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66 results for “Phloem”
Impacts of Phloem Chilling on Mature Red Maples at Harvard Forest 2019
Whether tree growth is limited by carbon supply or demand is a crucial question due to wide-ranging repercussions for projections of carbon sequestration on land. By temporarily restricting phloem transport using stem chilling, which increases phloem sap viscosity to create local bottlenecks to phloem transport, we created gradients of carbon supply in stems of mature red maples during the first half of the growing season. These carbon supply gradients had clear effects on tree physiology with radial growth in particular varying up to almost seven-fold with carbon supply. Local bulk nonstructural carbon concentrations in stems and roots remained relatively stable, suggesting that they are not rapidly modulated in response to changes in supply and demand. However, phloem and leaf nonstructural carbon accumulated above chilling-induced bottlenecks and were associated with reductions in photosynthetic capacity as well as the advancement of leaf coloration and fall, supporting the idea of within-tree feedbacks reducing carbon supply when supply exceeds demand. Most strikingly, radial growth varied systematically with carbon supply up to almost seven-fold, indicating that growth of red maple during the early growing season is strongly carbon-supply limited. The code to process these data and reproduce our results is available at https://github.com/TTRademacher/Exp2019Analysis. For more details pertaining to the methods see Rademacher et al. (2021) and contact the investigator.
Impacts of Phloem Chilling and Compression on Mature White Pine at Harvard Forest 2018
Wood formation is a crucial process for carbon sequestration on land, yet how variations in phloem-transported carbon and temperature affect wood formation, respiration and nonstructural carbon pools remains poorly understood. To better understand the role of carbon supply on allocation to wood formation, we constrained phloem transport using compression and chilling around the stem of 15 mature white pines to monitor the effects of contrasting carbon supply (enriched above and reduced below the manipulations) on local wood formation and respiration, as well as on nonstructural carbon pools in stems and roots. This data set contains all data measured during the experiment. This includes wood anatomical, xylogenetic, dendrochronological, stem CO2 efflux, and nonstructural carbon measurements in coarse roots and stems, as well as pre-dawn water potential measurements of needles and branches. Furthermore, we provide basic allometric measurements for all trees. The code to process these data and reproduce our results is available at https://github.com/TTRademacher/Exp2018Analysis. For more details pertaining to the methods see Rademacher et al. (2021) and contact the investigator.
Phloem anatomy constraints root system architecture development: theoretical clues from in silico experiments [software and dataset]
<p>Simulation software and results for "<strong>Phloem anatomy constraints root system architecture development: theoretical clues from in silico experiments</strong>"</p>
Text-fig. 14. Photomicrographs of thin sections of specimen BP/16/1732 Palmoxylon dutoitii from Mhengere Hill, Gorongosa, Mozambique. a: transverse section (TS) with four fibre vascular bundles (fvb) and poorly preserved parenchyma between; b: diagram of one of the fvbs in (a) of the reniform type (f – fibres, mx – metaxylum, p – phloem, px – protoxylum); c: close up of the vascular part of a fvb with 2 metaxylem elements and the collapsed cells to the lower left represents the phloem; d: fvb with 2 metaxylem elements, fibrous part to the left and parencymarous ground tissue to the right; e: lower magnification of fvb in (c); f: fvb with three metaxylem elements and phloem patch below; g: longitudinal section (LS) showing the vascular sections alternating with the fibrous sections; h: LS showing the horizontal thickening on the walls of the metaxylem vessels and a patch of parenchyma to the right (darker cells); i: spheroid echinate phytoliths that are typical of Hyphaene and Borassus. in Stratigraphy, Chronology And Palaeontology Of The Tertiary Rocks Of The Cheringoma Plateau, Mozambique
Text-fig. 14. Photomicrographs of thin sections of specimen BP/16/1732 Palmoxylon dutoitii from Mhengere Hill, Gorongosa, Mozambique. a: transverse section (TS) with four fibre vascular bundles (fvb) and poorly preserved parenchyma between; b: diagram of one of the fvbs in (a) of the reniform type (f – fibres, mx – metaxylum, p – phloem, px – protoxylum); c: close up of the vascular part of a fvb with 2 metaxylem elements and the collapsed cells to the lower left represents the phloem; d: fvb with 2 metaxylem elements, fibrous part to the left and parencymarous ground tissue to the right; e: lower magnification of fvb in (c); f: fvb with three metaxylem elements and phloem patch below; g: longitudinal section (LS) showing the vascular sections alternating with the fibrous sections; h: LS showing the horizontal thickening on the walls of the metaxylem vessels and a patch of parenchyma to the right (darker cells); i: spheroid echinate phytoliths that are typical of Hyphaene and Borassus.
