Light regulation of assimilatory sulphate reduction in Arabidopsis thaliana

Adenosine 5′-phosphosulphate reductase (APR) is considered to be a key enzyme of sulphate assimilation in higher plants. We analysed the diurnal fluctuations of total APR activity and protein accumulation together with the mRNA levels of three APR isoforms of Arabidopsis thaliana. The APR activity reached maximum values 4 h after light onset in both shoots and roots; the minimum activity was detected at the beginning of the night. During prolonged light, the activity remained stable and low in shoots, but followed the normal rhythm in roots. On the other hand, the activity decreased rapidly to undetectable levels within 24 h of prolonged darkness both in shoots and roots. Subsequent re-illumination restored the activity to 50% in shoots and to 20% in roots within 8 h. The mRNA levels of all three APR isoforms showed a diurnal rhythm, with a maximum at 2 h after light onset. The variation of APR2 mRNA was more prominent compared to APR1 and APR3. 35SO42– feeding experiments showed that the incorporation of 35S into reduced sulphur compounds in vivo was significantly higher in light than in the dark. A strong increase of mRNA and protein accumulation as well as enzyme activity during the last 4 h of the dark period was observed, implying that light was not the only factor involved in APR regulation. Indeed, addition of 0.5% sucrose to the nutrient solution after 38 h of darkness led to a sevenfold increase of root APR activity over 6 h. We therefore conclude that changes in sugar concentrations are also involved in APR regulation.

Interactions and structural analysis of the zinc -binding motif in decorin, a small leucine rich proteoglycan in extracellular matrix

Decorin, a dermatan/chondroitin sulfate proteoglycan, is ubiquitously distributed in the extracellular matrix (ECM) of mammals. Decorin belongs to the small leucine rich proteoglycan (SLRP) family, a proteoglycan family characterized by a core protein dominated by Leucine Rich Repeat motifs. The decorin core protein appears to mediate the binding of decorin to ECM molecules, such as collagens and fibronectin. It is believed that the interactions of decorin with these ECM molecules contribute to the regulation of ECM assembly, cell adhesions, and cell proliferation. These basic biological processes play critical roles during embryonic development and wound healing and are altered in pathological conditions such as fibrosis and tumorgenesis. ^ In this dissertation, we discover that decorin core protein can bind to Zn2+ ions with high affinity. Zinc is an essential trace element in mammals. Zn2+ ions play a catalytic role in the activation of many enzymes and a structural role in the stabilization of protein conformation. By examining purified recombinant decorin and its core protein fragments for Zn2+ binding activity using Zn2+-chelating column chromatography and Zn2+-equilibrium dialysis approaches, we have located the Zn2+ binding domain to the N-terminal sequence of the decorin core protein. The decorin N-terminal domain appears to contain two Zn2+ binding sites with similar high binding affinity. The sequence of the decorin N-terminal domain does not resemble any other reported zinc-binding motifs and, therefore, represents a novel Zn 2+ binding motif. By investigating the influence of Zn2+ ions on decorin binding interactions, we found a novel Zn2+ dependent interaction with fibrinogen, the major plasma protein in blood clots. Furthermore, a recombinant peptide (MD4) consisting of a 41 amino acid sequence of mouse decorin N-terminal domain can prolong thrombin induced fibrinogen/fibrin clot formation. This suggests that in the presence of Zn2+ the decorin N-terminal domain has an anticoagulation activity. The changed Zn2+-binding activities of the truncated MD4 peptides and site-directed mutagenesis generated mutant peptides revealed that the functional MD4 peptide might contain both a structural zinc-binding site in the cysteine cluster region and a catalytic zinc site that could be created by the flanking sequences of the cysteine cluster region. A model of a loop-like structure for MD4 peptide is proposed. ^

Glyphosate, Manganese, and Zinc Soybean Trial

Often there is yellowing of soybeans following glyphosate applications that has been attributed by some as manganese or zinc deficiency. There have been varied reports of impacts of this ‘yellow flash’ on soybean yields. The trial was conducted to investigate such claims.

Isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate-reducing bacteria (SRB) at different cold seep provinces

Anaerobic methane-oxidizing microbial communities in sediments at cold methane seeps are important factors in controlling methane emission to the ocean and atmosphere. Here, we investigated the distribution and carbon isotopic signature of specific biomarkers derived from anaerobic methanotrophic archaea (ANME groups) and sulphate-reducing bacteria (SRB) responsible for the anaerobic oxidation of methane (AOM) at different cold seep provinces of Hydrate Ridge, Cascadia margin. The special focus was on their relation to in situ cell abundances and methane turnover. In general, maxima in biomarker abundances and minima in carbon isotope signatures correlated with maxima in AOM and sulphate reduction as well as with consortium biomass. We found ANME-2a/DSS aggregates associated with high abundances of sn-2,3-di-O-isoprenoidal glycerol ethers (archaeol, sn-2-hydroxyarchaeol) and specific bacterial fatty acids (C16:1omega5c, cyC17:0omega5,6) as well as with high methane fluxes (Beggiatoa site). The low to medium flux site (Calyptogena field) was dominated by ANME-2c/DSS aggregates and contained less of both compound classes but more of AOM-related glycerol dialkyl glycerol tetraethers (GDGTs). ANME-1 archaea dominated deeper sediment horizons at the Calyptogena field where sn-1,2-di-O-alkyl glycerol ethers (DAGEs), archaeol, methyl-branched fatty acids (ai-C15:0, i-C16:0, ai-C17:0), and diagnostic GDGTs were prevailing. AOM-specific bacterial and archaeal biomarkers in these sediment strata generally revealed very similar d13C-values of around -100 per mill. In ANME-2-dominated sediment sections, archaeal biomarkers were even more 13C-depleted (down to -120 per mill), whereas bacterial biomarkers were found to be likewise 13C-depleted as in ANME-1-dominated sediment layers (d13C: -100 per mill). The zero flux site (Acharax field), containing only a few numbers of ANME-2/DSS aggregates, however, provided no specific biomarker pattern. Deeper sediment sections (below 20 cm sediment depth) from Beggiatoa covered areas which included solid layers of methane gas hydrates contained ANME-2/DSS typical biomarkers showing subsurface peaks combined with negative shifts in carbon isotopic compositions. The maxima were detected just above the hydrate layers, indicating that methane stored in the hydrates may be available for the microbial community. The observed variations in biomarker abundances and 13C-depletions are indicative of multiple environmental and physiological factors selecting for different AOM consortia (ANME-2a/DSS, ANME-2c/DSS, ANME-1) along horizontal and vertical gradients of cold seep settings.

Sediment and pore water geochemistry of sediment cores, Potter Cove, King George Island

Redox-sensitive trace metals (Mn, Fe, U, Mo, Re), nutrients and terminal metabolic products (NO3-, NH4+, PO43-, total alkalinity) were for the first time investigated in pore waters of Antarctic coastal sediments. The results of this study reveal a high spatial variability in redox conditions in surface sediments from Potter Cove, King George Island, western Antarctic Peninsula. Particularly in the shallower areas of the bay the significant correlation between sulphate depletion and total alkalinity, the inorganic product of terminal metabolism, indicates sulphate reduction to be the major pathway of organic matter mineralisation. In contrast, dissimilatory metal oxide reduction seems to be prevailing in the newly ice-free areas and the deeper troughs, where concentrations of dissolved iron of up to 700 µM were found. We suggest that the increased accumulation of fine-grained material with high amounts of reducible metal oxides in combination with the reduced availability of metabolisable organic matter and enhanced physical and biological disturbance by bottom water currents, ice scouring and burrowing organisms favours metal oxide reduction over sulphate reduction in these areas. Based on modelled iron fluxes we calculate the contribution of the Antarctic shelf to the pool of potentially bioavailable iron (Feb) to be 6.9x10**3 to 790x10**3 t/yr. Consequently, these shelf sediments would provide an Feb flux of 0.35-39.5/mg/m**2/yr (median: 3.8 mg/m**2/yr) to the Southern Ocean. This contribution is in the same order of magnitude as the flux provided by icebergs and significantly higher than the input by aeolian dust. For this reason suboxic shelf sediments form a key source of iron for the high nutrient-low chlorophyll (HNLC) areas of the Southern Ocean. This source may become even more important in the future due to rising temperatures at the WAP accompanied by enhanced glacier retreat and the accumulation of melt water derived iron-rich material on the shelf.

