Discovery of differentially expressed genes in the intestines of Pelteobagrus vachellii within a light/dark cycle

References

• Arriza JL, Fairman WA, Wadiche JI, Murdoch GH, Kavanaugh MP, Amara SG. 1994. Functional comparisons of three glutamate transporter subtypes cloned from human motor cortex. J Neurosci. 14(9):5559–5569.
   PubMed Web of Science ®Google Scholar
• Azzaydi M, Martinez FJ, Zamora S, Sánchez-Vázquez FJ, Madrid JA. 2000. The influence of nocturnal vs. diurnal feeding under winter conditions on growth and feed conversion of European sea bass (Dicentrarchus labrax L.). Aquaculture. 182(3–4):329–338.
   Web of Science ®Google Scholar
• Bailey SM, Udoh US, Young ME. 2014. Circadian regulation of metabolism. J Endocrinol. 222(2):R75–96.
   PubMed Web of Science ®Google Scholar
• Barattini P, Larsen KR, Moore JG, Dayton MT. 1993. Circadian rhythm of pepsin efflux in the fasting rat stomach. Chronobiol Int. 10(6):403–409.
   PubMed Web of Science ®Google Scholar
• Bodosi B, Gardi J, Hajdu I, Szentirmai E, Obal F Jr., Krueger JM. 2004. Rhythms of ghrelin, leptin, and sleep in rats: effects of the normal diurnal cycle, restricted feeding, and sleep deprivation. Am J Physiol Regul Integr Comp Physiol. 287(5):R1071–1079.
   PubMed Web of Science ®Google Scholar
• Brody T. 1999. Nutritional biochemistry. Pittsburgh (PA): Academic Press; p. 69–70.
   Google Scholar
• Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. 2005. Blast2 GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics. 21(18):3674–3676.
   PubMed Web of Science ®Google Scholar
• Crane BR, Young MW. 2014. Interactive features of proteins composing eukaryotic circadian clocks. Annu Rev Biochem. 83:191–219.
   PubMed Web of Science ®Google Scholar
• Dato SM, Catala A, Brenner RR. 1973. Circadian rhythm of fatty acid desaturation in mouse liver. Lipids. 8(1):1–6. doi:10.1007/BF02533231.
   PubMed Web of Science ®Google Scholar
• Davie D, Minghetti M, Migaud H. 2009. Seasonal variations in clock-gene expression in Atlantic salmon (Salmo salar). Chronobiol Int. 26(3):379–395.
   PubMed Web of Science ®Google Scholar
• Del Pozo A, Montoya A, Vera LM, Sánchez-Vázquez FJ. 2012. Daily rhythms of clock gene expression, glycaemia and digestive physiology in diurnal/nocturnal European seabass. Physiol Behav. 106(4):446–450.
   PubMed Web of Science ®Google Scholar
• Dibner C, Schibler U, Albrecht U. 2010. The mammalian circadian timing system: organization and coordination of central and peripheral clocks. Annu Rev Physiol. 72:517–549.
   PubMed Web of Science ®Google Scholar
• Fatima J, Iqbal CW, Houghton SG, Kasparek MS, Duenes JA, Zheng Y, Sarr MG. 2009. Hexose transporter expression and function in mouse small intestine: role of diurnal rhythm. J Gastrointest Surg. 13(4):634–641.
   PubMed Web of Science ®Google Scholar
• Fujii A, Kurokawa Y, Kawai S, Yoseda K, Dan S, Kai A, Tanaka M. 2007. Diurnal variation of tryptic activity in larval stage and development of proteolytic enzyme activities of malabar grouper (Epinephelus malabaricus) after hatching. Aquaculture. 270(1–4):68–76.
   Web of Science ®Google Scholar
• Furuya S, Yugari Y. 1974. Daily rhythmic change of L-histidine and glucose absorptions in rat small intestine in vivo. Biochim Biophys Acta. 343(3):558–564.
