High resolution geochemical analyses of ODP Leg 119 samples

Higher resolution pore-water samples were recovered at intervals of 0.3 to 3 m from selected cores during Leg 119 in order to identify zones where active geochemical reactions were occurring. In addition to shipboard measurements, solid- and dissolved-phase samples were analyzed at my shore-based laboratory. Solid-phase samples were analyzed for redox conditions, carbon, total metals, and leachable metals. Pore-water samples were analyzed for ammonia, silica, sulfate, and major cations. Data are presented in tables for 400 samples from Site 739 in Prydz Bay, East Antarctica, and Sites 736, 737, 738, 744, 745, and 746 at the Kerguelen Ridge, South Indian Ocean.

Nitrogen isotopic composition and chemical composition of altered oceanic crust from ODP Legs 129 and 185

Knowledge of the subduction input flux of nitrogen (N) in altered oceanic crust (AOC) is critical in any attempt to mass-balance N across arc-trench systems on a global or individual-margin basis. We have employed sealed-tube, carrier-gas-based methods to examine the N concentrations and isotopic compositions of AOC. Analyses of 53 AOC samples recovered on DSDP/ODP legs from the North and South Pacific, the North Atlantic, and the Antarctic oceans (with larger numbers of samples from Site 801 outboard of the Mariana trench and Site 1149 outboard of the Izu trench), and 14 composites for the AOC sections at Site 801, give N concentrations of 1.3 to 18.2 ppm and d15N_air of -11.6? to +8.3?, indicating significant N enrichment probably during the early stages of hydrothermal alteration of the oceanic basalts. The N-d15N modeling for samples from Sites 801 and 1149 (n=39) shows that the secondary N may come from (1) the sedimentary N in the intercalated sediments and possibly overlying sediments via fluid-sediment/rock interaction, and (2) degassed mantle N2 in seawater via alteration-related abiotic reduction processes. For all Site 801 samples, weak correlation of N and K2O contents indicates that the siting of N in potassic alteration phases strongly depends on N availability and is possibly influenced by highly heterogeneous temperature and redox conditions during hydrothermal alteration. The upper 470-m AOC recovered by ODP Legs 129 and 185 delivers approximately 800 kg/km N annually into the Mariana margin. If the remaining less-altered oceanic crust (assuming 6.5 km, mostly dikes and gabbros) has MORB-like N of 1.5 ppm, the entire oceanic crust transfers 5100 kg/km N annually into that trench. This N input flux is twice as large as the annual N input of 2500 kg/km in seafloor sediments subducting into the same margin, demonstrating that the N input in oceanic crust, and its isotopic consequences, must be considered in any assessment of convergent margin N flux.

Description of, and 238U, 234U, 232Th and 230Th measurements on a nodule from R/V Sonne station SO79_62KD, Central East Pacific Ocean

Two diagenetic manganese nodules from the Peru Basin were investigated by thermal ionization mass spectrometry and high resolution alpha spectrometry for uranium and thorium. The TIMS concentrations for nodule 62KD (63KG) vary as follows: 0.12-1.01 ppb (0.06-0.59) 230Th, 0.51-1.98 ppm (0.43-1.40) 232Th, 0.13-0.80 ppb (0.09-0.49) 234U, and 1.95-13.47 ppm (1.66-8.24) 238U. Both nodules have average growth rates of ~110 mm per million years. However, from the variations of excess 230Th with depth we estimate partial accumulation rates which range from 50 to 400 mm per million years. The 234U dating method cannot be applied due to remobilization of U from the sediment and subsequent incorporation into the nodules' crystal lattice, reflected by decay corrected 234U values far above the ocean water value. Sections of fast nodule growth are related to those layers having high Mn/Fe ratios (up to 200) and higher densities. As a possible explanation we develop a scenario that describes similar glacial/interglacial trends in both nodules as a record of regional changes of sediment and/or deep water chemistry.

