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Sagan, C, Khare BN, Thompson WR, McDonald GD, Wing MR, Bada JL, Tuan VD, Arakawa ET.  1993.  Polycyclic Aromatic-Hydrocarbons in the Atmospheres of Titan and Jupiter. Astrophysical Journal. 414:399-405.   10.1086/173086   AbstractWebsite

Polycyclic aromatic hydrocarbons (PAHs) are important components of the interstellar medium and carbonaceous chondrites, but have never been identified in the reducing atmospheres of the outer solar system. Incompletely characterized complex organic solids (tholins) produced by irradiating simulated Titan atmospheres reproduce well the observed UV/visible/IR optical constants of the Titan stratospheric haze. Titan tholin and a tholin generated in a crude simulation of the atmosphere of Jupiter are examined by two-step laser desorption/multiphoton ionization mass spectrometry. A range of two- to four-ring PAHs, some with one to four alkylation sites are identified, with net abundance approximately 10(-4) g g-1 (grams per gram) of tholins produced. Synchronous fluorescence techniques confirm this detection. Titan tholins have proportionately more one- and two-ring PAHs than do Jupiter tholins, which in turn have more four-ring and larger PAHs. The four-ringed PAH chrysene, prominent in some discussions of interstellar grains, is found in Jupiter tholins. Solid state C-13 NMR spectroscopy suggests congruent-to 25% of the total C in both tholins is tied up in aromatic and/or aliphatic alkenes. IR spectra indicate an upper limit in both tholins of congruent-to 6% by mass in benzenes, heterocyclics, and PAHs with more than four rings. Condensed PAHs may contribute at most approximately 10% to the observed detached limb haze layers on Titan. As with interstellar PAHs, the synthesis route of planetary PAHs is likely to be via acetylene addition reactions.

Schoeninger, MJ, Bada JL, Masters PM, Bettinger RL, White TD.  2011.  Unexamined Bodies of Evidence. Science. 332:916-916.Website
Schroeder, RA, Bada JL.  1976.  Review of Geochemical Applications of Amino-Acid Racemization Reaction. Earth-Science Reviews. 12:347-391.   10.1016/0012-8252(76)90011-8   Website
Schroeder, RA, Bada JL.  1977.  Kinetics and Mechanism of Epimerization and Decomposition of Threonine in Fossil Foraminifera. Geochimica Et Cosmochimica Acta. 41:1087-1095.   10.1016/0016-7037(77)90103-x   Website
Schroeder, RA, Bada JL.  1978.  Aspartic-Acid Racemization in Late Wisconsin Lake-Ontario Sediments. Quaternary Research. 9:193-204.   10.1016/0033-5894(78)90067-4   Website
Schwarz, C, Debruyne R, Kuch M, McNally E, Schwarcz H, Aubrey AD, Bada J, Poinar H.  2009.  New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic Acids Research. 37:3215-3229.   10.1093/nar/gkp159   AbstractWebsite

Despite being plagued by heavily degraded DNA in palaeontological remains, most studies addressing the state of DNA degradation have been limited to types of damage which do not pose a hindrance to Taq polymerase during PCR. Application of serial qPCR to the two fractions obtained during extraction (demineralization and protein digest) from six permafrost mammoth bones and one partially degraded modern elephant bone has enabled further insight into the changes which endogenous DNA is subjected to during diagenesis. We show here that both fractions exhibit individual qualities in terms of the prevailing type of DNA (i.e. mitochondrial versus nuclear DNA) as well as the extent of damage, and in addition observed a highly variable ratio of mitochondrial to nuclear DNA among the six mammoth samples. While there is evidence suggesting that mitochondrial DNA is better preserved than nuclear DNA in ancient permafrost samples, we find the initial DNA concentration in the bone tissue to be as relevant for the total accessible mitochondrial DNA as the extent of DNA degradation post-mortem. We also evaluate the general applicability of indirect measures of preservation such as amino-acid racemization, bone crystallinity index and thermal age to these exceptionally well-preserved samples.

