Publications

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2014
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.

2011
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.

2009
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.

2007
Bump, JK, Fox-Dobbs K, Bada JL, Koch PL, Peterson RO, Vucetich JA.  2007.  Stable isotopes, ecological integration and environmental change: wolves record atmospheric carbon isotope trend better than tree rings. Proceedings of the Royal Society B-Biological Sciences. 274:2471-2480.   10.1098/rspb.2007.0700   AbstractWebsite

Large-scale patterns of isotope ratios are detectable in the tissues of organisms, but the variability in these patterns often obscures detection of environmental trends. We show that plants and animals at lower trophic levels are relatively poor indicators of the temporal trend in atmospheric carbon isotope ratios (delta C-13) when compared with animals at higher trophic levels. First, we tested how differences in atmospheric delta C-13 values were transferred across three trophic levels. Second, we compared contemporary delta C-13 trends (1961 - 2004) in atmospheric CO2 to delta C-13 patterns in a tree species ( jack pine, Pinus banksiana), large herbivore (moose, Alces alces) and large carnivore (grey wolf, Canis lupus) from North America. Third, we compared palaeontological (approx. 30 000 to 12 000 14 C years before present) atmospheric CO2 trends to delta C-13 patterns in a tree species (Pinus flexilis, Juniperus sp.), a megaherbivore (bison, Bison antiquus) and a large carnivore (dire wolf, Canis dirus) from the La Brea tar pits ( southern California, USA) and Great Basin (western USA). Contrary to previous expectations, we found that the environmental isotope pattern is better represented with increasing trophic level. Our results indicate that museum specimens of large carnivores would best reflect large-scale spatial and temporal patterns of carbon isotopes in the palaeontological record because top predators can act as ecological integrators of environmental change.

2006
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.

2004
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.

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.

2003
Kminek, G, Bada JL, Pogliano K, Ward JF.  2003.  Radiation-dependent limit for the viability of bacterial spores in halite fluid inclusions and on Mars. Radiation Research. 159:722-729.   10.1667/0033-7587(2003)159[0722:rlftvo]2.0.co;2   AbstractWebsite

When claims for the long-term survival of viable organisms are made, either within terrestrial minerals or on Mars, considerations should be made of the limitations imposed by the naturally occurring radiation dose to which they have been exposed. We investigated the effect of ionizing radiation on different bacterial spores by measuring the inactivation constants for B. subtilis and S. marismortui spores in solution as well as for dry spores of B. subtilis and B. thuringiensis. S. marismortui is a halophilic spore that is genetically similar to the recently discovered 2-9-3 bacterium from a halite fluid inclusion, claimed to be 250 million years old (Vreeland et al, Nature 407, 897-900, 2000). B. thuringiensis is a soil bacterium that is genetically similar to the human pathogens B. anthracis and B. cereus (Helgason et al., Appl. Environ. Microbiol 66, 2627-2630, 2000). To relate the inactivation constant to some realistic environments, we calculated the radiation regimen in a halite fluid inclusion and in the Martian subsurface over time. Our conclusion is that the ionizing dose of radiation in those environments limits the survival of viable bacterial spores over long periods. In the absence of an active repair mechanism in the dormant state, the long-term survival of spores is limited to less than 109 million years in halite fluid inclusions, to 100 to 160 million years in the Martian subsurface below 3 m, and to less than 600,000 years in the uppermost meter of Mars. (C) 2003 by Radiation Research Society.

2002
Kminek, G, Botta O, Glavin DP, Bada JL.  2002.  Amino acids in the Tagish Lake meteorite. Meteoritics & Planetary Science. 37:697-701. AbstractWebsite

