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  • 1
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    Widely rhythmic transcriptome in Calanus finmarchicus during the high Arctic summer solstice period (2021)
    Cell Press
    Details
    Publication Date: 2021-01-01
    Electronic ISSN: 2589-0042
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Natural Sciences in General , Physics
    Published by Cell Press
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  • 2
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    Daily transcriptomes of the copepod Calanus finmarchicus during the summer solstice at high Arctic latitudes (2020)
    Springer Nature
    Details
    Publication Date: 2020-11-24
    Description: The zooplankter Calanus finmarchicus is a member of the so-called “Calanus Complex”, a group of copepods that constitutes a key element of the Arctic polar marine ecosystem, providing a crucial link between primary production and higher trophic levels. Climate change induces the shift of C. finmarchicus to higher latitudes with currently unknown impacts on its endogenous timing. Here we generated a daily transcriptome of C. finmarchicus at two high Arctic stations, during the more extreme time of Midnight Sun, the summer solstice. While the southern station (74.5 °N) was sea ice-free, the northern one (82.5 °N) was sea ice-covered. The mRNAs of the 42 samples have been sequenced with an average of 126 ± 5 million reads (mean ± SE) per sample, and aligned to the reference transcriptome. We detail the quality assessment of the datasets and the complete annotation procedure, providing the possibility to investigate daily gene expression of this ecologically important species at high Arctic latitudes, and to compare gene expression according to latitude and sea ice-coverage.
    Electronic ISSN: 2052-4463
    Topics: Nature of Science, Research, Systems of Higher Education, Museum Science
    Published by Springer Nature
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  • 3
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    Circadian Clock Involvement in Zooplankton Diel Vertical Migration (2017)
    Cell Press
    Details
    Publication Date: 2017-07-01
    Print ISSN: 0960-9822
    Electronic ISSN: 1879-0445
    Topics: Biology
    Published by Cell Press
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  • 4
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    Sequences of Taqman® probes/primers for gene expression measurements in Calanus finmarchicus (2018)
    PANGAEA
    In:  Supplement to: Häfker, N Sören; Teschke, Mathias; Last, Kim; Pond, David W; Hüppe, Lukas; Meyer, Bettina (2018): Calanus finmarchicus seasonal cycle and diapause in relation to gene expression, physiology, and endogenous clocks. Limnology and Oceanography, https://doi.org/10.1002/lno.11011
    Details
    Publication Date: 2023-03-16
    Description: The copepod Calanus finmarchicus plays a crucial role in the north Atlantic food web. Its seasonal life cycle involves reproduction and development in surface waters before overwintering in diapause at depth. Although diapause has been studied for more than a century, the factors responsible for the initiation and termination of it are still unclear. Endogenous clocks have been identified as potent tools for photoperiod measurement and seasonal rhythmicity in many terrestrial species, but knowledge of these remains scarce in the marine realm. Focusing on the dominant CV copepodid stage, we sampled a population of C. finmarchicus from a Scottish sea loch to characterize population dynamics, several physiological parameters, and diel and seasonal expression rhythms of 35 genes representing different metabolic pathways, including the circadian clock machinery. This generated a detailed overview of the seasonal cycle of C. finmarchicus including the most extensive field dataset on circadian clock gene expression in a marine species to date. Gene expression patterns revealed distinct gene clusters upregulated at different phases of the copepod's seasonal cycle. While diel clock cycling was restricted to the active spring/summer phase, many clock genes exhibited the highest expression during diapause. Our results provide new insights into diapause on physiological and genetic levels. We suggest that photoperiod, in interaction with internal and external factors (lipid content, temperature, food availability) and the endogenous clock mechanism, plays an important role in the timing of diapause in C. finmarchicus.
