Transcriptomic profiling of spleen in grass-fed and grain-fed angus cattle

PLoS ONE

Volumn 10, Issue 9, 2015, Pages

  Li, Yaokun ^a   Carrillo, José A ^b   Ding, Yi ^b   He, Yanghua ^b   Zhao, Chunping ^a   Liu, Jianan ^b   Liu, George E ^c   Zan, Linsen ^a   Song, Jiuzhou ^b  

^a NORTHWEST A F UNIVERSITY   (China)

^b UNIVERSITY OF MARYLAND   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CD9 ANTIGEN; HLA DR ANTIGEN; NUCLEAR RECEPTOR NUR77; TRANSCRIPTOME;

ANGUS CATTLE; ARTICLE; CD9 GENE; COMPARATIVE STUDY; CONTROLLED STUDY; DIET; DOCK6 GENE; ENDOU GENE; FGFBP1 GENE; GENE; GENE EXPRESSION; GENE IDENTIFICATION; GENE ONTOLOGY; GENE REGULATORY NETWORK; HADH GENE; HLA DRA GENE; INGENUITY PATHWAY ANALYSIS; LOC534630 GENE; NONHUMAN; NR4A1 GENE; ONLINE ANALYSIS; OVOL1 GENE; QUANTITATIVE ANALYSIS; RBMX2 GENE; REAL TIME POLYMERASE CHAIN REACTION; RNA SEQUENCE; SLC4A9 GENE; SPLENIC TISSUE; TMEM45B GENE; ANIMAL; ANIMAL FOOD; BOVINE; GENETICS; METABOLISM; PHYSIOLOGY; SPLEEN;

ANIMAL FEED; ANIMALS; CATTLE; GENE REGULATORY NETWORKS; SPLEEN; TRANSCRIPTOME;

EID: 84947565801     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0135670     Document Type: Article

References (40)

