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3. Characterization of the chicken orthologues of mammalian CD154 and CD40

Author

Tregaskes, Clive

Subjects
636.50896079
Abstract

In mammals CD 154 (CD40 ligand, TNFSF5) and its cognate receptor CD40 (TNFRSF5) are essential for the generation of an adaptive immune response. To date very few members of either the TNF or TNF receptor superfamily have been identified in the chicken, and none of those that have share a high degree of homology with CD40 or CD 154. An EST derived from an activated chicken spleen cDNA library was identified as having a high homology to mammalian CD 154 sequences. A full-length cDNA containing this EST sequence was cloned, and used to generate a soluble form of the encoded protein. This soluble protein was to identify cells that expressed the receptor for this protein, and to clone a cDNA encoding this receptor. The protein was demonstrated to bind to chicken B cells and macrophages. The receptor to this putative chicken CD 154 protein shared a high degree of sequence homology to mammalian CD40 sequences. The sequence data alone was insufficient to identify these two proteins as orthologues of mammahan CD 154 and CCD40. The fusion protein was shown to have biological activity similar to its mammalian counterpart in three different bioassays, suggesting that these two proteins are functional and structural homologues of mammalian CD 154 and CD40.

Published
2007

4. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun

Abstract

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Published
2023

7. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, primary, Alfieri, James M., additional, Anthony, Nick, additional, Arensburger, Peter, additional, Athrey, Giridhar N., additional, Balacco, Jennifer, additional, Balic, Adam, additional, Bardou, Philippe, additional, Barela, Paul, additional, Bigot, Yves, additional, Blackmon, Heath, additional, Borodin, Pavel M., additional, Carroll, Rachel, additional, Casono, Meya C., additional, Charles, Mathieu, additional, Cheng, Hans, additional, Chiodi, Maddie, additional, Cigan, Lacey, additional, Coghill, Lyndon M., additional, Crooijmans, Richard, additional, Das, Neelabja, additional, Davey, Sean, additional, Davidian, Asya, additional, Degalez, Fabien, additional, Dekkers, Jack M., additional, Derks, Martijn, additional, Diack, Abigail B., additional, Djikeng, Appolinaire, additional, Drechsler, Yvonne, additional, Dyomin, Alexander, additional, Fedrigo, Olivier, additional, Fiddaman, Steven R., additional, Formenti, Giulio, additional, Frantz, Laurent A.F., additional, Fulton, Janet E., additional, Gaginskaya, Elena, additional, Galkina, Svetlana, additional, Gallardo, Rodrigo A., additional, Geibel, Johannes, additional, Gheyas, Almas, additional, Godinez, Cyrill John P., additional, Goodell, Ashton, additional, Graves, Jennifer A. M., additional, Griffin, Daren K., additional, Haase, Bettina, additional, Han, Jian-Lin, additional, Hanotte, Olivier, additional, Henderson, Lindsay J., additional, Hou, Zhuo-Cheng, additional, Howe, Kerstin, additional, Huynh, Lan, additional, Ilatsia, Evans, additional, Jarvis, Erich, additional, Johnson, Sarah M., additional, Kaufman, Jim, additional, Kelly, Terra, additional, Kemp, Steve, additional, Kern, Colin, additional, Keroack, Jacob H., additional, Klopp, Christophe, additional, Lagarrigue, Sandrine, additional, Lamont, Susan J., additional, Lange, Margaret, additional, Lanke, Anika, additional, Larkin, Denis M., additional, Larson, Greger, additional, Layos, John King N., additional, Lebrasseur, Ophélie, additional, Malinovskaya, Lyubov P., additional, Martin, Rebecca J., additional, Martin Cerezo, Maria Luisa, additional, Mason, Andrew S., additional, McCarthy, Fiona M., additional, McGrew, Michael J., additional, Mountcastle, Jacquelyn, additional, Muhonja, Christine Kamidi, additional, Muir, William, additional, Muret, Kévin, additional, Murphy, Terence, additional, Ng’ang’a, Ismael, additional, Nishibori, Masahide, additional, O’Connor, Rebecca E., additional, Ogugo, Moses, additional, Okimoto, Ron, additional, Ouko, Ochieng, additional, Patel, Hardip R., additional, Perini, Francesco, additional, Pigozzi, María Ines, additional, Potter, Krista C., additional, Price, Peter D., additional, Reimer, Christian, additional, Rice, Edward S., additional, Rocos, Nicolas, additional, Rogers, Thea F., additional, Saelao, Perot, additional, Schauer, Jens, additional, Schnabel, Robert, additional, Schneider, Valerie, additional, Simianer, Henner, additional, Smith, Adrian, additional, Stevens, Mark P., additional, Stiers, Kyle, additional, Tiambo, Christian Keambou, additional, Tixier-Boichard, Michele, additional, Torgasheva, Anna A., additional, Tracey, Alan, additional, Tregaskes, Clive A., additional, Vervelde, Lonneke, additional, Wang, Ying, additional, Warren, Wesley C., additional, Waters, Paul D., additional, Webb, David, additional, Weigend, Steffen, additional, Wolc, Anna, additional, Wright, Alison E., additional, Wright, Dominic, additional, Wu, Zhou, additional, Yamagata, Masahito, additional, Yang, Chentao, additional, Yin, Zhong-Tao, additional, Young, Michelle C., additional, Zhang, Guojie, additional, Zhao, Bingru, additional, and Zhou, Huaijun, additional

