{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T02:23:17Z","timestamp":1789957397295,"version":"4.0.1"},"reference-count":78,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T00:00:00Z","timestamp":1652659200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T00:00:00Z","timestamp":1652659200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001801","name":"University of Western Australia","doi-asserted-by":"crossref","award":["PS-2(11) FDP\/17\/8071"],"award-info":[{"award-number":["PS-2(11) FDP\/17\/8071"]}],"id":[{"id":"10.13039\/501100001801","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001801","name":"University of Western Australia","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001801","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Funct Integr Genomics"],"published-print":{"date-parts":[[2022,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Gastrointestinal helminths are a global health issue, for humans as well as domestic animals. Most studies focus on the tissues that are infected with the parasite, but here we studied the ileum, a tissue that is rarely infected by helminths. We tested whether inflammation in the ileum contributes to the development and severity of diarrhoea, by comparing sheep that are susceptible (n = 4) or resistant (n = 4) to the disease. We analyzed the ileum transcriptome using RNASeq sequencing approach and various bioinformatics tools including FastQC, STAR, featureCounts, DESeq2, DAVID, clusterProfiler, Cytoscape (ClusterONE) and EnrichR. We identified 243 differentially expressed genes (DEGs), of which 118 were up-regulated and 125 were down-regulated DEGs in the diarrhoea-susceptible animals compared to the diarrhoea-resistant animals. The resulting DEGs were functionally enriched for biological processes, pathways and gene set enrichment analysis. The up-regulated DEGs suggested that an inflammatory immune response was coupled with genes involved in \u2018Th2 immune response\u2019 and \u2018anti-inflammatory response\u2019. The down-regulated DEGs were related to ion transport, muscle contraction and pathways preventing inflammation. We conclude that i) susceptibility to helminth-induced diarrhoea involves an inflammatory response at a non-infectious site; ii) down-regulation of pathways preventing inflammation can contribute to the severity of diarrhoea; and iii) genes involved in anti-inflammatory responses can reduce the inflammation and diarrhoea.<\/jats:p>","DOI":"10.1007\/s10142-022-00864-6","type":"journal-article","created":{"date-parts":[[2022,5,16]],"date-time":"2022-05-16T10:03:00Z","timestamp":1652695380000},"page":"865-877","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Contribution of the Immune Response in the Ileum to the Development of Diarrhoea caused by Helminth Infection: Studies with the Sheep Model"],"prefix":"10.1007","volume":"22","author":[{"given":"Shamshad Ul","family":"Hassan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eng Guan","family":"Chua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Parwinder","family":"Kaur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erwin A.","family":"Paz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chin Yen","family":"Tay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan C.","family":"Greeff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shimin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1905-7934","authenticated-orcid":false,"given":"Graeme B.","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,5,16]]},"reference":[{"issue":"8","key":"864_CR1","doi-asserted-by":"publisher","first-page":"591","DOI":"10.2174\/138920210793360907","volume":"11","author":"L Akhabir","year":"2010","unstructured":"Akhabir L, Sandford A (2010) Genetics of interleukin 1 receptor-like 1 in immune and inflammatory diseases. Curr Genomics 11(8):591\u2013606","journal-title":"Curr Genomics"},{"key":"864_CR2","doi-asserted-by":"crossref","unstructured":"Al Nabhani Z, Dietrich G, Hugot J-P, Barreau F (2017) Nod2: The intestinal gate keeper. PLOS Pathogens [Internet]. [cited 2021 May 27];13(3). Available from: https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC5333895\/.","DOI":"10.1371\/journal.ppat.1006177"},{"key":"864_CR3","doi-asserted-by":"crossref","unstructured":"Asano K, Takahashi N, Ushiki M, Monya M, Aihara F, Kuboki