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2016
Parker, ET, Cleaves HJ, Bada JL, Fernandez FM.  2016.  Quantitation of alpha-hydroxy acids in complex prebiotic mixtures via liquid chromatography/tandem mass spectrometry. Rapid Communications in Mass Spectrometry. 30:2043-2051.   10.1002/rcm.7684   AbstractWebsite

RationaleSpark discharge experiments, like those performed by Stanley Miller in the 1950s, generate complex, analytically challenging mixtures that contain biopolymer building blocks. Recently, -amino acids and -hydroxy acids (AHAs) were subjected to environmental cycling to form simple depsipeptides (peptides with both amide and ester linkages). The synthesis of AHAs under possible primordial environments must be examined to better understand this chemistry. MethodsWe report a direct, quantitative method for AHAs using ultrahigh-performance liquid chromatography and triple quadrupole mass spectrometry. Hexylamine ion-pairing chromatography and selected reaction monitoring detection were combined for the rapid analysis of ten AHAs in a single run. Additionally, prebiotic simulation experiments, including the first-ever reproduction of Miller's 1958 cyanamide spark discharge experiment, were performed to evaluate AHA synthesis over a wide range of possible primitive terrestrial environments. ResultsThe quantitating transition for each of the AHAs targeted in this study produced a limit of detection in the nanomolar concentration range. For most species, a linear response over a range spanning two orders of magnitude was found. The AHAs glycolic acid, lactic acid, malic acid, and -hydroxyglutaric acid were detected in electric discharge experiments in the low micromolar concentration range. ConclusionsThe results of this work suggest that the most abundant building blocks available for prebiotic depsipeptide synthesis would have been glycolic, lactic, malic, and -hydroxyglutaric acids, and their corresponding amino acids, glycine, alanine, and aspartic and glutamic acids. Copyright (c) 2016 John Wiley & Sons, Ltd.

Bada, JL, Chalmers JH, Cleaves HJ.  2016.  Is formamide a geochemically plausible prebiotic solvent? Physical Chemistry Chemical Physics. 18:20085-20090.   10.1039/c6cp03290g   AbstractWebsite

From a geochemical perspective, significant amounts of pure formamide (HCONH2) would have likely been rare on the early Earth. There may have been mixed formamide-water solutions, but even in the presence of catalyst, solutions with >= 20 weight% water in formamide would not have produced significant amounts of prebiotic compounds. It might be feasible to produce relatively pure formamide by a rare occurrence of freezing formamide/water mixtures at temperatures lower than formamide's freezing point (2.55 degrees C) but greater than the freezing point of water. Because of the high density of formamide ice it would have sunk and accumulated at the bottom of the solution. If the remaining water froze on the surface of this ice, and was then removed by a sublimation-ablation process, a small amount of pure formamide ice might have been produced. In addition a recent report suggested that similar to 85 weight% formamide could be prepared by a geochemical type of fractional distillation process, offering another possible route for prebiotic formamide production.

Raggi, L, Bada JL, Lazcano A.  2016.  On the lack of evolutionary continuity between prebiotic peptides and extant enzymes. Physical Chemistry Chemical Physics. 18:20028-20032.   10.1039/c6cp00793g   AbstractWebsite

The significance of experiments that claim to simulate the properties of prebiotic small peptides and polypeptides as models of the polymers that may have preceded proteins is critically addressed. As discussed here, most of these experiments are based only on a small number of a larger set of amino acids that may have been present in the prebiotic environment, supported by both experimental simulations and the repertoire of organic compounds reported in carbonaceous chondrites. Model experiments with small peptides may offer some insights into the processes that contributed to generate the chemical environment leading to the emergence of informational oligomers, but not to the origin of proteins. The large body of circumstantial evidence indicating that catalytic RNA played a key role in the origin of protein synthesis during the early stages of cellular evolution implies that the emergence of the genetic code and of protein biosynthesis are no longer synonymous with the origin of life. Hence, reports on the abiotic synthesis of small catalytic peptides under potential prebiotic conditions do not provide information on the origin of triplet encoded protein biosynthesis, but in some cases may serve as models to understand the properties of the earliest proteins.

2014
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.

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.

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.

2013
Bada, JL.  2013.  New insights into prebiotic chemistry from Stanley Miller's spark discharge experiments. Chem Soc Rev. 42:2186-96.   10.1039/c3cs35433d   Abstract