Data from: A cucumber protein, Phloem Phosphate Stress Repressed 1, rapidly degrades in response to a phosphate stress condition
<p>Under depleted external phosphate (Pi), many plant species adapt to this stress by initiating downstream signalling cascades. In plants, the vascular system delivers nutrients and signalling agents to control physiological and developmental processes. Currently, limited information is available regarding the direct role of phloem-borne long-distance signals in plant growth and development under Pi-stress conditions. Here, we report on the identification and characterization of a cucumber protein, <em>Cucumis sativus</em> Phloem Phosphate-Stress-Repressed 1 (CsPPSR1), whose level in the phloem translocation stream rapidly responds to imposed Pi-limiting conditions. CsPPSR1 degradation is mediated by the 26S proteasome; under Pi-sufficient conditions, CsPPSR1 is stabilized by its phosphorylation, within the sieve tube system, through the action of CsPPSR1 Kinase. Further, we discovered that CsPPSR1 Kinase was susceptible to Pi-starvation-induced degradation, in the sieve tube system. Our findings offer insight into a molecular mechanism underlying the response of phloem-borne proteins to Pi-limited stress conditions.</p>
Data from: Phloem-feeding insects creat parasitoid free space for caterpillars
<p>Seemingly small ecological changes can have large, ramifying effects that defy expectations. Such are keystone effects in ecosystems. Phloem-feeding insect herbivores can act as keystone species by altering community structure and species interactions via plant-mediated or ant-mediated mechanisms. Plant responses triggered by phloem-feeders can disrupt tri-trophic interactions induced by leaf-chewing herbivores, while ants that tend phloem-feeders can deter or prey on other arthropods. Here, we investigate how phloem-feeding herbivores change caterpillar-parasitoid interactions on <em>Quercus alba</em> (white oak) trees in natural forests. We factorially manipulated the presence of phloem-feeding insects as well as ant access on <em>Q. alba</em> branches over multiple years and sites, and measured parasitism rates of co-occurring caterpillars. While 19.3% of caterpillars were parasitized when phloem-feeders were removed, the presence of phloem-feeders completely suppressed parasitism of caterpillars (0%). This stark pattern was consistent across the diverse community of phloem-feeders and caterpillars. Our manipulation of ant access had no effect on parasitism of caterpillars, implicating a plant-mediated mechanism. We further assessed the mechanistic hypothesis that phloem-feeders suppress plant emission of caterpillar-induced volatile compounds, which could disrupt host location behavior by parasitoids of caterpillars. Phloem-feeders indeed reduced concentrations of four volatile compounds, consistent with the putative plant volatile-mediated mechanism. Given the important role of parasitoids in controlling herbivore populations, this keystone effect of phloem-feeders offers novel insight into community dynamics in forests and potentially other terrestrial ecosystems.</p>
Data from: A cucumber protein, Phloem Phosphate Stress Repressed 1, rapidly degrades in response to a phosphate stress condition
Open the record for dataset details and reuse information.
Data from: Phloem-feeding insects creat parasitoid free space for caterpillars
Open the record for dataset details and reuse information.
