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Dar MA, Ahmad SM, Bhat BA, Dar TA, Haq ZU, Wani BA, Shabir N, Kashoo ZA, Shah RA, Ganai NA, Heidari M. Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry. Genomics 2022; 114:110475. [PMID: 36064074 DOI: 10.1016/j.ygeno.2022.110475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 07/07/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Salmonella, one of the major infectious diseases in poultry, causes considerable economic losses in terms of mortality and morbidity, especially in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line Kashmir faverolla, and commercial broiler were selected. RNA-seq was performed after challenging the chicken with Salmonella Typhimurium. Comparative differential expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The genes that were differentially expressed included interleukins, cytokines, NOS2, Avβ-defensins, toll-like receptors, and other immune-related gene families. Most of the genes and signaling pathways involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla. Pathway analysis revealed that most of the enriched pathways were MAPK signaling pathway, NOD-like receptor signaling pathway, TLR signaling pathway, PPAR signaling pathway, endocytosis, etc. Surprisingly some immune-related genes like TLRs were upregulated in the susceptible chicken breed. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and RNA sequencing results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla. Here we also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.
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Affiliation(s)
- Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India; Department of Clinical Biochemistry/Biochemistry, University of Kashmir, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India.
| | - Basharat A Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Tanveer Ali Dar
- Department of Clinical Biochemistry/Biochemistry, University of Kashmir, India
| | - Zulfqar Ul Haq
- Division of Livestock Poultry and Management, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Basharat A Wani
- Division of Veterinary Pathology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Zahid Amin Kashoo
- Division of Veterinary Microbiology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | | | - Mohammad Heidari
- USDA, Agricultural Research Service, Avian Disease and Oncology Laboratory, 4279 E. Mount Hope Rd., East Lansing, MI 48823, USA
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Drauch V, Mitra T, Liebhart D, Hess M, Hess C. Infection dynamics of Salmonella Infantis vary considerably between chicken lines. Avian Pathol 2022; 51:561-573. [PMID: 35938538 DOI: 10.1080/03079457.2022.2108373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractSalmonella (S.) Infantis is the most common serovar in broilers and broiler meat in the European Union. In the field, fast-growing broilers are reported to be more affected than slow-growing and layer birds. The present study investigated the infection dynamics and immunological response of four chicken lines in the course of a S. Infantis infection. Two commercial chicken lines, Ross 308 and Hubbard ISA-JA-757, and two experimentally chicken lines, specific pathogen free (SPF) layers and broilers, were infected at 2 days of age. Investigations focused on faecal shedding, bacterial colonisation, humoral and cellular immune response in the blood. Ross and SPF broilers were mainly attributed as high shedders followed by Hubbard. SPF layers showed the least shedding. This is in agreement with the caecal colonisation, SPF layers harboured significant less bacteria. Systemic spread of S. Infantis to liver and spleen was highest in Ross being statistically significant at 7 days of age compared to the other lines. Spread of infection to in-contact birds, was noticed 5 days post infection in every line. Antibody response occurred in every chicken line from day 21 of age onwards. In contrast to the other chicken lines, significant differences in T cell subsets and monocytes/macrophages were found between infected and negative Hubbard birds at 7 days of age. Uninfected SPF birds had significant higher immune cell counts (T cell subsets, B cells and monocytes /macrophages) compared to uninfected commercial birds, a fact important for future experimental settings. The results illustrate that the infection dynamics of S. Infantis is influenced by the chicken line resulting in a higher risk of transmission to humans from fast-growing broilers.
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Affiliation(s)
- V Drauch
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - T Mitra
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - D Liebhart
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - M Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - C Hess
- Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
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Kaiser MG, Hsieh J, Kaiser P, Lamont SJ. Differential immunological response detected in mRNA expression profiles among diverse chicken lines in response to Salmonella challenge. Poult Sci 2022; 101:101605. [PMID: 34936953 PMCID: PMC8703071 DOI: 10.1016/j.psj.2021.101605] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/13/2021] [Indexed: 10/28/2022] Open
Abstract
Salmonella enterica serovar Enteritidis is a bacterial pathogen that contributes to poultry production losses and human foodborne illness. The bacterium elicits a broad immune response involving both the innate and adaptive components of the immune system. Coordination of the immune response is largely directed by cytokines. The objective of the current study was to characterize the expression of a select set of cytokines and regulatory immune genes in three genetically diverse chicken lines after infection with S. Enteritidis. Leghorn, Fayoumi and broiler day-old chicks were orally infected with pathogenic S. Enteritidis or culture medium. At 2 and 18 h postinfection, spleens and ceca were collected and mRNA expression levels for 7 genes (GM-CSF, IL2, IL15, TGF-β1, SOCS3, P20K, and MHC class IIβ) were evaluated by real-time quantitative PCR. Genetic line had a significant effect on mRNA expression levels of IL15, TGF-β1, SOCS3 and P20K in the spleen and on P20K and MHC class IIβ in the cecum. Comparing challenged vs. unchallenged birds, the expression of SOCS3 and P20K mRNA were significantly higher in the spleen and cecum, while MHC class IIβ mRNA was significantly lower in spleen. Combining the current RNA expression results with those of previously reported studies on the same samples reveals distinct RNA expression profiles among the three genetic chicken lines and the 2 tissues. This study illustrates that these diverse genetic lines have distinctively different immune response to S. Enteritidis challenge within the spleen and the cecum.
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Affiliation(s)
- Michael G Kaiser
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - John Hsieh
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - Pete Kaiser
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG, United Kingdom
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA.
