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Lai, Floriana; Fagernes, Cathrine E; Bernier, Nicholas J; Miller, Garielle M; Munday, Philip L; Jutfelt, Fredrik; Nilsson, Göran E (2023): Seawater carbonate chemistry and genes regulating neurogenesis and neuroplasticity in brains of three-spined stickleback, cinnamon anemonefish and spiny damselfish exposed to elevated CO2 [dataset]. PANGAEA, https://doi.org/10.1594/PANGAEA.958748

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Abstract:
The continuous increase of anthropogenic CO2 in the atmosphere resulting in ocean acidification has been reported to affect brain function in some fishes. During adulthood, cell proliferation is fundamental for fish brain growth and for it to adapt in response to external stimuli, such as environmental changes. Here we report the first expression study of genes regulating neurogenesis and neuroplasticity in brains of three-spined stickleback (Gasterosteus aculeatus), cinnamon anemonefish (Amphiprion melanopus) and spiny damselfish (Acanthochromis polyacanthus) exposed to elevated CO2. The mRNA expression levels of the neurogenic differentiation factor (NeuroD) and doublecortin (DCX) were upregulated in three-spined stickleback exposed to high-CO2 compared with controls, while no changes were detected in the other species. The mRNA expression levels of the proliferating cell nuclear antigen (PCNA) and the brain-derived neurotrophic factor (BDNF) remained unaffected in the high-CO2 exposed groups compared to the control in all three species. These results indicate a species-specific regulation of genes involved in neurogenesis in response to elevated ambient CO2 levels. The higher expression of NeuroD and DCX mRNA transcripts in the brain of high-CO2–exposed three-spined stickleback, together with the lack of effects on mRNA levels in cinnamon anemonefish and spiny damselfish, indicate differences in coping mechanisms among fish in response to the predicted-future CO2 level.
Keyword(s):
Acanthochromis polyacanthus; Amphiprion melanopus; Animalia; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or < 1 m**2); Gasterosteus aculeatus; Gene expression (incl. proteomics); Laboratory experiment; Nekton; North Atlantic; Pelagos; Single species; South Pacific; Temperate; Tropical
Supplement to:
Lai, Floriana; Fagernes, Cathrine E; Bernier, Nicholas J; Miller, Garielle M; Munday, Philip L; Jutfelt, Fredrik; Nilsson, Göran E (2017): Responses of neurogenesis and neuroplasticity related genes to elevated CO 2 levels in the brain of three teleost species. Biology Letters, 13(8), 20170240, https://doi.org/10.1098/rsbl.2017.0240
Source:
Lai, Floriana; Fagernes, Cathrine E; Bernier, Nicholas J; Miller, Garielle M; Munday, Philip L; Jutfelt, Fredrik; Nilsson, Göran E (2017): Data from: Responses of neurogenesis and neuroplasticity related genes to elevated CO2 levels in the brain of three teleost species. Dryad, https://doi.org/10.5061/dryad.pn397
