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Parker, ET, Cleaves JH, Burton AS, Glavin DP, Dworkin JP, Zhou MS, Bada JL, Fernandez FM.  2014.  Conducting Miller-Urey experiments. Jove-Journal of Visualized Experiments.   10.3791/51039   AbstractWebsite

In 1953, Stanley Miller reported the production of biomolecules from simple gaseous starting materials, using an apparatus constructed to simulate the primordial Earth's atmosphere-ocean system. Miller introduced 200 ml of water, 100 mmHg of H-2, 200 mmHg of CH4, and 200 mmHg of NH3 into the apparatus, then subjected this mixture, under reflux, to an electric discharge for a week, while the water was simultaneously heated. The purpose of this manuscript is to provide the reader with a general experimental protocol that can be used to conduct a Miller-Urey type spark discharge experiment, using a simplified 3 L reaction flask. Since the experiment involves exposing inflammable gases to a high voltage electric discharge, it is worth highlighting important steps that reduce the risk of explosion. The general procedures described in this work can be extrapolated to design and conduct a wide variety of electric discharge experiments simulating primitive planetary environments.

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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.

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Kminek, G, Bada JL.  2006.  The effect of ionizing radiation on the preservation of amino acids on Mars. Earth and Planetary Science Letters. 245:1-5.   10.1016/j.epsl.2006.03.008   AbstractWebsite

Amino acids are excellent biomarkers in the search for life on Mars because they are essential for biology as we know it and they are robust enough to survive for billions of years in the cold and dry Martian environment. However, amino acids and other organic compounds on Mars are exposed to the ionizing radiation from space and from the decay of radionuclides. This process and its role in the preservation of organic compounds has not been adequately addressed in the past. Based on measured radiolysis constants of amino acids and radiation dose estimates for Mars we show that the detection of an amino acid signature derived from an early Martian biosphere is not limited by its radiolytic decomposition as long as the amino acids are shielded adequately from space radiation. This indicates clearly the need to access the Martian subsurface in the search for molecular traces of an extinct Martian biosphere. (c) 2006 Elsevier B.V. All rights reserved.

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.

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Keefe, AD, Miller SL, McDonald G, Bada J.  1995.  Investigation of the Prebiotic Synthesis of Amino-Acids and Rna Bases from Co2 Using Fes/H2s as a Reducing Agent. Proceedings of the National Academy of Sciences of the United States of America. 92:11904-11906.   10.1073/pnas.92.25.11904   AbstractWebsite

An autotrophic theory of the origin of metabolism and life has been proposed in which carbon dioxide is reduced by ferrous sulfide and hydrogen sulfide by means of a reversed citric acid cycle, leading to the production of amino acids. Similar processes hale been proposed for purine synthesis. Ferrous sulfide is a strong reducing agent in the presence of hydrogen sulfide and can produce hydrogen as web as reduce alkenes, alkynes, and thiols to saturated hydrocarbons and reduce ketones to thiols. However, the reduction of carbon dioxide has not been demonstrated. We show here that no amino acids, purines, or pyrimidines are produced from carbon dioxide with the ferrous sulfide and hydrogen sulfide system. Furthermore, this system does not produce amino acids from carboxylic acids by reductive amination and carboxylation. Thus, the proposed autotrophic theory, using carbon dioxide, ferrous sulfide, and hydrogen sulfide, lacks the robustness needed to be a geological process and is, therefore, unlikely to have played a role in the origin of metabolism or the origin of life.

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Parker, ET, Zhou MS, Burton AS, Glavin DP, Dworkin JP, Krishnamurthy R, Fernandez FM, Bada JL.  2014.  A plausible simultaneous synthesis of amino acids and simple peptides on the primordial earth. Angewandte Chemie-International Edition. 53:8132-8136.   10.1002/anie.201403683   AbstractWebsite

Following his seminal work in 1953, Stanley Miller conducted an experiment in 1958 to study the polymerization of amino acids under simulated early Earth conditions. In the experiment, Miller sparked a gas mixture of CH4, NH3, and H2O, while intermittently adding the plausible prebiotic condensing reagent cyanamide. For unknown reasons, an analysis of the samples was not reported. We analyzed the archived samples for amino acids, dipeptides, and diketopiperazines by liquid chromatography, ion mobility spectrometry, and mass spectrometry. A dozen amino acids, 10 glycine-containing dipeptides, and 3 glycine-containing diketopiperazines were detected. Miller's experiment was repeated and similar polymerization products were observed. Aqueous heating experiments indicate that Strecker synthesis intermediates play a key role in facilitating polymerization. These results highlight the potential importance of condensing reagents in generating diversity within the prebiotic chemical inventory.

Parker, ET, Cleaves HJ, Callahan MP, Dworkin JP, Glavin DP, Lazcano A, Bada JL.  2011.  Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment. Origins of Life and Evolution of Biospheres. 41:201-212.   10.1007/s11084-010-9228-8   AbstractWebsite

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH(4)), hydrogen sulfide (H(2)S), ammonia (NH(3)), and carbon dioxide (CO(2)). Racemic methionine was formed in significant yields, together with other sulfur-bearing organic compounds. The formation of methionine and other compounds from a model prebiotic atmosphere that contained H(2)S suggests that this type of synthesis is robust under reducing conditions, which may have existed either in the global primitive atmosphere or in localized volcanic environments on the early Earth. The presence of a wide array of sulfur-containing organic compounds produced by the decomposition of methionine and cysteine indicates that in addition to abiotic synthetic processes, degradation of organic compounds on the primordial Earth could have been important in diversifying the inventory of molecules of biochemical significance not readily formed from other abiotic reactions, or derived from extraterrestrial delivery.

