The Feeding Tube of Cyst Nematodes: Characterisation of Protein Exclusion
Publication Date
January 28, 2014
Journal
PLOS ONE
Authors
Sebastian Eves Van Den Akker, Catherine J. Lilley, James R. Ault, Alison E. Ashcroft, et al
Volume
9
Issue
1
Pages
e87289
DOI
https://dx.plos.org/10.1371/journal.pone.0087289
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0087289
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24489891
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905015
Europe PMC
http://europepmc.org/abstract/MED/24489891
Web of Science
000330510000125
Scopus
84900332488
Mendeley
http://www.mendeley.com/research/feeding-tube-cyst-nematodes-characterisation-protein-exclusion
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1364279"], "description"=>"<p>Size predictions shown for MOBCAL Exact Hard Sphere Scattering (EHSS) in grey bars, and Projection Approximation (PA) in white bars, compared to RotaMol, in black bars, for a range of proteins (PDB code given) from published sources. For the majority of predictions (70%) RotaMol lies between that of PA and EHSS (• indicates the cases where RotaMol predictions are not between PA and EHSS) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087289#pone.0087289-Shelimov1\" target=\"_blank\">[23]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087289#pone.0087289-Valentine2\" target=\"_blank\">[28]</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087289#pone.0087289-Hopper1\" target=\"_blank\">[29]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "rotamol", "predictions"], "article_id"=>916353, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g004", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_RotaMol_predictions_and_existing_prediction_methods_/916353", "title"=>"Comparison between RotaMol predictions and existing prediction methods.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364281"], "description"=>"<p>In each case, left represents mass spectrum and right represents the corresponding drift plot. (<b>A</b>) GFP drift plot shows both monomeric species of 27334 Da and a dimeric species at 54627 Da only (red). (<b>B</b>) mRFP drift plot shows a monomeric species at 25786 Da and a less intense dimeric species at 51575 Da (red). (<b>C</b>) Dual PI drift plot shows a single weak dimeric species below the measurement threshold and two monomeric species, both at 21690 Da, presumed to be folded and unfolded variants.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "mrfp", "dual"], "article_id"=>916355, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g005", "stats"=>{"downloads"=>3, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ESI_TWIMS_MS_drift_plots_of_GFP_mRFP_and_Dual_PI_/916355", "title"=>"ESI-TWIMS-MS drift plots of GFP, mRFP and Dual PI.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364283"], "description"=>"<p>Dual PI migrates as multiple bands under native conditions indicating multimerisation.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "dual", "pi"], "article_id"=>916357, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g006", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Native_PAGE_comparison_between_Dual_PI_and_mRFP_/916357", "title"=>"Native-PAGE comparison between Dual PI and mRFP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364284"], "description"=>"<p>For all samples, sedimentation coefficient is plotted against concentration distribution, c(s). A single monomeric species was detected for mRFP (red), both monomeric and dimeric species were detected for GFP (green). A monomeric form and large heterogeneous multimers estimated at >150 kDa were detected for Dual PI (black).</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "analytical", "ultra-centrifugation", "gfp", "dual"], "article_id"=>916358, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g007", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Absorbance_data_from_analytical_ultra_centrifugation_for_mRFP_GFP_and_Dual_PI_/916358", "title"=>"Absorbance data from analytical ultra-centrifugation for mRFP, GFP and Dual PI.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364285"], "description"=>"_", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "uptake", "proteins", "cyst", "nematodes", "correlated", "molecular"], "article_id"=>916359, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.t001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observed_uptake_of_proteins_by_cyst_nematodes_correlated_with_their_molecular_mass_and_size_/916359", "title"=>"Observed uptake of proteins by cyst nematodes correlated with their molecular mass and size.