Data from: Microbiome responses during virulence adaptation by a phloem-feeding insect to resistant near-isogenic rice lines
The microbiomes of phloem feeding insects include functional bacteria and yeasts essential for herbivore survival and development. Changes in microbiome composition are implicated in virulence adaptation by herbivores to host plant species or host populations (including crop varieties). We examined patterns in adaptation by the green leafhopper, Nephotettix virescens, to near-isogenic rice lines (NILs) with one or two resistance genes and the recurrent parent T65, without resistance genes. Only the line with two resistance genes was effective in reducing leafhopper fitness. After 20 generations on the resistant line, selected leafhoppers attained similar survival, weight gain and egg laying to leafhoppers that were continually reared on the susceptible recurrent parent, indicating that they had adapted to the resistant host. By sequencing the 16s rRNA gene, we described the microbiome of leafhoppers from colonies associated with five collection sites, and continually reared or switched between NILs. The microbiomes included 69-119 OTUs of which 44 occurred in ≥ 90% of samples. Of these, 14 OTUs were assigned to the obligate symbiont Candidatus sulcia clade. After 20 generations of selection, collection site had a greater effect than host plant on microbiome composition. Six bacteria genera, including Candidatus sulcia, were associated with leafhopper virulence. However, there was significant within-treatment, site-related variability in the prevalence of these taxa such that the mechanisms underlying their association with virulence remain to be determined. Our results imply that these taxa are associated with leafhopper nutrition. Ours is the first study to describe microbiome diversity and composition in rice leafhoppers. We discuss our results in light of the multiple functions of herbivore microbiomes during virulence adaptation in insect herbivores.
Extreme Poisson's Ratios Recorded In The Secondary Phloem Of Malvaceae (online data)
<p>This zip file contains two dataset (in xl format), namely the experimental results and the parametric study in relation to the published article</p>
Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV
<p>The dataset contains all the original raw files sorted by figure and figure panel. NGS data has been deposited on GEO (GSE176378). The content of each file is the following:</p> <p> </p> <p><strong>FIGURE 1:</strong></p> <p>-<strong>1A</strong>: Northern blots raw TIFF image files for the detection of TuYVs81 RNA on membrane HMW7 and methylene blue staining of the same membrane.</p> <p>-<strong>1B</strong>: Pictures of Col-0, <em>ago1-57</em>, <em>ago1-27</em> and <em>ago1-38</em> infected with TuYVs81 WT and -P0.</p> <p>-<strong>1C</strong>: Axiozoom pictures of TuMV-GFP AS9 infected plants of Col-0, <em>ago2-1</em>, <em>ago1-57</em> (sup149.1) and <em>ago2-1/ago1-57</em>. Both raw czi and jpg files are provided. Additional pictures for each genotype are also provided.</p> <p>-<strong>1D</strong>: Western blot (W579) and Coomassie staining raw image files for the detection of GFP from TuMV-AS9-GFP infected plants.</p> <p>-<strong>1E&G</strong>: Northern blots raw film scan for the detection of TuYVs81 RNA and TRV-PDS RNS on membrane HMW24 and HMW25 respectively. Methylene blue staining of the same membrane. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p>-<strong>1F&H</strong>:</p> <p>-<strong>1I</strong>: Signal quantification of HMW24/25 using imageJ (spreadsheet).