59 Works

Data from: Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

Jim Downie, Andy F. S. Taylor, Glenn Iason, Ben Moore, Jonathan Silvertown, Stephen Cavers & Richard Ennos
1. For successful colonisation of host roots, ectomycorrhizal (EM) fungi must overcome host defence systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defence systems, but it is not yet understood whether variation in these constitutive defences can result in variation in colonisation of hosts by specific fungal species. 2. We planted seedlings from...

Pathogen dynamics across the diversity of ageing

Jessica Clark, Luke McNally & Tom Little
Reproduction, mortality and immune function often change with age, but do not invariably deteriorate. Across the tree of life, there is extensive variation in age-specific performance and changes to key life-history traits. These changes occur on a spectrum from classic senescence, where performance declines with age, to juvenescence, where performance improves with age. Reproduction, mortality and immune function are also important factors influencing the spread of infectious disease, yet there exists no comprehensive investigation into...

Data from: Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus

Alex Twyford
An understanding of genetic structure is essential for answering many questions in population genetics. However, complex population dynamics and scale-dependent processes can make it difficult to detect if there are distinct genetic clusters present in natural populations. Inferring discrete population structure is particularly challenging in the presence of continuous genetic variation such as isolation by distance. Here, we use the plant species Mimulus guttatus as a case study for understanding genetic structure at three spatial...

Interference in the shared-stroop task: a comparison of self- and other-monitoring

Martin Pickering, Janet F. McLean & Chiara Gambi
Co-acting participants represent and integrate each other’s actions, even when they are not required to monitor one another. However, monitoring the actions of a partner is an important component of successful interactions, and particularly of linguistic interactions. Moreover, monitoring others may rely on similar mechanisms to those that are involved in self-monitoring. In order to investigate the effect of monitoring on shared linguistic representations, we combined a monitoring task with the shared Stroop task. In...

Data from: Integrated population models poorly estimate the demographic contribution of immigration

Matthieu Paquet, Jonas Knape, Debora Arlt, Pär Forslund, Tomas Pärt, Øystein Flagstad, Carl G. Jones, Malcolm A. C. Nicoll, Ken Norris, Josephine M. Pemberton, Håkan Sand, Linn Svensson, Vikash Tatayah, Petter Wabakken, Camilla Wikenros, Mikael Åkesson & Matthew Low
Estimating the contribution of demographic parameters to changes in population growth is essential for understanding why populations fluctuate. Integrated Population Models (IPMs) offer a possibility to estimate contributions of additional demographic parameters, for which no data have been explicitly collected: typically immigration. Such parametersare often subsequently highlighted as important drivers of population growth. Yet, accuracy in estimating their temporal variation, and consequently their contribution to changes in population growth rate, has not been investigated. To...

Data from: Sex-specific associations between life history traits and a novel reproductive polymorphism in the Pacific field cricket

Jon Richardson, Justa Heinen-Kay & Marlene Zuk
Associations between heritable polymorphisms and life-history traits, such as development time or reproductive investment, may play an underappreciated role in maintaining polymorphic systems. This is because selection acting on a particular morph could be bolstered or disrupted by correlated changes in life-history or vice versa. In a Hawaiian population of the Pacific field cricket (Teleogryllus oceanicus), a novel mutation (flatwing) on the X-chromosome is responsible for a heritable polymorphism in male wing structure. We used...

