Genome-Wide Identification of Molecular Mimicry Candidates in Parasites
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{"title"=>"Genome-wide identification of molecular mimicry candidates in parasites", "type"=>"journal", "authors"=>[{"first_name"=>"Philipp", "last_name"=>"Ludin", "scopus_author_id"=>"37063392400"}, {"first_name"=>"Daniel", "last_name"=>"Nilsson", "scopus_author_id"=>"35477528100"}, {"first_name"=>"Pascal", "last_name"=>"Mäser", "scopus_author_id"=>"6603316531"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"361404848", "sgr"=>"79952417222", "issn"=>"19326203", "arxiv"=>"1203.2655", "pmid"=>"21408160", "scopus"=>"2-s2.0-79952417222", "doi"=>"10.1371/journal.pone.0017546", "isbn"=>"0011-3891"}, "id"=>"4706adc4-569f-31b1-ac4c-01f446ffacd3", "abstract"=>"Among the many strategies employed by parasites for immune evasion and host manipulation, one of the most fascinating is molecular mimicry. With genome sequences available for host and parasite, mimicry of linear amino acid epitopes can be investigated by comparative genomics. Here we developed an in silico pipeline for genome-wide identification of molecular mimicry candidate proteins or epitopes. The predicted proteome of a given parasite was broken down into overlapping fragments, each of which was screened for close hits in the human proteome. Control searches were carried out against unrelated, free-living eukaryotes to eliminate the generally conserved proteins, and with randomized versions of the parasite proteins to get an estimate of statistical significance. This simple but computation-intensive approach yielded interesting candidates from human-pathogenic parasites. From Plasmodium falciparum, it returned a 14 amino acid motif in several of the PfEMP1 variants identical to part of the heparin-binding domain in the immunosuppressive serum protein vitronectin. And in Brugia malayi, fragments were detected that matched to periphilin-1, a protein of cell-cell junctions involved in barrier formation. All the results are publicly available by means of mimicDB, a searchable online database for molecular mimicry candidates from pathogens. To our knowledge, this is the first genome-wide survey for molecular mimicry proteins in parasites. The strategy can be adopted to any pair of host and pathogen, once appropriate negative control organisms are chosen. MimicDB provides a host of new starting points to gain insights into the molecular nature of host-pathogen interactions.", "link"=>"http://www.mendeley.com/research/genomewide-identification-molecular-mimicry-candidates-parasites-2", "reader_count"=>53, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>4, "Researcher"=>14, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>6, "Student > Master"=>5, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>1, "Student > Doctoral Student"=>4, "Researcher"=>14, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>6, "Student > Master"=>5, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>38, "Medicine and Dentistry"=>3, "Neuroscience"=>1, "Psychology"=>1, "Computer Science"=>3, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>38}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"United States"=>3, "Brazil"=>2, "United Kingdom"=>2, "Australia"=>1, "France"=>1, "Switzerland"=>1, "Spain"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/792801"], "description"=>"<p>Numbers of amino acid identities between the 14-mers and their best hit in the human proteome are color-coded as indicated.</p>", "links"=>[], "tags"=>["molecular", "mimicry", "14-mers", "parasite", "proteomes", "randomized", "versions", "thereof"], "article_id"=>463166, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Numbers_of_identified_candidate_molecular_mimicry_14_mers_from_parasite_proteomes_and_randomized_versions_thereof_R_/463166", "title"=>"Numbers of identified candidate molecular mimicry 14-mers from parasite proteomes and randomized versions thereof (R).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-08 00:52:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/793042"], "description"=>"<p>Hits from <i>B. malayi</i> (<i>Bma</i>), <i>S. mansoni</i> (<i>Sma</i>) and <i>P. falciparum</i> (<i>Pfa</i>) and their human match (Ent, Shannon entropy in bits; Id, number of identities).</p>", "links"=>[], "tags"=>["mimicry"], "article_id"=>463419, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.t003", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_mimicry_candidates_/463419", "title"=>"Selected mimicry candidates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-08 00:56:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/792902"], "description"=>"<p>Identities to vitronectin are printed in bold black, similarities in black. The known vitronectin domains are the signal sequence (blue), somatomedin-B (green), and hemopexin (red). The known PfEMP1 domains are the N-terminal segment (dark blue), Duffy Binding Like α (light blue), cysteine-rich interdomain region α (yellow), Duffy Binding Like 2d (orange), cysteine-rich interdomain region ß (purple), transmembrane domain (cyan), acidic terminal segment (green).</p>", "links"=>[], "tags"=>["vitronectin", "pfemp1", "variants"], "article_id"=>463271, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.g005", "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_human_vitronectin_top_and_P_falciparum_PfEMP1_variants_bottom_/463271", "title"=>"Alignment of human vitronectin (top) and <i>P. falciparum</i> PfEMP1 variants (bottom).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-08 00:54:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/792612"], "description"=>"<p>The SH2 domain is shaded in yellow, the SOCS box domain in blue. The N-terminal parts of the two proteins do not share any similarity (not shown).</p>", "links"=>[], "tags"=>["alignment", "mimicry", "a8npn8"], "article_id"=>462983, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ClustalW_alignment_of_the_candidate_mimicry_region_in_A8NPN8_from_B_malayi_to_H_sapiens_SOCS5_/462983", "title"=>"ClustalW alignment of the candidate mimicry region in A8NPN8 from <i>B. malayi</i> to <i>H. sapiens</i> SOCS5.