Publications

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Book Chapter
Msters, PM, Bada J, Hoopes E, Darling D.  1979.  The Dating of Fossil Bones Using Amimo Acid Racemization. Radiocarbon and other dating methods. ( and Rainer B, Ed.).:757-773., Berkley: UC Press
Journal Article
Bada, JL.  1972.  Dating of Fossil Bones Using Racemization of Isoleucine. Earth and Planetary Science Letters. 15:223-&.   10.1016/0012-821x(72)90167-7   Website
Lumley, HD, Lumley MAD, Bada JL, Turekian KK.  1977.  Dating of Pre-Neanderthal Remains at Caune-de-Larago, Tautavel, Pyrenees-Orientales, France. Journal of Human Evolution. 6:223-224.Website
Bada, JL, Fegley B, Miller SL, Lazcano A, Cleaves HJ, Hazen RM, Chalmers J.  2007.  Debating evidence for the origin of life on Earth. Science. 315:937-938.Website
Bada, JL, Shou MY, Man EH, Schroeder RA.  1978.  Decomposition of Hydroxy Amino-Acids in Foraminiferal Tests - Kinetics, Mechanism and Geochronological Implications. Earth and Planetary Science Letters. 41:67-76.   10.1016/0012-821x(78)90042-0   Website
Bennett, RV, Cleaves HJ, Davis JM, Sokolov DA, Orlando TM, Bada JL, Fernandez FM.  2013.  Desorption Electrospray Ionization Imaging Mass Spectrometry as a Tool for Investigating Model Prebiotic Reactions on Mineral Surfaces. Analytical Chemistry. 85:1276-1279.   10.1021/ac303202n   AbstractWebsite

Mineral-assisted thermal decomposition of formamide (HCONH2) is a heavily studied model prebiotic reaction that has offered valuable insights into the plausible pathways leading to the chemical building blocks of primordial informational polymers. To date, most efforts have focused on the analysis of formamide reaction products released in solution, although several studies have examined the role of mineral catalysts in promoting this chemistry. We show here that the direct investigation of reactive mineral surfaces by desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) gives a new perspective on the important role of the mineral surface in the formation of reaction products. As a proof-of-principle example, we show that DESI-MSI allows interrogation of the molecular products produced on heterogeneous granite samples with minimal sample preparation. Purine and pyrimidine nucleobases and their derivatives are successfully detected by DESI-MSI, with a strong correlation of the spatial product distribution with the mineral microenvironment. To our knowledge, this study is the first application of DESI-MSI to the study of complex and porous mineral surfaces and their roles in chemical evolution. This DESI-MSI approach is generally applicable to a wide range of reactions or other processes involving minerals.

Bada, J.  1974.  Details of amino acid racemization dating. McGraw-Hill yearbook of science and technology. :212-213.
Bada, JL, McDonald GD.  1996.  Detecting amino acids on Mars. Analytical Chemistry. 68:A668-A673.Website
Glavin, DP, Schubert M, Botta O, Kminek G, Bada JL.  2001.  Detecting pyrolysis products from bacteria on Mars. Earth and Planetary Science Letters. 185:1-5.   10.1016/s0012-821x(00)00370-8   AbstractWebsite

A pyrolysis/sublimation technique was developed to isolate volatile amine compounds from a Mars soil analogue inoculated with similar to 10 billion Escherichia coli cells. In this technique, the inoculated soil is heated to 500 degreesC for several seconds at Martian ambient pressure and the sublimate, collected by a cold finger, then analyzed using high performance liquid chromatography. Methylamine and ethylamine, produced from glycine and alanine decarboxylation, were the most abundant amine compounds detected after pyrolysis of the cells. A heating cycle similar to that utilized in our experiment was also used to release organic compounds from the Martian soil in the 1976 Viking gas chromatography/mass spectrometry (GC/MS) pyrolysis experiment. The Viking GC/MS did not detect any organic compounds of Martian origin above a level of a few parts per billion in the Martian surface soil. Although the Viking GC/MS instruments were not specifically designed to search for the presence of living cells on Mars, our experimental results indicate that at the part per billion level, the degradation products generated from several million bacterial cells per gram of Martian soil would not have been detected. (C) 2001 Elsevier Science B.V. All rights reserved.

Zhao, MX, Bada JL.  1995.  Determination of Alpha-Dialkylamino Acids and Their Enantiomers in Geological Samples by High-Performance Liquid-Chromatography after Derivatization with a Chiral Adduct of O-Phthaldialdehyde. Journal of Chromatography A. 690:55-63.   10.1016/0021-9673(94)00927-2   AbstractWebsite

Derivatization with o-phthaldialdehyde (OPA) and the chiral thiol N-acetyl-L-cysteine (NAG) is a convenient and sensitive technique for the HPLC detection and resolution of protein amino acid enantiomers. The kinetics of the reaction of OPA-NAC with alpha-dialkylamino acids was investigated. The fluorescence yield of alpha-dialkylamino acids was only about 10% of that of protein amino acids when the derivatization was carried out at room temperature for 1-2 min, which is the procedure generally used for protein amino acid analyses. The fluorescence yield of alpha-dialkylamino acids can be enhanced by up to ten-fold when the derivatization reaction time is increased to 15 min at room temperature. The OPA-NAC technique was optimized for the detection and enantiomeric resolution of alpha-dialkylamino acids in geological samples which contain a large excess of protein amino acids. The estimated detection limit for alpha-dialkylamino acids is 1-2 pmol, comparable to that for protein amino acids.

