Publications

Export 20 results:
Sort by: Author Title Type [ Year  (Asc)]
1989
1993
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.

1995
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.

1999
Arrhenius, G, Bada JL, Joyce GF, Lazcano A, Miller S, Orgel LE.  1999.  Origin and ancestor: Separate environments. Science. 283:792-792.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
Ambler, RP, Bada JL, Finch P, Grocke DR, Eglinton G, Macko SA.  1999.  Preservation of key biomolecules in the fossil record: current knowledge and future challenges - Discussion. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences. 354:86-87.Website
2000
Orgel, L, A'Hearn M, Bada J, Baross J, Chapman C, Drake M, Kerridge J, Race M, Sogin M, Squyres S.  2000.  Sample return from small solar system bodies. Advances in Space Research. 25:239-48.   10.1016/s0273-1177(99)00954-0   AbstractWebsite

With plans for multiple sample return missions in the next decade, NASA requested guidance from the National Research Council's Space Studies Board on how to treat samples returned from solar system bodies such as planetary satellites, asteroids and comets. A special task group assessed the potential for a living entity to be included in return samples from various bodies as well as the potential for large scale effects if such an entity were inadvertently introduced into the Earth's biosphere. The group also assessed differences among solar system bodies, identified investigations that could reduce uncertainty about the bodies, and considered risks of returned samples compared to the natural influx of material to the Earth in the form of interplanetary dust particles, meteorites and other small impactors. The final report (NRC, 1998) provides a decision making framework for future missions and makes recommendations on how to handle samples from different planetary satellites and primitive solar system bodies

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.

2005
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.

2006
Glavin, DP, Dworkin JP, Aubrey A, Botta O, Doty JH, Martins Z, Bada JL.  2006.  Amino acid analyses of Antarctic CM2 meteorites using liquid chromatography-time of flight-mass spectrometry. Meteoritics & Planetary Science. 41:889-902. AbstractWebsite

Amino acid analyses of the Antarctic CM2 chondrites Allan Hills (ALH) 83100 and Lewis Cliff (LEW) 90500 using liquid chromatography-time of flight-mass spectrometry (LC-ToF-MS) Coupled with UV fluorescence detection revealed that these carbonaceous meteorites contain a suite of indigenous amino acids not present in Antarctic ice. Several amino acids were detected in ALH 83100, including glycine, alanine, beta-alanine, gamma-amino-n-butyric acid (gamma-ABA), and alpha-aminoisobutyric acid (AIB) with concentrations ranging from 250 to 340 parts per billion (ppb). In contrast to ALH 83 100, the CM2 meteorites LEW 90500 and Murchison had a much higher total abundance of these amino acids (440-3200 ppb). In addition, ALL! 83 100 was found to have lower abundances of the alpha-dialkyl amino acids AIB and isovaline than LEW 90500 and Murchison. There are three possible explanations for the depleted amino, acid content in ALH 83100: 1) amino acid leaching from ALH 83100 during exposure to Antarctic ice meltwater, 2) a higher degree of aqueous alteration on the ALH 83 100 parent body, or 3) ALH 83 100 originated on a chemically distinct parent body from the other two CM2 meteorites. The high relative abundance of epsilon-amino-n-caproic acid (EACA) in the ALH 83100 meteorite as well as the Antarctic ice indicates that Nylon-6 contamination from the Antarctic sample storage bags may have occurred during collection.

Aubrey, A, Cleaves HJ, Chalmers JH, Skelley AM, Mathies RA, Grunthaner FJ, Ehrenfreund P, Bada JL.  2006.  Sulfate minerals and organic compounds on Mars. Geology. 34:357-360.   10.1130/g22316.1   AbstractWebsite

Strong evidence for evaporitic sulfate minerals such as gypsum and jarosite has recently been found on Mars. Although organic molecules are often codeposited with terrestrial evaporitic minerals, there have been no systematic investigations of organic components in sulfate minerals. We report here the detection of organic material, including amino acids and their amine degradation products, in ancient terrestrial sulfate minerals. Amino acids and amines appear to be preserved for geologically long periods in sulfate mineral matrices. This suggests that sulfate minerals should be prime targets in the search for organic compounds, including those of biological origin, on Mars.

2007
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.

2008
Aubrey, AD, Chalmers JH, Bada JL, Grunthaner FJ, Amashukeli X, Willis P, Skelley AM, Mathies RA, Quinn RC, Zent AP, Ehrenfreund P, Amundson R, Glavin DP, Botta O, Barron L, Blaney DL, Clark BC, Coleman M, Hofmann BA, Josset JL, Rettberg P, Ride S, Robert F, Sephton MA, Yen A.  2008.  The Urey instrument: An advanced in situ organic and oxidant detector for Mars exploration. Astrobiology. 8:583-595.   10.1089/ast.2007.0169   AbstractWebsite

The Urey organic and oxidant detector consists of a suite of instruments designed to search for several classes of organic molecules in the martian regolith and ascertain whether these compounds were produced by biotic or abiotic processes using chirality measurements. These experiments will also determine the chemical stability of organic molecules within the host regolith based on the presence and chemical reactivity of surface and atmospheric oxidants. Urey has been selected for the Pasteur payload on the European Space Agency's (ESA's) upcoming 2013 ExoMars rover mission. The diverse and effective capabilities of Urey make it an integral part of the payload and will help to achieve a large portion of the mission's primary scientific objective: "to search for signs of past and present life on Mars." This instrument is named in honor of Harold Urey for his seminal contributions to the fields of cosmochemistry and the origin of life.

