Recent trends in the abundance of plaice Pleuronectes platessa and cod Gadus morhua in shallow coastal waters of the Northeastern Atlantic continental shelf – a review

Shallow, near-shore water habitats on the continental shelf of the Northeast Atlantic have been productive fishing areas in the past. Here, we review the present knowledge about (i) recent trends in the abundance of plaice and cod in these habitats and (ii) hypotheses regarding the factors responsible for any trends. At present, only a few studies exist on the trends of abundance of plaice or cod, namely from the Bay of Biscay, the North Sea and the Skagerrak/Kattegat. They suggest a declining abundance in coastal, shallow areas and – at least for plaice – a latitudinal gradient with an erosion of the southern distribution boundary in the Bay of Biscay and deepening of stocks in the North Sea. In contrast, no trend in shallow water abundance of plaice similar to a decline in deep-water stocks during the 1970s and their slow recovery during the 2000s is apparent in the Skagerrak/Kattegat. Although shallow habitats fundamentally differ from deeper areas by the prevalence of juvenile stages, the declining trends coincide with decreasing abundance/landings and spatial stock relocations in the deeper areas. Whether this indicates a common trend pointing at connectivity between shallow and deep water remains open. Fundamental differences exist in the suggested causes of the trends in different geographical areas. High fishing pressure together with low local recruitment apparently prevents the recovery of overexploited plaice and cod stocks in the Skagerrak/Kattegat. In contrast, the responses of juveniles and adult fish to increasing seawater temperature are the main hypotheses for changes in distribution and abundance of both fish species in the North Sea/Bay of Biscay. However, temperature alone cannot explain the observed decline of fish in coastal areas, and the causes may be more complex, involving nutrient loading, primary productivity or food availability, although at present, knowledge of these factors is insufficient.     

Identification of Rabbit Oviductal Fluid Proteins Involved in Pre‐Fertilization Processes by Quantitative Proteomics

Oviductal fluid (ODF) proteins modulate and support reproductive processes in the oviduct. In the present study, proteins involved in the biological events that precede fertilization have been identified in the rabbit ODF proteome, isolated from the ampulla and isthmus of the oviduct at different time points within 8 h after intrauterine insemination. A workflow is used that integrates lectin affinity capture with stable‐isotope dimethyl labeling prior to nanoLC‐MS/MS analysis. In total, over 400 ODF proteins, including 214 lectin enriched glycoproteins, are identified and quantified. Selected data are validated by Western blot analysis. Spatiotemporal alterations in the abundance of ODF proteins in response to insemination are detected by global analysis. A subset of 63 potentially biologically relevant ODF proteins is identified, including extracellular matrix components, chaperones, oxidoreductases, and immunity proteins. Functional enrichment analysis reveals an altered peptidase regulator activity upon insemination. In addition to protein identification and abundance changes, N‐glycopeptide analysis further identifies 281 glycosites on 199 proteins. Taken together, these results show, for the first time, the evolving oviductal milieu early upon insemination. The identified proteins are likely those that modulate in vitro processes, including spermatozoa function.     

Sectioned or whole otoliths? A global review of hard structure preparation techniques used in ageing sparid fishes

Reviews in Fish Biology and Fisheries - While otoliths are considered the most reliable structure to accurately age fish, a variety of otolith preparation techniques are available, which have...     

Redirecting the lipid metabolism of the yeast Starmerella bombicola from glycolipid to fatty acid production

Journal of Industrial Microbiology & Biotechnology - Free fatty acids are basic oleochemicals implemented in a range of applications including surfactants, lubricants, paints, plastics, and...     

Purification and properties of NAD(P)-independent polyol dehydrogenase complex from the plasma membrane of Gluconobacter oxydans

Gluconobacter oxydans rapidly oxidizes many different polyhydroxy alcohols (polyols). Polyol oxidations are catalyzed by constitutively synthesized membrane-bound dehydrogenases directly linked to the electron transport chain. A polyol-oxidizing enzyme was isolated from the membranes of G. oxydans and tested for its ability to oxidize various substrates. The enzyme was composed of three subunits: a 67 kDa catalytic unit, a 46 kDa c-type cytochrome, and a 15 kDa subunit. The enzyme oxidized compounds containing three or more hydroxyl groups but did not oxidize mono-, di-, or cyclic alcohols; aldehydes; carboxylic acids; or mono- or di-saccharides. Therefore, we propose this enzyme be considered a polyol dehydrogenase.     

