Shigella flexneri 3a Outer Membrane Protein C Epitope Is Recognized by Human Umbilical Cord Sera and Associated with Protective Activity
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{"title"=>"Shigella flexneri 3a Outer Membrane Protein C Epitope Is Recognized by Human Umbilical Cord Sera and Associated with Protective Activity", "type"=>"journal", "authors"=>[{"first_name"=>"Anna", "last_name"=>"Jarzab", "scopus_author_id"=>"7801321788"}, {"first_name"=>"Danuta", "last_name"=>"Witkowska", "scopus_author_id"=>"7004093029"}, {"first_name"=>"Edmund", "last_name"=>"Ziomek", "scopus_author_id"=>"57190808211"}, {"first_name"=>"Anna", "last_name"=>"Dabrowska", "scopus_author_id"=>"36149961500"}, {"first_name"=>"Zbigniew", "last_name"=>"Szewczuk", "scopus_author_id"=>"7003671954"}, {"first_name"=>"Andrzej", "last_name"=>"Gamian", "scopus_author_id"=>"7006609635"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"369491982", "doi"=>"10.1371/journal.pone.0070539", "pmid"=>"23940590", "issn"=>"19326203", "scopus"=>"2-s2.0-84881115842", "sgr"=>"84881115842"}, "id"=>"8ff72d29-e322-3ee3-a26e-68a73e8d023a", "abstract"=>"Shigella flexneri 3a is one of the five major strains of the Shigella genus responsible for dysentery, especially among children, in regions of high poverty and poor sanitation. The outer membrane proteins (OMP) of this bacterium elicit immunological responses and are considered a prime target for vaccine development. When injected into mice they elicit a protective immunological response against a lethal dose of the pathogen. The OMPs from S. flexneri 3a were isolated and resolved by two-dimension-SDS-PAGE. Two 38-kDa spots were of particular interest since in our earlier studies OMPs of such molecular mass were found to interact with umbilical cord sera. These two spots were identified as OmpC by ESI-MS/MS spectrometry. By DNA sequencing, the ompC gene from S. flexneri 3a was identical to ompC from S. flexneri 2a [Gene Bank: 24113600]. A 3D model of OmpC was built and used to predict B-cell type (discontinuous) antigenic epitopes. Six epitopes bearing the highest score were selected and the corresponding peptides were synthesized. Only the peptides representing loop V of OmpC reacted strongly with the umbilical cord serum immunoglobulins. To determine which amino acids are essential for the antigenic activity of the epitope, the loop V was scanned with a series of dodecapeptides. The peptide RYDERY was identified as a minimal sequence for the loop V epitope. Truncation at either the C- or N-terminus rendered this peptide inactive. Apart from C-terminal tyrosine, substitution of each of the remaining five amino acids with glycine, led to a precipitous loss of immunological activity. This peptide may serve as a ligand in affinity chromatography of OmpC-specific antibodies and as a component of a vaccine designed to boost human immune defenses against enterobacterial infections.", "link"=>"http://www.mendeley.com/research/shigella-flexneri-3a-outer-membrane-protein-c-epitope-recognized-human-umbilical-cord-sera-associate", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>7, "Lecturer > Senior Lecturer"=>1, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>4, "Student > Master"=>7, "Lecturer > Senior Lecturer"=>1, "Other"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>6, "Medicine and Dentistry"=>2, "Chemical Engineering"=>1, "Chemistry"=>2, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Poland"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1142198"], "description"=>"*<p>epitopes synthesized based on the highest score from continuous and discontinuous prediction method.</p>**<p><i>Shigella flexneri</i> 3a OmpC loops assigned according to <i>E. coli</i> OmpC structure <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070539#pone.0070539-Basl1\" target=\"_blank\">[28]</a>.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "epitopes", "corresponding", "loops", "ompc"], "article_id"=>763917, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.t004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synthetic_epitopes_and_their_corresponding_loops_in_Shigella_flexneri_OmpC_model_/763917", "title"=>"Synthetic epitopes and their corresponding loops in <i>Shigella flexneri</i> OmpC model.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142197"], "description"=>"<p>Series of pin-tethered RYDERY derivatives were synthesized as described in Fig. 3. In one series individual amino acids were replaced with glycine, and in the other series amino acids were truncated one-by-one from the N-terminus. For both series antigenic activity for the peptides was determined as described in Fig. 3. The results are the average of three independent assays.