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  • 1
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Limnology and Oceanography 60 (2015): 957–966, doi:10.1002/lno.10062.
    Description: We present a time series of data for temperature, salinity, nitrate, and carbonate chemistry from September 2011 to July 2013 at the University of Washington's Friday Harbor Laboratories. Samples were collected at the Friday Harbor dock and pump house. Seawater conditions at Friday Harbor were high nitrate-low chlorophyll, with average nitrate and pCO2 concentrations of ∼ 25 ± 5 μmol L−1 and ∼ 700 ± 103 μatm (pH 7.80 ± 0.06). Transient decreases in surface water nitrate and pCO2 corresponded with the timing of a spring bloom (April through June). The high nitrate and pCO2 originate from the high values for these parameters in the source waters to the Salish Sea from the California Undercurrent (CU). These properties are due to natural aerobic respiration in the region where the CU originates, which is the oxygen minimum zone in the eastern tropical North Pacific. Alkalinity varies little so the increase in pCO2 is due to inputs of dissolved inorganic carbon (DIC). This increase in DIC can come from both natural aerobic respiration within the ocean and input of anthropogenic CO2 from the atmosphere when the water was last at the sea surface. We calculated that the anthropogenic “ocean acidification” contribution to DIC in the source waters of the CU was 36 μmol L−1. This contribution ranged from 13% to 22% of the total increase in DIC, depending on which stoichiometry was used for C/O2 ratio (Redfield vs. Hedges). The remaining increase in DIC was due to natural aerobic respiration.
    Description: We thank The Educational Foundation of America (EFA) and National Science Foundation Field Station Marine Lab Program (FSML) (NSF DBI 0829486) for essential initial funding to JWM to develop the Ocean Acidification Experimental Lab (OAEL). Additional support was provided by NSF award EF1041213 to E. Carrington Ken Sebens for encouragement to involve students in this research as part of a FHL mini-apprenticeship course.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Publication Date: 2022-05-26
    Description: Submitted in partial fulfillment of the requirements of the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June, 1973
    Description: An experimental study of the interaction of metal ions with the surface of hydrous manganese dioxide has been completed. The results of these experiments have greatly improved our qualitative understanding of the adsorption mechanism and have also provided a means of testing quantitatively the proposal that the concentration of cobalt in manganese rich marine samples is due to adsorption of cobalt from sea water by hydrous manganese dioxide. This study has shown that there are two reasons why manganese dioxide is an efficient scavenger of metal ions from sea water. These are coulombic attraction and specific adsorption. The coulombic attraction is in response to the surface charge that originates because of acid-base reactions at the surface. The surface charge is pH dependent, and the pH of zero point of charge for the hydrous manganese dioxide used in this study was 2.25. The surface charge increases rapidly for pH values greater than the pH of zero point of charge and reaches values of -100 μcoul/cm2 by pH 8.0. However, the high surface charge cannot explain all the adsorption. This is because some metal ions exhibìt a strong specific adsorption on the surface. This specific adsorption is a direct reaction of the metal ions with the surface, releasing one proton from the surface for each metal ion adsorbed. The energy of this specific interaction is frequently greater than the energy of electrostatic attraction. Adsorption on hydrous manganese dioxide and the magnitude of the specific adsorption both increased in the order: Na = K 〈 Mn 〈 Ca 〈 Sr 〈 Ba 〈 Ni 〈 Zn 〈 Mn ≤ Co This suggests that the specific adsorption potential controls the adsorption selectivity of δMn02. An adsorption isotherm was constructed for cobalt, and these data were used to test the hypothesis that the enrichment of cobalt in the suspended matter of the Black Sea and in ferromanganoan sediments from the East Pacific Rise is due to adsorption of cobalt from sea water by manganese dioxide. The calculations indicate that adsorption is a feasible explanation for these examples.
    Description: This research has been supported for various periods by funds granted by the National Science Foundation (GA-l3574) and U. S. Atomic Energy Commission Contract AT-(30-1)3566 and Graduate Fellowships provided by the Pan American Petroleum Foundation and by the Woods Hole Oceanographic Institution.
