Sampling the fish gill microbiome : a comparison of tissue biopsies and swabs

Funding Information: The research costs of this work were supported by the BBSRC EASTBIO DTP and Marine Alliance for Science and Technology Scotland (MASTS) small grants funding scheme. Acknowledgements The authors would like to thank Scottish Sea Farms (SSF) for the kind facilitation of fieldwork that provided material in this project, particularly the staff at the Loch Spelve facility, and the health team at SSF, particularly Dr. Ralph Bickerdike. Thanks are due as well to Professor Matt Holden and Kerry Pettigrew of the Infection Group within the Biomedical Sciences Research Complex, School of Medicine, University of St Andrews, for assistance within the laboratory, as well as Dr. David Bass at the Centre for Environment Fisheries and Aquaculture Science for helpful proofreading.Peer reviewedPublisher PD

Comparative Analysis of Gene Expression in Virulent and Attenuated Strains of Infectious Bronchitis Virus at Subcodon Resolution.

Like all coronaviruses, avian infectious bronchitis virus (IBV) possesses a long, single-stranded, positive-sense RNA genome (∼27 kb) and has a complex replication strategy that includes the production of a nested set of subgenomic mRNAs (sgmRNAs). Here, we used whole-transcriptome sequencing (RNASeq) and ribosome profiling (RiboSeq) to delineate gene expression in the IBV M41-CK and Beau-R strains at subcodon resolution. RNASeq facilitated a comparative analysis of viral RNA synthesis and revealed two novel transcription junction sites in the attenuated Beau-R strain, one of which would generate a sgmRNA encoding a ribosomally occupied open reading frame (dORF) located downstream of the nucleocapsid coding region. RiboSeq permitted quantification of the translational efficiency of virus gene expression and identified, for the first time, sites of ribosomal pausing on the genome. Quantification of reads flanking the programmed ribosomal frameshifting (PRF) signal at the genomic RNA ORF1a/ORF1b junction revealed that PRF in IBV is highly efficient (33 to 40%). Triplet phasing of RiboSeq data allowed precise determination of reading frames and revealed the translation of two ORFs (ORF4b and ORF4c on sgmRNA IR), which are widely conserved across IBV isolates. Analysis of differential gene expression in infected primary chick kidney cells indicated that the host cell response to IBV occurs primarily at the level of transcription, with global upregulation of immune-related mRNA transcripts following infection and comparatively modest changes in the translation efficiencies of host genes. Cellular genes and gene networks differentially expressed during virus infection were also identified, giving insights into the host cell response to IBV infection.IMPORTANCE IBV is a major avian pathogen and presents a substantial economic burden to the poultry industry. Improved vaccination strategies are urgently needed to curb the global spread of this virus, and the development of suitable vaccine candidates will be aided by an improved understanding of IBV molecular biology. Our high-resolution data have enabled a precise study of transcription and translation in cells infected with both pathogenic and attenuated forms of IBV and expand our understanding of gammacoronaviral gene expression. We demonstrate that gene expression shows considerable intraspecies variation, with single nucleotide polymorphisms being associated with altered production of sgmRNA transcripts, and our RiboSeq data sets enabled us to uncover novel ribosomally occupied ORFs in both strains. The numerous cellular genes and gene networks found to be differentially expressed during virus infection provide insights into the host cell response to IBV infection.Wellcome Trust European Research Counci

Variability in prey field structure drives inter-annual differences in prey encounter by a marine predator, the little penguin

