Shifts in the microbial community structure in different temperatures during sample storage from IODP Hole 325-M0058A

The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4��C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80��C. Storage at 4��C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.

Composition of bottom sediments, rocks, and ores from the Tropical Atlantic

Geological features of some areas of the Tropical Atlantic (stratigraphy, tectonic structure, lithology, distribution of ore components in bottom sediments, petrography of bedrocks, etc.) are under consideration in the book. Regularities of concentration of trace elements in iron-manganese nodules, features of these nodules in bottom sediments, distribution of phosphorite nodules and other phosphorites have been studied. Much attention is paid to rocks of the ocean crust. A wide range of mineralization represented by magnetite, chromite, chalcopyrite, pyrite, pentlandite, and other minerals has been found.

Oxygen and sulfur isotopes of peridotite and gabbro from the Mid-Atlantic Ridge

Whole rock sulfur and oxygen isotope compositions of altered peridotites and gabbros from near the 15��20'N Fracture Zone on the Mid-Atlantic Ridge were analyzed to investigate hydrothermal alteration processes and test for a subsurface biosphere in oceanic basement. Three processes are identified. (1) High-temperature hydrothermal alteration (~250-350��C) at Sites 1268 and 1271 is characterized by 18O depletion (2.6-4.4 per mil), elevated sulfide-S, and high delta34S (up to ~2 wt% and 4.4-10.8 per mil). Fluids were derived from high-temperature (>350��C) reaction of seawater with gabbro at depth. These cores contain gabbroic rocks, suggesting that associated heat may influence serpentinization. (2) Low-temperature (<150��C) serpentinization at Sites 1272 and 1274 is characterized by elevated delta18O (up to 8.1 per mil), high sulfide-S (up to ~3000 ppm), and negative delta34S (to -32.1 per mil) that reflect microbial reduction of seawater sulfate. These holes penetrate faults at depth, suggesting links between faulting and temperatures of serpentinization. (3) Late low-temperature oxidation of sulfide minerals caused loss of sulfur from rocks close to the seafloor. Sulfate at all sites contains a component of oxidized sulfide minerals. Low delta34S of sulfate may result from kinetic isotope fractionation during oxidation or may indicate readily oxidized low-delta34S sulfide derived from microbial sulfate reduction. Results show that peridotite alteration may be commonly affected by fluids +/- heat derived from mafic intrusions and that microbial sulfate reduction is widespread in mantle exposed at the seafloor.

Liquid lead and Lithium. A Comprehensive molecular dynamics study

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues in these programs is the problem of liquid metals breeder blanket behavior. Structural material of the blanket should meet high requirements because of extreme operating conditions. Therefore the knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT=f(PT), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Simulations of liquids can provide much information to the community; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to lead to the deeper understanding and better predictive behavior.

New simulations to qualify eutectic lithium-lead as breeder material

Pb17Li is today a reference breeder material in diverse fusion R&D programs worldwide. One of the main issues is the problem of liquid metals breeder blanket behavior. The knowledge of eutectic properties like optimal composition, physical and thermodynamic behavior or diffusion coefficients of Tritium are extremely necessary for current designs. In particular, the knowledge of the function linking the tritium concentration dissolved in liquid materials with the tritium partial pressure at a liquid/gas interface in equilibrium, CT =f(PT ), is of basic importance because it directly impacts all functional properties of a blanket determining: tritium inventory, tritium permeation rate and tritium extraction efficiency. Nowadays, understanding the structure and behavior of this compound is a real goal in fusion engineering and materials science. Atomistic simulations of liquids can provide much information; not only supplementing experimental data, but providing new tests of theories and ideas, making specific predictions that require experimental tests, and ultimately helping to a deeper understanding

Crack mechanical failure in lithium niobate crystal under ion irradiation; novel simulation by extended finite elements