    Keywords: Chemical oceanography ; Metal ions ; Atlantis II (Ship : 1963-) Cruise AII49
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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  • 3
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: Arabian Gulf Carbonate System Chemistry
    Description: The data show that the average value of pCO2 in surface seawater in the Exclusive Economic Zone of Qatar is supersaturated with respect to the atmosphere. The excess pCO2 reflects a balance between a source due to the impact of increasing T and S on the carbonate system equilibrium constants and a sink due to CO2 loss due to gas exchange from surface seawater after it enters the Gulf through the Strait of Hormuz. Nevertheless, CaCO3 formation was still more important, relative to net biological production, than in the open ocean. The tracer Alk* has values determined by CaCO3 formation and had values suggesting substantial CaCO3 formation. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/833517
    Description: International Research Co-Fund Collaboration Program of QU (IRCC) IRCC-2019-002
    Keywords: Carbonate chemistry ; Persian/Arabian Gulf ; EEZ of Qatar ; DIC ; Alkalinity ; PCO2
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 4
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2006. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Marine Chemistry 100 (2006): 250-268, doi:10.1016/j.marchem.2005.10.024.
    Description: Since the 1960’s, thorium isotopes occupy a special place in the oceanographer’s toolbox as tracers for determining rates and mechanisms of oceanic scavenging, particle dynamics, and carbon fluxes. Due to their unique and constant production rates from soluble parent nuclides of uranium and radium, their disequilibrium can be used to calculate rates and time scales of sinking particles. In addition, by ratio-ing particulate 234Th (as well, in principle, other Thnuclides) to carbon (and other elements), and linking this ratio to the parent-daughter disequilibrium in the water column, it is possible to calculate fluxes of carbon and other elements. Most of these applications are possible with little knowledge of the dissolved chemical properties of thorium, other than its oxidation state (IV) and tendency to strongly sorb to surfaces, i.e., its “particle- or surface-activity”. However, the use of any tracer is hindered by a lack of knowledge of its chemical properties. Recent observations in the variability of carbon to 234Th ratios in different particle types, as well as of associations of Th(IV) with various marine organic biomolecules has led to the need for a review of current knowledge and what future endeavors should be taken to understand the marine chemistry of thorium.
    Description: The writing of this paper was supported, in parts by NSF (OCE-0351559; OCE-0350758, and OCE 0354757).
    Keywords: Thorium ; Speciation ; Seawater ; Colloids ; Exopolymeric substances ; Transparent exopolymeric particles ; Amphiphiles ; Biosurfactant ligand
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: 1607662 bytes
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  • 5
    ISSN: 1365-3091
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences
    Notes: Modern terrigenous sediments cemented by low-magnesian calcite are found in distributary channels and adjacent shallow-water marine localities at the front of the Fraser River delta. These permanently submerged areas are usually covered by sea water, including sea water intruded upstream along bottoms of river channels. The cemented sediments occur as irregular to platy nodular masses at or near to sediment-water interface, where they are frequently encountered during dredging. The cement consists of small crystals arranged in fibrous rims and other aggregates around and between sand grains. Processes leading to cementation are not yet known, but may include dissolution of calcareous shells by pore waters in buried sediments, followed by precipitation of calcite at higher levels from these fluids as they are expelled upward during compaction.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Sedimentology 28 (1981), S. 0 
    ISSN: 1365-3091
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences
    Notes: Boundary Bay tidal flats on the inactive southern flank of the Fraser Delta have surface sediments consisting almost entirely of very fine to fine, well to very well sorted sands which show a gradual fining-shorewards trend. Five floral/sedimentological zones form distinct biofacies. These are, from the shoreline seaward, the saltmarsh, algal mat, upper sand wave, eelgrass and lower sand wave zones. The lower limit of the saltmarsh lies at a constant level above which the maximum duration of continuous exposure rises abruptly from ∼ 12 to 40 days. Similarly, at the lower limit of the algal mat zone the maximum duration of continuous exposure jumps from 1 to ∼ 2 days, and at the upper limit of the eelgrass zone from ∼ 0·5 to ∼ 0·8 days. These correlations between exposure and zonation are suggested to be causal.In the algal mat and eelgrass zones microtopography of biogenic origin, only a few centimetres high, creates lateral heterogeneity within the zonal biofacies. In the upper sand wave zone, very low amplitude (a∼ 0·1 m) symmetrical sand waves (λ∼ 30 m) of probable storm-wave origin have a similar effect. In the lower sand wave zone, sand waves (a∼ 0·5 m, λ∼ 60 m) are formed by tidal currents or wave action and physical sedimentary structures dominate over biogenic ones.The densities of the following macrofaunal organisms which produce distinctive biogenic sedimentary structures were determined on two surveyed transects: Callianassa californiensis and Upogebia pugettensis, both thalassinidean shrimps; three polychaete worms, Abarenicola sp., Spio sp. and Clymenella sp.; the bivalve Mya arenaria and the gastropods Batillaria attramentaria and Nassarius mendicus. Callianassa excavate unlined temporary feeding burrows, whereas Upogebia build mud-lined permanent dwelling burrows. Upogebia are restricted to below mean sea-level where continuous exposure is 〈 0·5 days, whereas Callianassa extend up to a level, just below mean higher high water, where maximum continuous exposure rises abruptly from 4 to 9 days. This difference in range is probably due to the latter's greater anoxia tolerance—a necessary adaptation for life in an unlined feeding burrow.
