Ge 145 - Isotopic Biogeochemistry Seminar

Dr. Alex Sessions, Fall 2007

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General Info

• Time: Tuesdays 1-4pm, NM015 (Geochem conference room)
• Syllabus

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Topic

This year we will consider the question: How can we explain the tremendous variability in D/H ratios of biochemicals found throughout the biological world? Selected readings will cover subjects ranging from the controls on intracellular and leaf water, to metabolic fractionations and biosynthetic processes.

Week

1 2 3 4 5 6 7 8 9 10

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Reading Materials

Week 1 (Oct-2) - Controls on Intracellular Water

discussion leader: Anne Dekas

Papers for discussion:

• Kreuzer-Martin H. W., Lott M. J., Ehleringer J. R., and Hegg E. L. (2006) Metabolic processes account for the majority of the intracellular water in log-phase Escherichia coli cells as revealed by hydrogen isotopes. Biochemistry 45(45), 13622-13630.
• Booth I. R. and Louis P. (1999) Managing hypoosmotic stress: aquaporins and mechanosensitive channels in Escherichia coli. Current Opinions in Microbiology 2(2), 166-169.
• Haines T. H. (1994) Water transport across biological membranes. FEBS Letters 346, 115-122.

Supplemental references:

• Fu D. and Lu M. (2007) The structural basis of water permeation and proton exclusion in aquaporins. Molecular Membrane Biology 24(5-6), 366-374.
• Mamonov A. B., Coalson R. D., Zeidel M. L., and Mathai J. C. (2007) Water and deuterium oxide permeability through aquaporin 1: MD predictions and experimental verification. Journal of General Physiology 130(1), 111-116.
• Kreuzer-Martin H. W., Ehleringer J. R., and Hegg E. L. (2005) Oxygen isotopes indicate most intracellular water in log-phase Escherichia coli is derived from metabolism. Proceedings of the National Academy of Sciences 102(48), 17337-17341.
• Wang Y., Schulten K., and Tajkhorshid E. (2005) What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF. Structure 13(8), 1107-1118.
• King L. S., Kozono D., and Agre P. (2004) From structure to disease: The evolving tale of aquaporin biology. Nature Reviews Molecular Cell Biology 5(9), 687-698.
• Ronsch H., Kramer R., and Morbach S. (2003) Impact of osmotic stress on volume regulation, cytoplasmic solute composition and lysine production in Corynebacterium glutamicum MH20-22B. Journal of Biotechnology 104(1-3), 87-97.
Mathai J. C., Sprott G. D., and Zeidel M. L. (2001) Molecular mechanisms of water and solute transport across archaebacterial lipid membranes. Journal of Biological Chemistry 276(29), 27266-27271.
Chrispeels M. J., Morillon R., Maurel C., Gerbeau P., Kjellbom P., and Johansson I. (2001) Aquaporins of plants: Structure, function, regulation, and role in plant water relations. Aquaporins 51, 277-334.
Johansson I., Karlsson M., Johanson U., Larsson C., and Kjellbom P. (2000) The role of aquaporins in cellular and whole plant water balance. Biochimica Et Biophysica Acta-Biomembranes 1465(1-2), 324-342.
• Borgnia M., Nielsen S., Engel A., and Agre P. (1999) Cellular and molecular biology of the aquaporin water channels. Annual Review of Biochemistry 68, 425-458.

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Week 2 (Oct-9) - Controls on Plant Tissue Water

discussion leader: Sarah Feakins

Papers for discussion:

• Cernusak L. A., Pate J. S., and Farquhar G. D. (2002) Diurnal variation in the stable isotope composition of water and dry matter in fruiting Lupinus angustifolius under field conditions. Plant Cell and Environment 25(7), 893-907.
• Roden J. S. and Ehleringer J. R. (1999) Observations of hydrogen and oxygen isotopes in leaf water confirm the Craig-Gordon model under wide-ranging environmental conditions. Plant Physiology 120(4), 1165-1173.
• Barbour M. M. and Farquhar G. D. (2003) Do pathways of water movement and leaf anatomical dimensions allow development of gradients in (H2O)-O-18 between veins and the sites of evaporation within leaves? Plant Cell and Environment 27(1), 107-121.