    Keywords: AWI_BioOce; Biological Oceanography @ AWI
    Type: Dataset
    Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, 15.5 kBytes
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  • 5
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    Circadian clock involvement in zooplankton diel vertical migration, link to supplementary material (2017)
    PANGAEA
    In:  Supplement to: Häfker, N Sören; Meyer, Bettina; Last, Kim; Pond, David W; Hüppe, Lukas; Teschke, Mathias (2017): Circadian clock involvement in zooplankton diel vertical migration. Current Biology, 27(14), 2194-2201.e3, https://doi.org/10.1016/j.cub.2017.06.025
    Details
    Publication Date: 2023-01-13
    Description: Genetic clocks are a ubiquitous ancient and adaptive mechanism enabling organisms to anticipate environmental rhythms and to regulate behavioral, physiological and behavioral processes accordingly. Whilst terrestrial circadian clocks are well studied and understood, knowledge about the clock systems in marine organisms is still limited. This is particularly true for abundant species displaying large-scale rhythms like diel vertical migration (DVM) that contribute significantly to shaping their respective ecosystems. Here, we describe endogenous and highly rhythmic patterns in the biology of the ecologically important and highly abundant planktic copepod Calanus finmarchicus. This species shows circadian rhythms of DVM, metabolism, and most core circadian clock genes (clock, period1, period2, timeless, cryptochrome2, clockwork orange) in the laboratory. In the field, copepods from shallow water (0-50m) have more robust rhythmic clock gene oscillations than those caught in deeper water (140-50m). Further, peak expressions of clock genes generally occurred at either sunset or sunrise coinciding with peak migration times. Providing one of the first field investigations of clock gene rhythmicity in a marine species this study further couples clock genes measurements with laboratory and field data on DVM. While the mechanistic connection remains elusive, our results imply a high degree of causality between clock gene expression and one of the planet's largest daily migration of biomass. This could increase zooplankton fitness by optimizing the temporal trade-off between feeding and predator avoidance.
    Type: Dataset
    Format: application/zip, 201.7 kBytes
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  • 6
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    Free fatty acids in the digestive system of Antarctic krill measured with GC-MS (2023)
    PANGAEA
    Details
    Publication Date: 2024-01-04
    Description: Antarctic krill, Euphausia superba, is a key species in the Southern Ocean with an immense biomass. Ongoing climate change affects their food availability, habitat and survivability. Therefore, markers documenting changes in this species are important to monitor and discover future issues, also because krill-derived products are manufactured for human consumption. While many studies focus on the analysis of the fatty acid composition after the hydrolysis of lipids, the composition of intact lipids has rarely been evaluated. Krill was caught with a continuous krill pumping system in May of 2021 in the Bransfield Strait and in January and March of 2022 at the South Orkney Islands aboard the commercial krill fishing vessel Antarctic Endurance. The stomach, digestive gland and hind gut were dissected and analysed individually. Samples were extracted with an optimized Bligh&Dyer protocol. Free fatty acids from the digestive system of Antarctic krill, Euphausia superba, were prepared as methyl esters from the total lipid extract and measured via gas chromatography - mass spectrometry. Identification was confirmed with standards and based on retention orders.
    Keywords: ANT_END_KiGuMi_1; ANT_END_KiGuMi_17; ANT_END_KiGuMi_19; ANT_END_KiGuMi_5; ANT_END_LEG_3; ANT_END_LEG2; Antarctic Endurance; Antarctic krill; Antarctic Peninsula; Bransfield Strait; Continous krill pumping system; Date/Time of event; DEPTH, water; Elevation of event; Euphausia superba; Event label; Fatty acid of total lipids; fatty acids; Gas chromatography - Mass spectrometry (GC-MS); Intact phospholipids; Krill, length; Latitude of event; liquid chromatography high-resolution mass spectrometry; Location of event; Longitude of event; Organ; Phosphatidylcholine; Phosphatidylethanolamine; Sample ID; Sex; Southern Ocean; South Orkney Islands; Very long chain polyunsaturated fatty acids
    Type: Dataset
    Format: text/tab-separated-values, 4478 data points
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  • 7
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    Intact phospholipids in the digestive system of Antarctic krill measured with LC-HRMS (2023)
    PANGAEA
    Details
    Publication Date: 2024-01-04
    Description: Antarctic krill, Euphausia superba, is a key species in the Southern Ocean with an immense biomass. Ongoing climate change affects their food availability, habitat and survivability. Therefore, markers documenting changes in this species are important to monitor and discover future issues, also because krill-derived products are manufactured for human consumption. While many studies focus on the analysis of the fatty acid composition after the hydrolysis of lipids, the composition of intact lipids has rarely been evaluated. Krill was caught with a continuous krill pumping system in May of 2021 in the Bransfield Strait and in January and March of 2022 at the South Orkney Islands aboard the commercial krill fishing vessel Antarctic Endurance. The stomach, digestive gland and hind gut were dissected and analysed individually. Samples were extracted with an optimized Bligh&Dyer protocol. Intact phospholipids from the digestive system of Antarctic krill, Euphausia superba, were measured with liquid chromatography - high-resolution mass spectrometry on an Orbitrap mass spectrometer. Identification of intact phospholipids was based on characteristic fragments of the head group in MS2 experiments in positive electrospray ionization mode, while the fatty acid compositions of intact phospholipids were determined by characteristic fragments occurring during MS2 measurements using negative electrospray ionization.