1953 was a banner year for biological chemistry: The double helix structure of DNA was published by Watson and Crick, Sanger's group announced the first amino acid sequence of a protein (insulin) and the synthesis of key biomolecules using simulated primordial Earth conditions has demonstrated by Miller. Miller's studies in particular transformed the study of the origin of life into a respectable field of inquiry and established the basis of prebiotic chemistry, a field of research that investigates how the components of life as we know it can be formed in a variety of cosmogeochemical environments. In this review, I cover the continued advances in prebiotic syntheses that Miller's pioneering work has inspired. The main focus is on recent state-of-the-art analyses carried out on archived samples of Miller's original experiments, some of which had never before been analyzed, discovered in his laboratory material just before his death in May 2007. One experiment utilized a reducing gas mixture and an apparatus configuration (referred to here as the "volcanic" apparatus) that could represent a water-rich volcanic eruption accompanied by lightning. Another included H(2)S as a component of the reducing gas mixture. Compared to the limited number of amino acids Miller identified, these new analyses have found that over 40 different amino acids and amines were synthesized, demonstrating the potential robust formation of important biologic compounds under possible cosmogeochemical conditions. These experiments are suggested to simulate long-lived volcanic island arc systems, an environment that could have provided a stable environment for some of the processes thought to be involved in chemical evolution and the origin of life. Some of the alternatives to the Miller-based prebiotic synthesis and the "primordial soup" paradigm are evaluated in the context of their relevance under plausible planetary conditions.

Bennett, RV, Cleaves HJ, Davis JM, Sokolov DA, Orlando TM, Bada JL, Fernandez FM.  2013.  Desorption Electrospray Ionization Imaging Mass Spectrometry as a Tool for Investigating Model Prebiotic Reactions on Mineral Surfaces. Analytical Chemistry. 85:1276-1279.   10.1021/ac303202n   AbstractWebsite

Mineral-assisted thermal decomposition of formamide (HCONH2) is a heavily studied model prebiotic reaction that has offered valuable insights into the plausible pathways leading to the chemical building blocks of primordial informational polymers. To date, most efforts have focused on the analysis of formamide reaction products released in solution, although several studies have examined the role of mineral catalysts in promoting this chemistry. We show here that the direct investigation of reactive mineral surfaces by desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) gives a new perspective on the important role of the mineral surface in the formation of reaction products. As a proof-of-principle example, we show that DESI-MSI allows interrogation of the molecular products produced on heterogeneous granite samples with minimal sample preparation. Purine and pyrimidine nucleobases and their derivatives are successfully detected by DESI-MSI, with a strong correlation of the spatial product distribution with the mineral microenvironment. To our knowledge, this study is the first application of DESI-MSI to the study of complex and porous mineral surfaces and their roles in chemical evolution. This DESI-MSI approach is generally applicable to a wide range of reactions or other processes involving minerals.

Rosa, C, Zeh J, George JC, Botta O, Zauscher M, Bada J, O'Hara TM.  2013.  Age estimates based on aspartic acid racemization for bowhead whales (Balaena mysticetus) harvested in 1998-2000 and the relationship between racemization rate and body temperature. Marine Mammal Science. 29:424-445.   10.1111/j.1748-7692.2012.00593.x   AbstractWebsite

Fifty-two eyes were collected and analyzed to estimate ages of 42 bowhead whales using the aspartic acid racemization aging technique. Between-eye and within-eye variance components for the ratio of the D and L optical isomers (D/L ratio) were estimated via analysis of variance using multiple measurements from nine whales with both eyes sampled and analyzed. For whales with more than one (D/L)(act) value, an inverse variance weighted average of the values was used as (D/L)(act) for the whale. Racemization rate (k(Asp)) and D/L ratio at birth (D/L)(0) were estimated using (D/L)(act) from 27 bowhead whales with age estimates based on baleen or ovarian corpora data and two term fetuses. The estimates were k(Asp) = 0.977x10(-3)/yr and (D/L)(0) = 0.0250. The nonlinear least squares analysis that produced these estimates also estimated female age at sexual maturity as ASM=25.86yr. SE(age) was estimated via a bootstrap that took into account the SE of (D/L)(act) and the variances and covariance of k(Asp) and (D/L)(0). One male exceeded 100yr of age; the oldest female was 88. A strong linear relationship between k(Asp) and body temperature was estimated by combining bowhead data with independent data from studies of humans and fin whales. Using this relationship, we estimated k(Asp) and ASM for North Atlantic minke whales.

2012
Elsila, JE, Glavin DP, Dworkin JP, Martins Z, Bada JL.  2012.  Inconclusive evidence for nonterrestrial isoleucine enantiomeric excesses in primitive meteorites. Proceedings of the National Academy of Sciences of the United States of America. 109:E3288-E3288.   10.1073/pnas.1213261109   Abstract

Pizzarello et al. (1) recently described the soluble organic content of eight Antarctic Renazzo-type (CR) carbonaceous chondrites and reported large enantiomeric excesses (ee) of l-isoleucine and d-alloisoleucine. The reported values of ee decrease with inferred increases in aqueous alteration. We believe the conclusions presented in the paper are not fully justified and the data are potentially flawed.

