1. Ashraf S, Zaneb H, Yousaf MS, Ijaz A, Sohail MU, Muti S, et al. Effect of dietary supplementation of prebiotics and probiotics on intestinal microarchitecture in broilers reared under cyclic heat stress. J Anim Physiol Anim Nutr (Berl). 2013;97 Suppl 1:68–73. Epub 2013/05/10. https://doi.org/10.1111/jpn.12041 PMID: 23639019.
2. Nardone A, Ronchi B, Lacetera N, Ranieri MS, Bernabucci U. Effects of climate changes on animal production and sustainability of livestock systems. Livestock Science. 2010; 130(1–3):57–69.
3. Ghazi S, Habibian M, Moeini M, Abdolmohammadi A. Effects of different levels of organic and inorganic chromium on growth performance and immunocompetence of broilers under heat stress. Biological trace element research. 2012; 146:309–17. https://doi.org/10.1007/s12011-011-9260-1 PMID: 22127829
4. Imik H, Ozlu H, Gumus R, Atasever MA, Urcar S, Atasever M. Effects of ascorbic acid and α-lipoic acid on performance and meat quality of broilers subjected to heat stress. British Poultry Science. 2012; 53 (6):800–8.
5. Marder J, Arad Z. Panting and acid-base regulation in heat stressed birds. Comp Biochem Physiol A Comp Physiol. 1989; 94(3):395–400. Epub 1989/01/01. https://doi.org/10.1016/0300-9629(89)90112-6 PMID: 2574090.
6. Butts CL, Sternberg EM. Neuroendocrine factors alter host defense by modulating immune function. Cell Immunol. 2008; 252(1–2):7–15. Epub 2008/03/11. https://doi.org/10.1016/j.cellimm.2007.09.009 PMID: 18329009; PubMed Central PMCID: PMC2590632.
7. Marketon JIW, Glaser RJCi. Stress hormones and immune function. 2008; 252(1–2):16–26. https://doi. org/10.1016/j.cellimm.2007.09.006 PMID: 18279846
8. Ruff J, Barros TL, Tellez G Jr, Blankenship J, Lester H, Graham BD, et al. Research Note: Evaluation of a heat stress model to induce gastrointestinal leakage in broiler chickens. Poultry Science. 2020; 99 (3):1687–92. https://doi.org/10.1016/j.psj.2019.10.075 PMID: 32115037
9. Renaudeau D, Collin A, Yahav S, De Basilio V, Gourdine J-L, Collier R. Adaptation to hot climate and strategies to alleviate heat stress in livestock production. Animal. 2012; 6(5):707–28. https://doi.org/10. 1017/S1751731111002448 PMID: 22558920
10. Habashy WS, Milfort MC, Rekaya R, Aggrey SE. Cellular antioxidant enzyme activity and biomarkers for oxidative stress are affected by heat stress. International journal of biometeorology. 2019; 63:1569– 84. https://doi.org/10.1007/s00484-019-01769-z PMID: 31352522
11. Dubey JP, Jenkins MC. Re-evaluation of the life cycle of Eimeria maxima Tyzzer, 1929 in chickens (Gallus domesticus). Parasitology. 2018; 145(8):1051–8. Epub 2017/12/15. https://doi.org/10.1017/ S0031182017002153 PMID: 29239290.
12. Schnitzler BE, Shirley MW. Immunological aspects of infections with Eimeria maxima: a short review. Avian Pathology. 1999; 28(6):537–43.
13. Schneiders G, Foutz J, Milfort M, Ghareeb A, Sorhue U, Richter J, et al. Ontogeny of intestinal permeability in chickens infected with Eimeria maxima: implications for intestinal health. J Adv Parasitol. 2019; 6(3):41–50.
14. Schneiders GH, Foutz JC, Milfort MC, Ghareeb AF, Fuller AL, Rekaya R, et al. Heat stress reduces sexual development and affects pathogenesis of Eimeria maxima in meat-type chickens. Scientific Reports. 2020; 10(1):10736.