    Keywords: ANT_END_KiGuMi_1; ANT_END_KiGuMi_17; ANT_END_KiGuMi_19; ANT_END_KiGuMi_5; ANT_END_LEG_3; ANT_END_LEG2; Antarctic Endurance; Antarctic krill; Antarctic Peninsula; Bransfield Strait; Continous krill pumping system; Date/Time of event; DEPTH, water; Elevation of event; Euphausia superba; Event label; fatty acids; Intact phospholipids; Krill, length; Latitude of event; liquid chromatography high-resolution mass spectrometry; Liquid chromatography-high resolution mass spectrometry (LC-HRMS) with Orbitrap; Location of event; Longitude of event; Organ; Phosphatidylcholine; Phosphatidylcholine 14:0/17:1; Phosphatidylcholine 14:0/18:1; Phosphatidylcholine 14:0/19:2; Phosphatidylcholine 14:1/16:0; Phosphatidylcholine 15:0/16:1; Phosphatidylcholine 15:1/14:0; Phosphatidylcholine 16:0/13:0; Phosphatidylcholine 16:0/16:1; Phosphatidylcholine 16:0/17:1; Phosphatidylcholine 16:0/17:2; Phosphatidylcholine 16:0/18:1; Phosphatidylcholine 16:0/19:1; Phosphatidylcholine 16:0/20:3; Phosphatidylcholine 16:0/22:5; Phosphatidylcholine 16:0/22:6; Phosphatidylcholine 16:1/13:0; Phosphatidylcholine 16:1/14:0; Phosphatidylcholine 16:1/16:1; Phosphatidylcholine 16:1/17:1; Phosphatidylcholine 16:1/22:1; Phosphatidylcholine 16:4/14:0; Phosphatidylcholine 16:4/16:0; Phosphatidylcholine 18:1/15:0; Phosphatidylcholine 18:1/15:1; Phosphatidylcholine 18:1/17:0; Phosphatidylcholine 18:1/18:1; Phosphatidylcholine 18:1/20:1; Phosphatidylcholine 18:1/20:5; Phosphatidylcholine 18:1/23:1; Phosphatidylcholine 18:1/28:8; Phosphatidylcholine 18:2/15:0; Phosphatidylcholine 18:2/18:1; Phosphatidylcholine 18:3/16:0; Phosphatidylcholine 18:3/22:1; Phosphatidylcholine 18:4/14:0; Phosphatidylcholine 18:4/20:5; Phosphatidylcholine 18:4/22:1; Phosphatidylcholine 18:4/24:1; Phosphatidylcholine 18:4/34:5; Phosphatidylcholine 20:4/19:2; Phosphatidylcholine 20:4/24:1; Phosphatidylcholine 20:5/14:1; Phosphatidylcholine 20:5/16:0; Phosphatidylcholine 20:5/17:0; Phosphatidylcholine 20:5/18:3; Phosphatidylcholine 20:5/19:1; Phosphatidylcholine 20:5/20:1; Phosphatidylcholine 20:5/20:4; Phosphatidylcholine 20:5/20:5; Phosphatidylcholine 20:5/21:1; Phosphatidylcholine 20:5/22:0; Phosphatidylcholine 20:5/22:1; Phosphatidylcholine 20:5/22:6; Phosphatidylcholine 20:5/24:0; Phosphatidylcholine 20:5/24:1; Phosphatidylcholine 20:5/25:1; Phosphatidylcholine 20:5/25:5; Phosphatidylcholine 20:5/26:4; Phosphatidylcholine 20:5/26:6; Phosphatidylcholine 20:5/28:8; Phosphatidylcholine 20:5/32:6; Phosphatidylcholine 20:5/34:5; Phosphatidylcholine 20:5/36:8; Phosphatidylcholine 21:5/16:0; Phosphatidylcholine 21:5/18:1; Phosphatidylcholine 22:1/18:1; Phosphatidylcholine 22:5/17:1; Phosphatidylcholine 22:5/23:1; Phosphatidylcholine 22:6/17:0; Phosphatidylcholine 22:6/18:1; Phosphatidylcholine 22:6/18:3; Phosphatidylcholine 22:6/19:1; Phosphatidylcholine 22:6/19:2; Phosphatidylcholine 22:6/22:6; Phosphatidylcholine 22:6/23:1; Phosphatidylcholine 22:6/24:1; Phosphatidylcholine 