Sulphur and iron species in Dvurechenskii mud volcano sediments

The deep Black Sea is known to be depleted in electron-acceptors for sulphide oxidation. This study on depth distributions of sulphur species (S(II), S(0),S(n)**2-,S2O3**2-,SO3**2-,SO4**2-) in the Dvurechenskii mud volcano, a cold seep situated in the permanently anoxic eastern Black Sea basin (Sorokin Trough, 2060 m water depth), showed remarkable concentrations of sulphide oxidation products. Sulphite concentrations of up to 11 µmol L**1-, thiosulphate concentrations of up to 22 µmol L**1-, zero-valent sulphur concentrations of up to 150 µmol L**1- and up to five polysulphide species were measured in the upper 20 cm of the sediment. Electron-acceptors found to be available in the Dvurechenskii mud volcano (DMV) for the oxidation of hydrogen sulphide to sulphide oxidation intermediates are iron-minerals, and probably also reactive manganese phases. Up to 60 µmol g**1- of reactive iron-minerals and up to 170 µmol L**1- dissolved iron was present in the central summit with the highest fluid upflow and fresh mud outflow. Thus, the source for the oxidative power in the DMV are reactive iron phases extruded with the mud from an ancient source in the deeply buried sediments, leading to the formation of various sulphur intermediates in comparably high concentrations. Another possible source of sulphide oxidation intermediates in DMV sediments could be the formation of zero-valent sulphur by sulphate dependent anaerobic microbial oxidation of methane followed by disproportionation of zero-valent sulphur. Sulphide oxidation intermediates, which are produced by these processes, do not reach thermodynamic equilibrium with rhombic sulphur, especially close to the active center of the DMV due to a short equilibration time. Thus, mud volcano sediments, such as in the DMV, can provide oxidizing niches even in a highly reduced environment like the abyssal part of the Black Sea.

The distribution of zinc, cadmium, copper and iron in seawater of the Iceland-Faroe Ridge area

During the International ICES Expedition "Overflow '73" a total of 174 samples from 18 stations were collected by R. V. "Meteor" in the waters of the Iceland-Faroe Ridge area. They were filtered on board ship (through 0.4 mym "Nuclepore" filters), then stored in 500 cm**3 quartz bottles (at -20 °C) and analyzed in air-filtered laboratories on land for zinc and cadmium by means of the differential pulse anodic stripping voltammetry technique and copper and iron by flameless atomic absorption spectrometry. The overall averages of 1.9 myg Zn l**-1, 0.07 myg Cd l**-1, 0.5 myg Cu l**-1 and 0.9 myg Fe l**-1 are in good agreement with recent "baseline" studies of open-ocean waters. The mixture of low salinity water masses from the North Iceland Shelf/Arctic Intermediate Waters seem to maintain distinctly lower concentration of Cd, Cu and Fe than the waters from the North Atlantic and the Norwegian Sea where quite similar mean values are found. There is only little evidence for the assumption that overflow events on the ridge are influencing the concentrations of dissolved metals in the near-bottom layers.