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics"], "article_id"=>763916, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Defining_epitope_8217_s_minimal_sequence_/763916", "title"=>"Defining epitope’s minimal sequence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142193"], "description"=>"<p>Six peptides were synthesized on polyethylene pins (MIMOTOPES, Clayton, Victoria, Australia) as the solid phase and by using the Fmoc strategy. After the synthesis peptides remained attached to the pins and were used in the ELISA assay. Unlike in a regular ELISA, formation of the [antigen]-[primary Ab] complex took place on the pin, rather than on the wall of the 96-well polystyrene plate. The primary antibody (Ab) adsorbed to the pin was detected with goat-anti-human IgG-AP conjugate, followed by reaction with orthonitrophenyl phosphate (ONPP) as the AP substrate. The IgG fraction was obtained from the mixture of thirteen umbilical cord sera. The results are the average of three independent assays.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "pin-tethered", "peptides"], "article_id"=>763913, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Antigenic_activity_of_the_pin_tethered_peptides_representing_predicted_epitopes_/763913", "title"=>"Antigenic activity of the pin-tethered peptides representing predicted epitopes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142191"], "description"=>"<p>100 µg of crude preparation of the outer membrane proteins was precipitated with TCA. The pellet was washed with 12.5% TCA, acetone and air dried. The precipitate was dissolved in 125 µl of the sample buffer (pH 4–7). The IPG strip (11 cm) was soaked in the sample solution placed in the ceramic container provided with the IPGphor system. The first dimension of the electrophoretic separation was done according to the manufacturer’s recommendations. Proteins resolved on the buffer strip were reduced with DTT and alkylated with iodoacetamide. For the second dimension the IPG strip was placed over a vertical slab of 12.5% polyacrylamide gel prepared according to Laemmli <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070539#pone.0070539-McCarty1\" target=\"_blank\">[40]</a>. Protein spots were visualized using the silver staining method as described by Shevchenko et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070539#pone.0070539-Baldridge1\" target=\"_blank\">[41]</a>. Spots 13_1 and 13_2 were identified as OmpC and spot 13_3 as OmpA (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070539#pone-0070539-t002\" target=\"_blank\">Table 2</a>).</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "flexneri", "membrane"], "article_id"=>763911, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.g001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_2D_SDS_PAGE_of_S_flexneri_3a_outer_membrane_proteins_/763911", "title"=>"2D-SDS-PAGE of <i>S. flexneri 3a</i> outer membrane proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142192"], "description"=>"<p>A - epitope distribution on the surface of <i>S. flexneri</i> 3a OmpC 3D model; epitopes 1 to 5 represent outer membrane loops (1– loop II, 2– loop IV, 3– loop V, 4– loop VII, 5– loop VIII) and epitope number 6 corresponds to inner-membrane loop and has been used as a control, B – location of the epitope No. 3 (RYDERY) on the OmpC surface. Images were created by using ElliPro Prediction, and edited with Chimera Software.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "bioinformatic", "studies"], "article_id"=>763912, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_bioinformatic_studies_on_the_OmpC_/763912", "title"=>"Summary of the bioinformatic studies on the OmpC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142200"], "description"=>"*<p>the score is the average of the scores obtained for each residue.</p>**<p>inner-membrane loop.</p><p>Underlined are amino acids with their side-chains exposed to the surface of the bacterial membrane and the highest probability of contributing to the antigenic epitope.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "discontinuous", "epitopes", "3a"], "article_id"=>763919, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.t003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prediction_of_the_discontinuous_and_continuous_epitopes_for_S_flexneri_3a_OmpC_/763919", "title"=>"Prediction of the discontinuous and continuous epitopes for <i>S. flexneri</i> 3a OmpC.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142201"], "description"=>"*<p>This group received OmpC intraperitoneally in three doses: 1.6 µg, 3.2 µg and 1.6 µg at week intervals.</p>**<p>These mice received subcutaneous OmpC injection.