22:6/25:5; Phosphatidylcholine 22:6/26:4; Phosphatidylcholine 22:6/26:6; Phosphatidylcholine 22:6/28:8; Phosphatidylcholine 22:6/36:8; Phosphatidylcholine 28:8/20:4; Phosphatidylcholine 28:8/22:1; Phosphatidylcholine 28:8/26:6; Phosphatidylethanolamine; Phosphatidylethanolamine 14:0/20:5; Phosphatidylethanolamine 16:0/20:5; Phosphatidylethanolamine 16:0/22:6; Phosphatidylethanolamine 16:1/16:1; Phosphatidylethanolamine 16:2/16:0; Phosphatidylethanolamine 18:1/14:1; Phosphatidylethanolamine 18:1/16:0; Phosphatidylethanolamine 18:1/16:4; Phosphatidylethanolamine 18:1/17:1; Phosphatidylethanolamine 18:1/18:1; Phosphatidylethanolamine 18:1/20:5; Phosphatidylethanolamine 18:1/22:5; Phosphatidylethanolamine 18:1/22:6; Phosphatidylethanolamine 18:1/28:8; Phosphatidylethanolamine 18:2/14:0; Phosphatidylethanolamine 18:2/18:1; Phosphatidylethanolamine 18:4/16:0; Phosphatidylethanolamine 18:4/16:1; Phosphatidylethanolamine 18:4/20:4; Phosphatidylethanolamine 19:1/22:6; Phosphatidylethanolamine 20:1/18:1; Phosphatidylethanolamine 20:1/20:5; Phosphatidylethanolamine 20:1/22:6; Phosphatidylethanolamine 20:3/16:0; Phosphatidylethanolamine 20:4/14:0; Phosphatidylethanolamine 20:4/18:1; Phosphatidylethanolamine 20:5/14:1; Phosphatidylethanolamine 20:5/18:0; Phosphatidylethanolamine 20:5/18:3; Phosphatidylethanolamine 20:5/20:4; Phosphatidylethanolamine 20:5/20:5; Phosphatidylethanolamine 20:5/22:5; Phosphatidylethanolamine 20:5/22:6; Phosphatidylethanolamine 20:5/26:6; Phosphatidylethanolamine 20:5/28:8; Phosphatidylethanolamine 22:6/12:0; Phosphatidylethanolamine 22:6/16:2; Phosphatidylethanolamine 22:6/18:3; Phosphatidylethanolamine 22:6/20:4; Phosphatidylethanolamine 22:6/22:6; Phosphatidylethanolamine 26:7/18:1; Phosphatidylethanolamine 28:8/16:0; Phosphatidylethanolamine 28:8/22:6; Phosphatidylglycerol 16:0/18:1; Phosphatidylglycerol 16:0/20:2; Phosphatidylglycerol 16:0/20:5; Phosphatidylglycerol 18:1/20:5; Phosphatidylglycerol 20:1/16:0; Phosphatidylglycerol 20:5/20:5; Phosphatidyl-N,N'-dimethylethanolamine 14:0/18:1; Phosphatidyl-N,N'-dimethylethanolamine 16:0/16:1; Phosphatidyl-N,N'-dimethylethanolamine 16:0/18:1; Phosphatidyl-N,N'-dimethylethanolamine 16:0/22:6; Phosphatidyl-N,N'-dimethylethanolamine 18:1/18:1; Phosphatidyl-N,N'-dimethylethanolamine 18:1/20:5; Phosphatidyl-N,N'-dimethylethanolamine 18:1/22:6; Phosphatidyl-N,N'-dimethylethanolamine 20:5/16:0; Phosphatidyl-N,N'-dimethylethanolamine 20:5/18:0; Phosphatidyl-N,N'-dimethylethanolamine 20:5/20:1; Phosphatidyl-N,N'-dimethylethanolamine 20:5/20:5; Phosphatidyl-N,N'-dimethylethanolamine 20:5/22:1; Phosphatidyl-N,N'-dimethylethanolamine 20:5/22:6; Phosphatidyl-N,N'-dimethylethanolamine 20:5/23:1; Phosphatidyl-N,N'-dimethylethanolamine 22:6/22:6; Phosphatidyl-N-methylethanolamine 16:0/20:5; Phosphatidyl-N-methylethanolamine 16:0/22:6; Phosphatidyl-N-methylethanolamine 18:1/20:5; Phosphatidyl-N-methylethanolamine 18:1/22:6; Phosphatidyl-N-methylethanolamine 