Deep drilling of glaciers: Russian projects in the Arctic (1975-1995)

The data collection "Deep Drilling of Glaciers: Soviet-Russian projects in Arctic, 1975-1995" was collected by the following basic considerations: - compilation of deep (>100 m) drilling projects on Arctic glaciers, using data of (a) publications; (b) archives of IGRAN; (c) personal communication of project participants; - documentation of parameters, references. Accuracy of data and techniques applied to determine different parameters are not evaluated. The accuracy of some geochemical parameters (up to 1984 and heavy metalls) is uncertain. Most reconstructions of ice core age and of annual layer thickness are discussed; - digitizing of published diagrams (in case, when original numerical data were lost) and subsequent data conversion to equal range series and adjustment to the common units. Therefore, the equal-range series were calculated from original data or converted from digitized chart values as indicated in the metadata. For the methodological purpose, the equal-range series obtained from original and reconstructed data were compared repeatedly; the systematic difference was less then 5-7%. Special attention should be given to the fact, that the data for individual ice core parameters varies, because some parameters were originally measured or registered. Parameters were converted in equal-range series using 2 m steps; - two or more parameter values were determined, then the mean-weighted (i.e. accounting the sample length) value is assigned to the entire interval; - one parameter value was determined, measured or registered independently from the parameter values in depth intervals which over- and underlie it, then the value is assigned to the entire interval; - one parameter value was determined, measured or registered for two adjoining depth intervals, then the specific value is assigned to the depth interval, which represents >75% of sample length ; if each of adjoining depth intervals represents <75% of sample length, then the correspondent parameter value is assigned to both intervals of depth. This collection of ice core data (version 2000) was made available through the EU funded QUEEN project by S.M. Arkhipov, Moscow.

Chemical and Sr isotopic compositions of 3 step leachates and residues of bulk samples, zeolites, and smectites from Lower Miocene sediments at ODP Site 166-1007

Massive clinoptilolite authigenesis was observed at about 1105 meters below sea floor (mbsf) in lower Miocene wellcompacted carbonate periplatform sediments from the Great Bahama Bank [Ocean Drilling Program, ODP Leg 166, Site 1007]. The diagenetic assemblage comprises abundant zeolite crystallized within foraminifer tests and sedimentary matrix, as well as Mg smectites. In carbonate-rich deposits, the formation of the zeolite requires a supply of silica. Thus, the objective of the study is to determine the origin of the silica supply, its diagenetic evolution, and consequently the related implications on interpretation of the sedimentary record, in terms of local or global paleoceanographic change. For lack of evidence for any volcaniclastic input or traces of Si-enriched deep fluids circulation, an in situ biogenic source of silica is validated by isotopic data and chemical modeling for the formation of such secondary minerals in shallow-water carbonate sequences. Geochemical and strontium isotopic data clearly establish the marine signature of the diagenetic zeolite, as well as its contemporaneous formation with the carbonate deposition (Sr model ages of 19.6-23.2 Ma). The test of saturation for the pore fluids specifies the equilibrium state of the present mineralogical assemblage. Seawater-rock modeling specifies that clinoptilolite precipitates from the dissolution of biogenic silica, which reacts with clay minerals. The amount of silica (opal-A) involved in the reaction has to be significant enough, at least 10 wt.%, to account for the observed content of clinoptilolite occurring at the most zeolite-rich level. Modeling also shows that the observed amount of clinoptilolite (~19%) reflects an in situ and short-term reaction due to the high reactivity of primary biogenic silica (opal-A) until its complete depletion. The episodic occurrence of these well-lithified zeolite-rich levels is consistent with the occurrence of seismic reflectors, particularly the P2 seismic sequence boundary located at 1115 mbsf depth and dated as 23.2 Ma. The age range of most zeolitic sedimentary levels (biostratigraphic ages of 21.5-22 Ma) correlates well with that of the early Miocene glaciation Mi-1 and Mi-1a global events. Thus, the clinoptilolite occurrence in the shallow carbonate platform environment far from volcanogenic supply, or in other sensitive marine areas, is potentially a significant new proxy for paleoproductivity and oceanic global events, such as the Miocene events, which are usually recognized in deep-sea pelagic sediments and high latitude deposits.

