A novel approach to using seabed geomorphology as a predictor of habitat use in highly mobile marine predators : implications for ecology and conservation

Department for Business, Energy, and Industrial Strategy (BEIS, formerly DECC) Offshore Energy Strategic Environmental Assessment programme funded the purchase of the tags and their deployment (OESEA-14-47) and supported HMEW (OESEA-20-118). DJFR was supported by NERC National Public Good- National Capability funding to SMRU (NE/R015007/1). MIDC was supported by project EcoSTAR, funded under NERC INSITE Phase II (grant no. NE/T010614/1). Funds for open access publication fees were from the research grants of supervisors at University of St Andrews.Understanding how marine predators find patchily distributed prey resources in a dynamic environment is key to identifying important ecological areas for ecosystem-level conservation management. However, the mechanisms underpinning important foraging areas often result from complex interactions between static and dynamic covariates (e.g. topography and currents). Modelling habitat associations with hydrodynamic processes is rarely useful when attempting to identify and characterise foraging areas across an individual’s foraging range. Investigating the influence of static habitat features on predator behaviour can provide a more tractable baseline understanding of habitat associations, upon which additional complexity can be added. Seabed gradient covariates (e.g. slope and aspect) are often used, yet such metrics are computed at singular user-defined resolutions, and provide limited ecological insight when used in isolation. Instead, categorising the seabed into geomorphological features may provide better characterisation of seabed structure. Here we explore the utility of a pattern recognition algorithm to delineate whole geomorphological features (“geomorphons”) on the seabed (e.g. valleys, ridges, footslopes) from bathymetry data, and examine the influence of geomorphology on marine predator habitat use. We demonstrate the potential application of this approach in a case study, examining the influence of geomorphons on the at-sea behaviour of a highly mobile predator inhabiting shelf seas: the grey seal (Halichoerus grypus). We analyse GPS tracking data from three seals tagged in the southern North Sea, an area with heterogeneous geomorphology. We use hidden Markov models (HMMs) to infer foraging and travelling behaviour and model the effect of different feature types on the probability of switching between states. All three seals showed an increased probability of transitioning from travelling to foraging when encountering slopes, footslopes and hollows, and foraging activity was concentrated at slopes on the fringes of the Dogger Bank. We hypothesise that such features may host prey aggregations, or lead to increased prey capture success. The results suggest the importance of such areas for grey seals in the southern North Sea, a region undergoing rapid and widespread anthropogenic habitat change. This method could be incorporated into future species distribution models to improve estimates of predator distribution, informing conservation management and marine spatial planning.Publisher PDFPeer reviewe

Polymorphism in TGFB1 is associated with worse non-relapse mortality and overall survival after stem cell transplantation with unrelated donors.

Transforming growth factor beta-1, encoded by the TGFB1 gene, is a cytokine that plays a central role in many physiological and pathogenic processes. We have sequenced TGFB1 regulatory region and assigned allelic genotypes in a large cohort of hematopoietic stem cell transplantation patients and donors. In this study, we analyzed 522 unrelated donor-patient pairs and examined the combined effect of all the common polymorphisms in this genomic region. In univariate analysis, we found that patients carrying a specific allele, 'p001', showed significantly reduced overall survival (5-year overall survival 30.7% for p001/ p001 patients vs. 41.6% others; P=0.032) and increased non-relapse mortality (1-year nonrelapse mortality: 39.0% vs. 25.4%; P=0.039) after transplantation. In multivariate analysis, the presence of a p001/ p001 genotype in patients was confirmed as an independent factor for reduced overall survival [hazard ratio=1.53 (1.04-2.24); P=0.031], and increased non-relapse mortality [hazard ratio=1.73 (1.06-2.83); P=0.030]. In functional experiments we found a trend towards a higher percentage of surface transforming growth factor beta-1-positive regulatory T cells after activation when the cells had a p001 allele (P=0.07). Higher or lower production of transforming growth factor beta-1 in the inflammatory context of hematopoietic stem cell transplantation may influence the development of complications in these patients. Findings indicate that TGFB1 genotype could potentially be of use as a prognostic factor in hematopoietic stem cell transplantation risk assessment algorithms

Cluster J Mycobacteriophages: Intron Splicing in Capsid and Tail Genes

Bacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution. © 2013 Pope et al

Reinforcement learning of normative monitoring intensities

Choosing actions within norm-regulated environments involves balancing achieving one’s goals and coping with any penalties for non-compliant behaviour. This choice becomes more complicated in environments where there is uncertainty. In this paper, we address the question of choosing actions in environments where there is uncertainty regarding both the outcomes of agent actions and the intensity of monitoring for norm violations. Our technique assumes no prior knowledge of probabilities over action outcomes or the likelihood of norm violations being detected by employing reinforcement learning to discover both the dynamics of the environment and the effectiveness of the enforcer. Results indicate agents become aware of greater rewards for violations when enforcement is lax, which gradually become less attractive as the enforcement is increased

Comparative transcriptome analysis by RNAseq of necrotic enteritis <i>Clostridium perfringens</i> during <i>in vivo</i> colonization and <i>in vitro</i> conditions

