Mid and hindgut transcriptome profiling analysis of Atlantic salmon (Salmon salar) under unpredictable chronic stress

The intestinal epithelium is a selectively permeable barrier for nutrients, electrolytes and water, while maintaining effective protection against pathogens. Combinations of stressors throughout an animal's life, especially in agriculture and aquaculture settings, may affect the regular operativity of this organ with negative consequences for animal welfare. In the current study, we report the effects of a three-week unpredictable chronic stress (UCS) period on the intestinal morphology and transcriptome response of Atlantic salmon (Salmon salar) parr midgut and hindgut. Midgut and hindgut from both control and UCS fish were collected for histology and RNA-sequencing analysis to identify respective changes in the membrane structures and putative genes and pathways responding to UCS. Histological analysis did not show any significant effect on morphometric parameters. In the midgut, 1030 genes were differentially expressed following UCS, resulting in 279 genes which were involved in 13 metabolic pathways, including tissue repair pathways. In the hindgut, following UCS, 591 differentially expressed genes were detected with 426 downregulated and 165 upregulated. A total of 53 genes were related to three pathways. Downregulated genes include cellular senescence pathways, p53 signalling and cytokine–cytokine receptor pathways. The overall results corroborate that salmon parr were at least partly habituating to the UCS treatment. In midgut, the main upregulation was related to cell growth and repair, while in the hindgut there were indications of the activated apoptotic pathway, reduced cell repair and inhibited immune/anti-inflammatory capacity. This may be the trade-off between habituating to UCS and health resilience. This study suggests possible integrated genetic regulatory mechanisms that are tuned when farmed Atlantic salmon parr attempt to cope with UCS.publishedVersio

The β-oxidation pathway is downregulated during diapause termination in Calanus copepods

Calanus copepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist of C. finmarchicus. However, the identification of C. glacialis in some samples underlines the need for performing molecular analyses to reliably identify Calanus species. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.publishedVersio

Montana Kaimin, August 28, 2008

Student newspaper of the University of Montana, Missoula.https://scholarworks.umt.edu/studentnewspaper/6186/thumbnail.jp

Assessing the Value of a Citizen Science Approach for Ctenophore Identification

During the era of biodiversity loss, a complete species census and understanding where the different species occur is of high priority. Even though this knowledge has increased tremendously, mainly with expanded use of integrated taxonomic identification, there are groups where our knowledge is very limited, both in terms of diversity and distribution. Ctenophores are such a group. Due to a lack of identification literature, damage to specimens during net sampling and sample processing, difficulties with preservation and a considerably undescribed diversity within the phylum, this group is often hard to work with. A citizen science approach was applied during a mapping campaign on ctenophore diversity along the Norwegian coast in order to have a broad geographical coverage. This was achieved by a collaboration with five diving clubs along a south-north geographical gradient that were briefly introduced to ctenophore taxonomy and ecology and sampling techniques using Whatman® FTA® Cards. The data collected by the participating divers gave a broad spatial coverage and provided information on ctenophore diversity in these regions. The use of FTA® Cards in the sampling allowed successful species and genus level identification using DNA barcodes. However, small obstacles such as accurate morphological species identification and labor-intensive issues were identified that can impede the use of large-scale citizen science approaches to map ctenophore diversity and thus recommendations for future implications that address these issues are proposed here

Assessing the Value of a Citizen Science Approach for Ctenophore Identification

During the era of biodiversity loss, a complete species census and understanding where the different species occur is of high priority. Even though this knowledge has increased tremendously, mainly with expanded use of integrated taxonomic identification, there are groups where our knowledge is very limited, both in terms of diversity and distribution. Ctenophores are such a group. Due to a lack of identification literature, damage to specimens during net sampling and sample processing, difficulties with preservation and a considerably undescribed diversity within the phylum, this group is often hard to work with. A citizen science approach was applied during a mapping campaign on ctenophore diversity along the Norwegian coast in order to have a broad geographical coverage. This was achieved by a collaboration with five diving clubs along a south-north geographical gradient that were briefly introduced to ctenophore taxonomy and ecology and sampling techniques using Whatman® FTA® Cards. The data collected by the participating divers gave a broad spatial coverage and provided information on ctenophore diversity in these regions. The use of FTA® Cards in the sampling allowed successful species and genus level identification using DNA barcodes. However, small obstacles such as accurate morphological species identification and labor-intensive issues were identified that can impede the use of large-scale citizen science approaches to map ctenophore diversity and thus recommendations for future implications that address these issues are proposed here

Hiding in plain sight - Euplokamis dunlapae (Ctenophora) in Norwegian waters

Cydippid ctenophores of genus Euplokamis have been rarely reported from the north-east Atlantic in the scientific literature. The conspicuous lack of previous records is likely attributable to methodological constraints detrimental to sampling ctenophores, including the use of plankton nets and preservation of samples as well as poor identification literature and a lack of taxonomic expertise on gelatinous zooplankton. Here, we have compiled published and novel records as well as documented diver observations, of Euplokamis spp. in Norwegian waters. Despite scant earlier reports, our data suggest that the genus Euplokamis is widely distributed and relatively common along the entire Norwegian coast, including Svalbard. Euplokamis was recorded from samples taken from several hundred meters depth to surface, from fjords as well as offshore. Most of the observations reported in this study are from the period between April and July, whereas specimens have been found nearly throughout the year. Specimens from Norwegian waters were morphologically most similar to Euplokamis dunlapae, and conservative 18S rDNA sequences of some specimens had a 100% match with an E. dunlapae specimen from Friday Harbor, USA, the type locality for the species. However, the morphological and molecular variation of Euplokamis demonstrates the need for systematic global sampling of multiple individuals of many ctenophore species