Bada, JL, Wang XYS, Hamilton H.  1999.  Preservation of key biomolecules in the fossil record: current knowledge and future challenges. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences. 354:77-86.   10.1098/rstb.1999.0361   AbstractWebsite

We have developed a model based on the analyses of modern and Pleistocene eggshells and mammalian bones which can be used to understand the preservation of amino acids and other important biomolecules such as DNA in fossil specimens. The model is based on the following series of diagenetic reactions and processes involving amino acids: the hydrolysis of proteins and the subsequent loss of hydrolysis products from the fossil matrix with increasing geologic age; the racemization of amino acids which produces totally racemized amino acids in 10(5)-10(6) years in most environments on the Earth; the introduction of contaminants into the fossil that lowers the enantiomeric (D:L) ratios produced via racemization; and the condensation reactions between amino acids, as well as other compounds with primary amino groups, and sugars which yield humic acid-like polymers. This model was used to evaluate whether useful amino acid and DNA sequence information is preserved in a variety of human, amber-entombed insect and dinosaur specimens. Most skeletal remains of evolutionary interest with respect to the origin of modern humans are unlikely to preserve useful biomolecular information although those from high latitude sites may be an exception. Amber-entombed insects contain well-preserved unracemized amino acids, apparently because of the anhydrous nature of the amber matrix, and thus may contain DNA fragments which have retained meaningful genetic information. Dinosaur specimens contain mainly exogenous amino acids, although traces of endogenous amino acids may be present in some cases. Future ancient biomolecule research which takes advantage of new methologies involving, for example, humic acid cleaving reagents and microchip-based DNA-protein detection and sequencing, along with investigations of very slow biomolecule diagenetic reactions such as the racemization of isoleucine at the beta-carbon, will lead to further enhancements of our understanding of biomolecule preservation in the fossil record.

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Glavin, DP, Matrajt G, Bada JL.  2004.  Re-examination of amino acids in Antarctic micrometeorites. Space Life Sciences: Steps toward Origin(S) of Life. 33( Bernstein MP, Kress M, NavarroGonzalez R, Eds.).:106-113., Kidlington: Pergamon-Elsevier Science Ltd   10.1016/j.asr.2003.02.011   Abstract

The delivery of amino acids by micrometeorites to the early Earth during the period of heavy bombardment (4.5-3.5 Ga) could have been a significant source of the Earth's prebiotic organic inventory. Antarctic micrometeorites (AMMs) in the 100-200 mum size range represent the dominant mass fraction of extraterrestrial material accreted by the Earth today. However, one problem is that these 'large' micrometeorite grains can be heated to very high temperatures (1000 to 1500 degreesC) during atmospheric deceleration, causing the amino acids to decompose. In this study, we have analyzed the acid-hydrolyzed, hot water extracts from 455 AMMs for the presence of amino acids using high performance liquid chromatography. For comparison, a 5 mg sample of the CM meteorite Murchison was also investigated. In the Murchison sample we found high levels (similar to3-4 parts-per-million, ppm) of alpha-aminoisobutyric acid (AIB) and isovaline, two non-protein amino acids that are extremely rare on Earth and are characteristic of amino acids of apparent extraterrestrial origin. In contrast, we were unable to detect any AIB above the 0.1 ppm level in the AMM samples studied. Only in one AMM sample from a previous study has AIB been detected (similar to300 ppm). To date, more than 600 AMMs have been analyzed for extraterrestrial amino acids. Although our results indicate that less than 5% of all AMMs contain detectable levels of AIB, we cannot rule out the possibility that AIB can be delivered to the Earth intact by a small percentage of AMMs that escaped extensive heating during atmospheric entry. (C) 2003 COSPAR. Published by Elsevier Ltd. All rights reserved.

Botta, O, Glavin DP, Kminek G, Bada JL.  2002.  Relative amino acid concentrations as a signature for parent body processes of carbonaceous chondrites. Origins of Life and Evolution of Biospheres. 32:143-163.   10.1023/a:1016019425995   AbstractWebsite

Most meteorites are thought to have originated from objects in the asteroid belt. Carbonaceous chondrites, which contain significant amounts of organic carbon including complex organic compounds, have also been suggested to be derived from comets. The current model for the synthesis of organic compounds found in carbonaceous chondrites includes the survival of interstellar organic compounds and the processing of some of these compounds on the meteoritic parent body. The amino acid composition of five CM carbonaceous chondrites, two CIs, one CR, and one CV3 have been measured using hot water extraction-vapor hydrolysis, OPA/NAC derivatization and high-performance liquid chromatography (HPLC). Total amino acid abundances in the bulk meteorites as well as the amino acid concentrations relative to glycine = 1.0 for beta-alanine, alpha-aminoisobutyric acid and D-alanine were determined. Additional data for three Antarctic CM meteorites were obtained from the literature. All CM meteorites analyzed in this study show a complex distribution of amino acids and a high variability in total concentration ranging from similar to15 300 to similar to5800 parts per billion (ppb), while the CIs show a total amino acid abundance of similar to4300 ppb. The relatively (compared to glycine) high AIB content found in all the CMs is a strong indicator that Strecker-cyanohydrin synthesis is the dominant pathway for the formation of amino acids found in these meteorites. The data from the Antarctic CM carbonaceous chondrites are inconsistent with the results from the other CMs, perhaps due to influences from the Antarctic ice that were effective during their residence time. In contrast to CMs, the data from the CI carbonaceous chondrites indicate that the Strecker synthesis was not active on their parent bodies.

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.

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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.