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Cleaves, HJ, Chalmers JH, Lazcano A, Miller SL, Bada JL.  2008.  A reassessment of prebiotic organic synthesis in neutral planetary atmospheres. Origins of Life and Evolution of Biospheres. 38:105-115.   10.1007/s11084-007-9120-3   AbstractWebsite

The action of an electric discharge on reduced gas mixtures such as H(2)O, CH(4) and NH(3) (or N(2)) results in the production of several biologically important organic compounds including amino acids. However, it is now generally held that the early Earth's atmosphere was likely not reducing, but was dominated by N(2) and CO(2). The synthesis of organic compounds by the action of electric discharges on neutral gas mixtures has been shown to be much less efficient. We show here that contrary to previous reports, significant amounts of amino acids are produced from neutral gas mixtures. The low yields previously reported appear to be the outcome of oxidation of the organic compounds during hydrolytic workup by nitrite and nitrate produced in the reactions. The yield of amino acids is greatly increased when oxidation inhibitors, such as ferrous iron, are added prior to hydrolysis. Organic synthesis from neutral atmospheres may have depended on the oceanic availability of oxidation inhibitors as well as on the nature of the primitive atmosphere itself. The results reported here suggest that endogenous synthesis from neutral atmospheres may be more important than previously thought.

Cleaves, HJ, Aubrey AD, Bada JL.  2009.  An Evaluation of the Critical Parameters for Abiotic Peptide Synthesis in Submarine Hydrothermal Systems. Origins of Life and Evolution of Biospheres. 39:109-126.   10.1007/s11084-008-9154-1   AbstractWebsite

It has been proposed that oligopeptides may be formed in submarine hydrothermal systems (SHSs). Oligopeptides have been synthesized previously under simulated SHS conditions which are likely geochemically implausible. We have herein investigated the oligomerization of glycine under SHS-like conditions with respect to the limitations imposed by starting amino acid concentration, heating time, and temperature. When 10(-1) M glycine solutions were heated at 250A degrees C for < 20 min glycine oligomers up to tetramers and diketopiperazine (DKP) were detectable. At 200A degrees C, less oligomerization was noted. Peptides beyond glycylglycine (gly(2)) and DKP were not detected below 150A degrees C. At 10(-2) M initial glycine concentration and below, only gly(2), DKP, and gly(3) were detected, and then only above 200A degrees C at < 20 min reaction time. Gly(3) was undetectable at longer reaction times. The major parameters limiting peptide synthesis in SHSs appear to be concentration, time, and temperature. Given the expected low concentrations of amino acids, the long residence times and range of temperatures in SHSs, it is unlikely that SHS environments were robust sources of even simple peptides. Possible unexplored solutions to the problems presented here are also discussed.

Chen, RF, Bada JL.  1992.  The Fluorescence of Dissolved Organic-Matter in Seawater. Marine Chemistry. 37:191-221.   10.1016/0304-4203(92)90078-o   AbstractWebsite

A total of 28 vertical profiles of seawater fluorescence was measured in the Sargasso Sea, the Straits of Florida, the Southern California Borderlands, and the central Pacific Ocean. In all cases, surface seawater fluorescence was low as a result of photochemical bleaching which occurs on the timescale of hours. Fluorescence of deep water was 2-2.5 times higher than that of surface waters, and was constant, implying a long residence time for fluorescent organic matter, possibly of the order of thousands of years. Fluorescence correlates well with nutrients (NO3-, PO43-) in mid-depth waters ( 100-1000 m) in the Sargasso Sea and the central North Pacific, consistent with results in the central Pacific and the coastal seas of Japan. This suggests that regeneration or formation of fluorescent materials accompanies the oxidation and remineralization of settling organic particles. The various sources and sinks of fluorescent organic matter in the global oceans are assessed. The major sources are particles and in situ formation; rivers, rain, diffusion from sediments, and release from organisms are minor sources. The major sink is photochemical bleaching.

Chen, RF, Bada JL, Suzuki Y.  1993.  The Relationship between Dissolved Organic-Carbon (Doc) and Fluorescence in Anoxic Marine Porewaters - Implications for Estimating Benthic Doc Fluxes. Geochimica Et Cosmochimica Acta. 57:2149-2153.   10.1016/0016-7037(93)90102-3   AbstractWebsite

Fluorescence and dissolved organic carbon (DOC) measurements of porewaters from the Santa Barbara Basin, the Guaymas Basin, and the upper sections of the Nankai Trough suggest that ultraviolet fluorescence (lambda(ex) = 325 nm, lambda(em) = 450 nm) may be used as a first order estimate of DOC in anoxic marine porewaters. The majority of porewater organic carbon appears to be fluorescent, while a constant approximately 1 mM DOC, probably the low molecular weight compounds, is not fluorescent. These data are consistent with a model in which low molecular weight compounds dissolved in porewater act as the common intermediate between labile sedimentary organic matter and remineralization or polymerization products. Fluorescence may also be used to sensitively estimate benthic DOC fluxes to the overlying water column. Results from the Santa Barbara Basin, if representative of global anoxic oceanic regions, indicate that DOC release from anoxic sediments is not a major source of oceanic DOC when compared to internal recycling rates, but may be comparable to external input or permanent removal processes.

Chen, RF, Bada JL.  1989.  Seawater and Porewater Fluorescence in the Santa-Barbara Basin. Geophysical Research Letters. 16:687-690.   10.1029/GL016i007p00687   Website
Chen, RF, Bada JL.  1994.  The Fluorescence of Dissolved Organic-Matter in Porewaters of Marine-Sediments. Marine Chemistry. 45:31-42.   10.1016/0304-4203(94)90089-2   AbstractWebsite

The fluorescence of porewaters from marine sediment cores from six different areas was measured. In most cases, fluorescence was affected primarily by the diagenesis of organic carbon first through sulfate reduction and subsequently by methane generation. Typically, fluorescence, dissolved organic carbon (DOC), absorbance, alkalinity, and ammonium ion concentrations correlate quite well, increasing in the upper sections of anoxic sediments and co-varying in deeper sections of these cores. The good correlation of DOC with fluorescence in the three cores in which DOC was measured indicates that fluorescence can be used to make a first order estimate of DOC concentration in anoxic porewaters. Data are consistent with a model in which labile organic matter in the sediments is broken down by sulfur reducing bacteria to low molecular weight monomers. These monomers are either remineralized to CO2 or polymerize to form dissolved, fluorescent, high molecular weight molecules. The few exceptions to this model involve hydrothermally generated hydrocarbons that are formed in situ in the Guaymas Basin or are horizontally advected along the decollement in the Nankai Trench.

Chen, RF, Bada JL.  1990.  A Laser-Based Fluorometry System for Investigations of Seawater and Porewater Fluorescence. Marine Chemistry. 31:219-230.   10.1016/s0304-4203(05)80014-3   AbstractWebsite

A highly sensitive laser-induced fluorescence (LIF) system has been developed to study the fluorescence of dissolved organic carbon (DOC) in the marine environment. The LIF detector has a detection limit of approximately 10 attomoles (10x10(-18) moles) of pterin and eliminates internal quenching in highly fluorescent samples such as anoxic porewaters encountered when using conventional fluorometry. LIF analysis is rapid, reproducible, and uses only 100 mu-l of a sample. This small size requirement permits fluorescence analyses of samples often available only in limited amounts, such as pore-waters, hydrothermal vent waters, and rainwaters. In addition, the LIF detection system may greatly simplify extraction and separation procedures required to characterize the fluorescent components of DOC.