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PubMed1977

Life and the outer planets I. Performance of terrestrial organisms in ammonia-rich systems.

Survival and growth of organisms has been demonstrated at 298 degrees K in NH3 atmospheres, including ammonia-methane mixtures. Included are bacteria such as Clostridium perfringens, Pseudomonas aeruginosa, fungi such as Penicillium notatum and Torula utilis. Although the biological response in onion and other species of Allium is limited to germination, standard metabolic poisons were active even in 15 M aqueous NH3, at 250 degrees K. The most extreme example of compatibility between NH3-rich environments and terrestrial life was the retention of metabolic capabilities by conidia of Penicillium after 6 months at 233 degrees K in a liquid ammonia-glycerol medium. Tritiated thymidine, uridine and amino acids were incorporated by these conidia unless subjected to intense gamma-radiation. Observations spanning the past decade suggest that the analogies between H2O and NH3 as solvent media or -OH and -NH2, as functional groups are probably valid. Chemical-biological evolution similar to early terrestrial evolution could be compatible with chemical conditions presumed to exist on the outer planets and some of their satellites.

Ammonia↗

PubMed2003

Evolution of phage with chemically ambiguous proteomes.

BACKGROUND: The widespread introduction of amino acid substitutions into organismal proteomes has occurred during natural evolution, but has been difficult to achieve by directed evolution. The adaptation of the translation apparatus represents one barrier, but the multiple mutations that may be required throughout a proteome in order to accommodate an alternative amino acid or analogue is an even more daunting problem. The evolution of a small bacteriophage proteome to accommodate an unnatural amino acid analogue can provide insights into the number and type of substitutions that individual proteins will require to retain functionality. RESULTS: The bacteriophage Qbeta initially grows poorly in the presence of the amino acid analogue 6-fluorotryptophan. After 25 serial passages, the fitness of the phage on the analogue was substantially increased; there was no loss of fitness when the evolved phage were passaged in the presence of tryptophan. Seven mutations were fixed throughout the phage in two independent lines of descent. None of the mutations changed a tryptophan residue. CONCLUSIONS: A relatively small number of mutations allowed an unnatural amino acid to be functionally incorporated into a highly interdependent set of proteins. These results support the 'ambiguous intermediate' hypothesis for the emergence of divergent genetic codes, in which the adoption of a new genetic code is preceded by the evolution of proteins that can simultaneously accommodate more than one amino acid at a given codon. It may now be possible to direct the evolution of organisms with novel genetic codes using methods that promote ambiguous intermediates.

Allolevivirus↗

PubMed1992

Chemistry of the interstellar medium--an evolutionary dead end?

An analysis of the experimental data available and of the present theoretical concepts shows that even the initial physicochemical chemical precellular stages of biological evolution are impossible in the interstellar medium, while biomonomers possibly formed on asteroids and comets might have participated after transportation to the Earth in the final stages of the origin of the first precellular biological structures and then in the first living cells.

Aluminum Silicates↗

PubMed1986

Is there a single origin of life?

The emergence of the first life on the earth is now established as an early event, and closely related to the evolving earth. Laboratory experiments examining possible chemical events have revealed a multitude of plausible pathways. Lack of knowledge of the primitive terrestrial conditions contemporary with the evolving prebolic organic chemistry limits reconstruction techniques. The primitive earth's aqueous history is essential to unraveling this problem. Based on our current knowledge of other planets of the solar system, we do not expect close analogues to the early earth. We still do not know if there was a second origin or if only earth has life. This may depend upon the question of the survival of information bearing chemical systems in a dynamic or chaotic environment and the chemical protection afforded within such a system. Water is the central molecule of controversy: the blessing and the curse of the chemist. New and novel chemical mechanisms and systems abound.

Enzymes↗

PubMed2004

In phase selective excitation of overlapping multiplets by gradient-enhanced chemical shift selective filters.

