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  • 1
    Publication Date: 2023-01-13
    Description: Chinese sturgeon (Acipenser sinensis), mainly distributed in the Yangtze River, has been listed as a grade I protected animal in China because of a dramatic decline in population owing to loss of natural habitat for reproduction and interference by human activities. Understanding the proteome profile of Chinese sturgeon liver would provide an invaluable resource for protecting and increasing the stocks of this species. In this study, we have analyzed proteome profiles of juvenile Chinese sturgeon liver using a one-dimensional gel electrophoresis coupled to LC-MS/MS approach. A total of 1059 proteins and 2084 peptides were identified. The liver proteome was found to be associated with diverse biological processes, cellular components and molecular functions. The proteome profile identified a variety of significant pathways including carbohydrate metabolism, fatty acid metabolism and amino acid metabolism pathways. It also established a network for protein biosynthesis, folding and catabolic processes. The proteome profile established in this study can be used for understanding the development of Chinese sturgeon and studying the molecular mechanisms of action under environmental or chemical stress, providing very useful omics information that can be applied to preserve this species.
    Type: Dataset
    Format: application/zip, 3 datasets
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  • 2
    Publication Date: 2023-01-13
    Keywords: Database accession number; Isoelectric point; Molecular mass; Name; Organisms; Peptide; Peptide, unique; Peptide sequence; Sequence coverage
    Type: Dataset
    Format: text/tab-separated-values, 1660 data points
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  • 3
    Publication Date: 2023-01-13
    Keywords: Biological process; Cellular component; Database accession number; Molecular function; Name; Peptide; Peptide, unique
    Type: Dataset
    Format: text/tab-separated-values, 336 data points
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  • 4
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    PANGAEA
    In:  Supplement to: Kao, Shuh-Ji; Zheng, Li-Wei; Hsiao, Silver Sung-Yun (2015): Isotopic compositions and speciation of sedimentary nitrogen and carbon in the Okinawa Trough over past 30 ka. Paleoceanography, 30(10), 1233-1244, https://doi.org/10.1002/2015PA002782
    Publication Date: 2023-06-27
    Description: Total organic carbon to total nitrogen ratio (C/N) and their isotopic composition (d13CTOC vs. d15NTN) are oft-applied proxies to discern terrigenous from marine sourced organics and to unravel the ancient environmental information. In high depositional Asian marginal seas, matrixes, including N-bearing minerals, dilution leads to illusive and even contradictive interpretations. We use KOH-KOBr to separate operationally defined total organic matter into oxidizable (labile) and residual fractions for content and isotope measurements. In a sediment core in the Okinawa Trough, significant amounts of carbon and nitrogen existed in the residual phase, in which the C/N ratio was ~9 resembling most documented sedimentary bulk C/N ratios in the China marginal seas. Such similarity creates a pseudo-C/N interrupting the application of bulk C/N. The residual carbon, though composition unknown, it displayed a d13C range (-22.7 to -18.9 per mil, mean -20.7 per mil) similar to black carbon (-24.0 to -22.8 per mil) in East China Sea surface sediments. After removing residual fraction, we found the temporal pattern of d13CLOC in labile fraction (LOC) was more variable but broadly agreed with the atmospheric pCO2-induced changes in marine endmember d13C. Thus, we suggested adding pCO2-induced endmember modulation into two-endmember mixing model for paleo-environment reconstruction. Meanwhile, the residual nitrogen revealed an intimate association with illite content suggesting its terrestrial origin. Additionally, d15N in residual fraction likely carried the climate imprint from land. Further studies are required to explore the controlling factors for carbon and nitrogen isotopic speciation and to retrieve the information locked in the residual fraction.
    Keywords: AGE; Carbon, organic, residual; Carbon, organic, total; DEPTH, sediment/rock; East China Sea, Pacific Ocean; Giant piston corer; GPC; IMAGES; IMAGES VII - WEPAMA; International Marine Global Change Study; Marion Dufresne (1995); MD012404; MD01-2404; MD122; Nitrogen, carbonate free fraction; Nitrogen, inorganic; δ13C, organic carbon; δ13C, residual organic carbon; δ15N, carbonate free fraction; δ15N, inorganic
    Type: Dataset
    Format: text/tab-separated-values, 536 data points
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  • 5
    Publication Date: 2023-07-10
    Keywords: Database accession number; Isoelectric point; Molecular mass; Peptide; Peptide, unique; Peptide sequence; Protein name; Sequence coverage
    Type: Dataset
    Format: text/tab-separated-values, 4128 data points
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  • 6
    Publication Date: 2024-01-04
    Description: Here we present the dynamic elastic properties, strains, density, porosity, thin sections, XRD, and XRF of 8 metamorphic samples, including one augen gneiss, one schist, one proto-mylonite, three mylonites, and two ultramylonites, collected near the Alpine Faults.