15. Ghareeb AF, Schneiders GH, Foutz JC, Milfort MC, Fuller AL, Yuan J, et al. Heat Stress Alters the Effect of Eimeria maxima Infection on Ileal Amino Acids Digestibility and Transporters Expression in Meat-Type Chickens. Animals. 2022; 12(12):1554.
16. Ghareeb AFA, Schneiders GH, Richter JN, Foutz JC, Milfort MC, Fuller AL, et al. Heat stress modulates the disruptive effects of Eimeria maxima infection on the ileum nutrient digestibility, molecular transporters, and tissue morphology in meat-type chickens. PLoS One. 2022; 17(6):e0269131. Epub 2022/0 04. https://doi.org/10.1371/journal.pone.0269131 PMID: 35657942; PubMed Central PMCID: PMC9165794.
17. Adams JJNE. Transcriptome: connecting the genome to gene function. Nature Education. 2008; 1 (1):195.
18. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170 P
19. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA seq aligner. Bioinformatics. 2013; 29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635 PMID: 23104886
20. Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014; 30(7):923–30. https://doi.org/10.1093/bioinformatics/ btt656 PMID: 24227677
21. Dodt M, Roehr JT, Ahmed R, Dieterich C. FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms. Biology. 2012; 1(3):895–905. https://doi.org/10.3390/ biology1030895 PMID: 24832523
22. Barnett DW, Garrison EK, Quinlan AR, Stro¨mberg MP, Marth GT. BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics. 2011; 27(12):1691–2. https://doi.org/10.1093/ bioinformatics/btr174 PMID: 21493652
23. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature protocols. 2012; 7(3):562–78. https://doi.org/10.1038/nprot.2012.016 PMID: 22383036
24. Anders S, Huber W. Differential expression analysis for sequence count data. Nature Precedings. 2010:1-. https://doi.org/10.1186/gb-2010-11-10-r106 PMID: 20979621
25. Benjamini Y, Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological). 1995; 57(1):289– 300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
26. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research. 2003; 13 (11):2498–504. https://doi.org/10.1101/gr.1239303 PMID: 14597658
27. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009; 25(8):1091–3. https://doi.org/10.1093/bioinformatics/btp101 PMID: 19237447
28. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic acids research. 1999; 27(1):29–34. https://doi.org/10.1093/nar/27.1.29 PMID: 9847135
29. Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M. KEGG: integrating viruses and cellular organisms. Nucleic acids research. 2021; 49(D1):D545–D51. https://doi.org/10.1093/nar/ gkaa970 PMID: 33125081
30. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2− ΔΔCT method. methods. 2001; 25(4):402–8.
31. Syafwan S, Kwakkel R, Verstegen M. Heat stress and feeding strategies in meat-type chickens. World’s Poultry Science Journal. 2011; 67(4):653–74.
32. Habashy W, Milfort M, Adomako K, Attia Y, Rekaya R, Aggrey S. Effect of heat stress on amino acid digestibility and transporters in meat-type chickens. Poultry science. 2017; 96(7):2312–9. https://doi. org/10.3382/ps/pex027 PMID: 28339933
33. Habashy WS, Milfort MC, Fuller AL, Attia YA, Rekaya R, Aggrey SE. Effect of heat stress on protein utilization and nutrient transporters in meat-type chickens. International Journal of Biometeorology. 2017; 61:2111–8. https://doi.org/10.1007/s00484-017-1414-1 PMID: 28799035
34. Brocker C, Lassen N, Estey T, Pappa A, Cantore M, Orlova VV, et al. Aldehyde dehydrogenase 7A1 (ALDH7A1) is a novel enzyme involved in cellular defense against hyperosmotic stress. Journal of Biological Chemistry. 2010; 285(24):18452–63. https://doi.org/10.1074/jbc.M109.077925 PMID: 20207735
35. Feher JJ. Quantitative human physiology: an introduction: Academic press; 2017.
36. Petrova B, Kanarek N. Potential Benefits and Pitfalls of Histidine Supplementation for Cancer Therapy Enhancement. J Nutr. 2020; 150(Suppl 1):2580S–7S. Epub 2020/10/02. https://doi.org/10.1093/jn/ nxaa132 PMID: 33000153.
