A Novel HURRAH Protocol Reveals High Numbers of Monomorphic MHC Class II Loci and Two Asymmetric Multi-Locus Haplotypes in the Père David's Deer
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{"title"=>"A Novel HURRAH protocol reveals high numbers of monomorphic MHC class ii loci and two asymmetric multi-locus haplotypes in the Père David's deer", "type"=>"journal", "authors"=>[{"first_name"=>"Qiu Hong", "last_name"=>"Wan", "scopus_author_id"=>"7102267004"}, {"first_name"=>"Pei", "last_name"=>"Zhang", "scopus_author_id"=>"57198754300"}, {"first_name"=>"Xiao Wei", "last_name"=>"Ni", "scopus_author_id"=>"8296803100"}, {"first_name"=>"Hai Long", "last_name"=>"Wu", "scopus_author_id"=>"55703658200"}, {"first_name"=>"Yi Yan", "last_name"=>"Chen", "scopus_author_id"=>"36192740000"}, {"first_name"=>"Ye Ye", "last_name"=>"Kuang", "scopus_author_id"=>"37461632400"}, {"first_name"=>"Yun Fa", "last_name"=>"Ge", "scopus_author_id"=>"16743905500"}, {"first_name"=>"Sheng Guo", "last_name"=>"Fang", "scopus_author_id"=>"7402422369"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-79251552828", "sgr"=>"79251552828", "pui"=>"361185821", "isbn"=>"1932-6203", "pmid"=>"21267075", "doi"=>"10.1371/journal.pone.0014518"}, "id"=>"93610325-dff1-35f8-aa9b-d1f6cb4ee8db", "abstract"=>"The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated \"HURRAH\" based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1) All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2) these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ∼ DRB1 ∼ DRB3 ∼ DQA1 ∼ DQB2 (H1) and DRA1*02 ∼ DRB2 ∼ DRB4 ∼ DQA2 ∼ DQB1 (H2). The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens.", "link"=>"http://www.mendeley.com/research/novel-hurrah-protocol-reveals-high-numbers-monomorphic-mhc-class-ii-loci-two-asymmetric-multilocus-h", "reader_count"=>18, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>5, "Student > Master"=>1, "Student > Bachelor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>5, "Student > Master"=>1, "Student > Bachelor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/806118"], "description"=>"<p>Dots indicate identity to the first sequence and gaps represent missing amino acids. The box indicates antigen-presenting exon 2, and crosses indicate putative antigen-binding sites, as determined based on the HLA equivalents <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014518#pone.0014518-Reche1\" target=\"_blank\">[42]</a>. The letters and numbers following the <i>Elda</i>-MHC genes indicate their corresponding cDNA sequences, and the names of loci and alleles identified by the HURRAH protocol. The shaded areas indicate nucleotide differences among the <i>Elda</i>-MHC loci.</p>", "links"=>[], "tags"=>["alignments", "amino", "sequences", "deduced", "full-length"], "article_id"=>476475, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014518.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_sequence_alignments_of_the_amino_acid_sequences_deduced_from_the_full_length_cDNAs_/476475", "title"=>"Multiple sequence alignments of the amino acid sequences deduced from the full-length cDNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-18 01:47:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/402374", "https://ndownloader.figshare.com/files/402459", "https://ndownloader.figshare.com/files/402481", "https://ndownloader.figshare.com/files/402504", "https://ndownloader.figshare.com/files/402535", "https://ndownloader.figshare.com/files/402548", "https://ndownloader.figshare.com/files/402580", "https://ndownloader.figshare.com/files/402600"], "description"=>"<div><p>The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated “HURRAH” based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1) All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2) these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ∼ DRB1 ∼ DRB3 ∼ DQA1 ∼ DQB2 (H1) and DRA1*02 ∼ DRB2 ∼ DRB4 ∼ DQA2 ∼ DQB1 (H2). The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens.</p></div>", "links"=>[], "tags"=>["hurrah", "reveals", "numbers", "monomorphic", "mhc", "ii", "loci", "asymmetric", "multi-locus", "haplotypes"], "article_id"=>139509, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0014518.s001", "https://dx.doi.org/10.1371/journal.pone.0014518.s002", "https://dx.doi.org/10.1371/journal.pone.0014518.s003", "https://dx.doi.org/10.1371/journal.pone.0014518.s004", "https://dx.doi.org/10.1371/journal.pone.0014518.s005", "https://dx.doi.org/10.1371/journal.pone.0014518.s006", "https://dx.doi.org/10.1371/journal.pone.0014518.s007", "https://dx.doi.org/10.1371/journal.pone.0014518.s008"], "stats"=>{"downloads"=>26, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Novel_HURRAH_Protocol_Reveals_High_Numbers_of_Monomorphic_MHC_Class_II_Loci_and_Two_Asymmetric_Multi_Locus_Haplotypes_in_the_P_re_David_s_Deer/139509", "title"=>"A Novel HURRAH Protocol Reveals High Numbers of Monomorphic MHC Class II Loci and Two Asymmetric Multi-Locus Haplotypes in the Père David's Deer", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-01-18 02:38:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/806514"], "description"=>"<p>Species distribution and locus identification of 148 MHC class II cDNA sequences of wild carnivores and ungulates obtained from NCBI.</p>", "links"=>[], "tags"=>["locus", "148", "mhc", "ii", "cdna", "sequences", "carnivores", "ungulates"], "article_id"=>476867, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014518.