AI3SD Video: Skills4Scientists - Poster & Careers Symposium - Poster Compilation

András Vekassy, Aspen Fenzl, Erhan Gulsen, Hewan Zewdu, Jamie Longio, Maximilian Hoffman, Rhyan Barrett, Rubaiyat Khondaker, Anna Catton, Hongyang Dong, Kevin Calvache, Kaylee Patel, King Wong, Louis Greenhalgh, Rebecca Jane Clements, Thomas Allam, Sarah Scripps, Gavin Man, Samuel Munday, Michael Blakey, Graeme M. Day, Chris-Kriton Skylaris, Simon J. Coles, Stephen Gow & William Brocklesby
This video forms part of the Skills4Scientists Series which has been organised as a joint venture between the Artificial Intelligence for Scientific Discovery Network+ (AI3SD) and the Physical Sciences Data-Science Service (PSDS). This series ran over summer 2021 and aims to educate and improve scientists skills in a range of areas including research data management, python, version control, ethics, and career development. This series is primarily aimed at final year undergraduates / early stage PhD...

Data from: Using singleton densities to detect recent selection in Bos taurus

Matthew Hartfield, Nina Aagaard Poulsen, Bernt Guldbrandtsen & Thomas Bataillon
Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the ‘Singleton Density Score’, to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as...

Epigenome-wide association study of global cortical volumes in generation Scotland: Scottish family health study

Miruna Carmen Barbu, Mat Harris, Xueyi Shen, Stolicyn Aleks, Claire Green, Carmen Amador, Rosie Walker, Stewart Morris, Mark Adams, Anca Sandu, Christopher McNeil, Gordon Waiter, Kathryn Evans, Archie Campbell, Joanna Wardlaw, Douglas Steele, Alison Murray, David Porteous, Andrew McIntosh & Heather Whalley
A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores. We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two...

Long noncoding RNA PP7080 promotes hepatocellular carcinoma development by sponging mir-601 and targeting SIRT1

Weifang Song, Zhang Wenhui, Yao Ruiqiang, Xinli Hu, Ting Shi, Meijiao Wang & Haijuan Zhang
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy in adults, ranking the second leading cause of cancer-related death. To date, the underlying mechanisms of HCC pathogenesis are still unclear. Recently, more and more studies have reported that long noncoding RNAs (lncRNAs) are involved in the occurrence and development of HCC. This study aims to investigate the expressions, clinical significance and roles of lncRNA PP7080 in HCC. We analyzed the transcriptome data of HCC...

Data from: Burrowing by translocated boodie (Bettongia lesueur) populations alters soils but has limited effects on vegetation

Bryony Palmer, Leonie Valentine, Cheryl Lohr, Gergana Daskalova & Richard Hobbs
Digging and burrowing mammals modify soil resources, creating shelter for other animals and influencing vegetation and soil biota. The use of conservation translocations to reinstate the ecosystem functions of digging and burrowing mammals is becoming more common. However, in an increasingly altered world, the roles of translocated populations, and their importance for other species, may be different. Boodies (Bettongia lesueur), a commonly translocated species in Australia, construct extensive warrens, but how their warrens affect soil...

Fossilization processes have little impact on tip-calibrated divergence time analyses

Joseph O'Reilly
The importance of palaeontological data in divergence time estimation has increased with the introduction of Bayesian Total-Evidence Dating methods which utilise fossil taxa directly for calibration, facilitated by the joint analysis of morphological and molecular data. Fossil taxa are invariably incompletely known as a consequence of taphonomic processes, resulting in the decidedly non-random distribution of missing data. The impact of non-random missing data on the accuracy and precision of clade age estimation is unknown. In...

Data from: Phylogenetic sampling affects evolutionary patterns of morphological disparity

Thomas Smith, Mark Puttick, Joseph O'Reilly, Davide Pisani & Philip Donoghue
Cladistic character matrices are routinely repurposed in analyses of morphological disparity. Unfortunately, the sampling of taxa and characters within such datasets reflects their intended application - to resolve phylogeny, rather than distinguish between phenotypes - resulting in tree shapes that often misrepresent broader taxonomic and morphological diversity. Here we use tree shape as a proxy to explore how sampling can affect perceptions of evolving morphological disparity. Through analyses of simulated and empirical data, we demonstrate...

