Publications

Export 212 results:
Sort by: [ Author  (Desc)] Title Type Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Z
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.

Zenobi, R, Philippoz JM, Zare RN, Wing MR, Bada JL, Marti K.  1992.  Organic-Compounds in the Forest Vale, H4 Ordinary Chondrite. Geochimica Et Cosmochimica Acta. 56:2899-2905.   10.1016/0016-7037(92)90366-q   AbstractWebsite

We have analyzed the H4 ordinary chondrite Forest Vale for polycyclic aromatic hydrocarbons (PAHs) using two-step laser mass spectrometry (L2MS) and for amino acids using a standard chromatographic method. Indigenous PAHs were identified in the matrices of freshly cleaved interior faces but could not be detected in pulverized silicates and chondrules. No depth dependence of the PAHs was found in a chipped interior piece. Amino acids, taken from the entire sample, consisted of protein amino acids that were nonracemic, indicating that they are terrestrial contaminants. The presence of indigenous PAHs and absence of indigenous amino acids provides support for the contention that different processes and environments contributed to the synthesis of the organic matter in the solar system.

W
Wing, MR, Bada JL.  1992.  The Origin of the Polycyclic Aromatic-Hydrocarbons in Meteorites. Origins of Life and Evolution of the Biosphere. 21:375-383. AbstractWebsite

Polycyclic aromatic hydrocarbons (PAHs) in Cl and C2 Carbonaceous Chondrites appear to be the product of a high-temperature synthesis. This observation counters a prevailing view that PAHs in meteorites are a thermal alternation product of preexisting aliphatic compounds, which in turn required the presence of low-temperature mineral phases such as magnetite and hydrated phyllosilicates for their formation. Such a process would necessarily lead to a more low-temperature assemblage of PAHs, as many low-temperature minerals and compounds are extant in meteorites. Ivuna, a C1 carbonaceous chondrite, has been shown to contain abundant amounts of the three-ring PAHs phenanthrene/anthracene, but no detectable levels of the two- and four-ring PAHs naphthalene and pyrene/fluoranthene. Ivuna and other C1 carbonaceous chondrites are known to have been extensively altered by water. The aqueous solubilities of PAHs indicate that some PAHs would have been mobilized during the aqueous alteration phase in meteorite parent bodies. Model geochromatography experiments using crushed serpentine or beach sand as the solid phase and water for elution suggest that the complete separation of two, three, and four-ring PAHs could be expected to occur in the parent body of C1 carbonaceous chondrites. It is proposed that aqueous fluids driven by heat in the parent body of Ivuna migrated from the interior to the surface, in the process transporting, separating and concentrating PAHs at various zones in the parent body. The presence of indigenous PAHs and absence of indigenous amino acids in the H4 ordinary chondrite Forest Vale provides support for the contention that different processes and environments contributed to the synthesis of the organic matter in the solar system.

Wing, MR, Bada JL.  1991.  Geochromatography on the Parent Body of the Carbonaceous Chondrite Ivuna. Geochimica Et Cosmochimica Acta. 55:2937-2942.   10.1016/0016-7037(91)90458-h   AbstractWebsite

Ivuna, a CI carbonaceous chondrite, has been found to contain abundant amounts of the three-ring polycyclic aromatic hydrocarbons (PAHs) phenanthrene/anthracene, but no detectable levels of the two- and four-ring PAHs naphthalene and pyrene/fluoranthene. Either the three-ring PAHs in Ivuna were synthesized in a process that did not produce the two- or four-ring PAHs, or all these compounds were synthesized together and subsequently separated. Thermodynamical considerations and studies of hydrocarbon pyrolysis and combustion do not support the former possibility. Ivuna and other CI carbonaceous chondrites are known to have been extensively altered by water. The aqueous solubilities suggest that some PAHs would have been mobilized during the aqueous alteration phase in carbonaceous meteorite parent bodies. In a model geochromatography experiment, naphthalene, phenanthrene, and pyrene were partially resolved at a low pressure and flow rate utilizing columns containing crushed serpentine or beach sand, and water for elution. This laboratory geochromatography experiment suggests that complete separation of PAHs could be expected to occur in the parent body of CI carbonaceous chondrites. Such processes on Earth are known to lead to the formation of hydrothermal PAH minerals such as pendletonite. It is proposed that aqueous fluids driven by heat in the parent body of Ivuna migrated from the interior to the surface, in the process transporting, separating, and concentrating PAHs at various zones in the parent body.

Wills, C, iBada J.  2000.  The Spark of LIfe: Darwin and the Primeval soup. : Perseus publishing
Wang, XS, Poinar HN, Poinar GO, Bada JL.  1995.  Amino acids in the amber matrix and in entombed insects. Amber, Resinite, and Fossil Resins. 617( Anderson KB, Crelling JC, Eds.).:255-262., Washington: Amer Chemical Soc Abstract

We have investigated the amino acids in both the bulk matrix and in insect inclusions in tree resins ranging in age from <100 years to 130 million years. The amino acid content of the resin matrix averages about 5 ppm and does not systematically vary with the age of the resin. The amino acids in the matrix are likely derived from either plant cells, or microorganisms, encapsulated when the resin solidified. The amino acid content of the insect tissues entombed in amber is less than that in modern insect specimens; this loss may be the result of oxidation reactions. The amino acid compositions of a fly and bee entombed in 30-40 million year old amber are somewhat different from the amino acid profiles of modern insects; this finding suggests that the preserved amino acid pattern under anhydrous conditions may not be the same as in aqueous environments. The amino acid racemization rate in amber insect inclusions is retarded by a factor of >10(4) compared to other geochemical environments on the surface of the Earth. This is also apparently due to the anhydrous properties of the amber matrix. The excellent preservation of amino acids in amber insect inclusions suggests that other biomolecules would also be preserved much better than in other geochemical environments. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

S
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
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, 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, 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.

Shou, PM, Bada JL.  1980.  Pks of Amino-Acids at Elevated-Temperatures Estimated from Racemization Data. Naturwissenschaften. 67:37-38.   10.1007/bf00424503   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.

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
Schoeninger, MJ, Bada JL, Masters PM, Bettinger RL, White TD.  2011.  Unexamined Bodies of Evidence. Science. 332:916-916.Website
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.