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Species_distribution_and_locus_identification_of_148_MHC_class_II_cDNA_sequences_of_wild_carnivores_and_ungulates_obtained_from_NCBI_/476867", "title"=>"Species distribution and locus identification of 148 MHC class II cDNA sequences of wild carnivores and ungulates obtained from NCBI.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-18 01:54:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/806231"], "description"=>"<p>The trees were generated based on exon 3-exon 5 cDNA sequences (A, B, C, and D), intron 1 sequences (G, I, and K), intron 2 sequences (E, H, J and L), and 5′UTR-exon 1 (F). The complete intron 1 sequence of <i>Ovar</i>-DRA was unavailable, so we show only those based on the intron 2 sequences. The <i>Elda</i>-MHC genes are shaded, to allow them to be easily distinguished from the cow and sheep genes. Numbers indicate bootstrap percentages (values smaller than 50% are not shown). The numbers outside and inside the parentheses are bootstrap values for the MP and Bayesian trees, respectively. The bootstrap percentages of the NJ trees were very similar to those of the MP trees, and thus are not shown. As the branch lengths differed among trees, only the topologies are shown here. The information near each <i>Elda</i>-MHC gene indicates the initial cDNA sequence (a, b, c and d) and identified loci (1, 2, 3 and 4). For this analysis, the expressed HLA, BoLA and <i>Ovar</i>-MHC loci were identified from the relevant completely sequenced MHC class II regions of the human (HLA; NT_007592), cow (BoLA; Btau 3.1) and sheep (<i>Ovar</i>-MHC; EU176819).</p>", "links"=>[], "tags"=>["trees", "dqb"], "article_id"=>476590, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014518.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_trees_for_the_DRA_DRB_DQA_and_DQB_loci_/476590", "title"=>"Phylogenetic trees for the DRA, DRB, DQA, and DQB loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-18 01:49:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/805926"], "description"=>"<p>Here we show only profile reconstitution of the simplest SSCP-HD banding patterns, i.e. those representing a homozygous haplotype. For practical use, the most complicate SSCP-HD profile should also be reconstituted for comparison.</p>", "links"=>[], "tags"=>["hurrah", "isolating", "mhc", "ii"], "article_id"=>476284, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014518.g001", "stats"=>{"downloads"=>2, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Technical_design_of_the_novel_HURRAH_protocol_for_isolating_MHC_class_II_loci_/476284", "title"=>"Technical design of the novel HURRAH protocol for isolating MHC class II loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-18 01:44:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/806396"], "description"=>"<p>For comparison, the BoLA- and <i>Ovar</i>-MHC genes were included. The four BoLA class II multi-locus haplotypes shown (ABCD) are based on Ballingall et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014518#pone.0014518-Ballingall1\" target=\"_blank\">[28]</a>, Ellis and Ballingall <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014518#pone.0014518-Ellis1\" target=\"_blank\">[29]</a>, and the <i>Bos taurus</i> genome sequencing project (NCBI Btau 3.1). The <i>Ovar</i>-MHC class II multi-locus haplotype shown was revised according to Herrmann-Hoesing et al. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014518#pone.0014518-HerrmannHoesing1\" target=\"_blank\">[10]</a>. Recombination events are shown by the dashed-line marked conversion of two adjacent rectangles, which represent intron 1 (left) and intron 2 (right). The colors show corresponding relationships among the MHC class II loci in the three ruminants. Dotted rectangles indicate historical existence of inferred genes. UND indicates “undetected.” We also show a powerful ancestral <i>Elda</i>-MHC class II haplotype (F) containing all of the identified loci.</p>", "links"=>[], "tags"=>["depiction", "ii"], "article_id"=>476755, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014518.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_depiction_of_the_evolution_of_the_Elda_MHC_class_II_genes_/476755", "title"=>"Schematic depiction of the evolution of the <i>Elda</i>-MHC class II genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-18 01:52:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/806551"], "description"=>"<p>Comparison of the number of MHC class II loci expressed among different mammals.</p>", "links"=>[], "tags"=>["mhc", "ii", "loci"], "article_id"=>476915, "categories"=>["Immunology", "Ecology"], "users"=>["Qiu-Hong Wan", "Pei Zhang", "Xiao-Wei Ni", "Hai-Long Wu", "Yi-Yan Chen", "Ye-Ye Kuang", "Yun-Fa Ge", "Sheng-Guo Fang"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014518.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_the_number_of_MHC_class_II_loci_expressed_among_different_mammals_/476915", "title"=>"Comparison of the number of MHC class II loci expressed among different mammals.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-01-18 01:55:15"}

PMC Usage Stats | Further Information

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Relative Metric

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