Swift heavy ion irradiation (ions with mass heavier than 15 and energy exceeding MeV/amu) transfer their energy mainly to the electronic system with small momentum transfer per collision. Therefore, they produce linear regions (columnar nano-tracks) around the straight ion trajectory, with marked modifications with respect to the virgin material, e.g., phase transition, amorphization, compaction, changes in physical or chemical properties. In the case of crystalline materials the most distinctive feature of swift heavy ion irradiation is the production of amorphous tracks embedded in the crystal. Lithium niobate is a relevant optical material that presents birefringence due to its anysotropic trigonal structure. The amorphous phase is certainly isotropic. In addition, its refractive index exhibits high contrast with those of the crystalline phase. This allows one to fabricate waveguides by swift ion irradiation with important technological relevance. From the mechanical point of view, the inclusion of an amorphous nano-track (with a density 15% lower than that of the crystal) leads to the generation of important stress/strain fields around the track. Eventually these fields are the origin of crack formation with fatal consequences for the integrity of the samples and the viability of the method for nano-track formation. For certain crystal cuts (X and Y), these fields are clearly anisotropic due to the crystal anisotropy. We have used finite element methods to calculate the stress/strain fields that appear around the ion-generated amorphous nano-tracks for a variety of ion energies and doses. A very remarkable feature for X cut-samples is that the maximum shear stress appears on preferential planes that form +/-45�� with respect to the crystallographic planes. This leads to the generation of oriented surface cracks when the dose increases. The growth of the cracks along the anisotropic crystal has been studied by means of novel extended finite element methods, which include cracks as discontinuities. In this way we can study how the length and depth of a crack evolves as function of the ion dose. In this work we will show how the simulations compare with experiments and their application in materials modification by ion irradiation.

Crack mechanical failure in ceramic materials under ion irradiation: case of lithium niobate crystal

Swift heavy ion irradiation (ions with mass heavier than 15 and energy exceeding MeV/amu) transfer their energy mainly to the electronic system with small momentum transfer per collision. Therefore, they produce linear regions (columnar nano-tracks) around the straight ion trajectory, with marked modifications with respect to the virgin material, e.g., phase transition, amorphization, compaction, changes in physical or chemical properties. In the case of crystalline materials the most distinctive feature of swift heavy ion irradiation is the production of amorphous tracks embedded in the crystal. Lithium niobate is a relevant optical material that presents birefringence due to its anysotropic trigonal structure. The amorphous phase is certainly isotropic. In addition, its refractive index exhibits high contrast with those of the crystalline phase. This allows one to fabricate waveguides by swift ion irradiation with important technological relevance. From the mechanical point of view, the inclusion of an amorphous nano-track (with a density 15% lower than that of the crystal) leads to the generation of important stress/strain fields around the track. Eventually these fields are the origin of crack formation with fatal consequences for the integrity of the samples and the viability of the method for nano-track formation. For certain crystal cuts (X and Y), these fields are clearly anisotropic due to the crystal anisotropy. We have used finite element methods to calculate the stress/strain fields that appear around the ion- generated amorphous nano-tracks for a variety of ion energies and doses. A very remarkable feature for X cut-samples is that the maximum shear stress appears on preferential planes that form +/-45�� with respect to the crystallographic planes. This leads to the generation of oriented surface cracks when the dose increases. The growth of the cracks along the anisotropic crystal has been studied by means of novel extended finite element methods, which include cracks as discontinuities. In this way we can study how the length and depth of a crack evolves as function of the ion dose. In this work we will show how the simulations compare with experiments and their application in materials modification by ion irradiation.

