Monovalent ions modulate the flux through multiple folding pathways of an RNA pseudoknot

The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is important to elucidate the general principles governing their thermodynamics/folding mechanisms. Here, we combine experiments and simulations to examine the folding/unfolding pathways of the VPK pseudoknot, a variant of the Mouse Mammary Tumor Virus (MMTV) PK involved in ribosomal frameshifting. Fluorescent nucleotide analogs (2-aminopurine and pyrrolocytidine) placed at different stem/loop positions in the PK, and laser temperature-jump approaches serve as local probes allowing us to monitor the order of assembly of VPK with two helices with different intrinsic stabilities. The experiments and molecular simulations show that at 50 mM KCl the dominant folding pathway populates only the more stable partially folded hairpin. As the salt concentration is increased a parallel folding pathway emerges, involving the less stable hairpin structure as an alternate intermediate. Notably, the flux between the pathways is modulated by the ionic strength. The findings support the principle that the order of PK structure formation is determined by the relative stabilities of the hairpins, which can be altered by sequence variations or salt concentrations. Our study not only unambiguously demonstrates that PK folds by parallel pathways, but also establishes that quantitative description of RNA self-assembly requires a synergistic combination of experiments and simulations.Comment: Supporting Information include

Family differences on triploid induction, sexual maturation and its contribution to sea cage performance of Atlantic cod, Gadus morhua

Early maturation has been one of the biological bottlenecks of commercializing Atlantic cod culture. To overcome the bottleneck, production of sterile fish through triploidy and other molecular techniques have been suggested and attempted. Although studies have been carried out on triploid performance of Atlantic cod, no studies have been conducted to see the performance of triploid fish at family level. We produced 29 triploid sibling families using standard hydrostatic pressure technique of newly fertilized eggs with parallel, untreated diploid families. Larvae were reared in separate tanks using standard rearing protocols until reaching 20 g and were PIT tagged. PIT tagged juveniles were transferred to sea cages in duplicate. At 34 months post-hatch, all the fish were sampled and body weight, liver weight and gonadal weight were recorded. Results showed that significant family differences exist between diploid and triploid families in gonadal development, especially for the females. Fish from triploid families had significantly smaller gonadosomatic index than fish from diploid families, but diploid families were heavier than the triploid families. Our result highlight the need for considering a parallel strategy for triploid family selection within the conventional diploid breeding program to exploit the existing variation in triploid performance.acceptedVersio

Broodstock exposure to warming and elevated pCO<inf>2</inf> impairs gamete quality and narrows the temperature window of fertilisation in Atlantic cod

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Optimizing intensive culture protocols for Atlantic cod (Gadus morhua) larvae

Larval cod require live prey as food, and prey concentration (PC) and feeding frequency (FF) often afect their growth and survival. Apart from this, water exchange rates/water fow (WER/WF) and water current (WC) also afect the prey resident time in the tank and larval/early juvenile behaviour, respectively. High water current is also known to induce stress in fnfsh larvae, and this stress response is believed to be dependent on larval developmental stage. Thus, we conducted a study to evaluate three larval rearing protocols varying in prey concentration, feeding frequency, and water current/exchange rate. Three protocols were used: low prey concentration (PC), low feeding frequency (FF), and low water fow (protocol 1); medium PC, medium FF, and medium WF (protocol 2); and high PC, high FF, and high WF (protocol 3) (see Table 1). Larvae were sampled periodically for growth and cortisol measurements. Cortisol extraction and radioimmunoassay (RIA) were conducted using methods previously validated for cod larvae. Larvae reared using protocols 2 and 3 were signifcantly bigger and heavier than larvae reared using protocol 1. Rearing protocol had a signifcant efect on the cortisol level in larval cod. Larvae showed a developmental stage-dependent stress response. Protocol 2 had signifcantly higher survival than protocols 1 and 3. Our results indicate that an intermediate PC, FF, and WF (protocol 2) is suitable during cod larval rearing

