Publications

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2011
Kua, J, Bada JL.  2011.  Primordial Ocean Chemistry and its Compatibility with the RNA World. Origins of Life and Evolution of Biospheres. 41:553-558.   10.1007/s11084-011-9250-5   AbstractWebsite

We examine the stability of three key components needed to establish an RNA World under a range of potential conditions present on the early earth. The stability of ribose, cytosine, and the phosphodiester bond are estimated at different pH values and temperatures by extrapolating available experimental data. The conditions we have chosen range from highly acidic or alkaline hydrothermal vents, to the milder conditions in a primordial ocean at a range of atmospheric CO2 partial pressures.

2004
Glavin, DP, Cleaves HJ, Schubert M, Aubrey A, Bada JL.  2004.  New method for estimating bacterial cell abundances in natural samples by use of sublimation. Applied and Environmental Microbiology. 70:5923-5928.   10.1128/aem.70.10.5923-5928.2004   AbstractWebsite

We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500degreesC for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from similar to10(5) to 10(9) E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DA-PI (4,6-diamidino-2-phenylindole) staining.

2003
Kminek, G, Bada JL, Pogliano K, Ward JF.  2003.  Radiation-dependent limit for the viability of bacterial spores in halite fluid inclusions and on Mars. Radiation Research. 159:722-729.   10.1667/0033-7587(2003)159[0722:rlftvo]2.0.co;2   AbstractWebsite

When claims for the long-term survival of viable organisms are made, either within terrestrial minerals or on Mars, considerations should be made of the limitations imposed by the naturally occurring radiation dose to which they have been exposed. We investigated the effect of ionizing radiation on different bacterial spores by measuring the inactivation constants for B. subtilis and S. marismortui spores in solution as well as for dry spores of B. subtilis and B. thuringiensis. S. marismortui is a halophilic spore that is genetically similar to the recently discovered 2-9-3 bacterium from a halite fluid inclusion, claimed to be 250 million years old (Vreeland et al, Nature 407, 897-900, 2000). B. thuringiensis is a soil bacterium that is genetically similar to the human pathogens B. anthracis and B. cereus (Helgason et al., Appl. Environ. Microbiol 66, 2627-2630, 2000). To relate the inactivation constant to some realistic environments, we calculated the radiation regimen in a halite fluid inclusion and in the Martian subsurface over time. Our conclusion is that the ionizing dose of radiation in those environments limits the survival of viable bacterial spores over long periods. In the absence of an active repair mechanism in the dormant state, the long-term survival of spores is limited to less than 109 million years in halite fluid inclusions, to 100 to 160 million years in the Martian subsurface below 3 m, and to less than 600,000 years in the uppermost meter of Mars. (C) 2003 by Radiation Research Society.

1994
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.

1993
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.