E et al (2015) Intestinal CD169+ macrophages initiate mucosal inflammation by secreting CCL8 that recruits inflammatory monocytes. Nature Communications [Internet]. [cited 2021 May 25];6. Available from: https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4518321\/","DOI":"10.1038\/ncomms8802"},{"issue":"3","key":"864_CR4","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1111\/j.1365-3024.2006.00816.x","volume":"28","author":"A Balic","year":"2006","unstructured":"Balic A, Cunningham CP, Meeusen ENT (2006) Eosinophil interactions with Haemonchus contortus larvae in the ovine gastrointestinal tract. Parasite Immunol 28(3):107\u2013115","journal-title":"Parasite Immunol"},{"issue":"3","key":"864_CR5","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.4049\/jimmunol.1102310","volume":"188","author":"NK Banda","year":"2012","unstructured":"Banda NK, Hyatt S, Antonioli AH, White JT, Glogowska M, Takahashi K et al (2012) Role of C3a receptors, C5a receptors, and complement protein C6 deficiency in collagen antibody-induced arthritis in mice. J Immunol 188(3):1469\u20131478","journal-title":"J Immunol"},{"issue":"1","key":"864_CR6","first-page":"C88","volume":"287","author":"NC Browner","year":"2004","unstructured":"Browner NC, Sellak H, Lincoln TM (2004) Downregulation of cGMP-dependent protein kinase expression by inflammatory cytokines in vascular smooth muscle cells. Am J Phys Cell Phys 287(1):C88\u2013C96","journal-title":"Am J Phys Cell Phys"},{"issue":"7","key":"864_CR7","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1016\/0020-7519(92)90053-N","volume":"22","author":"BM Buddle","year":"1992","unstructured":"Buddle BM, Jowett G, Green RS, Douch PGC, Risdon PL (1992) Association of blood eosinophilia with the expression of resistance in Romney lambs to nematodes. Int J Parasitol 22(7):955\u2013960","journal-title":"Int J Parasitol"},{"issue":"1","key":"864_CR8","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1186\/1471-2105-14-128","volume":"14","author":"EY Chen","year":"2013","unstructured":"Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles G et al (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14(1):128","journal-title":"BMC Bioinformatics"},{"issue":"8","key":"864_CR9","doi-asserted-by":"publisher","first-page":"3542","DOI":"10.4049\/jimmunol.1403068","volume":"194","author":"LG Coulthard","year":"2015","unstructured":"Coulthard LG, Woodruff TM (2015) Is the complement activation product C3a a proinflammatory molecule? Re-evaluating the evidence and the myth. J Immunol 194(8):3542\u20133548","journal-title":"J Immunol"},{"key":"864_CR10","doi-asserted-by":"crossref","unstructured":"Craig TM (2009) CHAPTER 22 - Helminth Parasites of the Ruminant Gastrointestinal Tract. In: Anderson DE, Rings DM, editors. Food Animal Practice (Fifth Edition) [Internet]. Saint Louis: W.B. Saunders [cited 2021 Mar 1]. p. 78\u201391. Available from: https:\/\/www.sciencedirect.com\/science\/article\/pii\/B9781416035916100223.","DOI":"10.1016\/B978-141603591-6.10022-3"},{"issue":"1","key":"864_CR11","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/1746-6148-10-87","volume":"10","author":"NM Craig","year":"2014","unstructured":"Craig NM, Smith DW, Pate JA, Morrison IW, Knight PA (2014) Local cytokine transcription in na\u00efve and previously infected sheep and lambs following challenge with Teladorsagia circumcincta. BMC Vet Res 10(1):87","journal-title":"BMC Vet Res"},{"issue":"1","key":"864_CR12","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.jcmgh.2018.02.009","volume":"6","author":"S Das","year":"2018","unstructured":"Das S, Jayaratne R, Barrett KE (2018) The role of ion transporters in the pathophysiology of infectious diarrhea. Cell Mol Gastroenterol Hepatol 6(1):33\u201345","journal-title":"Cell Mol Gastroenterol Hepatol"},{"issue":"9","key":"864_CR13","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1016\/S0161-5890(02)00210-9","volume":"39","author":"S Diehl","year":"2002","unstructured":"Diehl S, Rinc\u00f3n M (2002) The two faces of IL-6 on Th1\/Th2 differentiation. Mol Immunol 39(9):531\u2013536","journal-title":"Mol Immunol"},{"issue":"6","key":"864_CR14","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1016\/s1074-7613(00)00078-9","volume":"13","author":"S Diehl","year":"2000","unstructured":"Diehl S, Anguita J, Hoffmeyer A, Zapton T, Ihle JN, Fikrig E (2000) Inhibition of Th1 differentiation by IL-6 Is mediated by SOCS. Immunity. 