Effects of bottom trawling on fish foraging and feeding

The effects of bottom trawling on benthic invertebrates include reductions of biomass, diversity and body size. These changes may negatively affect prey availability for demersal fishes, potentially leading to reduced food intake, body condition and yield of fishes in chronically trawled areas. Here, the effect of trawling on the prey availability and diet of two commercially important flatfish species, plaice (Pleuronectes platessa) and dab (Limanda limanda), was investigated over a trawling intensity gradient in the Irish Sea. Previous work in this area has shown that trawling negatively affects the condition of plaice but not of dab. This study showed that reductions in local prey availability did not result in reduced feeding of fish. As trawling frequency increased, both fish and prey biomass declined, such that the ratio of fish to prey remained unchanged. Consequently, even at frequently trawled sites with low prey biomass, both plaice and dab maintained constant levels of stomach fullness and gut energy contents. However, dietary shifts in plaice towards energy-poor prey items were evident when prey species were analysed individually. This, together with a potential decrease in foraging efficiency due to low prey densities, was seen as the most plausible cause for the reduced body condition observed. Understanding the relationship between trawling, benthic impacts, fish foraging and resultant body condition is an important step in designing successful mitigation measures for future management strategies in bottom trawl fisheries.     

The Allosteric Regulatory Mechanism of the Escherichia coli MetNI Methionine ATP Binding Cassette (ABC) Transporter

The MetNI methionine importer of Escherichia coli, an ATP binding cassette (ABC) transporter, uses the energy of ATP binding and hydrolysis to catalyze the high affinity uptake of d- and l-methionine. Early in vivo studies showed that the uptake of external methionine is repressed by the level of the internal methionine pool, a phenomenon termed transinhibition. Our understanding of the MetNI mechanism has thus far been limited to a series of crystal structures in an inward-facing conformation. To understand the molecular mechanism of transinhibition, we studied the kinetics of ATP hydrolysis using detergent-solubilized MetNI. We find that transinhibition is due to noncompetitive inhibition by l-methionine, much like a negative feedback loop. Thermodynamic analyses revealed two allosteric methionine binding sites per transporter. This quantitative analysis of transinhibition, the first to our knowledge for a structurally defined transporter, builds upon the previously proposed structurally based model for regulation. This mechanism of regulation at the transporter activity level could be applicable to not only ABC transporters but other types of membrane transporters as well.     

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures.     

In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry

Affinity purification coupled to mass spectrometry provides a reliable method for identifying proteins and their binding partners. In this study we have used Drosophila melanogaster proteins triple tagged with Flag, Strep II, and Yellow fluorescent protein in vivo within affinity pull-down experiments and isolated these proteins in their native complexes from embryos. We describe a pipeline for determining interactomes by Parallel Affinity Capture (iPAC) and show its use by identifying partners of several protein baits with a range of sizes and subcellular locations. This purification protocol employs the different tags in parallel and involves detailed comparison of resulting mass spectrometry data sets, ensuring the interaction lists achieved are of high confidence. We show that this approach identifies known interactors of bait proteins as well as novel interaction partners by comparing data achieved with published interaction data sets. The high confidence in vivo protein data sets presented here add new data to the currently incomplete D. melanogaster interactome. Additionally we report contaminant proteins that are persistent with affinity purifications irrespective of the tagged bait.     

Investigating the status of biological stimuli as objects of attention in multiple object tracking

Background

Humans are able to track multiple simultaneously moving objects. A number of factors have been identified that can influence the ease with which objects can be attended and tracked. Here, we explored the possibility that object tracking abilities may be specialized for tracking biological targets such as people.

Methodology/Principal Findings

We used the Multiple Object Tracking (MOT) paradigm to explore whether the high-level biological status of the targets affects the efficiency of attentional selection and tracking. In Experiment 1, we assessed the tracking of point-light biological motion figures. As controls, we used either the same stimuli or point-light letters, presented in upright, inverted or scrambled configurations. While scrambling significantly affected performance for both letters and point-light figures, there was an effect of inversion restricted to biological motion, inverted figures being harder to track. In Experiment 2, we found that tracking performance was equivalent for natural point-light walkers and ‘moon-walkers’, whose implied direction was incongruent with their actual direction of motion. In Experiment 3, we found higher tracking accuracy for inverted faces compared with upright faces. Thus, there was a double dissociation between inversion effects for biological motion and faces, with no inversion effect for our non-biological stimuli (letters, houses).

Conclusions/Significance

MOT is sensitive to some, but not all naturalistic aspects of biological stimuli. There does not appear to be a highly specialized role for tracking people. However, MOT appears constrained by principles of object segmentation and grouping, where effectively grouped, coherent objects, but not necessarily biological objects, are tracked most successfully.     

KINETICS OF AMMONIUM ASSIMILATION IN TWO SEAWEEDS, ENTEROMORPHA SP. (CHLOROPHYCEAE) AND OSMUNDARIA COLENSOI (RHODOPHYCEAE)

The kinetics of ammonium assimilation were investigated in two seaweeds from northeastern New Zealand, Enteromorpha sp. (Chlorophyceae, Ulvales) and Osmundaria colensoi (Hook. f. et Harvey) R.E. Norris (Rhodophyceae, Ceramiales), with the use of a recently developed method for measuring assimilation. In contrast to ammonium uptake, which was nonsaturable, ammonium assimilation exhibited Michaelis–Menten kinetics in both species. Maximum rates of assimilation (V_max) were 27 and 12 μmol·(g DW)⁻¹·h⁻¹ for Enteromorpha sp. and O. colensoi, respectively, with half-saturation (K_m) constants for assimilation of 18 and 41 μM. At environmentally relevant concentrations, assimilation accounted for all of the ammonium taken up by both species. The maximum rate of assimilation in Enteromorpha sp. resembled very closely that of the ammonium assimilatory enzyme, glutamine synthetase, when activities of the latter were measured in the presence of subsaturating substrate (glutamate and ATP) concentrations. Moreover, the initial rate of glutamine production (measured with HPLC) following ammonium enrichment was almost identical to the rates determined above. The rate of ammonium assimilation was therefore determined by three independent methods, two of which involve in vivo measurements, and it is suggested that the use of assimilation kinetics may be useful when examining the nutrient relations of seaweeds.     

Spectroscopic origin of conformation-sensitive contributions to polysaccharide optical activity: Vacuum-ultraviolet circular dichroism of agarose

The vacuum-uv CD of agarose solid films has been measured to 145 nm and shows a positive band near 180 nm and a larger negative band at around 152 nm. The positive band remains accessible in aqueous solution and has been used to characterize changes in molecular conformation and interaction during the sol–gel transition. The temperature profile of vacuum-uv CD shows sharp, discontinuous changes around the melting and setting points of the gel, which are interpreted in terms of cooperative intermolecular association through double helices, and pronounced hysteresis, which is discussed in terms of helix–helix aggregation.     

The relation between melanocortin 1 receptor (MC1R) variation and the generation of phenotypic diversity in the cutaneous response to ultraviolet radiation

The melanocortin 1 receptor (MC1R) is known to play an important role in determining physiological variation in human pigmentation, and consequently human susceptibility to ultraviolet radiation. A reason for wider interest is that the considerable phenotypic diversity has been in part generated by the effects of gene dosage, and the presence of a large number of mutations at this G-protein coupled receptor that are not functionally equivalent. Thus, a range of mutations at a single receptor locus can lead to a complex range of graded phenotypes.