Geochemistry of abyssal peridotites from ODP Hole 209-1274A

Aqueous dihydrogen (H2,aq) is produced in copious amounts when seawater interacts with peridotite and H2O oxidizes ferrous iron in olivine to ferric iron in secondary magnetite and serpentine. Poorly understood in this process is the partitioning of iron and its oxidation state in serpentine, although both impose an important control on dihydrogen production. We present results of detailed petrographic, mineral chemical, magnetic and Mößbauer analyses of partially to fully serpentinized peridotites from the Ocean Drilling Program (ODP) Leg 209, Mid-Atlantic Ridge (MAR) 15°N area. These results are used to constrain the fate of iron during serpentinization and are compared with phase equilibria considerations and peridotite-seawater reaction path models. In samples from Hole 1274A, mesh-rims reveal a distinct in-to-out zoning from brucite at the interface with primary olivine, followed by a zone of serpentine + brucite ± magnetite and finally serpentine + magnetite in the outermost mesh-rim. The compositions of coexisting serpentine (Mg# 95) and brucite (Mg# 80) vary little throughout the core. About 30-50% of the iron in serpentine/brucite mesh-rims is trivalent, irrespective of subbasement depth and protolith (harzburgite versus dunite). Model calculations suggest that both partitioning and oxidation state of iron are very sensitive to temperature and water-to-rock ratio during serpentinization. At temperatures above 330 °C the dissolution of olivine and coeval formation of serpentine, magnetite and dihydrogen depends on the availability of an external silica source. At these temperatures the extent of olivine serpentinization is insufficient to produce much hydrogen, hence conditions are not reducing enough to form awaruite. At T < 330 °C, hydrogen generation is facilitated by the formation of brucite, as dissolution of olivine to form serpentine, magnetite and brucite requires no addition of silica. The model calculations suggest that the iron distribution observed in serpentine and brucite is consistent with formation temperatures ranging from <150 to 250 °C and bulk water-to-rock ratios between 0.1 and 5. These conditions coincide with peak hydrogen fugacities during serpentinization and are conducive to awaruite formation during main stage serpentinization. The development of the common brucite rims around olivine is either due to an arrested reaction olivine -> brucite -> serpentine + brucite, or reflects metastable olivine-brucite equilibria developing in the strong gradient in silica activity between orthopyroxene (talc-serpentine) and olivine (serpentine-brucite).

Mineralogy and geochemistry of Mg-phyllosilicates from Middle Valley, northern Juan de Fuca Ridge

We present results of a detailed mineralogical and geochemical study of the progressive hydrothermal alteration of clastic sediments recovered at ODP Site 858 in an area of active hydrothermal venting at the sedimented, axial rift valley of Middle Valley (northern Juan de Fuca Ridge). These results allow a characterization of newly formed phyllosilicates and provide constraints on the mechanisms of clay formation and controls of mineral reactions on the chemical and isotopic composition of hydrothermal fluids. Hydrothermal alteration at Site 858 is characterized by a progressive change in phyllosilicate assemblages with depth. In the immediate vent area, at Hole 858B, detrital layers are intercalated with pure hydrothermal precipitates at the top of the section, with a predominance of hydrothermal phases at depth. Sequentially downhole in Hole 858B, the clay fraction of the pure hydrothermal layers changes from smectite to corrensite to swelling chlorite and finally to chlorite. In three pure hydrothermal layers in the deepest part of Hole 858B, the clay minerals coexist with neoformed quartz. Neoformed and detrital components are clearly distinguished on the basis of morphology, as seen by SEM and TEM, and by their chemical and stable isotope compositions. Corrensite is characterized by a 24 Å stacking sequence and high Si- and Mg-contents, with Fe/(Fe+Mg) ratio of = 0.08. We propose that corrensite is a unique, possibly metastable, mineralogical phase and was precipitated directly from seawater-dominated hydrothermal fluids. Hydrothermal chlorite in Hole 858B has a stacking sequence of 14 Å with Fe/(Fe+Mg) ratios of ? 0.35. The chemistry and structure of swelling chlorite suggest that it is a corrensiteychlorite mixed-layer phase. The mineralogical zonation in Hole 858B is accompanied by a systematic decrease in d18O, reflecting both the high thermal gradients that prevail at Site 858 and extensive sediment-fluid interaction. Precipitation of the Mg-phyllosilicates in the vent region directly controls the chemical and isotopic compositions of the pore fluids. This is particularly evident by decreases in Mg and enrichments in deuterium and salinity in the pore fluids at depths at which corrensite and chlorite are formed. Structural formulae calculated from TEM-EDX analyses were used to construct clay-H2O oxygen isotope fractionation curves based on oxygen bond models. Our results suggest isotopic disequilibrium conditions for corrensite-quartz and swelling chlorite-quartz precipitation, but yield an equilibrium temperature of 300° C ± 30° for chlorite-quartz at 32 m below the surface. This estimate is consistent with independent estimates and indicates steep thermal gradients of 10-11°/m in the vent region.

