. A. ER signal domain at the start of each precursor sequence is highlighted in blue where cleavage of the signal domain is predicted to occur between blue and pink residues (Dutton et al., 2004). The precursor is organised with an N-terminal propeptide domain, NTPP (black), N-terminal repeat, NTR (green), mature cyclotide domain (red) and C-terminal propeptide domain, CTPP (purple). An AEP mediated cleavage potentially occurs at the conserved Asn/Asp adjacent to the CTPP of all cyclotide sequences; B. New cyclotides are named vibe 1–25. In varv A/kalata S and vibe 24 transcripts, two repeating mature domains are present. In acyclotides, either the conserved Asn/Asp or CTPP sequence is absent. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 1. Example structures and sequences from the three main cyclotide subfamilies. The structures are based on the PDB files for kalata B1 (1nb1), cycloviolacin O1 (1nbj) and Momordica cochinchinensis II (MCoTI-II) (1ib9). The unique cyclic cystine knot (CCK) topology of cyclotides arises when the ring formed by CysI-CysIV and CysII-CysV together with the backbone loops 1 and 4 are penetrated by the third disulfide between CysIII and CysVI. The cyclotide producing plant families are denoted by RRubiaceae VViolaceae, FFabaceae, SSolanaceae and CCucurbitaceae. The conserved Cys residues are highlighted in yellow and the cis-pro in loop 5 that defines the M¨obius subfamily is highlighted in blue. The conserved Asn/Asp residue at which cyclisation occurs is highlighted in red. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 5. Multiple sequence alignment of vibe AEPs and other functionally verified ligase- and protease-type AEPs identified in cyclic peptide producing plants. The AEP conserved catalytic triad residues Asn, Cys and His are highlighted in red. In the aligned AEPs, ligase activity determinant 1 (LAD1) containing gate keeper residue (highlighted in green/cyan, position orthologous to CYS247 in OaAEP1b (Harris et al., 2015) and ligase activity determinant 2 (LAD2) regions (highlighted in pink/blue) (Hemu et al., 2019), poly-proline region (Jackson et al., 2018) and marker of ligase activity region (MLA) (Jackson et al., 2018) are highlighted in boxes. VyPAL2 from V. yedoensis (Hemu et al., 2019), HeAEP3 from H. enneaspermus (Jackson et al., 2018), OaAEP1b from O. affinis (Harris et al., 2015) and butelase 1 from C. ternatea (Nguyen et al., 2014) are functionally verified ligases. MCoAEP2 has also shown efficient in vitro ligase activity, despite the presence of protease-type ligase activity determinant regions (Du et al., 2020). VyAEP1 from V. yedoensis and HaAEP1 from H. annus are protease-type AEPs with weaker ligase activity at high/neural pH (Haywood et al., 2018; Hemu et al., 2019). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry

Fig. 5. Spatio-temporal distribution of target phytohormones in different tissue of rapeseed germination.

Fig. 2 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry

Fig. 2. XRD spectrum (a), FI-TR pattern (b), Raman spectrum (c) of the composite material, and magnetization hysteresis loop of Fe3O4@Ti3C2@β-CD (d).

Fig. 1 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry

Fig. 1. Schematic of the synthetic route for Fe3O4@Ti3C2@β-CD and the sample pre-treatment procedure.

Fig. 4 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry

Fig. 4. Effects of different cleanup sorbents (a), effects of the amount of magnetic solid-phase extraction sorbents (b), effects of the simultaneous derivatization and magnetic solid phase extraction time (c), effects of the desorption time (d). 5 mg rapeseed spiked with 10 ng/g of each analyte.

Fig. 3 in Magnetic Ti C MXene functionalized with β-cyclodextrin as magnetic solid-phase extraction and in situ derivatization for determining 12 phytohormones in oilseeds by ultra-performance liquid chromatography-tandem mass spectrometry

Fig. 3. SEM image of Ti3C2 (a) and Fe3O4@Ti3C2@β-CD (b), TEM image of Ti3C2(c) and Fe3O4@Ti3C2@β-CD (d), elemental mapping and chemical composition of Fe3O4@Ti3C2@β-CD (e).

opencc-by-4.0Aug 2023View details →

Raw data: Validation of a method for surveillance of nanoparticles in mussels using single particle inductively coupled plasma mass spectrometry

The compressed archive contains SP-ICP-MS data to reproduce results for the paper with the working title "Validation of a method for surveillance of nanoparticles in mussels using single particle inductively coupled plasma mass spectrometry"". The remaining data to produce all other results, visualizations and statistics for the paper is included in the supplementary or GitHub. Associated code is deposited in a GitHub repository, github.com/arebruvold/mussel_validation .