Impaired neuromuscular function by conjoint actions of organophosphorus insecticide metabolites omethoate and cyclohexanol with implications for treatment of respiratory failure

Kosala N. Dissanayake, Robert Chang-Chih Chou, Adrian Thompson, Filip Margetiny, Charlotte Davie, Scott McKinnon, Vishwendra Patel, Lester Sultatos, Joseph J. McArdle, Richard E. Clutton, Michael Eddleston & Richard R. Ribchester
Ingestion of agricultural organophosphorus insecticides is a significant cause of death in rural Asia. Patients often show acute respiratory failure and/or delayed, unexplained signs of neuromuscular paralysis, sometimes diagnosed as “Intermediate Syndrome”. We tested the hypothesis that omethoate and cyclohexanol, circulating metabolites of one agricultural formulation, cause muscle weakness and paralysis. Acetylcholinesterase activity of insecticide components and metabolites was measured using purified enzyme from eel electroplaque or muscle homogenates. Mechanomyographic recording of pelvic limb responses...

Impaired neuromuscular function by conjoint actions of organophosphorus insecticide metabolites omethoate and cyclohexanol with implications for treatment of respiratory failure

Kosala N. Dissanayake, Robert Chang-Chih Chou, Adrian Thompson, Filip Margetiny, Charlotte Davie, Scott McKinnon, Vishwendra Patel, Lester Sultatos, Joseph J. McArdle, Richard E. Clutton, Michael Eddleston & Richard R. Ribchester
Ingestion of agricultural organophosphorus insecticides is a significant cause of death in rural Asia. Patients often show acute respiratory failure and/or delayed, unexplained signs of neuromuscular paralysis, sometimes diagnosed as “Intermediate Syndrome”. We tested the hypothesis that omethoate and cyclohexanol, circulating metabolites of one agricultural formulation, cause muscle weakness and paralysis. Acetylcholinesterase activity of insecticide components and metabolites was measured using purified enzyme from eel electroplaque or muscle homogenates. Mechanomyographic recording of pelvic limb responses...

Data from: Palaeontology meets metacommunity ecology: The Maastricthian dinosaur fossil record of North America as a case study

Jorge García-Girón, Jani Heino, Janne Alahuhta, Alfio Alessandro Chiarenza & Steve Brusatte
Documenting the patterns and potential associated processes of ancient biotas has always been a central challenge in palaeontology. Over the last decades, intense debate has focused on the organisation of dinosaur–dominated communities, yet no general consensus has been reached on how these communities were organised in a spatial context and if primarily affected by abiotic or biotic agents. Here, we used analytical routines typically applied in metacommunity ecology to provide novel insights into dinosaurian distributions...

Centre for Research in Digital Education Annual Report 2019

Sian Bayne

Data from: Selection on growth rate and local adaptation drive genomic adaptation during experimental range expansions in the protist Tetrahymena thermophila

Felix Moerman, Emanuel Fronhofer, Florian Altermatt & Andreas Wagner
1. Populations that expand their range can undergo rapid evolutionary adaptation of life-history traits, dispersal behaviour, and adaptation to the local environment. Such adaptation may be aided or hindered by sexual reproduction, depending on the context. 2. However, few empirical and experimental studies have investigated the genetic basis of adaptive evolution during range expansions. Even less attention has been given to the question how sexual reproduction may modulate such adaptive evolution during range expansions. 3....

UK dogs data from: Genome-wide association studies for canine hip dysplasia in single and multiple populations – implications and potential novel risk loci

Juliane Friedrich, Shizhi Wang, Erling Strandberg, Per Arvelius, Dylan N Clements & Pamela Wiener
Background: Association mapping studies of quantitative trait loci (QTL) for canine hip dysplasia (CHD) can contribute to the understanding of the genetic background of this common and debilitating disease and might contribute to its genetic improvement. The power of association studies for CHD is limited by relatively small sample numbers for CHD records within countries, suggesting potential benefits of joining data across countries. However, this is complicated due to the use of different scoring systems...

