49 Works

Data from: Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response

William D. K. Reid, Andrew J. Close, Suzanne Humphrey, Gemma Chaloner, Lizeth Lacharme-Lora, Lisa Rothwell, Pete Kaiser, Nicola J. Williams, Thomas J. Humprey, Paul Wigley, Stephen P. Rushton & Tom J. Humphrey
Development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. The immune response against pathogen challenge depends on the specific threat to the host. Here, we show that broiler chickens mount a breed-dependent immune response to Campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and Bayesian structural equation models (SEM). SEM provides a framework by which cytokine interdependencies,...

Data from: Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

Ignacio Mena, Martha I. Nelson, Francisco Quezada-Monroy, Jayeeta Dutta, Refugio Cortes-Fernández, J. Horacio Lara-Puente, Felipa Castro-Peralta, Luis F. Cunha, Nídia Sequeira-Trovão, Bernardo Lozano-Dubernard, Andrew Rambaut, Harm Van Bakel & Adolfo García-Sastre
Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of...

Data from: Automated single particle detection and tracking for large microscopy datasets

Rhodri S. Wilson, Lei Yang, Alison Dun, Annya M. Smyth, Rory R. Duncan, Colin Rickman & Weiping Lu
Recent advances in optical microscopy have enabled the acquisition of very large datasets from living cells with unprecedented spatial and temporal resolutions. Our ability to process these datasets now plays an essential role in order to understand many biological processes. In this paper, we present an automated particle detection algorithm capable of operating in low signal-to-noise fluorescence microscopy environments and handling large datasets. When combined with our particle linking framework, it can provide hitherto intractable...

Soil thaw depth from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This datasets contains measures of soil thaw depth from permafrost in subarctic Canada. Soil thaw depth was measured in 2013 and 2014 in sites from Yukon and Northwest Territories.

Soil temperature profiles from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of soil temperature profiles from permafrost in subarctic Canada. Soil temperature profiles were monitored during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, thawing features of peatland plateaus, unburnt and burnt black spruce forests, and additional sites.

Bulk density, carbon and nitrogen content in soil profiles from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of measurements of bulk density, carbon and nitrogen content in soil profiles from permafrost in subarctic Canada. Soil cores were sampled during early summer in 2013 and 2014. Soil cores were sampled from a peatland plateau and thawing features of the peatland plateau, and from an unburnt and burnt black spruce forest, and additional sites in Yukon and Northwest Territories.

Soil respired radiocarbon as CO2 and CH4 from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset contains measures of soil respired radiocarbon as CO2 and CH4 from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada. The radiocarbon content of soil respired CO2 and CH4 was measured during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, thawing features of peatland plateaus and unburnt and burnt black spruce forests.

Data from: Cellular and humoral immunity in a wild mammal: Variation with age & sex and association with overwinter survival

Rebecca L. Watson, Tom N. McNeilly, Kathryn A. Watt, Josephine M. Pemberton, Jill G. Pilkington, Martin Waterfall, Phoebe R. T. Hopper, Daniel Cooney, Rose Zamoyska, Daniel H. Nussey & Phoebe R.T. Hopper
Immune defenses are expected to be crucial for survival under the considerable parasite pressures experienced by wild animals. However, our understanding of the association between immunity and fitness in nature remains limited due to both the complexity of the vertebrate immune system and the often-limited availability of immune reagents in nonmodel organisms. Here, we use methods and reagents developed by veterinary researchers for domestic ungulates on blood samples collected from a wild Soay sheep population,...

Data from: Rodents: food or pests in Neolithic Orkney

Andrzej A. Romaniuk, Alexandra N. Shepherd, David V. Clarke, Alison J. Sheridan, Sheena Fraser, László Bartosiewicz & Jeremy S. Herman
Rodents have important effects on contemporary human societies, sometimes providing a source of food but more often as agricultural pests, or as vectors and reservoirs of disease. Skeletal remains of rodents are commonly found in archaeological assemblages from around the world, highlighting their potential importance to ancient human populations. However, there are few studies of the interactions between people and rodents at such sites and most of these are confined to locations where rodents have...

Data from: Multihost Bartonella parasites display covert host specificity even when transmitted by generalist vectors

Susan M. Withenshaw, Godefroy Devevey, Amy B. Pedersen & Andy Fenton
Many parasites infect multiple sympatric host species, and there is a general assumption that parasite transmission between co-occurring host species is commonplace. Such between-species transmission could be key to parasite persistence within a disease reservoir and is consequently an emerging focus for disease control. However, while a growing body of theory indicates the potential importance of between-species transmission for parasite persistence, conclusive empirical evidence from natural communities is lacking, and the assumption that between-species transmission...

