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  • Armstrong J, Armstrong W. 2009. Record rates of pressurized gas-flow in the great horsetail, Equisetum telmateia. Were Carboniferous Calamites similarly aerated? New Phytologist 184: 202215.
  • Armstrong W, Drew MC. 2002. Root growth and metabolism under oxygen deficiency. In: WaiselY, EshelA, KafkafiU, eds. Plant roots: the hidden half, 3rd edn. New York, NY, USA: Marcel Dekker, 729761.
  • Armstrong W, Strange ME, Cringle S, Beckett PM. 1994. Microelectrode and modelling study of oxygen distribution in roots. Annals of Botany (London) 74: 287299.
  • Armstrong W, Webb T, Darwent M, Beckett PM. 2009. Measuring and interpreting respiratory critical oxygen pressures in roots. Annals of Botany (London) 103: 281293.
  • Bailey-Serres J, Voesenek LA. 2008. Flooding stress: acclimations and genetic diversity. Annual Review of Plant Biology 59: 313339.
  • Baldi P, Long AD. 2001. A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509519.
  • Banti V, Mafessoni F, Loreti E, Alpi A, Perata P. 2010. The heat-inducible transcription factor HsfA2 enhances anoxia tolerance in Arabidopsis. Plant Physiology 152: 14711483.
  • Benamar A, Rolletschek H, Borisjuk L, Avelange-Macherel MH, Curien G, Mostefai HA, Andriantsitohaina R, Macherel D. 2008. Nitrite–nitric oxide control of mitochondrial respiration at the frontier of anoxia. Biochimica et Biophysica Acta 1777: 12681275.
  • Bologa KL, Fernie AR, Leisse A, Loureiro ME, Geigenberger P. 2003. A bypass of sucrose synthase leads to low internal oxygen and impaired metabolic performance in growing potato tubers. Plant Physiology 132: 20582072.
  • Borisjuk L, Rolletschek H. 2009. The oxygen status of the developing seed. New Phytologist 182: 1730.
  • Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J. 2008. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant Journal 56: 743755.
  • Burke PV, Poyton RO. 1998. Structure/function of oxygen-regulated isoforms in cytochrome c oxidase. Journal of Experimental Biology 201: 11631175.
  • Carroll AD, Fox GG, Laurie S, Phillips R, Ratcliffe RG, Stewart GR. 1994. Ammonium assimilation and the role of [gamma]-aminobutyric acid in pH homeostasis in carrot cell suspensions. Plant Physiology 106: 513520.
  • Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. 2010a. Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.). Plant Cell Physiology 51: 2137.
  • Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW. 2010b. Comparisons of early transcriptome responses to low-oxygen environments in three dicotyledonous plant species. Plant Signalling and Behaviour 30: 10061009.
  • Colmer TD, Voesenek LACJ. 2009. Flooding tolerance: suites of plant traits in variable environments. Functional Plant Biology 36: 665681.
  • Crawford LA, Bown AW, Breitkreuz KE, Guinel FC. 1994. The synthesis of [gamma]-aminobutyric acid in response to treatments reducing cytosolic pH. Plant Physiology 104: 865871.
  • van Dongen JT, Fröhlich A, Ramírez-Aguilar SJ, Schauer N, Fernie AR, Erban A, Kopka J, Clark J, Langer A, Geigenberger P. 2009. Transcript and metabolite profiling of the adaptive response to mild decreases in oxygen concentration in the roots of arabidopsis plants. Annals of Botany (London) 103: 269280.
  • van Dongen JT, Schurr U, Pfister M, Geigenberger P. 2003. Phloem metabolism and function have to cope with low internal oxygen. Plant Physiology 131: 15291543.
  • Ferrari TE, Varner JE. 1971. Intact tissue assay for nitrite reductase in barley aleurone layers. Plant Physiology 47: 790794.
  • Fukao T, Xu K, Ronald PC, Bailey-Serres J. 2006. A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18: 20212034.
  • Garrocho-Villegas V, Gopalasubramaniam SK, Arredondo-Peter R. 2007. Plant hemoglobins: what we know six decades after their discovery. Gene 398: 7885.
  • Geigenberger P. 2003. Response of plant metabolism to too little oxygen. Current Opinions in Plant Biology 6: 247256.