    Keywords: Alpine Faults; anisotropy; dynamic elastic proerties; File format; File name; File size; Metamorphic rocks; MULT; Multiple investigations; pulse transmission; South-Island_New-Zealand; Uniform resource locator/link to file
    Type: Dataset
    Format: text/tab-separated-values, 32 data points
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  • 7
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    PANGAEA
    In:  Supplement to: Li, Wei; Gao, Kunshan; Beardall, John (2015): Nitrate limitation and ocean acidification interact with UV-B to reduce photosynthetic performance in the diatom Phaeodactylum tricornutum. Biogeosciences, 12(8), 2383-2393, https://doi.org/10.5194/bg-12-2383-2015
    Publication Date: 2024-03-20
    Description: It has been proposed that ocean acidification (OA) will interact with other environmental factors to influence the overall impact of global change on biological systems. Accordingly we investigated the influence of nitrogen limitation and OA on the physiology of diatoms by growing the diatom Phaeodactylum tricornutum Bohlin under elevated (1000 µatm; high CO2- HC) or ambient (390 µatm; low CO2-LC) levels of CO2 with replete (110 µmol/L; high nitrate-HN) or reduced (10 ?mol/L; low nitrate-LN) levels of NO3- and subjecting the cells to solar radiation with or without UV irradiance to determine their susceptibility to UV radiation (UVR, 280-400 nm). Our results indicate that OA and UVB induced significantly higher inhibition of both the photosynthetic rate and quantum yield under LN than under HN conditions. UVA or/and UVB increased the cells' non-photochemical quenching (NPQ) regardless of the CO2 levels. Under LN and OA conditions, activity of superoxide dismutase and catalase activities were enhanced, along with the highest sensitivity to UVB and the lowest ratio of repair to damage of PSII. HC-grown cells showed a faster recovery rate of yield under HN but not under LN conditions. We conclude therefore that nutrient limitation makes cells more prone to the deleterious effects of UV radiation and that HC conditions (ocean acidification) exacerbate this effect. The finding that nitrate limitation and ocean acidification interact with UV-B to reduce photosynthetic performance of the diatom P. tricornutum implies that ocean primary production and the marine biological C pump will be affected by OA under multiple stressors.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Aragonite saturation state; Bicarbonate ion; Bicarbonate ion, standard deviation; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Catalase activity, standard deviation; Catalase activity, unit per cell; Catalase activity, unit per protein mass; Charophyta; Chromista; Coulometric titration; Damage/repair ratio; Damage/repair ratio, standard deviation; Damage rate; Damage rate, standard deviation; Effective quantum yield; Effective quantum yield, standard deviation; Exponential rate constant for recovery; Exponential rate constant for recovery, standard deviation; Figure; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Laboratory experiment; Laboratory strains; Light; Macro-nutrients; Non photochemical quenching; Non photochemical quenching, standard deviation; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Ochrophyta; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Phaeodactylum tricornutum; Photosynthetic carbon fixation rate, per cell; Photosynthetic carbon fixation rate, per chlorophyll a; Photosynthetic carbon fixation rate, standard deviation; Phytoplankton; Potentiometric; Primary production/Photosynthesis; Protein per cell; Proteins, standard deviation; Repair rate; Repair rate, standard deviation; Salinity; Single species; Species; Superoxide dismutase activity, standard deviation; Superoxide dismutase activity, unit per cell; Superoxide dismutase activity, unit per protein mass; Table; Temperature, water; Time, standard deviation; Time in minutes; Treatment; Ultraviolet-a radiation-induced inhibition of carbon fixation; Ultraviolet-a radiation-induced inhibition of carbon fixation, standard deviation; Ultraviolet-a radiation-induced inhibition of effective photochemical quantum yield; Ultraviolet-a radiation-induced inhibition of effective photochemical quantum yield, standard deviation; Ultraviolet-b radiation-induced inhibition of carbon fixation; Ultraviolet-b radiation-induced inhibition of carbon fixation, standard deviation; Ultraviolet-b radiation-induced inhibition of effective photochemical quantum yield; Ultraviolet-b radiation-induced inhibition of effective photochemical quantum yield, standard deviation
    Type: Dataset
    Format: text/tab-separated-values, 7864 data points