</p> <p>-<strong>1J</strong>: Northern blots raw film scan and TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, 5’, TuYV siRNA, mir159 and U6 probe on membrane PPM70. For the detection of PDS, mir408 and U6 on membrane PPM71 Pictures of Col-0, <em>ago2-1</em>, <em>ago1-57</em> (sup149.1) and <em>ago2-1/ago1-57</em> infected with TuYVs81 WT and TRV-PDS at 20dpi. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p>-<strong>1K</strong>: Shortstack quantification of normalized reads per category (see legend). Original bargraph and html document retracing the analysis steps.</p> <p>-<strong>1L</strong>: Distribution of TuYVs81-derived sRNA reads (20-nt to 25-nt) along the TuYVs81 genome in Col-0 total RNA (library JBT5) and AGO1 IP replicate 1 (library JBT13), with MISIS. Output files from MISIS and final .png image of the distribution.</p> <p> </p> <p><strong>FIGURE 2:</strong></p> <p>-<strong>2A&C</strong>: Kinetic of systemic TuYVs81 and TuMV-GFP WT infection in Col-0, <em>ago1-57</em>, <em>ago1-27 </em>and <em>ago1-38 </em>represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs.</p> <p>-<strong>2B</strong>: Northern blots raw TIFF image files for the detection of TuYVs81 RNA on membrane HMW22 and methylene blue staining of the same membrane.</p> <p>-<strong>2D</strong>: Western blot (W555) and Coomassie staining raw image files for the detection of GFP from TuMV-GFP infected plants.</p> <p>-<strong>2E</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in inoculated leaves of Col-0<em>, ago1-27</em> and <em>ago1-57</em>.</p> <p><strong>2F</strong>: Western blot (W779) and Coomassie staining raw image files for the detection of RT viral proteins from TuYVs81 inoculated leaves.</p> <p><strong>2G</strong>: Western blot (W626-W629) and Coomassie staining raw image files for the detection of CFP-AGO1 and P0-myc in N. benthamiana leaves. Northern blot raw TIFF image files for the detection of P0 CABYV, P0 BMYV and P0 PLRV on membrane HMW28 and methylene blue staining of the same membrane. Protein sequence of the P0 constructs used.</p> <p><strong>2H&I</strong>: DAS-ELISA result and fresh weight of Col-0 and <em>ago1-57</em> plants infected via aphids with WT TuYV.</p> <p> </p> <p><strong>FIGURE 3</strong>:</p> <p>-<strong>3A</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, TuYV siRNA, siR255, IR71, siR1003 and U6 probe on membrane PPM102. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p>-<strong>3B</strong>: Pictures of Col-0, <em>dcl2-1</em>, <em>dcl4-2</em>, <em>ago1-57, dcl2-1/dcl4-2, dcl2-5/dcl3-1, dcl2-1/ago1-57, dcl4-2/ago1-57, dcl2-1/dcl4-2/ago1-57 </em>infected with TuYVs81 WT at 16dpi.</p> <p>-<strong>3C</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in TuYVs81 infected Col-0, <em>dcl2-1</em>, <em>dcl4-2</em>, <em>ago1-57, dcl2-1/dcl4-2, dcl2-5/dcl3-1, dcl2-1/ago1-57, dcl4-2/ago1-57, dcl2-1/dcl4-2/ago1-57 </em>leaves.</p> <p>-<strong>3D</strong>: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP, DCL2-tRFP and DCL4-tRFP are in the folder Figure S5 (related to this panel)</p> <p> </p> <p><strong>FIGURE 4:</strong></p> <p><strong>4A</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in TuYVs81 infected leaves and vasculature of Col-0 and <em>dcl2-1</em> at 17dpi.</p> <p><strong>4B</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYVs81 RNA 3’, TuYV siRNA, siR255, IR71, miR822, miR168, miR162 and U6 probe on membrane PPM90. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p><strong>4C</strong>: Western blot and Coomassie staining raw image files for the detection of DCL1 (W746) and the RT viral protein (W721) from TuYVs81 infected leaves and vasculatures.</p> <p><strong>4D</strong>: qPCR data for the quantification of <em>DCL2 </em><em>and </em><em>DCL4</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 and <em>dcl2-1</em> plants.