| WEEK # | TOPICS | READINGS |
|---|---|---|
| 1-4 | Archaea | Week 1 Introduction (PDF - 1.5 MB) Hayes, J. M. "Fractionation of the Isotopes of Carbon and Hydrogen in Biosynthetic Processes." In Stable Isotopic Geochemistry. Edited by J. W. Valley and D. R. Cole. Reviews in Mineralogy and Geochemistry 43, (2001): 225-278. Rohmer, M. "Mevalonate-independent Methylerythritol Phosphate Pathway for Isoprenoid Biosynthesis," and "Elucidation and Distribution." Pure Appl Chem 75, nos. 2-3 (2003): 375-387. Week 2 Boucher, Y., M. Kamekura, and W. Ford Doolittle. "Origins and Evolution of Isoprenoid Biosynthesis in Archaea." Molecular Microbiology 52, no. 2 (2004): 515-527. Chen, A., D. Zhang, and C. D. Poulter. "(S)-Geranylgeranylglyceryl Phosphate Synthase." The Journal of Biological Chemistry 268, no. 29 (October 15, 1993): 21701-21705. Eguchi, T., Y. Nishimura, and K. Kakinuma. "Importance of the Isopropylidene Terminal of Geranylgeranyl Group for the Formation of Tetraether Lipid in Methangoenic Archaea." Tetrahedron Letters 44 (2003): 3275-3279. Smit, A., and A. Mushegian. "Biosynthesis of Isoprenoids via Mevalonate in Archaea: The Lost Pathway." Genome Res 10, (2000): 1468-1484. Kon, T., and N. Nemoto, et al. "Effects of a Squalene Epoxidase Inhibitor, Terbinafine, on Ether Lipid Biosyntheses in a Thermoacidophilic Archaeon, and Thermoplasma Acidophilum." Journal of Bacteriology 184, no.5 (March 2002): 1395-1401. Week 3 Blumenberg, M., and R. Seifert, et al. "Membrane Lipid Patterns Typify Distinct Anaerobic Methanotrophic Consortia." PNAS 101, no. 30 (July 27, 2004): 11111-11116. Koga, Y., and H. Morii. "Recent Advances in Structural Research on Ether Lipids from Archaea Including Comparative and Physiological Aspect." Biosci Biotechnol Biochem 69, no. 11 (2005): 2019-2034. S., Schouten, and E. C. Hopmans, et al. "Widespread Occurence of Structurally Diverse Tetraether Membrane Lipids: Evidence for the Ubiquitous Presence of Low-Temperature Relatives of Hyperthermophiles." Proceedings of the National Academy of Sciences of the United States of America 97, no. 26 (2000): 14421-14426. S., Gribaldo, and C. Brochier-Armanet. "The Origin and Evolution of Archaea: A State of the Art." Phil Trans R Soc B 361, (2006): 1007-1022. H., Daiyasu, et al. "A Study of Archaeal Enzymes Involved in Polar Lipid Synthesis Linking Amino Acid Sequence Information, Genomic Contexts and Lipid Composition." Archaea 1, (2005): 399-410. B. F., Lutnaes, et al. "Archaeal C80 Isoprenoid Tetraacids Responsible for Napthenate Deposition in Crude Oil Processing." Org Biomol Chem 4, (2006): 616-620. A., Gattinger, et al. "Phospholipid Etherlipid and Phospholipid Fatty Acid Fingerprints in Selected Euryarchaeotal Monocultures for Taxonomic Profiling." FEMS Microbiology Letters 213, (2002): 133-139. H., Morii, et al. "A Novel Ether Core Lipid with H-shaped C80-isoprenoid Hydrocarbon Chain from the Hyperthermophilic Methanogen Methanothermus Fervidus." Biochimica et Biophysica Acta 1390, (1998): 339-345. Week 4 Koga, Y., and H. Morii. "Special Methods for the Analysis of Ether Lipid Structure and Metabolism in Archaea." Analytical Biochemistry 348, (2006): 1-14. G. C., Baker, et al. "Review and Re-analysis of Domain-specific 16S Primers." Journal of Microbiological Methods 55 (2003): 541-555. E. C., Hopmans, et al. "Analysis of Intact Tetraether Lipids in Archaeal Cell Material and Sediments by High Performance Liquid Chromatography/Atmospheric Pressure Chemical Ionization Mass Spectrometry." Rapid Commun Mass Spectrom 14 (2000): 585-589. H. F., Sturt, et al. "Intact Polar Membrane Lipids in Prokaryotes and Sediments Deciphered by High-performance Liquid Chromatography/Electrospray Ionization Multistage Mass Spectrometry - New Biomarkers for Biogeochemistry and Microbial Ecology." Rapid Commun Mass Spectrom 18, (2004): 617-628. C., Huguet, et al. "An Improved Method to Determine the Absolute Abundance of Glycerol Dibiphytanyl Glycerol Tetraether Lipids." Organic Geochemistry 37 (2006): 1036-1041. |