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4
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Monson MS, Bearson BL, Sylte MJ, Looft T, Lamont SJ, Bearson SMD. Transcriptional response of blood leukocytes from turkeys challenged with Salmonella enterica serovar Typhimurium UK1. Vet Immunol Immunopathol 2020; 232:110181. [PMID: 33401108 DOI: 10.1016/j.vetimm.2020.110181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 12/25/2022]
Abstract
Non-typhoidal Salmonella is one of the most common causes of bacterial foodborne disease and consumption of contaminated poultry products, including turkey, is one source of exposure. Minimizing Salmonella colonization of commercial turkeys could decrease the incidence of Salmonella-associated human foodborne illness. Understanding host responses to these bacteria is critical in developing strategies to minimize colonization and reduce food safety risk. In this study, we evaluated bacterial load and blood leukocyte transcriptomic responses of 3-week-old turkeys challenged with the Salmonella enterica serovar Typhimurium (S. Typhimurium) UK1 strain. Turkeys (n = 8/dose) were inoculated by oral gavage with 108 or 1010 colony forming units (CFU) of S. Typhimurium UK1, and fecal shedding and tissue colonization were measured across multiple days post-inoculation (dpi). Fecal shedding was 1-2 log10 higher in the 1010 CFU group than the 108 CFU group, but both doses effectively colonized the crop, spleen, ileum, cecum, colon, bursa of Fabricius and cloaca without causing any detectable clinical signs in either group of birds. Blood leukocytes were isolated from a subset of the birds (n = 3-4/dpi) both pre-inoculation (0 dpi) and 2 dpi with 1010 CFU and their transcriptomic responses assayed by RNA-sequencing (RNA-seq). At 2 dpi, 647 genes had significant differential expression (DE), including large increases in expression of immune genes such as CCAH221, IL4I1, LYZ, IL13RA2, IL22RA2, and ACOD1. IL1β was predicted as a major regulator of DE in the leukocytes, which was predicted to activate cell migration, phagocytosis and proliferation, and to impact the STAT3 and toll-like receptor pathways. These analyses revealed genes and pathways by which turkey blood leukocytes responded to the pathogen and can provide potential targets for developing intervention strategies or diagnostic assays to mitigate S. Typhimurium colonization in turkeys.
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Affiliation(s)
- Melissa S Monson
- Iowa State University, Department of Animal Science, Ames, IA, United States
| | - Bradley L Bearson
- USDA, ARS, National Laboratory for Agriculture and the Environment, Ames, IA, United States
| | - Matthew J Sylte
- USDA, ARS, National Animal Disease Center, Ames, IA, United States
| | - Torey Looft
- USDA, ARS, National Animal Disease Center, Ames, IA, United States
| | - Susan J Lamont
- Iowa State University, Department of Animal Science, Ames, IA, United States
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5
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Wang F, Zhang J, Zhu B, Wang J, Wang Q, Zheng M, Wen J, Li Q, Zhao G. Transcriptome Analysis of the Cecal Tonsil of Jingxing Yellow Chickens Revealed the Mechanism of Differential Resistance to Salmonella. Genes (Basel) 2019; 10:genes10120979. [PMID: 31795199 PMCID: PMC6947646 DOI: 10.3390/genes10120979] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/21/2019] [Accepted: 11/26/2019] [Indexed: 11/16/2022] Open
Abstract
Salmonella is one of the most common food-borne pathogens. It can be transmitted between chickens, as well as to people by contaminated poultry products. In our study, we distinguished chickens with different resistances mainly based on bacterial loads. We compared the cecal tonsil transcriptomes between the susceptible and resistant chickens after Salmonella infection, aiming to identify the crucial genes participating in the antibacterial activity in the cecal tonsil. A total of 3214 differentially expressed genes (DEGs), including 2092 upregulated and 1122 downregulated genes, were identified between the two groups (fold change ≥ 2.0, padj < 0.05). Many DEGs were mainly involved in the regulation of two biological processes: crosstalk between the cecal tonsil epithelium and pathogenic bacteria, such as focal adhesion, extracellular-matrix-receptor interaction, and regulation of the actin cytoskeleton and host immune response including the cytokine-receptor interaction. In particular, the challenged resistant birds exhibited strong activation of the intestinal immune network for IgA production, which perhaps contributed to the resistance to Salmonella infection. These findings give insight into the mRNA profile of the cecal tonsil between the two groups after initial Salmonella stimulation, which may extend the known complexity of molecular mechanisms in chicken immune response to Salmonella.
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Affiliation(s)
- Fei Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Jin Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Jie Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Qiao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
- State Key Laboratory of Animal Nutrition, Beijing 100193, China
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (F.W.); (J.Z.); (B.Z.); (J.W.); (Q.W.); (M.Z.); (J.W.)
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
- Correspondence:
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6
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Li P, Fan W, Everaert N, Liu R, Li Q, Zheng M, Cui H, Zhao G, Wen J. Messenger RNA Sequencing and Pathway Analysis Provide Novel Insights Into the Susceptibility to Salmonella enteritidis Infection in Chickens. Front Genet 2018; 9:256. [PMID: 30061915 PMCID: PMC6055056 DOI: 10.3389/fgene.2018.00256] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022] Open
Abstract
Salmonella enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Controlling poultry SE infection will have great practical significance for human public health, as poultry are considered to be important sources and carriers of the disease. In this study, the splenic transcriptomes of challenged-susceptible (S), challenged-resistant (R) and non-challenged (C) chicks (3-days old, specific-pathogen-free White Leghorn) were characterized in order to identify the immune-related gene markers and pathways. A total of 934 significant differentially expressed genes (DEGs) were identified in comparisons among the C, R and S birds. First reported here, the DEGs involved in the Forkhead box O (FoxO) signaling pathway, especially FoxO3, were identified as potential markers for host resistance to SE infection. The challenged-susceptible birds exhibited strong activation of the FoxO signaling pathway, which may be a major defect causing immune cell apoptosis as part of SE-induced pathology; these S birds also showed weak activation of mitogen-activated protein kinase (MAPK)-related genes, contrasting with strong splenic activation in the R birds. Interestingly, suppression of several pathways in the immune response against Salmonella, including cytokine-cytokine receptor interaction and Jak-STAT, was only found in S birds and there was evidence of cross-talk among these pathways, perhaps contributing to susceptibility to Salmonella infection. These findings will help facilitate understanding resistance and susceptibility to SE infection in the earliest phases of the host immune response through Salmonella-induced pathways, provide new approaches to develop strategies for SE prevention and treatment, and may enhance innate resistance by genetic selection in animals.
