Photoperiodic control of smoltification
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34224 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3503560.fastq.gz | Fastqsanger.gz | |||
| ERR3503570.fastq.gz | Fastqsanger.gz | |||
| ERR3503580.fastq.gz | Fastqsanger.gz | |||
| ERR3503590.fastq.gz | Fastqsanger.gz | |||
| ERR3503600.fastq.gz | Fastqsanger.gz |
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Project description:This experiment is intended to provide information about transcriptional changes in the gill of Atlantic salmon during smoltification, in comparison with juvenile salmon not given the appropriate photoperiodic stimuli. Also, transcriptional changes due to osmotic stress (24H salt water challenged) will be recorded. This to better understand the transformation of the gill from a fresh water-type to a salt water-type, and possibly identify novel and important genes that are dependent upon a specific photoperiodic history for their expression. Additionally the data can be used to observe the shift in salt water response as the juvenile salmon goes through smoltification. Experimental workflow: All fish started on 24H light (LL), after one week, half of the fish were moved to short photoperiod (8:16, SP). The rest remained on LL throughout. After eight weeks, half of the fish on short photoperiod were moved back onto 24H light (SPLL). Remaining fish continued under 8:16. After another eight weeks the experiment was ended. Fish were sampled on days 0, 32, 53, 68, 89 and 110. On each sampling occasion fish were sampled directly from fresh water (FW), and from a 24H salt water (SW) stay, transferred the previous day. Weight and length was noted. Gill tissue was the taken and placed in RNAlater. Additionally plasma for measuring hypoosmoregulatory capacity was taken.
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Project description:Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic responses at the protein level, we quantified the proteome of the model plant Arabidopsis thaliana by mass spectrometry across four photoperiods. This revealed coordinated changes of abundance in the proteins of photosynthesis, primary metabolism and secondary metabolic processes such as pigment biosynthesis, consistent with higher metabolic activity in long photoperiods. Higher translation rates during the day than during the night likely contribute to these changes, but rhythmic RNA profiles will alter their effects. Photoperiodic control of protein levels might be greatest if high translation rates only coincide with high transcript levels in some photoperiods. We term this mechanism ‘translational coincidence’, mathematically model its components, and demonstrate its effect on the Arabidopsis proteome. Datasets from a green alga and a cyanobacterium suggest that this mechanism is general, contributing to the seasonal control of the proteome in many phototrophic organisms, and favouring RNA rhythms even for stable proteins.
2018-02-27 | PXD006848 | Pride
Project description:Atlantic salmon (Salmo salar) move from fresh- to seawater environments following a seasonally timed preparative transition called smoltification, which takes place under photoperiodic control in the freshwater environment. In masu salmon (Oncorhynchus masou), coordination of photoperiodic sexual maturation is proposed to involve in a fish-specific circumventricular organ, the saccus vasculosus (SV), through its intrinsic opsin-based light sensitivity, thyrotrophin secretion and modulation of deiodinase activity (TSH-DIO cascade). The saccus vasculosus is a highly vascularized structure located on the ventral side of the hypothalamus and its interface between the blood and cerebrospinal fluid also hints at a role in ionic balance of the cerebrospinal fluid (CSF). Both the potential photoperiodic and ionic functions of the SV led us to perform transcriptome analysis of the SV in smoltification in Atlantic salmon. Our data show that SV response to seawater exposure is highly dependent on photoperiodic history and identifies ependymin as a major secretory output of the SV, consistent with a role in control of CSF composition. Conversely, we could not detect crucial elements of the opsin-TSH-DIO cascade suggesting that the photoperiodic history-dependence of the SV to seawater exposure is unlikely to stem from SV-intrinsic responses to photoperiod.
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Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate a transcriptome data from livers throughout smoltification and after seawater transfer. In this experiment two groups of Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the experiment group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. The second control group received constant light throughout the experiment. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
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Project description:The anadromous Atlantic salmon undergo preparatory physiological transformations before seawater entry, referred to as smoltification. Little is known about the photoperiod-influence and genome regulatory processes driving smoltification such as the large scale changes in lipid metabolism and energy homeostasis in the developing smolt liver. To shed light on this, we performed a smoltification trial using contrasting photoperiod regimes and generate ATAC-seq data from livers throughout smoltification and after seawater transfer to assess the differences in chromatin accessibility. In this experiment Atlantic salmon were reared for a total of 46 weeks from the parr stage, through smoltification, and seawater transfer. After 21 week from first feeding, the group was given artificial winter photoperiod (8 hours light, 16 hours dark) for 8 weeks to induce smoltification before returning to constant light. Liver tissue was sampled from individuals first at week 1, 21 weeks after first feeding, then again at week 10, after the winter period, at week 19, after the expected smoltification time, and lastly at week 25, after transfer to seawater.
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Project description:In order to identify genes specifically involved in the photoperiodic control of the mobilisation programme for starch reserve in Arabidopsis thaliana transcription profiling was performed on the following genotypes Columbia wild type (Col-0), CO overexpressor (35S::CO), CO muntant (co-10), GBSSI mutant (gbs-1), aps1 mutant (aps1) and Columbia with sucrose. The different Arabidopsis thaliana genotype seedlings were cultivated in long day conditions (16 h day/ 8 h dark) at 22 C in controlled environment cabinets for two weeks. Samples were collected at ZT 4, immediately frozen in liquid nitrogen and processed.
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