VECTORS of change in the marine environment: Ecosystem and economic impacts and management implications

Human use of the European marine environment is increasing and diversifying. This is creating new mechanisms for human induced-changes in marine life which need to be understood and quantified as well as the impact of these changes on ecosystems, their structures (e.g. biodiversity) and functioning (e.g. productivity), and the social and economic consequences that arise. The current and emerging pressures are multiple and interacting, arising, for example, from transport, platforms for renewable and nonrenewable energy, exploitation of living and non-living resources, agricultural and industrial discharges, together with wider environmental changes (including climate change). Anticipating the future consequences of these pressures and vectors of change for marine life and of adaptation and mitigation measures (such as the introduction of new technologies and structures, new ballast water practices, ocean and offshore wind energy devices and new fishing strategies) is a prerequisite to the development and implementation of strategies, policies and regulations to manage the marine environment, such as the IMO Convention on ballast water management and the EU Maritime Policy and Marine Strategy Framework Directive

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A

Grip Force Reveals the Context Sensitivity of Language-Induced Motor Activity during “Action Words

Studies demonstrating the involvement of motor brain structures in language processing typically focus on \ud time windows beyond the latencies of lexical-semantic access. Consequently, such studies remain inconclusive regarding whether motor brain structures are recruited directly in language processing or through post-linguistic conceptual imagery. In the present study, we introduce a grip-force sensor that allows online measurements of language-induced motor activity during sentence listening. We use this tool to investigate whether language-induced motor activity remains constant or is modulated in negative, as opposed to affirmative, linguistic contexts. Our findings demonstrate that this simple experimental paradigm can be used to study the online crosstalk between language and the motor systems in an ecological and economical manner. Our data further confirm that the motor brain structures that can be called upon during action word processing are not mandatorily involved; the crosstalk is asymmetrically\ud governed by the linguistic context and not vice versa

Heat in optical tweezers

Laser-induced thermal effects in optically trapped microspheres and single cells have been investigated by Luminescence Thermometry. Thermal spectroscopy has revealed a non-localized temperature distribution around the trap that extends over tens of microns, in agreement with previous theoretical models. Solvent absorption has been identified as the key parameter to determine laser-induced heating, which can be reduced by establishing a continuous fluid flow of the sample. Our experimental results of thermal loading at a variety of wavelengths reveal that an optimum trapping wavelength exists for biological applications close to 820 nm. This has been corroborated by a simultaneous analysis of the spectral dependence of cellular heating and damage in human lymphocytes during optical trapping. Minimum intracellular heating, well below the cytotoxic level (43 °C), has been demonstrated to occur for optical trapping with 820 nm laser radiation, thus avoiding cell damage

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

<p>Abstract</p> <p>Background</p> <p>We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using <it>in silico </it>simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence.</p> <p>Results</p> <p>The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on <it>Arabidopsis</it>. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most.</p> <p>Conclusions</p> <p>BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.</p

Facial expressions depicting compassionate and critical emotions: the development and validation of a new emotional face stimulus set

Attachment with altruistic others requires the ability to appropriately process affiliative and kind facial cues. Yet there is no stimulus set available to investigate such processes. Here, we developed a stimulus set depicting compassionate and critical facial expressions, and validated its effectiveness using well-established visual-probe methodology. In Study 1, 62 participants rated photographs of actors displaying compassionate/kind and critical faces on strength of emotion type. This produced a new stimulus set based on N = 31 actors, whose facial expressions were reliably distinguished as compassionate, critical and neutral. In Study 2, 70 participants completed a visual-probe task measuring attentional orientation to critical and compassionate/kind faces. This revealed that participants lower in self-criticism demonstrated enhanced attention to compassionate/kind faces whereas those higher in self-criticism showed no bias. To sum, the new stimulus set produced interpretable findings using visual-probe methodology and is the first to include higher order, complex positive affect displays

Heisenberg pseudo-exchange and emergent anisotropies in field-driven pinwheel artificial spin ice

Rotating all islands in square artificial spin ice (ASI) uniformly about their centers gives rise to the recently reported pinwheel ASI. At angles around 45∘, the antiferromagnetic ordering changes to ferromagnetic and the magnetic configurations of the system exhibit near degeneracy, making it particularly sensitive to small perturbations. We investigate through micromagnetic modeling the influence of dipolar fields produced by physically extended islands in field-driven magnetization processes in pinwheel arrays and compare the results to hysteresis experiments performed in situ using Lorentz transmission electron microscopy. We find that magnetization end states induce a Heisenberg pseudoexchange interaction that governs both the interisland coupling and the resultant array reversal process. Symmetry reduction gives rise to anisotropies and array-corner mediated avalanche reversals through a cascade of nearest-neighbor (NN) islands. The symmetries of the anisotropy axes are related to those of the geometrical array but are misaligned to the array axes as a result of the correlated interactions between neighboring islands. The NN dipolar coupling is reduced by decreasing the island size and, using this property, we track the transition from the strongly coupled regime towards the pure point dipole one and observe modification of the ferromagnetic array reversal process. Our results shed light on important aspects of the interactions in pinwheel ASI and demonstrate a mechanism by which their properties may be tuned for use in a range of fundamental research and spintronic applications

Letter processing and font information during reading: beyond distinctiveness, where vision meets design

Letter identification is a critical front end of the reading process. In general, conceptualizations of the identification process have emphasized arbitrary sets of distinctive features. However, a richer view of letter processing incorporates principles from the field of type design, including an emphasis on uniformities across letters within a font. The importance of uniformities is supported by a small body of research indicating that consistency of font increases letter identification efficiency. We review design concepts and the relevant literature, with the goal of stimulating further thinking about letter processing during reading

Deception has no acute or residual effect on cycling time trial performance but negatively effects perceptual responses.

Feedback deception is used to explore the importance of expectations on pacing strategy and performance in self-paced exercise. The deception of feedback from a previous performance explores the importance of experience knowledge on exercise behaviour. This study aimed to explore the acute and residual effects of the deception of previous performance speed on perceptual responses and performance in cycling time trials.A parallel-group design.Twenty cyclists were assigned to a control or deception group and performed 16.1km time trials. Following a ride-alone baseline time trial (FBL), participants performed against a virtual avatar representing their FBL performance (PACER), then completed a subsequent ride-alone time trial (SUB). The avatar in the deception group, however, was unknowingly set 2% faster than their FBL.Both groups performed faster in PACER than FBL and SUB (p<0.05), but SUB was not significantly different to FBL. Affect was more negative and Ratings of Perceived Exertion (RPE) were higher in PACER than FBL in the deception group (p<0.05).The presence of a visual pacer acutely facilitated time trial performance, but deceptive feedback had no additional effect on performance. The deception group, however, experienced more negative affect and higher RPE in PACER, whereas these responses were absent in the control group. The performance improvement was not sustained in SUB, suggesting no residual performance effects occurred