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Affiliation(s)
- Peng Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Wenlei Fan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
| | - Nadia Everaert
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Ranran Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qinghe Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maiqing Zheng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huanxian Cui
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guiping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Wen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,State Key Laboratory of Animal Nutrition, Beijing, China
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Tohidi R, Javanmard A, Idris I. Immunogenetics applied to control salmonellosis in chicken: a review. JOURNAL OF APPLIED ANIMAL RESEARCH 2018. [DOI: 10.1080/09712119.2017.1301256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Reza Tohidi
- Department of Animal Science, Torbat-e Jam University of Agriculture, Torbat-e Jam, Iran
| | - Arash Javanmard
- Department of Animal Science, University of Tabriz, Tabriz, Iran
| | - Ismail Idris
- Department of Animal Science, Universiti Putra Malaysia, Serdang, Malaysia
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8
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The immune-genes regulation mediated mechanisms of probiotics to control salmonella infection in chicken. WORLD POULTRY SCI J 2017. [DOI: 10.1017/s0043933917000265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Hu Y, Chen WW, Liu HX, Shan YJ, Zhu CH, Li HF, Zou JM. Genetic differences in ChTLR15 gene polymorphism and expression involved in Salmonella enterica natural and artificial infection respectively, of Chinese native chicken breeds, with a focus on sexual dimorphism. Avian Pathol 2017; 45:13-25. [PMID: 26488442 DOI: 10.1080/03079457.2015.1110849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chicken Toll-like receptor 15 (ChTLR15) has been shown to participate in immune activation in response to various pathogens and in the innate defence against infection. Two genetically distinct Chinese breeds of chicken (Qinyuan Partridge and Baier breeds) were used to study the correlation between ChTLR15 single nucleotide polymorphisms and the natural infection status of salmonella in hens, and also to examine genetic and sex-specific effects on ChTLR15 mRNA expression in heterophils and spleen during acute infection with Salmonella enterica serovar Enteritidis (SE) from 1 to 10 days after experimental infection. Three single-nucleotide polymorphisms (G168A, C726T and A1166G) in a single exon of ChTLR15 were identified in the two breeds, but only C726T showed a significant association with salmonella infection. Compared with layer-type Baier chicks, meat-type Qingyuan chicks showed a higher tolerance for capture stress and (SE) infection, as measured, respectively, by the modified body weight of chicks in the control group and in the infection group. Meanwhile, ChTLR15 down-regulation in heterophils and up-regulation in spleen were involved in the response to pathogenic SE colonization during the acute infection period. These significant genetic effects in females led to greater differences in both innate and adaptive immune responses than those exhibited in males. These results suggest that genetics, time and gender play important roles in the modulation of ChTLR15 mRNA level elicited by the SE-mediated immune response differentially in the two genetically distinct breeds, with a focus on sexual dimorphism.
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Affiliation(s)
- Y Hu
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , Jiangsu 225003 , P.R. China.,b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu 225009 , P.R. China
| | - W W Chen
- c Luoyang Pu-like Bio-engineering Co., Ltd , Luoyang , Henan 471000 , P.R. China
| | - H X Liu
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , Jiangsu 225003 , P.R. China
| | - Y J Shan
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , Jiangsu 225003 , P.R. China
| | - C H Zhu
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , Jiangsu 225003 , P.R. China
| | - H F Li
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , Jiangsu 225003 , P.R. China
| | - J M Zou
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , Jiangsu 225003 , P.R. China.,b Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses , Yangzhou , Jiangsu 225009 , P.R. China
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Hu Y, Shan YJ, Zhu CH, Song WT, Xu WJ, Zhu WQ, Zhang SJ, Li HF. Upregulation of NRAMP1 mRNA confirms its role in enhanced host immunity in post-artificial infections of Salmonella enteritidis in chicks. Br Poult Sci 2016; 56:408-15. [PMID: 26181686 DOI: 10.1080/00071668.2015.1052371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
1. Salmonella enteritidis (SE) is reported as the most common food-borne pathogen transmitted through poultry products. The natural resistance-associated macrophage protein 1 (NRAMP1) is a candidate gene associated with SE-mediated immune response and is related to the phagocytosis of SE. In this study, the classical single-nucleotide polymorphism (SNP) G2357A in exon 8 of the NRAMP1 gene was detected. The expression of NRAMP1 mRNA was first investigated in heterophil granulocytes and spleen in chicks from two different Chinese native breeds at 1, 3 and 10 d post-infection. In addition, the association with the effect of SE challenge was identified. 2. The G2357A SNP showed no significant association with Salmonella natural infection in birds from two different Chinese native breeds. 3. The upregulation of NRAMP1 mRNA in heterophils and spleen was involved in the response to pathogenic SE colonisation during the acute infection period in chicks. The results suggest that genetics, age, gender and interactions among these factors play important roles in the modulation of NRAMP1 mRNA expression and copy number by SE-mediated immune response in different Chinese chickens. 4. In conclusion, the enhancement of host immunity mediated by the upregulation of NRAMP1 mRNA in heterophil granulocytes and spleen might be more obvious and earlier in the chicks resistant to infections with SE than in susceptible chicks.