BACKGROUND: Necrotic enteritis (NE) caused by netB-positive type A Clostridium perfringens is an important bacterial disease of poultry. Through its complex regulatory system, C. perfringens orchestrates the expression of a collection of toxins and extracellular enzymes that are crucial for the development of the disease; environmental conditions play an important role in their regulation. In this study, and for the first time, global transcriptomic analysis was performed on ligated intestinal loops in chickens colonized with a netB-positive C. perfringens strain, as well as the same strain propagated in vitro under various nutritional and environmental conditions. RESULTS: Analysis of the respective pathogen transcriptomes revealed up to 673 genes that were significantly expressed in vivo. Gene expression profiles in vivo were most similar to those of C. perfringens grown in nutritionally-deprived conditions. CONCLUSIONS: Taken together, our results suggest a bacterial transcriptome responses to the early stages of adaptation, and colonization of, the chicken intestine. Our work also reveals how netB-positive C. perfringens reacts to different environmental conditions including those in the chicken intestine. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12866-016-0792-6) contains supplementary material, which is available to authorized users

Perturbation drives changing metapopulation dynamics in a top marine predator

Funding: O.E.G. was supported by the Marine Alliance for Science and Technology for Scotland, funded by the Scottish Funding Council (grant no. HR09011). E.L.C. was supported by a Newton Fellowship (Royal Society of London), Marie Curie Fellowship (EU Horizon2020) and a Rutherford Discovery Fellowship (Royal Society of New Zealand). A.J.H. and D.J.F.R. were supportedby NERC (grant no. SMRU 10/001).Metapopulation theory assumes a balance between local decays/extinctions and local growth/new colonisations. Here we investigate whether recent population declines across part of the UK harbour seal range represent normal metapopulation dynamics or are indicative of perturbations potentially threatening the metapopulation viability, using 20 years of population trends, location tracking data (n = 380), and UK-wide, multi-generational population genetic data (n = 269). First, we use microsatellite data to show that two genetic groups previously identified are distinct metapopulations: northern and southern. Then, we characterize the northern metapopulation dynamics in two different periods, before and after the start of regional declines (pre-/peri-perturbation). We identify source-sink dynamics across the northern metapopulation, with two putative source populations apparently supporting three likely sink populations, and a recent metapopulation-wide disruption of migration coincident with the perturbation. The northern metapopulation appears to be in decay, highlighting that changes in local populations can lead to radical alterations in the overall metapopulation's persistence and dynamics.PostprintPeer reviewe

The origin of defects induced in ultra-pure germanium by Electron Beam Deposition

The creation of point defects in the crystal lattices of various semiconductors by subthreshold events has been reported on by a number of groups. These observations have been made in great detail using sensitive electrical techniques but there is still much that needs to be clarified. Experiments using Ge and Si were performed that demonstrate that energetic particles, the products of collisions in the electron beam, were responsible for the majority of electron-beam deposition (EBD) induced defects in a two-step energy transfer process. Lowering the number of collisions of these energetic particles with the semiconductor during metal deposition was accomplished using a combination of static shields and superior vacuum resulting in devices with defect concentrations lower than $10^{11}\,$cm$^{-3}$, the measurement limit of our deep level transient spectroscopy (DLTS) system. High energy electrons and photons that samples are typically exposed to were not influenced by the shields as most of these particles originate at the metal target thus eliminating these particles as possible damage causing agents. It remains unclear how packets of energy that can sometimes be as small of 2eV travel up to a $\mu$m into the material while still retaining enough energy, that is, in the order of 1eV, to cause changes in the crystal. The manipulation of this defect causing phenomenon may hold the key to developing defect free material for future applications.Comment: 18 pages, 9 figure

Cognitive appraisal of environmental stimuli induces emotion-like states in fish

The occurrence of emotions in non-human animals has been the focus of debate over the years. Recently, an interest in expanding this debate to non-tetrapod vertebrates and to invertebrates has emerged. Within vertebrates, the study of emotion in teleosts is particularly interesting since they represent a divergent evolutionary radiation from that of tetrapods, and thus they provide an insight into the evolution of the biological mechanisms of emotion. We report that Sea Bream exposed to stimuli that vary according to valence (positive, negative) and salience (predictable, unpredictable) exhibit different behavioural, physiological and neuromolecular states. Since according to the dimensional theory of emotion valence and salience define a two-dimensional affective space, our data can be interpreted as evidence for the occurrence of distinctive affective states in fish corresponding to each the four quadrants of the core affective space. Moreover, the fact that the same stimuli presented in a predictable vs. unpredictable way elicited different behavioural, physiological and neuromolecular states, suggests that stimulus appraisal by the individual, rather than an intrinsic characteristic of the stimulus, has triggered the observed responses. Therefore, our data supports the occurrence of emotion-like states in fish that are regulated by the individual's perception of environmental stimuli.European Commission [265957 Copewell]; Fundacao para a Ciencia e Tecnologia [SFRH/BD/80029/2011, SFRH/BPD/72952/2010]info:eu-repo/semantics/publishedVersio

MMS observations of electron-scale filamentary currents in the reconnection exhaust and near the X line

© 2016. American Geophysical Union. All Rights Reserved.We report Magnetospheric Multiscale observations of macroscopic and electron-scale current layers in asymmetric reconnection. By intercomparing plasma, magnetic, and electric field data at multiple crossings of a reconnecting magnetopause on 22 October 2015, when the average interspacecraft separation was ~10km, we demonstrate that the ion and electron moments are sufficiently accurate to provide reliable current density measurements at 30ms cadence. These measurements, which resolve current layers narrower than the interspacecraft separation, reveal electron-scale filamentary Hall currents and electron vorticity within the reconnection exhaust far downstream of the X line and even in the magnetosheath. Slightly downstream of the X line, intense (up to 3μA/m2) electron currents, a super-Alfvénic outflowing electron jet, and nongyrotropic crescent shape electron distributions were observed deep inside the ion-scale magnetopause current sheet and embedded in the ion diffusion region. These characteristics are similar to those attributed to the electron dissipation/diffusion region around the X line