Genome-Wide Transcriptomic Analysis of Intestinal Tissue to Assess the Impact of Nutrition and a Secondary Nematode Challenge in Lactating Rats
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{"title"=>"Genome-wide transcriptomic analysis of intestinal tissue to assess the impact of nutrition and a secondary nematode challenge in lactating rats", "type"=>"journal", "authors"=>[{"first_name"=>"Spiridoula", "last_name"=>"Athanasiadou", "scopus_author_id"=>"6602505749"}, {"first_name"=>"Leigh A.", "last_name"=>"Jones", "scopus_author_id"=>"24537225200"}, {"first_name"=>"Stewart T.G.", "last_name"=>"Burgess", "scopus_author_id"=>"23983990900"}, {"first_name"=>"Ilias", "last_name"=>"Kyriazakis", "scopus_author_id"=>"7006474425"}, {"first_name"=>"Alan D.", "last_name"=>"Pemberton", "scopus_author_id"=>"7004405886"}, {"first_name"=>"Jos G.M.", "last_name"=>"Houdijk", "scopus_author_id"=>"6701864224"}, {"first_name"=>"John F.", "last_name"=>"Huntley", "scopus_author_id"=>"26643191400"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"79959216454", "scopus"=>"2-s2.0-79959216454", "pui"=>"361966398", "pmid"=>"21698235", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0020771"}, "id"=>"f85fb379-8353-3515-8371-e2e2ade67f2d", "abstract"=>"BACKGROUND Gastrointestinal nematode infection is a major challenge to the health and welfare of mammals. Although mammals eventually acquire immunity to nematodes, this breaks down around parturition, which renders periparturient mammals susceptible to re-infection and an infection source for their offspring. Nutrient supplementation reduces the extent of periparturient parasitism, but the underlying mechanisms remain unclear. Here, we use a genome wide approach to assess the effects of protein supplementation on gene expression in the small intestine of periparturient rats following nematode re-infection. METHODOLOGY/PRINCIPAL FINDINGS The use of a rat whole genome expression microarray (Affymetrix Gene 1.0ST) showed significant differential regulation of 91 genes in the small intestine of lactating rats, re-infected with Nippostrongylus brasiliensis compared to controls; affected functions included immune cell trafficking, cell-mediated responses and antigen presentation. Genes with a previously described role in immune response to nematodes, such as mast cell proteases, and intelectin, and others newly associated with nematode expulsion, such as anterior gradient homolog 2 were identified. Protein supplementation resulted in significant differential regulation of 64 genes; affected functions included protein synthesis, cellular function and maintenance. It increased cell metabolism, evident from the high number of non-coding RNA and the increased synthesis of ribosomal proteins. It regulated immune responses, through T-cell activation and proliferation. The up-regulation of transcription factor forkhead box P1 in unsupplemented, parasitised hosts may be indicative of a delayed immune response in these animals. CONCLUSIONS/SIGNIFICANCE This study provides the first evidence for nutritional regulation of genes related to immunity to nematodes at the site of parasitism, during expulsion. Additionally it reveals genes induced following secondary parasite challenge in lactating mammals, not previously associated with parasite expulsion. This work is a first step towards defining disease predisposition, identifying markers for nutritional imbalance and developing sustainable measures for parasite control in domestic mammals.", "link"=>"http://www.mendeley.com/research/genomewide-transcriptomic-analysis-intestinal-tissue-assess-impact-nutrition-secondary-nematode-chal", "reader_count"=>17, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Materials Science"=>1, "Agricultural and Biological Sciences"=>9, "Veterinary Science and Veterinary Medicine"=>2, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United Kingdom"=>1, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/765251"], "description"=>"<p>*The P value reported here is a range between the most and least significant result, for the various molecules represented in each biological process.</p>", "links"=>[], "tags"=>["processes", "affected", "supplementation", "lactating"], "article_id"=>435619, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_biological_processes_significantly_affected_by_protein_supplementation_in_lactating_rats_/435619", "title"=>"Top biological processes significantly affected by protein supplementation in lactating rats.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:33:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/765213"], "description"=>"<p>Canonical pathways significantly affected by protein supplementation in lactating rats.</p>", "links"=>[], "tags"=>["pathways", "affected", "supplementation", "lactating"], "article_id"=>435574, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Canonical_pathways_significantly_affected_by_protein_supplementation_in_lactating_rats_/435574", "title"=>"Canonical pathways significantly affected by protein supplementation in lactating rats.