</p><p>PBS – phosphate buffered saline, MPL – monophosphoryl lipid A;</p>***<p>Mice were challenged with 0.2 ml of live <i>S. flexneri</i> 3a (1.23×10<sup>8</sup> cells per mouse). The number of animals surviving the challenge is shown. In brackets is the total number of animals in the experimental group.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "mice", "immunization", "ompc"], "article_id"=>763920, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.t001", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protective_effect_of_mice_immunization_with_OmpC_against_a_challenge_with_live_S_flexneri_3a_/763920", "title"=>"Protective effect of mice immunization with OmpC against a challenge with live <i>S. flexneri</i> 3a.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142199"], "description"=>"<p>Protein spots were extracted from 2D- polyacrylamide gel with an Eppendorf pipette and approx. 1 mm in diameter gel pieces were destained according to the procedure described by Gharahdaghi et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070539#pone.0070539-Arcidiacono1\" target=\"_blank\">[42]</a>. In-gel tryptic digestion of proteins was done using Promega (Madison, WI, USA) Gold Label trypsin, following the manufacturer’s protocol with only minor alterations. The tryptic digest sample (1–10 µl) was injected on a trap column coupled to a C18 Waters NanoEase capillary column 75 µm×50 mm. The ESI-MS/MS experiments were carried out on a QTOF-Global mass spectrometer (Micromass, Manchester, UK).</p>*<p>Mascot score was obtained after submitting raw data (PKL format) to the Matrix Science website for evaluation (<a href=\"http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=MIS\" target=\"_blank\">http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=MIS</a>).</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "spots", "extracted"], "article_id"=>763918, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.t002", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_selected_protein_spots_extracted_from_2D_SDS_PAGE_/763918", "title"=>"Identification of selected protein spots extracted from 2D-SDS-PAGE.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142196"], "description"=>"<p>Series of 29 dodecapeptides corresponding to the loop V sequence were synthesized using the pin method (Experimental Procedures). Each peptide in the series differed from its predecessor by one amino acid. The “ruler” has been moved from the C- to the N-end, allowing for complete coverage of the loop sequence. Binding of the IgG fraction from the umbilical cord serum was performed as described in Fig. 3. The results represent the average of the nine most active umbilical cord sera.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics"], "article_id"=>763915, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.g005", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Probing_loop_V_by_using_8220_sliding_ruler_8221_approach_/763915", "title"=>"Probing loop V by using “sliding ruler” approach.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 02:52:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1142195"], "description"=>"<p>Mice and rabbits were immunized with purified OmpC as described in Experimental Procedures. Peptides corresponding to predicted epitopes were synthesized as described in Fig. 3. To determine immunological activity mouse and rabbit sera were used as the primary antibody (Ab) and detected with goat-anti-mouse IgG-AP conjugate, or goat-anti-rabbit IgG-AP conjugate, respectively. Sera from non-immunized animals were used as controls.</p>", "links"=>[], "tags"=>["Biochemistry", "biotechnology", "Computational biology", "Sequence analysis", "immunology", "microbiology", "Model organisms", "Animal models", "mouse", "proteomics", "sequencing", "Diagnostic medicine", "Infectious diseases", "pediatrics", "epitope"], "article_id"=>763914, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Anna Jarząb", "Danuta Witkowska", "Edmund Ziomek", "Anna Dąbrowska", "Zbigniew Szewczuk", "Andrzej Gamian"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0070539.g004", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_OmpC_epitope_recognition_by_mouse_and_rabbit_sera_/763914", "title"=>"OmpC epitope recognition by mouse and rabbit sera.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-05 02:52:52"}

PMC Usage Stats | Further Information

  • {"unique-ip"=>"22", "full-text"=>"17", "pdf"=>"6", "abstract"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"8"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"5"}
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  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"14", "full-text"=>"14", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
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Relative Metric

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