Hoopes, EA, Peltzer ET, Bada JL.  1978.  Determination of Amino-Acid Enantiomeric Ratios by Gas-Liquid Chromatography of N-Trifluoroacetyl-L-Prolyl-Peptide Methyl-Esters. Journal of Chromatographic Science. 16:556-560.Website
Skelley, AM, Scherer JR, Aubrey AD, Grover WH, Ivester RHC, Ehrenfreund P, Grunthaner FJ, Bada JL, Mathies RA.  2005.  Development and evaluation of a microdevice for amino acid biomarker detection and analysis on Mars. Proceedings of the National Academy of Sciences of the United States of America. 102:1041-1046.   10.1073/pnas.0406798102   AbstractWebsite

The Mars Organic Analyzer (MOA), a microfabricated capillary electrophoresis (CE) instrument for sensitive amino acid biomarker analysis, has been developed and evaluated. The microdevice consists of a four-wafer sandwich combining glass CE separation channels, microfabricated pneumatic membrane valves and pumps, and a nanoliter fluidic network. The portable MOA instrument integrates high voltage CE power supplies, pneumatic controls, and fluorescence detection optics necessary for field operation. The amino acid concentration sensitivities range from micromolar to 0.1 nM, corresponding to part-per-trillion sensitivity. The MOA was first used in the lab to analyze soil extracts from the Atacama Desert, Chile, detecting amino acids ranging from 10-600 parts per billion. Field tests of the MOA in the Panoche Valley, CA, successfully detected amino acids at 70 parts per trillion to 100 parts per billion in jarosite, a sulfate-rich mineral associated with liquid water that was recently detected on Mars. These results demonstrate the feasibility of using the MOA to perform sensitive in situ amino acid biomarker analysis on soil samples representative of a Mars-like environment.

Steinberg, SM, Bada JL.  1983.  The Diagenetic Production of Alpha-Keto Acids in Heated and Fossil Chione Shells. Geochimica Et Cosmochimica Acta. 47:1481-1486.   10.1016/0016-7037(83)90307-1   Website
Man, EH, Bada JL.  1987.  Dietary D-Amino Acids. Annual Review of Nutrition. 7:209-225.   10.1146/annurev.nutr.7.1.209   Website
Glavin, DP, Schubert M, Bada JL.  2002.  Direct isolation of purines and pyrimidines from nucleic acids using sublimation. Analytical Chemistry. 74:6408-6412.   10.1021/ac0259663   AbstractWebsite

A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (similar to 0.5 Torr) at temperatures of > 150 degreesC. With the exception of guanine, approximately 60-75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 T. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

Lee, C, Bada JL.  1977.  Dissolved Amino-Acids in Equatorial Pacific, Sargasso Sea, and Biscayne Bay. Limnology and Oceanography. 22:502-510.Website
Ambler, RP, Macko SA, Sykes B, Griffiths JB, Bada J, Eglinton G.  1999.  Documenting the diet in ancient human populations through stable isotope analysis of hair - Discussion. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences. 354:75-76.Website
Onstott, TC, Magnabosco C, Aubrey AD, Burton AS, Dworkin JP, Elsila JE, Grunsfeld S, Cao BH, Hein JE, Glavin DP, Kieft TL, Silver BJ, Phelps TJ, van Heerden E, Opperman DJ, Bada JL.  2014.  Does aspartic acid racemization constrain the depth limit of the subsurface biosphere? Geobiology. 12:1-19.   10.1111/gbi.12069   AbstractWebsite

Previous studies of the subsurface biosphere have deduced average cellular doubling times of hundreds to thousands of years based upon geochemical models. We have directly constrained the in situ average cellular protein turnover or doubling times for metabolically active micro-organisms based on cellular amino acid abundances, D/L values of cellular aspartic acid, and the in vivo aspartic acid racemization rate. Application of this method to planktonic microbial communities collected from deep fractures in South Africa yielded maximum cellular amino acid turnover times of similar to 89years for 1km depth and 27 degrees C and 1-2years for 3km depth and 54 degrees C. The latter turnover times are much shorter than previously estimated cellular turnover times based upon geochemical arguments. The aspartic acid racemization rate at higher temperatures yields cellular protein doubling times that are consistent with the survival times of hyperthermophilic strains and predicts that at temperatures of 85 degrees C, cells must replace proteins every couple of days to maintain enzymatic activity. Such a high maintenance requirement may be the principal limit on the abundance of living micro-organisms in the deep, hot subsurface biosphere, as well as a potential limit on their activity. The measurement of the D/L of aspartic acid in biological samples is a potentially powerful tool for deep, fractured continental and oceanic crustal settings where geochemical models of carbon turnover times are poorly constrained. Experimental observations on the racemization rates of aspartic acid in living thermophiles and hyperthermophiles could test this hypothesis. The development of corrections for cell wall peptides and spores will be required, however, to improve the accuracy of these estimates for environmental samples.