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:32:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/384312", "https://ndownloader.figshare.com/files/384374"], "description"=>"<div><h3>Background</h3><p>Gastrointestinal nematode infection is a major challenge to the health and welfare of mammals. Although mammals eventually acquire immunity to nematodes, this breaks down around parturition, which renders periparturient mammals susceptible to re-infection and an infection source for their offspring. Nutrient supplementation reduces the extent of periparturient parasitism, but the underlying mechanisms remain unclear. Here, we use a genome wide approach to assess the effects of protein supplementation on gene expression in the small intestine of periparturient rats following nematode re-infection.</p> <h3>Methodology/Principal Findings</h3><p>The use of a rat whole genome expression microarray (Affymetrix Gene 1.0ST) showed significant differential regulation of 91 genes in the small intestine of lactating rats, re-infected with <em>Nippostrongylus brasiliensis</em> compared to controls; affected functions included immune cell trafficking, cell-mediated responses and antigen presentation. Genes with a previously described role in immune response to nematodes, such as mast cell proteases, and intelectin, and others newly associated with nematode expulsion, such as anterior gradient homolog 2 were identified. Protein supplementation resulted in significant differential regulation of 64 genes; affected functions included protein synthesis, cellular function and maintenance. It increased cell metabolism, evident from the high number of non-coding RNA and the increased synthesis of ribosomal proteins. It regulated immune responses, through T-cell activation and proliferation. The up-regulation of transcription factor forkhead box P1 in unsupplemented, parasitised hosts may be indicative of a delayed immune response in these animals.</p> <h3>Conclusions/Significance</h3><p>This study provides the first evidence for nutritional regulation of genes related to immunity to nematodes at the site of parasitism, during expulsion. Additionally it reveals genes induced following secondary parasite challenge in lactating mammals, not previously associated with parasite expulsion. This work is a first step towards defining disease predisposition, identifying markers for nutritional imbalance and developing sustainable measures for parasite control in domestic mammals.</p> </div>", "links"=>[], "tags"=>["genome-wide", "transcriptomic", "intestinal", "nutrition", "nematode", "lactating", "rats"], "article_id"=>135878, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0020771.s001", "https://dx.doi.org/10.1371/journal.pone.0020771.s002"], "stats"=>{"downloads"=>14, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Transcriptomic_Analysis_of_Intestinal_Tissue_to_Assess_the_Impact_of_Nutrition_and_a_Secondary_Nematode_Challenge_in_Lactating_Rats/135878", "title"=>"Genome-Wide Transcriptomic Analysis of Intestinal Tissue to Assess the Impact of Nutrition and a Secondary Nematode Challenge in Lactating Rats", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-06-16 01:37:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/765044"], "description"=>"<p>Canonical pathways significantly affected by secondary challenge with <i>Nippostrongylus brasiliensis</i> in lactating rats.</p>", "links"=>[], "tags"=>["pathways", "affected", "lactating"], "article_id"=>435414, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Canonical_pathways_significantly_affected_by_secondary_challenge_with_Nippostrongylus_brasiliensis_in_lactating_rats_/435414", "title"=>"Canonical pathways significantly affected by secondary challenge with <i>Nippostrongylus brasiliensis</i> in lactating rats.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:30:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/764663"], "description"=>"<p>Network score = 38. Individual nodes represent protein functions with relationships represented by edges. Nodes are colored by change in gene expression, red indicating up-regulation in infected rats, green indicating down-regulation in infected rats and white indicating that the gene/factor was not differentially expressed but showed a defined relationship to the other genes in the network. Arrows indicate directional relationships between genes.</p>", "links"=>[], "tags"=>["affected", "parasite"], "article_id"=>435030, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphical_representation_of_network_1_as_affected_by_secondary_parasite_challenge_/435030", "title"=>"Graphical representation of network 1 as affected by secondary parasite challenge.