Comparative analysis of gene expression profiles in ruminal tissue from Holstein dairy cows fed high or low concentrate diets

Ashwell, 2006, The many paths to p38 mitogen-activated protein kinase activation in the immune system, Nat. Rev. Immunol., 6, 532, 10.1038/nri1865 Beachy, 2004, Tissue repair and stem cell renewal in carcinogenesis, Nature, 432, 324, 10.1038/nature03100 Carmona-Saez, 2007, GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists, Genome Biol., 8, R3, 10.1186/gb-2007-8-1-r3 Chen, 2001, MAP kinases, Chem. Rev., 101, 2449, 10.1021/cr000241p Chomczynski, 1987, Single-stepmethod of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction, Anal. Biochem., 162, 156, 10.1016/0003-2697(87)90021-2 Cohen, 2003, The hedgehog signaling network, Am. J. Med. Genet. A, 123A, 5, 10.1002/ajmg.a.20495 Díaz, 2009, Model selection in a global analysis of a microarray experiment, J. Anim. Sci., 87, 88, 10.2527/jas.2007-0713 Doreau, 1997, Effects of level of intake and of available volatile fatty acids on the absorptive capacity of sheep rumen, Small Ruminant Res., 25, 99, 10.1016/S0921-4488(96)00982-0 Fujisawa, 2007, ASK family proteins in stress response and disease, Mol. Biotechnol., 37, 13, 10.1007/s12033-007-0053-x Gäbel, 1989, Interrelations between short-chain fatty acids and sodium absorption in the rumen of sheep, Acta Vet. Scand. Suppl., 86, 134 Gäbel, 1991, Influences of diet, short-chain fatty acids, lactate and chloride on bicarbonate movement across the reticulo-rumen wall of sheep, Zentralbl. Veterinärmed. A, 38, 523, 10.1111/j.1439-0442.1991.tb01043.x Griffioen, 2002, Molecular mechanisms controlling the localisation of protein kinase A, Curr. Genet., 41, 199, 10.1007/s00294-002-0308-9 Harmon, 1991, Influence of dietary forage and energy intake on metabolism and acyl-CoA synthetase activity in bovine ruminal epithelial tissue, J. Anim. Sci., 69, 4117, 10.2527/1991.69104117x Khaniya, 2009, Microarray analysis of differentially expressed genes from peyer's patches of cattle orally challenged with bovine spongiform encephalopathy, J. Toxicol. Environ. Health A, 72, 1008, 10.1080/15287390903084199 Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method, Methods, 25, 402, 10.1006/meth.2001.1262 Lodemann, 2006, Effects of diet and osmotic pressure on Na+transport and tissue conductance of sheep isolated rumen epithelium, Exp. Physiol., 91, 539, 10.1113/expphysiol.2005.032078 Lum, 2004, The hedgehog response network: sensors, switches, and routers, Science, 304, 1755, 10.1126/science.1098020 Miyamoto, 1996, Integrins can collaborate with growth factors for phosphorylation of receptor tyrosine kinases and MAP kinase activation: roles of integrin aggregation and occupancy of receptors, J. Cell Biol., 135, 1633, 10.1083/jcb.135.6.1633 Nogales-Cadenas, 2009, vol. 37, W317 Owens, 1998, Acidosis in cattle: a review, J. Anim. Sci., 76, 275, 10.2527/1998.761275x Penner, 2006, An evaluation of the accuracy and precision of a stand-alone submersible continuous ruminal pH measurement system, J. Dairy Sci., 89, 2132, 10.3168/jds.S0022-0302(06)72284-6 Penner, 2007, Severity of ruminal acidosis in primiparous holstein cows during the periparturient period, J. Dairy Sci., 90, 365, 10.3168/jds.S0022-0302(07)72638-3 Penner, 2009, Effect of dietary forage to concentrate ratio on volatile fatty acid absorption and the expression of genes related to volatile fatty acid absorption