We have developed gradient-enhanced chemical shift selective filters (ge-CSSF) for inphase excitation of overlapping multiplets 1H. This method relies on the constructive addition of on resonance signal while off resonance magnetization is eliminated by destructive interference due to variable chemical shift evolution. This is achieved by co-addition of several FIDs acquired with a gradually incremented chemical shift evolution period. Two variable-time and one constant-time ge-CSSFs are proposed that can be combined with TOCSY, NOESY, and ROESY mixing schemes yielding highly selective 1D experiments. Analytical and numerical expressions are derived to calculate the excitation profiles of the ge-CSSFs and to examine the effects of spin-spin relaxation, the length of the CSSF increment, and selective inversion pulses. We demonstrate, both theoretically and experimentally, that CSSFs yield fast signal separation for compounds with a range of spin-spin relaxation times and chemical shift differences as small as 1-2 Hz. The use of pulsed field gradients ensures that very clean spectra are obtained. The main application of these techniques lies in analysis of mixtures where severe spectral overlap prevents the use of simple 1D selective methods.

Journal Article↗

PubMed2004

Dynamic co-evolution of peptides and chemical energetics, a gateway to the emergence of homochirality and the catalytic activity of peptides.

We propose a scenario for the dynamic co-evolution of peptides and energy on the primitive Earth. From a multi component system consisting of hydrogen cyanide, several carbonyl compounds, ammonia, alkyl amine, carbonic anhydride, borate and isocyanic acid, we show that the reversibility of this system leads to several intermediate nitriles, that irreversibly evolve to alpha-amino acids and N-carbamoyl amino acids via selective catalytic processes. On the primitive Earth these N-carbamoyl amino acids combined with energetic molecules (NOx) may have been the core of a molecular engine producing peptides permanently and assuring their recycling and evolution. We present this molecular engine, a production example, and its various selectivities. The perspectives for such a dynamic approach to the emergence of peptides are evoked in the conclusion.

Amino Acids↗

PubMed2003

[Cryptobiosphere of Mars].

The US Viking missions (1975-1976) failed to discover any biological activity on the surface of Mars. Yet, life may exist in the planet lithosphere which was found to contain a substantial amount of water. Martian interior can also provide microbial cryptolife with sources of carbon (CO, CO2, CH4) and energy (reduced elements and compounds, e.g. H2, CO, H2S, NH4+, CH4, Fe3+). Microorganisms identical to the Earth's anaerobic methanogens, sulfate reducers, acetogens, denitrifiers etc. are the most probable Martian aborigines. Well-balanced continuous functioning of the Martian cryptobiosphere implies closure of biochemical carbon, sulfur and nitrogen cycles which cannot be reached but with participation of organotrophic and anaerobic hydrolytic and zymotic organisms, ammonifiers and denitrifiers. Considering the low intensity of biological and chemical processes in the absence of surface hydrosphere, low-power atmosphere and cryptobiosphere closure on Mars, and slow global energy matter cycles, evolution of the presumable Martian cryptolife should also go at a slack pace and directions and forms of the evolution of living substance can have little in common with those on Earth. Comprehensive investigations of the Martian biota will employ a great variety of geochemical, radi- and stable isotope, microbiological, enzymatic and molecular biology methods.

Aerobiosis↗

PubMed1998

The diffuse interstellar bands: a tracer for organics in the diffuse interstellar medium?

The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.

Astronomical Phenomena↗

PubMed2003

The interface between the biological and inorganic worlds: iron-sulfur metalloclusters.

Complex iron-sulfur metalloclusters form the active sites of the enzymes that catalyze redox transformations of N2, CO, and H2, which are likely components of Earth's primordial atmosphere. Although these centers reflect the organizational principles of simpler iron-sulfur clusters, they exhibit extensive elaborations that confer specific ligand-binding and catalytic properties. These changes were probably achieved through evolutionary processes, including the fusion of small clusters, the addition of new metals, and the development of cluster assembly pathways, driven by selective pressures resulting from changes in the chemical composition of the biosphere.

Aldehyde Oxidoreductases↗

PubMed2006

alpha-Hydroxy and alpha-amino acids under possible Hadean, volcanic origin-of-life conditions.

To test the theory of a chemoautotrophic origin of life in a volcanic, hydrothermal setting, we explored mechanisms for the buildup of bio-organic compounds by carbon fixation on catalytic transition metal precipitates. We report the carbon monoxide-dependent formation of carbon-fixation products, including an ordered series of alpha-hydroxy and alpha-amino acids of the general formula R-CHA-COOH (where R is H, CH3,C2H5,orHOCH2 and A is OH or NH2) by carbon fixation at 80 degrees to 120 degrees C, catalyzed by nickel or nickel,iron precipitates with carbonyl, cyano, and methylthio ligands as carbon sources, with or without sulfido ligands. Calcium or magnesium hydroxide was added as a pH buffer. The results narrow the gap between biochemistry and volcanic geochemistry and open a new gateway for the exploration of a volcanic, hydrothermal origin of life.