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Affiliation(s)
- Y Hu
- a Jiangsu Provincial Key Laboratory of Poultry Genetics & Breeding , Institute of Poultry Science of Jiangsu Province , Yangzhou , China
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11
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Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont SJ, Hu S, Zhou H, Li N. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics 2015; 16:851. [PMID: 26497311 PMCID: PMC4619007 DOI: 10.1186/s12864-015-2098-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/15/2015] [Indexed: 12/30/2022] Open
Abstract
Background DNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals. Avian species hold a crucial position in evolutionary history. In this study, we used whole-genome bisulfite sequencing (MethylC-seq) to generate single base methylation profiles of lungs in two genetically distinct and highly inbred chicken lines (Fayoumi and Leghorn) that differ in genetic resistance to multiple pathogens, and we explored the potential regulatory role of DNA methylation associated with immune response differences between the two chicken lines. Methods The MethylC-seq was used to generate single base DNA methylation profiles of Fayoumi and Leghorn birds. In addition, transcriptome profiling using RNA–seq from the same chickens and tissues were obtained to interrogate how DNA methylation regulates gene transcription on a genome-wide scale. Results The general DNA methylation pattern across different regions of genes was conserved compared to other species except for hyper-methylation of repeat elements, which was not observed in chicken. The methylation level of miRNA and pseudogene promoters was high, which indicates that silencing of these genes may be partially due to promoter hyper-methylation. Interestingly, the promoter regions of more recently evolved genes tended to be more highly methylated, whereas the gene body regions of evolutionarily conserved genes were more highly methylated than those of more recently evolved genes. Immune-related GO (Gene Ontology) terms were significantly enriched from genes within the differentially methylated regions (DMR) between Fayoumi and Leghorn, which implicates DNA methylation as one of the regulatory mechanisms modulating immune response differences between these lines. Conclusions This study establishes a single-base resolution DNA methylation profile of chicken lung and suggests a regulatory role of DNA methylation in controlling gene expression and maintaining genome transcription stability. Furthermore, profiling the DNA methylomes of two genetic lines that differ in disease resistance provides a unique opportunity to investigate the potential role of DNA methylation in host disease resistance. Our study provides a foundation for future studies on epigenetic modulation of host immune response to pathogens in chickens. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2098-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinxiu Li
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rujiao Li
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Xiaoxiang Hu
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yiqiang Zhao
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Li Li
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chungang Feng
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaorong Gu
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China
| | - Fang Liang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA. .,Department of Poultry Science, Texas A&M University, College Station, TX, 77845, USA.
| | - Ning Li
- The State Key Laboratory for Agro-biotechnology, China Agricultural University, Beijing, 100193, China. .,National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China. .,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
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12
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Susceptibility to Salmonella carrier-state: a possible Th2 response in susceptible chicks. Vet Immunol Immunopathol 2014; 159:16-28. [PMID: 24694400 DOI: 10.1016/j.vetimm.2014.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 01/13/2014] [Accepted: 03/02/2014] [Indexed: 11/23/2022]
Abstract
Infection of chicken with Salmonella may lead to a carrier-state characterized by the persistence of bacteria in the ceca for a long period of time and result in their excretion in feces. This excretion is the source of contamination of their congeners and food. During infection, enterocytes are the primary target cells for Salmonella, the producers of soluble factors which launch immune response and cells which are reciprocally responsive to surrounding immune cells. This study used microarrays to compare the gene expression profile during carrier-state of enterocytes purified from infected and control chicks which are either resistant or susceptible to Salmonella Enteritidis carrier-state. In total, we identified 271 genes significantly differentially expressed with an absolute fold change greater than 1.5. A global analysis determined interaction networks between differentially regulated genes. Using an a priori approach, our analyses focused on differentially expressed genes which were transcriptionally linked to cytokines playing a major role in the fate of the immune response. The expression of genes transcriptionally linked to type I interferon and TGF-β was down-regulated in infected chicks from both lines. Gene expression linked to the Th1 axis suggests the latter is inhibited in both lines. Finally, the expression of genes linked to IL-4, IL-5 and IL-13 indicates that susceptibility to carrier-state could be associated with a Th2 bias. Overall, these results highlight that the response to Salmonella during the acute phase and carrier-state is different and that enterocytes play a central role in this response.
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13
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Genetic differ in TLR4 gene polymorphisms and expression involved in Salmonella natural and artificial infection respectively in Chinese native chicken breeds. Mol Biol Rep 2013; 40:5005-12. [PMID: 23666058 DOI: 10.1007/s11033-013-2601-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 04/29/2013] [Indexed: 10/26/2022]
Abstract
Salmonella enteritidis (SE) is a foodborne pathogen that negatively affects both animal and human health. Genetic variations in response to pathogenic SE colonization or to SE vaccination were measured in chicken resource populations. Toll-like receptor 4 (TLR4) is part of a group of evolutionarily conserved pattern recognition receptors involved in the activation of the immune system in response to various pathogens and in the innate defense against infection. In this study, TLR4 was investigated the association of TLR4 gene polymorphisms with Salmonella natural infection situation of birds from two distinct Chinese genetic breeds. One SNP G1894C in the second intron of chicken TLR4 (chTLR4) was scanned in the two hens breed, which showed significant association with Salmonella natural infection situation (P<0.05). Genetic variations in response to pathogenic SE colonization also existed in distinct Chinese chicken resource population. In this study, mRNA expression of TLR4 was detected to investigate the association with the effect of artificial SE challenge in heterophil granulocytes and spleen of chicks from two distinct Chinese genetic breeds at 1, 3 and 10 day post-infection during the acute infection period. It clearly showed that young chicks' response to SE infection was regulated by TLR4 mRNA expression. The results suggest that genetics, time, gender, and interactions among these factors, play important roles in TLR4 mRNA basic values and copies modulation of SE mediated immune response in distinct Chinese chickens.
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14
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A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue. J Theor Biol 2013; 330:75-87. [PMID: 23603730 DOI: 10.1016/j.jtbi.2013.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 04/05/2013] [Accepted: 04/09/2013] [Indexed: 12/28/2022]
Abstract
The aim of this study was to create a dynamic mathematical model of the development of the cellular branch of the intestinal immune system of poultry during the first 42 days of life and of its response towards an oral infection with Salmonella enterica serovar Enteritidis. The system elements were grouped in five important classes consisting of intra- and extracellular S. Enteritidis bacteria, macrophages, CD4+, and CD8+ cells. Twelve model variables were described by ordinary differential equations, including 50 parameters. Parameter values were estimated from literature or from own immunohistochemistry data. The model described the immune development in non-infected birds with an average R² of 0.87. The model showed less accuracy in reproducing the immune response to S. Enteritidis infection, with an average R² of 0.51, although model response did follow observed trends in time. Evaluation of the model against independent data derived from several infection trials showed strong/significant deviations from observed values. Nevertheless, it was shown that the model could be used to simulate the effect of varying input parameters on system elements response, such as the number of immune cells at hatch. Model simulations allowed one to study the sensitivity of the model outcome for varying model inputs. The initial number of immune cells at hatch was shown to have a profound impact on the predicted development in the number of systemic S. Enteritidis bacteria after infection. The theoretical contribution of this work is the identification of responses in system elements of the developing intestinal immune system of poultry obtaining a mathematical representation which allows one to explore the relationships between these elements under contrasting environmental conditions during different stages of intestinal development.