</p> <p><strong>4E</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of PDS, TRV 3’UTR and U6 (PPM96) and TRV 3’UTR (HMW38) in leaf and vasculature of plants infected with TRV-PDS. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p><strong>4F</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in TuYVs81 WT and P0- infected leaves and vasculature of Col-0 plants. Raw Ct and calculation spreadsheet are with Figure 4A.</p> <p><strong>4G</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of TuYV RNA 3’, TuYV siRNA and U6 (PPM102) in leaf and vasculature of Col-0 and <em>dcl2-1</em> plants infected withTuYVs81 WT or P0-. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p> </p> <p><strong>FIGURE 5:</strong></p> <p>-<strong>5A</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 and <em>ago1-57</em> plants.</p> <p>-<strong>5B</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 (W758) and AGO2(W759) from TuYVs81 infected leaves and vasculatures.</p> <p>-<strong>5C</strong>: AGO1 signal quantification across five biological replicates in Mock and TuYVs81 infected leaves and vasculatures.</p> <p>-<strong>5D&E</strong>: All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP-AGO1 and P0-tRFP are in the folder Figure S8 (related to this panel).</p> <p>-<strong>5F</strong>: qPCR data for the quantification of <em>AGO1 </em><em>and</em><em> AGO2</em> RNA in TuYVs81 infected leaves and vasculature of Col-0 and <em>ago1-57</em> plants. Raw Ct and calculation spreadsheet are with Figure 5A.</p> <p>-<strong>5G</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W809) and AGO2 (W810) from TuYVs81 WT and TuYVs81 P0- infected leaves and vasculatures.</p> <p>-<strong>5H</strong>: Pictures of SUC-SUL (SS, parental), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) adult plants.</p> <p>-<strong>5I</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and P0-HA (W723) from SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) leaves and vasculatures.</p> <p>-<strong>5J</strong>: Northern blots TIFF images/raw phoshphoimager .gel files for the detection of SUL siRNA, miR160c, miR160*, miR168, miR159 and U6 (PPM89) in leaf and vasculature from SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) plants. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p>-<strong>5K</strong>: qPCR data for the quantification of <em>CHLI1</em>, <em>CHLI2</em> and <em>AGO1 </em>RNA in leaves and vasculature of SUC-SUL (SS), SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV-P0-HA LP1 (CLSS6-3) plants.</p> <p>-<strong>5L</strong>: Raw heatmap of all AGO1 IP libraries (DESeq2). Top 20 most deregulated loci.</p> <p> </p> <p><strong>FIGURE S1:</strong></p> <p><strong>S1A</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in whole leaves of TuYVs81 infected Col-0 and different ago single and combination mutants.</p> <p><strong>S1B</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and AGO2 (W603) from Col-0, <em>ago2-1</em>, <em>ago1-57</em> and <em>ago2-1/ago1-57</em> infected with TuYVs81 WT and TRV-PDS</p> <p><strong>S1C</strong>: Northern blots raw TIFF image files for the detection of TuYV RNA 3’, TuYV siRNA, s81 insert siRNA, miR403, miR408, miR159 and U6 on membrane PPM60 (AGO1 IP) and PPM62 (AGO2 IP). Total RNA quantification and input volumes on gel (spreadsheet).</p> <p><strong>S1D:</strong> Western blot and Coomassie staining raw image files for the detection of AGO1 (W537) and AGO2 (W538) from Col-0, <em>ago1-57</em>, <em>ago1-27</em> infected with TuYVs81 WT.