# Readings

## Texts

McLafferty, Fred W., and František Tureček. Interpretation of Mass Spectra (Organic Chemistry Series). University Science Books, 1993. ISBN: 9780935702040. [Preview with Google Books]

Hayes, J. M. "Fractionation of the Isotopes of Carbon and Hydrogen in Biosynthetic Processes." In Stable Isotopic Geochemistry (Reviews in Mineralogy and Geochemistry 43). Edited by J. W. Valley and D. R. Cole. Mineralogical Society of America, 2001, pp. 225–78. ISBN: 9780939950553.

Killops, S., and V. Killops. An Introduction to Organic Geochemistry. Wiley-Blackwell, 2005. ISBN: 9780632065042.

Gaines, S. M., G. Eglinton, and J. Rullkötter. Echoes of Life: What Fossil Molecules Reveal about Earth History. Oxford University Press, 2009. ISBN: 9780195176193.

Fahy, E., Shankar Subramaniam, et al. "A Comprehensive Classification System for Lipids." J Lipid Research 46 (2005): 839–61.

Geobiology Laboratory Manual

Course readings.
WEEK # | READINGS
--- | ---
1 & 2 | McLafferty, F. W. and František Tureček. Chapters 1 to 4 in Interpretation of Mass Spectra (Organic Chemistry Series). University Science Books, 1993. ISBN: 9780935702255. [Preview with Google Books]
3 | Allard, B., M. N. Rager, et al. "Occurrence of High Molecular Weight Lipids (C80+) in the Trilaminar Outer Cell Walls of Some Freshwater Microalgae. A Reappraisal of Algaenan Structure." Org Geochem 33, no. 7 (2002): 789–801. Derenne, S., and C. Largeau. "A Review of Some Important Families of Refractory Macromolecules: Composition, Origin and Fate in Soils and Sediments." Soil Science 166, no. 11 (2001): 833–47. Gelin, F., I. Boogers, et al. "Resistant Biomacromolecules in Marine Microalgae of the Classes Eustigmatophyceae and Chlorophyceae: Geochemical Implications." Org Geochem 26, no. 11–12 (1997): 659–75. Köster, J., J. K. Volkman, et al. "Mono-, Di- and Trimethyl-branched Alkanes in Cultures of the Filamentous Cyanobacterium Calothrix Scopulorum." Org Geochem 30, no. 11 (1999): 1367–79. Rieley, G., J. W. Collister, et al. "Gas Chromatography/Isotope Ratio Mass Spectrometry of Leaf Wax n-alkanes from Plants of Differing Carbon Dioxide Metabolisms." Rapid Communications in Mass Spectrometry 7, no. 6 (1993): 488–91. Tegelaar, E. W., J. W. de Leeuw, et al. "A Reappraisal of Kerogen Formation." Geochim Cosmochim Acta 53, no. 11 (1989): 3103–6. Hayes, J. M. "Fractionation of the Isotopes of Carbon and Hydrogen in Biosynthetic Processes." In Stable Isotopic Geochemistry (Reviews in Mineralogy and Geochemistry, Volume 43). Edited by J. W. Valley and D. R. Cole. Mineralogical Society of America, 2001, pp. 225–78. ISBN: 9780939950553.
4 | Kates, M., ed. "Membrane Lipids of Archaea." In The Biochemistry of Archaea (Archaebacteria). Edited by D. J. Krushner and Alistair T. Matheson. Elsevier Science Ltd., 1993, pp. 261–95. ISBN: 9780444817136. [Preview with Google Books] Sinninghe, Damsté J. S., W. I. C. Rijpstra, et al. "Distribution of Membrane Lipids of Planktonic Crenarchaeota in the Arabian Sea." Applied and Environmental Microbiology 68, no. 6 (2002): 2997–3002. Tornabene, T. G., T. A. Langworthy, et al. "Squalenes, Phytanes and other Isoprenoids as Major Neutral Lipids of Methanogenic and Thermoacidophilic Archaebacteria." J Mol Evol 13, no. 1 (1979): 73–83. Volkman, J. K., and J. R. Maxwell. "Acyclic Isoprenoids as Biological Markers." In Biological Markers and the Sedimentary Record (Methods in