1. Alfaia CPM, Alves SP, Martins SIV, Costa ASH, Fontes CMGA, Lemos JPC, et al. (2009) Effect of the feeding system on intramuscular fatty acids and conjugated linoleic acid isomers of beef cattle, with emphasis on their nutritional value and discriminatory ability. Food Chemistry 114: 939-946.
2. Leheska JM, Thompson LD, Howe JC, Hentges E, Boyce J, Brooks JC, et al. (2008) Effects of conventional and grass-feeding systems on the nutrient composition of beef. Journal Of Animal Science 86: 3575-3585. doi: 10.2527/jas.2007-0565 PMID: 18641180
3. Garcia PT, Pensel NA, Sancho AM, Latimori NJ, Kloster AM, Amigone MA, et al. (2008) Beef lipids in relation to animal breed and nutrition in Argentina. Meat Science 79: 500-508. doi: 10.1016/j.meatsci. 2007.10.019 PMID: 22062910
4. Descalzo AM, Insani EM, Biolatto A, Sancho AM, Garcia PT, Pensel NA, et al. (2005) Influence of pasture or grain-based diets supplemented with vitamin E on antioxidant/oxidative balance of Argentine beef. Meat Science 70: 35-44. doi: 10.1016/j.meatsci.2004.11.018 PMID: 22063278
5. Smith DR, Wood R, Tseng S, Smith SB (2002) Increased beef consumption increases apolipoprotein A-I but not serum cholesterol of mildly hypercholesterolemic men with different levels of habitual beef intake. Experimental Biology And Medicine 227: 266-275. PMID: 11910049
6. Hunninghake DB, Maki KC, Kwiterovich PO, Davidson MH, Dicklin MR, Kafonek SD. (2000) Incorporation of lean red meat into a National Cholesterol Education Program Step I diet: A long-term, randomized clinical trial in free-living persons with hypercholesterolemia. Journal Of the American College Of Nutrition 19: 351-360. PMID: 10872897
7. Beauchesne-Rondeau E, Gascon A, Bergeron J, Jacques H (2003) Plasma lipids and lipoproteins in hypercholesterolemic men fed a lipid-lowering diet containing lean beef, lean fish, or poultry. American Journal Of Clinical Nutrition 77: 587-593. PMID: 12600847
8. Melanson K, Gootman J, Myrdal A, Kline G, Rippe JM (2003) Weight loss and total lipid profile changes in overweight women consuming beef or chicken as the primary protein source. Nutrition 19: 409-414. PMID: 12714091
9. De la Fuente J, Diaz MT, Alvarez I, Oliver MA, Furnols MFI, Sanudo C, et al. (2009) Fatty acid and vitamin E composition of intramuscular fat in cattle reared in different production systems. Meat Science 82: 331-337. doi: 10.1016/j.meatsci.2009.02.002 PMID: 20416720
10. Yang A, Brewster MJ, Lanari MG, Tume RK (2002) Effect of vitamin E supplementation on alphatocopherol and beta-carotene concentrations in tissues from pasture- and grain-fed cattle. Meat Science 60: 35-40. PMID: 22063103
11. Insani EM, Eyherabide A, Grigioni G, Sancho AM, Pensel NA, Descalzo AM. (2008) Oxidative stability and its relationship with natural antioxidants during refrigerated retail display of beef produced in Argentina. Meat Science 79: 444-452. doi: 10.1016/j.meatsci.2007.10.017 PMID: 22062904
12. Cross ML, Gill HS (1999) Modulation of immune function by a modified bovine whey protein concentrate. Immunology And Cell Biology 77: 345-350. PMID: 10457202
13. Brunner FS, Schmid-Hempel P, Barribeau SM (2014) Protein-poor diet reduces host-specific immune gene expression in Bombus terrestris. Proceedings Of the Royal Society B-Biological Sciences 281.
14. Smith RA (1998) Impact of disease on feedlot performance: A review. Journal Of Animal Science 76: 272-274. PMID: 9464908
15. Bronte V, Pittet MJ (2013) The Spleen in Local and Systemic Regulation of Immunity. Immunity 39: 806-818. doi: 10.1016/j.immuni.2013.10.010 PMID: 24238338
16. Li RW, Schroeder SG (2012) Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection. Funct Integr Genomics 12: 35-44. doi: 10.1007/s10142-011-0259-7 PMID: 22203460
17. S. A (2010) FastQC: a quality control tool for high throughput sequence data. Available online at: http://wwwbioinformaticsbabrahamacuk/projects/fastqc.
18. Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11: R14. doi: 10.1186/gb-2010-11-2-r14 PMID: 20132535
19. Abdel-Aziz HO, Takasaki I, Tabuchi Y, Nomoto K, Murai Y, Tsuneyama K, et al. (2007) High-density oligonucleotide microarrays and functional network analysis reveal extended lung carcinogenesis pathway maps and multiple interacting genes in NNK [4-(methylnitrosamino)-1-(3-pyridyle)-1-butanone] induced CD1 mouse lung tumor. J Cancer Res Clin Oncol 133: 107-115. PMID: 16977459