Documentation:
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 (2022): seacarb: seawater carbonate chemistry with R. R package version 3.3.1. https://cran.r-project.org/web/packages/seacarb/index.html
Comment:
In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Gattuso et al, 2022) 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 2023-05-08.
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
Type of studyStudy typeLai, Floriana
Species, unique identificationSpecies UIDLai, Floriana
Species, unique identification (URI)Species UID (URI)Lai, Floriana
Species, unique identification (Semantic URI)Species UID (Semantic URI)Lai, Floriana
Individual IDInd IDLai, Floriana
TreatmentTreatLai, Floriana
mRNA gene expression, relativemRNA expressLai, FlorianaPCNA (ubc/rpl13A)
mRNA gene expression, relativemRNA expressLai, FlorianaNeuroD (ubc/rpl13A)
mRNA gene expression, relativemRNA expressLai, FlorianaDCX (ubc/rpl13A)
10 mRNA gene expression, relativemRNA expressLai, FlorianaBDNF (ubc/rpl13A)
11 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmLai, Floriana
12 Partial pressure of carbon dioxide, standard deviationpCO2 std dev±Lai, Floriana
13 Alkalinity, totalATµmol/kgLai, Floriana
14 Alkalinity, total, standard deviationAT std dev±Lai, Floriana
15 SalinitySalLai, Floriana
16 Salinity, standard deviationSal std dev±Lai, Floriana
17 Temperature, waterTemp°CLai, Floriana
18 Temperature, water, standard deviationTemp std dev±Lai, Floriana
19 pHpHLai, Florianatotal scale
20 pH, standard deviationpH std dev±Lai, Floriana
21 Aragonite saturation stateOmega ArgLai, Floriana
22 Aragonite saturation state, standard deviationOmega Arg std dev±Lai, Floriana
23 Calcite saturation stateOmega CalLai, Floriana
24 Calcite saturation state, standard deviationOmega Cal std dev±Lai, Floriana
25 pHpHLai, FlorianaNBS scale
26 pH, standard deviationpH std dev±Lai, Floriana
27 Carbonate system computation flagCSC flagYang, YanCalculated using seacarb after Nisumaa et al. (2010)
28 pHpHYang, YanCalculated using seacarb after Nisumaa et al. (2010)
29 Carbon dioxideCO2µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
30 Fugacity of carbon dioxide (water) at sea surface temperature (wet air)fCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
31 Partial pressure of carbon dioxide (water) at sea surface temperature (wet air)pCO2water_SST_wetµatmYang, YanCalculated using seacarb after Nisumaa et al. (2010)
32 Bicarbonate ion[HCO3]-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
33 Carbonate ion[CO3]2-µmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
34 Carbon, inorganic, dissolvedDICµmol/kgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
35 Aragonite saturation stateOmega ArgYang, YanCalculated using seacarb after Nisumaa et al. (2010)
36 Calcite saturation stateOmega CalYang, YanCalculated using seacarb after Nisumaa et al. (2010)
Status:
Curation Level: Enhanced curation (CurationLevelC)
Size:
1474 data points