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15
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Cheng HH, Kaiser P, Lamont SJ. Integrated Genomic Approaches to Enhance Genetic Resistance in Chickens. Annu Rev Anim Biosci 2013; 1:239-60. [DOI: 10.1146/annurev-animal-031412-103701] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hans H. Cheng
- Avian Disease and Oncology Laboratory, USDA, ARS, East Lansing, Michigan 48823;
| | - Pete Kaiser
- The Roslin Institute & Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom;
| | - Susan J. Lamont
- Department of Animal Science, Iowa State University, Ames, Iowa 50011;
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16
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Coble DJ, Sandford EE, Ji T, Abernathy J, Fleming D, Zhou H, Lamont SJ. Impacts ofSalmonella enteritidisinfection on liver transcriptome in broilers. Genesis 2012; 51:357-64. [DOI: 10.1002/dvg.22351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - Tieming Ji
- Department of Statistics; Iowa State University; Ames; Iowa
| | - Jason Abernathy
- Department of Animal Science; University of California Davis; Davis; California
| | | | - Huaijun Zhou
- Department of Animal Science; University of California Davis; Davis; California
| | - Susan J. Lamont
- Department of Animal Science; Iowa State University; Ames; Iowa
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17
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Bottje WG, Kong BW, Song JJ, Lee JY, Hargis BM, Lassiter K, Wing T, Hardiman J. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K microarray. II. Differentially expressed focus genes. Poult Sci 2012; 91:2576-87. [PMID: 22991544 DOI: 10.3382/ps.2012-02204] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated using microarray analysis. Microarray procedures and validation were reported previously. By using an overlay function of a software program (Ingenuity Pathway Analysis, IPA) in which canonical pathways are projected onto a set of genes, a subset of 27 differentially expressed focus genes were identified. Focus genes that were upregulated in the high FE phenotype were associated with important signal transduction pathways (Jnk, G-coupled, and retinoic acid) or in sensing cell energy status and stimulating energy production that would likely enhance growth and development of muscle tissue. In contrast, focus genes that were upregulated in the low FE muscle phenotype were associated with cytoskeletal architecture (e.g., actin-myosin filaments), fatty acid oxidation, growth factors, or ones that would likely be induced in response to oxidative stress. The results of this study provide additional information on gene expression and the cellular basis of feed efficiency in broilers.
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Affiliation(s)
- W G Bottje
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA.
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18
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Schokker D, Peters THF, Hoekman AJW, Rebel JMJ, Smits MA. Differences in the early response of hatchlings of different chicken breeding lines to Salmonella enterica serovar Enteritidis infection. Poult Sci 2012; 91:346-53. [PMID: 22252347 DOI: 10.3382/ps.2011-01758] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Poultry products are the major source of food-borne Salmonella infection in humans. Broiler lines selected to be more resistant to Salmonella could reduce the transfer of Salmonella to humans. To investigate differences in the susceptibility of newly hatched chicks to oral infection with Salmonella enterica serovar Enteritidis, 3 commercial broiler lines (A, B, and C) were infected immediately after hatch and compared to healthy controls at 0.33, 1, and 2 d postinfection. Weight, bacteriological examination, and the jejunal influx of CD4, CD8, TCRαβ, TCRγδ, and KUL01 (macrophages and dendritic cells) cells that are positive was investigated. In addition, the jejunal transcriptional response was analyzed using whole-genome chicken cDNA arrays. Salmonella colony-forming unit counts from cecal content and liver revealed that Salmonella enterica entered the body at 0.33 d postinfection. Broiler line A appeared most susceptible to intestinal colonization and the systemic spread of Salmonella. In addition, the Salmonella-induced jejunal influx of macrophages in this line showed a clear increase in time, which is in contrast to lines B and C. On the other hand, all lines showed a peak of CD4(+) cells at 1 d postinfection when infected chicks were compared to control chicks. The transcriptional response of line A clearly differed from the responses in lines B and C. Functional analysis indicated that the majority of the differentially expressed genes at 0.33 d postinfection in line A were involved in cell-cycle functions, whereas at 2 d postinfection the majority of the differentially expressed genes could be assigned to inflammatory disorder, differentiation and proliferation of (T) lymphocytes. These data indicate that hatchlings of different broiler lines differ in their systemic spread of Salmonella and suggest that intestinal barrier functions, as well as immunological responses, may be the underlying factors. We hypothesize that the differences between genetic chicken lines divergent in their response to Salmonella infection at a young age include developmental differences of the gut.
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Affiliation(s)
- D Schokker
- Wageningen UR Livestock Research, Animal Breeding and Genomics Centre, Wageningen, the Netherlands.
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19
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Sandford EE, Orr M, Shelby M, Li X, Zhou H, Johnson TJ, Kariyawasam S, Liu P, Nolan LK, Lamont SJ. Leukocyte transcriptome from chickens infected with avian pathogenic Escherichia coli identifies pathways associated with resistance. RESULTS IN IMMUNOLOGY 2012; 2:44-53. [PMID: 24371566 DOI: 10.1016/j.rinim.2012.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 02/17/2012] [Accepted: 02/21/2012] [Indexed: 12/13/2022]
Abstract
Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which is responsible for morbidity and mortality in chickens. Gene expression patterns have previously been demonstrated to differ between chicken populations that are resistant vs. susceptible to bacterial infection, but little is currently known about gene expression response to APEC. Increased understanding of gene expression patterns associated with resistance will facilitate genetic selection to increase resistance to APEC. Male broiler chicks were vaccinated at 2 weeks of age and challenged with APEC at 4 weeks of age. Peripheral blood leukocytes were collected at 1 and 5 day post-infection. Lesions on the liver, pericardium, and air sacs were used to assign a mild or severe pathology status to non-vaccinated, challenged chicks. Ten treatment groups were therefore generated with a priori factors of vaccination, challenge, day post-infection, and the a posteriori factor of pathology status. Global transcriptomic response was evaluated using the Agilent 44K chicken microarray. APEC infection resulted in more up-regulation than down-regulation of differentially expressed genes. Immune response and metabolic processes were enriched with differentially expressed genes. Although vaccination significantly reduced lesions in challenged bird, there was no detectable effect of vaccination on gene expression. This study investigated the transcriptomic differences in host responses associated with mild vs. severe pathology, in addition to the effects of vaccination and challenge, thus revealing genes and networks associated with response to APEC and providing a foundation for future studies on, and genetic selection for, genetic resistance to APEC.
