Ecological Archives A025-104-A3
Bharath Ananthasubramaniam, Edward McCauley, Kurt A. Gust, Alan J. Kennedy, Erik B. Muller, Edward J. Perkins, and Roger M. Nisbet. 2015. Relating suborganismal processes to exotoxological and population level endpoints using a bioenergetics model. Ecological Applications 25:1691–1710. http://dx.doi.org/10.1890/14-0498.1
Appendix C. Literature summary of papers investigating global transcript expression in Daphnia.
Our observations are arranged into five transcriptomics-based categories relevant to the DEB sensitivity analysis including: (1) Energy Utilization, (2) Oxygen Transport for Aerobic Respiration, (3) Feeding and Assimilation, (4) Carapace and Molting and (5) Reproduction. Further, the results are sorted against apical (organism level) effects on growth, reproduction or combined growth and reproduction effects to provide phenotypic anchoring for changes in gene transcript expression. (Particular effects on growth and reproduction are indicated in bold letters).
Table C1. Energy Utilization (Based on Transcript Expression Data).
Exposure |
Apical Effect |
Sub-Organismal Effect |
Genomic Effect (Function) |
Expression |
Reference |
Cd |
Negative effects on Population Growth Rate (PGR) - Survivorship, Growth & Reproduction |
Carbohydrate & Fat Metab (Glycoloysis / Gluconeogenesis) |
increased |
(Connon et al. 2008) |
|
Cd |
Negative effects on Population Growth Rate (PGR) - Survivorship, Growth & Reproduction |
Energy Metabolism |
mixed |
(Connon et al. 2008) |
|
Cd |
Decreased Growth, Reproduction & Fitness - Length, Number of Clutches, Total neonates, Per Capita Birth Rate |
Lipid-Ovary Index |
Response to Metals Stress |
increased |
(Shaw et al. 2007) |
P limited food |
Negative effects on Growth |
arachidonic acid metabolism |
decreased |
(Jeyasingh et al. 2011) |
|
propiconazole |
Negative effects on Growth & Juvenile Development |
ATP Synthesis |
increased |
(Soetaert et al. 2006) |
|
P limited food |
Negative effects on Growth |
biosynthesis of alkaloids derived from histidine and purine |
increased |
(Jeyasingh et al. 2011) |
|
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Carbohydrate Metabolism |
increased |
(Soetaert et al. 2007a) |
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Carbohydrate Metabolism |
mixed |
(Vandenbrouck et al. 2009) |
Polar & Nonpolar Narcotics |
Negative effects on Growth |
Decreased caloric content: carbs, lipid, & protein |
Carbohydrate Metabolism |
mixed |
(Dom et al. 2012) |
P limited food |
Negative effects on Growth |
glycerolipid metabolism |
increased |
(Jeyasingh et al. 2011) |
|
Polar & Nonpolar Narcotics |
Negative effects on Growth |
Decreased caloric content: carbs, lipid, & protein |
Lipid binding / lipid transport |
mixed |
(Dom et al. 2012) |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Lipid Metabolism (alpha-esterase) |
increased |
(Soetaert et al. 2007a) |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Lipid Metabolism (Vitellogenin - embryo nutrition) |
decreased |
(Soetaert et al. 2007a) |
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Lipid Metabolism (Vitellogenin) |
decreased |
(Vandenbrouck et al. 2009) |
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Protein Metabolism |
increased |
(Vandenbrouck et al. 2009) |
Polar & Nonpolar Narcotics |
Negative effects on Growth |
Decreased caloric content: carbs, lipid, & protein |
Protein Metabolism |
increased |
(Dom et al. 2012) |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Protein Metabolism (proteolysis) |
mixed |
(Soetaert et al. 2007a) |
fungicide fenarimol |
Negative effects on Growth & Embryo development |
Protein Metabolism (Proteolysis) |
increased |
(Soetaert et al. 2007b) |
|
propiconazole |
Negative effects on Growth & Juvenile Development |
Stress Response |
mixed |
(Soetaert et al. 2006) |
|
P limited food |
Negative effects on Growth |
tryptophan metabolism |
decreased |
(Jeyasingh et al. 2011) |
|
Ibuprophen |
Negative effects on Reproduction |
Negative impacts on oogeneis and juvenile development |
Carbohydrate Metabolism |
increased |
(Heckmann et al. 2008) |
Ibuprophen |
Negative effects on Reproduction |
Negative impacts on oogeneis and juvenile development |
Lipid Metabolism |
increased |
(Heckmann et al. 2008) |
Zn |
Negative effects on Reproduction and juvenile growth |
Lipid Transport, (All Vitellogenin-fused to SOD) |
increased |
(Vandegehuchte et al. 2010) |
|
Zn |
Negative effects on Reproduction and juvenile growth |
Lipid Transport, (Vitellogenin) |
decreased |
(Vandegehuchte et al. 2010) |
|
Zn |
Negative effects on Reproduction and juvenile growth |
Proteolysis |
increased |
(Vandegehuchte et al. 2010) |
|
Cd |
None measured - 1/10 LC50 Exposure |
Fatty Acid Biosynthesis |
decreased |
(Poynton et al. 2011) |
|
Cd |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Lipid Metabolism & Transport |
decreased |
(Poynton et al. 2008a) |
|
Cu |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Lipid Metabolism & Transport |
decreased |
(Poynton et al. 2008b) |
|
Zn |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
|
Lipid Metabolism & Transport |
decreased |
(Poynton et al. 2008a) |
Table C2. Oxygen Transport for Aerobic Respiration (Based on Transcript Expression Data).