Data

Download dataset as tab-delimited text — use the following character encoding:


Study type

Species UID

Species UID (URI)

Species UID (Semantic URI)

Ind ID

Treat

mRNA express
(PCNA (ubc/rpl13A))

mRNA express
(NeuroD (ubc/rpl13A))

mRNA express
(DCX (ubc/rpl13A))
10 
mRNA express
(BDNF (ubc/rpl13A))
11 
pCO2water_SST_wet [µatm]
12 
pCO2 std dev [±]
13 
AT [µmol/kg]
14 
AT std dev [±]
15 
Sal
16 
Sal std dev [±]
17 
Temp [°C]
18 
Temp std dev [±]
19 
pH
(total scale)
20 
pH std dev [±]
21 
Omega Arg
22 
Omega Arg std dev [±]
23 
Omega Cal
24 
Omega Cal std dev [±]
25 
pH
(NBS scale)
26 
pH std dev [±]
27 
CSC flag
28 
pH
29 
CO2 [µmol/kg]
30 
fCO2water_SST_wet [µatm]
31 
pCO2water_SST_wet [µatm]
32 
[HCO3]- [µmol/kg]
33 
[CO3]2- [µmol/kg]
34 
DIC [µmol/kg]
35 
Omega Arg
36 
Omega Cal
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265051Control0.0217200.0747300.0286600.013680333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265052Control0.0178900.0847700.0439500.009950333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265053Control333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265054Control0.0207900.0909400.0376600.007400333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265055Control0.0200600.0887700.0223100.015430333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265056Control0.0227600.0744300.0374400.008880333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265057Control0.0217100.011400333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265058Control0.0171900.0413000.0427700.009720333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265059Control0.0133100.0529100.0238200.009440333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:12650510Control0.0171600.0804300.0070300.009190333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:12650511Control0.0269400.012940333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:12650512Control0.0234300.1053300.0317500.014690333.033.0189038624.203.4017.61.208.080.0852.090.743.341.19248.0812.21331.841597.07119.821729.111.913.07
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265051High CO20.0158400.1026700.0437200.009680991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265052High CO20.0231870.1027400.0683500.015800991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265053High CO2991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265054High CO20.0160300.0946100.0500200.011590991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265055High CO20.0179070.0375200.008410991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265056High CO20.0167150.0783500.0397400.011280991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265057High CO20.0187040.0973000.015210991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265058High CO20.0114420.0321100.013900991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:1265059High CO20.0296790.1037500.0623000.010990991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:12650510High CO20.0243630.1000100.0491300.011150991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:12650511High CO20.0182370.117810991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryGasterosteus aculeatusmarinespecies.orgurn:lsid:marinespecies.org:taxname:12650512High CO20.0227350.0932300.0344800.012080991.356.6183913124.203.4017.61.207.650.0310.820.111.310.18247.6436.36987.831723.6446.891806.890.751.20
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783981Control0.1112940.3232060.2326720.07681420581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783982Control0.0928870.2541690.2997070.06148120581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783983Control0.0751780.2001220.2540040.07432620581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783984Control0.0430950.3577130.2069660.08670220581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783985Control0.0725550.2525170.1585310.04307220581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783986Control0.0719740.3416390.2460800.07892320581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783987Control0.0630400.2446630.1552910.04353720581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783988Control0.0705400.2111160.2399050.02857420581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783989Control0.0614260.4178380.1275300.06011520581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:27839810Control0.0631190.2608210.2099000.04970720581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:27839811Control0.0644640.3448610.2797690.06602420581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:27839812Control0.0503890.1623440.0927960.04977020581633.320.1228.40.018.150.005268.0010.55400.20401.431588.36188.491787.403.084.63
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783981High CO20.0964090.2795350.3562230.0749072168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783982High CO20.0805760.2684870.2705700.0883272168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783983High CO20.0774240.2541140.3541970.0467042168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783984High CO20.0634840.4328520.1403860.0791002168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783985High CO20.0442180.1549552168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783986High CO20.0572280.2812620.2756700.0440962168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783987High CO20.0690040.2427870.1835510.0399572168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783988High CO20.0599930.2422120.2070010.0415662168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2783989High CO20.0672250.2773520.1386630.0390112168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:27839810High CO20.0776300.3650160.1325250.0383472168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:27839811High CO20.0599460.1993070.1721150.0343702168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAmphiprion melanopusmarinespecies.orgurn:lsid:marinespecies.org:taxname:27839812High CO20.0679490.1972850.2159530.0413162168733.620.0928.50.017.810.008267.6627.621052.161055.401910.32104.762042.701.712.57
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794691Control0.0802620.790239
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794692Control0.0820391.1374870.8677780.044666
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794693Control0.0744611.0434080.9790920.049268
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794694Control0.0828730.6832940.8413970.062533
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794695Control0.0740440.6111290.8822740.057876
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794696Control0.0703320.6686550.7160810.048454
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794697Control0.0894360.7699320.8918410.061506
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794698Control0.0869970.9104580.837442
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794691High CO20.0854750.9455600.8223500.055372
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794692High CO20.0752920.7401890.7359700.056902
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794693High CO20.0741560.9514150.6525180.051310
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794694High CO20.0798410.6737900.8662540.050147
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794695High CO20.0769850.6339291.0126940.054828
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794696High CO20.0860200.9985480.8165000.057033
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794697High CO20.0802940.7216990.8721650.065348
laboratoryAcanthochromis polyacanthusmarinespecies.orgurn:lsid:marinespecies.org:taxname:2794698High CO20.0803280.8822140.8177610.049871