Amino Acids↗

PubMed1990

Prebiotic synthesis of histidine.

The prebiotic formation of histidine (His) has been accomplished experimentally by the reaction of erythrose with formamidine followed by a Strecker synthesis. In the first step of this reaction sequence, the formation of imidazole-4-acetaldehyde took place by the condensation of erythrose and formamidine, two compounds that are known to be formed under prebiotic conditions. In a second step, the imidazole-4-acetaldehyde was converted to His, without isolation of the reaction products by adding HCN and ammonia to the reaction mixture. LC, HPLC, thermospray liquid chromatography-mass spectrometry, and tandem mass spectrometry were used to identify the product, which was obtained in a yield of 3.5% based on the ratio of His/erythrose. This is a new chemical synthesis of one of the basic amino acids which had not been synthesized prebiotically until now.

Aldehydes↗

PubMed1996

Possible role of volcanic ash-gas clouds in the Earth's prebiotic chemistry.

Volcanic ash-gas clouds represent versatile local atmospheric environments appropriate for abiotic synthesis of rather complex organic molecules due to the simultaneous presence of various gaseous reagents, catalytically active inorganic particles, electric discharges, pressure and temperature gradients. They are relatively readily attainable for the scientists, contrary to objects or events of space origin (interstellar and planetary dust, meteoritic/cometary impacts, etc.), providing excellent opportunities for in situ studies and grounded simulating experiments. This paper reviews the available data on this environment, its most important chemical and physical parameters. Based on this analysis, it is suggested in brief experimental conditions for the simulation.

Atmospheric Pressure↗

PubMed2001

Experimental simulation of early Martian volcanic lightning.

A mixture of possible Martian volcanic gases were reproduced and irradiated by a high-energy infrared laser to reproduce the effects of lightning on the production of prebiotic molecules. The analysis of products were performed by a gas chromatograph interfaced in parallel with a FTIR-detector and a quadrupole mass spectrometer equipped with an electron impact and chemical ionization modes. The main products identified were hydrocarbons and an uncharacterized yellow film deposit. Preliminary results indicate the presence of hydrogen cyanide among the resultant compounds.

Evolution, Chemical↗

PubMed2004

Drug evolution concept in drug design: 1. Hybridization method.

A novel concept, "drug evolution", is proposed to develop chemical libraries that have a high probability of finding drugs or drug candidates. It converts biological evolution into chemical evolution. In this paper, we present "hybridization" drug evolution, which is the equivalent of sexual recombination of parental genomes in biological evolution. The hybridization essentially shuffles the building blocks of the parent drugs and ought to drug(s); no drug evolution can otherwise occur. We hybridized two drugs, benzocaine and metoclopramide and generated 16 molecules that include the parent drugs, four known drugs, and two molecules whose therapeutic activities are reported. The unusually high number of drugs and drug candidates in the library encourages high expectations of finding new drug(s) or drug candidate(s) within the remaining eight compounds. Interestingly, the therapeutic applications of the eight drugs or drug candidates in the library are fairly diverse as 38 therapeutic applications and 25 molecular targets are counted. Therefore, the library fits as a general chemical library for unspecified therapeutic activities. The hybridization of other two drugs, aspirin and cresotamide, is also described to demonstrate the generality of the method.

4-Aminobenzoic Acid↗

PubMed1984

Self-instructed condensation of amino acids into polymers.

In contemporary cells biological information is largely stored in nucleic acids. Therefore, a prerequisite in many theories on the origin of cellular life is the pre-existence of self-replicating polynucleotides that had to be formed by abiotic processes on the prebiotic Earth. It is usually assumed that the spontaneous synthesis of a self-replicating polynucleotide could take place readily. However, serious stereochemical obstacles exist which make Such a synthesis extremely improbable. Amino acids on the other hand, which are abundantly formed in prebiotic simulation experiments, are relatively easily polymerized to macromolecules (protoproteins) that share with modern proteins many properties: e.g., definable non-random structure, selected amino acid sequences, enzyme-like activities and self-assembly into supramolecular structures. Prebiotic polyamino acids are therefore regarded by some scientists, including the present author, as the first informational macromolecules. The origin of this information is the chemical reactivity of the various prebiotic amino acids and their chemical response to their environment. The first informational polynucleotides were likely formed by a polynucleotide polymerase activity of prebiotic protoproteins. A contemporary model for this process is seen, e.g., in the activity of template-free Q beta-replicase.