</p> <p><strong>S1E:</strong> Northern blots TIFF images/raw phoshphoimager .gel files for the detection of SUL siRNA, miR408, miR159 and U6 (PPM93) in AGO1 and AGO2 IPs from Col-0, SUC-SUL (SS), SS/<em>ago1-57 </em>rosette leaves. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p><strong>S1F</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 and AGO2 (W766) from Col-0, SUC-SUL (SS), SS/<em>ago1-57 </em>rosette leaves before and after AGO1 and AGO2 IP.</p> <p> </p> <p><strong>FIGURE S2:</strong></p> <p><strong>S2A:</strong> Total RNA quantification of TuYVs81 infected Col-0 and <em>ago1-57</em> plant pools (#1 and #2) used for sRNA deepseq. Powerpoint presentation of all plant pool used, WB results and bioanalyzer profile of the total RNA. Spreadsheet with sequencing and mapping statistic for all 16 JBT libraries.</p> <p><strong>S2B</strong>: Western blot and Coomassie staining raw image files for the detection of AGO1 (W398-W402) before and after AGO1 IP for sRNA deepseq samples.</p> <p><strong>S2C:</strong> See figure 1K. Original bargraphs for 21-nt, 22-nt and 24-nt mapped reads in all JBT libraries.</p> <p><strong>S2D</strong>: Distribution of TuYVs81-derived sRNA reads (20-nt to 25-nt) along the TuYVs81 genome in Col-0 total RNA (libraries JBT5 and JBT6), <em>ago1-57</em> total RNA (libraries JBT7 and JBT8), Col-0 AGO1 IP (libraries JBT13 and JBT14) and <em>ago1-57</em> AGO1 IP (libraries JBT15 and JBT16), with MISIS. Output files from MISIS and final .png image of the distribution.</p> <p><strong>S2E:</strong> TuYVs81 nucleotide composition % (spreadsheet) and 5’ nucleotide frequency of the vsiRNA reads mapped to the TuYVs81 genome in JBT5, JBT7, JBT13 and JBT15 (.png). 5’ graphs were generated using MISIS.</p> <p> </p> <p><strong>FIGURE S3:</strong></p> <p><strong>S3A</strong>: Kinetic of systemic TuYVs81, TuMV-GFP and TRV-PDS infection in Col-0 and <em>ago1-57</em>, represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs.</p> <p><strong>S3B</strong>: qPCR data for the quantification of <em>TuYV</em> RNA in inoculated leaves of Col-0<em>, ago1-27</em> and <em>ago1-57</em>. Biological replicate to the experiment in Figure 2E.</p> <p> </p> <p><strong>FIGURE S4:</strong></p> <p><strong>S4A:</strong> Leaf pictures of Col-0, <em>dcl2-1</em>, <em>dcl4-2</em>, <em>dcl2-1/dcl4-2, rdr6-12, sgs3-14 </em>infected with TuYVs81 WT at 17dpi. Leaves are from two different individuals.</p> <p><strong>S4B:</strong> Northern blots raw TIFF images and scans files for the detection of TuYVs81 RNA 3’ siRNA and U6 in Col-0, <em>ago1-57, dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14</em> infected with TuYVs81 WT on membrane PPM39. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p><strong>S4C:</strong> Northern blots raw TIFF images files for the detection of TuYVs81 RNA 3’ in Col-0, <em>ago1-57, dcl2-1, rdr6-12, sgs3-14</em> infected with TuYVs81 WT on membrane HMW8. Methylene blue stain of the membrane. Total RNA quantification and input volumes on gel (spreadsheet) with figure S4B.</p> <p><strong>S4D</strong>: Kinetic of systemic TuYVs81 infection in Col-0, <em>ago1-57</em>, <em>dcl2-1, dcl4-2, dcl2-1/dcl4-2, rdr6-12, sgs3-14</em> represented as the cumulated percentage of infected plants in the inoculated population. Raw spreadsheet with day to day counting. Original graphs.</p> <p> </p> <p><strong>FIGURE S5:</strong></p> <p>All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP, DCL2-tRFP and DCL4-tRFP. Note that more images are available that those in the manuscript.</p> <p> </p> <p><strong>FIGURE S6:</strong></p> <p><strong>S6A:</strong> qPCR data for the quantification of <em>TuYV</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0.