13(6):805\u2013815. https:\/\/doi.org\/10.1016\/s1074-7613(00)00078-9","journal-title":"Immunity."},{"issue":"5\u20136","key":"864_CR15","doi-asserted-by":"publisher","first-page":"457","DOI":"10.3109\/08830189809043005","volume":"16","author":"CA Dinarello","year":"1998","unstructured":"Dinarello CA (1998) Interleukin-1, interleukin-1 receptors and interleukin-1 receptor antagonist. Int Rev Immunol 16(5\u20136):457\u2013499","journal-title":"Int Rev Immunol"},{"issue":"1","key":"864_CR16","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S et al (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15\u201321","journal-title":"Bioinformatics"},{"issue":"3","key":"864_CR17","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1016\/0304-4017(84)90045-1","volume":"16","author":"PGC Douch","year":"1984","unstructured":"Douch PGC, Harrison GBL, Buchanan LL, Brunsdon RV (1984) Relationship of histamine in tissues and antiparasitic substances in gastrointestinal mucus to the development of resistance to trichostrongyle infections in young sheep. Vet Parasitol 16(3):273\u2013288","journal-title":"Vet Parasitol"},{"issue":"1","key":"864_CR18","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/j.scr.2015.06.008","volume":"15","author":"R Ebert","year":"2015","unstructured":"Ebert R, Benisch P, Krug M, Zeck S, Mei\u00dfner-Weigl J, Steinert A et al (2015) Acute phase serum amyloid A induces proinflammatory cytokines and mineralization via toll-like receptor 4 in mesenchymal stem cells. Stem Cell Res 15(1):231\u2013239","journal-title":"Stem Cell Res"},{"key":"864_CR19","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/1476-9255-3-5","volume":"3","author":"M Eisenhut","year":"2006","unstructured":"Eisenhut M (2006) Changes in ion transport in inflammatory disease. J Inflamm 3:5","journal-title":"J Inflamm"},{"key":"864_CR20","unstructured":"Elias JA, Zitnik RJ (2012) Cytokine-cytokine interactions in the context of cytokine networking. Am J Respir Cell Mol Biol [Internet]. [cited 2021 May 27]; Available from: https:\/\/www.atsjournals.org\/doi\/pdf\/10.1165\/ajrcmb\/7.4.365"},{"issue":"5","key":"864_CR21","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.1084\/jem.179.5.1563","volume":"179","author":"FD Finkelman","year":"1994","unstructured":"Finkelman FD, Madden KB, Cheever AW, Katona IM, Morris SC, Gately MK, Hubbard BR, Gause WC, Urban JF Jr (1994) Effects of interleukin 12 on immune responses and host protection in mice infected with intestinal nematode parasites. J Exp Med 179(5):1563\u20131572","journal-title":"J Exp Med"},{"issue":"2","key":"864_CR22","doi-asserted-by":"publisher","first-page":"e0008119","DOI":"10.1371\/journal.pntd.0008119","volume":"14","author":"SJ Frohberger","year":"2020","unstructured":"Frohberger SJ, Fercoq F, Neumann A-L, Surendar J, Stamminger W, Ehrens A et al (2020) S100A8\/S100A9 deficiency increases neutrophil activation and protective immune responses against invading infective L3 larvae of the filarial nematode Litomosoides sigmodontis. PLoS Negl Trop Dis 14(2):e0008119","journal-title":"PLoS Negl Trop Dis"},{"issue":"Suppl 2","key":"864_CR23","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1186\/ar1917","volume":"8","author":"C Gabay","year":"2006","unstructured":"Gabay C (2006) Interleukin-6 and chronic inflammation. Arthritis Res Ther 8(Suppl 2):S3","journal-title":"Arthritis Res Ther"},{"issue":"3","key":"864_CR24","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1046\/j.1365-2567.2000.00974.x","volume":"99","author":"HS Gill","year":"2000","unstructured":"Gill HS, Altmann K, Cross ML, Husband AJ (2000) Induction of T helper 1- and T helper 2-type immune responses during Haemonchus contortus infection in sheep. Immunology 99(3):458\u2013463","journal-title":"Immunology"},{"issue":"7796","key":"864_CR25","doi-asserted-by":"publisher","first-page":"527","DOI":"10.1038\/s41586-020-2025-2","volume":"578","author":"DB Graham","year":"2020","unstructured":"Graham DB, Xavier RJ (2020) Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature 578(7796):527\u2013539","journal-title":"Nature"},{"issue":"13","key":"864_CR26","doi-asserted-by":"publisher","first-page":"1630","DOI":"10.1071\/AN19038","volume":"60","author":"JC Greeff","year":"2020","unstructured":"Greeff