This study was funded by Australian Research Council Linkage Grants (grant nos. LP110200603 and LP160100162), with contributions from the Taronga Conservation Society Australia.Understanding how marine predators encounter prey across patchy landscapes remains challenging due to difficulties in measuring the three-dimensional structure of pelagic prey fields at scales relevant to animal movement. We measured at-sea behaviour of a central-place forager, the little penguin (Eudyptula minor), over 5 years (2015–2019) using GPS and dive loggers. We made contemporaneous measurements of the prey field within the penguins' foraging range via boat-based acoustic surveys. We developed a prey encounter index by comparing estimates of acoustic prey density encountered along actual penguin tracks to those encountered along simulated penguin tracks with the same characteristics as real tracks but that moved randomly through the prey field. In most years, penguin tracks encountered prey better than simulated random movements greater than 99% of the time, and penguin dive depths matched peaks in the vertical distribution of prey. However, when prey was unusually sparse and/or deep, penguins had worse than random prey encounter indices, exhibited dives that mismatched depth of maximum prey density, and females had abnormally low body mass (5.3% lower than average). Reductions in prey encounters owing to decreases in the density or accessibility of prey may ultimately lead to reduced fitness and population declines in central-place foraging marine predators.Publisher PDFPeer reviewe

Review of the influence of noise in X-ray computed tomography measurement uncertainty

Different aspects of noise in X-ray computed tomography (XCT) for industrial purposes are examined. An overview of the most common noise metrics is given, together with a description of XCT noise influence quantities. We address the current state of the art in understanding the contribution of noise to XCT measurement uncertainty, giving a chronological view of the different attempts that have been made to account for the contribution from noise to XCT measurement uncertainty. We conclude that approaches to estimating the contribution of noise to XCT measurement uncertainty that account for not only noise, but also other factors that affect image quality (e.g., scattering, beam hardening and blurring) are preferable to approaches that only account for noise

Coastal seascape variability in the intensifying East Australian Current Southern Extension

Funding: This study was funded by Australian Research Council Linkage Grants (LP110200603 awarded to RH, DS and Iain Field, and LP160100162 awarded to IJ, Martina Doublin, MC, GC, DS, Iain Suthers and RH) with contributions from the Taronga Conservation Society Australia, NSW National Parks and the Australian Antarctic Division.Coastal pelagic ecosystems are highly variable in space and time, with environmental conditions and the distribution of biomass being driven by complex processes operating at multiple scales. The emergent properties of these processes and their interactive effects result in complex and dynamic environmental mosaics referred to as “seascapes”. Mechanisms that link large-scale oceanographic processes and ecological variability in coastal environments remain poorly understood, despite their importance for predicting how ecosystems will respond to climate change. Here we assessed seascape variability along the path of the rapidly intensifying East Australian Current (EAC) Southern Extension in southeast Australia, a hotspot of ocean warming and ecosystem tropicalisation. Using satellite and in situ measures of temperature, salinity and current velocity coupled with contemporaneous measurements of pelagic biomass distribution from nine boat-based active acoustic surveys in five consecutive years, we investigated relationships between the physical environment and the distribution of pelagic biomass (zooplankton and fish) at multiple timescales. Survey periods were characterised by high variability in oceanographic conditions, with variation in coastal conditions influenced by meso-to-large scale processes occurring offshore, including the position and strength of eddies. Intra-annual variability was often of a similar or greater magnitude to inter-annual variability, suggesting highly dynamic conditions with important variation occurring at scales of days to weeks. Two seascape categories were identified being characterised by (A) warmer, less saline water and (B) cooler, more saline water, with the former indicating greater influence of the EAC on coastal processes. Warmer waters were also associated with fewer, deeper and less dense biological aggregations. As the EAC continues to warm and penetrate further south, it is likely that this will have substantial effects on biological activity in coastal pelagic ecosystems, including a potential reduction in the accessibility of prey aggregations to surface-feeding predators and to fisheries. These results highlight the import role of offshore oceanographic processes in driving coastal seascape variability and biological activity in a region undergoing rapid oceanic warming and ecological change.Publisher PDFPeer reviewe

Using predicted patterns of 3D prey distribution to map king penguin foraging habitat

