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Xie, Jinling; Li, Baolin; Zhou, Tangjian; Wang, Xiaojie (2024): Seawater carbonate chemistry and water content, apoptosis, and proliferation of the brain in marine medaka [dataset]. PANGAEA, https://doi.pangaea.de/10.1594/PANGAEA.973670 (DOI registration in progress)

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Abstract:
Here, we studied structural changes in medaka (Oryzias melastigma) brain regions contacting cerebrospinal fluid (CSF) after short-term (7 days) CO2 exposure.
This dataset is included in the OA-ICC data compilation maintained in the framework of the IAEA Ocean Acidification International Coordination Centre (see https://oa-icc.ipsl.fr). Original data were provided by the author of the related paper (see Related to) to the OA-ICC data curator. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2024) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation by seacarb is 2024-11-26.
Keyword(s):
Animalia; Bottles or small containers/Aquaria (<20 L); Chordata; Gene expression (incl. proteomics); Laboratory experiment; Nekton; Oryzias melastigma; Other studied parameter or process; Pelagos; Single species
Related to:
Xie, Jinling; Li, Baolin; Zhou, Tangjian; Wang, Xiaojie (2024): The water content, apoptosis, and proliferation of the brain in marine medaka affected by seawater acidification. Integrative Zoology, 1749-4877.12872, https://doi.org/10.1111/1749-4877.12872
References:
Nisumaa, Anne-Marin; Pesant, Stephane; Bellerby, Richard G J; Delille, Bruno; Middelburg, Jack J; Orr, James C; Riebesell, Ulf; Tyrrell, Toby; Wolf-Gladrow, Dieter A; Gattuso, Jean-Pierre (2010): EPOCA/EUR-OCEANS data compilation on the biological and biogeochemical responses to ocean acidification. Earth System Science Data, 2(2), 167-175, https://doi.org/10.5194/essd-2-167-2010
Yang, Yan; Brockmann, Patrick; Galdino, Carolina; Schindler, Uwe; Gazeau, Frédéric (2024): An update of data compilation on the biological response to ocean acidification and overview of the OA-ICC data portal. Earth System Science Data, 16(8), 3771-3780, https://doi.org/10.5194/essd-16-3771-2024
Yang, Yan; Hansson, L; Gattuso, Jean-Pierre (2016): Data compilation on the biological response to ocean acidification: an update. Earth System Science Data, 8(1), 79-87, https://doi.org/10.5194/essd-8-79-2016
Related code / software:
Gattuso, Jean-Pierre; Epitalon, Jean-Marie; Lavigne, Héloïse; Orr, James; Gentili, Bernard; Hagens, Mathilde; Hofmann, Andreas; Mueller, Jens-Daniel; Proye, Aurélien; Rae, James; Soetaert, Karline (2024): seacarb: seawater carbonate chemistry with R. R package version 3.3.3. https://cran.r-project.org/web/packages/seacarb/index.html
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Type of studyStudy typeWang, Xiaojie
2Species, unique identificationSpecies UIDWang, Xiaojie
3Species, unique identification (URI)Species UID (URI)Wang, Xiaojie
4Species, unique identification (Semantic URI)Species UID (Semantic URI)Wang, Xiaojie
5Treatment: carbon dioxide, partial pressureT:pCO2ppmvWang, Xiaojie
6Gene nameGeneWang, Xiaojie
7Gene expressionGene expressionWang, XiaojieRelative
8Gene abundance, relativeGA relWang, XiaojieQuantitative analysis of Cleaved Caspase-3 abundance (standardized against GAPDH)
9Gene abundance, relativeGA relWang, XiaojieQuantitative analysis of PCNA abundance (standardized against GAPDH)
10PercentagePerc%Wang, XiaojiePCNA+ / DAPI in the telencephalon
11PercentagePerc%Wang, XiaojiePCNA+ / DAPI in the hypothalamus
12Cell, lengthCell lµmWang, XiaojieTUNEL+ cells in tectum opticum
13PercentagePerc%Wang, XiaojieBrain water
14Number of cellsNo cells#Wang, XiaojieTUNEL+ cells in tectum opticum
15Number of cellsNo cells#Wang, XiaojieTUNEL+ cells in hypothalamus
16Temperature, waterTemp°CWang, Xiaojie
17Temperature, water, standard errorT std e±Wang, Xiaojie
18Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmWang, XiaojieCalculated using CO2SYS
19Partial pressure of carbon dioxide (water) at sea surface temperature (wet air), standard errorpCO2water_SST_wet std e±Wang, XiaojieCalculated using CO2SYS
20pH, NBS scalepH NBSWang, XiaojiePotentiometricNBS scale
21pH, standard errorpH std e±Wang, XiaojiePotentiometricNBS scale
22Alkalinity, totalATµmol/kgWang, XiaojiePotentiometric titration
23Alkalinity, total, standard errorAT std e±Wang, XiaojiePotentiometric titration
24SalinitySalWang, Xiaojie
25Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
26pH, total scalepHTYang, YanCalculated using seacarb after Nisumaa et al. (2010)total scale
27Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
28Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
30Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Size:
5646 data points

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