Data from: Marker-dependent associations among oxidative stress, growth and survival during early life in a wild mammal

Louise L. Christensen, Colin Selman, Jonathan D. Blount, Jill G. Pilkington, Kathryn A. Watt, Josephine M. Pemberton, Jane M. Reid & Daniel H. Nussey
Oxidative stress (OS) is hypothesized to be a key physiological mechanism mediating life-history trade-offs, but evidence from wild populations experiencing natural environmental variation is limited. We tested the hypotheses that increased early life growth rate increases OS, and that increased OS reduces first-winter survival, in wild Soay sheep (Ovis aries) lambs. We measured growth rate and first-winter survival for four consecutive cohorts, and measured two markers of oxidative damage (malondialdehyde (MDA), protein carbonyls (PC)) and...

Data from: Distribution and abundance of glucocorticoid and mineralocorticoid receptors throughout the brain of the great tit Parus major

Rebecca A. Senft, Simone L. Meddle & Alexander T. Baugh
The glucocorticoid stress response, regulated by the hypothalamic-pituitary-adrenal (HPA) axis, enables individuals to cope with stressors through transcriptional effects in cells expressing the appropriate receptors. The two receptors that bind glucocorticoids—the mineralocorticoid receptor (MR) and glucocorticoid receptor (GR)—are present in a variety of vertebrate tissues, but their expression in the brain is especially important. Neural receptor patterns have the potential to integrate multiple behavioral and physiological traits simultaneously, including self-regulation of glucocorticoid secretion through negative...

Data from: Sibling competition does not exacerbate inbreeding depression in the burying beetle Nicrophorus vespilloides

Natalie Pilakouta, Daniel J. Sieber & Per T. Smiseth
Inbreeding results from matings between relatives and can cause a reduction in offspring fitness, known as inbreeding depression. Previous work has shown that a wide range of environmental stresses, such as extreme temperatures, starvation, and parasitism, can exacerbate inbreeding depression. It has recently been argued that stresses due to intraspecific competition should have a stronger effect on the severity of inbreeding depression than stresses due to harsh physical conditions. Here, we tested whether an increase...

Data from: Relative costs of offspring sex and offspring survival in a polygynous mammal

Hannah Froy, Craig A. Walling, Josephine M. Pemberton, Tim H. Clutton-Brock, Loeske E.B. Kruuk & Loeske E. B. Kruuk
Costs of reproduction are expected to be ubiquitous in wild animal populations and understanding the drivers of variation in these costs is an important aspect of life-history evolution theory. We use a 43 year dataset from a wild population of red deer to examine the relative importance of two factors that influence the costs of reproduction to mothers, and to test whether these costs vary with changing ecological conditions. Like previous studies, our analyses indicate...

Data from: The genome of the yellow potato cyst nematode Globodera rostochiensis reveals insights into the basis of parasitism and virulence

Sebastian Eves-Van Den Akker, Dominik Laetsch, Peter Thorpe, Catherine Lilley, Etienne Danchin, Martine Da Rocha, Corinne Rancurel, Nancy Holroyd, James Cotton, Amir Szitenberg, Eric Grenier, Josselin Montarry, Benjamin Mimee, Marc-Olivier Duceppe, Ian Boyes, Jessica Marvin, Laura Jones, Hazijah Yusup, Joël Lafond-Lapalme, Magali Esquibet, Michael Sabeh, Michael Rott, Hein Overmars, Anna Finkers-Tomczak, Geert Smant … & John Jones
Background: The yellow potato cyst nematode Globodera rostochiensis is a devastating plant pathogen of global economic importance. This biotrophic parasite secretes effectors from pharyngeal glands, some of which were acquired by horizontal gene transfer, to manipulate host processes and promote parasitism. G. rostochiensis is classified into pathotypes with different plant resistance-breaking phenotypes. Results: We generate a high-quality genome assembly for G. rostochiensis pathotype Ro1, identify putative effectors and horizontal gene transfer events, map gene expression...

Data from: Accounting for female space sharing in St. Kilda Soay sheep (Ovis aries) results in little change in heritability estimates

Charlotte E. Regan, Jill G. Pilkington, Camillo Bérénos, Josephine M. Pemberton, Per T. Smiseth & Alastair J. Wilson
When estimating heritability in free-living populations, it is common practice to account for common environment effects, because of their potential to generate phenotypic covariance among relatives thereby biasing heritability estimates. In quantitative genetic studies of natural populations, however, philopatry, which results in relatives being clustered in space, is rarely accounted for. The two studies to have done so suggest absolute declines in heritability estimates of up to 43% when accounting for space sharing by relatives....

Data from: Use of novel psychoactive substances by inpatients on general adult psychiatric wards

Jack L. Stanley, Daniel V. Mogford, Rebecca J. Lawrence & Stephen M. Lawrie
Objectives: Non-illicit alternatives to controlled drugs, known as Novel Psychoactive Substances (NPS) have recently risen to prominence. They are readily available with uncertain pharmacology and no widely available assay. Given that psychiatric patients are at risk of comorbid substance abuse, we hypothesized that NPS use would be present in the psychiatric population, and sought to determine its prevalence and investigate the characteristics of those who use these drugs with a retrospective review of discharge letters....