Exposure |
Apical Effect |
Sub-Organismal Effect |
Genomic Effect (Function) |
Expression |
Reference |
Cd |
Decreased Growth, Reproduction & Fitness - Length, Number of Clutches, Total neonates, Per Capita Birth Rate |
Lipid-Ovary Index |
Oxygen Transport |
increased |
(Shaw et al. 2007) |
Cd |
Negative effects on Population Growth Rate (PGR) - Survivorship, Growth & Reproduction |
Oxygen Transport |
decreased |
(Connon et al. 2008) |
|
fungicide fenarimol |
Negative effects on Growth & Embryo development |
Oxygen Transport |
increased |
(Soetaert et al. 2007b) |
|
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Oxygen Transport |
decreased |
(Vandenbrouck et al. 2009) |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Oxygen Transport (hemoglobin) |
decreased |
(Soetaert et al. 2007a) |
Zn (dietary) |
Negative effects on Reproduction (2nd brood onward), No effect on survival growth or feeding rate |
Effect on time-to molt |
Mitochondrial Function |
increased |
(De Schamphelaere et al. 2008) |
Ibuprophen |
Negative effects on Reproduction |
Negative impacts on oogeneis and juvenile development |
Oxidative phoshorylation |
mixed |
(Heckmann et al. 2008) |
Zn |
Negative effects on Reproduction and juvenile growth |
Oxygen Transport (hemoglobin) |
decreased |
(Vandegehuchte et al. 2010) |
|
Cd |
None measured - 1/10 LC50 Exposure |
Oxygen Transport |
increased |
(Poynton et al. 2011) |
|
Cd |
None measured - 1/10 LC50 Exposure |
|
Oxygen Transport |
increased |
(Poynton et al. 2011) |
Table C3. Feeding and Assimilation (Based on Transcript Expression Data).
Exposure |
Apical Effect |
Sub-Organismal Effect |
Genomic Effect (Function) |
Expression |
Reference |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Digestion |
increased |
(Soetaert et al. 2007a) |
fungicide fenarimol |
Negative effects on Growth & Embryo development |
Digestion & Nutrition Absorbtion |
increased |
(Soetaert et al. 2007b) |
|
Dietary Differences |
None measured |
Gut Physiology |
mixed |
(Dudycha et al. 2012) |
|
Cd |
None measured - 1/10 LC50 Exposure |
Digestion & Nutrition Absorbtion |
decreased |
(Poynton et al. 2007) |
|
Cu |
None measured - 1/10 LC50 Exposure |
Digestion & Nutrition Absorbtion |
decreased |
(Poynton et al. 2007) |
|
Zn |
None measured - 1/10 LC50 Exposure |
Digestion & Nutrition Absorbtion |
decreased |
(Poynton et al. 2007) |
|
Cd |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Digestion & Nutrition Absorbtion |
decreased |
(Poynton et al. 2008a) |
|
Cu |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Digestion & Nutrition Absorbtion |
decreased |
(Poynton et al. 2008a) |
|
Zn |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
|
Digestion & Nutrition Absorbtion |
decreased |
(Poynton et al. 2008a) |
Table C4. Carapace and Molting (Based on Transcript Expression Data).
