Observations of two deep-sea chimaeroids in Icelandic waters.

Long-term survey time series repeated occurrence of the deep-sea chimaeroid species small-eyed rabbitfish Hydrolagus affinis and large-eyed rabbitfish H. mirabilis have been observed at same but few locations in Icelandic waters over 23 years. For H. affinis the catch at one specific station has consisted almost exclusively of mature males over the time period. Identification of potential aggregation locations is of vital importance to natural resource management because such aggregation may render these species vulnerable to potential fishing activities.

The effect of growth rate on otolith-based discrimination of cod (Gadus morhua) ecotypes.

Otolith shape has previously been used to identify ecotypes within the Icelandic cod (Gadus morhua) stock, using DST profiles to validate the results. Fish otolith shape variation has repeatedly been found to be largely determined by growth rate. To examine the effect of growth rate on the relationship between otolith shape and cod ecotypes (using the Pan I genotype as a proxy for ecotype), 826 archived sagittal otoliths collected over a 58 year sampling period were retrieved, the individual growth rate calculated, and otolith shape described using both Normalized Elliptic Fourier transform and Discrete Wavelet transform. Discriminant functions of otolith shape successfully classified ecotype, whether using Fourier or Wavelet descriptors, but only when excluding a heterozygous genotype from the analysis. The otolith shape variability of this genotype lowered the classification success, while otolith shape, in turn, was significantly affected by growth rate and cohort. Growth rate differences previously reported for the ecotypes were present, but were less marked than expected and indeed, growth rate variance attributable to ecotype identity was dwarfed by cohort- and location-related variance in growth. Such a strong effect of growth rate suggests that cod ecotype discrimination based on otolith shape is sensitive to both temporal and spatial variations in growth, which can mask the effect of ecotype-related growth rate differences on otolith shape.

The microbiome of deep-sea fish reveals new microbial species and a sparsity of antibiotic resistance genes.

Adaptation to life in the deep-sea can be dramatic, with fish displaying behaviors and appearances unlike those seen in any other aquatic habitat. However, the extent of which adaptations may have developed at a microbial scale is not as clear. Shotgun metagenomic sequencing of the intestinal microbiome of 32 species of deep-sea fish from across the Atlantic Ocean revealed that many of the associated microbes differ extensively from those previously identified in reference databases. 111 individual metagenome-assembled genomes (MAGs) were constructed representing individual microbial species from the microbiomes of these fish, many of which are potentially novel bacterial taxa and provide a window into the microbial diversity in this underexplored environment. These MAGs also demonstrate how these microbes have adapted to deep-sea life by encoding a greater capacity for several cellular processes such as protein folding and DNA replication that can be inhibited by high pressure. Another intriguing feature was the almost complete lack of genes responsible for acquired resistance to known antibiotics in many of the samples. This highlights that deep-sea fish microbiomes may represent one of few animal-associated microbiomes with little influence from human activity. The ability of the microbes in these samples to bioluminesce is lower than expected given predictions that this trait has an important role in their life cycle at these depths. The study highlights the uniqueness, complexity and adaptation of microbial communities living in one of the largest and harshest environments on Earth.

Requirement for the RIIbeta isoform of PKA, but not calcium-stimulated adenylyl cyclase, in visual cortical plasticity.

The cAMP-dependent protein kinase (PKA) signaling pathway plays a key role in visual cortical plasticity. Inhibitors that block activation of all PKA regulatory subunits (RIalpha,RIbeta, RIIalpha, RIIbeta) abolish long-term potentiation (LTP) and long-term depression (LTD) in vitro and ocular dominance plasticity (ODP) in vivo. The details of this signaling cascade, however, including the source of PKA signals and which PKA subunits are involved, are unknown. To investigate these issues we have examined LTP, LTD, and ODP in knock-out mice lacking either the two cortically expressed Ca2+-stimulated adenylyl cyclases (AC1 and AC8) or the predominant neocortical subunit of PKA (RIIbeta). Here we show that plasticity remains intact in AC1/AC8-/- mice, whereas ODP and LTD, but not LTP, are absent in RIIbeta-/- mice. We conclude that (1) plasticity in the visual cortex does not require the activity of known Ca2+-stimulated adenylyl cyclases, (2) the PKA dependence of ODP and LTD, but not LTP, is mediated by RIIbeta-PKA, and (3) multiple isoforms of PKA contribute to LTD.

A new way to rapidly create functional, fluorescent fusion proteins: random insertion of GFP with an in vitro transposition reaction.

BACKGROUND: The jellyfish green fluorescent protein (GFP) can be inserted into the middle of another protein to produce a functional, fluorescent fusion protein. Finding permissive sites for insertion, however, can be difficult. Here we describe a transposon-based approach for rapidly creating libraries of GFP fusion proteins. RESULTS: We tested our approach on the glutamate receptor subunit, GluR1, and the G protein subunit, alphas. All of the in-frame GFP insertions produced a fluorescent protein, consistent with the idea that GFP will fold and form a fluorophore when inserted into virtually any domain of another protein. Some of the proteins retained their signaling function, and the random nature of the transposition process revealed permissive sites for insertion that would not have been predicted on the basis of structural or functional models of how that protein works. CONCLUSION: This technique should greatly speed the discovery of functional fusion proteins, genetically encodable sensors, and optimized fluorescence resonance energy transfer pairs.

Historical changes in genotypic frequencies at the Pantophysin locus in Atlantic cod (Gadus morhua) in Icelandic waters: evidence of fisheries-induced selection?

The intense fishing mortality imposed on Atlantic cod in Icelandic waters during recent decades has resulted in marked changes in stock abundance, as well as in age and size composition. Using a molecular marker known to be under selection (Pan I) along with a suite of six neutral microsatellite loci, we analysed an archived data set and revealed evidence of distinct temporal changes in the frequencies of genotypes at the Pan I locus among spawning Icelandic cod, collected between 1948 and 2002, a period characterized by high fishing pressure. Concurrently, temporal stability in the composition of the microsatellite loci was established within the same data set. The frequency of the Pan I(BB) genotype decreased over a period of six decades, concomitant with considerable spatial and technical changes in fishing effort that resulted in the disappearance of older individuals from the fishable stock. Consequently, these changes have likely led to a change in the genotype frequencies at this locus in the spawning stock of Icelandic cod. The study highlights the value of molecular genetic approaches that combine functional and neutral markers examined in the same set of individuals for investigations of the selective effects of harvesting and reiterates the need for an evolutionary dimension to fisheries management.

Are vertical behaviour patterns related to the pantophysin locus in the Atlantic cod (Gadus morhua L.)?

Throughout their geographic distribution, marine fish species often form subpopulations with limited connectivity, among which individuals display a variety of migratory behaviours. Fish behaviour experiments using Data Storage Tags (DSTs) have been useful to define the natural movement of individuals. In Icelandic waters, such experiments have indicated the presence of two distinct behaviour types of the Atlantic cod Gadus morhua, related to vertical migrations and habitat choice in feeding migrations. Some individuals have been shown to stay most of the time in shallow waters characterised by the seasonal trend in temperature for the shelf waters, while other migrate to deeper and colder waters where most of them forage in temperature fronts characterized by highly variable temperatures. The analysis of the pantophysin locus (Pan I) of the same individuals revealed that individuals carrying the Pan I AA genotype are likely to display a shallow water feeding migrations while individuals carrying the Pan I BB genotype preferred deeper waters and forage near thermal fronts. The heterozygote exhibited both type of behaviours. This study therefore suggests that further research need to be done on the pantophysin locus and its potential effects on cod phenotypes to assess the potential relationship between this locus and the behavioural types described.