Influence of Development and Dietary Phospholipid Content and Composition on Intestinal Transcriptome of Atlantic Salmon (Salmo salar)
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{"title"=>"Influence of development and dietary phospholipid content and composition on intestinal transcriptome of Atlantic salmon (Salmo salar)", "type"=>"journal", "authors"=>[{"first_name"=>"Christian", "last_name"=>"De Santis", "scopus_author_id"=>"22953181300"}, {"first_name"=>"John F.", "last_name"=>"Taylor", "scopus_author_id"=>"7405408226"}, {"first_name"=>"Laura", "last_name"=>"Martinez-Rubio", "scopus_author_id"=>"26633983000"}, {"first_name"=>"Sebastian", "last_name"=>"Boltana", "scopus_author_id"=>"8899247500"}, {"first_name"=>"Douglas R.", "last_name"=>"Tocher", "scopus_author_id"=>"7005072840"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"607159329", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0140964", "pmid"=>"26488165", "sgr"=>"84949446128", "scopus"=>"2-s2.0-84949446128"}, "id"=>"02568f91-51b6-3f60-866a-d99d4e035057", "abstract"=>"The inclusion of intact phospholipids in the diet is essential during larval development and can improve culture performance of many fish species. The effects of supplementation of dietary phospholipid from marine (krill) or plant (soy lecithin) sources were investigated in Atlantic salmon, Salmo salar. First feeding fry were fed diets containing either krill oil or soybean lecithin supplying phospholipid at 2.6%, 3.2%, 3.6% and 4.2% of diet. Fish were sampled at ~ 2.5 g (~1,990°day post fertilization, dpf) and ~10 g (2,850°dpf). By comparison of the intestinal transcriptome in specifically chosen contrasts, it was determined that by 2,850°dpf fish possessed a profile that resembled that of mature and differentiated intestinal cell types with a number of changes specific to glycerophospholipid metabolism. It was previously shown that intact phospholipids and particularly phosphatidylcholine are essential during larval development and that this requirement is associated with the inability of enterocytes in young fry to endogenously synthesize sufficient phospholipid for the efficient export of dietary lipid. In the immature phase (~1,990°dpf), the dietary phospholipid content as well as its class composition impacted on several biochemical and morphological parameters including growth, but these differences were not associated with differences in intestinal transcriptomes. The results of this study have made an important contribution to our understanding of the mechanisms associated with lipid transport and phospholipid biosynthesis in early life stages of fish.", "link"=>"http://www.mendeley.com/research/influence-development-dietary-phospholipid-content-composition-intestinal-transcriptome-atlantic-sal", "reader_count"=>25, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>3, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>3, "Student > Master"=>6, "Other"=>3, "Student > Bachelor"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2367975"], "description"=>"<p>Expression values are reported for each individual replicate (n = 6) compared to.fry (2.5g) fed the basal unsupplemented (low phospholipid) diet. Only gene-sets with <i>q</i> < 0.05 are shown. Pathways are colour-coded based on the broad classification category (Kegg). Further details are provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140964#pone.0140964.s002\" target=\"_blank\">S2 Table</a>. Gene-sets marked with an “a” are differentially expressed in S2.6 compared to B, “b” in S3.6 vs B and “c” in K2.6 vs B. Data were plotted using heatmap.2 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140964#pone.0140964.ref037\" target=\"_blank\">37</a>] and rows were clustered according to Euclidean distance.</p>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581805, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140964.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_plotting_GAGE_results_from_the_1d_test_in_the_intestine_of_2_5_g_fry_fed_diets_S2_6_S3_6_and_K2_6_/1581805", "title"=>"Heatmap plotting GAGE results from the <i>1d</i> test in the intestine of 2.5 g fry fed diets S2.6, S3.6 and K2.6.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-21 02:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2367974"], "description"=>"<p>Values represent expression in the intestine of 2.5 g fish fed diet S2.6, S3.6 and K2.6. Expression values are reported for each individual replicate compared to average of 1.5g fish fed the basal unsupplemented diet (1.5% phospholipid content). Kegg identifiers (Kxxxxx) are specified for each gene. Data were plotted using heatmap.2 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140964#pone.0140964.ref037\" target=\"_blank\">37</a>] and rows were clustered according to Euclidean distance.</p>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581804, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140964.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_participating_to_the_glycerophospholipid_metabolism_Kegg_ID_ko00564_/1581804", "title"=>"Genes participating to the glycerophospholipid metabolism (Kegg ID ko00564).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-21 02:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2367977"], "description"=>"<p><i>p</i> Value is the FDR-uncorrected <i>p</i> value</p><p>FC is fold change, positive values denote up-regulation compared to control diet B and vice versa</p><p>Genes differentially expressed (p < 0.005; absolute fold change > 1.3) in both S3.6 and K2.6 compared with the control diet B.</p>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581807, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140964.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_differentially_expressed_p_lt_0_005_absolute_fold_change_gt_1_3_in_both_S3_6_and_K2_6_compared_with_the_control_diet_B_/1581807", "title"=>"Genes differentially expressed (p < 0.005; absolute fold change > 1.3) in both S3.6 and K2.6 compared with the control diet B.