</p> <p><strong>S6B:</strong> See Figure 4B</p> <p><strong>S6C:</strong> qPCR data for the quantification of <em>DCL2 </em><em>and </em><em>DCL4</em> RNA in whole leaves and vasculatures of TuYVs81 infected Col-0 plants.</p> <p> </p> <p><strong>FIGURE S7:</strong></p> <p><strong>S7A:</strong> qPCR data for the quantification of <em>TuYV</em> RNA in vasculatures and protoplast cells of TuYVs81 infected Col-0.</p> <p><strong>S7B:</strong> Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W283), AGO2 and AGO4 (W328) in vasculatures and protoplast cells of TuYVs81 infected Col-0 and <em>ago1-57</em>.</p> <p><strong>S7C:</strong> Northern blots raw TIFF images for the detection of miR168 and U6 on membrane PPM47 in vasculatures and protoplast cells of TuYVs81 infected Col-0. Total RNA quantification and input volumes on gel (spreadsheet).</p> <p><strong>S7D:</strong> qPCR data for the quantification of <em>TuYV</em> and <em>AGO1</em> RNA in mock and TuYVs81 infected leaves of Col-0, <em>ago1-57</em>, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1).</p> <p><strong>S7E:</strong> qPCR data for the quantification of <em>AGO1</em> RNA in TuYVs81 WT and P0- infected leaves and vasculature of Col-0 and <em>dcl2-1</em> plants.</p> <p><strong>S7F:</strong> Western blot and Coomassie staining raw image files for the detection of AGO1 and RT viral protein (W708) in whole leaves of TuYVs81 infected Col-0, <em>ago1-57</em>, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1).</p> <p><strong>S7G</strong>: qPCR data for the quantification of <em>Flag-AGO1</em> RNA in mock and TuYVs81 infected leaves of Col-0, pSUC:Flag-AGO1 #1 (ASWW1b3) and #2 (ASWW2b1).</p> <p> </p> <p><strong>FIGURE S8:</strong></p> <p><strong>S8A:</strong> All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with tRFP-AGO1. Note that more images are available that those in the manuscript.</p> <p><strong>S8B:</strong> All raw .lif files and Fiji processed TIFF microscopy images of B2-GFP expressing <em>N. benthamiana</em> plants infiltrated with P0-tRFP. Note that more images are available that those in the manuscript.</p> <p> </p> <p><strong>FIGURE S9:</strong></p> <p><strong>S9A: </strong>Pictures of 11-day old seedlings grown on MS media: Col-0, SUC-SUL (SS), SS/pSuc:P15-FHA, SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV:P0-HA LP1 (CLSS6-3).</p> <p><strong>S9B:</strong> qPCR data for the quantification of <em>P0-HA </em><em>and</em><em> AGO1</em> RNA in seedlings of Col-0, SUC-SUL (SS), SS/pSuc:P15-FHA, SS/pCoYMV:P0-HA WT (CWSS6-3) and SS/pCoYMV:P0-HA LP1 (CLSS6-3).</p> <p> </p> <p><strong>FIGURE S10:</strong></p> <p><strong>S10A:</strong> Raw heatmap of all AGO1 Total RNA libraries (DESeq2). Top 18 most deregulated loci.</p> <p><strong>S10B:</strong> MA plot of AGO1 IP in Col-0 TuYV <em>vs.</em> AGO1 IP in Col-0 mock (DESeq2). MA plot of AGO1 IP in <em>ago1-57</em> TuYV <em>vs.</em> AGO1 IP in <em>ago1-57</em> mock (DESeq2).</p> <p><strong>S10C:</strong> Northern blots raw TIFF images/raw phoshphoimager .gel files for the detection of SUL3’ siRNA, TuYV 3’ siRNA and U6 on membrane PPM64 (Col-0<em>, ago1-57, dcl2-1, dcl4-2, dcl2/4</em> infected with TuYVs81 and Col-0 plus ago1-57 infected with aphid transmitted TuYV WT) and PPM68 (Col-0<em>, ago1-57, rdr6-12, sgs3-14, dcl2/4 </em>infected with TuYVs81 as well as Col-0 and<em> ago1-57</em> infected with TuMV-GFP). Total RNA quantification and input volumes on gel (spreadsheet).</p>
Fig. 5 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants
Fig. 5. Extracted-ion chromatograms (EIC; m/z 124, 127) obtained by HS-SPME–GCxGC-ToF-MS-analysis after feeding [2H]- -leucine to several fruit tissues of 10 Lunripe bell peppers (Capsicum annuum cv. Allrounder).