Shou, PM, Bada JL.  1980.  Pks of Amino-Acids at Elevated-Temperatures Estimated from Racemization Data. Naturwissenschaften. 67:37-38.   10.1007/bf00424503   Website
Skelley, AM, Aubrey AD, Willis PA, Amashukeli X, Ehrenfreund P, Bada JL, Grunthaner FJ, Mathies RA.  2007.  Organic amine biomarker detection in the Yungay region of the Atacama Desert with the Urey instrument. Journal of Geophysical Research-Biogeosciences. 112   10.1029/2006jg000329   AbstractWebsite

The Urey in situ organic compound analysis instrument, consisting of a subcritical water extractor ( SCWE) and a portable microchip capillary electrophoresis instrument called the Mars Organic Analyzer ( MOA), was field tested in the Atacama Desert, Chile, in June 2005. Soil samples from the most arid Yungay region were collected, biomarkers were extracted by the SCWE, and organic amine composition and amino acid chirality analysis was performed by the MOA. Samples collected from the top 1 cm of duracrust soil but shielded from the ambient environment by rocks were compared to the exposed duracrust. The shielded duracrust yielded amines and amino acids ranging from 50 to 100 ppb, while amino acid signals from the exposed duracrust were below blank levels. Samples from buried gypsum deposits located directly above a water flow channel contained amino acids ranging from 13 to 90 ppb. Chiral analysis revealed D/L ratios of 0.39 +/- 0.08 and 0.34 +/- 0.07 for alanine/serine and 0.78 +/- 0.06 for aspartic acid, indicating significant racemization of biologically produced amino acids. On the basis of the D/L ratios, we estimate sample ages ranging from 10(3) to 10(5) years. These results demonstrate the successful field testing of the Urey instrument, as well as the detection of biomarkers from past terrestrial life in one of the most arid and Mars-like regions on Earth.

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.

Skelley, AM, Cleaves HJ, Jayarajah CN, Bada JL, Mathies RA.  2006.  Application of the mars organic analyzer to nucleobase and amine biomarker detection. Astrobiology. 6:824-837.   10.1089/ast.2006.6.824   AbstractWebsite

The Mars Organic Analyzer (MOA), a portable microfabricated capillary electrophoresis instrument being developed for planetary exploration, is used to analyze a wide variety of fluorescamine-labeled amine-containing biomarker compounds, including amino acids, mono-and diaminoalkanes, amino sugars, nucleobases, and nucleobase degradation products. The nucleobases cytosine and adenine, which contain an exocyclic primary amine, were effectively labeled, separated, and detected at concentrations < 500 nM. To test the general applicability of the MOA for biomarker detection, amino acids and mono- and diamines were extracted from bacterial cells using both hydrolysis and sublimation followed by analysis. The extrapolated limit of detection provided by the valine biomarker was similar to 4 x 10(3) cells per sample. Products of an NH4CN polymerization that simulate a prebiotic synthesis were also successfully isolated via sublimation and analyzed. Adenine and alanine/serine were detected with no additional sample cleanup at 120 +/- 13 mu M and 4.1 +/- mu M, respectively, corresponding to a reaction yield of 0.04% and 0.0003%, respectively. This study demonstrates that the MOA provides sensitive detection and analysis of low levels of a wide variety of amine-containing organic compounds from both biological and abiotic sources.

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
Steinberg, SM, Bada JL.  1983.  Peptide Decomposition in the Neutral Ph-Region Via the Formation of Diketopiperazines. Journal of Organic Chemistry. 48:2295-2298.   10.1021/jo00161a036   Website
Steinberg, SM, Bada JL.  1984.  Oxalic, Glyoxalic and Pyruvic Acids in Eastern Pacific-Ocean Waters. Journal of Marine Research. 42:697-708.Website