37. Rougier JS, Abriel H. Cardiac voltage-gated calcium channel macromolecular complexes. Biochim Biophys Acta. 2016; 1863(7 Pt B):1806–12. Epub 2015/12/29. https://doi.org/10.1016/j.bbamcr.2015.12. 014 PMID: 26707467.
38. Jin W, Broedl UC, Monajemi H, Glick JM, Rader DJ. Lipase H, a new member of the triglyceride lipase family synthesized by the intestine. Genomics. 2002; 80(3):268–73. https://doi.org/10.1006/geno.2002. 6837 PMID: 12213196
39. Cronje PJRAiANiA. Heat stress in livestock—The role of the gut in its aetiology and a potential role for betaine in its alleviation. 2005; 15:107–22.
40. Norris K, Evans MRJBE. Ecological immunology: life history trade-offs and immune defense in birds. 2000; 11(1):19–26.
41. Lucas LD, French SSJPo. Stress-induced tradeoffs in a free-living lizard across a variable landscape: consequences for individuals and populations. 2012; 7(11):e49895.
42. Borish LC, Steinke JW. 2. Cytokines and chemokines. Journal of Allergy and Clinical Immunology. 2003; 111(2):S460–S75. https://doi.org/10.1067/mai.2003.108 PMID: 12592293
43. Van Parijs L, Abbas AK. Role of Fas-mediated cell death in the regulation of immune responses. Current opinion in immunology. 1996; 8(3):355–61. https://doi.org/10.1016/s0952-7915(96)80125-7 PMID: 8793992
44. Lebratti T, Lim YS, Cofie A, Andhey P, Jiang X, Scott J, et al. A sustained type I IFN-neutrophil-IL-18 axis drives pathology during mucosal viral infection. Elife. 2021; 10:e65762. https://doi.org/10.7554/ eLife.65762 PMID: 34047696
45. Ito T, Carson IV WF, Cavassani KA, Connett JM, Kunkel SL. CCR6 as a mediator of immunity in the lung and gut. Experimental cell research. 2011; 317(5):613–9. https://doi.org/10.1016/j.yexcr.2010.12. 018 PMID: 21376174
46. Schwarz DS, Blower MD. The endoplasmic reticulum: structure, function and response to cellular signaling. Cellular and molecular life sciences. 2016; 73:79–94. https://doi.org/10.1007/s00018-015-2052- 6 PMID: 26433683
47. Azad Kalam M, Motoi K, Hoque Azharul M, Masaaki T. Effect of Chronic Heat Stress on Performance and Oxidative Damage in Different Strains of Chickens. 日本家禽学会誌. 2010; 47(4):333–7.
48. Lee M, Park H, Heo JM, Choi HJ, Seo S. Multi-tissue transcriptomic analysis reveals that L-methionine supplementation maintains the physiological homeostasis of broiler chickens than D-methionine under acute heat stress. PLoS One. 2021; 16(1):e0246063. Epub 2021/01/28. https://doi.org/10.1371/journal. pone.0246063 PMID: 33503037; PubMed Central PMCID: PMC7840013.
49. Kanehisa M. Toward understanding the origin and evolution of cellular organisms. Protein Science. 2019; 28(11):1947–51. https://doi.org/10.1002/pro.3715 PMID: 31441146
50. Memon FU, Yang Y, Leghari IH, Lv F, Soliman AM, Zhang W, et al. Transcriptome analysis revealed ameliorative effects of Bacillus based probiotic on immunity, gut barrier system, and metabolism of chicken under an experimentally induced Eimeria tenella infection. Genes. 2021; 12(4):536. https://doi. org/10.3390/genes12040536 PMID: 33917156
51. Powell N, Canavan J, MacDonald T, Lord G. Transcriptional regulation of the mucosal immune system mediated by T-bet. Mucosal immunology. 2010; 3(6):567–77. https://doi.org/10.1038/mi.2010.53 PMID: 20844482
52. Bremner A, Kim S, Morris KM, Nolan MJ, Borowska D, Wu Z, et al. Kinetics of the cellular and transcriptomic response to Eimeria maxima in relatively resistant and susceptible chicken lines. Frontiers in Immunology. 2021; 12:653085.