Potential terrestrial contamination of meteoritic amino acid data must always be considered. The manuscript states that “terrestrial contamination levels… were evaluated based on the presence of proteinogenic amino acids’ l-excesses and accounted for when needed,” but this “accounting” is not described. A wide range of l-proteinogenic amino acid excesses was measured …

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

Parker, ET, Cleaves HJ, Callahan MP, Dworkin JP, Glavin DP, Lazcano A, Bada JL.  2011.  Enhanced Synthesis of Alkyl Amino Acids in Miller's 1958 H2S Experiment. Origins of Life and Evolution of Biospheres. 41:569-574.   10.1007/s11084-011-9253-2   AbstractWebsite

Stanley Miller's 1958 H2S-containing experiment, which included a simulated prebiotic atmosphere of methane (CH4), ammonia (NH3), carbon dioxide (CO2), and hydrogen sulfide (H2S) produced several alkyl amino acids, including the alpha-, beta-, and gamma-isomers of aminobutyric acid (ABA) in greater relative yields than had previously been reported from his spark discharge experiments. In the presence of H2S, aspartic and glutamic acids could yield alkyl amino acids via the formation of thioimide intermediates. Radical chemistry initiated by passing H2S through a spark discharge could have also enhanced alkyl amino acid synthesis by generating alkyl radicals that can help form the aldehyde and ketone precursors to these amino acids. We propose mechanisms that may have influenced the synthesis of certain amino acids in localized environments rich in H2S and lightning discharges, similar to conditions near volcanic systems on the early Earth, thus contributing to the prebiotic chemical inventory of the primordial Earth.

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.

Grew, ES, Bada JL, Hazen RM.  2011.  Borate Minerals and Origin of the RNA World. Origins of Life and Evolution of Biospheres. 41:307-316.   10.1007/s11084-010-9233-y   AbstractWebsite

The RNA World is generally thought to have been an important link between purely prebiotic (>3.7 Ga) chemistry and modern DNA/protein biochemistry. One concern about the RNA World hypothesis is the geochemical stability of ribose, the sugar moiety of RNA. Prebiotic stabilization of ribose by solutions associated with borate minerals, notably colemanite, ulexite, and kernite, has been proposed as one resolution to this difficulty. However, a critical unresolved issue is whether borate minerals existed in sufficient quantities on the primitive Earth, especially in the period when prebiotic synthesis processes leading to RNA took place. Although the oldest reported colemanite and ulexite are 330 Ma, and the oldest reported kernite, 19 Ma, boron isotope data and geologic context are consistent with an evaporitic borate precursor to 2400-2100 Ma borate deposits in the Liaoning and Jilin Provinces, China, as well as to tourmaline-group minerals at 33003450 Ma in the Barberton belt, South Africa. The oldest boron minerals for which the age of crystallization could be determined are the metamorphic tourmaline species schorl and dravite in the Isua complex (metamorphism between ca. 3650 and ca. 3600 Ma). Whether borates such as colemanite, ulexite and kernite were present in the Hadean (>4000 Ma) at the critical juncture when prebiotic molecules such as ribose required stabilization depends on whether a granitic continental crust had yet differentiated, because in its absence we see no means for boron to be sufficiently concentrated for borates to be precipitated.

Rivas, M, Becerra A, Pereto J, Bada JL, Lazcano A.  2011.  Metalloproteins and the Pyrite-based Origin of Life: A Critical Assessment. Origins of Life and Evolution of Biospheres. 41:347-356.   10.1007/s11084-011-9238-1   AbstractWebsite

We critically examine the proposal by W chtersh user (Prokaryotes 1: 275-283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787-1808, 2006b) that putative transition metal binding sites in protein components of the translation machinery of hyper-thermophiles provide evidence of a direct relationship with the FeS clusters of pyrite and thus indicate an autotrophic origin of life in volcanic environments. Analysis of completely sequenced cellular genomes of Bacteria, Archaea and Eucarya does not support the suggestion by W chtersh user (Prokaryotes 1: 275-283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787-1808, 2006b) that aminoacyl-tRNA synthetases and ribosomal proteins bear sequence signatures typical of strong covalent metal bonding whose absence in mesophilic species reveals a process of adaptation towards less extreme environments.

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.

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.

Bada, JL.  2010.  DISTANCES TO THE BEACH. Chemical & Engineering News. 88:6-6.Website
2009
Pereto, J, Bada JL, Lazcano A.  2009.  Charles Darwin and the Origin of Life. Origins of Life and Evolution of Biospheres. 39:395-406.   10.1007/s11084-009-9172-7   AbstractWebsite

When Charles Darwin published The Origin of Species 150 years ago he consciously avoided discussing the origin of life. However, analysis of some other texts written by Darwin, and of the correspondence he exchanged with friends and colleagues demonstrates that he took for granted the possibility of a natural emergence of the first life forms. As shown by notes from the pages he excised from his private notebooks, as early as 1837 Darwin was convinced that "the intimate relation of Life with laws of chemical combination, & the universality of latter render spontaneous generation not improbable". Like many of his contemporaries, Darwin rejected the idea that putrefaction of preexisting organic compounds could lead to the appearance of organisms. Although he favored the possibility that life could appear by natural processes from simple inorganic compounds, his reluctance to discuss the issue resulted from his recognition that at the time it was possible to undertake the experimental study of the emergence of life.

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.

Bada, JL.  2009.  Enantiomeric excesses in the Murchison meteorite and the origin of homochirality in terrestrial biology. Proceedings of the National Academy of Sciences of the United States of America. 106:E85-E85.   10.1073/pnas.0906490106   Website
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.