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The major components of the mucosal immune system are the gut-associated lymphoid tissues (GALT), comprising lymphoid aggregates ([[Peyer's Patches - Anatomy & Physiology|Peyer's patches]] in the jejunum and ileum), individual intra-epithelial lymphocytes (IELs) and the mesenteric lymph nodes.  These lymphoid structures are in close contact with specialised 'follicle-associated' epithelium, a tissue that contains microfold (M) cells capable of sampling antigens from the intestinal lumen.  Many other cell types, including neurones and the enterocytes themselves are able to contribute to immune responses through the production of cytokines and chemokines.  The B cells of the Peyers patches differentiate to produce antibodies of mainly the [[IgA]] isotype which is then transported into the intestinal lumen by a specific transporter.  This antibody is thought to control bacterial growth in the GI tract and also to help to maintain tolerance to benign antigens by complexing with them and reducing their local availability, a phenomenon called '''immune exclusion'''.

The major components of the mucosal immune system are the gut-associated lymphoid tissues (GALT), comprising lymphoid aggregates ([[Peyer's Patches - Anatomy & Physiology|Peyer's patches]] in the jejunum and ileum), individual intra-epithelial lymphocytes (IELs) and the mesenteric lymph nodes.  These lymphoid structures are in close contact with specialised 'follicle-associated' epithelium, a tissue that contains microfold (M) cells capable of sampling antigens from the intestinal lumen.  Many other cell types, including neurones and the enterocytes themselves are able to contribute to immune responses through the production of cytokines and chemokines.  The B cells of the Peyers patches differentiate to produce antibodies of mainly the [[IgA]] isotype which is then transported into the intestinal lumen by a specific transporter.  This antibody is thought to control bacterial growth in the GI tract and also to help to maintain tolerance to benign antigens by complexing with them and reducing their local availability, a phenomenon called '''immune exclusion'''.

The mucosal immune system of the host and the enteric bacterial flora interact constantly in the gastro-intestinal (GI) tract.  The host must remain tolerant of the enteric flora but must still be able to recognise and respond to potentially pathogenic organisms.  These apparently contradictory tasks are resolved by the ability of the immune system to [[Immune Tolerance - WikiBlood|'tolerate']] certain antigens if these are presented to macrophages and dendritic cells in an appropriate manner.  The major factors that enforce tolerance are immunosuppressive [[Cytokines - WikiBlood|cytokines]] (particularly interleukin 10 and transforming growth factor beta) and immunoregulatory clades of T lymphocytes, although the exact mechanisms by which tolerance is actually achieved are the subject of much research and debate.  '''Most of the recent theories regarding ARD suggest that it results from alterations in the interaction between the mucosal immune system and the enteric flora, particularly a loss of immune tolerance to commensal bacteria.'''

The mucosal immune system of the host and the enteric bacterial flora interact constantly in the gastro-intestinal (GI) tract.  The host must remain tolerant of the enteric flora but must still be able to recognise and respond to potentially pathogenic organisms.  These apparently contradictory tasks are resolved by the ability of the [[Immune Tolerance|immune system to 'tolerate']] certain antigens if these are presented to macrophages and dendritic cells in an appropriate manner.  The major factors that enforce tolerance are immunosuppressive [[Cytokines - WikiBlood|cytokines]] (particularly interleukin 10 and transforming growth factor beta) and immunoregulatory clades of T lymphocytes, although the exact mechanisms by which tolerance is actually achieved are the subject of much research and debate.  '''Most of the recent theories regarding ARD suggest that it results from alterations in the interaction between the mucosal immune system and the enteric flora, particularly a loss of [[Immune Tolerance|immune tolerance]] to commensal bacteria.'''