Supplemental references:

• Barbour M. M., Roden J. S., Farquhar G. D., and Ehleringer J. R. (2004) Expressing leaf water and cellulose oxygen isotope ratios as enrichment above source water reveals evidence of a Peclet effect. Oecologia 138(3), 426-435.
• Farquhar G. D., Cernusak L. A., and Barnes B. (2007) Heavy water fractionation during transpiration. Plant Physiology 143(1), 11-18.
• Leaney F. W., Osmond C. B., Allison G. B., and Ziegler H. (1985) Hydrogen-Isotope Composition of Leaf Water in C-3 and C-4 Plants - Its Relationship to the Hydrogen-Isotope Composition of Dry-Matter. Planta 164(2), 215-220.
• Yakir D., DeNiro M. J., and Rundel P. W. (1989) Isotopic inhomogeneity of leaf water: Evidence and implications for the use of isotopic signals transduced by plants. Geochimica et Cosmochimica Acta 53, 2769-2773.

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Week 4 (Oct-23) - Isotope Effects in Photosynthesis

discussion leader: Laurent

Papers for discussion:

• Haumann M., Bogershausen O., Cherepanov D., Ahlbrink R., and Junge W. (1997) Photosynthetic oxygen evolution: H/D isotope effects and the coupling between electron and proton transfer during the redox reactions at the oxidizing side of Photosystem II. Photosynthesis Research 51, 193-208.
• Luo Y.-H., Sternberg L., Suda S., Kumazawa S., and Mitsui A. (1991) Extremely low D/H ratios of photoproduced hydrogen by cyanobacteria. Plant and Cell Physiology 32(6), 897-900.
• Estep M. F. and Hoering T. C. (1981) Stable hydrogen isotope fractionations during autotrophic and mixotrophic growth of microalgae. Plant Physiology 67, 474-477.

Supplemental references:

• (help?)

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Week 5 (Oct-30) - Isotope Effects in Carbohydrate Metabolism

discussion leader: Ashley Jones

Papers for discussion:

• Roden J. S., Lin G. G., and Ehleringer J. R. (2000) A mechanistic model for interpretation of hydrogen and oxygen isotope ratios in tree-ring cellulose. Geochimica Et Cosmochimica Acta 64(1), 21-35.
• Yakir D. and DeNiro M. J. (1990) Oxygen and hydrogen isotope fractionation during cellulose metabolism in Lemna gibba L. Plant Physiology 93, 325-332.
• Schleucher J., Vanderveer P., Markley J. L., and Sharkey T. D. (1999) Intramolecular deuterium distributions reveal disequilibrium of chloroplast phophoglucose isomerase. Plant, Cell, and Environment 22, 525-533.

Supplemental references:

• Schleucher J., Vanderveer P. J., and Sharkey T. D. (1998) Export of carbon from chloroplasts at night. Plant Physiology 118, 1439-1445.
• Sternberg L. d. S. L., DeNiro M. J., and Savidge R. A. (1986) Oxygen isotope exchange between metabolites and water during biochemical reactions leading to cellulose synthesis. Plant Physiology 82, 423-427.
• Yakir D. (1992) Variations in the natural abundance of oxygen-18 and deuterium in plant carbohydrates. Plant, Cell, and Environment 15, 1005-1020.
• Luo Y. H. and Sternberg L. (1991) Deuterium heterogeneity in starch and cellulose nitrate of CAM and C3 plants. Phytochemistry 30(4), 1095-1098.
• Augusti A., Betson T. R., and Schleucher J. (2006) Hydrogen exchange during cellulose synthesis distinguishes climatic and biochemical isotope fractionations in tree rings. New Phytologist 172(3), 490-499.
• Schmidt H. L. and Eisenreich W. (2001) Systematic and regularities in the origin of H-2 patterns in natural compounds. Isotopes in Environmental and Health Studies 37(3), 253-254.
• Schmidt H.L., Werner R.A., and Eisenreich W. (2003) Systematics of 2H patterns in natural compounds and its importance for the elucidation of biosynthetic pathways. Phytochemistry Reviews 2, 61-85.
• Terwilliger V. J. and DeNiro M. J. (1995) Hydrogen isotope fractionation in wood-producing avocado seedlings: Biological constraints to paleoclimatic interpretations of dD values in tree ring cellulose nitrate. Geochimica et Cosmochimica Acta 59(24), 5199-5207.
• Terwilliger V. J., Kitajima K., Le Roux-Swarthout D. J., Mulkey S., and Wright S. J. (2001) Influences of heterotrophic and autotrophic resource use on carbon and hydrogen isotopic compositions of tropical tree leaves. Isotopes in Environmental and Health Studies 37, 133-160.
• Terwilliger V. J., Betancourt J. L., Leavitt S. W., and Van de Water P. K. (2002) Leaf cellulose delta D and delta O-18 trends with elevation differ in direction among co-occurring, semiarid plant species. Geochimica Et Cosmochimica Acta 66(22), 3887-3900.

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Week 6 (Nov-8) - Isotope Effects in Isoprenoid vs n-Alkyl Lipids

discussion leader: Ying Wang

Papers for discussion:

• Chikaraishi Y., Naraoka H., and Poulson S. R. (2004) Carbon and hydrogen isotopic fractionation during lipid biosynthesis in a higher plant (Cryptomeria japonica). Phytochemistry 65(3), 323-330.
• Rohmer M. (2003) Mevalonate-independent methylerythritol phosphate pathway for isoprenoid biosynthesis. Elucidation and distribution. Pure and Applied Chemistry 75(2-3), 375-387.
• Magnuson K., Jackowski S., Rock C. O., and Cronan J. E., Jr. (1993) Regulation of Fatty Acid Biosynthesis in Escherichia coli. Microbiological Reviews 57(3), 522-542.

Supplemental references:

• Rohmer M. (1999) The mevalonate-independent methylerythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis, including carotenoids. Pure and Applied Chemistry 71(12), 2279-2284.
• Lange B. M., Rujan T., Martin W., and Croteau R. (2000) Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes. Proceedings of the National Academy of Science 97(24), 13172-13177.
• Bach T. J. (1995) Some New Aspects of Isoprenoid Biosynthesis in Plants - a Review. Lipids 30(3), 191-202.
• Boucher Y. and Doolittle W. F. (2000) The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Molecular Microbiology 37(4), 703-716.
• Boucher Y., Kamekura M., and Doolittle W. F. (2004) Origins and evolution of isoprenoid lipid biosynthesis in archaea. Molecular Microbiology 52(2), 515-527.
• Chappell J. (1995) Biochemistry and Molecular-Biology of the Isoprenoid Biosynthetic-Pathway in Plants. Annual Review of Plant Physiology and Plant Molecular Biology 46, 521-547.
• Chappell J. (1995) The Biochemistry and Molecular-Biology of Isoprenoid Metabolism. Plant Physiology 107(1), 1-6.
• Laule O., Furholz A., Chang H. S., Zhu T., Wang X., Heifetz P. B., Gruissem W., and Lange B. M. (2003) Crosstalk between cytosolic and plastidial pathways of isoprenoid biosynthesis in Arabidopsis thaliana. Proceedings of the National Academy of Sciences 100(11), 6866-6871.