Geochemistry and Geophysics). Edited by R. B. Johns. Elsevier Science Ltd., 1987, pp. P1–42. ISBN: 9780444425980. Woese, C. R., O. Kandler, et al. "Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya." Proc Natl Acad Sci USA 87, no. 12 (1990): 4576–9. Michaelis, W., R. Seifert, et al. "Microbial Reefs in the Black Sea Fueled by Anaerobic Oxidation of Methane." Science 297, no. 5583 (2002): 1013–5. Thiel, V., M. Blumenberg, et al. "Unexpected Occurrence of Hopanoids at Gas Seeps in the Black Sea." Org Geochem 34, no. 1 (2003): 81–7. Thiel, V., J. Peckmann, et al. "Highly Isotopically Depleted Soprenoids: Molecular Markers for Ancient Methane Venting." Geochim Cosmochim Acta 63, no. 23–24 (1999): 3959–66.
5 & 6 | Neunlist, Serge, and Michel Rohmer. "A Novel Hopanoid, 30-(5'-adenosyl) Hopane, from the Purple Non-sulphur Bacterium Rhodopseudomonas Acidophila, with Possible DNA Interactions." Biochem J 228, no. 3 (1985): 769–71. Doughty, D. M., R. C. Hunter, et al. "2-Methylhopanoids are Maximally Produced in Akinetes of Nostoc Punctiforme: Geobiological Implications." Geobiology 7, no. 5 (2009): 524–32. Welander, Paula V., Maureen L. Coleman, et al. "Identification of a Methylase Required for 2-methylhopanoid Production and Implications for the Interpretation of Sedimentary Hopanes." PNAS 107, no. 19 (2010): 1–6. Poralla, Karl, G. Muth, et al. "Hopanoids are Formed During Transition from Substrate to Aerial Hyphae in Streptomyces Coelicolor A3(2)." FEMS Microbiology Letters 189, no. 1 (2000): 93–5. Härtner, Thomas, Kristina L. Straub, et al. "Occurrence of Hopanoid Lipids in Anaerobic Geobacter Species." FEMS Microbiology Letters 243, no. 1 (2005): 59–64. Fischer, W. W., R. E. Summons, et al. "Targeted Genomic Detection of Biosynthetic Pathways: Anaerobic Production of Hopanoid Biomarkers by a Common Sedimentary Microbe." Geobiology 3, no. 1 (2005): 33–40. Kannenberg, Elmar L., and Karl Poralla. "Hopanoid Biosynthesis and Function in Bacteria." Naturwissenschaften 86, no. 4 (1999): 168–76.
7 | Tchen, T. T., and Konrad Bloch. "On the Mechanism of Enzymatic Cyclization of Squalene*." The Journal of Biological Chemistry (1956): 931–9. (From the Converse Memorial Chemical Laboratory, Harvard University, Cambridge, Massachusetts) Jahnke, Linda, and Harold P. Klein. "Oxygen Requirements for Formation and Activity of the Squalene Epoxidase in Saccharomyces Cerevisiae." Journal of Bacteriology 155, no. 2 (1983): 488–92. Kopp, Robert E., Joseph L. Kirschvink, et al. "The Paleoproterozoic Snowball Earth: A Climate Disaster Triggered by the Evolution of Oxygenic Photosynthesis." PNAS 102, no. 32 (2005): 11131–6.
8 | Raymond, Jason, and Daniel Segrè. "The Effect of Oxygen on Biochemical Networks and the Evolution of Complex Life." Science 311 (2006): 1764–7. Kodner, Robin B., Roger E. Summons, et al. "Sterols in a Unicellular Relative of the Metazoans." PNAS 105, no. 29 (2008): 9897–902. Kodner, R. B., A. Pearson, et al. "Sterols in Red and Green Algae: Quantification, Phylogeny, and Relevance for the Interpretation of Geologic Steranes." Geobiology 6, no. 4 (2008): 411–20.
9 | Brocks, Jochen J., Gordon D. Love, et al. "Biomarker Evidence for Green and Purple Sulphur Bacteria in a Stratified Palaeoproterozoic Sea." Nature 437, no. 6 (2005): 866–70.
10 | Summons, Roger E., Pierre Albrecht, et al. "Molecular Biosignatures." Space Science Reviews 135, no. 1–4 (2008): 133–59.