FUNDING The at-sea data collection and 50% of CLG’s Ph.D. studentship was provided by the Swiss Polar Institute as a grant ‘Unlocking the Secrets of the False Bottom’ to ASB. The School of Biology, University of St Andrews, funded the other 50% of CLG’s studentship. Work at South Georgia was supported by the Natural Environment Research Council’s Collaborative Antarctic Science Scheme (CASS-129), a grant from the TransAntarctic Association grant to RBS, and a British Antarctic Survey Collaborative Gearing Scheme grant to RBS and ASB. ASB and RP were supported in part by UKRI/NERC under grant NE/R012679/1. ACKNOWLEDGMENTS We thank the staff at the British Antarctic Survey base at King Edward Point (South Georgia), Quark Expeditions and the crew and staff of the Ocean Endeavour and the FPV Pharos South Georgia for their help with the fieldwork logistics. We also thank the Swiss Polar Institute and the ACE foundation for funding our ACE project, and all our colleagues who assisted with acoustic data collection at sea: Matteo Bernasconi, Inigo Everson, and Joshua Lawrence. We thank Yves Cherel for fruitful discussion on the role of prey patches for king penguins in the Kerguelen region. We also thank C. Ribout and the Centre for Biological Studies of Chizé for conducting the sexing analyses of the birdsPeer reviewedPublisher PD

An experimental analysis of the optical, thermal and power to weight performance of plastic and glass optics with AR coatings for embedded CPV windows

A low concentrator photovoltaic is presented and the optical losses within a double glazed window assembly are described. The use of plastic instead of glass is analyzed for its reduced weight and hence greater power to weight ratios. Although the transmittance of glass is higher, the power to weight ratio of the plastic devices was almost double that of the glass counterparts and even higher than the original non concentrating silicon cell. The plastic Topas material was found to be the best performing material overall. Crystal Clear, a plastic resin, had a higher average transmittance but had a lower optical efficiency due to the cold cast manufacturing process in comparison to injection moulding of the other materials. This proves the importance of considering both the materials and their associated manufacturing quality

Adenine nucleotide translocation in liver mitochondria of hypothyroid rats

In measurements using a disc filtration method, liver mitochondria obtained from hypothyroid rats translocate external ADP at 0 [deg]C via the atractyloside-sensitive carrier much more slowly than do mitochondria from normal rats, confirming the findings of Portnay et al. (Biochem. Biophys. Res. Commun. 55, 17, 1973). The hypothyroid mitochondria contain 60% more ATP + ADP than do mitochondria from normals, but the excess nucleotides are not exchangeable and so do not contribute to translocation. A decrease in the first-order rate constant accounts for the decreased velocity. Neither a decrease in the number of translocator sites nor changes in ADP phosphorylation or ATPase activity seem to account for the abnormal kinetics of translocation. Although the filtration method limits the maximal translocation rate observed in normal mitochondria at temperatures above 17 [deg]C that induce a fluid membrane state, no such transition is seen in mitochondria from hypothyroid rats up to 35 [deg]C, indicating that the translocator is in an altered environment in hypothyroidism. Injecting a hypothyroid rat once with -thyroxine corrects the abnormal compartmentation and produces a temperature-rate relationship like that in normal mitochondria in 3 days, a period which would accommodate the hormone actions reported on translation, membrane phospholipid synthesis, or fatty acid desaturation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22994/1/0000562.pd

Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A

Chromothripsis, the process of catastrophic shattering and haphazard repair of chromosomes, is a common event in cancer. Whether chromothripsis might constitute an actionable molecular event amenable to therapeutic targeting remains an open question. We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ∼25% of patients (‘chr21amp’). We report that chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. The chr21amp event is highly clonal and present throughout the hematopoietic hierarchy. DYRK1A, a serine threonine kinase and transcription factor, is the only gene in the 2.7Mb minimally amplified region which showed both increased expression and chromatin accessibility compared to non-chr21amp BP-MPN controls. We demonstrate that DYRK1A is a central node at the nexus of multiple cellular functions critical for BP-MPN development, including DNA repair, STAT signalling and BCL2 overexpression. DYRK1A is essential for BP-MPN cell proliferation in vitro and in vivo, and DYRK1A inhibition synergises with BCL2 targeting to induce BP-MPN cell apoptosis. Collectively, these findings define the chr21amp event as a prognostic biomarker in BP-MPN and link chromothripsis to a druggable target