Ultrasonic imaging as a means of monitoring gonadal development in lumpfish (Cyclopterus lumpus)

The commercial farming of juvenile lumpfish requires monitoring of gonadal development to achieve synchronized production. Conventional methods such as gonadosomatic index (GSI), sex hormone analyses, gonadal histology, endoscopy, and gene expression analyses are costly, invasive, and often involve sacrificing the fish. We assessed the efficiency of ultrasound as a non-invasive method for monitoring gonadal development in lumpfish. Based on ultrasound observations, we categorized the fish into six stages; F0 to F5 for females and M0 to M5 for males, that represented maturity levels from immature to spent. Importantly, the ultrasound gonadal stages aligned with histological gonadal stages. Additionally, ultrasound stages aligned with profiles of GSI, testosterone (T), 11-ketotestosterone, and 17β-estradiol throughout gonadal development including the spawning period. Moreover, these parameters exhibited significant positive correlations with each other reflecting their parallel trends during gonadal development. To minimize the frequency of ultrasound usage and fish handling, we established F3 and M3/M4 as arbitrary thresholds for identifying ripe females and males, respectively. By using these thresholds, the need for regular ultrasound monitoring could be reduced during most of the rearing period. Ultrasound proves to be useful and reliable for monitoring gonadal development in lumpfish, enabling synchronized production of juvenile fish

Northern cod species face spawning habitat losses if global warming exceeds 1.5°C

Source at: http://doi.org/10.1126/sciadv.aas8821 Rapid climate change in the Northeast Atlantic and Arctic poses a threat to some of the world’s largest fish populations. Impacts of warming and acidification may become accessible through mechanism-based risk assessments and projections of future habitat suitability. We show that ocean acidification causes a narrowing of embryonic thermal ranges, which identifies the suitability of spawning habitats as a critical life-history bottleneck for two abundant cod species. Embryonic tolerance ranges linked to climate simulations reveal that ever-increasing CO2 emissions [Representative Concentration Pathway (RCP) 8.5] will deteriorate suitability of present spawning habitat for both Atlantic cod (Gadus morhua) and Polar cod (Boreogadus saida) by 2100. Moderate warming (RCP4.5) may avert dangerous climate impacts on Atlantic cod but still leaves few spawning areas for the more vulnerable Polar cod, which also loses the benefits of an ice-covered ocean. Emissions following RCP2.6, however, support largely unchanged habitat suitability for both species, suggesting that risks are minimized if warming is held “below 2°C, if not 1.5°C,” as pledged by the Paris Agreement

Development of cod farming in Norway: Past and current biological and market status and future prospects and directions

Atlantic cod is a historically abundant species in the North Atlantic region and has contributed to the prosperity of many nations. But a decline in stocks in the last century has prompted to initiate commercial farming of cod in captive conditions. Several approaches have been employed ranging from stock enhancement, capture-based aquaculture and intensive cod farming. However, except for the enhancement efforts which were carried out for almost a century, efforts on other methods were intermittent coinciding with lower quotas. Intensive farming was attempted in Norway, Scotland, Ireland, Canada, Iceland and Faroe Islands in the 2000s. But it was carried out hastily to cash in the demand for cod in the market even though there were many biological knowledge gaps that are required for a successful aquaculture venture. The reasons for the failure of commercial farming in Norway during the 2000s were not only because of limited knowledge of the biology of cod but also the economic meltdown in Europe in 2008. Cod farming came to a halt; however, the Norwegian National Cod Breeding Program (NCBP) initiated in 2003 continued to operate and produced a fifth generation of a domesticated cod in 2019. Efforts to fill the gaps and the selective breeding for better growth and disease resistance within NCBP have improved the quality of the juveniles produced. We will discuss the past efforts and reasons for failure in farming of cod, how the current situation looks and the future direction in terms of cod biology, political atmosphere and market.publishedVersio

Effects of weathered polyethylene microplastic ingestion on sexual maturation, fecundity and egg quality in maturing broodstock Atlantic cod Gadus morhua