JC, Liu S, Palmer D, Martin GB, Greeff JC, Liu S et al (2020) Temporal changes in circulatory blood cell parameters of sheep genetically different for faecal worm egg count and diarrhoea from late summer to spring in a Mediterranean environment. Anim Prod Sci 60(13):1630\u20131642","journal-title":"Anim Prod Sci"},{"issue":"2","key":"864_CR27","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1111\/j.1365-2249.1995.tb03667.x","volume":"100","author":"MC Grimm","year":"1995","unstructured":"Grimm MC, Pavli P, Van de Pol E, Doe WF (1995) Evidence for a CD14+ population of monocytes in inflammatory bowel disease mucosa--implications for pathogenesis. Clin Exp Immunol 100(2):291\u2013297","journal-title":"Clin Exp Immunol"},{"key":"864_CR28","doi-asserted-by":"crossref","unstructured":"Gutierrez-Pajares JL, Iturrieta J, Dulam V, Wang Y, Pavlides S, Malacari G et al (2015) Caveolin-3 Promotes a Vascular Smooth Muscle Contractile Phenotype. Front Cardiovasc Med [Internet]. [cited 2021 Feb 23];2. Available from: https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4671348\/","DOI":"10.3389\/fcvm.2015.00027"},{"issue":"3","key":"864_CR29","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1016\/S0020-7519(98)00221-5","volume":"29","author":"GB Harrison","year":"1999","unstructured":"Harrison GB, Pulford HD, Gatehouse TK, Shaw RJ, Pfeffer A, Shoemaker CB (1999) Studies on the role of mucus and mucosal hypersensitivity reactions during rejection of Trichostrongylus colubriformis from the intestine of immune sheep using an experimental challenge model. Int J Parasitol 29(3):459\u2013468","journal-title":"Int J Parasitol"},{"issue":"1","key":"864_CR30","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1046\/j.1365-3024.2003.00602.x","volume":"25","author":"GBL Harrison","year":"2003","unstructured":"Harrison GBL, Pulford HD, Hein WR, Barber TK, Shaw RJ, Mcneill M et al (2003) Immune rejection of Trichostrongylus colubriformis in sheep; a possible role for intestinal mucus antibody against an L3-specific surface antigen. Parasite Immunol 25(1):45\u201353","journal-title":"Parasite Immunol"},{"key":"864_CR31","doi-asserted-by":"publisher","first-page":"2207","DOI":"10.1038\/s41598-022-06001-4","volume":"12","author":"SU Hassan","year":"2022","unstructured":"Hassan SU, Chua EG, Paz EA, Kaur P, Tay CY, Greeff JC, Liu S, Martin GB (2022) Investigating the development of diarrhoea through gene expression analysis in sheep genetically resistant to gastrointestinal helminth infection. Sci Rep 12:2207. https:\/\/doi.org\/10.1038\/s41598-022-06001-4","journal-title":"Sci Rep"},{"issue":"1","key":"864_CR32","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1016\/j.vetimm.2006.03.012","volume":"112","author":"NG Henderson","year":"2006","unstructured":"Henderson NG, Stear MJ (2006) Eosinophil and IgA responses in sheep infected with Teladorsagia circumcincta. Vet Immunol Immunopathol 112(1):62\u201366","journal-title":"Vet Immunol Immunopathol"},{"issue":"1","key":"864_CR33","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44\u201357","journal-title":"Nat Protoc"},{"issue":"3\u20134","key":"864_CR34","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1016\/j.ijpara.2007.07.012","volume":"38","author":"A Ingham","year":"2008","unstructured":"Ingham A, Reverter A, Windon R, Hunt P, Menzies M (2008) Gastrointestinal nematode challenge induces some conserved gene expression changes in the gut mucosa of genetically resistant sheep. Int J Parasitol 38(3\u20134):431\u2013442","journal-title":"Int J Parasitol"},{"issue":"1","key":"864_CR35","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1084\/jem.180.1.203","volume":"180","author":"R Badolato","year":"1994","unstructured":"Badolato R, Wang JM, Murphy WJ, Lloyd AR, Michiel DF, Bausserman LL, Kelvin DJ, Oppenheim JJ (1994) Serum amyloid A is a chemoattractant: induction of migration, adhesion, and tissue infiltration of monocytes and polymorphonuclear leukocytes. J Exp Med 180(1):203\u2013209","journal-title":"J Exp Med"},{"issue":"282","key":"864_CR36","doi-asserted-by":"publisher","first-page":"109139","DOI":"10.1016\/j.vetpar.2020.109139","volume":"1","author":"C Jacobson","year":"2020","unstructured":"Jacobson C, Larsen JW, Besier RB, Lloyd JB, Kahn LP (2020) Diarrhoea associated with gastrointestinal parasites in grazing