Published
2023
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11. RNA-seq raw reads of chicken hypothalamus and breast muscle

Author

Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun

Abstract

The objective of the study was to identify genes, gene networks, and signaling pathways associated with heat stress under Newcastle disease virus (NDV infection in the hypothalamus and the breast muscle of chickens by transcriptome profiling, using two highly genetically distinct inbred chicken lines (Leghorn and Fayoumi).

Published
2022

12. The Diverse Major Histocompatibility Complex Haplotypes of a Common Commercial Chicken Line and Their Effect on Marek’s Disease Virus Pathogenesis and Tumorigenesis

Author

Bertzbach, Luca D., primary, Tregaskes, Clive A., additional, Martin, Rebecca J., additional, Deumer, Undine-Sophie, additional, Huynh, Lan, additional, Kheimar, Ahmed M., additional, Conradie, Andelé M., additional, Trimpert, Jakob, additional, Kaufman, Jim, additional, and Kaufer, Benedikt B., additional

Published
2022
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13. The Diverse Major Histocompatibility Complex Haplotypes of a Common Commercial Chicken Line and Their Effect on Marek’s Disease Virus Pathogenesis and Tumorigenesis

Author

Bertzbach, Luca D, Tregaskes, Clive A, Martin, Rebecca J, Deumer, Undine-Sophie, Huynh, Lan, Kheimar, Ahmed M, Conradie, Andelé M, Trimpert, Jakob, Kaufman, Jim, Kaufer, Benedikt B, Bertzbach, Luca D [0000-0002-0698-5395], and Apollo - University of Cambridge Repository

Subjects
major histocompatibility complex (MHC), animal structures, Carcinogenesis, animal diseases, B9, B19, Immunology, VALO, susceptibility, Major Histocompatibility Complex, resistance, major histocompatibility complex (MHC, Haplotypes, Histocompatibility Antigens, Marek Disease, Immunology and Allergy, Animals, B15, B21, Chickens, Herpesvirus 2, Gallid, Disease Resistance, 600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft::632 Schäden, Krankheiten, Schädlinge an Pflanzen
Abstract

The major histocompatibility complex (MHC) is crucial for appropriate immune responses against invading pathogens. Chickens possess a single predominantly-expressed class I molecule with strong associations between disease resistance and MHC haplotype. For Marek's disease virus (MDV) infections of chickens, the MHC haplotype is one of the major determinants of genetic resistance and susceptibility. VALO specific pathogen free (SPF) chickens are widely used in biomedical research and vaccine production. While valuable findings originate from MDV infections of VALO SPF chickens, their MHC haplotypes and associated disease resistance remained elusive. In this study, we used several typing systems to show that VALO SPF chickens possess MHC haplotypes that include B9, B9:02, B15, B19 and B21 at various frequencies. Moreover, we associate the MHC haplotypes to MDV-induced disease and lymphoma formation and found that B15 homozygotes had the lowest tumor incidence while B21 homozygotes had the lowest number of organs with tumors. Finally, we found transmission at variable levels to all contact birds except B15/B21 heterozygotes. These data have immediate implications for the use of VALO SPF chickens and eggs in the life sciences and add another piece to the puzzle of the chicken MHC complex and its role in infections with this oncogenic herpesvirus.