Microplastics (MPs) have become a global issue as they are omnipresent in the ocean. Fish ingesting MPs through feed could be affected in their physiological function, e.g., disrupted enzyme production and function, reduction of feeding and reproductive failure. This study assessed the effects of feed containing naturally weathered MPs from the Oslofjord (Norway) on the reproductive physiology of Atlantic cod (Gadus morhua). Farmed cod broodstock were fed either control (C-diet) or feeds containing 1% microplastic (MP-diet) starting nine months prior to spawning, from June until May. No major differences were found between diet groups in overall biometrics or gonad histology. Sex steroid levels (testosterone, 11-ketotestosterone and 17β-estradiol) resulted in expected profiles increasing over time without any significant differences between treatments. Gene expression levels of the steroidogenic enzyme 20β-hydroxysteroid dehydrogenase (20β-hsd) and vitellogenin1 (vtg1) showed significant differences between dietary treatments with lower expression in the control group. This can be a direct effect of MPs, but endocrine disrupting effects of potentially leachable plastic additives cannot be completely ruled out. Thus, these enzymes could be indicators of exposure to contaminants that disrupt sexual maturation by affecting the production of primarily maturation-inducing steroid. Although the concentration of MPs employed in this study may not be high enough to elicit any observable short-term biological effects, the observed gene expression suggests that long-term consequences should be considered caused by an expected increase of MPs in marine environments

Ocean Acidification Effects on Atlantic Cod Larval Survival and Recruitment to the Fished Population

-How fisheries will be impacted by climate change is far from understood. While some fish populations may be able to escape global warming via range shifts, they cannot escape ocean acidification (OA), an inevitable consequence of the dissolution of anthropogenic carbon dioxide (CO2) emissions in marine waters. How ocean acidification affects population dynamics of commercially important fish species is critical for adapting management practices of exploited fish populations. Ocean acidification has been shown to impair fish larvae’s sensory abilities, affect the morphology of otoliths, cause tissue damage and cause behavioural changes. Here, we obtain first experimental mortality estimates for Atlantic cod larvae under OA and incorporate these effects into recruitment models. End-of-century levels of ocean acidification (~1100 μatm according to the IPCC RCP 8.5) resulted in a doubling of daily mortality rates compared to present-day CO2 concentrations during the first 25 days post hatching (dph), a critical phase for population recruitment. These results were consistent under different feeding regimes, stocking densities and in two cod populations (Western Baltic and Barents Sea stock). When mortality data were included into Ricker-type stock-recruitment models, recruitment was reduced to an average of 8 and 24% of current recruitment for the two populations, respectively. Our results highlight the importance of including vulnerable early life stages when addressing effects of climate change on fish stocks

Divergent responses of Atlantic cod to ocean acidification and food limitation

In order to understand the effect of global change on marine fishes, it is imperative to quantify the effects on fundamental parameters such as survival and growth. Larval survival and recruitment of the Atlantic cod (Gadus morhua) were found to be heavily impaired by end-of-century levels of ocean acidification. Here, we analysed larval growth among 35–36 days old surviving larvae, along with organ development and ossification of the skeleton. We combined CO2treatments (ambient: 503 µatm, elevated: 1,179 µatm) with food availability in order to evaluate the effect of energy limitation in addition to the ocean acidification stressor. As expected, larval size (as a proxy for growth) and skeletogenesis were positively affected by high food availability. We found significant interactions between acidification and food availability. Larvae fed ad libitum showed little difference in growth and skeletogenesis due to the CO2 treatment. Larvae under energy limitation were significantly larger and had further developed skeletal structures in the elevated CO2 treatment compared to the ambient CO2 treatment. However, the elevated CO2 group revealed impairments in critically important organs, such as the liver, and had comparatively smaller functional gills indicating a mismatch between size and function. It is therefore likely that individual larvae that had survived acidification treatments will suffer from impairments later during ontogeny. Our study highlights important allocation trade-off between growth and organ development, which is critically important to interpret acidification effects on early life stages of fish