   PubMedGoogle Scholar
• Gamble KL, Allen GC, Zhou T, McMahon DG. 2007. Gastrin-releasing peptide mediates light-like resetting of the suprachiasmatic nucleus circadian pacemaker through cAMP response element binding protein and Per1 activation. J Neurosci. 27(44):12078–12087.
   PubMed Web of Science ®Google Scholar
• Gamble KL, Berry R, Frank SJ, Young ME. 2014. Circadian clock control of endocrine factors. Nat Rev Endocrinol. 10(8):466–475.
   PubMed Web of Science ®Google Scholar
• Goel N, Stunkard AJ, Rogers NL, Van Dongen HP, Allison KC, O'Reardon JP, Ahima RS, Cummings DE, Heo M,Dinges DF. 2009. Circadian rhythm profiles in women with night eating syndrome. J Biol Rhythms. 24(1):85–94.
   PubMed Web of Science ®Google Scholar
• Grabherr MG, Haas BJ, Yassour M, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29(7):644–652.
   PubMed Web of Science ®Google Scholar
• Gregory P, Dagmar R. 2004. Protein structure and function. London (UK): New Science Press; p. 78–79.
   Google Scholar
• Guerra-Santos B, López-Olmeda JF, Mattos BO, Baião AB, Pereira DS, Sánchez-Vázquez FJ, Cerqueira RB, Albinati RC, Fortes-Silva R. 2016. Synchronization to light and mealtime of daily rhythms of locomotor activity, plasma glucose and digestive enzymes in the Nile tilapia (Oreochromis niloticus). Comp Biochem Physiol Part A. 204:40–47.
   PubMed Web of Science ®Google Scholar
• Hopman WPM, van Battum PLH, Salemans JMJI, Kuijpers HJH,Nagengast FM. 1996. Plasma peptide YY in patients with proctocolectomy and ileal pouch-anal anastomosis; relation with plasma cholecystokinin. Regulatory Peptides. 64(1–3):72.
   Google Scholar
• Hossain MAR, Haylor GS,Beveridge MCM. 2001. Effect of feeding time and frequency on the growth and feed utilization of African catfish Clarias gariepinus (Burchell 1822) fingerlings. Aquaculture Res. 32(12):999–1004.
   Web of Science ®Google Scholar
• Huang W, Ramsey KM, Marcheva B, Bass J. 2011. Circadian rhythms, sleep, and metabolism. J Clin Invest. 121(6):2133–2141.
   PubMed Web of Science ®Google Scholar
• Hussain MM,Pan X. 2009. Clock genes, intestinal transport and plasma lipid homeostasis. Trends Endocrinol Metab. 20(4):177–185.
   PubMed Web of Science ®Google Scholar
• Hussain MM, Pan X. 2014. Circadian regulators of intestinal lipid absorption. J Lipid Res. 56(4):761–770.
   PubMed Web of Science ®Google Scholar
• Kalsbeek A, Verhagen LA, Schalij I, Foppen E, Saboureau M, Bothorel B, Buijs RM, Pevet P. 2008. Opposite actions of hypothalamic vasopressin on circadian corticosterone rhythm in nocturnal versus diurnal species. Eur J Neurosci. 27(4):818–827.
   PubMed Web of Science ®Google Scholar
• Kanehisa M,Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28(1):29–34.
   Web of Science ®Google Scholar
• Konturek PC, Brzozowski T, Konturek SJ. 2011. Gut clock: implication of circadian rhythms in the gastrointestinal tract. J Physiol Pharmaco. 62(2):139–150.
   PubMed Web of Science ®Google Scholar
• Kotani T, Fushimi H. 2011. Determination of appropriate feeding schedules from diel feeding rhythms in finfish larviculture. Aquaculture. 315(1–3):104–113.
   Web of Science ®Google Scholar
• Li B,Dewey CN. 2011. Rsem: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 12:323.
   PubMed Web of Science ®Google Scholar
• Livak KJ,Schmittgen TD. 2001. Analysis of relative gene expression data using Q realtime quantitative PCR and the 2−ΔΔCt method. Methods. 25(4):402–408.