In-field assessment of batteries and PV modules in a large photovoltaic rural electrification programme

Assuring the sustainability of quality in photovoltaic rural electrification programmes involves enhancing the reliability of the components of solar home systems as well as the characterization of the overall programme cost structure. Batteries and photovoltaic modules have a great impact on both the reliability and the cost assessment, the battery being the weakest component of the solar home system and consequently the most expensive element of the programme. The photovoltaic module, despite being the most reliable component, has a significant impact cost-wise on the initial investment, even at current market prices. This paper focuses on the in-field testing of both batteries and photovoltaic modules working under real operating conditions within a sample of 41 solar home systems belonging to a large photovoltaic rural electrification programme with more than 13,000 installed photovoltaic systems. Different reliability parameters such as lifetime have been evaluated, taking into account different factors, for example energy consumption rates, or the manufacturing quality of batteries. A degradation model has been proposed relating both loss of capacity and time of operation. The user e solar home system binomial is also analysed in order to understand the meaning of battery lifetime in rural electrification.

Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose

The SQD1 enzyme is believed to be involved in the biosynthesis of the sulfoquinovosyl headgroup of plant sulfolipids, catalyzing the transfer of SO3��� to UDP-glucose. We have determined the structure of the complex of SQD1 from Arabidopsis thaliana with NAD+ and the putative substrate UDP-glucose at 1.6-��� resolution. Both bound ligands are completely buried within the binding cleft, along with an internal solvent cavity which is the likely binding site for the, as yet, unidentified sulfur-donor substrate. SQD1 is a member of the short-chain dehydrogenase/reductase (SDR) family of enzymes, and its structure shows a conservation of the SDR catalytic residues. Among several highly conserved catalytic residues, Thr-145 forms unusually short hydrogen bonds with both susceptible hydroxyls of UDP-glucose. A His side chain may also be catalytically important in the sulfonation.

Crystal structures of bovine milk xanthine dehydrogenase and xanthine oxidase: Structure-based mechanism of conversion

Mammalian xanthine oxidoreductases, which catalyze the last two steps in the formation of urate, are synthesized as the dehydrogenase form xanthine dehydrogenase (XDH) but can be readily converted to the oxidase form xanthine oxidase (XO) by oxidation of sulfhydryl residues or by proteolysis. Here, we present the crystal structure of the dimeric (Mr, 290,000) bovine milk XDH at 2.1-��� resolution and XO at 2.5-��� resolution and describe the major changes that occur on the proteolytic transformation of XDH to the XO form. Each molecule is composed of an N-terminal 20-kDa domain containing two iron sulfur centers, a central 40-kDa flavin adenine dinucleotide domain, and a C-terminal 85-kDa molybdopterin-binding domain with the four redox centers aligned in an almost linear fashion. Cleavage of surface-exposed loops of XDH causes major structural rearrangement of another loop close to the flavin ring (Gln 423���Lys 433). This movement partially blocks access of the NAD substrate to the flavin adenine dinucleotide cofactor and changes the electrostatic environment of the active site, reflecting the switch of substrate specificity observed for the two forms of this enzyme.

Sulfur K-edge x-ray absorption spectroscopy: A spectroscopic tool to examine the redox state of S-containing metabolites in vivo

The sulfur K-edge x-ray absorption spectra for the amino acids cysteine and methionine and their corresponding oxidized forms cystine and methionine sulfoxide are presented. Distinct differences in the shape of the edge and the inflection point energy for cysteine and cystine are observed. For methionine sulfoxide the inflection point energy is 2.8 eV higher compared with methionine. Glutathione, the most abundant thiol in animal cells, also has been investigated. The x-ray absorption near-edge structure spectrum of reduced glutathione resembles that of cysteine, whereas the spectrum of oxidized glutathione resembles that of cystine. The characteristic differences between the thiol and disulfide spectra enable one to determine the redox status (thiol to disulfide ratio) in intact biological systems, such as unbroken cells, where glutathione and cyst(e)ine are the two major sulfur-containing components. The sulfur K-edge spectra for whole human blood, plasma, and erythrocytes are shown. The erythrocyte sulfur K-edge spectrum is similar to that of fully reduced glutathione. Simulation of the plasma spectrum indicated 32% thiol and 68% disulfide sulfur. The whole blood spectrum can be simulated by a combination of 46% disulfide and 54% thiol sulfur.