Published
2022
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30. A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems

Author

Afrache, Hassnae, Tregaskes, Clive A., and Kaufman, Jim

Subjects
BF1, BF2, BLB2, BLB1, Nomenclature, databases and bioinformatics in Immunogenetics, BF-BL region, Review, Recombination, 3. Good health
Abstract

Among the genes with the highest allelic polymorphism and sequence diversity are those encoding the classical class I and class II molecules of the major histocompatibility complex (MHC). Although many thousands of MHC sequences have been deposited in general sequence databases like GenBank, the availability of curated MHC sequences with agreed nomenclature has been enormously beneficial. Along with the Immuno Polymorphism Database-IMunoGeneTics/human leukocyte antigen (IPD-IMGT/HLA) database, a collection of databases for curated sequences of immune importance has been developed. A recent addition is an IPD-MHC database for chickens. For many years, the nomenclature system for chicken MHC genes has been based on a list of standard, presumed to be stable, haplotypes. However, these standard haplotypes give different names to identical sequences. Moreover, the discovery of new recombinants between haplotypes and a rapid increase in newly discovered alleles leaves the old system untenable. In this review, a new nomenclature is considered, for which alleles of different loci are given names based on the system used for other MHCs, and then haplotypes are named according to the alleles present. The new nomenclature system is trialled, first with standard haplotypes and then with validated sequences from the scientific literature. In the trial, some class II B sequences were found in both class II loci, presumably by gene conversion or inversion, so that identical sequences would receive different names. This situation prompts further suggestions to the new nomenclature system. In summary, there has been progress, but also problems, with the new IPD-MHC system for chickens.

31. A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems

Author

Afrache, Hassnae, Tregaskes, Clive A, and Kaufman, Jim

Subjects
BF1, BF2, Polymorphism, Genetic, Databases, Factual, Recombination, 3. Good health, Major Histocompatibility Complex, BLB2, BLB1, BF-BL region, Terminology as Topic, Immunogenetics, Animals, Chickens
Abstract

Among the genes with the highest allelic polymorphism and sequence diversity are those encoding the classical class I and class II molecules of the major histocompatibility complex (MHC). Although many thousands of MHC sequences have been deposited in general sequence databases like GenBank, the availability of curated MHC sequences with agreed nomenclature has been enormously beneficial. Along with the Immuno Polymorphism Database-IMunoGeneTics/human leukocyte antigen (IPD-IMGT/HLA) database, a collection of databases for curated sequences of immune importance has been developed. A recent addition is an IPD-MHC database for chickens. For many years, the nomenclature system for chicken MHC genes has been based on a list of standard, presumed to be stable, haplotypes. However, these standard haplotypes give different names to identical sequences. Moreover, the discovery of new recombinants between haplotypes and a rapid increase in newly discovered alleles leaves the old system untenable. In this review, a new nomenclature is considered, for which alleles of different loci are given names based on the system used for other MHCs, and then haplotypes are named according to the alleles present. The new nomenclature system is trialled, first with standard haplotypes and then with validated sequences from the scientific literature. In the trial, some class II B sequences were found in both class II loci, presumably by gene conversion or inversion, so that identical sequences would receive different names. This situation prompts further suggestions to the new nomenclature system. In summary, there has been progress, but also problems, with the new IPD-MHC system for chickens.

32. A potential nomenclature for the Immuno Polymorphism Database (IPD) of chicken MHC genes: progress and problems

Author

Afrache, Hassnae, Tregaskes, Clive A., and Kaufman, Jim

Subjects
BF1, BF2, BLB2, BLB1, Nomenclature, databases and bioinformatics in Immunogenetics, BF-BL region, Review, Recombination, 3. Good health
Abstract

Among the genes with the highest allelic polymorphism and sequence diversity are those encoding the classical class I and class II molecules of the major histocompatibility complex (MHC). Although many thousands of MHC sequences have been deposited in general sequence databases like GenBank, the availability of curated MHC sequences with agreed nomenclature has been enormously beneficial. Along with the Immuno Polymorphism Database-IMunoGeneTics/human leukocyte antigen (IPD-IMGT/HLA) database, a collection of databases for curated sequences of immune importance has been developed. A recent addition is an IPD-MHC database for chickens. For many years, the nomenclature system for chicken MHC genes has been based on a list of standard, presumed to be stable, haplotypes. However, these standard haplotypes give different names to identical sequences. Moreover, the discovery of new recombinants between haplotypes and a rapid increase in newly discovered alleles leaves the old system untenable. In this review, a new nomenclature is considered, for which alleles of different loci are given names based on the system used for other MHCs, and then haplotypes are named according to the alleles present. The new nomenclature system is trialled, first with standard haplotypes and then with validated sequences from the scientific literature. In the trial, some class II B sequences were found in both class II loci, presumably by gene conversion or inversion, so that identical sequences would receive different names. This situation prompts further suggestions to the new nomenclature system. In summary, there has been progress, but also problems, with the new IPD-MHC system for chickens.