Fig. 6 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants
Fig. 6. Extracted-ion chromatograms (EIC; m/z 124, 127) obtained by HS-SPME–GCxGC-ToF-MS-analysis after feeding [2H]- -leucine to several organs of bell 10 Lpepper plants (Capsicum annuum cv. Allrounder).
Fig. 3 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants
Fig. 3. IBMP-content (means ± standard deviations (n = 5–8) expressed as ng/g FW (fresh weight)) in the various parts of unripe (A) and ripe (B) bell pepper fruits (Capsicum annuum cv. Allrounder). Ripening stages of bell pepper fruits: unripe (fully green), breaking point (green and yellow) and ripe (fully yellow) (C). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants
Fig. 4. Structure (A) and electron ionization (EI) mass spectra (B) of the biosynthetic product ([2H]-IBMP) after incorporation of stable-isotope labelled [2H]- 9 10 L-leucine.
Fig. 2 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants
Fig. 2. EI-MS spectra and fragmentation pattern of IBMP (A) and EI-MS spectra and fragmentation pattern of [2H]-IBMP (B).
Fig. 1 in Sites of biosynthesis, distribution and phloem transport of 3-isobutyl-2- Methoxypyrazine in Capsicum annuum (bell pepper) plants
Fig. 1. Total ion chromatogram (TIC) (A) and extracted ion chromatogram (EIC) (B) of ripe bell pepper pericarp (Capsicum annuum cv. Allrounder) analyzed by HSSPME–GC-ToF-MS.
Fig. 1 in Cucurbitaceae phloem exudate lectins: Purification, molecular characterization and carbohydrate binding characteristics
Fig. 1. Multiple sequence alignment of the amino acid sequence of PP2 proteins from Cucurbitaceae species as well as from A. thaliana and A. graveolens. Sequences of A. graveolens (CBC70481.1), A. thaliana (CAB78986.1), Coccinia indica agglutinin CIA17 (P0DSP5.1), Cucumis sativus (KAE8649724.1), Cucumis melo (AAM74924.1), Luffa acutangula (C0HJV2.1), Cucurbita argyrosperma (CBC70491.1), Cucurbita arg. sororia (AAM82558.1), Cucurbita moschata (AAF74345.1), Cucurbita pepo (023518987.1), Cucurbita maxima (AAA33117.1), Cucurbita digitata (AAM82559.1) were taken from NCBI gene bank. Multiple sequence alignment was performed using Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/). The highly conserved amino acids 100-Leu-Ile-Glu-Val-Ser-Trp-105 and 199-Trp- Lys-200, which are important for chitooligosaccharide binding are shown in boxes. The residue numbers correspond to the primary structure of PPL.
Fig. 6 in Cucurbitaceae phloem exudate lectins: Purification, molecular characterization and carbohydrate binding characteristics
Fig. 6. Interaction of chitohexaose with the carbohydrate binding cleft of PPL, showing the amino acid residues involved in carbohydrate binding. The binding site was divided into three subsites as indicated by arrows: subsite 1 (Leu-100, Glu-102), subsite 2 (Ile-101, Ser-104, Trp-105) and subsite 3 (Trp-199, Lys- 200). Only three GlcNAc residues from the non-reducing end of chitohexaose are seen to interact with the binding cleft. GlcNAc residues at the reducing end interact with another PPL monomer (shown in the circle at the top left corner). Reproduced from Bobbili et al. (2014). Copyright (2014) Elsevier.
Fig. 3. A LigPlot depicting the interactions between CIA17 in Cucurbitaceae phloem exudate lectins: Purification, molecular characterization and carbohydrate binding characteristics
Fig. 3. A LigPlot depicting the interactions between CIA17 and bound chitotetraose. Adapted from the Supporting Information of Bobbili et al. (2019). Copyright (2019) Elsevier.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.