Research Article
The Cyborg Astrobiologist: scouting red beds for uncommon features with geological significance
- Patrick Charles McGuire, Enrique Díaz-Martínez, Jens Ormö, Javier Gómez-Elvira, José Antonio Rodríguez-Manfredi, Eduardo Sebastián-Martínez, Helge Ritter, Robert Haschke, Markus Oesker, Jörg Ontrup
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- Published online by Cambridge University Press:
- 04 October 2005, pp. 101-113
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The ‘Cyborg Astrobiologist’ has undergone a second geological field trial, at a site in northern Guadalajara, Spain, near Riba de Santiuste. The site at Riba de Santiuste is dominated by layered deposits of red sandstones. The Cyborg Astrobiologist is a wearable computer and video camera system that has demonstrated a capability to find uncommon interest points in geological imagery in real time in the field. In this second field trial, the computer vision system of the Cyborg Astrobiologist was tested at seven different tripod positions, on three different geological structures. The first geological structure was an outcrop of nearly homogeneous sandstone, which exhibits oxidized-iron impurities in red areas and an absence of these iron impurities in white areas. The white areas in these ‘red beds’ have turned white because the iron has been removed. The iron removal from the sandstone can proceed once the iron has been chemically reduced, perhaps by a biological agent. In one instance the computer vision system found several (iron-free) white spots to be uncommon and therefore interesting, as well as several small and dark nodules. The second geological structure was another outcrop some 600 m to the east, with white, textured mineral deposits on the surface of the sandstone, at the bottom of the outcrop. The computer vision system found these white, textured mineral deposits to be interesting. We acquired samples of the mineral deposits for geochemical analysis in the laboratory. This laboratory analysis of the crust identifies a double layer, consisting of an internal millimetre-size layering of calcite and an external centimetre-size efflorescence of gypsum. The third geological structure was a 50 cm thick palaeosol layer, with fossilized root structures of some plants. The computer vision system also found certain areas of these root structures to be interesting. A quasi-blind comparison of the Cyborg Astrobiologist's interest points for these images with the interest points determined afterwards by a human geologist shows that the Cyborg Astrobiologist concurred with the human geologist 68% of the time (true-positive rate), with a 32% false-positive rate and a 32% false-negative rate. The performance of the Cyborg Astrobiologist's computer vision system was by no means perfect, so there is plenty of room for improvement. However, these tests validate the image-segmentation and uncommon-mapping technique that we first employed at a different geological site (Rivas Vaciamadrid) with somewhat different properties for the imagery.
Effect of metallic cations on the efficiency of DNA amplification. Implications for nucleic acid replication during early stages of life
- María Arribas, Aránzazu de Vicente, Armando Arias, Ester Lázaro
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- 04 October 2005, pp. 115-123
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The process of catalysis of biochemical reactions has been essential since the first organic molecules appeared on Earth. As the complexity of the ensemble of primitive biomolecules was very low, primitive catalysts had necessarily to be very simple molecules or ions. The evolution of catalysts had to be in parallel with the evolution of the molecular species reacting. An example of this parallel evolution is nucleic acid polymerization. Synthesis of primitive short oligonucleotides could have been catalysed by metal ions either in solution or on the surface of minerals such as montmorillonite clays. Some oligonucleotides could start to function as templates for the synthesis of complementary copies and there is experimental evidence supporting the role also played by metal ions in this process. In later stages of evolution, a group of enzymatic proteins, nucleic acid polymerases, has been selected to catalyse nucleic acid replication. The presence of Mg2+ in the active centre of these enzymes suggests that evolution has preserved some of the primitive catalysts, including them as cofactors of more complex molecules. However, the reasons why Mg2+ was selected among other ions that possibly were present in primitive environments are unknown. In this paper we try to approach this question by analysing the amplification efficiency of the polymerase chain reaction of a DNA fragment in the presence of different metal ions. In some cases the conditions of the reaction have been displaced from optimum (by the presence of nucleotide imbalances and a suboptimal Mg2+concentration). The results obtained permit one to draw interesting conclusions about how some metallic cations can help replication to proceed in conditions of limited substrate availability, a circumstance that could have been frequent at prebiotic stages, when nucleic acid synthesis was dependent on the physico-chemical conditions of the environment.
