A structural view of evolutionary divergence

Two directed evolution experiments on p-nitrobenzyl esterase yielded one enzyme with a 100-fold increased activity in aqueous-organic solvents and another with a 17°C increase in thermostability. Structures of the wild type and its organophilic and thermophilic counterparts are presented at resolutions of 1.5 Å, 1.6 Å, and 2.0 Å, respectively. These structures identify groups of interacting mutations and demonstrate how directed evolution can traverse complex fitness landscapes. Early-generation mutations stabilize flexible loops not visible in the wild-type structure and set the stage for further beneficial mutations in later generations. The mutations exert their influence on the esterase structure over large distances, in a manner that would be difficult to predict. The loops with the largest structural changes generally are not the sites of mutations. Similarly, none of the seven amino acid substitutions in the organophile are in the active site, even though the enzyme experiences significant changes in the organization of this site. In addition to reduction of surface loop flexibility, thermostability in the evolved esterase results from altered core packing, helix stabilization, and the acquisition of surface salt bridges, in agreement with other comparative studies of mesophilic and thermophilic enzymes. Crystallographic analysis of the wild type and its evolved counterparts reveals networks of mutations that collectively reorganize the active site. Interestingly, the changes that led to diversity within the α/β hydrolase enzyme family and the reorganization seen in this study result from main-chain movements.

Biochemical evolution II: Origin of life in tubular microstructures on weathered feldspar surfaces

Mineral surfaces were important during the emergence of life on Earth because the assembly of the necessary complex biomolecules by random collisions in dilute aqueous solutions is implausible. Most silicate mineral surfaces are hydrophilic and organophobic and unsuitable for catalytic reactions, but some silica-rich surfaces of partly dealuminated feldspars and zeolites are organophilic and potentially catalytic. Weathered alkali feldspar crystals from granitic rocks at Shap, north west England, contain abundant tubular etch pits, typically 0.4–0.6 μm wide, forming an orthogonal honeycomb network in a surface zone 50 μm thick, with 2–3 × 106 intersections per mm2 of crystal surface. Surviving metamorphic rocks demonstrate that granites and acidic surface water were present on the Earth’s surface by ∼3.8 Ga. By analogy with Shap granite, honeycombed feldspar has considerable potential as a natural catalytic surface for the start of biochemical evolution. Biomolecules should have become available by catalysis of amino acids, etc. The honeycomb would have provided access to various mineral inclusions in the feldspar, particularly apatite and oxides, which contain phosphorus and transition metals necessary for energetic life. The organized environment would have protected complex molecules from dispersion into dilute solutions, from hydrolysis, and from UV radiation. Sub-micrometer tubes in the honeycomb might have acted as rudimentary cell walls for proto-organisms, which ultimately evolved a lipid lid giving further shelter from the hostile outside environment. A lid would finally have become a complete cell wall permitting detachment and flotation in primordial “soup.” Etch features on weathered alkali feldspar from Shap match the shape of overlying soil bacteria.

Mineralogy and chemistry of bentonitic clays from the Wombat and Exmouth Plateaus

Bentonites (i.e., smectite-dominated, altered volcanic ash layers) were recovered in Berriasian to Valanginian hemipelagic sediments of the Wombat Plateau (Site 761) and southern Exmouth Plateau (Site 763). They are compared to coeval bentonites in eupelagic sediments of the adjacent Argo Abyssal Plain (Sites 261 and 765) and Gascoyne Abyssal Plain (Site 766). A volcaniclastic origin with dacitic to rhyolitic ash as parent material is suggested by the abundance of well-ordered montmorillonite, fresh to altered silicic glass shards, volcanogenic minerals (euhedral sanidine, apatite, and long-prismatic zircon), and volcanic rock fragments, and by a vitroclastic ultrafabric (smectitized glass shards). We distinguish (1) pure smectite bentonites with a white, pink, or light gray color, a waxy appearance, and a very homogeneous, cryptocrystalline smectite matrix (water-free composition at Site 761: 68.5% SiO2, 0.27% TiO2, 19.1% Al2O3, 3.3% Fe2O3, 0.4%-1.1% Na2O, and 0.6% K2O) and (2) impure bentonitic claystones containing mixtures of volcanogenic smectite and pyroclastic grains with terrigenous and pelagic components. The ash layers were progressively altered during diagenesis. Silicic glass was first hydrated, then slightly altered (etched with incipient smectite authigenesis), then moderately smectitized (with shard shape still intact), and finally completely homogenized to a pure smectite matrix without obvious relict structures. Euhedral clinoptilolite is the latest pore-filling or glass-replacing mineral, postdating smectite authigenesis. Volcanic activity was associated with continental breakup and rapid subsidence during the "juvenile ocean phase." Potential source areas for a Neocomian post-breakup volcanism include the Wombat Plateau, Joey and Roo rises, Scott Plateau, and Wallaby Plateau/Cape Range Fracture Zone. Westward-directed trade winds transported silicic ash from these volcanic source areas to the Exmouth Plateau into the adjacent abyssal plains. The Wombat Plateau bentonites are interpreted as proximal ash turbidites.