33. Conservation of biological properties of the CD40 ligand, CD154 in a non-mammalian vertebrate

Author

Tregaskes, Clive A., Glansbeek, Harrie L., Gill, Andrew C., Hunt, Lawrence G., Burnside, Joan, Young, John R., Tregaskes, Clive A., Glansbeek, Harrie L., Gill, Andrew C., Hunt, Lawrence G., Burnside, Joan, and Young, John R.

Abstract

Signals delivered by the CD40 ligand, CD154, have crucial roles in immune responses in mammals, being required for development of germinal centres, maturation of T-dependent antibody responses, and generation of B-cell memory. To determine whether these functions were conserved in a non-mammalian species, a putative chicken CD154 cDNA was used to make an oligomeric fusion protein, and to raise monoclonal antibodies. The antibodies detected surface expression on activated T-cells. The fusion protein detected expression of a receptor on B-cells, thrombocytes and macrophages. Biological effects of the fusion protein included induction of NO synthesis in a macrophage cell line, enhancement of splenic B-cell survival, and induction of apoptosis in a bursal lymphoma cell line. These observations demonstrated substantial functional equivalence with mammalian CD154 and thus provided evidence for the early evolutionary emergence of the set of functions associated with this molecule, and its central role in the vertebrate immune system.

35. Surface expression, peptide repertoire, and thermostability of chicken class I molecules correlate with peptide transporter specificity

Author

Lawrence G. Hunt, Olli Vainio, James C. Kaufman, Andy van Hateren, Michael Harrison, Clive A. Tregaskes, Anna K. Sowa, Tregaskes, Clive [0000-0002-5750-0853], Kaufman, Jim [0000-0002-7216-8422], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Heterozygote, Erythrocytes, Molecular Sequence Data, Peptide, permissive, Major histocompatibility complex, Epitope, Substrate Specificity, 03 medical and health sciences, Epitopes, overdominance, MHC class I, Animals, restrictive, Amino Acid Sequence, Peptide sequence, heterozygous advantage, chemistry.chemical_classification, Genetics, Multidisciplinary, biology, Beta-2 microglobulin, Protein Stability, Cell Membrane, Histocompatibility Antigens Class I, Homozygote, Temperature, Membrane Transport Proteins, Heterozygote advantage, Biological Transport, MHC restriction, Biological Sciences, Molecular biology, 3. Good health, 030104 developmental biology, chemistry, Haplotypes, biology.protein, ABC transporter, Peptides, beta 2-Microglobulin, Chickens
Abstract

The chicken major histocompatibility complex (MHC) has strong genetic associations with resistance and susceptibility to certain infectious pathogens. The cell surface expression level of MHC class I molecules varies as much as 10-fold between chicken haplotypes and is inversely correlated with diversity of peptide repertoire and with resistance to Marek's disease caused by an oncogenic herpesvirus. Here we show that the average thermostability of class I molecules isolated from cells also varies, being higher for high-expressing MHC haplotypes. However, we find roughly the same amount of class I protein synthesized by high- and low-expressing MHC haplotypes, with movement to the cell surface responsible for the difference in expression. Previous data show that chicken TAP genes have high allelic polymorphism, with peptide translocation specific for each MHC haplotype. Here we use assembly assays with peptide libraries to show that high-expressing B15 class I molecules can bind a much wider variety of peptides than are found on the cell surface, with the B15 TAPs restricting the peptides available. In contrast, the translocation specificity of TAPs from the low-expressing B21 haplotype is even more permissive than the promiscuous binding shown by the dominantly expressed class I molecule. B15/B21 heterozygote cells show much greater expression of B15 class I molecules than B15/B15 homozygote cells, presumably as a result of receiving additional peptides from the B21 TAPs. Thus, chicken MHC haplotypes vary in several correlated attributes, with the most obvious candidate linking all these properties being molecular interactions within the peptide-loading complex (PLC).

Published
2015

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