Publications

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Metabolic Flux Analysis

  • Chen XW, Alonso AP, Allen DK, Reed JL, Shachar-Hill Y (2011) Synergy between 13C-Metabolic Flux Analysis and Flux Balance Analysis for understanding metabolic adaption to anaerobiosis in E. coli. Metabolic Engineering 13:38-48 PDF
  • Alonso AP, Val DL, Shachar-Hill Y (2011) Central metabolic fluxes in the endosperm of developing maize seeds and their implications for metabolic engineering. Metabolic Engineering 13:96-107 PDF
  • Alonso AP, Piasecki RJ, Wang Y, LaClair RW, Shachar-Hill Y (2010) Quantifying the labeling and the levels of plant cell wall precursors using ion chromatography tandem mass spectrometry. Plant Physiology 153: 915-924 PDF
  • Alonso AP, Dale VL, Shachar-Hill Y (2010) Understanding fatty acid synthesis in developing maize embryos using metabolic flux analysis. Metabolic Engineering 12: 488-497 PDF
  • Allen DK, Libourel IGL, Shachar-Hill Y (2009) Metabolic flux analysis in plants: coping with complexity. Plant Cell and Environment. 32: 1241-1257  PDF
  • Allen DK, Ohlrogge JB, Shachar-Hill Y (2009) The role of light in soybean seed filling metabolism. Plant Journal. 58:220-234  PDF
  • Libourel IGL, Shachar-Hill Y (2008) Metabolic flux analysis in plants: from intelligent design to rational engineering.  Annual Review of Plant Biology 59: 625-650  PDF
  • Alonso AP, Raymond P, Hernould M, Rondeau-Mouro C, de Graaf A, Chourey P, Lahaye M, Shachar-Hill Y, Rolin D, Dieuaide-Noubhani M (2007) A metabolic flux analysis to study the role of sucrose synthase in the regulation of the carbon partitioning in central metabolism in maize root tips. Metabolic Engineering 9: 419-432  PDF
  • Alonso AP, Goffman FD, Ohlrogge JB, Shachar-Hill Y (2007) Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos. Plant Journal 52: 296-308  PDF
  • Libourel I, Gehan J, Shachar-Hill Y (2007) Design of substrate label for steady state flux measurements in plant systems using the metabolic network of Brassica napus embryos. Phytochemistry 68: 2211-2221  PDF
  • Allen DK, Shachar-Hill Y, Ohlrogge JB (2007) Compartment-specific labeling information in 13C metabolic flux analysis of plants. Phytochemistry. 68: 2197-2210  PDF
  • McKinlay JB, Shachar-Hill Y, Zeikus JG, Vieille C (2007) Determining Actinobacillus succinogenes metabolic pathways and fluxes by NMR and GC-MS analyses of 13C-labeled metabolic product isotopomers. Metabolic Engineering.  9: 177–192 PDF
  • Schwender J, Shachar-Hill Y, Ohlrogge JB (2006) Mitochondrial metabolism in developing embryos of brassica napus. Journal of Biological Chemistry 281: 34040-34047  PDF
  • Ratcliffe RG and Shachar-Hill Y (2006) Measuring multiple fluxes through plant metabolic networks. Plant Journal 45: 490-511  PDF
  •  Goffman FD, Alonso AP, Schwender J, Shachar-Hill Y, Ohlrogge JB (2005) Light enables a very high efficiency of carbon storage in developing embryos of Brassica napus. Plant Physiology 138: 2269-2279  PDF
  • Schwender J, Goffman F, Ohlrogge JB, Shachar-Hill Y (2004) Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds. Nature 432: 779-782  PDF
  • Schwender J, Ohlrogge JB, Shachar-Hill Y (2004) Understanding flux in plant metabolic networks Current Opinion in Plant Biology 7: 309-317  PDF
  • Schwender J, Ohlrogge JB, Shachar-Hill Y (2003) A flux model of glycolysis and the oxidative pentosephosphate pathway in developing Brassica napus embryos. Journal of Biological Chemistry 278: 29442-29453  PDF
  • Alonso AP, Dale VL, Shachar-Hill Y (2011) Central metabolic fluxes in the endosperm of developing maize seeds and their implications for metabolic engineering. Metabolic Engineering 13: 96-107 PDF
  • Chen XW, Alonso AP, Allen DK, Reed JL, Shachar-Hill Y (2011) Synergy between 13C-Metabolic Flux Analysis and Flux Balance Analysis for understanding metabolic adaption to anaerobiosis in E. coli. Metabolic Engineering 13:38-48 PDF

 