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364287", "https://ndownloader.figshare.com/files/1364288", "https://ndownloader.figshare.com/files/1364289"], "description"=>"<div><p>Plant parasitic nematodes comprise several groups; the most economically damaging of these are the sedentary endoparasites. Sedentary endoparasitic nematodes are obligate biotrophs and modify host root tissue, using a suite of effector proteins, to create a feeding site that is their sole source of nutrition. They feed by withdrawing host cell assimilate from the feeding site though a structure known as the feeding tube. The function, composition and molecular characteristics of feeding tubes are poorly characterised. It is hypothesised that the feeding tube facilitates uptake of host cell assimilate by acting as a molecular sieve. Several studies, using molecular mass as the sole indicator of protein size, have given contradictory results about the exclusion limits of the cyst nematode feeding tube. In this study we propose a method to predict protein size, based on protein database coordinates <i>in silico</i>. We tested the validity of these predictions using travelling wave ion mobility spectrometry – mass spectrometry, where predictions and measured values were within approximately 6%. We used the predictions, coupled with mass spectrometry, analytical ultracentrifugation and protein electrophoresis, to resolve previous conflicts and define the exclusion characteristics of the cyst nematode feeding tube. Heterogeneity was tested in the liquid, solid and gas phase to provide a comprehensive evaluation of three proteins of particular interest to feeding tube size exclusion, GFP, mRFP and Dual PI. The data and procedures described here could be applied to the design of plant expressed defence compounds intended for uptake into cyst nematodes. We also highlight the need to assess protein heterogeneity when creating novel fusion proteins.</p> </div>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "feeding", "cyst", "characterisation"], "article_id"=>916361, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087289.s001", "https://dx.doi.org/10.1371/journal.pone.0087289.s002", "https://dx.doi.org/10.1371/journal.pone.0087289.s003"], "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Feeding_Tube_of_Cyst_Nematodes_Characterisation_of_Protein_Exclusion_/916361", "title"=>"The Feeding Tube of Cyst Nematodes: Characterisation of Protein Exclusion", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364274"], "description"=>"<p>The nematode feeds by inserting the stylet through the wall of the feeding cell. A feeding tube is formed within the host cell cytoplasm, and host cell assimilate is withdrawn through the walls of the feeding tube in the direction of the arrows. Inset shows a cross section of a feeding tube induced by <i>Globodera pallida</i> in potato (<i>Solanum tuberosum</i>) and viewed under a transmission electron microscope.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "diagram", "cyst", "nematode", "feeding"], "article_id"=>916348, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g001", "stats"=>{"downloads"=>10, "page_views"=>199, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_diagram_of_the_cyst_nematode_feeding_process_/916348", "title"=>"Schematic diagram of the cyst nematode feeding process.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364275"], "description"=>"<p>The images represent every pixel analysed at varying Pixelskips for a single viewing angle of the green fluorescent protein PDB file. At a Pixelskip of 1 every pixel is measured, at a Pixelskip of 50, 1 in every 50 pixels is measured. The number of pixels is then multiplied by the Pixelskip for X and Y.</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "varying", "pixelskip"], "article_id"=>916349, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g002", "stats"=>{"downloads"=>2, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RotaMol_Varying_Pixelskip_and_its_effect_on_measurement_accuracy_/916349", "title"=>"RotaMol: Varying Pixelskip and its effect on measurement accuracy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/1364277"], "description"=>"<p>(<b>A</b>) RotaMol analysis of mRFP at θ = 30° varying Pixelskip in a stepwise manner from 3 to 100. Average area (black) in Angstroms<sup>2</sup> plotted against Pixelskip. Computation time (red) plotted on left axis in seconds, shows exponential increase with decreasing Pixelskip. The optimum value for Pixelskip was defined as 20, as it has the highest accuracy with the shortest computational time (arrow). (<b>B</b>) RotaMol analysis of Luteinising hormone-releasing hormone (LHRH) using a Pixelskip of 20 and varying the number of viewing angles from 1 to 32,400 (θ = 180° to 1°). The optimum value for the number of viewing angles is defined as 32 (θ = 30°) as it has no appreciable difference when compared to 32,400 viewing angles (θ = 1°).</p>", "links"=>[], "tags"=>["Computational biology", "Macromolecular structure analysis", "protein structure", "Plant science", "Plant biotechnology", "Transgenic plants", "Plant pathology", "Plant pathogens", "proteomics", "Spectrometric identification of proteins", "Zoology", "Nematology", "algorithms", "rotamol"], "article_id"=>916351, "categories"=>["Biological Sciences"], "users"=>["Sebastian Eves-van den Akker", "Catherine J. Lilley", "James R. Ault", "Alison E. Ashcroft", "John T. Jones", "Peter E. Urwin"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087289.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimum_values_for_RotaMol_parameters_/916351", "title"=>"Optimum values for RotaMol parameters.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-28 03:22:32"}

PMC Usage Stats | Further Information

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Relative Metric

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