Synthetic zeolites and other microporous oxide molecular sieves

Use of synthetic zeolites and other microporous oxides since 1950 has improved insulated windows, automobile air-conditioning, refrigerators, air brakes on trucks, laundry detergents, etc. Their large internal pore volumes, molecular-size pores, regularity of crystal structures, and the diverse framework chemical compositions allow ���tailoring��� of structure and properties. Thus, highly active and selective catalysts as well as adsorbents and ion exchangers with high capacities and selectivities were developed. In the petroleum refining and petrochemical industries, zeolites have made possible cheaper and lead-free gasoline, higher performance and lower-cost synthetic fibers and plastics, and many improvements in process efficiency and quality and in performance. Zeolites also help protect the environment by improving energy efficiency, reducing automobile exhaust and other emissions, cleaning up hazardous wastes (including the Three Mile Island nuclear power plant and other radioactive wastes), and, as specially tailored desiccants, facilitating the substitution of new refrigerants for the ozone-depleting chlorofluorocarbons banned by the Montreal Protocol.

Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.

The x-ray crystal structures of the sulfide oxidase antibody 28B4 and of antibody 28B4 complexed with hapten have been solved at 2.2-angstrom and 1.9-angstrom resolution, respectively. To our knowledge, these structures are the highest resolution catalytic antibody structures to date and provide insight into the molecular mechanism of this antibody-catalyzed monooxygenation reaction. Specifically, the data suggest that entropic restriction plays a fundamental role in catalysis through the precise alignment of the thioether substrate and oxidant. The antibody active site also stabilizes developing charge on both sulfur and periodate in the transition state via cation-pi and electrostatic interactions, respectively. In addition to demonstrating that the active site of antibody 28B4 does indeed reflect the mechanistic information programmed in the aminophosphonic acid hapten, these high-resolution structures provide a basis for enhancing turnover rates through mutagenesis and improved hapten design.

X-ray absorption fine structure as a monitor of zinc coordination sites during oogenesis of Xenopus laevis.

The x-ray absorption fine structure (XAFS) zinc K-edge steps for intact stages I,II and V,VI Xenopus laevis oocytes demonstrate that the zinc concentration is about 3 and 1 mM, respectively. However, the chi(k) function for the early stage oocytes differs markedly from that for the late one. Analysis of the XAFS data for stage I,II oocytes indicates that zinc is bound to 2.0 +/- 0.5 sulfur atoms at an average coordination distance of 2.29 +/- 0.02 angstroms and 2.0 +/- 0.5 nitrogen or oxygen (N/O) atoms at 2.02 +/- 0.02 angstroms. In marked contrast, in stage V,VI oocytes, zinc is bound to 4.1 +/- 0.4 N/O atoms at an average distance of 1.98 +/- 0.01 angstroms. Our previous studies demonstrated that 90% of the zinc in stage VI oocytes is sequestered within yolk platelets, associated with a single molecule, lipovitellin, the proteolytically processed product of vitellogenin. XAFS analysis of yolk platelets, lipovitellin, and vitellogenin demonstrates that zinc is bound to 4.0 +/- 0.5 N/O ligands at an average distance of 1.98 +/- 0.01 angstroms in each case, identical to that of stage V,VI oocytes. The higher shell contributions in the Fourier transforms indicate that two of the N/O zinc ligands are His in both stage V,VI and I,II oocytes. The results show that in stage I,II oocytes, there is a high concentration of a zinc protein whose zinc coordination site likely is composed of (His)2(Cys)2, such as, e.g., TFIIIA. As the oocytes develop, the predominant zinc species becomes one that exhibits the (His)2(N/0)2 zinc site found in lipovitellin. Hence, the ligands to the zinc atoms in intact oocytes and the changes that take place as a function of oogenesis and after their fertilization, during embryogenesis, now can be examined and explored.