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The availability of suitable prey during the early life of fish may determine recruitment to the adult population. Since larval and juvenile feeding can be highly selective, their preferences for certain prey species and sizes should be considered when estimating the availability of prey. In this study, diet composition (and prey preferences) of 4984 (1366) Faroe Plateau cod (Gadus morhua) larvae and juveniles between 3 and 63 mm sampled on the central Faroe shelf (62°N, 6.8°W) over an 8-year period was investigated. Cod preyed on successively larger food items as they grew. Yolk-sac larvae consumed phytoplankton, copepod eggs and nauplii before the yolk sac was exhausted. Copepod eggs followed by calanoid nauplii were the predominant and preferred food items in the early larval stage. In the late larval stage these were replaced by small to medium sized (0.6–1.2 mm) copepod species mainly Pseudocalanus sp., Acartia sp. and early stage Calanus finmarchicus, of which the two former species appeared most preferred. Temora longicornis was highly abundant in juvenile cod, but the preference for this species was neutral. Positive selection and high abundance of late stage (≥ 1.5 mm) C. finmarchicus was observed in early juveniles, but C. finmarchicus was replaced by decapod larvae in late juveniles. Other abundant prey species such as Oithona sp. and barnacle larvae occurred in varying numbers in the guts, but were generally not positively selected at any stage. Late larval and early juvenile cod appeared to suffer from unfavourable feeding conditions as they fed on smaller prey than what they prefer potentially indicating bottle necks in the feeding at these development stages.

Non-invasive computed tomography (CT) of an adult sand tiger shark Carcharias taurus Rafinesque, 1810 is used to provide an interactive three-dimensional ‘general’ shark (Selachimorpha) anatomy atlas. Given its post-cranial body morphology, the sand tiger shark appeared to be a well-chosen candidate and through comparison of the sand tiger shark with several other representatives of all eight established orders of sharks, we confirm that the relatively large degree of mineralization of the endoskeleton, along with the overall size, makes the sand tiger shark an ideal candidate for skeletal segmentation and construction of a skeletal atlas using conventional CT. This atlas both increases accessibility to the internal morphological features of the sand tiger shark and provides a more generalized overview of the skeletal anatomy of sharks and can aid as a supplement to destructive fresh dissection of specimens in the future and the construction of future skeletal atlases of other less mineralized sharks.

The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this study will support the ongoing research for this particular animal model and provides a new molecular tool to assist biological research in cartilaginous fishes.

Hepatic encephalopathy (HE) is a neuropsychiatric disorder caused by hepatic dysfunction. Numerous studies dictate that ammonia plays an important role in the pathogenesis of HE, and hyperammonemia can lead to alterations in amino acid homeostasis. Glutamine and glycine are both ammoniagenic amino acids that are increased in liver failure. Modulating the levels of glutamine and glycine has shown to reduce ammonia concentration in hyperammonemia. Ornithine Phenylacetate (OP) has consistently been shown to reduce arterial ammonia levels in liver failure by modulating glutamine levels. In addition to this, OP has also been found to modulate glycine concentration providing an additional ammonia removing effect. Data support that glycine also serves an important role in N-methyl D-aspartate (NMDA) receptor mediated neurotransmission in HE. This potential important role for glycine in the pathogenesis of HE merits further investigations.

Alterations in interorgan metabolism of ammonia play an important role in the onset of hyperammonemia in liver failure. Glutamine synthetase (GS) in muscle is an important target for ammonia removal strategies in hyperammonemia. Ornithine Phenylacetate (OP) is hypothesized to remove ammonia by providing glutamate as a substrate for increased GS activity and hence glutamine production. The newly generated glutamine conjugates with phenylacetate forming phenylacetylglutamine which can be excreted in the urine, providing an excretion pathway for ammonia. We have also shown that OP targets glycine metabolism, providing an additional ammonia reducing effect.

Recruitment to the Faroe Plateau cod (Gadus morhua) stock (62°N, 6.8°W) is highly variable between years, and availability of suitable prey during the early life stages may determine the year class strength. Here we first investigate interannual variability in recruitment (1983–2017) of cod based on survey data and data from stock assessments. Positive relationships between the spawning stock biomass and larval abundance and between juvenile abundance and recruitment at year 1 were detected. However, the relationship between larval abundance and juvenile abundance was not statistically significant, indicating variable survival during the larval/early juvenile stages. We then investigated if food availability at the larval and early juvenile stages could explain the variability in recruitment using an 8-year long time series of larval and juvenile gut content. Feeding at the early larval stage, present during the pre-bloom, was relatively stable between years. However, large interannual variability in feeding at the early juvenile stage was detected. When juvenile survival and mean length were high, juveniles clearly had less food in their guts. This contradiction is suggested to be due to intense grazing pressure on the zooplankton at high juvenile abundances. However, years with high larval survival coincided with years when the phytoplankton spring bloom was early and intense, suggesting that production of suitable prey during the larval stages determines larval growth and survival and that this production is dependent on the phytoplankton spring bloom characteristics.

Non-invasive computed tomography (CT) of an adult sand tiger shark Carcharias taurus Rafinesque, 1810 is used to provide an interactive three-dimensional 'general' shark (Selachimorpha) anatomy atlas. Given its post-cranial body morphology the sand tiger shark appeared to be a well-chosen candidate and through comparison of the sand tiger shark with several other representatives of all eight established orders of sharks, we confirm that the relatively large degree of mineralization of the endoskeleton, along with the overall size, makes the sand tiger shark an ideal candidate for skeletal segmentation and construction of a skeletal atlas using conventional CT. This atlas both increases accessibility to the internal morphological features of the sand tiger shark and provides a more generalized overview of the skeletal anatomy of sharks and can aid as a supplement to destructive fresh dissection of specimens in the future and the construction of future skeletal atlases of other less mineralized sharks.

The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads were assembled with the Trinity de novo assembler both within each tissue and across all tissues combined resulting in 362,690 transcripts in the combined assembly which represent 289,515 Trinity genes. BUSCO analysis determined a level of 87% completeness for the combined transcriptome. In total, 123,110 proteins were predicted of which 78,679 and 83,164 had significant hits against the SwissProt and Uniref90 protein databases, respectively. Additionally, 61,215 proteins aligned to known protein domains, 7,208 carried a signal peptide and 15,971 possessed at least one transmembrane region. Based on the annotation, 81,582 transcripts were assigned to gene ontology terms and 42,078 belong to known clusters of orthologous groups (eggNOG). To demonstrate the value of our molecular resource, we show that the improved transcriptome data enhances the current possibilities of osmoregulation research in spiny dogfish by utilizing the novel gene and protein annotations to investigate a set of genes involved in urea synthesis and urea, ammonia and water transport, all of them crucial in osmoregulation. We describe the presence of different gene copies and isoforms of key enzymes involved in this process, including arginases and transporters of urea and ammonia, for which sequence information is currently absent in the databases for this model species. The transcriptome assemblies and the derived annotations generated in this study will support the ongoing research for this particular animal model and provides a new molecular tool to assist biological research in cartilaginous fishes.