 The Arbuscular Micorrhizal Symbiosis

  • Tian C, Kasiborski B, Koul R, Lammers PJ, Bucking H, Shachar-Hill Y (2010) Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbosis: gene characterization and the coordination of the expression with notrogen flux. Plant Physiology 153: 1175-1187 PDF
  •  GachomoE, Allen JW, Pfeffer PE, Govindarajulu M, JinH, Nagahashi G, Lammers PJ, Shachar-Hill Y, Bücking H (2009) Germinating spores of Glomus intraradices can use internal and exogenous nitrogen sources for de novo biosynthesis of amino acids. New Phytologist 184: 399-411 PDF
  • Allen JW, Shachar-Hill Y (2009) Sulfur transfer through an Arbuscular Mycorrhiza. Plant Physiology 149: 549-560  PDF
  • Martin F, Gianinazzi-Pearson V, Hijri M,  Lammers P, Requena N, Sanders IR, Shachar-Hill Y, Shapiro H, Tuskan GA,Young JPW (2008) The long hard road to a completed Glomus intraradices genome. New Phytologist 180: 735-750 PDF
  • Bucking H, Abubaker J, Govindarajulu M, Tala M, Pfeffer PE, Nagahashi G, Lammers P Shachar-Hill Y (2008) Root exudates stimulate the uptake and metabolism of organic carbon in germinating spores of Glomus intraradices. New Phytologist 180: 684-695  PDF
  • Shachar-Hill Y (2007) Quantifying flows through metabolic networks and the prospects for fluxomic studies of mycorrhizas. New Phytologist 174: 235-240.  PDF
  • Jin H, Pfeffer PE, Douds DD, Piotrowski E, Lammers PJ, Shachar-Hill Y (2005) The uptake, metabolism, transport and transfer of nitrogen in an arbuscular mycorrhizal symbiosis. New Phytologist 168: 687-696  PDF
  • Govindarajulu M, Pfeffer PE, Jin H, Abubaker J, Douds DD, Allen JW, Bücking H, Lammers PJ, Shachar-Hill Y (2005) Nitrogen transfer in the arbuscular mycorrhizal symbiosis. Nature 435: 819-823  PDF
  • Bücking H, Shachar-Hill Y (2005) Phosphate uptake, transport and transfer by the arbuscular mycorrhizal fungus Glomus intraradices is stimulated by increased carbohydrate availability. New Phytologist 165: 899-912  PDF
  • Pfeffer PE, Douds DD, Bücking H, Schwartz DP, Shachar-Hill Y (2004) The fungus does not transfer carbon to or between roots in an arbuscular mycorrhizal symbiosis. New Phytologist 163: 617–627    PDF
  • Bago B, Pfeffer PE, Abubaker J, Jun J, Allen JW, Brouillette J, Douds DD, Lammers PJ, Shachar-Hill Y (2003)  Carbon export from arbuscular mycorrhizal roots involves the translocation of carbohydrate as well as lipid. Plant Physiology 131: 1496-1507  PDF
  • Bago B, Zipfel W, Williams R, Jun J, Arreola R, Lammers P, Pfeffer PE, Shachar-Hill Y (2002) Translocation and utilization of fungal lipid in the arbuscular mycorrhizal symbiosis. Plant Physiology 128: 108-124  PDF
  • Lammers PJ, Jun J, Abubaker J, Arreola R, Gopalan A, Bago B, Hernandez-Sebastia C, Allen JW, Douds DD, Pfeffer PE, Shachar-Hill Y (2001) The glyoxylate cycle in an arbuscular mycorrhizal fungus: gene expression and carbon flow. Plant Physiology 127:1287-1298  PDF
  • Bago B, Pfeffer P, Shachar-Hill Y (2001) Could the urea cycle be transporting nitrogen in the arbuscular mycorrhzal symbiosis? New Phytologist 149: 4-8 PDF
  • Bago B, Pfeffer PE, Shachar-Hill Y (2000) Carbon metabolism and transport in arbuscular mycorrhizas. Plant Physiology 124: 949-957  PDF
  • Bago, B, Pfeffer PE, Douds DD, Brouillette J, Becard G, Shachar-Hill Y (1999) Carbon metabolism in spores of  the arbuscular mycorrhizal fungus Glomus  intraradices as revealed by NMR  spectroscopy. Plant Physiology 121: 263-272  PDF
  • Pfeffer PE, Douds DD, Bécard G, Shachar-Hill Y (1999) Carbon Uptake and the Metabolism and Transport of Lipids in an Arbuscular Mycorrhiza. Plant Physiology 120: 587-598  PDF
  • Shachar-Hill Y, Pfeffer PE, Douds D, Osman SF, Doner LW, Ratcliffe RG (1995) Partitioning of intermediary carbon metabolism in VAM-colonized leek. Plant Physiology 108: 7-15 [cover article]  PDF

