Publications

Export 15 results:
Sort by: Author [ Title  (Asc)] 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   [Show ALL]
P
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
Shou, PM, Bada JL.  1980.  Pks of Amino-Acids at Elevated-Temperatures Estimated from Racemization Data. Naturwissenschaften. 67:37-38.   10.1007/bf00424503   Website
Beaty, DW, Miller S, Zimmerman W, Bada J, Conrad P, Dupuis E, Huntsberger T, Ivlev R, Kim SS, Lee BG, Lindstrom D, Lorenzoni L, Mahaffy P, McNamara K, Papanastassiou D, Patrick S, Peters S, Rohatgi N, Simmonds JJ, Spray J, Swindle TD, Tamppari L, Treiman A, Wolfenbarger JK, Zent A.  2004.  Planning for a Mars in situ sample preparation and distribution (SPAD) system. Planetary and Space Science. 52:55-66.   10.1016/j.pss.2003.08.016   AbstractWebsite

For Mars in situ landed missions, it has become increasingly apparent that significant value may be provided by a shared system that we call a Sample Preparation and Distribution (SPAD) System. A study was conducted to identify the issues and feasibility of such a system for these missions that would provide common functions for: receiving a variety of sample types from multiple sample acquisition systems; conducting preliminary characterization of these samples with non-destructive science instruments and making decisions about what should happen to the samples; performing a variety of sample preparation functions- and, finally, directing the prepared samples to additional science instruments for further analysis. Scientific constraints on the functionality of the system were identified, such as triage, contamination management, and various sample preparation steps, e.g., comminution, splitting, rock surfacing, and sieving. Some simplifying strategies were recommended and an overall science flow was developed. Engineering functional requirements were also investigated and example architectures developed. Preliminary conclusions are that shared SPAD facility systems could indeed add value to future Mars in situ landed missions if they are designed to respond to the particular requirements and constraints of those missions, that such a system appears feasible for consideration, and that certain standards should be developed for key SPAD interfaces. (C) 2003 Elsevier Ltd. All rights reserved.

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.

Becker, L, Glavin DP, Bada JL.  1997.  Polycyclic aromatic hydrocarbons (PAHs) in Antarctic Martian meteorites, carbonaceous chondrites and polar ice. Abstracts of Papers of the American Chemical Society. 213:240-GEOC.Website
Botta, O, Martins Z, Emmenegger C, Dworkin JP, Glavin DP, Harvey RP, Zenobi R, Bada JL, Ehrenfreund P.  2008.  Polycyclic aromatic hydrocarbons and amino acids in meteorites and ice samples from LaPaz Icefield, Antarctica. Meteoritics & Planetary Science. 43:1465-1480. AbstractWebsite

We have analyzed ice samples and meteorites from the LaPaz region of Antarctica to investigate the composition of polycyclic aromatic hydrocarbons (PAHs) and amino acids with the goal to understand whether or not there is a compositional relationship between the two reservoirs. Four LL5 ordinary chondrites (OCs) and one CK carbonaceous chondrite were collected as part of the 2003/2004 ANSMET season. Ice samples collected from directly underneath the meteorites were extracted. In addition, exhaust particles from the snowmobiles used during the expedition were collected to investigate possible contributions from this source. The meteorite samples, the particulate matter and solid-state extracts of the ice samples and the exhaust filters were subjected to two-step laser mass spectrometry (L2MS) to investigate the PAH composition. For amino acids analysis, the meteorites were extracted with water and acid hydrolyzed, and the extracts were analyzed with offline OPA/NAC derivatization combined with liquid chromatography with UV fluorescence detection and time of flight mass spectrometry (LC-FC/ToF-MS). PAHs in the particulate matter of the ice were found to be qualitatively similar to the meteorite samples, indicating that micron-sized grains of the meteorite may be embedded in the ice samples. The concentration levels of dissolved PAHs in all the ice samples were found to be below the detection limit of the L2MS. The PAH composition of the snowmobile exhaust is significantly different to the one in particulate matter, making it an unlikely Source of contamination for Antarctic meteorites. The amino acids glycine, beta-alanine and gamma-amino-n-butyric acid that were detected at concentrations of 3 to 19 parts per billion (ppb) are probably indigenous to the Antarctic meteorites. Some of the LaPaz ice samples were also found to contain amino acids at concentration levels of 1 to 33 parts per trillion (ppt), in particular alpha-aminoisobutyric acid (AIB), an abundant non-protein amino acid of extraterrestrial Origin found in some carbonaceous chondrites. We hypothesize that this amino acid could have been extracted from Antarctic micrometeorites and the particulate matter of the meteorites during the concentration procedure of the ice samples.

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.

Bada, JL, Lazcano A.  2003.  Prebiotic soup - Revisiting the Miller experiment. Science. 300:745-746.   10.1126/science.1085145   Website
Levy, M, Miller SL, Brinton K, Bada JL.  2000.  Prebiotic synthesis of adenine and amino acids under Europa-like conditions. Icarus. 145:609-613.   10.1006/icar.2000.6365   AbstractWebsite

In order to simulate prebiotic synthetic processes on Europa and other ice-covered planets and satellites, we have investigated the prebiotic synthesis of organic compounds from dilute solutions of NH(4)CN frozen for 25 years at -20 and -78 degrees C. In addition, the aqueous products of spark discharge reactions from a reducing atmosphere were frozen for 5 years at -20 degrees C. We find that both adenine and guanine, as well as a simple set of amino acids dominated by glycine, are produced in substantial yields under these conditions, These results indicate that some of the key components necessary for the origin of life may have been available on Europa throughout its history and suggest that the circumstellar zone where life might arise may be wider than previously thought. (C) 2000 Academic Press.

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.

Grutters, M, van Raaphorst W, Epping E, Helder W, de Leeuw JW, Glavin DP, Bada J.  2002.  Preservation of amino acids from in situ-produced bacterial cell wall peptidoglycans in northeastern Atlantic continental margin sediments. Limnology and Oceanography. 47:1521-1524. AbstractWebsite

In this study we present the results of total hydrolysable amino acids (THAA) and amino acid D/L-enantiomers in northeastern Atlantic continental margin sediments. There is increasing evidence that intrinsically labile amino acids are present in old marine sediments as part of a refractory network of peptide-like material. We used amino acid enantiomers to identify the contribution of amino acids from bacterial cell walls to THAA in organic matter ranging from relatively young to 18,000 yr old. The ratio of D/L-amino acids increased with depth in the sediment mixed layer. Application of a transport-racemization-degradation model excludes a significant production of D-amino acids by racemization and implies in situ bacterial production as the main source. Amino acids associated with a refractory pool of bacterial cell walls could account for approximately one third of the THAA deeper in the sediments. We propose that in situ bacterial production and the primary flux of labile organic matter from the water column result in a small but highly reactive pool of amino acids in the surface mixed sediment only, whereas amino acids associated with refractory cell walls persist in marine sediments.

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.

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
Kua, J, Bada JL.  2011.  Primordial Ocean Chemistry and its Compatibility with the RNA World. Origins of Life and Evolution of Biospheres. 41:553-558.   10.1007/s11084-011-9250-5   AbstractWebsite

We examine the stability of three key components needed to establish an RNA World under a range of potential conditions present on the early earth. The stability of ribose, cytosine, and the phosphodiester bond are estimated at different pH values and temperatures by extrapolating available experimental data. The conditions we have chosen range from highly acidic or alkaline hydrothermal vents, to the milder conditions in a primordial ocean at a range of atmospheric CO2 partial pressures.

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.