Effects of population size and mutation rate on the evolution of mutational robustness

It is often assumed that the efficiency of selection for mutational robustness would be proportional to mutation rate and population size, thus being inefficient in small populations. However, Krakauer and Plotkin (2002) hypothesized that selection in small populations would favor robustness mechanisms, such as redundancy, that mask the effect of deleterious mutations. In large populations, by contrast, selection is more effective at removing deleterious mutants and fitness would be improved by eliminating mechanisms that mask the effect of deleterious mutations and thus impede their removal. Here, we test whether these predictions are supported in experiments with evolving populations of digital organisms. Digital organisms are self-replicating programs that inhabit a virtual world inside a computer. Like their organic counterparts, digital organisms mutate, compete, evolve, and adapt by natural selection to their environment. In this study, 160 populations evolved at different combinations of mutation rate and population size. After 10(4) generations, we measured the mutational robustness of the most abundant genotype in each population. Mutational robustness tended to increase with mutation rate and to decline with population size, although the dependence with population size was in part mediated by a negative relationship between fitness and robustness. These results are independent of whether genomes were constrained to their original length or allowed to change in size.     

Thermodynamics of neutral protein evolution

Naturally evolving proteins gradually accumulate mutations while continuing to fold to stable structures. This process of neutral evolution is an important mode of genetic change and forms the basis for the molecular clock. We present a mathematical theory that predicts the number of accumulated mutations, the index of dispersion, and the distribution of stabilities in an evolving protein population from knowledge of the stability effects (delta deltaG values) for single mutations. Our theory quantitatively describes how neutral evolution leads to marginally stable proteins and provides formulas for calculating how fluctuations in stability can overdisperse the molecular clock. It also shows that the structural influences on the rate of sequence evolution observed in earlier simulations can be calculated using just the single-mutation delta deltaG values. We consider both the case when the product of the population size and mutation rate is small and the case when this product is large, and show that in the latter case the proteins evolve excess mutational robustness that is manifested by extra stability and an increase in the rate of sequence evolution. All our theoretical predictions are confirmed by simulations with lattice proteins. Our work provides a mathematical foundation for understanding how protein biophysics shapes the process of evolution.     

Heregulin-induced epigenetic regulation of the utrophin-A promoter

Utrophin is the autosomal homolog of dystrophin, the product of the Duchenne's muscular dystrophy (DMD) locus. Utrophin is of therapeutic interest since its over-expression can compensate dystrophin's absence. Utrophin is enriched at neuromuscular junctions due to heregulin-mediated utrophin-A promoter activation. We demonstrate that heregulin activated MSK1/2 and phosphorylated histone H3 at serine 10 in cultured C2C12 muscle cells, in an ERK-dependent manner. MSK1/2 inhibition suppressed heregulin-mediated utrophin-A activation. MSK1 over-expression potentiated heregulin-mediated utrophin-A activation and chromatin remodeling at the utrophin-A promoter. These results identify MSK1/2 as key effectors modulating utrophin-A expression as well as identify novel targets for DMD therapy.     

Effects of two weeks' mandatory snack consumption on energy intake and energy balance

Objective: Our goal was to compare the effects of mandatory consumption of commercial snack products (CSPs) on energy intakes and energy balance in free‐living adults and to assess the interaction between habitual level of CSP consumption and the interventions. Research Methods and Procedures: Four groups of 18 subjects (lean and overweight, males and females) were studied using a crossover design. Subjects consumed one type of CSP (high‐carbohydrate, high‐fat, or mixed composition) at three manipulations of energy 0 MJ (control), 1.5 MJ (low‐energy), and 3.0 MJ (high‐energy) each day during three 14‐day interventions. The study design was parallel for type of CSP (macronutrient composition) and within‐subjects for energy level. Subjects self‐recorded food intakes between Days 8 and 14, and body weights were investigator‐recorded on Days 1, 8, and 15 of each intervention period. Daily energy expenditure was estimated by heart rate monitoring. Results: Daily energy intakes increased from 10.4 MJ (control) to 11.1 MJ (low‐energy) and 11.5 MJ (high‐energy) (p < 0.001), resulting in a trend (not significant) for body weight gain. Energy balance was more positive when subjects were not recording their food intakes than when they were (p < 0.001). There was a trend (not significant) for greater increases in energy intake with increasing fat content, and energy density, of the interventions. Frequent CSP consumers compensated more for the interventions than did infrequent CSP consumers (R² = 0.125, p = 0.003). Discussion: Subjects partially compensated for energy when supplemented with CSPs over 14‐day periods, although this was insufficient to prevent some increase in energy balance. The level of compensation correlated with habitual energy intake from CSPs.