   PubMed Web of Science ®Google Scholar
• López-Olmeda JF, Montoya A, Oliveira C, Sánchez-Vázquez FJ. 2009. Synchronization to light and restricted-feeding schedules of behavioral and humoral daily rhythms in gilthead seabream (Sparus aurata). Chronobiol Int. 26(7):1389–1408.
   PubMed Web of Science ®Google Scholar
• López-Olmeda JF, Tartaglione EV, de la Iglesia HO, Sánchez-Vázquez FJ. 2010. Feeding entrainment of food-anticipatory activity and per1 expression in the brain and liver of zebrafish under different lighting and feeding conditions. Chronobiol Int. 27(7):1380–1400.
   PubMed Web of Science ®Google Scholar
• Lucas RJ, Lall GS, Allen AE, Brown TM. 2012. How rod, cone, and melanopsin photoreceptors come together to enlighten the mammalian circadian clock. Prog Brain Res. 199:1–18.
   PubMed Web of Science ®Google Scholar
• Marinho G, Peres H, Carvalho AP. 2014. Effect of feeding time on dietary protein utilization and growth of juvenile Senegalese sole (Solea senegalensis). Aquac Res. 45(5):828–833.
   Web of Science ®Google Scholar
• Martín-Robles ÁJ, Isorna E, Whitmore D, Muñoz-Cueto JA, Pendón C. 2011. The clock gene Period3 in the nocturnal flatfish Solea senegalensis: molecular cloning, tissue expression and daily rhythms in central areas. Comp Biochem Physiol A Mol Integr Physiol. 159(1):7–15.
   PubMed Web of Science ®Google Scholar
• Matsuzaka T, Shimano H. 2009. Elovl6: a new player in fatty acid metabolism and insulin sensitivity. J Mol Med. 87(4): 379–384.
   PubMed Web of Science ®Google Scholar
• Mazurais D, Porter M, Lethimonier G, LeDrean G, Le Goff P, Randall C, Pakdel F, Bromage N, Kah O. 2000. Effects of melatonin on liver estrogen receptor and vitellogenin expression in rainbow trout: an in vitro and in vivo study. Gen Comp Endocrinol. 118(2):344–353.
   PubMed Web of Science ®Google Scholar
• Miller BH, McDearmon EL, Panda S, Hayes KR, Zhang J, Andrews JL, Antoch MP, Walker JR, Esser KA, Hogenesch JB, et al. 2007. Circadian and CLOCK-controlled regulation of the mouse transcriptome and cell proliferation. Proc Natl Acad Sci U S A. 104(9):3342–3347. doi:10.1073/pnas.0611724104.
   PubMed Web of Science ®Google Scholar
• Mistlberger RE. 2011. Neurobiology of food anticipatory circadian rhythms. Physiol Behav. 104(4):535–545.
   PubMed Web of Science ®Google Scholar
• Montoya A, López-Olmeda JF, Yúfera M, Sánchez-Muros MJ, Sánchez-Vázquez FJ. 2010. Feeding time synchronises daily rhythms of behaviour and digestive physiology in gilthead seabream (Sparus aurata). Aquaculture. 306(1–4):315–321. doi:10.1016/j.aquaculture.2010.06.023.
   Web of Science ®Google Scholar
• Mukherji A, Kobiita A, Chambon P. 2015. Shifting the feeding of mice to the rest phase creates metabolic alterations, which, on their own, shift the peripheral circadian clocks by 12 hours. Proc Natl Acad Sci USA. 112(48):6683–6690.
   Web of Science ®Google Scholar
• Navarro-Guillén C, Engrola S, Yúfera M. 2018.Daily dynamic of digestive processes in Senegalese sole (Solea senegalensis) larvae and post-larvae. Aquaculture. 493:100–106.