Organic matter based proxies from surface sediments along three transects on the Pakistan continental margin

A valid assessment of selective aerobic degradation on organic matter (OM) and its impact on OM-based proxies is vital to produce accurate environmental reconstructions. However, most studies investigating these effects suffer from inherent environmental heterogeneities. In this study, we used surface samples collected along two meter-scale transects and one longer transect in the northeastern Arabian Sea to constrain initial OM heterogeneity, in order to evaluate selective aerobic degradation on temperature, productivity and alteration indices at the sediment-water interface. All of the studied alteration indices, the higher plant alkane index, alcohol preservation index, and diol oxidation index, demonstrated that they are sensitive indicators for changes in the oxygen regime. Several export production indices, a cholesterol-based stanol/stenol index and dinoflagellate lipid- and cyst-based ratios, showed significant (more than 20%) change only over the lateral oxygen gradients. Therefore, these compounds do not exclusively reflect surface water productivity, but are significantly altered after deposition. Two of the proxies, glycerol dibiphytanyl glycerol tetraether-based TEX86 sea surface temperature indices and indices based on phytol, phytane and pristane, did not show any trends related to oxygen. Nevertheless, unrealistic sea surface temperatures were obtained after application of the TEX86, TEX86L, and TEX86H proxies. The phytol-based ratios were likely affected by the sedimentary production of pristane. Our results demonstrate the selective impact of aerobic organic matter degradation on the lipid and palynomorph composition of surface sediments along a short lateral oxygen gradient and suggest that some of the investigated proxies may be useful tracers of changing redox conditions at the sediment-water interface.

Total organic carbon, metal concentrations and metal and aluminium ratios in bulk sediment from the ODP sample 169-1033B-4H-4,54-74

Holocene laminated sediments in Saanich Inlet, British Columbia, are interrupted by frequent, non-laminated, massive layers. These layers may be debris flows released by earthquakes or bioturbated sediments deposited during periods of relatively high bottom water oxygen concentration and/or low surface productivity, or both. We determined the organic carbon content and the concentration of a suite of redox-sensitive metals in bulk sediments at approximately 1-cm resolution across a laminated-massive-laminated interval (ODP Leg 169S Sample 1033B-4H-4,54-74), to determine the redox conditions under which the massive layer was deposited. Our results indicate that this massive interval was deposited under anoxic bottom waters. Manganese/Al ratios are consistently low throughout the massive section, while Mo/Al, Cd/Al, Re/Al, and U/Al ratios are enriched relative to their metal/Al ratios in detrital material (represented by Cowichan River suspended sediments). The concentration of organic carbon in the lower portion of the massive layer is higher than in the upper portion, which has a concentration similar to that in the overlying and underlying laminated sediments. Well-defined peaks in Mo/Al, Cd/Al, and Re/Al and a broad peak in U/Al occur in the lower portion of the massive layer. The positions of the Cd/Al, Re/Al, and Mo/Al peaks, as well as the increase in organic carbon content with depth in the massive layer, are best explained by a process of diagenetic redistribution of metals that occurred after the massive layer was emplaced.

The refolding of different alpha-fetoprotein variants

The effect of glycosylation on AFP foldability was investigated by parallel quantitative and qualitative analyses of the refolding of glycosylated and nonglycosylated AFP variants. Both variants were successfully refolded by dialysis from the denatured-reduced state, attaining comparable ``refolded peak'' profiles and refolding yields as determined by reversed-phase HPLC analysis. Both refolded variants also showed comparable spectroscopic fingerprints to each other and to their native counterparts, as determined by circular dichroism spectroscopy. Inclusion body-derived AFP was also readily refolded via dilution under the same redox conditions as dialysis refolding, showing comparable circular dichroism fingerprints as native nonglycosylated AFP. Quantitative analyses of inclusion body-derived AFP showed sensitivity of AFP aggregation to proteinaceous and nonproteinaceous inclusion body contaminants, where refolding yields increased with increasing AFP purity. All of the refolded AFP variants showed positive responses in ELISA that corresponded with the attainment of a bioactive conformation. Contrary to previous reports that the denaturation of cord serum AFP is an irreversible process, these results clearly show the reversibility of AFP denaturation when refolded under a redox-controlled environment, which promotes correct oxidative disulfide shuffling. The successful refolding of inclusion body-derived AFP suggests that fatty acid binding may not be required for the attainment of a rigid AFP tertiary structure, contrary to earlier studies. The overall results from this work demonstrate that foldability of the AFP molecule from its denatured-reduced state is independent of its starting source, the presence or absence of glycosylation and fatty acids, and the refolding method used (dialysis or dilution).