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:23:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/765165"], "description"=>"<p>*The P value reported here is a range between the most and least significant result, for the various molecules represented in each biological process.</p>", "links"=>[], "tags"=>["processes", "affected", "supplementation"], "article_id"=>435535, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_biological_processes_significantly_affected_by_the_interaction_between_protein_supplementation_and_secondary_challenge_/435535", "title"=>"Top biological processes significantly affected by the interaction between protein supplementation and secondary challenge.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:32:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/764882"], "description"=>"<p>Bars demonstrate fold change difference in mRNA of the genes shown in the x axes as a consequence of (a) secondary parasite challenge or (b) HP supplementation in comparison to non-infected or LP fed rats respectively.</p>", "links"=>[], "tags"=>["rt", "pcr"], "article_id"=>435248, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Confirmatory_q_RT_PCR_analysis_of_selected_genes_/435248", "title"=>"Confirmatory q RT PCR analysis of selected genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-06-16 01:27:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/765005"], "description"=>"<p>Pathways significantly affected by the interaction between protein supplementation and secondary challenge.</p>", "links"=>[], "tags"=>["affected", "supplementation"], "article_id"=>435380, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pathways_significantly_affected_by_the_interaction_between_protein_supplementation_and_secondary_challenge_/435380", "title"=>"Pathways significantly affected by the interaction between protein supplementation and secondary challenge.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:29:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/765082"], "description"=>"<p>*The P value reported here is a range between the most and least significant result, for the various molecules represented in each biological process.</p>", "links"=>[], "tags"=>["processes", "affected", "lactating"], "article_id"=>435446, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_biological_processes_significantly_affected_by_secondary_challenge_with_Nippostrongylus_brasiliensis_in_lactating_rats_/435446", "title"=>"Top biological processes significantly affected by secondary challenge with <i>Nippostrongylus brasiliensis</i> in lactating rats.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:30:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/765118"], "description"=>"<p>*For extended list of genes (FC>1.5) see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020771#pone.0020771.s001\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["differentially", "regulated", "lactating", "rats", "mtc"], "article_id"=>435481, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_significantly_differentially_regulated_by_secondary_challenge_with_N_brasiliensis_in_lactating_rats_P_2_MTC_0_05_/435481", "title"=>"Genes significantly differentially regulated by secondary challenge with <i>N.brasiliensis</i> in lactating rats (P<0.05, FC>2<sup>*</sup>, MTC 0.05).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:31:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/765301"], "description"=>"<p>Genes significantly differentially regulated by protein supplementation in lactating rats (P<0.05, FC>1.5, MTC 0.05).</p>", "links"=>[], "tags"=>["differentially", "regulated", "supplementation", "lactating", "rats", "mtc"], "article_id"=>435663, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_significantly_differentially_regulated_by_protein_supplementation_in_lactating_rats_P_lt_0_05_FC_gt_1_5_MTC_0_05_/435663", "title"=>"Genes significantly differentially regulated by protein supplementation in lactating rats (P<0.05, FC>1.5, MTC 0.05).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:34:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/764965"], "description"=>"<p>Primer sequence, annealing temperature (AT°C) and PCR product length for genes amplified using qPCR.</p>", "links"=>[], "tags"=>["annealing", "pcr", "genes", "amplified"], "article_id"=>435333, "categories"=>["Genetics", "Immunology"], "users"=>["Spiridoula Athanasiadou", "Leigh A. Jones", "Stewart T. G. Burgess", "Ilias Kyriazakis", "Alan D. Pemberton", "Jos G. M. Houdijk", "John F. Huntley"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0020771.t009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primer_sequence_annealing_temperature_AT_176_C_and_PCR_product_length_for_genes_amplified_using_qPCR_/435333", "title"=>"Primer sequence, annealing temperature (AT°C) and PCR product length for genes amplified using qPCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-06-16 01:28:53"}

PMC Usage Stats | Further Information

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