Amino Acids↗

PubMed2002

Geodynamic and seismic constraints on the thermochemical structure and dynamics of convection in the deep mantle.

We revisit a recent study by Forte & Mitrovica in which global geophysical observables associated with mantle convection were inverted and the existence of a strong increase in viscosity near a depth of 2000 km was inferred. Employing mineral-physics data and theory we also showed that, although there are chemical anomalies in the lowermost mantle, they are unable to inhibit the dominant thermal buoyancy of the deep-mantle mega-plumes below Africa and the Pacific Ocean. New Monte Carlo simulations are employed to explore the impact of uncertainties in current mineral-physics constraints on inferences of deep-mantle thermochemical structure. To explore the impact of the high-viscosity peak at a depth of 2000 km on the evolution of lower-mantle structure, we carried out time-dependent convection simulations. The latter show that the stability and longevity of the dominant long-wavelength heterogeneity in the lowermost mantle are controlled by this viscosity peak.

Computer Simulation↗

PubMed2002

On the origin of noble gases in mantle plumes.

The chemical differences between deep- and shallow-mantle sources of oceanic basalts provide evidence that several distinct components coexist within the Earth's mantle. Most of these components have been identified as recycled in origin. However, the noble-gas signature is still a matter of debate and questions the preservation of primitive regions in the convective mantle. We show that a model where the noble-gas signature observed in Hawaii and Iceland comes from a pristine homogeneous deep layer would imply a primitive (3)He content and (3)He/(22)Ne ratio that are very unlikely. On the contrary, mass balances show that the partly degassed peridotite of a marble-cake mantle can be the noble-gas end-member with an apparent 'primitive'-like composition. This component is mixed with recycled oceanic crust in different proportions in the plume sources and in the shallow mantle. A recycling model of the mantle, involving gravitational segregation of the oceanic crust at the bottom of the mantle, potentially satisfies trace-element as well as noble-gas constraints.

Argon↗

PubMed2002

The continental lithospheric mantle: characteristics and significance as a mantle reservoir.

The continental lithospheric mantle (CLM) is a small-volumed (ca. 2.5% of the total mantle), chemically distinct mantle reservoir that has been suggested to play a role in the source of continental and oceanic magmatism. It is our most easily identifiable reservoir for preserving chemical heterogeneity in the mantle. Petrological and geophysical constraints indicate that the maximum depth of the CLM is ca. 250 km. There is a clear secular variation of CLM composition, such that CLM formed in the last 2 Gyr is less depleted and therefore less dynamically stable than ancient CLM formed in the Archean. We present new trace-element data for kimberlite-hosted lithospheric peridotites and metasomites. These data, combined with other data for spinel peridotites from non-cratonic regions, show that neither hydrous nor anhydrous lithospheric mantle xenoliths make suitable sources for continental or oceanic basalts. Addition of a hydrous phase, either amphibole or phlogopite, to depleted peridotite results in positive Nb and Ti anomalies that are the opposite of those predicted for some flood-basalt sources on the basis of their trace-element abundances. Overall, the Sr and Nd isotopic composition of cratonic and non-cratonic CLM is close to bulk Earth, with cratonic CLM showing small numbers of extreme compositions. Thus, while the CLM is certainly ancient in many locations, its average composition is not significantly 'enriched' over primitive upper mantle, in terms of either radiogenic isotopes or trace elements. These characteristics, plus a change in lithospheric chemistry with depth, indicate that the elemental and isotopic composition of lithospheric mantle likely to be re-incorporated into convecting mantle via delamination/thermal erosion processes is probably not very distinct from that of the convecting mantle. These observations lead us to question the requirement for CLM participation in the source of oceanic magmas and to promote consideration of a mantle that is chemically heterogeneous on all scales. Hf and Nd isotope compositions identify a distinctive source component in deeply derived alkaline volcanics associated with continents. This component cannot be constrained to the CLM but may originate from a deeper reservoir of ancient, subducted oceanic crust stored in the mantle.

Earth, Planet↗