Seawater carbonate chemistry and proportion of different dissolution levels in live juvenile Limacina helicina antarctica from the natural environment and ship-board incubations

The carbonate chemistry of the surface ocean is rapidly changing with ocean acidification, a result of human activities. In the upper layers of the Southern Ocean, aragonite-a metastable form of calcium carbonate with rapid dissolution kinetics-may become undersaturated by 2050. Aragonite undersaturation is likely to affect aragonite-shelled organisms, which can dominate surface water communities in polar regions. Here we present analyses of specimens of the pteropod Limacina helicina antarctica that were extracted live from the Southern Ocean early in 2008. We sampled from the top 200 m of the water column, where aragonite saturation levels were around 1, as upwelled deep water is mixed with surface water containing anthropogenic CO2. Comparing the shell structure with samples from aragonite-supersaturated regions elsewhere under a scanning electron microscope, we found severe levels of shell dissolution in the undersaturated region alone. According to laboratory incubations of intact samples with a range of aragonite saturation levels, eight days of incubation in aragonite saturation levels of 0.94-1.12 produces equivalent levels of dissolution. As deep-water upwelling and CO2 absorption by surface waters is likely to increase as a result of human activities, we conclude that upper ocean regions where aragonite-shelled organisms are affected by dissolution are likely to expand.

(Table 1) Chemical and isotopic compositions of rudist aragonite and magnesian calcite cements from ODP Hole 144-877A

The classic paleotemperature record based on d18O data from pelagic foraminiferal calcite suggests that equatorial sea-surface temperatures during the Maastrichtian (~12-20°C) were much cooler than today (~27-29°C). Such cool equatorial temperatures contradict basic theories of tropical atmospheric and ocean dynamics. We report d18O data from remarkably well preserved rudist aragonite and magnesian calcite cements of Maastrichtian age (~69+/-1 Ma) from the carbonate platform of Wodejebato guyot in the western Pacific. These data suggest that equatorial sea-surface temperatures in the Maastrichtian (best estimate ~27-32°C) were at least as warm as today. This finding helps reconcile the geologic d18O record with ocean-atmospheric dynamic theory and implies a reduction in the poleward heat flux required by global climate simulations of greenhouse conditions.

Ion Beam irradiation of copper nitride: electronic vs elastic-collision mechanism

Copper nitride is a metastable material which results very attractive because of their potential to be used in functional device. Cu3 N easily decomposes into Cu and N2 by annealing [1] or irradiation (electron, ions, laser) [2, 3]. Previous studies carried out in N-rich Cu3 N films irradiated with Cu at 42MeV evidence a very efficient sputtering of N whose yield (5×10 3 atom/ion), for a film with a thickness of just 100 nm, suggest that the origin of the sputtering has an electronic nature. This N depletion was observed to be responsible for new phase formation ( Cu2 O) and pure Cu [4]

Magnetic properties of nanostructured systems based on TbFe2

The aim of this work is to study the magnetic properties of annealed [Fe3Ga/TbFe2]n heterostructures grown by sputtering at room temperature. The interest of investigating multilayers comprised of TbFe2 and Fe3Ga is their complementary properties in terms of coercivity and magnetostriction. We have studied the thickness combination which optimizes the magnetic and magnetostrictive properties of the annealed multilayers. The crystallization of the Laves phase upon the thermal treatment in heterostructures with thick TbFe2 layers promotes the increase of the coercivity. This crystallization seems to be prevented by the low mechanical stiffness of the Fe3Ga. [Fe3Ga/TbFe2]n heterostructures show promising characteristics, λ of 340 ppm and a HC of 220 Oe, for the development of new magnetostrictive devices.