   Web of Science ®Google Scholar
• Nisembaum LG, Velarde E, Tinoco AB, Azpeleta C, de Pedro N, Alonso-Gómez AL, Delgado MJ, Isorna E. 2012. Light-dark cycle and feeding time differentially entrains the gut molecular clock of the goldfish (Carassius auratus). Chronobiol Int. 29(6):665–673. doi:10.3109/07420528.2012.686947.
   PubMed Web of Science ®Google Scholar
• Pan X, Hussain MM. 2009. Clock is important for food and circadian regulation of macronutrient absorption in mice. J Lipid Res. 50(9):1800–1813.
   PubMed Web of Science ®Google Scholar
• Pan X, Terada T, Irie M, Saito H, Inui KI. 2002. Diurnal rhythm of H+-peptide cotransporter in rat small intestine. Am J Physiol Gastrointest Liver Physiol. 283(1):G57–64. doi:10.1152/ajpgi.00545.2001.
   PubMed Web of Science ®Google Scholar
• Pan X, Terada T, Okuda M, Inui KI. 2003. Altered diurnal rhythm of intestinal peptide transporter by fasting and its effects on the pharmacokinetics of ceftibuten. J Pharmacol Exp Ther. 307(2):626–632. doi:10.1124/jpet.103.055939.
   PubMed Web of Science ®Google Scholar
• Paredes JF, Vera LM, Martinez-Lopez F, Navarro I, Sánchez Vázquez FJ. 2014. Circadian rhythms of gene expression of lipid metabolism in Gilthead Sea bream liver: synchronisation to light and feeding time. Chronobiol Int. 31(5):613–626. doi:10.3109/07420528.2014.881837.
   PubMed Web of Science ®Google Scholar
• Polgár L. 2005. The catalytic triad of serine peptidases. Cell Mol Life Sci. 62(19–20):2161–2172.
   PubMed Web of Science ®Google Scholar
• Qin CJ, Gong Q, Wen ZY, Zou YC, Yuan DY, Shao T, Li HT. 2017. Comparative analysis of the liver transcriptome of Pelteobagrus vachellii with an alternative feeding time. Comp Biochem Physiol Part D Genomics Proteomics. 22:131–138.
   PubMed Web of Science ®Google Scholar
• Qin CJ, Shao T. 2015. The clock gene clone and its circadian rhythms in Pelteobagrus vachellii. Chin J Oceanol Limnol. 33(3):597–603.
   Web of Science ®Google Scholar
• Qin CJ, Sun JX, Wen ZY, Han YW, Liu YF, Yuan DY, Wang J. 2018. Comparative transcriptome sequencing of the intestine reveals differentially expressed genes in Pelteobagrus vachellii. Aquacult Res. 49:2560–2571.
   Web of Science ®Google Scholar
• Quintero JE, Kuhlman SJ, McMahon DG. 2003. The biological clock nucleus: a multiphasic oscillator network regulated by light. J Neurosci. 23(22):8070–8076.
   PubMed Web of Science ®Google Scholar
• Reppert SM, Weaver DR. 2002. Coordination of circadian timing in mammals. Nature. 418(6901):935–941.
   PubMed Web of Science ®Google Scholar
• Rideau N, De Sousa F, Larbier M. 1983. Diurnal variations in thee pancreatic proteases in the chicken fed with a meal. Ann Nutr Metab. 27(5):436–446.
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ,Smyth GK. 2010. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26(1):139–140.
   PubMed Web of Science ®Google Scholar
• Rutter J, Reick M, Wu LC, McKnight SL. 2001. Regulation of clock and NPAS2 DNA binding by the redox state of NAD cofactors. Science. 293(5529):510–514.
   PubMed Web of Science ®Google Scholar
• Sahar S, Masubuchi S, Eckel-Mahan K, Vollmer S, Galla L, Ceglia N, Masri S, Barth TK, Grimaldi B, Oluyemi O, Astarita G, Hallows WC, Piomelli D, Imhof A, Baldi P, Denu JM,Sassone-Corsi P. 2014. Circadian control of fatty acid elongation by SIRT1 protein-mediated deacetylation of acetyl-coenzyme A synthetase 1. J Biol Chem. 289(9):6091–6097.