Interstitial water and sediment chemistry at DSDP Sites 87-582 and 87-584

Two trenches off Japan were explored during DSDP Leg 87. One is the Nankai Trough and the other is the Japan Trench; Site 582 is located on the floor of the former and Site 584 is situated on the deep-sea terrace of the latter. Cores from Site 582 and 584 consist mainly of hemipelagic sediments and diatomaceous silts and mudstone, respectively. In this report we analyze the chemistry of the interstitial water and sediments, as well as the sediment mineralogy. Sulfate reduction is accompanied by the production of secondary pyrite, which is rich in the sediment at both sites. Dissolved Ca concentration is relatively low and changes only slightly at both sites, probably because of the formation of carbonate with high alkalinity. Concentrations of dissolved Mg decrease with depth at Site 584. The dissolved Mg depletion probably results from the formation of Mg-rich carbonate and/or ion exchange and reaction between interstitial water and clay minerals. Higher Si/Al values are due to biogenic opal in the sediments and roughly correlate with higher values of interstitial water SiO2. Increases in dissolved Li concentrations may be related to its release from clay minerals, to advection that results from dewatering, and/or to fluid transport.

Pore water methane characteristics and sulphate reduction rates of ODP Leg 164 sediments

Anaerobic methane oxidation (AMO) was characterized in sediment cores from the Blake Ridge collected during Ocean Drilling Program (ODP) Leg 164. Three independent lines of evidence support the occurrence and scale of AMO at Sites 994 and 995. First, concentration depth profiles of methane from Hole 995B exhibit a region of upward concavity suggestive of methane consumption. Diagenetic modeling of the concentration profile indicates a 1.85-m-thick zone of AMO centered at 21.22 mbsf, with a peak rate of 12.4 nM/d. Second, subsurface maxima in tracer-based sulfate reduction rates from Holes 994B and 995B were observed at depths that coincide with the model-predicted AMO zone. The subsurface zone of sulfate reduction was 2 m thick and had a depth integrated rate that compared favorably to that of AMO (1.3 vs. 1.1 nmol/cm**2/d, respectively). These features suggest close coupling of AMO and sulfate reduction in the Blake Ridge sediments. Third, measured d13CH4 values are lightest at the point of peak model-predicted methane oxidation and become increasingly 13C-enriched with decreasing sediment depth, consistent with kinetic isotope fractionation during bacterially mediated methane oxidation. The isotopic data predict a somewhat (60 cm) shallower maximum depth of methane oxidation than do the model and sulfate reduction data.

Mineralogy, chemistry and stable isotope composition of hydrothermal altered sheeted dikes of ODP Hole 111-504B

During ODP Leg 111 Hole 504B was extended 212 m deeper into the sheeted dikes of oceanic Layer 2, for a total penetration of 1288 m within basement. Study of the mineralogy, chemistry, and stable isotopic compositions of the rocks recovered on Leg 111 has confirmed and extended the previous model for hydrothermal alteration at the site: axial greenschist hydrothermal metamorphism was followed by seawater recharge and subsequent off-axis alteration. The dikes are depleted in 18O (mean delta18O = +5.1 ? +/- 0.6 ?) relative to fresh mid-ocean ridge basalt. Oxygen isotopic data on whole rocks and isolated secondary minerals indicate temperatures during axial metamorphism of 250°-350°C and water/rock ratios about one. Increasing amounts of actinolite with depth in the dike section, however, suggest that temperatures increased downward in the dikes. Pyrite + pyrrhotite + chalcopyrite + magnetite was the stable sulfide + oxide mineral assemblage during axial alteration, but these minerals partly re-equilibrated later at temperatures less than 200°C. The dikes sampled on Leg 111 contain an average of 500 ppm sulfur, slightly lower than igneous values. The delta34S values of sulfide average 0?, which indicates the presence of basaltic sulfide and incorporation of little or no seawater-derived sulfide into the rocks. These data are consistent with models for the presence of rock-dominated sulfur in deep hydrothermal fluids. The presence of anhydrite at 1176 m within basement indicates that unaltered seawater can penetrate to significant depths in the crust during recharge.