Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB
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{"title"=>"Epigenetic segregation of microbial genomes from complex samples using restriction endonucleases hpaii and McrB", "type"=>"journal", "authors"=>[{"first_name"=>"Guohong", "last_name"=>"Liu", "scopus_author_id"=>"57039315300"}, {"first_name"=>"Christopher Q.", "last_name"=>"Weston", "scopus_author_id"=>"57039675500"}, {"first_name"=>"Long K.", "last_name"=>"Pham", "scopus_author_id"=>"57039653600"}, {"first_name"=>"Shannon", "last_name"=>"Waltz", "scopus_author_id"=>"56533599900"}, {"first_name"=>"Helen", "last_name"=>"Barnes", "scopus_author_id"=>"57039625600"}, {"first_name"=>"Paula", "last_name"=>"King", "scopus_author_id"=>"57039519300"}, {"first_name"=>"Dan", "last_name"=>"Sphar", "scopus_author_id"=>"57039907700"}, {"first_name"=>"Robert T.", "last_name"=>"Yamamoto", "scopus_author_id"=>"57039532500"}, {"first_name"=>"R. Allyn", "last_name"=>"Forsyth", "scopus_author_id"=>"7102198947"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84954072795", "sgr"=>"84954072795", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0146064", "pmid"=>"26727463", "pui"=>"607558378"}, "id"=>"23e667c0-1b76-3b58-9345-cbf06a2abcaa", "abstract"=>"We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.", "link"=>"http://www.mendeley.com/research/epigenetic-segregation-microbial-genomes-complex-samples-using-restriction-endonucleases-hpaii-mcrb", "reader_count"=>20, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Student > Doctoral Student"=>1, "Researcher"=>2, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Student > Bachelor"=>6, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>4, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>7, "Social Sciences"=>1, "Immunology and Microbiology"=>2, "Computer Science"=>1, "Engineering"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "Australia"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2620264"], "description"=>"<p>The input DNA sample coverage (red line) and HpaII bound coverage (blue line) are plotted across the genome position of <i>M</i>. <i>tuberculosis</i>.</p>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632657, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146064.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genomic_sequencing_coverage_of_M_tuberculosis_improves_with_enrichment_/1632657", "title"=>"Genomic sequencing coverage of <i>M</i>. <i>tuberculosis</i> improves with enrichment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:56:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/2620267"], "description"=>"<p>(A) The percent of microbial ID reads (blue) increases and human ID reads (red) decrease with enrichment. (B) Normalized microbial Order sequence Identification reads are plotted for bound and input samples. Greater than 95% of identified microbes have increased sequenced reads. Many microbes (red points) are only detectable after enrichment. (C) Comparison of ratio of microbial sequence ID reads in sputum input and sputum bound samples. (D) Genomic sequencing coverage of bacteria such as <i>P</i>. <i>aeruginosa</i> improves with enrichment. The input DNA sample coverage (red line) and HpaII bound coverage (blue line) are plotted across the genome position of <i>P</i>. <i>aeruginosa</i>.</p>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632660, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146064.g005", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HpaII_mediated_enrichment_of_DNA_from_a_pooled_sputum_sample_improves_microbe_sequencing_detection_and_coverage_/1632660", "title"=>"HpaII mediated enrichment of DNA from a pooled sputum sample improves microbe sequencing detection and coverage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:56:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/2620270"], "description"=>"<p>(A) Biotinylated McrB-N enzyme is added to a DNA mixture. Following the addition of strepatavidin coated magnetic beads, the mixture is segregated into fractions that are bound (containing majority of human) or unbound (containing majority of microbes). (B) Sequence analysis demonstrates that McrB-N segregates human and rice DNA away from microbial genomes in the unbound fraction. The fold enrichment for each taxa is plotted for the unbound (blue) fraction.</p>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632663, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146064.g006", "stats"=>{"downloads"=>3, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_workflow_using_McrB_N_/1632663", "title"=>"Enrichment workflow using McrB-N.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:56:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2620277", "https://ndownloader.figshare.com/files/2620278", "https://ndownloader.figshare.com/files/2620279", "https://ndownloader.figshare.com/files/2620280", "https://ndownloader.figshare.com/files/2620281", "https://ndownloader.figshare.com/files/2620282", "https://ndownloader.figshare.com/files/2620283"], "description"=>"<div><p>We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.</p></div>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632666, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0146064.s001", "https://dx.doi.org/10.1371/journal.pone.0146064.s002", "https://dx.doi.org/10.1371/journal.pone.0146064.s003", "https://dx.doi.org/10.1371/journal.pone.0146064.s004", "https://dx.doi.org/10.1371/journal.pone.0146064.s005", "https://dx.doi.org/10.1371/journal.pone.0146064.s006", "https://dx.doi.org/10.1371/journal.pone.0146064.s007"], "stats"=>{"downloads"=>7, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Epigenetic_Segregation_of_Microbial_Genomes_from_Complex_Samples_Using_Restriction_Endonucleases_HpaII_and_McrB_/1632666", "title"=>"Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-05 14:56:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2620257"], "description"=>"<p>(A) Biotinylated HpaII enzyme is conjugated to streptavidin coated magnetic beads. A DNA mixture can then be added to the conjugated beads and following incubation the mixture is segregated into fractions that are bound (containing majority of <i>Y</i>. <i>pestis</i>) or unbound (containing majority of human) to the beads. (B) Adding salt to the binding buffer enhances segregation of human (blue bars) from <i>Y</i>. <i>pestis</i> (green bars).</p>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632651, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146064.g001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_workflow_using_HpaII_/1632651", "title"=>"Enrichment workflow using HpaII.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:56:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/2620259"], "description"=>"<p>(A) Recovery of decreasing levels of <i>Y</i>. <i>pestis</i> DNA (blue bars) from a fixed 1000 ng human DNA (green bars). (B) DNA recovery using 100 ng and 1000 ng <i>Y</i>. <i>pestis</i> DNA in a background of 1000 ng human DNA. (C) Recovery of a fixed 1 ng of <i>Y</i>. <i>pestis</i> DNA (blue bars) from increasing levels of human DNA (green bars).</p>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632653, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146064.g002", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Y_pestis_genomic_DNA_is_efficiently_segregated_from_human_DNA_/1632653", "title"=>"<i>Y</i>. <i>pestis</i> genomic DNA is efficiently segregated from human DNA.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:56:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/2620260"], "description"=>"<p>The fold enrichment (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0146064#pone.0146064.e001\" target=\"_blank\">Eq 1</a>) for each Eukaryote, Prokaryote and virus genome is listed. The GC content of microbial genomes are plotted above.</p>", "links"=>[], "tags"=>["methylation states", "Complex Samples", "offer promise", "Restriction Endonucleases", "population methylomes", "enrichment levels", "genomic detection", "enrichment results", "Microbial Genomes", "genome", "Restriction Endonucleases HpaII", "Epigenetic Segregation", "genomic DNA", "cytosine methylation", "bind CpG methylated DNA", "McrB"], "article_id"=>1632654, "categories"=>["Uncategorised"], "users"=>["Guohong Liu", "Christopher Q. Weston", "Long K. Pham", "Shannon Waltz", "Helen Barnes", "Paula King", "Dan Sphar", "Robert T. Yamamoto", "R. Allyn Forsyth"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0146064.g003", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequence_analysis_of_HpaII_mediated_enrichment_of_a_genomic_mixture_/1632654", "title"=>"Sequence analysis of HpaII mediated enrichment of a genomic mixture.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-05 14:56:23"}

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Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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