Data from: Selection on parental performance opposes selection for larger body mass in a wild population of blue tits

Caroline Elizabeth Thomson, Florian Bayer, Nicholas Crouch, Samantha Farrell, Elizabeth Heap, Elizabeth Mittell, Mar Zurita-Cassinello & Jarrod D. Hadfield
There is abundant evidence in many taxa for positive directional selection on body size, and yet little evidence for microevolutionary change. In many species, variation in body size is partly determined by the actions of parents, so a proposed explanation for stasis is the presence of a negative genetic correlation between direct and parental effects. Consequently, selecting genes for increased body size would result in a correlated decline in parental effects, reducing body size in...

Data from: Mode of resistance to viral lysis affects host growth across multiple environments in the marine picoeukaryote Ostreococcus tauri

Sarah E. Heath & Sinead Collins
Viruses play important roles in population dynamics and as drivers of evolution in single-celled marine phytoplankton. Viral infection of Ostreococcus tauri often causes cell lysis, but two spontaneously arising resistance mechanisms occur: resistant cells that cannot become infected and resistant producer cells that are infected but not lysed, and which may slowly release viruses. As of yet, little is known about how consistent the effects of viruses on their hosts are across different environments. To...

Data from: The effect of dietary restriction on reproduction: a meta-analytic perspective

Joshua P. Moatt, Shinichi Nakagawa, Malgorzata Lagisz & Craig A. Walling
Background: Dietary restriction (DR), a reduction in the amount of food or particular nutrients eaten, is the most consistent environmental manipulation to extend lifespan and protect against age related diseases. Current evolutionary theory explains this effect as a shift in the resolution of the trade-off between lifespan and reproduction. However, recent studies have questioned the role of reproduction in mediating the effect of DR on longevity and no study has quantitatively investigated the effect of...

Data from: Fine with heat, problems with water: microclimate alters water loss in a thermally adapted insular lizard

Anat Belasen, Kinsey Brock, Binbin Li, Dimitra Chremou, Efstratios Valakos, Panayiotis Pafilis, Barry Sinervo & Johannes Foufopoulos
Global change, including habitat isolation and climate change, has both short- and long-term impacts on wildlife populations. For example, genetic drift and inbreeding result in genetic impoverishment in small, isolated populations, while species undergo range shifts or adaptive phenotypic change in response to shifts in environmental temperatures. In this study, we utilize a model system in which Holocene landscape changes have occurred to examine long-term effects of population isolation. To examine how isolation may constrain...

Data from: The global antigenic diversity of swine influenza A viruses

Nicola S. Lewis, Colin A. Russell, Tavis K. Anderson, Kathryn Berger, David F. Burke, Judith M. Fonville, Ronald A.M. Fouchier, Paul Kellam, Bjorn F. Koel, Tung Nguyen, Bundit Nuansrichy, J. S. Malik Peiris, Takehiko Saito, Gaelle Simon, Eugene Skepner, Nobuhiro Takemae, ESNIP3 Consortium, Richard J. Webby, Kristien Van Reeth, Sharon M. Brookes, Lars Larsen, Ian H. Brown, Amy L. Vincent, Pinky Langat, Filip Bielejec … & JS Malik Peiris
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the...

Data from: Maternal effects alter the severity of inbreeding depression in the offspring

Natalie Pilakouta & Per T. Smiseth
A maternal effect is a causal influence of the maternal phenotype on the offspring phenotype over and above any direct effects of genes. There is abundant evidence that maternal effects can have a major impact on offspring fitness. Yet, no previous study has investigated the potential role of maternal effects in influencing the severity of inbreeding depression in the offspring. Inbreeding depression is a reduction in the fitness of inbred offspring relative to outbred offspring....

Autotrophic and heterotrophic soil respiration fluxes from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada

C. Estop-Aragones, J.P. Fisher, M.A. Cooper, A. Thierry, R. Treharne, J.B. Murton, G.K. Phoenix, D.J. Charman, M. Williams & I.P. Hartley
This dataset consists of autotrophic and heterotrophic soil respiration fluxes from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada. Autotrophic and heterotrophic soil respiration fluxes (CO2) were monitored during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, unburnt and burnt black spruce forests, and additional sites.

Registration Year

  • 2016
    49

Resource Types

  • Dataset
    49

Affiliations

  • University of Edinburgh
    49
  • University of Exeter
    13
  • University of Sheffield
    12
  • University of Sussex
    10
  • University of Cambridge
    4
  • University of Oxford
    3
  • Ghent University
    2
  • Centre for Ecology & Hydrology
    2
  • UK Centre for Ecology & Hydrology
    2
  • University of Glasgow
    2