Glassy State and Cryopreservation of Mint Shoot Tips

Vitrification refers to the physical process by which a liquid supercools to very low tem- peratures and finally solidifies into a metastable glass, without undergoing crystallization at a practical cooling rate. Thus, vitrification is an effective freeze-avoidance mechanism and living tissue cryopreservation is, in most cases, relying on it. As a glass is exceedingly vis- cous and stops all chemical reactions that require molecular diffusion, its formation leads to metabolic inactivity and stability over time. To investigate glassy state in cryopreserved plant material, mint shoot tips were submitted to the different stages of a frequently used cryopreservation protocol (droplet-vitrification) and evaluated for water content reduction and sucrose content, as determined by ion chromatography, frozen water fraction and glass transitions occurrence by differential scanning calorimetry, and investigated by low-tempera- ture scanning electron microscopy, as a way to ascertain if their cellular content was vitri- fied. Results show how tissues at intermediate treatment steps develop ice crystals during liquid nitrogen cooling, while specimens whose treatment was completed become vitrified, with no evidence of ice formation. The agreement between calorimetric and microscopic observations was perfect. Besides finding a higher sucrose concentration in tissues at the more advanced protocol steps, this level was also higher in plants precultured at 25/21?C than in plants cultivated at 25?C.

Magnetization reversal assisted by half antivortex states in nanostructured circular cobalt disks

The half antivortex, a fundamental topological structure which determines magnetization reversal of submicron magnetic devices with domain walls, has been suggested also to play a crucial role in spin torque induced vortex core reversal in circular disks. Here, we report on magnetization reversal in circular disks with nanoholes through consecutive metastable states with half antivortices. In-plane anisotropic magnetoresistance and broadband susceptibility measurements accompanied by micromagnetic simulations reveal that cobalt (Co) disks with two and three linearly arranged nanoholes directed at 45° and 135° with respect to the external magnetic field show reproducible step-like changes in the anisotropic magnetoresistance and magnetic permeability due to transitions between different intermediate states mediated by vortices and half antivortices confined to the dot nanoholes and edges, respectively. Our findings are relevant for the development of multi-hole based spintronic and magnetic memory devices.

Exploring the folding free energy surface of a three-helix bundle protein

The multidimensional free energy surface for a small fast folding helical protein is explored based on first-principle calculations. The model represents the 46-residue segment from fragment B of staphylococcal protein A. The relationship between collapse and tertiary structure formation, and the order of collapse and secondary structure formation, are investigated. We find that the initial collapse process gives rise to a transition state with about 30% of the native tertiary structure and 50–70% of the native helix content. We also observe two distinct distributions of native helix in this collapsed state (Rg ≈ 12 Å), one with about 20% of the native helical hydrogen bonds, the other with near 70%. The former corresponds to a local minimum. The barrier from this metastable state to the native state is about 2 kBT. In the latter case, folding is essentially a downhill process involving topological assembly. In addition, the order of formation of secondary structure among the three helices is examined. We observe cooperative formation of the secondary structure in helix I and helix II. Secondary structure in helix III starts to form following the formation of certain secondary structure in both helix I and helix II. Comparisons of our results with those from theory and experiment are made.

Studies using double mutants of the conformational transitions in influenza hemagglutinin required for its membrane fusion activity

Amino acid substitutions widely distributed throughout the influenza hemagglutinin (HA) influence the pH of its membrane fusion activity. We have combined a number of these substitutions in double mutants and determined the effects on the pH of fusion and on the pH at which the refolding of HA required for fusion occurs. By analyzing combinations of mutations in three regions of the metastable neutral-pH HA that are rearranged at fusion pH we obtain evidence for both additive and nonadditive effects and for an apparent order of dominance in the effects of amino acid substitutions in particular regions on the pH of fusion. We conclude that there are at least three components in the structural transition required for membrane fusion activity and consider possible pathways for the transition in relation to the known differences between neutral and fusion pH HA structures.

Spectral bifurcations in dispersive wave turbulence

Dispersive wave turbulence is studied numerically for a class of one-dimensional nonlinear wave equations. Both deterministic and random (white noise in time) forcings are studied. Four distinct stable spectra are observed—the direct and inverse cascades of weak turbulence (WT) theory, thermal equilibrium, and a fourth spectrum (MMT; Majda, McLaughlin, Tabak). Each spectrum can describe long-time behavior, and each can be only metastable (with quite diverse lifetimes)—depending on details of nonlinearity, forcing, and dissipation. Cases of a long-live MMT transient state dcaying to a state with WT spectra, and vice-versa, are displayed. In the case of freely decaying turbulence, without forcing, both cascades of weak turbulence are observed. These WT states constitute the clearest and most striking numerical observations of WT spectra to date—over four decades of energy, and three decades of spatial, scales. Numerical experiments that study details of the composition, coexistence, and transition between spectra are then discussed, including: (i) for deterministic forcing, sharp distinctions between focusing and defocusing nonlinearities, including the role of long wavelength instabilities, localized coherent structures, and chaotic behavior; (ii) the role of energy growth in time to monitor the selection of MMT or WT spectra; (iii) a second manifestation of the MMT spectrum as it describes a self-similar evolution of the wave, without temporal averaging; (iv) coherent structures and the evolution of the direct and inverse cascades; and (v) nonlocality (in k-space) in the transferral process.