sheep. Vet Parasitol 1(282):109139","journal-title":"Vet Parasitol"},{"issue":"D1","key":"864_CR37","doi-asserted-by":"publisher","first-page":"D545","DOI":"10.1093\/nar\/gkaa970","volume":"49","author":"M Kanehisa","year":"2020","unstructured":"Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M (2020) KEGG: integrating viruses and cellular organisms. Nucleic Acids Res 49(D1):D545\u2013D551","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"864_CR38","first-page":"100","volume":"1","author":"LJE Karlsson","year":"2004","unstructured":"Karlsson LJE, Pollott GE, Greeff JC, Bell A, Eady SJ (2004) Relationship between faecal worm egg counts and scouring in Australian Merino sheep. Sci Access 1(1):100\u2013103","journal-title":"Sci Access"},{"key":"864_CR39","unstructured":"Karlsson LJE, Greeff JC, Eady SJ, Pollott GE. Nematode resistance & hypersensitivity diarrhoea. In 6th International Sheep Veterinary Congress (Eds GC Fthenakis and QA McKaller) 17\u201321 June 2005, Hersonissos, Greece, pp. 203\u2013204. Hersonnios Hellenic Veterinary Medical Society, Athens"},{"issue":"6","key":"864_CR40","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1016\/j.cell.2010.03.002","volume":"140","author":"DL Kastner","year":"2010","unstructured":"Kastner DL, Aksentijevich I, Goldbach-Mansky R (2010) Autoinflammatory disease reloaded: a clinical perspective. Cell 140(6):784\u2013790","journal-title":"Cell"},{"issue":"5","key":"864_CR41","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1016\/j.febslet.2008.01.022","volume":"582","author":"T Koga","year":"2008","unstructured":"Koga T, Torigoshi T, Motokawa S, Miyashita T, Maeda Y, Nakamura M et al (2008) Serum amyloid A-induced IL-6 production by rheumatoid synoviocytes. FEBS Lett 582(5):579\u2013585","journal-title":"FEBS Lett"},{"issue":"5","key":"864_CR42","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/0092-8674(95)90349-6","volume":"80","author":"VK Kuchroo","year":"1995","unstructured":"Kuchroo VK, Prabhu Das M, Brown JA, Ranger AM, Zamvil SS, Sobel RA et al (1995) B7-1 and B7-2 costimulatory molecules activate differentially the Th1\/Th2 developmental pathways: application to autoimmune disease therapy. Cell. 80(5):707\u2013718","journal-title":"Cell."},{"issue":"11","key":"864_CR43","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1111\/j.1751-0813.1994.tb00930.x","volume":"71","author":"JW Larsen","year":"1994","unstructured":"Larsen JW, Anderson N, Vizard AL, Anderson GA, Hoste H (1994) Diarrhoea in merino ewes during winter: association with trichostrongylid larvae. Aust Vet J 71(11):365\u2013372","journal-title":"Aust Vet J"},{"issue":"6","key":"864_CR44","doi-asserted-by":"publisher","first-page":"893","DOI":"10.1016\/S0020-7519(99)00050-8","volume":"29","author":"JWA Larsen","year":"1999","unstructured":"Larsen JWA, Anderson N, Vizard AL (1999) The pathogenesis and control of diarrhoea and breech soiling in adult Merino sheep. Int J Parasitol 29(6):893\u2013902","journal-title":"Int J Parasitol"},{"issue":"5","key":"864_CR45","doi-asserted-by":"publisher","first-page":"1149","DOI":"10.1084\/jem.20081271","volume":"206","author":"CG Lee","year":"2009","unstructured":"Lee CG, Hartl D, Lee GR, Koller B, Matsuura H, Da Silva CA et al (2009) Role of breast regression protein 39 (BRP-39)\/chitinase 3-like-1 in Th2 and IL-13\u2013induced tissue responses and apoptosis. J Exp Med 206(5):1149\u20131166","journal-title":"J Exp Med"},{"issue":"7","key":"864_CR46","doi-asserted-by":"publisher","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","volume":"30","author":"Y Liao","year":"2014","unstructured":"Liao Y, Smyth GK, Shi W (2014) featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features. Bioinformatics 30(7):923\u2013930","journal-title":"Bioinformatics"},{"issue":"8","key":"864_CR47","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1002\/ibd.20890","volume":"15","author":"S Liu","year":"2009","unstructured":"Liu S, Russo PA, Baldassano RN, Sullivan KE (2009) CD68 expression is markedly different in Crohn\u02bcs disease and the colitis associated with chronic granulomatous disease. Inflamm Bowel Dis 15(8):1213\u20131217","journal-title":"Inflamm Bowel Dis"},{"issue":"12","key":"864_CR48","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550","journal-title":"Genome