Geochemistry, minerals, color, rare earth elements and d18O at DSDP Hole 92-504B

Investigations of borehole waters sampled in Hole 504B during Leg 92 revealed changes in major-ion composition similar to changes observed previously (during Leg 83). The uniformity of chloride concentrations with increasing depth suggests efficient downhole mixing processes along density gradients caused by large temperature gradients. Chemical and mineralogical studies of suspended drilling mud (bentonite) suggest that this material has undergone substantial alteration and that CaSO4 (anhydrite/gypsum) has precipitated in the deeper parts of the hole. Rare earth element studies suggest contributions of both the bentonites and the basalts to the REE distributions. Studies of the isotopic composition (87Sr/86Sr) of dissolved strontium indicate a strong contribution of basaltic nonradiogenic strontium, although differences between the Leg 83 and Leg 92 data indicate an influence of bentonite during Leg 92. The oxygen isotope composition of the water does not change appreciably downhole. This uniformity can be understood in terms of high water-rock ratios and suggests that the chemical changes observed are due either to alteration processes involving bentonites and basaltic material from the walls of the hole or to exchange with formation fluids from the surrounding basement, which may have altered in composition at relatively high water-rock ratios.

Rare earth element fractionation in authigenic illite–smectite from Late Permian clastic rocks, Bowen Basin, Australia: implications for physico-chemical environments of fluids during illitization

REE analyses were performed on authigenic illitic clay. minerals from Late Permian mudrocks, sandstones and bentonites from the Bowen Basin (Australia). The mixed-layer illite-smectite exhibit REE patterns with an obvious fractionation of the HREE from the LREE and MREE, which is an apparent function of degree of illitization reaction. The highly illitic (R greater than or equal to 3) illite-smectite from the northern Bowen Basin show a depletion of LREE relative to the less illitic (R=0 and 1) clays. In contrast, an enrichment of HREE for the illite-rich clays relative to less. illitic clays is evident for the southern Bowen Basin samples. The North American Shale Composite-normalized (La/Lu)(sn) ratios show negative correlations with the illite content in illite-smectite and positive correlations with the delta(18)O values of the clays for both the northern and southern Bowen Basin samples. These correlations indicate that the increasing depletion of LREE in hydrothermal fluids is a function of increasing water/rock ratios in the northern Bowen Basin. Good negative correlations between (La/Lu)(sn) ratios and illite content in illite-smectite from the southern Bowen Basin suggest the involvement of fluids with higher alkalinity and higher pH in low water/ rock ratio conditions. Increasing HREE enrichment with delta(18)O decrease indicates the effect of increasing temperature at low water/rock ratios in the southern Bowen Basin. Results of the present study confirm the conclusions of some earlier studies suggesting that REE in illitic clay minerals are mobile and fractionated during illitization and that this fact should be considered in studies of sedimentary processes and in identifying provenance. Moreover, our results show that REE systematic of illitic clay minerals can be applied as an useful technique to gain information about physico-chemical conditions during thermal and fluid flow events in certain sedimentary basins. (C) 2003 Elsevier Science B.V. All rights reserved.

Rheological Properties of Organoclay Suspensions in Epoxy Network Precursors

This paper deals with the evolution of the state of dispersion of organically modified montmorillonites in epoxy or amine precursors. The epoxy prepolymer is a diglycidyl ether of bisphenol A (DGEBA) and the curing agent is an aliphatic diamine with a polyoxypropylene backbone (Jeffamine D2000). The clay dispersion is evaluated at the platelet scale (nanoscopic scale) from X-ray spectrometry [wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS)] and at the aggregates scale (microscopic scale) from rheological analysis. The organoclays used form gels in the monomers above the percolation threshold if no shear is applied and present a mechanical gel/sol transition when shear stress increases. Gel strength and viscosity at high shear rates are linked to the nanometric state of dispersion and reveal the existence of two different organizations depending on organoclay/monomer interactions: (i) When the clay shows good interactions with the monomer, a significant swelling of the clay galleries by the monomer is obtained. These swollen particles lead to formation of weak gels which after shearing give high relative viscosity fluids. (ii) When the clay develops poor interactions with the monomer, the clay tends to reduce its exchange surface with the monomer and leads to a strongly connected gel. Shear breaks down this physical network leading to a very low relative viscosity fluid composed of nonswollen particles keeping a high aspect ratio. (C) 2003 Elsevier B.V All rights reserved.

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.

Mesoestruturas porosas a partir de materiais naturais

The MCM-41 mesoporous synthesis was done using rice hulls ash and chrysotile as natural alternative silica sources. For the using of these sources, chemical and thermic treatments were done in both materials. After chemical and thermic treatments, these materials were employed on the MCM-41 mesoctructures synthesis. The natural materials treated and employed in the synthesis were characterized by several techniques such as X-ray diffraction, N2 adsorption and desorption, scanning electronic microscopy and thermogravimetric analysis. MCM-41 standart samples synthetized with aerosil 200 commercial sílica were used to evaluation. The formed material from rice hulls ash showed values from BET specific area about 468 m².g-1, N2 adsorption and desorption isotherms and loss mass similar to reference materials. The silica from chrysotile calcined and leached was employed to mesoporous materials synthesis. The BET specific area showed values about 700 m².g-1, N2 adsorption and desorption isotherms type IV and loss mass similar to mesoporous materials. The formed material from calcined and leached chrysotile, without calcination, applied to phenol remotion carried high performance liquid chromatography and evaluated with organophilic clays with different treatments. By the characterization techniques were proved that mesoporous materials with lesser order that reference samples. The material formed from rice hulls ash without the calcination step achieved better adsorption results than organophilic clays