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Affiliation(s)
- Erin E Sandford
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Megan Orr
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Mandy Shelby
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Xianyao Li
- Department of Poultry Science, Texas A&M University, College Station, TX 77843, USA
| | - Huaijun Zhou
- Department of Poultry Science, Texas A&M University, College Station, TX 77843, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Subhashinie Kariyawasam
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16082, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Lisa K Nolan
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
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20
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Kong BW, Song JJ, Lee JY, Hargis BM, Wing T, Lassiter K, Bottje W. Gene expression in breast muscle associated with feed efficiency in a single male broiler line using a chicken 44K oligo microarray. I. Top differentially expressed genes. Poult Sci 2011; 90:2535-47. [PMID: 22010239 DOI: 10.3382/ps.2011-01435] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated. Pooled RNA samples (n = 6/phenotype) labeled with cyanine 3 or cyanine 5 fluorescent dyes to generate cRNA probes were hybridized on a 4 × 44K chicken oligo microarray. Local polynomial regression normalization was applied to background-corrected red and green intensities with a moderated t-statistic. Corresponding P-values were computed and adjusted for multiple testing by false discovery rate to identify differentially expressed genes. Microarray validation was carried out by comparing findings with quantitative reverse-transcription PCR. A 1.3-fold difference in gene expression was set as a cutoff value, which encompassed 20% (782 of 4,011) of the total number of genes that were differentially expressed between FE phenotypes. Using an online software program (Ingenuity Pathway Analysis), the top 10 upregulated genes identified by Ingenuity Pathway Analysis in the high-FE group were generally associated with anabolic processes. In contrast, 7 of the top 10 downregulated genes in the high-FE phenotype (upregulated in the low-FE phenotype) were associated with muscle fiber development, muscle function, and cytoskeletal organization, with the remaining 3 genes associated with self-recognition or stress-responding genes. The results from this study focusing on only the top differentially expressed genes suggest that the high-FE broiler phenotype is derived from the upregulation of genes associated with anabolic processes as well as a downregulation of genes associated with muscle fiber development, muscle function, cytoskeletal organization, and stress response.
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Affiliation(s)
- B-W Kong
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, USA
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21
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Sandford EE, Orr M, Balfanz E, Bowerman N, Li X, Zhou H, Johnson TJ, Kariyawasam S, Liu P, Nolan LK, Lamont SJ. Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. BMC Genomics 2011; 12:469. [PMID: 21951686 PMCID: PMC3190404 DOI: 10.1186/1471-2164-12-469] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 09/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Avian pathogenic Escherichia coli (APEC) is detrimental to poultry health and its zoonotic potential is a food safety concern. Regulation of antimicrobials in food-production animals has put greater focus on enhancing host resistance to bacterial infections through genetics. To better define effective mechanism of host resistance, global gene expression in the spleen of chickens, harvested at two times post-infection (PI) with APEC, was measured using microarray technology, in a design that will enable investigation of effects of vaccination, challenge, and pathology level. Results There were 1,101 genes significantly differentially expressed between severely infected and non-infected groups on day 1 PI and 1,723 on day 5 PI. Very little difference was seen between mildly infected and non-infected groups on either time point. Between birds exhibiting mild and severe pathology, there were 2 significantly differentially expressed genes on day 1 PI and 799 on day 5 PI. Groups with greater pathology had more genes with increased expression than decreased expression levels. Several predominate immune pathways, Toll-like receptor, Jak-STAT, and cytokine signaling, were represented between challenged and non-challenged groups. Vaccination had, surprisingly, no detectible effect on gene expression, although it significantly protected the birds from observable gross lesions. Functional characterization of significantly expressed genes revealed unique gene ontology classifications during each time point, with many unique to a particular treatment or class contrast. Conclusions More severe pathology caused by APEC infection was associated with a high level of gene expression differences and increase in gene expression levels. Many of the significantly differentially expressed genes were unique to a particular treatment, pathology level or time point. The present study not only investigates the transcriptomic regulations of APEC infection, but also the degree of pathology associated with that infection. This study will allow for greater discovery into host mechanisms for disease resistance, providing targets for marker assisted selection and advanced drug development.
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Affiliation(s)
- Erin E Sandford
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
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22
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Shift in chicken intestinal gene association networks after infection with Salmonella. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2011; 6:339-47. [PMID: 21885356 DOI: 10.1016/j.cbd.2011.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 07/19/2011] [Accepted: 07/19/2011] [Indexed: 12/11/2022]
Abstract
A primary infection of Salmonella enteritidis causes a spatial-temporal dependent change in the gene expression patterns in the intestine of chickens (Gallus gallus). This is the result of a dynamic intestinal response to adapt to the altered environment and to optimize its 'health' and functionality under the new circumstances. By inferring gene association networks (GANs), the complexities of and changes in biological networks can be uncovered. Within such GANs highly interacting (hub) genes can be identified, which are supposed to be high-level regulators connected to multiple processes. By exploring the intestinal expression of genes differing between control and Salmonella infected chicken in a time-dependent manner differences in GANs were found. In control chickens more developmental processes were observed, whereas in infected chickens relatively more processes were associated to 'defense/pathogen response'. Moreover the conserved protein domains of the identified hub genes in controls were nuclear-associated, whereas hub genes in infected chickens were involved in 'cellular communication'. The shift in topology and functionality of the intestinal GANs in control and Salmonella infected animals and the identification of GAN-specific hubs is a first step to understand the complexity of biological networks and processes regulating intestinal health and functionality under normal and disturbed conditions.