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Week 7 (Nov-13) - Intramolecular Distribution of D

discussion leader: Weifu Guo

Papers for discussion:

• Zhang B. L., Pionnier S., and Buddrus S. (2006) Deuterium NMR study of the origin of hydrogen in fatty acids produced in vivo by chicken. European Journal of Lipid Science and Technology 108(2), 125-133.
• Billault I., Duan J. R., Guiet S., and Robins R. J. (2005) Quantitative deuterium isotopic profiling at natural abundance indicates mechanistic differences for Delta(12)-epoxidase and Delta(12)-desaturase in Vernonia galamensis. Journal of Biological Chemistry 280(18), 17645-17651.
• Duan J. R., Billault I., Mabon F., and Robins R. (2002) Natural deuterium distribution in fatty acids isolated from peanut seed oil: A site-specific study by quantitative H-2 NMR spectroscopy. Chembiochem 3(8), 752-759.

Supplemental references:

• Billault I., Guiet S., Mabon F., and Robins R. (2001) Natural deuterium distribution in long-chain fatty acids is nonstatistical: A site-specific study by quantitative H-2 NMR spectroscopy. Chembiochem 2(6), 425-431.
• Markai S., Marchand P. A., Mabon F., Baguet E., Billault I., and Robins R. J. (2002) Natural deuterium distribution in branched-chain medium-length fatty acids is nonstatistical: A site-specific study by quantitative H-2 NMR spectroscopy of the fatty acids of capsaicinoids. Chembiochem 3(2-3), 212-218.
• Royer A., Naulet N., Mabon F., Lees M., and Martin G. J. (1999) Stable isotope characterization of olive oils. II - Deuterium distribution in fatty acids studied by nuclear magnetic resonance. Journal of the American Oil Chemists Society 76(3), 365-373.
• Chikaraishi Y., Suzuki Y., and Naraoka H. (2004) Hydrogen isotopic fractionations during desaturation and elongation associated with polyunsaturated fatty acid biosynthesis in marine macroalgae. Phytochemistry 65(15), 2293-2300.

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Week 8 (Nov-20) - D/H Differences in C3 vs C4 Plants

discussion leader: Alon Amrani

Papers for discussion:

• Smith F. A. and Freeman K. H. (2006) Influence of physiology and climate on delta D of leaf wax n-alkanes from C-3 and C-4 grasses. Geochimica Et Cosmochimica Acta 70(5), 1172-1187.
• Ogee J., Cuntz M., Peylin P., and Bariac T. (2007) Non-steady-state, non-uniform transpiration rate and leaf anatomy effects on the progressive stable isotope enrichment of leaf water along monocot leaves. Plant Cell and Environment 30(4), 367-387.
• Zhang B. L., Billault I., Li X., Mabon F., Remaud G., and Martin M. L. (2002) Hydrogen isotopic profile in the characterization of sugars. Influence of the metabolic pathway. Journal of Agriculture and Food Chemistry 50, 1574-1580.

Supplemental references:

• Leaney F. W., Osmond C. B., Allison G. B., and Ziegler H. (1985) Hydrogen-Isotope Composition of Leaf Water in C-3 and C-4 Plants - Its Relationship to the Hydrogen-Isotope Composition of Dry-Matter. Planta 164(2), 215-220.
• Chikaraishi Y. and Naraoka H. (2001) Organic hydrogen-carbon isotope signatures of terrestrial higher plants during biosynthesis for distinctive photosynthetic pathways. Geochemical Journal 35, 451-458.
• Chikaraishi Y. and Naraoka H. (2003) Compound-specific dD-d13C analyses of n-alkanes extracted from terrestrial and aquatic plants. Phytochemistry 63, 361-371.
• Chikaraishi Y., Naraoka H., and Poulson S. R. (2004) Hydrogen and carbon isotopic fractionations of lipid biosynthesis among terrestrial (C3, C4 and CAM) and aquatic plants. Phytochemistry 65(10), 1369-1381.
• Sternberg L., DeNiro M. J., and Ajie H. (1984) Stable hydrogen isotope ratios of saponifiable lipids and cellulose nitrate from CAM, C3 and C4 plants. Phytochemistry 23(11), 2475-2477.
• Sternberg L. d. S. L., DeNiro M. J., and Johnson H. B. (1986) Oxygen and hydrogen isotope ratios of water from photosynthetic tissues of CAM and C3 plants. Plant Physiology 82, 428-431.
• Flanagan L. B., Comstock J. P., and Ehleringer J. R. (1991) Comparison of Modeled and Observed Environmental-Influences on the Stable Oxygen and Hydrogen Isotope Composition of Leaf Water in Phaseolus-Vulgaris L. Plant Physiology 96(2), 588-596.