Theoretical study of prebiotic precursors: the peptide bond and its silicon, sulphur and phosphorous analogues
- J.M. Chiaramello, D. Talbi, G. Berthier, Y. Ellinger
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- 04 October 2005, pp. 125-133
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This paper looks at the possibility that the peptide bond may be more common than originally thought, leading to molecules of prebiotic interest containing heavier atoms of the second row of the periodic table. Ab initio Möller–Plesset (MP2) coupled-cluster molecular orbital methods and density functional theory have been used. A first investigation of the six-atom system [C,3H,O,N] showed that formamide, NH2[bond]CH[double bond]O, is the most stable system that can be formed. Systematic studies on this same system in which C, O and N were respectively replaced by Si, S and P were then carried out. It has been found that the peptide-like linkage is the most stable for [C,3H,S,N] and [Si,3H,O,N] where NH2[bond]CH[double bond]S and NH2[bond]SiH[double bond]O are about 10–14 kcal mol−1 more favourable than the corresponding enol tautomers and well below other isomers on the energy scale. For [C,3H,O,P], the most stable species is CH3[bond]P[double bond]O, which is found 18 kcal mol−1 below the PH2[bond]CH[double bond]O peptide analogue. By correcting the known inadequacies in the calculations with the average theoretical to experimental ratio from the benchmark molecules of the system, it is possible to obtain a best estimate of rotational constants and infrared frequencies that should be precise enough to initiate laboratory experiments and/or observations. The corrected values of B=6.0342 GHz and C=5.4921 GHz for NH2[bond]CH[double bond]S; B=9.2292 GHz and C=6.1164 GHz for NH2[bond]SiH[double bond]O; B=8.0275 GHz and C=6.4779 GHz for CH3[bond]P[double bond]O should be accurate to within a few tenths of a per cent. Theoretical infrared spectra are also provided to assist in identification of these exotic species.
Activity and stability of a complex bacterial soil community under simulated Martian conditions
- Aviaja Anna Hansen, Jonathan Merrison, Per Nørnberg, Bente Aagaard Lomstein, Kai Finster
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- 04 October 2005, pp. 135-144
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A simulation experiment with a complex bacterial soil community in a Mars simulation chamber was performed to determine the effect of Martian conditions on community activity, stability and survival. At three different depths in the soil core short-term effects of Martian conditions with and without ultraviolet (UV) exposure corresponding to 8 Martian Sol were compared. Community metabolic activities and functional diversity, measured as glucose respiration and versatility in substrate utilization, respectively, decreased after UV exposure, whereas they remained unaffected by Martian conditions without UV exposure. In contrast, the numbers of culturable bacteria and the genetic diversity were unaffected by the simulated Martian conditions both with and without UV exposure. The genetic diversity of the soil community and of the colonies grown on agar plates were evaluated by denaturant gradient gel electrophoresis (DGGE) on DNA extracts. Desiccation of the soil prior to experimentation affected the functional diversity by decreasing the versatility in substrate utilization. The natural dominance of endospores and Gram-positive bacteria in the investigated Mars-analogue soil may explain the limited effect of the Mars incubations on the survival and community structure. Our results suggest that UV radiation and desiccation are major selecting factors on bacterial functional diversity in terrestrial bacterial communities incubated under simulated Martian conditions. Furthermore, these results suggest that forward contamination of Mars is a matter of great concern in future space missions.
Prebiotic formation of polyamino acids in molten urea
- H. Mita, S. Nomoto, M. Terasaki, A. Shimoyama, Y. Yamamoto
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- 04 October 2005, pp. 145-154
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It is important for research into the origins of life to elucidate polyamino acid formation under prebiotic conditions. Only a limited set of amino acids has been reported to polymerize thermally. In this paper we demonstrate a novel thermal polymerization mechanism in a molten urea of alkylamino acids (i.e. glycine, alanine, β-alanine, α-aminobutyric acid, valine, norvaline, leucine and norleucine), which had been thought to be incapable of undergoing thermal polymerization. Also, aspartic acid was found to polymerize in molten urea at a lower temperature than that at which aspartic acid alone had previously been thermally polymerized. Individual oligomers produced in heating experiments on urea–amino acid mixtures were analysed using a liquid chromatograph mass spectrometer. Major products in the reaction mixture were three different types of polyamino acid derivatives: N-carbamoylpolyamino acids, polyamino acids containing a hydantoin ring at the N-terminal position and unidentified derivatives with molecular weights that were greater by 78 than those of the corresponding peptide forms. The polymerization reaction occurred by taking advantage of the high polarity of molten urea as well as its dehydrating ability. Under the presumed prebiotic conditions employed here, many types of amino acids were thus revealed to undergo thermal polymerization.
Biological potential of low-temperature aqueous environments on Mars
- Lindsey S. Link, Bruce M. Jakosky, Geoffrey D. Thyne
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- Published online by Cambridge University Press:
- 04 October 2005, pp. 155-164
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We have explored chemical weathering of probable martian materials at low temperatures based on the increasing evidence for non-hydrothermal water at or near the martian surface. Chemical weathering of minerals at low temperatures (as low as 0 °C) in aqueous environments on Mars can provide geochemical energy to support construction of potential martian organisms. Here, we examine the geochemical energy available from the interaction of the martian surface or near-surface materials with low-temperature water. We calculate the Gibbs free energy for 13 different weathering reactions that are likely to be important on Mars. The aqueous weathering of 1 kg of an ultramafic rock such as the Chassigny meteorite under present martian conditions can support the construction of ~30 g of microbes. The aqueous weathering of 1 kg of a basaltic rock on Mars can support the construction of ~26 g of biomass under present martian conditions and ~32 grams for conditions probable in the past. This means that ~1.3×1019 g of potential biomass could have been supported from weathering a global layer of rock 1 m thick. Thus, low-temperature water–rock reactions on Mars can produce abundant geochemical energy for potential martian microbes.