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  • 8
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    PANGAEA
    In:  Supplement to: Li, Wei; Gao, Kunshan (2012): A marine secondary producer respires and feeds more in a high CO2 ocean. Marine Pollution Bulletin, 64(4), 699-703, https://doi.org/10.1016/j.marpolbul.2012.01.033
    Publication Date: 2024-03-15
    Description: Climate change mediates marine chemical and physical environments and therefore influences marine organisms. While increasing atmospheric CO2 level and associated ocean acidification has been predicted to stimulate marine primary productivity and may affect community structure, the processes that impact food chain and biological CO2 pump are less documented. We hypothesized that copepods, as the secondary marine producer, may respond to future changes in seawater carbonate chemistry associated with ocean acidification due to increasing atmospheric CO2 concentration. Here, we show that the copepod, Centropages tenuiremis, was able to perceive the chemical changes in seawater induced under elevated CO2 concentration (〉1700 µatm, pH 〈 7.60) with avoidance strategy. The copepod's respiration increased at the elevated CO2 (1000 µatm), associated acidity (pH 7.83) and its feeding rates also increased correspondingly, except for the initial acclimating period, when it fed less. Our results imply that marine secondary producers increase their respiration and feeding rate in response to ocean acidification to balance the energy cost against increased acidity and CO2 concentration.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Arthropoda; Behaviour; Bicarbonate ion; Bicarbonate ion, standard deviation; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, partial pressure, standard deviation; Carbon dioxide, standard deviation; Centropages tenuiremis; Clark type oxygen electrode (5300A, YSI); Coast and continental shelf; EPOCA; EUR-OCEANS; European network of excellence for Ocean Ecosystems Analysis; European Project on Ocean Acidification; Experimental treatment; Feeding rate, standard deviation; Feeding rate of cells per individuum; Filtering rate; Filtering rate, standard deviation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Identification; Laboratory experiment; Measured; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; pH meter (Mettler Toledo, USA); Phosphate; Respiration; Respiration rate, oxygen, per individual; Respiration rate, standard deviation; Salinity; see reference(s); Silicate; Single species; Species; Temperate; Temperature, water; Zooplankton
    Type: Dataset
    Format: text/tab-separated-values, 424 data points
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  • 9
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    PANGAEA
    In:  Supplement to: Gao, Kunshan; Xu, Juntian; Gao, Guang; Li, Yahe; Hutchins, David A; Huang, Bangqin; Wang, Lei; Zheng, Ying; Jin, Peng; Cai, Xiaoni; Häder, Donat-Peter; Li, Wei; Xu, Kai; Liu, Nana; Riebesell, Ulf (2012): Rising CO2 and increased light exposure synergistically reduce marine primary productivity. Nature Climate Change, 2, 519–523, https://doi.org/10.1038/nclimate1507
    Publication Date: 2024-03-15
    Description: Carbon dioxide and light are two major prerequisites of photosynthesis. Rising CO2 levels in oceanic surface waters in combination with ample light supply are therefore often considered stimulatory to marine primary production. Here we show that the combination of an increase in both CO2 and light exposure negatively impacts photosynthesis and growth of marine primary producers. When exposed to CO2 concentrations projected for the end of this century, natural phytoplankton assemblages of the South China Sea responded with decreased primary production and increased light stress at light intensities representative of the upper surface layer. The phytoplankton community shifted away from diatoms, the dominant phytoplankton group during our field campaigns. To examine the underlying mechanisms of the observed responses, we grew diatoms at different CO2 concentrations and under varying levels (5-100%) of solar radiation experienced by the phytoplankton at different depths of the euphotic zone. Above 22-36% of incident surface irradiance, growth rates in the high-CO2-grown cells were inversely related to light levels and exhibited reduced thresholds at which light becomes inhibitory. Future shoaling of upper-mixed-layer depths will expose phytoplankton to increased mean light intensities. In combination with rising CO2 levels, this may cause a widespread decline in marine primary production and a community shift away from diatoms, the main algal group that supports higher trophic levels and carbon export in the ocean.