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Week 9 (Nov-27) - D/H Differences between Plant Forms

discussion leader: Meghan Kelleher

Papers for discussion:

• Hou J. Z., D'Andrea W. J., MacDonald D., and Huang Y. S. (2007) Hydrogen isotopic variability in leaf waxes among terrestrial and aquatic plants around Blood Pond, Massachusetts (USA). Organic Geochemistry 38(6), 977-984.
• Bi X., Sheng G., Liu X., Li C., and Fu J. (2005) Molecular and carbon and hydrogen isotopic composition of n-alkanes in plant leaf waxes. Organic Geochemistry 36, 1405-1417.
• Wang X. F., Yakir D., and Avishai M. (1998) Non-climatic variations in the oxygen isotopic compositions of plants. Global Change Biology 4(8), 835-849.
  

Supplemental references:

• (help?)

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Week 10 (Dec-4) - Microbial D/H Fractionations

discussion leader: Alex Sessions

Papers for discussion:

• Roger O., Lavigne R., Mahmoud M., Buisson C., Onno B., Zhang B. L., and Robins R. J. (2004) Quantitative H-2 NMR at natural abundance can distinguish the pathway used for glucose fermentation by lactic acid bacteria. Journal of Biological Chemistry 279(24), 24923-24928.
• Morasch B., Richnow H. H., Schink B., and Meckenstock R. U. (2001) Stable hydrogen and carbon isotope fractionation during microbial toluene degradation: Mechanistic and environmental aspects. Applied and Environmental Microbiology 67(10), 4842-4849.
• Valentine D. L., Sessions A. L., Tyler S. C., and Chidthaisong A. (2004) Hydrogen isotope fractionation during H2/CO2 acetogenesis: hydrogen utilization efficiency and the origin of lipid-bound hydrogen. Geobiology 2, 179-188.

Supplemental references:

• Sessions A. L., Jahnke L. L., Schimmelmann A., and Hayes J. M. (2002) Hydrogen isotope fractionation in lipids of the methane-oxidizing bacterium Methylococcus capsulatus. Geochimica et Cosmochimica Acta 66(22), 3955-3969.
• Valentine D. L., Chidthaisong A., Rice A., Reeburgh W. S., and Tyler S. C. (2004) Carbon and hydrogen isotope fractionation by moderately thermophilic methanogens. Geochimica Et Cosmochimica Acta 68(7), 1571-1590.
• Pionnier S., Robins R. J., and Zhang B. L. (2003) Natural abundance hydrogen isotope affiliation between the reactants and the products in glucose fermentation with yeast. Journal of Agriculture and Food Chemistry 51, 2076-2082.
• Sugimoto A. and Wada E. (1995) Hydrogen isotopic composition of bacterial methane: CO2/H2 reduction and acetate fermentation. Geochimica et Cosmochimica Acta 59(7), 1329-1337.
• Mancini S. A., Ulrich A. C., Lacrampe-Couloume G., Sleep B., Edwards E. A., and Lollar B. S. (2003) Carbon and hydrogen isotopic fractionation during anaerobic biodegradation of benzene. Applied and Environmental Microbiology 69(1), 191-198.
• Ward J. A. M., Ahad J. M. E., Lacrampe-Couloume G., Slater G. F., Edwards E. A., and Lollar B. S. (2000) Hydrogen isotope fractionation during methanogenic degradation of toluene: Potential for direct verification of bioremediation. Environmental Science & Technology 34(21), 4577-4581.