Hiding in plain sight—Euplokamis dunlapae (Ctenophora) in Norwegian waters

Cydippid ctenophores of genus Euplokamis have been rarely reported from the north-east Atlantic in the scientific literature. The conspicuous lack of previous records is likely attributable to methodological constraints detrimental to sampling ctenophores, including the use of plankton nets and preservation of samples as well as poor identification literature and a lack of taxonomic expertise on gelatinous zooplankton. Here, we have compiled published and novel records as well as documented diver observations, of Euplokamis spp. in Norwegian waters. Despite scant earlier reports, our data suggest that the genus Euplokamis is widely distributed and relatively common along the entire Norwegian coast, including Svalbard. Euplokamis was recorded from samples taken from several hundred meters depth to surface, from fjords as well as offshore. Most of the observations reported in this study are from the period between April and July, whereas specimens have been found nearly throughout the year. Specimens from Norwegian waters were morphologically most similar to Euplokamis dunlapae, and conservative 18S rDNA sequences of some specimens had a 100% match with an E. dunlapae specimen from Friday Harbor, USA, the type locality for the species. However, the morphological and molecular variation of Euplokamis demonstrates the need for systematic global sampling of multiple individuals of many ctenophore species

Hiding in plain sight - Euplokamis dunlapae (Ctenophora) in Norwegian waters

Cydippid ctenophores of genus Euplokamis have been rarely reported from the north-east Atlantic in the scientific literature. The conspicuous lack of previous records is likely attributable to methodological constraints detrimental to sampling ctenophores, including the use of plankton nets and preservation of samples as well as poor identification literature and a lack of taxonomic expertise on gelatinous zooplankton. Here, we have compiled published and novel records as well as documented diver observations, of Euplokamis spp. in Norwegian waters. Despite scant earlier reports, our data suggest that the genus Euplokamis is widely distributed and relatively common along the entire Norwegian coast, including Svalbard. Euplokamis was recorded from samples taken from several hundred meters depth to surface, from fjords as well as offshore. Most of the observations reported in this study are from the period between April and July, whereas specimens have been found nearly throughout the year. Specimens from Norwegian waters were morphologically most similar to Euplokamis dunlapae, and conservative 18S rDNA sequences of some specimens had a 100% match with an E. dunlapae specimen from Friday Harbor, USA, the type locality for the species. However, the morphological and molecular variation of Euplokamis demonstrates the need for systematic global sampling of multiple individuals of many ctenophore species

Mid and hindgut transcriptome profiling analysis of Atlantic salmon (Salmon salar) under unpredictable chronic stress

The intestinal epithelium is a selectively permeable barrier for nutrients, electrolytes and water, while maintaining effective protection against pathogens. Combinations of stressors throughout an animal's life, especially in agriculture and aquaculture settings, may affect the regular operativity of this organ with negative consequences for animal welfare. In the current study, we report the effects of a three-week unpredictable chronic stress (UCS) period on the intestinal morphology and transcriptome response of Atlantic salmon (Salmon salar) parr midgut and hindgut. Midgut and hindgut from both control and UCS fish were collected for histology and RNA-sequencing analysis to identify respective changes in the membrane structures and putative genes and pathways responding to UCS. Histological analysis did not show any significant effect on morphometric parameters. In the midgut, 1030 genes were differentially expressed following UCS, resulting in 279 genes which were involved in 13 metabolic pathways, including tissue repair pathways. In the hindgut, following UCS, 591 differentially expressed genes were detected with 426 downregulated and 165 upregulated. A total of 53 genes were related to three pathways. Downregulated genes include cellular senescence pathways, p53 signalling and cytokine–cytokine receptor pathways. The overall results corroborate that salmon parr were at least partly habituating to the UCS treatment. In midgut, the main upregulation was related to cell growth and repair, while in the hindgut there were indications of the activated apoptotic pathway, reduced cell repair and inhibited immune/anti-inflammatory capacity. This may be the trade-off between habituating to UCS and health resilience. This study suggests possible integrated genetic regulatory mechanisms that are tuned when farmed Atlantic salmon parr attempt to cope with UC

Mid and hindgut transcriptome profiling analysis of Atlantic salmon (Salmon salar) under unpredictable chronic stress

The intestinal epithelium is a selectively permeable barrier for nutrients, electrolytes and water, while maintaining effective protection against pathogens. Combinations of stressors throughout an animal's life, especially in agriculture and aquaculture settings, may affect the regular operativity of this organ with negative consequences for animal welfare. In the current study, we report the effects of a three-week unpredictable chronic stress (UCS) period on the intestinal morphology and transcriptome response of Atlantic salmon (Salmon salar) parr midgut and hindgut. Midgut and hindgut from both control and UCS fish were collected for histology and RNA-sequencing analysis to identify respective changes in the membrane structures and putative genes and pathways responding to UCS. Histological analysis did not show any significant effect on morphometric parameters. In the midgut, 1030 genes were differentially expressed following UCS, resulting in 279 genes which were involved in 13 metabolic pathways, including tissue repair pathways. In the hindgut, following UCS, 591 differentially expressed genes were detected with 426 downregulated and 165 upregulated. A total of 53 genes were related to three pathways. Downregulated genes include cellular senescence pathways, p53 signalling and cytokine–cytokine receptor pathways. The overall results corroborate that salmon parr were at least partly habituating to the UCS treatment. In midgut, the main upregulation was related to cell growth and repair, while in the hindgut there were indications of the activated apoptotic pathway, reduced cell repair and inhibited immune/anti-inflammatory capacity. This may be the trade-off between habituating to UCS and health resilience. This study suggests possible integrated genetic regulatory mechanisms that are tuned when farmed Atlantic salmon parr attempt to cope with UCS