20:5/20:4; Phosphatidyl-N-methylethanolamine 20:5/20:5; Phosphatidyl-N-methylethanolamine 20:5/22:6; Phosphatidyl-N-methylethanolamine 22:6/22:6; Phosphatidylserine 16:0/20:5; Phosphatidylserine 16:0/22:6; Phosphatidylserine 18:1/20:5; Phosphatidylserine 18:1/22:6; Phosphatidylserine 19:2/20:5; Phosphoinositide 16:0/20:5; Phosphoinositide 16:0/22:5; Phosphoinositide 16:0/22:6; Phosphoinositide 18:1/20:4; Phosphoinositide 18:1/20:5; Phosphoinositide 18:1/21:4; Phosphoinositide 18:1/22:6; Phosphoinositide 18:2/20:5; Phosphoinositide 18:3/20:4; Phosphoinositide 18:3/20:5; Phosphoinositide 20:4/17:0; Phosphoinositide 20:5/15:0; Phosphoinositide 20:5/17:0; Phosphoinositide 20:5/17:1; Phosphoinositide 20:5/18:0; Phosphoinositide 20:5/19:0; Phosphoinositide 21:4/16:0; Phosphoinositide 22:6/15:0; Sample ID; Sex; Southern Ocean; South Orkney Islands; Very long chain polyunsaturated fatty acids
    Type: Dataset
    Format: text/tab-separated-values, 14974 data points
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  • 8
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    Intact phospholipid and fatty acid compositions in the digestive system of Antarctic krill, Euphausia superba, sampled in January, March and May (2023)
    PANGAEA
    Details
    Publication Date: 2024-01-04
    Description: This dataset contains the seasonal composition of intact phospholipids as well as of free fatty acids from the digestive system of Antarctic krill, Euphausia superba. Krill was caught with a continuous krill pumping system in May of 2021 in the Bransfield Strait and in January and March of 2022 at the South Orkney Islands. The stomach, digestive gland and hind gut were dissected and analysed individually. Samples were extracted with an optimized Bligh&Dyer protocol. Intact phospholipids were measured with liquid chromatography - high-resolution mass spectrometry on an Orbitrap mass spectrometer. Identification of intact phospholipids was based on characteristic fragments of the head group in MS2 experiments in positive electrospray ionization mode, while the fatty acid composition of intact phospholipids were determined by characteristic fragments occurring during MS2 measurements with negative electrospray ionization. Free fatty acids from the total lipid extract were measured as methyl esters were via gas chromatography - mass spectrometry and identified with standards and based on their retention order.
    Keywords: Antarctic krill; Antarctic Peninsula; Euphausia superba; fatty acids; Intact phospholipids; liquid chromatography high-resolution mass spectrometry; Phosphatidylcholine; Phosphatidylethanolamine; Southern Ocean; Very long chain polyunsaturated fatty acids
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 9
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    Circadian rhythms in oxygen uptake rates and swimming behaviour of the copepod Calanus finmarchicus (2016)
    In:  EPIC350 p.