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-21 02:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2367978", "https://ndownloader.figshare.com/files/2367979"], "description"=>"<div><p>The inclusion of intact phospholipids in the diet is essential during larval development and can improve culture performance of many fish species. The effects of supplementation of dietary phospholipid from marine (krill) or plant (soy lecithin) sources were investigated in Atlantic salmon, <i>Salmo salar</i>. First feeding fry were fed diets containing either krill oil or soybean lecithin supplying phospholipid at 2.6%, 3.2%, 3.6% and 4.2% of diet. Fish were sampled at ~ 2.5 g (~1,990°day post fertilization, dpf) and ~10 g (2,850°dpf). By comparison of the intestinal transcriptome in specifically chosen contrasts, it was determined that by 2,850°dpf fish possessed a profile that resembled that of mature and differentiated intestinal cell types with a number of changes specific to glycerophospholipid metabolism. It was previously shown that intact phospholipids and particularly phosphatidylcholine are essential during larval development and that this requirement is associated with the inability of enterocytes in young fry to endogenously synthesize sufficient phospholipid for the efficient export of dietary lipid. In the immature phase (~1,990°dpf), the dietary phospholipid content as well as its class composition impacted on several biochemical and morphological parameters including growth, but these differences were not associated with differences in intestinal transcriptomes. The results of this study have made an important contribution to our understanding of the mechanisms associated with lipid transport and phospholipid biosynthesis in early life stages of fish.</p></div>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581808, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0140964.s001", "https://dx.doi.org/10.1371/journal.pone.0140964.s002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Influence_of_Development_and_Dietary_Phospholipid_Content_and_Composition_on_Intestinal_Transcriptome_of_Atlantic_Salmon_Salmo_salar_/1581808", "title"=>"Influence of Development and Dietary Phospholipid Content and Composition on Intestinal Transcriptome of Atlantic Salmon (<i>Salmo salar</i>)", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-10-21 02:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2367976"], "description"=>"<p>Fish were 1990°dpf (~2.5g) and 2850°dpf (~ 10g)</p><p>BH indicates Benjamini and Hochberg correction.</p><p>Number of differentially expressed genes between intestinal transcriptomes of fish at 1990°dpf fed the basal, unsupplemented diet (B, 2.5g) and fish fed the other treatments selected to enable effects of development (B, 10g), phospholipid content (S2.6 and S3.6) and phospholipid class (K2.6 and S2.6) to be determined.</p>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581806, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140964.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_differentially_expressed_genes_between_intestinal_transcriptomes_of_fish_at_1990_176_dpf_fed_the_basal_unsupplemented_diet_B_2_5g_and_fish_fed_the_other_treatments_selected_to_enable_effects_of_development_B_10g_phospholipid_content_S2_6_and_S3/1581806", "title"=>"Number of differentially expressed genes between intestinal transcriptomes of fish at 1990°dpf fed the basal, unsupplemented diet (B, 2.5g) and fish fed the other treatments selected to enable effects of development (B, 10g), phospholipid content (S2.6 and S3.6) and phospholipid class (K2.6 and S2.6) to be determined.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-10-21 02:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2367973"], "description"=>"<p>All gene-sets with <i>q</i> < 0.05 are shown. Pathways are colour-coded based on the broad classification category (Kegg). Further details are provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140964#pone.0140964.s002\" target=\"_blank\">S2 Table</a>. Data were plotted using heatmap.2 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140964#pone.0140964.ref037\" target=\"_blank\">37</a>] and rows were clustered according to Euclidean distance.</p>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581803, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140964.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmap_plotting_GAGE_results_from_the_1d_test_in_the_intestine_of_10_g_parr_compared_to_2_5_g_fry_fed_the_basal_unsupplemented_low_phospholipid_diet_/1581803", "title"=>"Heatmap plotting GAGE results from the <i>1d</i> test in the intestine of 10 g parr compared to 2.5 g fry fed the basal unsupplemented (low phospholipid) diet.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-21 02:54:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/2367972"], "description"=>"<p>Values represent expression in the intestine of 10 g parr compared to 2.5 g fry fed the basal unsupplemented (low phospholipid) diet and are presented for each replicate independently. Genes highlighted in green are statistically significant (<i>q</i> < 0.05). Kegg identifiers (Kxxxxx) are specified for each gene. Data were plotted using heatmap.2 [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140964#pone.0140964.ref037\" target=\"_blank\">37</a>] and rows were clustered according to Euclidean distance.</p>", "links"=>[], "tags"=>["Salmo salar", "phospholipid", "dpf", "diet"], "article_id"=>1581802, "categories"=>["Uncategorised"], "users"=>["Christian De Santis", "John F. Taylor", "Laura Martinez-Rubio", "Sebastian Boltaña", "Douglas R. Tocher"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0140964.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_participating_in_glycerophospholipid_metabolism_Kegg_ID_ko00564_/1581802", "title"=>"Genes participating in glycerophospholipid metabolism (Kegg ID ko00564).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-10-21 02:54:10"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"9", "full-text"=>"10", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"10", "full-text"=>"8", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
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  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
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  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
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  • {"unique-ip"=>"14", "full-text"=>"13", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2018", "month"=>"4"}
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  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"12", "full-text"=>"15", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"18", "full-text"=>"22", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"9", "full-text"=>"11", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"14", "full-text"=>"17", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"14", "full-text"=>"15", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"16", "full-text"=>"16", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"15", "full-text"=>"12", "pdf"=>"6", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"11", "full-text"=>"12", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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