   PubMed Web of Science ®Google Scholar
• Saltiel AR,Kahn CR. 2001. Insulin signalling and the regulation of glucose and lipid metabolism. Natural. 414(6865):799–806.
   PubMed Web of Science ®Google Scholar
• Sánchez JA, López-Olmeda JF, Blanco-Vives B, Sánchez-Vázquez FJ. 2009. Effects of feeding schedule on locomotor activity rhythms and stress response in sea bream. Physiol Behav. 98(1–2):125–129.
   PubMed Web of Science ®Google Scholar
• Silva Reis Y, Rodrigues Leite JL, Limade Almeida CA, Pereira DSP, Vidal LVO, de Araujo FG, Fortes-Silva R. 2019. New insights into tambaqui (Colossoma macropomum) feeding behavior and digestive physiology by the self-feeding approach: effects on growth, dial patterns of food digestibility, amylase activity and gastrointestinal transit time. Aquaculture. 498(1):116–122. doi:10.1016/j.aquaculture.2018.08.054.
   Google Scholar
• Stephan FK. 2002. The “other” circadian system: food as a Zeitgeber. J Biol Rhythms. 17(4):284–292.
   PubMed Web of Science ®Google Scholar
• Takahashi JS, Hong HK, Ko CH, McDearmon EL. 2008. The genetics of mammalian circadian order and disorder: implications for physiology and disease. Nat Rev Genet. 9(10):764–775. doi:10.1038/nrg2430.
   PubMed Web of Science ®Google Scholar
• Takeda Y, Kang HS, Lih FB, Jiang H, Blaner WS, Jetten AM. 2014. Retinoid acid- related orphan receptor, ROR, participates in diurnal transcriptional regulation of lipid metabolic genes. Nucleic Acids Res. 42(16):10448–10459.
   PubMed Web of Science ®Google Scholar
• Taylor IL. 1993. Role of peptide YY in the endocrine control of digestion. J Dairy Sci. 76(7):2094–2101.
   PubMed Web of Science ®Google Scholar
• Tillner R, Rønnestad I, Harboe T, Ueberschär B. 2013. Hormonal control of tryptic enzyme activity in Atlantic cod larvae (Gadus morhua): involvement of cholecystokinin during ontogeny and diurnal rhythm. Aquaculture. 402–403:133–140.
   Web of Science ®Google Scholar
• Velarde E, Haque R, Iuvone PM, Azpeleta C, Alonso-Gomez AL, Delgado MJ. 2009. Circadian clock genes of goldfish, Carassius auratus: cDNA cloning and rhythmic expression of period and cryptochrome transcripts in retina, liver and gut. J Biol Rhythms. 24(2):104–113.
   PubMed Web of Science ®Google Scholar
• Vera LM, Negrini P, Zagatti C, Frigato E, Sánchez-Vázquez FJ, Bertolucci C. 2013. Light and feeding entrainment of the molecular circadian clock in a marine teleost (Sparus aurata). Chronobiol Int. 30(5):649–661. doi:10.3109/07420528.2013.775143.
   PubMed Web of Science ®Google Scholar
• Völkl A, Poort C. 1983. Circadian rhythm of protein synthesis activity in the exocrine pancreas of fed and starved rats. J Cell Sci. 61:467–473.
   PubMed Web of Science ®Google Scholar
• Xie C, Mao X, Huang J, Ding Y, Wu J, Dong S,Wei L. 2011. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 39:316–322.
   PubMed Web of Science ®Google Scholar
• Yang RB, Xie CX, Wei KJ, Zheng WY, Lei CS, Feng K. 2006. The daily feeding rhythms of juvenile yellow catfish, Pelteobagrus fulvidraco at different feeding frequencies. J Huazhong Agric Univ. 25:274–276.
   Google Scholar
• Zabielski R. 2004. Reefs in experimental gastroenterology-cyclic activities of the gastrointestinal tract. J Physiol Pharmacol. 55:19–32.
   PubMedGoogle Scholar