    Details
    Publication Date: 2016-06-08
    Description: In the marine environment herbivorous copepods represent an important link between the level of primary production and higher predators. In its main distribution areas of the North Atlantic and subarctic waters, the herbivorous copepod Calanus finmarchicus (Gunnerus, 1765) dominates the zooplankton communities in biomass. As a main prey species for commercially important fish stocks, C. finmarchicus links energy from the basis of marine pelagic food webs to higher trophic levels. C. finmarchicus performs diel vertical migration (DVM), highly synchronized to the diel fluctuations in light (day and night). The normal DVM pattern is characterized by an ascend to the surface at dusk and a descent to deeper layers at dawn. Yet, researchers have not found what the migration directly triggers. Light is supposed to be the most important cue. However, a few studies suggested that a biological clock is involved in DVM. The recent identification of clock genes in C. finmarchicus support the suggestion that an endogenous timing system may be involved in rhythms like DVM in C. finmarchicus. Thus, the aim of this work was to assess the role of light (photoperiod) on DVM and diel metabolic processes in C. finmarchicus and to detect the possible involvement of endogenous rhythmicity in these processes. To test this, laboratory experiments to the diel swimming behaviour and oxygen uptake rates were performed under light/dark (16 h L:8 h D) and constant darkness (DD) conditions, using the CV stage of Calanus finmarchicus. Copepods were sampled from an isolated population in Loch Etive, Scotland. In the laboratory experiments copepods showed a migration behaviour that is highly synchronized to the LD cycle, whereas a damped migration continued under DD conditions. Significant 24-hour oscillations in the vertical distribution were found in the migration experiment during the first day under LD conditions and during all three days under constant darkness. Also an oscillation in oxygen uptake rates was found under DD conditions. Overall, the results stress the importance of light for DVM of C. finmarchicus and suggest the involvement of an endogenous rhythm in diel patterns of vertical migration and metabolic processes. Regarding some limitations especially in respiration measurements, this work may provide a basis for further investigations on the true cause zooplankton DVM, implicating the role of biological clocks.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Thesis , notRev
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  • 10
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    Clock gene oscillation in the copepod Calanus finmarchicus in the Arctic: the effect of latitude and season (2019)
    In:  EPIC3
    Details
    Publication Date: 2020-04-24
    Description: Life evolved under the permanent influence of environmental cycles, the most prominent being the daily light/dark cycle, caused by the earth’s rotation about its axis. As a consequence almost all organisms have developed biological clocks that allow them to anticipate cyclic changes in the environment and thus to adjust their behavior and physiology accordingly. A biological clock has also been identified in the copepod Calanus finmarchicus, where it is thought to underpin diel and seasonal rhythms in behavior and physiology. C. finmarchicus plays a central role in sustaining the food webs of the North Atlantic and Subarctic regions, however, climate change induced latitudinal range shifts have introduced C. finmarchicus into the Arctic region, where it experiences extreme light conditions, with almost constant light throughout the Summer months and constant darkness in Winter. Therefore, this thesis centers on the question whether the C. finmarchichus clock stays functional throughout the High Arctic Summer, when diel fluctuations in light reach a minimum. Net based 24 h samplings have been conducted at two stations along a latitudinal gradient from the southern Barents Sea (74.5 °N, 30 °E) to the Nansen Basin (82.56 °N, 30.85 °E) north of Svalbard, within 9 days of the Summer Solstice 2018. Further, temporal expression patterns of clock genes have been analyzed and the behavioral activity of individual C. finmarchicus has been assessed in onboard laboratory experiments. Results from gene expression analysis show significant rhythmic oscillations in a number of core clock genes in wild caught C. finmarchicus, suggesting a functional and synchronized endogenous clock during periods of minimal fluctuations in light intensity. Further, a period shortening could be observed in several clock genes at the northern station associated with lower diel oscillations in light properties. Results from behavioral experiments indicate overall low rhythmic behavioral activity during Summer in the High Arctic. The findings from this study are further discussed in the context of seasonal timing, concluding that the circadian clock likely stays functional throughout the whole active phase at high latitudes, including periods of Midnight Sun. This may further point out the importance of the circadian clock as a tool to track the progression of the season and help to time seasonal events, which is of fundamental importance for C. finmarchicus to survive in the extreme conditions of the Arctic.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Thesis , notRev
    Format: application/pdf
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