Equilibration rates in lipid monolayers

A theoretical analysis is given for the rate of change of domain sizes in lipid monolayers at the air–water interface. The calculation is applicable to liquid domains formed from binary mixtures of lipids that form two coexisting liquid phases. Under conditions where the two lipid molecules have approximately equal areas, the equilibration rate does not involve macroscopic hydrodynamic flow in the subphase but rather depends on the diffusion coefficient of the lipid molecules. The calculation shows that the equilibration rate in binary mixtures of cholesterol and phosphatidylcholine is remarkably slow, the radius of a typical 20-μm diameter domain changing by as little as a part in a million per second. Under these circumstances, equilibration times of the order of days or weeks are expected. Even with such long times, the final state reached by the monolayer will in general be a state of metastable equilibrium, rather than true equilibrium.

Structural determinants of oxidative folding in proteins

A method for determining the kinetic fate of structured disulfide species (i.e., whether they are preferentially oxidized or reshuffle back to an unstructured disulfide species) is introduced. The method relies on the sensitivity of unstructured disulfide species to low concentrations of reducing agents. Because a structured des species that preferentially reshuffles generally first rearranges to an unstructured species, a small concentration of reduced DTT (e.g., 260 μM) suffices to distinguish on-pathway intermediates from dead-end species. We apply this method to the oxidative folding of bovine pancreatic ribonuclease A (RNase A) and show that des[40–95] and des[65–72] are productive intermediates, whereas des[26–84] and des[58–110] are metastable dead-end species that preferentially reshuffle. The key factor in determining the kinetic fate of these des species is the relative accessibility of both their thiol groups and disulfide bonds. Productive intermediates tend to be disulfide-secure, meaning that their structural fluctuations preferentially expose their thiol groups, while keeping their disulfide bonds buried. By contrast, dead-end species tend to be disulfide-insecure, in that their structural fluctuations expose their disulfide bonds in concert with their thiol groups. This distinction leads to four generic types of oxidative folding pathways. We combine these results with those of earlier studies to suggest a general three-stage model of oxidative folding of RNase A and other single-domain proteins with multiple disulfide bonds.

Formation of a GNRA tetraloop in P5abc can disrupt an interdomain interaction in the Tetrahymena group I ribozyme

The secondary structure of a truncated P5abc subdomain (tP5abc, a 56-nucleotide RNA) of the Tetrahymena thermophila group I intron ribozyme changes when its tertiary structure forms. We have now used heteronuclear NMR spectroscopy to determine its conformation in solution. The tP5abc RNA that contains only secondary structure is extended compared with the tertiary folded form; both forms coexist in slow chemical exchange (the interconversion rate constant is slower than 1 s−1) in the presence of magnesium. Kinetic experiments have shown that tertiary folding of the P5abc subdomain is one of the earliest folding transitions in the group I intron ribozyme, and that it leads to a metastable misfolded intermediate. Previous mutagenesis studies suggest that formation of the extended P5abc structure described here destabilize a misfolded intermediate. This study shows that the P5abc RNA subdomain containing a GNRA tetraloop in P5c (in contrast to the five-nucleotide loop P5c in the tertiary folded ribozyme) can disrupt the base-paired interdomain (P14) interaction between P5c and P2.

Kinetic stability as a mechanism for protease longevity

The folding of the extracellular serine protease, α-lytic protease (αLP; EC 3.4.21.12) reveals a novel mechanism for stability that appears to lead to a longer functional lifetime for the protease. For αLP, stability is based not on thermodynamics, but on kinetics. Whereas this has required the coevolution of a pro region to facilitate folding, the result has been the optimization of native-state properties independent of their consequences on thermodynamic stability. Structural and mutational data lead to a model for catalysis of folding in which the pro region binds to a conserved β-hairpin in the αLP C-terminal domain, stabilizing the folding transition state and the native state. The pro region is then proteolytically degraded, leaving the active αLP trapped in a metastable conformation. This metastability appears to be a consequence of pressure to evolve properties of the native state, including a large, highly cooperative barrier to unfolding, and extreme rigidity, that reduce susceptibility to proteolytic degradation. In a test of survival under highly proteolytic conditions, homologous mammalian proteases that have not evolved kinetic stability are much more rapidly degraded than αLP. Kinetic stability as a means to longevity is likely to be a mechanism conserved among the majority of extracellular bacterial pro-proteases and may emerge as a general strategy for intracellular eukaryotic proteases subject to harsh conditions as well.