Dilution versus dialysis - A quantitative study of the oxidative refolding of recombinant human alpha-fetoprotein

Alpha-fetoprotein (AFP) is a commercially important polypeptide with important diagnostic. physiological and immunomodulatory functions. Previous studies into the refolding of this macromolecule are contradictory. and variously suggest that AFP denaturation may be irreversible or that refolding may be achieved by reducing denaturant concentration through dilution but not dialysis. Importantly, these same previous studies do not provide quantitative metrics by which the Success of refolding, and the potential for bioprocess development. can be assessed. Moreover, these same studies do not optimize and control refolding redox potential - an important factor considering that AFP contains 32 cysteines which form 16 disulfide bonds. In this current study, a quantitative comparison of recombinant human AFP (rhAFP) refolding by dilution and dialysis is conducted under optimized redox conditions. rhAFP refolding yields were > 35% (dialysis refolding) and > 75% (dilution refolding) as assessed by RP-HPLC and ELISA, with structural Similarity to the native state confirmed by UV spectroscopy. Dialysis refolding yield was believed to be lower because the gradual reduction in denaturant concentration allowed extended conformational searching. enabling more time for undesirable interaction with other protein molecules and/or the dialysis membrane, leading to a Sub-optimal process outcome. Significant yield sensitivity to redox environment was also observed, emphasizing the importance of physicochemical optimization. This study demonstrates that very high refolding yields can be obtained, for a physiologically relevant protein, with optimized dilution refolding. The study also highlights the quantitative metrics and macromolecular physical spectroscopic 'fingerprints' required to facilitate transition from laboratory to process scale.

Chemical and isotopic compositions of water, particulates, plankton, gases, sediments, and minerals from the Kara Sea and lower Ob and Yenisei Rivers

The Kara Sea is an area uniquely suitable for studying processes in the river-sea system. This is a shallow sea, into which two great Siberian rivers, Yenisei and Ob, flow. From 1995 to 2003, the sea was studied by six international expeditions onboard the R/V Akademik Boris Petrov. This publication summarizes the results obtained, within the framework of this project, at the Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Various hydrogeochemical parameters, concentrations and isotopic composition of organic and carbonate carbon of the sediments, plankton, particulate organic matter, hydrocarbons, and dissolved CO2 were examined throughout the whole sea area at more than 200 sites. The d13C varies from -22 and -24 per mil where Atlantic waters enter the Kara Sea and in the north-eastern part of the water area to -27 per mil in the Yenisei and Ob estuaries. The value of d13C of the plankton is only weakly correlated with the d13C of the organic matter from the sediments and is lower by as much as 3-4 per mil. The paper presents the results obtained from a number of meridional river-sea profiles. It was determined from the relations between the isotopic compositions of plankton and particulate matter that the river waters carry material consisting of 70% detrital-humus matter and 30% planktonogenic material in the river part, and the material contained in the offshore waters consists of 30% terrigenous components, with the contribution of bioproducers amounting to 70%. The carbon isotopic composition of the plankton ranges from -29 to -35 per mil in the riverine part, from -28 to -27 per mil in the estuaries, and from -27.0 to -25 per mil in the marine part. The relative lightness of the carbon isotopic composition of plankton in Arctic waters is explained by the temperature effect, elevated CO2 concentrations, and long-distance CO2 supply to the sea with river waters. The data obtained on the isotopic composition of CO2 in the surface waters of the Kara Sea were used to map the distribution of d13C. The complex of hydrocarbon gases extracted from the waters included methane, C2-C5, and unsaturated C2=-C4= hydrocarbons, for which variations in the concentrations in the waters were studied along river-estuary-sea profiles. The geochemistry of hydrocarbon gases in surface fresh waters is characterized by comparable concentrations of methane (0.3-5 µl/l) and heavier hydrocarbons, including unsaturated ones. Microbiological methane with d13C from -105 to -90 per mil first occurs in the sediments at depths of 40-200 cm. The sediments practically everywhere display traces of methane oxidation in the form of a shift of the d13C of methane toward higher values and the occurrence of autogenic carbonate material, including ikaite, enriched in the light isotope. Ikaite (d13C from -25 to -60 per mil) was found and examined in several profiles. The redox conditions in the sediments varied from normal in the southern part of the sea to highly oxidized along the Novaya Zemlya Trough. Vertical sections through the sediments of the latter exemplify the complete suppression of the biochemical activity of microorganisms. Our data provide insight into the biogeochemistry of the Kara Sea and make it possible to specify the background values needed for ecological control during the future exploration operations and extraction of hydrocarbons in the Kara Sea.