  • Geigenberger P, Fernie AR, Gibon Y, Christ M, Stitt M. 2000. Metabolic activity decreases as an adaptive response to low internal oxygen in growing potato tubers. Biological Chemistry 381: 723740.
  • Gibon Y, Vigeolas H, Tiessen A, Geigenberger P, Stitt M. 2002. Sensitive and high throughput metabolite assays for inorganic pyrophosphate, ADPGlc, nucleotide phosphates, and glycolytic intermediates based on a novel enzymic cycling system. Plant Journal 30: 221235.
  • Guglielminetti L, Busilacchi HA, Perata P, Alpi A. 2001. Carbohydrate–ethanol transition in cereal grains under anoxia. New Phytologist 151: 607612.
  • Gupta KJ, Kaiser WM. 2010. Production and scavenging of nitric oxide by barley root mitochondria. Plant Cell Physiology 51: 576584.
  • Gupta KJ, Zabalza A, van Dongen JT. 2009. Regulation of respiration when the oxygen availability changes. Physiologia Plantarum 137: 383391.
  • Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H. 2009. The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460: 10261030.
  • Hinz M, Wilson IW, Yang J, Buerstenbinder K, Llewellyn D, Dennis ES, Sauter M, Dolferus R. 2010. Arabidopsis RAP2.2: an ethylene response transcription factor that is important for hypoxia survival. Plant Physiology 153: 757772.
  • Hunag X, von Rad U, Durner J. 2005. Nitric oxide induces transcriptional activation of the nitric oxide-tolerant alternative oxidase in Arabidopsis suspension cells. Planta 215: 914923.
  • Igamberdiev AU, Bykova NV, Shah JK, Hill RD. 2010. Anoxic nitric oxide cycling in plants: participating reactions and possible mechanisms. Physiologia Plantarum 138: 393404.
  • Igamberdiev AU, Hill RD. 2009. Plant mitochondrial function during anaerobiosis. Annals of Botany (London) 103: 259268.
  • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511518.
  • Kreuzwieser J, Hauberg J, Howell KA, Carroll A, Rennenberg H, Millar AH, Whelan J. 2009. Differential response of gray poplar leaves and roots underpins stress adaptation during hypoxia. Plant Physiology 149: 461473.
  • Lee KW, Chen PW, Lu CA, Chen S, Ho TH, Yu SM. 2009. Coordinated responses to oxygen and sugar deficiency allow rice seedlings to tolerate flooding. Science Signalling 2: ra61.
  • Li Y, Green LS, Holtzapffel R, Day DA, Bergersen FJ. 2001. Supply of O2 regulates demand for O2 and uptake of malate by N2-fixing bacteroids from soybean nodules. Microbiology 147: 663670.
  • Licausi F, van Dongen JT, Giuntoli B, Novi G, Santaniello A, Geigenberger P, Perata P. 2010. HRE1 and HRE2, two hypoxia-inducible ethylene response factors, affect anaerobic responses in Arabidopsis thaliana. Plant Journal 62: 302315.
  • Licausi F, Weits DA, Pant BD, Scheible WR, Geigenberger P, van Dongen JT. 2011. Hypoxia responsive gene expression is mediated by various subsets of transcription factors and miRNAs that are determined by the actual oxygen availability. New Phytologist 190: 442456.
  • Matthew T, Zhou W, Rupprecht J, Lim L, Thomas-Hall SR, Doebbe A, Kruse O, Hankamer B, Marx UC, Smith SM. 2009. The metabolome of Chlamydomonas reinhardtii following induction of anaerobic H2 production by sulfur depletion. Journal Biological Chemistry 284: 2341523425.
  • Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J. 2010. Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses. Plant Physiology 152: 14841500.
  • Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, Galbraith DW, Girke T, Bailey-Serres J. 2009. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proceedings of the National Academy of Sciences, USA 106: 1884318848.
  • Nagai K, Hattori Y, Ashikari M. 2010. Stunt or elongate? Two opposite strategies by which rice adapts to floods. Journal Plant Research 123: 303309.
  • Narsai R, Howell KA, Carroll A, Ivanova A, Millar AH, Whelan J. 2009. Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiology 151: 306322.