Biol"},{"issue":"7","key":"864_CR49","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1111\/j.1365-3024.2009.01110.x","volume":"31","author":"TN McNeilly","year":"2009","unstructured":"McNeilly TN, Devaney E, Matthews JB (2009) Teladorsagia circumcincta in the sheep abomasum: defining the role of dendritic cells in T cell regulation and protective immunity. Parasite Immunol 31(7):347\u2013356. https:\/\/doi.org\/10.1111\/j.1365-3024.2009.01110.x","journal-title":"Parasite Immunol"},{"issue":"12","key":"864_CR50","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1111\/pim.12290","volume":"37","author":"KM McRae","year":"2015","unstructured":"McRae KM, Stear MJ, Good B, Keane OM (2015) The host immune response to gastrointestinal nematode infection in sheep. Parasite Immunol 37(12):605\u2013613","journal-title":"Parasite Immunol"},{"issue":"12","key":"864_CR51","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1038\/nri3084","volume":"11","author":"J Neefjes","year":"2011","unstructured":"Neefjes J, Jongsma MLM, Paul P, Bakke O (2011) Towards a systems understanding of MHC class I and MHC class II antigen presentation. Nat Rev Immunol 11(12):823\u2013836","journal-title":"Nat Rev Immunol"},{"key":"864_CR52","doi-asserted-by":"crossref","unstructured":"Nemeth ZH, Bogdanovski DA, Barratt-Stopper P, Paglinco SR, Antonioli L, Rolandelli RH (2017) Crohn\u2019s disease and ulcerative colitis show unique cytokine profiles. Cureus 9(4):e1177","DOI":"10.7759\/cureus.1177"},{"issue":"2","key":"864_CR53","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1084\/jem.191.2.303","volume":"191","author":"MJH Nicklin","year":"2000","unstructured":"Nicklin MJH, Hughes DE, Barton JL, Ure JM, Duff GW (2000) Arterial inflammation in mice lacking the interleukin 1 receptor antagonist gene. J Exp Med 191(2):303\u2013312","journal-title":"J Exp Med"},{"key":"864_CR54","unstructured":"Niu XY, Liu SM, Greeff JC, Palmer DG, Martin GB (2021) Immune cell changes in different gastrointestinal tissues of Merino sheep distinct in genotypes during spring in Western Australia. In preparation"},{"key":"864_CR55","unstructured":"Pirahanchi Y, Jessu R, Aeddula NR (2020) Physiology, Sodium Potassium Pump. In: StatPearls [Internet]. StatPearls Publishing, Treasure Island [cited 2021 Feb 23]. Available from: http:\/\/www.ncbi.nlm.nih.gov\/books\/NBK537088\/"},{"issue":"5","key":"864_CR56","doi-asserted-by":"publisher","first-page":"1170","DOI":"10.1084\/jem.20170277","volume":"216","author":"M Rapp","year":"2019","unstructured":"Rapp M, Wintergerst MWM, Kunz WG, Vetter VK, Knott MML, Lisowski D et al (2019) CCL22 controls immunity by promoting regulatory T cell communication with dendritic cells in lymph nodes. J Exp Med 216(5):1170\u20131181","journal-title":"J Exp Med"},{"issue":"1","key":"864_CR57","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/nri3341","volume":"13","author":"HF Rosenberg","year":"2013","unstructured":"Rosenberg HF, Dyer KD, Foster PS (2013) Eosinophils: changing perspectives in health and disease. Nat Rev Immunol 13(1):9\u201322","journal-title":"Nat Rev Immunol"},{"issue":"4","key":"864_CR58","doi-asserted-by":"publisher","first-page":"842","DOI":"10.1111\/j.1476-5381.2009.00559.x","volume":"159","author":"P Schafer","year":"2010","unstructured":"Schafer P, Parton A, Gandhi A, Capone L, Adams M, Wu L et al (2010) Apremilast, a cAMP phosphodiesterase-4 inhibitor, demonstrates anti-inflammatory activity in vitro and in a model of psoriasis. Br J Pharmacol 159(4):842\u2013855","journal-title":"Br J Pharmacol"},{"issue":"5","key":"864_CR59","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1016\/j.bbamcr.2011.01.034","volume":"1813","author":"J Scheller","year":"2011","unstructured":"Scheller J, Chalaris A, Schmidt-Arras D, Rose-John S (2011) The pro- and anti-inflammatory properties of the cytokine interleukin-6. Biochimica Biophys Acta (BBA) Mol Cell Res 1813(5):878\u2013888","journal-title":"Biochimica Biophys Acta (BBA) Mol Cell Res"},{"issue":"5","key":"864_CR60","doi-asserted-by":"publisher","first-page":"1978","DOI":"10.3892\/ijo.2015.2917","volume":"46","author":"M Shiiba","year":"2015","unstructured":"Shiiba M, Saito K, Yamagami H, Nakashima D, Higo M, Kasamatsu A et al (2015) Interleukin-1 receptor antagonist (IL1RN) is associated with suppression of early carcinogenic events in human oral malignancies. Int J Oncol 