20. Pospisil P, Iyer LK, Adelstein SJ, Kassis AI (2006) A combined approach to data mining of textual and structured data to identify cancer-related targets. BMC Bioinformatics 7: 354. PMID: 16857057
21. Mayburd AL, Martlinez A, Sackett D, Liu H, Shih J, Tauler J, et al. (2006) Ingenuity network-assisted transcription profiling: Identification of a new pharmacologic mechanism for MK886. Clin Cancer Res 12: 1820-1827. PMID: 16551867
22. Mitra A, Luo J, Zhang H, Cui K, Zhao K, Song J. (2012) Marek's disease virus infection induces widespread differential chromatin marks in inbred chicken lines. BMC Genomics 13: 557. doi: 10.1186/1471-2164-13-557 PMID: 23072359
23. Bjorklund EA, Heins BJ, Dicostanzo A, Chester-Jones H (2014) Growth, carcass characteristics, and profitability of organic versus conventional dairy beef steers. J Dairy Sci 97: 1817-1827. doi: 10.3168/jds.2013-6983 PMID: 24472124
24. Bjorklund EA, Heins BJ, Dicostanzo A, Chester-Jones H (2014) Fatty acid profiles, meat quality, and sensory attributes of organic versus conventional dairy beef steers. J Dairy Sci 97: 1828-1834. doi: 10.3168/jds.2013-6984 PMID: 24472126
25. Holtcamp W(2012) Suspect sweetener: arsenic detected in organic brown rice syrup. Environ Health Perspect 120: A204.
26. Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 10: 135-151. doi: 10.1146/annurev-genom-082908-145957 PMID: 19715439
27. Ma X, Zhu YJ, Li CF, Xue P, Zhao YM, Chen SL, et al. (2014) Characterisation of Caenorhabditis elegans sperm transcriptome and proteome. Bmc Genomics 15.
28. Morita T, Koike H, Hagiwara H, Ito E, Machida M, Sato S, et al. (2014) Genome and Transcriptome Analysis of the Basidiomycetous Yeast Pseudozyma antarctica Producing Extracellular Glycolipids, Mannosylerythritol Lipids. Plos One 9.
29. Blanco-Ulate B, Vincenti E, Powell ALT, Cantu D (2013) Tomato transcriptome and mutant analyses suggest a role for plant stress hormones in the interaction between fruit and Botrytis cinerea. Frontiers In Plant Science 4.
30. Naeem A, Drackley JK, Lanier JS, Everts RE, Rodriguez-Zas SL, Loor JJ. (2014) Ruminal epithelium transcriptome dynamics in response to plane of nutrition and age in young Holstein calves. Functional & Integrative Genomics 14: 261-273.
31. Descalzo AM, Rossetti L, Grigioni G, Irurueta M, Sancho AM, Carrete J, et al. (2007) Antioxidant status and odour profile in fresh beef from pasture or grain-fed cattle. Meat Science 75: 299-307. doi: 10.1016/j.meatsci.2006.07.015 PMID: 22063662
32. Gatellier P, Mercier Y, Renerre M (2004) Effect of diet finishing mode (pasture or mixed diet) on antioxidant status of Charolais bovine meat. Meat Science 67: 385-394. doi: 10.1016/j.meatsci.2003.11.009 PMID: 22061512
33. Matulova M, Rajova J, Vlasatikova L, Volf J, Stepanova H, Havlickova H, et al. (2012) Characterization of chicken spleen transcriptome after infection with Salmonella enterica serovar Enteritidis. PLoS One 7: e48101. doi: 10.1371/journal.pone.0048101 PMID: 23094107
34. Rocha-Perugini V, Gonzalez-Granado JM, Tejera E, Lopez-Martin S, Yanez-Mo M, Sanchez-Madrid F. (2014) Tetraspanins CD9 and CD151 at the immune synapse support T-cell integrin signaling. Eur J Immunol 44: 1967-1975. doi: 10.1002/eji.201344235 PMID: 24723389
35. Wu F, Su P, Chen L, Li M, Liu X, Li Q. (2012) Cloning of arctic lamprey Lethenteron camtschaticum cd9 with roles in the immune response. J Fish Biol 81: 1147-1157. doi: 10.1111/j.1095-8649.2012.03299.x PMID: 22957860
36. Hoffman BG, Williams KL, Tien AH, Lu V, de Algara TR, Ting JP, et al. (2006) Identification of novel genes and transcription factors involved in spleen, thymus and immunological development and function. Genes And Immunity 7: 101-112. PMID: 16355110
37. MacKenzie F, Duriez P, Wong F, Noseda M, Karsan A (2004) Notch4 inhibits endothelial apoptosis via RBP-Jkappa-dependent and-independent pathways. J Biol Chem 279: 11657-11663. PMID: 14701863
38. Baltes N, Tonpitak W, Gerlach GF, Hennig-Pauka I, Hoffmann-Moujahid A, Ganter M, et al. (2001) Actinobacillus pleuropneumoniae iron transport and urease activity: effects on bacterial virulence and host immune response. Infect Immun 69: 472-478. PMID: 11119539
39. Altmann DM, Takacs K, Trowsdale J, Elliott JI (1993) Mouse mammary tumor virus-mediated T-cell receptor negative selection in HLA-DRA transgenic mice. Hum Immunol 37: 149-156. PMID: 8244778
40. Lee SO, Li X, Khan S, Safe S (2011) Targeting NR4A1 (TR3) in cancer cells and tumors. Expert Opin Ther Targets 15: 195-206. doi: 10.1517/14728222.2011.547481 PMID: 21204731