| 5-7 | Bacteria | Week 5 Seminar readings only. Week 6 R. D., Pancost, et al. "Biomarker Evidence for Widespread Anaerobic Methane Oxidation in Mediterranean Sediments by a Consortium of Methanogenic Archaea and Bacteria." Applied and Environmental Microbiology 66, no. 3 (March 2000): 1126-1132. V., Thiel, et al. "Unexpected Occurrence of Hopanoids at Gas Seeps in the Black Sea." Organic Geochemistry 34 (2003): 81-87. H. R., Harvey, et al. "Impact of DOM Composition on Bacterial Lipids and Community Structure in Estuaries." Aquat Microb Ecol 42 (2006): 105-117. M., Rohmer, et al. "Distribution of Hopanoid Triterpenes in Prokaryotes." Journal of General Microbiology 130 (1984): 1137-1150. M., Blumenberg, et al. "Biosynthesis of Hopanoids by Sulfate-reducing Bacteria (Genus Desulfovibrio)." Environmental Microbiology 8, no. 7 (2006): 1220-1227. Jean-Michel, Bravo, et al. "Novel Methylated Triterpenoids of the Gammacerane Series from the Nitrogen-fixing Bacterium Bradyhizobium Japonicum USDA 110." Eur J Biochem 268 (2001): 1323-1331. Week 7 A. M., Berry, et al. "Hopanoid Lipids Compose the Frankia Vesicle Envelope, Presumptive Barrier of Oxygen Diffusion to Nitrogenase." Proc Natl Acad Sci U.S.A. 90 (July 1993): 6091-6094. G., Flesch, and M. Rohmer. "Growth Inhibition of Hopanoid Synthesizing Bacteria by Squalene Cyclase Inhibitors." Arch Microbiol 147 (1987): 100-104. E. L., Kannenberg, and K. Poralla. "Hopanoid Biosynthesis and Function in Bacteria." Naturwissenschaften 86 (1999): 168-176. R., Rajamani, and J. Gao. "Balancing Kinetic and Thermodynamic Control: the Mechanism of Carbocation Cyclization by Squalene Cyclase." J Am Chem Soc 125 (2003): 12768-12781. K. U., Wendt, et al. "Structure and Function of a Squalene Cyclase." Science 277 (September 19, 1997): 1811-1815. |
| 8-10 | Eukarya | Week 8 Blumenberg, M., et al. "The Steroids of Hexactinellid Sponges." Naturwissenschaften 89 (2002): 415-419. V., Thiel, et al. "Mid-chain Branched Alkanoic Acids from "Living Fossil" Demosponges: a Link to Ancient Sedimentary Lipids?" Organic Geochemistry 30 (1999): 1-14. V., Thiel, and M. Blumenberg, et al. "A Chemical View of the Most Ancient Metazoi - Biomarker Chemotaxonomy of Hexactinellid Sponges." Naturwissenschaften 89 (2002): 60-66. H., Gross, et al. "Isolation and Structure Elucidation of Azoricasterol, a New Sterol of the Deepwater Sponge Macandrewia azorica." Naturwissenschaften 91 (2004): 441-446. M. A., McCaffrey, et al. "Paleoenvironmental Impications of Novel C30 Steranes in Precambrian to Cenozoic Age Petroleum and Bitumen." Geochimica et Cosmochimica Acta 58 (1994): 529-532. W., Hofheinz, and G. Oesterhelt. "24-Isopropylcholesterol and 22-Dehydro-24-isopropylcholesterol, Novel Sterols from a Sponge." Helvetica Chimica Acta 62 (1994): 1307-1309. W. C., Kokke, and M. C., et al. "Minor and Trace Sterols in Marine Invertebrates. XII." Helvetica Chimica Acta 62 (1979): 1310-1318. R. G., Kerr, et al. "De Novo Sterol Biosynthesis in Sponges," and "Incorporation and Transformation of Cycloartenol and Lanosterol into Unconventional Sterols of Marine and Freshwater Sponges." Tetrahedron 45, no. 7 (1989): 1893-1904. C. W., Li, et al. "Precambrian Sponges with Cellular Structures." Science 279 (February 6, 1998): 879-882. |
| 11 | Structural Preservation | |
| 12 | Sterochemical Modifications | |
| 13 | Diageneticpathways |