and metabolism in ruminal tissue, J. Dairy Sci., 92, 2767, 10.3168/jds.2008-1716 Poueymirou, 1989, Regulation of mouse preimplantation development: inhibition of synthesis of proteins in the two-cell embryo that require transcription by inhibitors of cAMP-dependent protein kinase, Dev. Biol., 133, 588, 10.1016/0012-1606(89)90061-4 Pullikuth, 2007, Scaffold mediated regulation of MAPK signaling and cytoskeletal dynamics: a perspective, Cell. Signal., 19, 1621, 10.1016/j.cellsig.2007.04.012 Reverter, 2006, A gene coexpression network for bovine skeletal muscle inferred from microarray data, Physiol. Genomics, 28, 76, 10.1152/physiolgenomics.00105.2006 Reverter, 2008, Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes, BioData Min., 1, 8, 10.1186/1756-0381-1-8 Sakata, 1984, Influence of short chain fatty acids on the epithelial cell division of digestive tract, Q. J. Exp. Physiol., 69, 639, 10.1113/expphysiol.1984.sp002850 Sehested, 1999, Transport of butyrate across the isolated bovine rumen epithelium—interaction with sodium, chloride and bicarbonate, Comp. Biochem. Physiol. A, 123, 399, 10.1016/S1095-6433(99)00082-3 Shen, 2004, An energy-rich diet causes rumen papillae proliferation associated with more IGF type 1 receptors and increased plasma IGF-1 concentrations in young goats, J. Nutr., 134, 11, 10.1093/jn/134.1.11 Showers, 1986, A cloned bovine cDNA encodes an alternate form of the catalytic subunit of cAMP-dependent protein kinase, J. Biol. Chem., 261, 16288, 10.1016/S0021-9258(18)66561-5 Skålhegg, 2002, Mutation of the Calpha subunit of PKA leads to growth retardation and sperm dysfunction, Mol. Endocrinol., 16, 630, 10.1210/me.16.3.630 Stork, 2002, Crosstalk between cAMP and MAP kinase signaling in the regulation of cell proliferation, Trends Cell Biol., 12, 258, 10.1016/S0962-8924(02)02294-8 Tan, 2006, Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray, Funct. Integr. Genomics, 6, 235, 10.1007/s10142-005-0016-x Taniguchi, 2008, Gene expression patterns of bovine perimuscular preadipocytes during adipogenesis, Biochem. Biophys. Res. Commun., 366, 346, 10.1016/j.bbrc.2007.11.111 Tanoue, 2002, Docking interactions in the mitogen-activated protein kinase cascades, Pharmacol. Ther., 93, 193, 10.1016/S0163-7258(02)00188-2 Tasken, 2004, Localized effects of cAMP mediated by distinct routes of protein kinase A, Physiol. Revs., 84, 137, 10.1152/physrev.00021.2003 Uppal, 2003, Modulation of Na+transport across isolated rumen epithelium by short-chain fatty acids in hay- and concentrate-fed sheep, J. Anim. Physiol. Anim. Nutr., 87, 380, 10.1046/j.1439-0396.2003.00448.x Uppal, 2003, The effect of short chain fatty acids on calcium flux rates across isolated rumen epithelium of hay-fed and concentrate-fed sheep, J. Anim. Physiol. Anim. Nutr., 87, 12, 10.1046/j.1439-0396.2003.00401.x Wang, 2008, An integrated approach for the analysis of biological pathways using mixed models, PLoS Genet., 4, e1000115, 10.1371/journal.pgen.1000115 Wiemann, 1991, Isoform C beta 2, an unusual form of the bovine catalytic subunit of cAMP-dependent protein kinase, J. Biol. Chem., 266, 5140, 10.1016/S0021-9258(19)67766-5 Yang, 2003, Transcriptional regulation by the MAP kinase signaling cascades, Gene, 320, 3, 10.1016/S0378-1119(03)00816-3 Zhu, 2005, Genes encoding catalytic subunits of protein kinase A and risk of spina bifida, Birth Defects Res. A Clin. Mol. Teratol., 73, 591, 10.1002/bdra.20175