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  • 7
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 376 (1995), S. 755-758 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Water-column denitrification accounts for almost half (60-QOTgNyr™1) of the total oceanic loss of fixed nitrogen and occurs primarily in three areas: the eastern tropical North Pacific (ETNP), the eastern tropical South Pacific and the Arabian Sea4 6. Each of these regions is ...
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  • 8
    Publication Date: 2019-09-30
    Description: Plants, algae, and cyanobacteria fix carbon dioxide to organic carbon with the Calvin–Benson (CB) cycle. Phosphoribulokinase (PRK) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) are essential CB-cycle enzymes that control substrate availability for the carboxylation enzyme Rubisco. PRK consumes ATP to produce the Rubisco substrate ribulose bisphosphate (RuBP). GAPDH catalyzes the reduction step of the CB cycle with NADPH to produce the sugar glyceraldehyde 3-phosphate (GAP), which is used for regeneration of RuBP and is the main exit point of the cycle. GAPDH and PRK are coregulated by the redox state of a conditionally disordered protein CP12, which forms a ternary complex with both enzymes. However, the structural basis of CB-cycle regulation by CP12 is unknown. Here, we show how CP12 modulates the activity of both GAPDH and PRK. Using thermophilic cyanobacterial homologs, we solve crystal structures of GAPDH with different cofactors and CP12 bound, and the ternary GAPDH-CP12-PRK complex by electron cryo-microscopy, we reveal that formation of the N-terminal disulfide preorders CP12 prior to binding the PRK active site, which is resolved in complex with CP12. We find that CP12 binding to GAPDH influences substrate accessibility of all GAPDH active sites in the binary and ternary inhibited complexes. Our structural and biochemical data explain how CP12 integrates responses from both redox state and nicotinamide dinucleotide availability to regulate carbon fixation.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 9
    Publication Date: 2018-07-30
    Description: Robust photosynthesis in chloroplasts and cyanobacteria requires the participation of accessory proteins to facilitate the assembly and maintenance of the photosynthetic apparatus located within the thylakoid membranes. The highly conserved Ycf48 protein acts early in the biogenesis of the oxygen-evolving photosystem II (PSII) complex by binding to newly synthesized precursor D1 subunit and by promoting efficient association with the D2 protein to form a PSII reaction center (PSII RC) assembly intermediate. Ycf48 is also required for efficient replacement of damaged D1 during the repair of PSII. However, the structural features underpinning Ycf48 function remain unclear. Here we show that Ycf48 proteins encoded by the thermophilic cyanobacterium Thermosynechococcus elongatus and the red alga Cyanidioschyzon merolae form seven-bladed beta-propellers with the 19-aa insertion characteristic of eukaryotic Ycf48 located at the junction of blades 3 and 4. Knowledge of these structures has allowed us to identify a conserved “Arg patch” on the surface of Ycf48 that is important for binding of Ycf48 to PSII RCs but also to larger complexes, including trimeric photosystem I (PSI). Reduced accumulation of chlorophyll in the absence of Ycf48 and the association of Ycf48 with PSI provide evidence of a more wide-ranging role for Ycf48 in the biogenesis of the photosynthetic apparatus than previously thought. Copurification of Ycf48 with the cyanobacterial YidC protein insertase supports the involvement of Ycf48 during the cotranslational insertion of chlorophyll-binding apopolypeptides into the membrane.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 10
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