46(5):1978\u20131984","journal-title":"Int J Oncol"},{"issue":"D1","key":"864_CR61","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","volume":"47","author":"D Szklarczyk","year":"2019","unstructured":"Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J et al (2019) STRING v11: protein\u2013protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47(D1):D607\u2013D613","journal-title":"Nucleic Acids Res"},{"key":"864_CR62","doi-asserted-by":"crossref","unstructured":"Tanaka T, Narazaki M, Kishimoto T (2014) IL-6 in Inflammation, Immunity, and Disease. Cold Spring Harbor Perspect Biol [Internet]. [cited 2021 Feb 9];6(10). Available from: https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC4176007\/","DOI":"10.1101\/cshperspect.a016295"},{"issue":"1","key":"864_CR63","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1016\/j.vetpar.2012.03.027","volume":"189","author":"MA Taylor","year":"2012","unstructured":"Taylor MA (2012) Emerging parasitic diseases of sheep. Vet Parasitol 189(1):2\u20137","journal-title":"Vet Parasitol"},{"issue":"1 Supplement","key":"864_CR64","doi-asserted-by":"crossref","first-page":"189.1","DOI":"10.4049\/jimmunol.196.Supp.189.1","volume":"196","author":"AJ Thompson","year":"2016","unstructured":"Thompson AJ, Omer L, He RL (2016) Serum amyloid A induces T lymphocyte migration through chemokine receptor CXCR3. J Immunol 196(1 Supplement):189.1","journal-title":"J Immunol"},{"issue":"11","key":"864_CR65","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1016\/s0020-7519(96)00115-4","volume":"26","author":"BM Wagland","year":"1996","unstructured":"Wagland BM, Emery DL, McClure SJ (1996) Studies on the host-parasite relationship between Trichostrongylus colubriformis and susceptible and resistant sheep. Int J Parasitol 26(11):1279\u20131286. https:\/\/doi.org\/10.1016\/s0020-7519(96)00115-4","journal-title":"Int J Parasitol"},{"issue":"6","key":"864_CR66","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.coph.2009.08.003","volume":"9","author":"D Wang","year":"2009","unstructured":"Wang D, DuBois RN, Richmond A (2009) The role of chemokines in intestinal inflammation and cancer. Curr Opin Pharmacol 9(6):688\u2013696","journal-title":"Curr Opin Pharmacol"},{"issue":"17","key":"864_CR67","doi-asserted-by":"publisher","first-page":"7223","DOI":"10.7314\/APJCP.2014.15.17.7223","volume":"15","author":"R-J Wang","year":"2014","unstructured":"Wang R-J, Wu P, Cai G-X, Wang Z-M, Xu Y, Peng J-J et al (2014) Down-regulated MYH11 expression correlates with poor prognosis in stage II and III colorectal cancer. Asian Pac J Cancer Prev 15(17):7223\u20137228","journal-title":"Asian Pac J Cancer Prev"},{"key":"864_CR68","doi-asserted-by":"crossref","unstructured":"Wang S, Song R, Wang Z, Jing Z, Wang S, Ma J (2018) S100A8\/A9 in Inflammation. Front Immunol [Internet]. [cited 2021 Feb 17];9. Available from: https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2018.01298\/full#B1","DOI":"10.3389\/fimmu.2018.01298"},{"issue":"8","key":"864_CR69","doi-asserted-by":"publisher","first-page":"1260","DOI":"10.1096\/fj.05-5292fje","volume":"20","author":"JW Wegener","year":"2006","unstructured":"Wegener JW, Schulla V, Koller A, Klugbauer N, Feil R, Hofmann F (2006) Control of intestinal motility by the Cav1.2 L-type calcium channel in mice. FASEB J 20(8):1260\u20131262","journal-title":"FASEB J"},{"issue":"8","key":"864_CR70","doi-asserted-by":"publisher","first-page":"G848","DOI":"10.1152\/ajpgi.00176.2014","volume":"307","author":"MG Welch","year":"2014","unstructured":"Welch MG, Margolis KG, Li Z, Gershon MD (2014) Oxytocin regulates gastrointestinal motility, inflammation, macromolecular permeability, and mucosal maintenance in mice. Am J Phys Gastrointest Liver 307(8):G848\u2013G862","journal-title":"Am J Phys Gastrointest Liver"},{"issue":"3","key":"864_CR71","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/j.tvjl.2011.10.009","volume":"192","author":"AR Williams","year":"2012","unstructured":"Williams AR, Palmer DG (2012) Interactions between gastrointestinal nematode parasites and diarrhoea in sheep: pathogenesis and control. Vet J 192(3):279\u2013285","journal-title":"Vet J"},{"issue":"3\u20134","key":"864_CR72","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1016\/j.vetpar.2010.02.033","volume":"170","author":"AR Williams","year":"2010","unstructured":"Williams