    Keywords: A4_SCS; Alkalinity, total; Alkalinity, total, standard deviation; Aragonite saturation state; Bicarbonate ion; Bicarbonate ion, standard deviation; Bottles or small containers/Aquaria (〈20 L); C3_SCS; Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Chlorophyll a; Chromista; Coast and continental shelf; DATE/TIME; Duration; E606_SCS; East China Sea; Entire community; Event label; Figure; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Growth rate, standard deviation; In situ sampler; Irradiance; Irradiance, standard deviation; ISS; Laboratory experiment; LE04_SCS; Light; Non photochemical quenching; Non photochemical quenching, standard deviation; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Ochrophyta; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Phaeodactylum tricornutum; Phosphate; Phytoplankton; PN07_ECS; Potentiometric; Primary production/Photosynthesis; Primary production of carbon; Primary production of carbon, per chlorophyll a; Primary production of carbon, per volume of seawater; Primary production of carbon, standard deviation; Salinity; Season; SEATS_SCS; Single species; Skeletonema costatum; South China Sea; Species; Temperate; Temperature, water; Thalassiosira pseudonana; Time of day; Treatment; Tropical; Yield ratio
    Type: Dataset
    Format: text/tab-separated-values, 17109 data points
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  • 10
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    PANGAEA
    In:  Supplement to: Li, Wei; Gao, Kunshan; Beardall, John (2012): Interactive Effects of Ocean Acidification and Nitrogen-Limitation on the Diatom Phaeodactylum tricornutum. PLoS ONE, 7(12), e51590, https://doi.org/10.1371/journal.pone.0051590
    Publication Date: 2024-03-15
    Description: Climate change is expected to bring about alterations in the marine physical and chemical environment that will induce changes in the concentration of dissolved CO2 and in nutrient availability. These in turn are expected to affect the physiological performance of phytoplankton. In order to learn how phytoplankton respond to the predicted scenario of increased CO2 and decreased nitrogen in the surface mixed layer, we investigated the diatom Phaeodactylum tricornutum as a model organism. The cells were cultured in both low CO2 (390 µatm) and high CO2 (1000 µatm) conditions at limiting (10 µmol/L) or enriched (110 µmol/L) nitrate concentrations. Our study shows that nitrogen limitation resulted in significant decreases in cell size, pigmentation, growth rate and effective quantum yield of Phaeodactylum tricornutum, but these parameters were not affected by enhanced dissolved CO2 and lowered pH. However, increased CO2 concentration induced higher rETRmax and higher dark respiration rates and decreased the CO2 or dissolved inorganic carbon (DIC) affinity for electron transfer (shown by higher values for K1/2 DIC or K1/2 CO2). Furthermore, the elemental stoichiometry (carbon to nitrogen ratio) was raised under high CO2 conditions in both nitrogen limited and nitrogen replete conditions, with the ratio in the high CO2 and low nitrate grown cells being higher by 45% compared to that in the low CO2 and nitrate replete grown ones. Our results suggest that while nitrogen limitation had a greater effect than ocean acidification, the combined effects of both factors could act synergistically to affect marine diatoms and related biogeochemical cycles in future oceans.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Aragonite saturation state; Bicarbonate ion; Bicarbonate ion, standard deviation; Bottles or small containers/Aquaria (〈20 L); Calcite saturation state; Calculated using CO2SYS; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, reciprocal of photosynthetic affinity value; Carbon, inorganic, dissolved, reciprocal of photosynthetic affinity value, standard deviation; Carbon, inorganic, dissolved, standard deviation; Carbon, organic, particulate, per cell; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, reciprocal of photosynthetic affinity value; Carbon dioxide, reciprocal of photosynthetic affinity value, standard deviation; Carbon dioxide, standard deviation; Carotenoids, standard deviation; Carotenoids per cell; Cell biovolume; Cell biovolume, standard deviation; Cell counts, percent of total; Cell counts, standard deviation; Cell size; Cell size, standard deviation; Chlorophyll a, standard deviation; Chlorophyll a per cell; Chlorophyll c, standard deviation; Chlorophyll c per cell; Chromista; Coulometric titration; Effective quantum yield; Effective quantum yield, standard deviation; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Growth rate, standard deviation; Identification; Laboratory experiment; Laboratory strains; Macro-nutrients; Maximal electron transport rate, relative; Maximal electron transport rate, relative, standard deviation; Maximum photochemical quantum yield of photosystem II; Maximum photochemical quantum yield of photosystem II, standard deviation; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Ochrophyta; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Particulate organic carbon content per cell, standard deviation; Particulate organic nitrogen per cell; Particulate organic nitrogen per cell, standard deviation; pH; pH, standard deviation; Phaeodactylum tricornutum; Photochemical efficiency; Photochemical efficiency, standard deviation; Phytoplankton; Potentiometric; Primary production/Photosynthesis; Respiration; Respiration rate, oxygen, per cell; Respiration rate, oxygen, per chlorophyll a; Respiration rate, oxygen, standard deviation; Salinity; Single species; Species; Spectrophotometric; Temperature, water; Treatment
    Type: Dataset
    Format: text/tab-separated-values, 29292 data points
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