A model for the modular evolution of rna addressing open questions on the origin of life

A main unsolved problem in the RNA world scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers generated by random polymerization of ribonucleotides (Joyce and Orgel 2006). Current estimates establish a minimum size about 165 nt long for such a ribozyme (Johnston et al. 2001), a length three to four times that of the longest RNA oligomers obtained by random polymerization on clay mineral surfaces (Huang and Ferris 2003, 2006). To overcome this gap, we have developed a stepwise model of ligation-based, modular evolution of RNA (Briones et al. 2009) whose main conceptual steps are summarized in Figure 1. This scenario has two main advantages with respect to previous hypotheses put forward for the origin of the RNA world: i) short RNA....

Chemical modification of smectite clays

Today, speciality use organoclays are being developed for an increasingly large number of specific applications. Many of these, including use in cosmetics, polishes, greases and paints, require that the material be free from abrasive impurities so that the product retains a smooth `feel'. The traditional `wet' method preparation of organoclays inherently removes abrasives naturally present in the parent mineral clay, but it is time-consuming and expensive. The primary objective of this thesis was to explore the alternative `dry' method (which is both quicker and cheaper but which provides no refining of the parent clay) as a process, and to examine the nature of the organoclays produced, for the production of a wide range of commercially usable organophilic clays in a facile way. Natural Wyoming bentonite contains two quite different types of silicate surface (that of the clay mineral montmorillonite and that of a quartz impurity) that may interact with the cationic surfactant added in the `dry' process production of organoclays. However, it is oil shale, and not the quartz, that is chiefly responsible for the abrasive nature of the material, although air refinement in combination with the controlled milling of the bentonite as a pretreatment may offer a route to its removal. Ion exchange of Wyoming bentonite with a long chain quaternary ammonium salt using the `dry' process affords a partially exchanged, 69-78%, organoclay, with a monolayer formation of ammonium ions in the interlayer. Excess ion pairs are sorbed on the silicate surfaces of both the clay mineral and the quartz impurity phases. Such surface sorption is enhanced by the presence of very finely divided, super paramagnetic, Fe2O3 or Fe(O)(OH) contaminating the surfaces of the major mineral components. The sorbed material is labile to washing, and induces a measurable shielding of the 29Si nuclei in both clay and quartz phases in the MAS NMR experiment, due to an anisotropic magnetic susceptibility effect. XRD data for humidified samples reveal the interlamellar regions to be strongly hydrophobic, with the by-product sodium chloride being expelled to the external surfaces. Many organic cations will exchange onto a clay. The tetracationic cyclophane, and multipurpose receptor, cyclobis(paraquat-p-phenylene) undergoes ion exchange onto Wyoming bentonite to form a pillared clay with a very regular gallery height. The major plane of the cyclophane is normal to the silicate surfaces, thus allowing the cavity to remain available for complexation. A series of group VI substituted o-dimethoxybenzenes were introduced, and shown to participate in host/guest interactions with the cyclophane. Evidence is given which suggests that the binding of the host structure to a clay substrate offers advantages, not only of transportability and usability but of stability, to the charge-transfer complex which may prove useful in a variety of commercial applications. The fundamental relationship between particle size, cation exchange capacity and chemical composition of clays was also examined. For Wyoming bentonite the extent of isomorphous substitution increases with decreasing particle size, causing the CEC to similarly increase, although the isomorphous substitution site: edge site ratio remains invarient throughout the particle size range studied.

Petrology of weathered lower lias clays

In weak argillaceous rocks the unweathered strength may be barely sufficient to meet civil engineering reguirements and any reductjon due to weathering will be critical. This study investigates the weathering of the Lower Lias clays with particular reference to their petrography and engineering properties. Investigations revealed the Midland Basin of deposition to contain reasonable thicknesses of clay, relatively uniform in nature with a well developed weathered zone, From the available exposures, the weathering zone of the Blockley Clay pit was selected and sampled for laboratory investigations of; Structure, Mineralogy and Chemistry and Engineering Properties. The nature and orientation of the fissures in the unweathered clay were analysed. A close relationship was found to exist between the major joint set and the ground surface, with stress release due to excavation being almost negligible. Thin sections of the clay, examined for structural data, suggested that there exist layers or areas that have been disturbed as a result of density differences. Shear planes were found in both the unweathered and weathered clay, in the latter case often associated with remoulding of the material. A direct measure of remoulding was obtained from the birefringence ratio. The fabric was examined in closer detail using the scanning electron microscope. Mineralogy, as revealed by X-ray and optical techniques indicated illite as the dominant clay mineral, with kaolinite subsidiary; quartz, calcite, pyrite, chlorite/vermiculite are present as accessory minerals. Weathering changes this relationship, calcite and pyrite being removed early in the process, with illite being degraded. The cementing action of calcite and iron oxides was investigated however, this was shown to be negligible. Quantitative measurements of both fixed (with minerals) and free (oxide coatings) iron were obtained by atomic absorption, with the Fe 3+/ Fe2+ ratio obtained by Mossbauer spectroscopy, Evidence indicates that free iron oxide coatings only become important as a result of weathering with the maximum concentration in the very highly weathered material. Engineering index properties and shear strength values were taken throughout the profile, Relationships between moisture content and strength, liquid limit and iron (Fe) were obtained and a correlation between the weathering zomes and the shear strength/depth curve has been established.

The dawn of the RNA World:toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation- based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. Copyright © 2009 RNA Society.