Bada, JL, Ehrenfreund P, Grunthaner F, Blaney D, Coleman M, Farrington A, Yen A, Mathies R, Amudson R, Quinn R, Zent A, Ride S, Barron L, Botta O, Clark B, Glavin D, Hofmann B, Josset JL, Rettberg P, Robert F, Sephton M.  2008.  Urey: Mars Organic and Oxidant Detector. Space Science Reviews. 135:269-279.   10.1007/s11214-007-9213-3   AbstractWebsite

One of the fundamental challenges facing the scientific community as we enter this new century of Mars research is to understand, in a rigorous manner, the biotic potential both past and present of this outermost terrestrial-like planet in our solar system. Urey: Mars Organic and Oxidant Detector has been selected for the Pasteur payload of the European Space Agency's (ESA's) ExoMars rover mission and is considered a fundamental instrument to achieve the mission's scientific objectives. The instrument is named Urey in recognition of Harold Clayton Urey's seminal contributions to cosmochemistry, geochemistry, and the study of the origin of life. The overall goal of Urey is to search for organic compounds directly in the regolith of Mars and to assess their origin. Urey will perform a groundbreaking investigation of the Martian environment that will involve searching for organic compounds indicative of life and prebiotic chemistry at a sensitivity many orders of magnitude greater than Viking or other in situ organic detection systems. Urey will perform the first in situ search for key classes of organic molecules using state-of-the-art analytical methods that provide part-per-trillion sensitivity. It will ascertain whether any of these molecules are abiotic or biotic in origin and will evaluate the survival potential of organic compounds in the environment using state-of-the-art chemoresistor oxidant sensors.

2009
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.

Aubrey, AD, Cleaves HJ, Bada JL.  2009.  The Role of Submarine Hydrothermal Systems in the Synthesis of Amino Acids. Origins of Life and Evolution of Biospheres. 39:91-108.   10.1007/s11084-008-9153-2   AbstractWebsite

There is little consensus regarding the plausibility of organic synthesis in submarine hydrothermal systems (SHSs) and its possible relevance to the origin of life. The primary reason for the persistence of this debate is that most experimental high temperature and high-pressure organic synthesis studies have neglected important geochemical constraints with respect to source material composition. We report here the results of experiments exploring the potential for amino acid synthesis at high temperature from synthetic seawater solutions of varying composition. The synthesis of amino acids was examined as a function of temperature, heating time, starting material composition and concentration. Using very favorable reactant conditions (high concentrations of reactive, reduced species), small amounts of a limited set of amino acids are generated at moderate temperature conditions (similar to 125-175A degrees C) over short heating times of a few days, but even these products are significantly decomposed after exposure times of approximately 1 week. The high concentration dependence observed for these synthetic reactions are demonstrated by the fact that a 10-fold drop in concentration results in orders of magnitude lower yields of amino acids. There may be other synthetic mechanisms not studied herein that merit investigation, but the results are likely to be similar. We conclude that although amino acids can be generated from simple likely environmentally available precursors under SHS conditions, the equilibrium at high temperatures characteristic of SHSs favors net amino acid degradation rather than synthesis, and that synthesis at lower temperatures may be more favorable.

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.

2010
Glavin, DP, Aubrey AD, Callahan MP, Dworkin JP, Elsila JE, Parker ET, Bada JL, Jenniskens P, Shaddad MH.  2010.  Extraterrestrial amino acids in the Almahata Sitta meteorite. Meteoritics & Planetary Science. 45:1695-1709.   10.1111/j.1945-5100.2010.01094.x   AbstractWebsite

Amino acid analysis of a meteorite fragment of asteroid 2008 TC(3) called Almahata Sitta was carried out using reverse-phase liquid chromatography coupled with UV fluorescence detection and time-of-flight mass spectrometry (LC-FD/ToF-MS) as part of a sample analysis consortium. LC-FD/ToF-MS analyses of hot-water extracts from the meteorite revealed a complex distribution of two- to seven-carbon aliphatic amino acids and one- to three-carbon amines with abundances ranging from 0.5 to 149 parts-per-billion (ppb). The enantiomeric ratios of the amino acids alanine, beta-amino-n-butyric acid, 2-amino-2-methylbutanoic acid (isovaline), and 2-aminopentanoic acid (norvaline) in the meteorite were racemic (d/l similar to 1), indicating that these amino acids are indigenous to the meteorite and not terrestrial contaminants. Several other nonprotein amino acids were also identified in the meteorite above background levels including alpha-aminoisobutyric acid (alpha-AIB), 4-amino-2-methylbutanoic acid, 4-amino-3-methylbutanoic acid, and 3-, 4-, and 5-aminopentanoic acid. The total abundances of isovaline and alpha-AIB in Almahata Sitta are approximately 1000 times lower than the abundances of these amino acids found in the CM carbonaceous chondrite Murchison. The extremely low abundances and unusual distribution of five-carbon amino acids in Almahata Sitta compared to CI, CM, and CR carbonaceous chondrites may reflect extensive thermal alteration of amino acids on the parent asteroid by partial melting during formation or subsequent impact shock heating. It is also possible that amino acids were synthesized by catalytic reactions on the parent body after asteroid 2008 TC(3) cooled to lower temperatures, or introduced as a contaminant from unrelated meteorite clasts and chemically altered by alpha-decarboxylation.

2011
Parker, ET, Cleaves HJ, Dworkin JP, Glavin DP, Callahan M, Aubrey A, Lazcano A, Bada JL.  2011.  Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proceedings of the National Academy of Sciences of the United States of America. 108:5526-5531.   10.1073/pnas.1019191108   AbstractWebsite

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H2S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H2S, CH4, NH3, and CO2. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples. The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment. The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H2S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H2S may have played an important role in prebiotic reactions in early solar system environments.

2014
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.