 

One Carbon Metabolism

  • Collakova E, Goyer A, Naponelli V, Krassovskaya I, Gregory JF, Hanson AD, Shachar-Hill Y (2008) Arabidopsis 10-Formyl tetrahydrofolate deformylases are essential for photorespiration. Plant Cell 20: 1818-1832  PDF
  • Goyer A, Collakova E, Shachar-Hill Y,  Hanson AD (2007) Functional Characterization of a Methionine γ-Lyase in Arabidopsis and its Implication in an Alternative to the Reverse Trans-sulfuration Pathway. Plant and Cell Physiology 48: 232–242  PDF
  • Goyer A, Collakova A, de la Garza RD, Quinlivan EP, Williamson J, Gregory JF, Shachar-Hill Y, Hanson AD (2005) 5-Formyltetrahydrofolate is an inhibitory but well tolerated metabolite in Arabidopsis leaves. Journal of Biological Chemistry 280: 26137-26142.   PDF
  • Goyer A, Johnson TL, Olsen LJ, Collakova E, Shachar-Hill Y, Rhodes D, Hanson AD (2004) Characterization and Metabolic Function of a Peroxisomal Sarcosine and Pipecolate Oxidase from Arabidopsis. Journal of Biological Chemistry 279: 16947-16953 PDF
  • Quinlivan EP, Roje S, Basset G, Shachar-Hill Y, Gregory JF(III), Hanson AD (2003) The Folate Precursor p-Aminobenzoate is reversibly converted to its glucose ester in the plant cytosol Journal of Biological Chemistry 278: 20731-20737 PDF
  • McNeil SD, Rhodes D, Russell BL, Nuccio ML, Shachar-Hill Y, Hanson AD (2000) Metabolic modeling identifies key constraints on an engineered glycine betaine synthesis pathway in tobacco.  Plant Physiology 124: 153-162 PDF
  • McNeil SD, Nuccio ML, Rhodes D, Shachar-Hill Y, Hanson AD (2000) Radiotracer and computer modeling evidence that phospho-base methylation is the main route of choline synthesis in tobacco. Plant Physiology 123: 371-380 PDF
  • Hanson AD, Gage DA, Shachar-Hill Y (2000) Plant one-carbon metabolism and its engineering. Trends in Plant Science 5: 206-213 PDF
  • Roje S, Wang H, McNeil SD, Raymond RK, Appling DR, Shachar-Hill Y, Bohnert  HJ, Hanson AD (1999) Isolation, characterization, and functional expression of cDNAs  encoding NADH-dependent  methylenetetrahydrofolate reductase from  higher plants. Journal of Biological Chemistry 274: 36089-36096 PDF

 

Other Interests

  • Miller R, Wu G, Desphande RR, Vieler A, Gaertner K, Li X, Moellering ER, Zäuner S, Cornish A, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, Shiu SH, Benning C (2010) Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen-deprivation predict diversion of metabolism. Plant Physiology 154: 1737-1752 PDF
  • Ohlrogge J, Allen D, Berguson W, DellaPenna D, Shachar-Hill Y, Sten Stymne (2009) Driving on Biomass. Science 324: 1019-1020  PDF
  • Last RL, Jones AD, Shachar-Hill Y (2007) Towards the plant metabolome and beyond. Nature Reviews Molecular Cell Biology 8: 167 – 174 PDF
  • Ratcliffe RG, Shachar-Hill Y (2005) Revealing metabolic phenotypes in plants: inputs from NMR analysis. Biological Reviews 80: 27–43 PDF
  • Goffman F, Ruckle M, Ohlrogge J, Shachar-Hill Y (2004)  CO2 concentration in developing oilseeds. Plant Physiology and Biochemistry 42: 703-708  PDF
  • Hill AE, Hill BS, Shachar-Hill Y (2004) What are Aquaporins for? Journal of Membrane Biology.  197:  1-32  PDF 
  • Shachar-Hill Y (2002) Nuclear Magnetic Resonance in plant metabolic engineering. Metabolic Engineering 4: 90-97 PDF
  • Quigley F, Rosenberg RM, Shachar-Hill Y, Bohnert HJ (2001) From Genome to Function – the Arabidopsis Aquaporins. Genome Biology 3: 1-17 PDF
  • Ratcliffe RG, Shachar-Hill Y (2001) Probing Plant metabolism with NMR Annual Review of Plant Physiology and Plant molecular Biology. 52: 499-526 PDF
  • Miller R, Wu G, Desphande RR, Vieler A, Gaertner K, Li X, Moellering ER, Zäuner S, Cornish A, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, Shiu SH, Benning C (2010) Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen-deprivation predict diversion of metabolism. Plant Physiology 154: 1737-1752 PDF