AR, Palmer DG, Williams IH, Vercoe PE, Karlsson LJ (2010) Faecal dry matter, inflammatory cells and antibodies in parasite-resistant sheep challenged with either Trichostrongylus colubriformis or Teladorsagia circumcincta. Vet Parasitol 170(3\u20134):230\u2013237","journal-title":"Vet Parasitol"},{"issue":"10","key":"864_CR73","doi-asserted-by":"publisher","first-page":"1904","DOI":"10.1093\/rheumatology\/kev207","volume":"54","author":"Q Yao","year":"2015","unstructured":"Yao Q, Shen M, McDonald C, Lacbawan F, Moran R, Shen B (2015) NOD2-associated autoinflammatory disease: a large cohort study. Rheumatology 54(10):1904\u20131912","journal-title":"Rheumatology"},{"issue":"6","key":"864_CR74","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.1084\/jem.20062076","volume":"204","author":"Q Yuan","year":"2007","unstructured":"Yuan Q, Bromley SK, Means TK, Jones KJ, Hayashi F, Bhan AK et al (2007) CCR4-dependent regulatory T cell function in inflammatory bowel disease. J Exp Med 204(6):1327\u20131334","journal-title":"J Exp Med"},{"issue":"3","key":"864_CR75","doi-asserted-by":"publisher","first-page":"808","DOI":"10.1016\/S0016-5085(97)70175-6","volume":"113","author":"K Z\u2019Graggen","year":"1997","unstructured":"Z\u2019Graggen K, Walz A, Mazzucchelli L, Strieter RM, Mueller C (1997) The C-X-C chemokine ENA-78 is preferentially expressed in intestinal epithelium in inflammatory bowel disease. Gastroenterology. 113(3):808\u2013816","journal-title":"Gastroenterology."},{"issue":"1","key":"864_CR76","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41392-019-0089-y","volume":"5","author":"T Zhao","year":"2020","unstructured":"Zhao T, Su Z, Li Y, Zhang X, You Q (2020) Chitinase-3 like-protein-1 function and its role in diseases. Signal Transduct Target Ther 5(1):1\u201320","journal-title":"Signal Transduct Target Ther"},{"issue":"4","key":"864_CR77","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1080\/09168451.2014.991680","volume":"79","author":"Y Zhou","year":"2015","unstructured":"Zhou Y, Ruan Z, Zhou X, Huang X, Li H, Wang L et al (2015) Lactosucrose attenuates intestinal inflammation by promoting Th2 cytokine production and enhancing CD86 expression in colitic rats. Biosci Biotechnol Biochem 79(4):643\u2013651","journal-title":"Biosci Biotechnol Biochem"},{"issue":"6","key":"864_CR78","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1002\/ibd.21898","volume":"18","author":"NP Zimmerman","year":"2012","unstructured":"Zimmerman NP, Kumar SN, Turner JR, Dwinell MB (2012) Cyclic AMP dysregulates intestinal epithelial cell restitution through PKA and RhoA. Inflamm Bowel Dis 18(6):1081\u20131091","journal-title":"Inflamm Bowel Dis"}],"container-title":["Functional &amp; Integrative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-022-00864-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10142-022-00864-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10142-022-00864-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,5]],"date-time":"2023-02-05T08:47:15Z","timestamp":1675586835000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10142-022-00864-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,16]]},"references-count":78,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,10]]}},"alternative-id":["864"],"URL":"https:\/\/doi.org\/10.1007\/s10142-022-00864-6","relation":{},"ISSN":["1438-793X","1438-7948"],"issn-type":[{"value":"1438-793X","type":"print"},{"value":"1438-7948","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,5,16]]},"assertion":[{"value":"24 February 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"18 April 2022","order":2,"name":"revised","label":"Revised","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 April 2022","order":3,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 May 2022","order":4,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All animal experimentation was approved by the Animal Ethics Committee of the WA Department of Primary Industry and Rural Development, under the guidelines of the National Health and Medical Research Council\u2019s Australian Code of Practice for the Care and Use of Animals for Scientific Purposes (approval no: AEC 17-1-02).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics declarations"}},{"value":"The author(s) declare no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}