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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.

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.

Bada, JL.  1991.  Amino-Acid Cosmogeochemistry. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences. 333:349-358.   10.1098/rstb.1991.0084   AbstractWebsite

Amino acids are ubiquitous components of living organisms and as a result they are widely distributed on the surface of the Earth. Whereas only 20 amino acids are found in proteins, a much more diverse mixture of amino acids has been detected in carbonaceous meteorites. Amino acids in living organisms consist exclusively of the L-enantiomers, but in meteorites, amino acids with chiral carbons are present as racemic mixtures. Protein amino acids undergo a variety of diagenetic reactions that produce some other amino acids but not the unique amino acids present in meteorites. Nevertheless, trace quantities of meteoritic amino acids may occur on the Earth, either as a result of bolide impact or from the capture of cosmic dust particles. The ensemble of amino acids present on the early Earth before life existed was probably similar to those in prebiotic experiments and meteorites. This generates a question about why the L-amino acids on which life is based were selected.