*When the serum antibody isotype concentrations were measured in different breeds of dog, normal German shepherd dogs were found to have lower serum concentrations of [[IgA]] than dogs of other breeds<ref>Batt RM, Barnes A, Rutgers HC, Carter SD. '''Relative IgA deficiency and small intestinal bacterial overgrowth in German shepherd dogs.''' ''Res Vet Sci. 1991 Jan;50(1):106-11.''</ref>.  It was suggested that this relative deficiency would prevent affected animals from controlling bacterial population size in the GI tract and lead to SIBO.  Another suggestion is that these animals would be less tolerant of the bacterial flora because the immune exclusion function of [[IgA]] would not be fulfilled.  Several efforts were then made to determine whether there was also a local intestinal deficiency in IgA in normal German shepherd dogs and measurement of faecal concentrations of the isotype produced conflicting results, with one study suggesting that its concentration was not significantly different from that of other breeds <ref>Peters IR, Calvert EL, Hall EJ, Day MJ. '''Measurement of immunoglobulin concentrations in the feces of healthy dogs.''' ''Clin Diagn Lab Immunol. 2004 Sep;11(5):841-8.''</ref> and another indicating that this was the case <ref>Littler RM, Batt RM, Lloyd DH. '''Total and relative deficiency of gut mucosal IgA in German shepherd dogs demonstrated by faecal analysis''' ''Vet Rec. 2006 Mar 11;158(10):334-41.''</ref>.  Since German shepherd dogs were found to have normal numbers of IgA positive plasma cells in the GALT<ref>German AJ, Hall EJ, Day MJ. '''Relative deficiency in IgA production by duodenal explants from German shepherd dogs with small intestinal disease.''' ''Vet Immunol Immunopathol. 2000 Aug 31;76(1-2):25-43.''</ref>, further work was directed at assessing whether the genes encoding the IgA transporter components are expressed correctly in this breed.  By measuring the levels of messenger RNA in intestinal biopsy samples, it was later shown that the transporter and its related genes are expressed normally <ref>Peters IR, Helps CR, Calvert EL, Hall EJ, Day MJ. '''Measurement of messenger RNA encoding the alpha-chain, polymeric immunoglobulin receptor, and J-chain in duodenal mucosa from dogs with and without chronic diarrhea by use of quantitative real-time reverse transcription-polymerase chain reaction assays.''' ''Am J Vet Res. 2005 Jan;66(1):11-6.''</ref>.  The degree to which relative IgA deficiency contributes to ARD in German shepherd dogs is currently unclear and this hypothesis contradicts the next, which suggests that a break in tolerance (partly manifesting as an increase in IgA production) underlies ARD.

*When the serum antibody isotype concentrations were measured in different breeds of dog, normal German shepherd dogs were found to have lower serum concentrations of [[IgA]] than dogs of other breeds<ref>Batt RM, Barnes A, Rutgers HC, Carter SD. '''Relative IgA deficiency and small intestinal bacterial overgrowth in German shepherd dogs.''' ''Res Vet Sci. 1991 Jan;50(1):106-11.''</ref>.  It was suggested that this relative deficiency would prevent affected animals from controlling bacterial population size in the GI tract and lead to SIBO.  Another suggestion is that these animals would be less tolerant of the bacterial flora because the immune exclusion function of [[IgA]] would not be fulfilled.  Several efforts were then made to determine whether there was also a local intestinal deficiency in IgA in normal German shepherd dogs and measurement of faecal concentrations of the isotype produced conflicting results, with one study suggesting that its concentration was not significantly different from that of other breeds <ref>Peters IR, Calvert EL, Hall EJ, Day MJ. '''Measurement of immunoglobulin concentrations in the feces of healthy dogs.''' ''Clin Diagn Lab Immunol. 2004 Sep;11(5):841-8.''</ref> and another indicating that this was the case <ref>Littler RM, Batt RM, Lloyd DH. '''Total and relative deficiency of gut mucosal IgA in German shepherd dogs demonstrated by faecal analysis''' ''Vet Rec. 2006 Mar 11;158(10):334-41.''</ref>.  Since German shepherd dogs were found to have normal numbers of IgA positive plasma cells in the GALT<ref>German AJ, Hall EJ, Day MJ. '''Relative deficiency in IgA production by duodenal explants from German shepherd dogs with small intestinal disease.''' ''Vet Immunol Immunopathol. 2000 Aug 31;76(1-2):25-43.''</ref>, further work was directed at assessing whether the genes encoding the IgA transporter components are expressed correctly in this breed.  By measuring the levels of messenger RNA in intestinal biopsy samples, it was later shown that the transporter and its related genes are expressed normally <ref>Peters IR, Helps CR, Calvert EL, Hall EJ, Day MJ. '''Measurement of messenger RNA encoding the alpha-chain, polymeric immunoglobulin receptor, and J-chain in duodenal mucosa from dogs with and without chronic diarrhea by use of quantitative real-time reverse transcription-polymerase chain reaction assays.''' ''Am J Vet Res. 2005 Jan;66(1):11-6.''</ref>.  The degree to which relative IgA deficiency contributes to ARD in German shepherd dogs is currently unclear and this hypothesis contradicts the next, which suggests that a break in tolerance (partly manifesting as an increase in IgA production) underlies ARD.