53. Lillehoj H, Min W, Dalloul R. Recent progress on the cytokine regulation of intestinal immune responses to Eimeria. Poultry Science. 2004; 83(4):611–23. https://doi.org/10.1093/ps/83.4.611 PMID: 15109059
54. Galli GM, Baldissera MD, Griss LG, Souza CF, Fortuoso BF, Boiago MM, et al. Intestinal injury caused by Eimeria spp. impairs the phosphotransfer network and gain weight in experimentally infected chicken chicks. Parasitology Research. 2019; 118:1573–9. https://doi.org/10.1007/s00436-019-06221-0 PMID: 30815727
55. Khatlab AdS Del Vesco AP, de Oliveira Neto AR, Fernandes RPM, Gasparino E. Dietary supplementation with free methionine or methionine dipeptide mitigates intestinal oxidative stress induced by Eimeria spp. challenge in broiler chickens. Journal of Animal Science and Biotechnology. 2019; 10(1):1–17.
56. Alehagen U, Opstad TB, Alexander J, Larsson A, Aaseth J. Impact of selenium on biomarkers and clinical aspects related to ageing. A review. Biomolecules. 2021; 11(10):1478. https://doi.org/10.3390/ biom11101478 PMID: 34680111
57. Hunt MC, Alexson SE. The role Acyl-CoA thioesterases play in mediating intracellular lipid metabolism. Progress in lipid research. 2002; 41(2):99–130. https://doi.org/10.1016/s0163-7827(01)00017-0 PMID: 11755680
58. Ho¨o¨g J-O, Stro¨mberg P, Hedberg JJ, Griffiths WJ. The mammalian alcohol dehydrogenases interact in several metabolic pathways. Chemico-biological interactions. 2003; 143:175–81. https://doi.org/10. 1016/s0009-2797(02)00225-9 PMID: 12604202
59. Aggrey SE, Milfort MC, Fuller AL, Yuan J, Rekaya R. Effect of host genotype and Eimeria acervulina infection on the metabolome of meat-type chickens. PLoS One. 2019; 14(10):e0223417. Epub 2019/ 10/17. https://doi.org/10.1371/journal.pone.0223417 PMID: 31618222; PubMed Central PMCID: PMC6795442.
60. Qing X, Zeng D, Wang H, Ni X, Lai J, Liu L, et al. Analysis of hepatic transcriptome demonstrates altered lipid metabolism following Lactobacillus johnsonii BS15 prevention in chickens with subclinical necrotic enteritis. Lipids in Health and Disease. 2018; 17:1–10.
61. Tang L-P, Li W-H, Liu Y-L, Lun J-C, He Y-M. Heat stress inhibits expression of the cytokines, and NF κB-NLRP3 signaling pathway in broiler chickens infected with salmonella typhimurium. Journal of Thermal Biology. 2021; 98:102945.
62. DORAN DJ. The migration of Eimeria acervulina sporozoites to the duodenal glands of Lieberku¨hn. The Journal of Protozoology. 1966; 13(1):27–33.
63. Trout J, Lillehoi H. Evidence of a role for intestinal CD8+ lymphocytes and macrophages in transport of Eimeria acervulina sporozoites. The Journal of parasitology. 1993; 79(5):790–2. PMID: 8105047
64. Beattie SE, Barta JR, Fernando M. Involvement of CD 8+ and CD 3+ lymphocytes in the transport of Eimeria necatrix sporozoites within the intestinal mucosa of chickens. Parasitology research. 2001; 87:405–8. https://doi.org/10.1007/s004360000371 PMID: 11403384
65. Schmid M, Lehmann MJ, Lucius R, Gupta N. Apicomplexan parasite, Eimeria falciformis, co-opts host tryptophan catabolism for life cycle progression in mouse. Journal of Biological Chemistry. 2012; 287 (24):20197–207. https://doi.org/10.1074/jbc.M112.351999 PMID: 22535959
66. McCauley R, Kong SE, Hall J. Glutamine and nucleotide metabolism within enterocytes. Journal of parenteral and enteral nutrition. 1998; 22(2):105–11. https://doi.org/10.1177/0148607198022002105 PMID: 9527969
67. Sakai R, Ooba Y, Watanabe A, Nakamura H, Kawamata Y, Shimada T, et al. Glutamate metabolism in a human intestinal epithelial cell layer model. Amino Acids. 2020; 52:1505–19. https://doi.org/10.1007/ s00726-020-02908-2 PMID: 33180203
68. Njålsson R. Glutathione synthetase deficiency. Cellular and Molecular Life Sciences CMLS. 2005; 62:1938–45. https://doi.org/10.1007/s00018-005-5163-7 PMID: 15990954
69. Lei XG, Cheng W-H, McClung JP. Metabolic regulation and function of glutathione peroxidase-1. Annu Rev Nutr. 2007; 27:41–61. https://doi.org/10.1146/annurev.nutr.27.061406.093716 PMID: 17465855
70. Zipprer EM, Neggers M, Kushwaha A, Rayavara K, Desai SA. A kinetic fluorescence assay reveals unusual features of Ca++ uptake in Plasmodium falciparum-infected erythrocytes. Malaria journal. 2014; 13(1):1–11.