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23
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Higgins SE, Wolfenden AD, Tellez G, Hargis BM, Porter TE. Transcriptional profiling of cecal gene expression in probiotic- and Salmonella-challenged neonatal chicks. Poult Sci 2011; 90:901-13. [PMID: 21406379 DOI: 10.3382/ps.2010-00907] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Probiotics are currently used to improve health and reduce enteric pathogens in poultry. However, the mechanisms by which they reduce or prevent disease are not known. Salmonella are intracellular pathogens that cause acute gastroenteritis in humans, and infections by nontyphoid species of Salmonella also can result in diarrhea, dehydration, and depression in poultry. Frequently, however, no clinical signs of infection are apparent in poultry flocks. In this study, day-of-hatch chicks were challenged with Salmonella enterica serovar Enteritidis (SE) and treated 1 h later with a poultry-derived, Lactobacillus-based probiotic culture (FloraMax-B11, Pacific Vet Group USA Inc., Fayetteville, AR). Cecae were collected 12 and 24 h posttreatment for Salmonella detection and RNA isolation for microarray analysis of gene expression. At both 12 and 24 h, SE was significantly reduced in chicks treated with the probiotic as compared with the birds challenged with only SE (P < 0.05). Microarray analysis revealed gene expression differences among all treatment groups. At 12 h, 170 genes were expressed at significantly different levels (P < 0.05), with a minimum difference in expression of 1.2-fold. At 24 h, the number of differentially regulated genes with a minimum 1.2-fold change was 201. Pathway analysis revealed that at both time points, genes associated with the nuclear factor kappa B complex, as well as genes involved in apoptosis, were significantly regulated. Based on this analysis, probiotic-induced differential regulation of the genes growth arrest-specific 2 (GAS2) and cysteine-rich, angiogenic inducer, 61 (CYR61) may result in increased apoptosis in the cecae of chicks. Because Salmonella is an intracellular pathogen, we suggest that increased apoptosis may be a mechanism by which the probiotic culture reduces Salmonella infection.
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Affiliation(s)
- S E Higgins
- Department of Animal and Avian Sciences, University of Maryland, College Park, 20742, USA.
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24
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Uthe JJ, Bearson SMD, Qu L, Dekkers JC, Nettleton D, Rodriguez Torres Y, O’Connor AM, McKean JD, Tuggle CK. Integrating comparative expression profiling data and association of SNPs with Salmonella shedding for improved food safety and porcine disease resistance. Anim Genet 2011; 42:521-34. [DOI: 10.1111/j.1365-2052.2010.02171.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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25
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Li X, Swaggerty CL, Kogut MH, Chiang HI, Wang Y, Genovese KJ, He H, Zhou H. Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PLoS One 2010; 5:e11827. [PMID: 20676366 PMCID: PMC2911375 DOI: 10.1371/journal.pone.0011827] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 07/05/2010] [Indexed: 11/19/2022] Open
Abstract
Campylobacter jejuni (C. jejuni) is one of the most common causes of human bacterial enteritis worldwide primarily due to contaminated poultry products. Previously, we found a significant difference in C. jejuni colonization in the ceca between two genetically distinct broiler lines (Line A (resistant) has less colony than line B (susceptible) on day 7 post inoculation). We hypothesize that different mechanisms between these two genetic lines may affect their ability to resist C. jejuni colonization in chickens. The molecular mechanisms of the local host response to C. jejuni colonization in chickens have not been well understood. In the present study, to profile the cecal gene expression in the response to C. jejuni colonization and to compare differences between two lines at the molecular level, RNA of ceca from two genetic lines of chickens (A and B) were applied to a chicken whole genome microarray for a pair-comparison between inoculated (I) and non-inoculated (N) chickens within each line and between lines. Our results demonstrated that metabolism process and insulin receptor signaling pathways are key contributors to the different response to C. jejuni colonization between lines A and B. With C. jejuni inoculation, lymphocyte activation and lymphoid organ development functions are important for line A host defenses, while cell differentiation, communication and signaling pathways are important for line B. Interestingly, circadian rhythm appears play a critical role in host response of the more resistant A line to C. jejuni colonization. A dramatic differential host response was observed between these two lines of chickens. The more susceptible line B chickens responded to C. jejuni inoculation with a dramatic up-regulation in lipid, glucose, and amino acid metabolism, which is undoubtedly for use in the response to the colonization with little or no change in immune host defenses. However, in more resistant line A birds the host defense responses were characterized by an up-regulation lymphocyte activation, probably by regulatory T cells and an increased expression of the NLR recognition receptor NALP1. To our knowledge, this is the first time each of these responses has been observed in the avian response to an intestinal bacterial pathogen.
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Affiliation(s)
- Xianyao Li
- Department of Poultry Science, Texas A&M University, College Station, Texas, United States of America
| | - Christina L. Swaggerty
- Southern Plains Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, College Station, Texas, United States of America
| | - Michael H. Kogut
- Southern Plains Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, College Station, Texas, United States of America
- * E-mail: (MHK); (HZ)
| | - Hsin-I Chiang
- Department of Poultry Science, Texas A&M University, College Station, Texas, United States of America
| | - Ying Wang
- Department of Poultry Science, Texas A&M University, College Station, Texas, United States of America
| | - Kenneth J. Genovese
- Southern Plains Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, College Station, Texas, United States of America
| | - Haiqi He
- Southern Plains Agricultural Research Center, United States Department of Agriculture, Agricultural Research Service, College Station, Texas, United States of America
| | - Huaijun Zhou
- Department of Poultry Science, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (MHK); (HZ)
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26
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Re-annotation is an essential step in systems biology modeling of functional genomics data. PLoS One 2010; 5:e10642. [PMID: 20498845 PMCID: PMC2871057 DOI: 10.1371/journal.pone.0010642] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 04/14/2010] [Indexed: 11/19/2022] Open
Abstract
One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data.