Data from: Carry on caring: infected females maintain their parental care despite suffering high mortality

Tom Ratz, Katy Monteith, Pedro Vale & Per Smiseth
Parental care is a key component of an organism’s reproductive strategy that is thought to trade-off with allocation towards immunity. Yet it is unclear how caring parents respond to pathogens: do infected parents reduce care as a sickness behaviour or simply from being ill, or do they prioritise their offspring by maintaining high levels of care? To address this issue, we investigated the consequences of infection by the pathogen Serratia marcescens on mortality, time spent...

Centre for Research in Digital Education Annual Report 2021

Sian Bayne

Benthic silica flux magnitudes and silicon isotopic composition of marine sediment pore waters and solid phase leachates for the Barents Sea (summer 2017-2019)

James PJ Ward, Sian F Henley, Johan C Faust & Felipe Sales de Freitas
This data product comprises 5 files, containing marine sediment pore water and solid phase leachate silicon (Si) isotopic and element concentration data, as well as benthic silica flux magnitudes derived from core incubation experiments and sediment biogenic silica contents. Samples were collected over three cruises of the Changing Arctic Ocean Seafloor (ChAOS) project summer sampling campaigns in the Barents Sea between 2017 and 2019 aboard the RRS James Clark Ross (cruises JR16006, JR17007 and JR18006)....

Genomic analysis reveals a polygenic architecture of antler morphology in wild red deer (Cervus elaphus)

Lucy Peters, Jisca Huisman, Loeske Kruuk, Josephine Pemberton & Susan Jonston
Sexually-selected traits show large variation and rapid evolution across the animal kingdom, yet genetic variation often persists within populations despite apparent directional selection. A key step in solving this long-standing paradox is to determine the genetic architecture of sexually-selected traits to understand evolutionary drivers and constraints at the genomic level. Antlers are a form of sexual weaponry in male red deer. On the island of Rum, Scotland, males with larger antlers have increased breeding success,...

Epigenome-wide association study of global cortical volumes in Generation Scotland: Scottish Family Health Study

Miruna Carmen Barbu, Mat Harris, Xueyi Shen, Stolicyn Aleks, Claire Green, Carmen Amador, Rosie Walker, Stewart Morris, Mark Adams, Anca Sandu, Christopher McNeil, Gordon Waiter, Kathryn Evans, Archie Campbell, Joanna Wardlaw, Douglas Steele, Alison Murray, David Porteous, Andrew McIntosh & Heather Whalley
A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores. We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two...

Epigenome-wide association study of global cortical volumes in generation Scotland: Scottish family health study

Miruna Carmen Barbu, Mat Harris, Xueyi Shen, Stolicyn Aleks, Claire Green, Carmen Amador, Rosie Walker, Stewart Morris, Mark Adams, Anca Sandu, Christopher McNeil, Gordon Waiter, Kathryn Evans, Archie Campbell, Joanna Wardlaw, Douglas Steele, Alison Murray, David Porteous, Andrew McIntosh & Heather Whalley
A complex interplay of genetic and environmental risk factors influence global brain structural alterations associated with brain health and disease. Epigenome-wide association studies (EWAS) of global brain imaging phenotypes have the potential to reveal the mechanisms of brain health and disease and can lead to better predictive analytics through the development of risk scores. We perform an EWAS of global brain volumes in Generation Scotland using peripherally measured whole blood DNA methylation (DNAm) from two...

Registration Year

  • 2021
    59

Resource Types

  • Dataset
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  • Output Management Plan
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Affiliations

  • University of Edinburgh
    59
  • University of Bristol
    5
  • Royal Adelaide Hospital
    3
  • Cardiff University
    3
  • Harvard University
    3
  • Massachusetts General Hospital
    2
  • Henan University
    2
  • Zhejiang University
    2
  • Chengdu Third People's Hospital
    2
  • Central South University
    2