High-performance liquid chromatography (HPLC) based amino acid analysis of a Tagish Lake meteorite sample recovered 3 months after the meteorite fell to Earth have revealed that the amino acid composition of Tagish Lake is strikingly different from that of the CM and Cl carbonaceous chondrites. We found that the Tagish Lake meteorite contains only trace levels of amino acids (total abundance = 880 ppb), which is much lower than the total abundance of amino acids in the Cl Orgueil (4100 ppb) and the CM Murchison (16 900 ppb). Because most of the same amino acids found in the Tagish Lake meteorite are also present in the Tagish Lake ice melt water, we conclude that the amino acids detected in the meteorite are terrestrial contamination. We found that the exposure of a sample of Murchison to cold water lead to a substantial reduction over a period of several weeks in the amount of amino acids that are not strongly bound to the meteorite matrix. However, strongly bound amino acids that are extracted by direct HCl hydrolysis are not affected by the leaching process. Thus even if there had been leaching of amino acids from our Tagish Lake meteorite sample during its 3 month residence in Tagish Lake ice and melt water, a Murchison type abundance of endogenous amino acids in the meteorite would have still been readily detectable. The low amino acid content of Tagish Lake indicates that this meteorite originated from a different type of parent body than the CM and CI chondrites. The parent body was apparently devoid of the reagents such as aldehyldes/ketones, HCN and ammonia needed for the effective abiotic synthesis of amino acids. Based on reflectance spectral measurements, Tagish Lake has been associated with P- or D-type asteroids. If the Tagish Lake meteorite was indeed derived from these types of parent bodies, our understanding of these primitive asteroids needs to be reevaluated with respect to their potential inventory of biologically important organic compounds.

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.

2001
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.

2000
Kminek, G, Bada JL, Botta O, Glavin DP, Grunthaner F.  2000.  MOD: an organic detector for the future robotic exploration of Mars. Planetary and Space Science. 48:1087-1091.   10.1016/s0032-0633(00)00082-9   AbstractWebsite

Searching for extinct or extant life on Mars is part of the future NASA surveyor class missions. Looking for key organic compounds that are essential for biochemistry as we know it or indicative of extraterrestrial organic influx is the primary goal of the Mars Organic Detector (MOD). MOD is able to detect amino acids, amines and PAHs with at least 100 times higher sensitivity than the Viking GCMS experiment. MOD is not capable of identifying specific organic molecules but can assess the organic inventory of amines and PAHs on the planet. MOD can also quantify adsorbed and chemisorbed water and evolved carbon dioxide in a stepped heating cycle to determine specific carbon-bearing minerals. All that comes with no sample preparation and no wet chemistry. The organics can be isolated from the carrier matrix by heating the sample and recovering the volatile organics on a cold finger. This sublimation technique can be used for extracting amino acids, amines and PAHs under Mars ambient conditions. The detection of amino acids, amines and PAHs is based on a fluorescence detection scheme. The MOD concept has functioned as a laboratory breadboard since 1998. A number of natural samples including shells, clays, bones, lambda -DNA and E.-coli bacteria have been used and organic molecules have been extracted successfully in each case. The first prototype of MOD is operational as of early fall of 1999. MOD has been selected for the definition phase of the NASA-MSR 2003 mission. (C) 2000 Elsevier Science Ltd. All rights reserved.

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

1995
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.

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.

1992
Becker, L, Bada JL, Kemper K, Suslick KS.  1992.  The Sonoluminescence Spectrum of Seawater. Marine Chemistry. 40:315-320.   10.1016/0304-4203(92)90029-a   AbstractWebsite

The sonoluminescence spectra of seawater and of a sodium chloride solution were determined by irradiation with ultrasound at 20 kHz. Ultrasound creates sonoluminescence through the process of acoustic cavitation: the formation, growth and implosive collapse of bubbles in a liquid. The sonoluminescence spectra of both seawater and NaCl in water are characterized by an emission line at 589 nm from excited-state sodium. Excited-state Na atoms are produced from the reaction of Na+ with high-energy hydroxyl radicals formed directly during the cavitation event. Emission at 589nm could be useful in determining whether sonochemical processes associated with cavitation occur in breaking waves or other turbulent flows.

1983
Bada, JL, Mitchell E, Kemper B.  1983.  Aspartic-Acid Racemization in Narwhal Teeth. Nature. 303:418-420.   10.1038/303418a0   Website
Bada, JL, Cronin JR, Ho MS, Kvenvolden KA, Lawless JG, Miller SL, Oro J, Steinberg S.  1983.  On the Reported Optical-Activity of Amino-Acids in the Murchison Meteorite. Nature. 301:494-496.   10.1038/301494a0   Website
1979
Ike, D, Bada JL, Masters PM, Kennedy G, Vogel JC.  1979.  Aspartic-Acid Racemization and Radiocarbon Dating of an Early Milling Stone Horizon Burial in California. American Antiquity. 44:524-530.   10.2307/279550   Website
1973
Bada, JL, Kvenvold.Ka, Peterson E.  1973.  Racemization of Amino-Acids in Bones. Nature. 245:308-310.   10.1038/245308a0   Website