Exposure |
Apical Effect |
Sub-Organismal Effect |
Genomic Effect (Function) |
Expression |
Reference |
Cd |
Negative effects on Population Growth Rate (PGR) - Survivorship, Growth & Reproduction |
Chitin Metabolism |
mixed |
(Connon et al. 2008) |
|
Cd |
Decreased Growth, Reproduction & Fitness - Length, Number of Clutches, Total neonates, Per Capita Birth Rate |
Lipid-Ovary Index |
Chitin Metabollism |
increased |
(Shaw et al. 2007) |
Cd |
Negative effects on Population Growth Rate (PGR) - Survivorship, Growth & Reproduction |
Cuticle Metabolism |
mixed |
(Connon et al. 2008) |
|
Cd |
Decreased Growth, Reproduction & Fitness - Length, Number of Clutches, Total neonates, Per Capita Birth Rate |
Lipid-Ovary Index |
Cuticle Protein metabolism |
increased |
(Shaw et al. 2007) |
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Chitin metabolism |
increased |
(Vandenbrouck et al. 2009) |
Polar & Nonpolar Narcotics |
Negative effects on Growth |
Decreased caloric content: carbs, lipid, & protein |
Cuticle Metabolism |
mixed |
(Dom et al. 2012) |
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Cuticle Metabolism (decreased at low Ni Conc, increased at high) |
mixed |
(Vandenbrouck et al. 2009) |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Cuticle Protein metabolism |
mixed |
(Soetaert et al. 2007a) |
fungicide fenarimol |
Negative effects on Growth & Embryo development |
Cuticle Protein metabolism |
decreased |
(Soetaert et al. 2007b) |
|
propiconazole |
Negative effects on Growth & Juvenile Development |
Cuticle Protein Metabolism |
mixed |
(Soetaert et al. 2006) |
|
Zn (dietary) |
Negative effects on Reproduction (2nd brood onward), No effect on survival growth or feeding rate |
Effect on time-to molt |
Chitin Binding |
decreased |
(De Schamphelaere et al. 2008) |
Zn |
Negative effects on Reproduction and juvenile growth |
Chitin Metabolism |
mixed |
(Vandegehuchte et al. 2010) |
|
Ibuprophen |
Negative effects on Reproduction |
Negative impacts on oogeneis and juvenile development |
Cuticle Metabolism |
mixed |
(Heckmann et al. 2008) |
Zn (dietary) |
Negative effects on Reproduction (2nd brood onward), No effect on survival growth or feeding rate |
Effect on time-to molt |
Cuticle Metabolism |
decreased |
(De Schamphelaere et al. 2008) |
Cd |
None measured - 1/10 LC50 Exposure |
Chitin Metabolism |
decreased |
(Poynton et al. 2007) |
|
Cu |
None measured - 1/10 LC50 Exposure |
Chitin Metabolism |
mixed |
(Poynton et al. 2007) |
|
Zn |
None measured - 1/10 LC50 Exposure |
Chitin Metabolism |
decreased |
(Poynton et al. 2007) |
|
Cd |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Chitin metabolism and cuticle metabolism |
mixed |
Poynton et al 2008 |
|
Cu |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Chitin metabolism and cuticle metabolism |
mixed |
(Poynton et al. 2008b) |
|
Zn |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Chitin metabolism and cuticle metabolism |
mixed |
Poynton et al 2008 |
|
Cd |
None measured - 1/10 LC50 Exposure |
|
Cuticle Metabolism |
increased |
Poynton et al 2011 |
Table C5. Reproduction (Based on Transcript Expression Data).
Exposure |
Apical Effect |
Sub-Organismal Effect |
Genomic Effect (Function) |
Expression |
Reference |
P limited food |
Negative effects on Growth |
androgen and oestrogen metabolism |
decreased |
(Jeyasingh et al. 2011) |
|
Polar & Nonpolar Narcotics |
Negative effects on Growth |
Decreased caloric content: carbs, lipid, & protein |
Lipid binding / lipid transport (Vitellogenin) |
mixed |
(Dom et al. 2012) |
fungicide fenarimol |
Negative effects on Growth & Embryo development |
Oogenesis - (Vitellogenin) |
decreased |
(Soetaert et al. 2007b) |
|
Ni |
Negative effects on Growth |
Mixed effects on energy parameters: Hormesis @ low concentrations, negative effects at high: Available Energy (Carbohydrates, Protein & Lipid), Cellular Energy Allocation, Consumed Energy) |
Oogenesis - (Vitellogenin) |
decreased |
(Vandenbrouck et al. 2009) |
Cd |
Negative effects on Growth |
Negative effects on energy parameters: Cellular Energy Allocation, Energy Available (Protein, Carbohydrate & Lipid Reserves), Energy Consumed |
Oogenesis and juvenile development (Vitellogenin) |
decreased |
(Soetaert et al. 2007a) |
propiconazole |
Negative effects on Growth & Juvenile Development |
Oogenesis -Yolk Proteins & Vitellogenin |
decreased |
(Soetaert et al. 2006) |
|
Zn (dietary) |
Negative effects on Reproduction (2nd brood onward), No effect on survival growth or feeding rate |
Effect on time-to molt |
Chitin Binding |
decreased |
(De Schamphelaere et al. 2008) |
Ibuprophen |
Negative effects on Reproduction |
Negative impacts on oogeneis and juvenile development |
crustacean eicosanoid metabolism |
mixed |
(Heckmann et al. 2008) |
Zn (dietary) |
Negative effects on Reproduction (2nd brood onward), No effect on survival growth or feeding rate |
Effect on time-to molt |
Cuticle Metabolism |
decreased |
(De Schamphelaere et al. 2008) |
Ibuprophen |
Negative effects on Reproduction |
Negative impacts on oogeneis and juvenile development |
Oogenesis |
decreased |
(Heckmann et al. 2008) |
Zn |
Negative effects on Reproduction and juvenile growth |
Oogenesis, (All Vitellogenin-fused to SOD) |
increased |
(Vandegehuchte et al. 2010) |
|
Zn |
Negative effects on Reproduction and juvenile growth |
Oogenesis, (Vitellogenin) |
decreased |
(Vandegehuchte et al. 2010) |
|
Cd |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Reproduction & Development |
decreased |
(Poynton et al. 2008a) |
|
Cu |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
Reproduction & Development |
decreased |
(Poynton et al. 2008b) |
|
Zn |
None measured - 1/20 EC50, 1/10 EC50, 1/10 LC50, NOEC |
|
Reproduction & Development |
decreased |
(Poynton et al. 2008a) |
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