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-08 00:49:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/396648", "https://ndownloader.figshare.com/files/396684", "https://ndownloader.figshare.com/files/396699", "https://ndownloader.figshare.com/files/396725", "https://ndownloader.figshare.com/files/396740"], "description"=>"<div><p>Among the many strategies employed by parasites for immune evasion and host manipulation, one of the most fascinating is molecular mimicry. With genome sequences available for host and parasite, mimicry of linear amino acid epitopes can be investigated by comparative genomics. Here we developed an <em>in silico</em> pipeline for genome-wide identification of molecular mimicry candidate proteins or epitopes. The predicted proteome of a given parasite was broken down into overlapping fragments, each of which was screened for close hits in the human proteome. Control searches were carried out against unrelated, free-living eukaryotes to eliminate the generally conserved proteins, and with randomized versions of the parasite proteins to get an estimate of statistical significance. This simple but computation-intensive approach yielded interesting candidates from human-pathogenic parasites. From <em>Plasmodium falciparum</em>, it returned a 14 amino acid motif in several of the PfEMP1 variants identical to part of the heparin-binding domain in the immunosuppressive serum protein vitronectin. And in <em>Brugia malayi</em>, fragments were detected that matched to periphilin-1, a protein of cell-cell junctions involved in barrier formation. All the results are publicly available by means of mimicDB, a searchable online database for molecular mimicry candidates from pathogens. To our knowledge, this is the first genome-wide survey for molecular mimicry proteins in parasites. The strategy can be adopted to any pair of host and pathogen, once appropriate negative control organisms are chosen. MimicDB provides a host of new starting points to gain insights into the molecular nature of host-pathogen interactions.</p> </div>", "links"=>[], "tags"=>["genome-wide", "molecular", "mimicry", "candidates", "parasites"], "article_id"=>138364, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0017546.s001", "https://dx.doi.org/10.1371/journal.pone.0017546.s002", "https://dx.doi.org/10.1371/journal.pone.0017546.s003", "https://dx.doi.org/10.1371/journal.pone.0017546.s004", "https://dx.doi.org/10.1371/journal.pone.0017546.s005"], "stats"=>{"downloads"=>7, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Identification_of_Molecular_Mimicry_Candidates_in_Parasites/138364", "title"=>"Genome-Wide Identification of Molecular Mimicry Candidates in Parasites", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-03-08 02:19:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/793074"], "description"=>"<p>Parasite (top), host (middle), and negative control species (bottom), their predicted number of protein-coding genes, and source of the predicted proteome file (EBI: European Bioinformatics Institute, JGI: Joint Genome Institute).</p>", "links"=>[], "tags"=>["genetics and genomics", "microbiology", "Computational biology", "Biochemistry"], "article_id"=>463446, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.t002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Organisms_used_in_this_study_/463446", "title"=>"Organisms used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-08 00:57:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/792557"], "description"=>"<p>Points below the blue dotted line represent parasite proteins with better scores to <i>H. sapiens</i> than to <i>C. elegans</i>.</p>", "links"=>[], "tags"=>["scores", "proteins"], "article_id"=>462931, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scatter_plot_of_the_blast_scores_of_all_proteins_from_B_malayi_left_and_S_mansoni_right_vs_the_host_H_sapiens_x_axis_and_the_control_C_elegans_y_axis_/462931", "title"=>"Scatter plot of the blast scores of all proteins from <i>B. malayi</i> (left) and <i>S. mansoni</i> (right) vs. the host <i>H. sapiens</i> (x-axis) and the control <i>C. elegans</i> (y-axis).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-08 00:48:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/792678"], "description"=>"<p>See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0017546#s3\" target=\"_blank\">Methods</a> for details. The process is illustrated with the actual numbers from the analysis of the <i>P. falciparum</i> proteome in blue, respectively a randomized version of it in grey, vs. the host <i>H. sapiens</i>.</p>", "links"=>[], "tags"=>["pipeline", "molecular", "mimicry", "candidates"], "article_id"=>463044, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_in_silico_pipeline_for_identification_of_molecular_mimicry_candidates_from_parasites_/463044", "title"=>"The <i>in silico</i> pipeline for identification of molecular mimicry candidates from parasites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-03-08 00:50:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/793025"], "description"=>"<p>Mimicry by transfer of nucleic acids or convergence of proteins can be identified <i>in silico</i> by comparative genomics (CRIT: Complement C2 receptor inhibitor trispanning (CRIT), C4BP: m<sup>7</sup>G, 7-methyl guanosine; CSP, circumsporozoite protein; Complement-binding protein, CR1: Complement receptor 1, FHL-1: factor-H-like protein-1, fH: factor H, MCP: Membrane cofactor protein, DAF: Decay-accelerating factor).</p>", "links"=>[], "tags"=>["molecular", "mimicry", "examples"], "article_id"=>463393, "categories"=>["Biological Sciences", "Biochemistry", "Genetics", "Microbiology"], "users"=>["Philipp Ludin", "Daniel Nilsson", "Pascal Mäser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0017546.t001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Possible_mechanism_for_molecular_mimicry_and_examples_from_pathogens_/463393", "title"=>"Possible mechanism for molecular mimicry and examples from pathogens.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-03-08 00:56:33"}

PMC Usage Stats | Further Information

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Relative Metric

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