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27
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Calenge F, Kaiser P, Vignal A, Beaumont C. Genetic control of resistance to salmonellosis and to Salmonella carrier-state in fowl: a review. Genet Sel Evol 2010; 42:11. [PMID: 20429884 PMCID: PMC2873309 DOI: 10.1186/1297-9686-42-11] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 04/29/2010] [Indexed: 12/30/2022] Open
Abstract
Salmonellosis is a frequent disease in poultry stocks, caused by several serotypes of the bacterial species Salmonella enterica and sometimes transmitted to humans through the consumption of contaminated meat or eggs. Symptom-free carriers of the bacteria contribute greatly to the propagation of the disease in poultry stocks. So far, several candidate genes and quantitative trait loci (QTL) for resistance to carrier state or to acute disease have been identified using artificial infection of S. enterica serovar Enteritidis or S. enterica serovar Typhimurium strains in diverse genetic backgrounds, with several different infection procedures and phenotypic assessment protocols. This diversity in experimental conditions has led to a complex sum of results, but allows a more complete description of the disease. Comparisons among studies show that genes controlling resistance to Salmonella differ according to the chicken line studied, the trait assessed and the chicken's age. The loci identified are located on 25 of the 38 chicken autosomal chromosomes. Some of these loci are clustered in several genomic regions, indicating the possibility of a common genetic control for different models. In particular, the genomic regions carrying the candidate genes TLR4 and SLC11A1, the Major Histocompatibility Complex (MHC) and the QTL SAL1 are interesting for more in-depth studies. This article reviews the main Salmonella infection models and chicken lines studied under a historical perspective and then the candidate genes and QTL identified so far.
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Affiliation(s)
- Fanny Calenge
- INRA, UR Unité de Recherches Avicoles, Nouzilly, France.
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van den Berg BHJ, Thanthiriwatte C, Manda P, Bridges SM. Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data. BMC Bioinformatics 2009; 10 Suppl 11:S9. [PMID: 19811693 PMCID: PMC3226198 DOI: 10.1186/1471-2105-10-s11-s9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The widespread availability of microarray technology has driven functional genomics to the forefront as scientists seek to draw meaningful biological conclusions from their microarray results. Gene annotation enrichment analysis is a functional analysis technique that has gained widespread attention and for which many tools have been developed. Unfortunately, most of these tools have limited support for agricultural species. Here, we evaluate and compare four publicly available computational tools (Onto-Express, EasyGO, GOstat, and DAVID) that support analysis of gene expression datasets in agricultural species. We use AgBase as the functional annotation reference for agricultural species. The selected tools were evaluated based on i) available features, usage and accessibility, ii) implemented statistical computational methods, and iii) annotation and enrichment performance analysis. Annotation was assessed using a randomly selected test gene annotation set and an experimental differentially expressed gene-set – both from chicken. The experimental set was also used to evaluate identification of enriched functional groups. Comparison of the tools shows that they produce different sets of annotations for the two datasets and different functional groups for the experimental dataset. While DAVID, GOstat and Onto-Express annotate comparable numbers of genes, DAVID provides by far the most annotations per gene. However, many of DAVID's annotations appear to be redundant or are at very high levels in the GO hierarchy. The GOSlim distribution of annotations shows that GOstat, Onto-Express and EasyGO provide similar GO distributions to those found in AgBase while annotations from DAVID show a different GOSlim distribution, again probably due to duplication and many non-specific terms. No consistent trends were found in results of GO term over/under representation analysis applied to the experimental data using different tools. While GOstat, David and Onto-Express could retrieve some significantly enriched terms, EasyGO did not show any significantly enriched terms. There was little agreement about the enriched terms identified by the tools. Conclusion Different tools for functionally annotating gene sets and identifying significantly enriched GO categories differ widely in their results when applied to a test annotation gene set and an experimental dataset from chicken. These results emphasize the need for care when interpreting the results of such analysis and the lack of standardization of approaches.
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Affiliation(s)
- Bart H J van den Berg
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Starkville, MS 39762, USA.
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Lim H, Choi K, Mandal P, Baatartsog O, Lee C, Lee J, Kim H. Transcriptional Profiling of Spleen Lymphocyte in Fowl Typhoid of Broilers. ACTA ACUST UNITED AC 2009. [DOI: 10.3923/ajava.2009.66.75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Chiang HI, Swaggerty CL, Kogut MH, Dowd SE, Li X, Pevzner IY, Zhou H. Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray. BMC Genomics 2008; 9:526. [PMID: 18990222 PMCID: PMC2588606 DOI: 10.1186/1471-2164-9-526] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Accepted: 11/06/2008] [Indexed: 08/30/2023] Open
Abstract
Background Salmonella enterica serovar Enteritidis (SE) is one of the most common food-borne pathogens that cause human salmonellosis and usually results from the consumption of contaminated poultry products. The mechanism of SE resistance in chickens remains largely unknown. Previously, heterophils isolated from broilers with different genetic backgrounds (SE-resistant [line A] and -susceptible [line B]) have been shown to be important in defending against SE infections. To dissect the interplay between heterophils and SE infection, we utilized large-scale gene expression profiling. Results The results showed more differentially expressed genes were found between different lines than between infection (SE-treated) and non-infection (control) samples within line. However, the numbers of expressed immune-related genes between these two comparisons were dramatically different. More genes related to immune function were down-regulated in line B than line A. The analysis of the immune-related genes indicated that SE infection induced a stronger, up-regulated gene expression of line heterophils A than line B, and these genes include several components in the Toll-like receptor (TLR) signaling pathway, and genes involved in T-helper cell activation. Conclusion We found: (1) A divergent expression pattern of immune-related genes between lines of different genetic backgrounds. The higher expression of immune-related genes might be more beneficial to enhance host immunity in the resistant line; (2) a similar TLR regulatory network might exist in both lines, where a possible MyD88-independent pathway may participate in the regulation of host innate immunity; (3) the genes exclusively differentially expressed in line A or line B with SE infection provided strong candidates for further investigating SE resistance and susceptibility. These findings have laid the foundation for future studies of TLR pathway regulation and cellular modulation of SE infection in chickens.
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Affiliation(s)
- Hsin-I Chiang
- Department of Poultry Science, Texas A&M University, College Station, TX 77843, USA.
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