71. Wasserman M, Alarco´n C, Mendoza PM. Effects of Ca++ depletion on the asexual cell cycle of Plasmodium falciparum. The American journal of tropical medicine and hygiene. 1982; 31(4):711–7. https://doi. org/10.4269/ajtmh.1982.31.711 PMID: 6808848
72. Gupta Y, Goicoechea S, Pearce CM, Mathur R, Romero JG, Kwofie SK, et al. The emerging paradigm of calcium homeostasis as a new therapeutic target for protozoan parasites. Medicinal Research Reviews. 2022; 42(1):56–82. https://doi.org/10.1002/med.21804 PMID: 33851452
73. Van Petegem FJJoBC. Ryanodine receptors: structure and function. 2012; 287(38):31624–32
74. Uurasmaa T-M, Streng T, Alkio M, Heinonen I, Anttila K. Short-term exercise affects cardiac function ex vivo partially via changes in calcium channel levels, without influencing hypoxia sensitivity. Journal of physiology and biochemistry. 2021; 77(4):639–51. https://doi.org/10.1007/s13105-021-00830-z PMID: 34449060
75. Hoth M, Niemeyer BAJCtim. The neglected CRAC proteins: Orai2, Orai3, and STIM2. 2013; 71:237– 71. https://doi.org/10.1016/B978-0-12-407870-3.00010-X PMID: 23890118
76. Roth W, Zadeh K, Vekariya R, Ge Y, Mohamadzadeh M. Tryptophan metabolism and gut-brain homeostasis. International journal of molecular sciences. 2021; 22(6):2973. https://doi.org/10.3390/ ijms22062973 PMID: 33804088
77. Saliba KJ, Kirk K. Nutrient acquisition by intracellular apicomplexan parasites: staying in for dinner. International journal for parasitology. 2001; 31(12):1321–30. https://doi.org/10.1016/s0020-7519(01) 00258-2 PMID: 11566300
78. Landfear SM. Nutrient transport and pathogenesis in selected parasitic protozoa. Eukaryotic cell. 2011; 10(4):483–93. https://doi.org/10.1128/EC.00287-10 PMID: 21216940
79. Gentile M, Latonen L, Laiho M. Cell cycle arrest and apoptosis provoked by UV radiation-induced DNA damage are transcriptionally highly divergent responses. Nucleic acids research. 2003; 31(16):4779– 90. https://doi.org/10.1093/nar/gkg675 PMID: 12907719
80. Kleinsimon S, Longmuss E, Rolff J, Ja¨ger S, Eggert A, Delebinski C, et al. GADD45A and CDKN1A are involved in apoptosis and cell cycle modulatory effects of viscumTT with further inactivation of the STAT3 pathway. Scientific reports. 2018; 8(1):5750. https://doi.org/10.1038/s41598-018-24075-x PMID: 29636527
81. Engeland KJCD, Differentiation. Cell cycle regulation: p53-p21-RB signaling. 2022; 29(5):946–60.
82. Singh D, Nishi K, Khambata K, Balasinor N. Introduction to epigenetics: basic concepts and advancements in the field. Elsevier; 2020. p. xxv–xliv