  • Paterson AH, Freeling M, Tang H, Wang X. 2010. Insights from the comparison of plant genome sequences. Annual Review of Plant Biology 61: 49372.
  • Perata P, Voesenek LA. 2007. Submergence tolerance in rice requires Sub1A, an ethylene-response-factor-like gene. Trends in Plant Science 12: 4346.
  • Pierik R, Millenaar FF, Peeters AJ, Voesenek LA. 2005. New perspectives in flooding research: the use of shade avoidance and Arabidopsis thaliana. Annals of Botany 96: 533540.
  • Remm M, Storm CE, Sonnhammer EL. 2001. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314: 10411052.
  • Rocha M, Licausi F, Araújo WL, Nunes-Nesi A, Sodek L, Fernie AR, Van Dongen JT. 2010a. Glycolysis and the tricarboxylic acid cycle are linked by alanine aminotransferase during hypoxia induced by waterlogging of Lotus japonicus. Plant Physiology 152: 15011513.
  • Rocha M, Sodek L, Licausi F, Hameed MW, Dornelas MC, van Dongen JT. 2010b. Analysis of alanine aminotransferase in various organs of soybean (Glycine max) and in dependence of different nitrogen fertilisers during hypoxic stress. Amino Acids 39: 10431053.
  • Rockel P, Strube F, Rockel A, Wildt J, Kaiser WM. 2002. Regulation of nitric oxide (NO) production by plant nitrate reductase in vivo and in vitro. Journal of Experimental Botany 53: 103110.
  • Semenza GL. 2007. Oxygen-dependent regulation of mitochondrial respiration by hypoxia-inducible factor 1. Biochemical Journal 405: 19.
  • Smagghe BJ, Hoy JA, Percifield R, Kundu S, Hargrove MS, Sarath G, Hilbert JL, Watts RA, Dennis ES, Peacock WJ. 2009. Correlations between oxygen affinity and sequence classifications of plant hemoglobins. Biopolymers 91: 10831096.
  • Summers JE, Ratcliffe RG, Jackson MB. 2000. Anoxia tolerance in the aquatic monocot Potamogeton pectinatus absence of oxygen stimulates elongation in association with an unusually large pasteur effect. Journal of Experimental Botany 51: 14131422.
  • Sweetlove LJ, Beard KF, Nunes-Nesi A, Fernie AR, Ratcliffe RG. 2010. Not just a circle: flux modes in the plant TCA cycle. Trends in Plant Science 15: 462470.
  • Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M. 2004. MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal 37: 914939.
  • Tronconi MA, Fahnenstich H, Gerrard Weehler MC, Andreo CS, Flügge UI, Drincovich MF, Maurino VG. 2008. Arabidopsis NAD-malic enzyme functions as a homodimer and heterodimer and has a major impact on nocturnal metabolism. Plant Physiology 146: 15401552.
  • Usadel B, Nagel A, Steinhauser D, Gibon Y, Blasing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F. 2006. PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7: 535.
  • Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D. 2005. Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses. Plant Physiology 138: 11951204.
  • Vanlerberghe GC, Horsey AK, Weger HG, Turpin DH. 1989. Anaerobic carbon metabolism by the tricarboxylic acid cycle: evidence for partial oxidative and reductive pathways during dark ammonium assimilation. Plant Physiology 91: 15511557.
  • Vinh le S, Von Haeseler A. 2004. IQPNNI: moving fast through tree space and stopping in time. Molecular Biology and Evolution 21: 15651571.
  • Wendehenne D, Durner J, Klessig DF. 2004. Nitric oxide: a new player in plant signalling and defence responses. Current Opinions in Plant Biology 7: 449455.
  • Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution 18: 691699.
  • Xu K, Xu X, Fukao T, Canlas P, Maghirang-Rodriguez R, Heuer S, Ismail AM, Bailey-Serres J, Ronald PC, Mackill DJ. 2006. Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442: 705708.
  • Zabalza A, van Dongen JT, Froehlich A, Oliver SN, Faix B, Gupta KJ, Schmälzlin E, Igal M, Orcaray L, Royuela M. 2009. Regulation of respiration and fermentation to control the plant internal oxygen concentration. Plant Physiology 149: 10871098.