194 Works

Data for the gene activity histogram

Alexander Phillip Turner

Mechanistic Studies into a Palladium-mediated Oxidation of Ketones to Enones

Paul Andrew Clarke
Data underpinning publication

Wann - Dimethylaminobenzonitrile data from calculations and from gas electron diffraction

Derek Alan Wann
Calculations and gas electron diffraction data related to the GED study of dimethylaminobenzonitrile prepared for publication.

\"Back-to-Front\" Indole Synthesis using Silver(I) Catalysis: Unexpected C-3 Pyrrole Activation Mode Supported by DFT

William Paul Unsworth & Aimee Kate Clarke
Raw data for "Back-to-Front" Indole Synthesis using Silver(I) Catalysis: Unexpected C-3 Pyrrole Activation Mode Supported by DFT. Unprocessed raw NMR data (1H and 13C) and copies of IR spectra and mass spectrometry data.

Dataset for \"Etheric Bimesogens and the Twist-Bend Nematic Phase\"

Richard Mandle
Spectral data for novel compounds and input files for the paper "Etheric Bimesogens and the Twist-Bend Nematic Phase". This dataset is embargoed until the end date of EPSRC grant EP/M020584/1 (31st of May 2018) as further publication and intellectual property may arise.

Data from: Agri-environment conservation set-asides have co-benefits for connectivity

Katie Threadgill, Colin McClean, Jenny Hodgson, Naomi Jones & Jane Hill
Widespread declines in farmland biodiversity have led to state-funded schemes which take land out of production to create (semi-)natural habitats for biodiversity (e.g. EU agri-environment schemes; US Conservation Reserve Program). Common features of such schemes are grassland strips at the edges of agricultural fields, and we examine potential co-benefits of these biodiversity set-asides for contributing to grassland connectivity. Although set-aside strips had negligible impact on landscape-scale species persistence (using metapopulation models parameterized for flying insects...

Nest choice in arboreal ants is an emergent consequence of network creation under spatial constraints

Matina Donaldson-Matasci, Joanna Chang, Scott Powell & Elva J. H. Robinson
Biological transportation networks must balance competing functional priorities. The self-organizing mechanisms used to generate such networks have inspired scalable algorithms to construct and maintain low-cost and efficient human-designed transport networks. The pheromone-based trail networks of ants have been especially valuable in this regard. Here, we use turtle ants as our focal system: In contrast to the ant species usually used as models for self-organized networks, these ants live in a spatially constrained arboreal environment where...

Integrating stakeholders’ perspectives and spatial modelling to develop scenarios of future land use and land cover change in northern Tanzania

Rebecca Kariuki, Linus Munishi, Colin Courtney-Mustaphi, Claudia Capitani, Anna Shoemaker, Paul Lane & Rob Marchant
Rapid rates of land use and land cover change (LULCC) in eastern Africa and limited instances of genuinely equal partnerships involving scientists, communities and decision makers challenge the development of robust pathways toward future environmental and socioeconomic sustainability. We use a participatory modelling tool, Kesho, to assess the biophysical, socioeconomic, cultural and governance factors that influenced past (1959-1999) and present (2000-2018) LULCC in northern Tanzania and to simulate four scenarios of land cover change to...

COVID-19 patient data from a study in Singapore curated for input into an in silico infection model

Farzad Fatehi, Richard J. Bingham, Eric C. Dykeman, Peter G. Stockley & Reidun Twarock
Within-host models of COVID-19 infection dynamics enable the merits of different forms of antiviral therapy to be assessed in individual patients. A stochastic agent-based model of COVID-19 intracellular dynamics is introduced here, that incorporates essential steps of the viral life cycle targeted by treatment options. Integration of model predictions with an intercellular ODE model of within-host infection dynamics, fitted to patient data, generates a generic profile of disease progression in patients that have recovered in...

No evidence for trade-offs between bird diversity, yield and water table depth on oil palm smallholdings: implications for tropical peatland landscape restoration

Eleanor Warren-Thomas, Fahmuddin Agus, Panji Akbar, Merry Crowson, Keith Hamer, Bambang Hariyadi, Jenny Hodgson, Winda Kartika, Mailys Lopes, Jennifer Lucey, Dedy Mustaqim, Nathalie Pettorelli, Asmadi Saad, Widia Sari, Gita Sukma, Lindsay Stringer, Caroline Ward & Jane Hill
Tropical peat swamp forests retain large carbon stocks and support unique biodiversity, but clearance and drainage for agriculture have resulted in fires, carbon emissions and biodiversity losses. Initiatives to re-wet cultivated peatlands may benefit biodiversity if this protects remaining forests from fire and agricultural encroachment, but there are concerns that re-wetting could reduce yields and damage livelihoods, as relationships between drainage, on-farm biodiversity, and crop yields have not been studied. We examined oil palm fruit...

Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models

Silvia Castiglione, Marina Melchionna, Antonio Profico, Gabriele Sansalone, Maria Modafferi, Alessandro Mondanaro, Stephen Wroe, Paolo Piras & Pasquale Raia
Modern phylogenetic comparative methods allow estimating evolutionary rates of phenotypic change, how these rates differ across clades, and assessing whether the rate remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, hence they do not allow us to determine rate variations among different parts of a single, complex phenotype, or charting of realized rate variation directly onto the phenotype. Herein, we present a new method...

Data from: Quantifying trade-offs between butterfly abundance and movement in the management of agricultural set-aside strips

Katie Threadgill, Jenny Hodgson, Naomi Jones, Colin McClean & Jane Hill
1. Agri-environment schemes (AES) create small areas of habitat within agricultural landscapes to support biodiversity. Here, we study butterfly flight behaviour within linear AES features and examine whether differences in resource availability affect the speed, linearity or directionality of local movements, thereby affecting their contribution to landscape connectivity. 2. We surveyed butterflies within three basic (naturally regenerating) and three wildflower-sown linear field margin strips (0.09-0.15 ha) on a farm in North Yorkshire, UK, and mapped...

Data from: An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor

Katherine E. Dunn, Mark C. Leake, Adam J. M. Wollman, Martin A. Trefzer, Steven Johnson & Andy M. Tyrrell
DNA has been used to construct a wide variety of nanoscale molecular devices. Inspiration for such synthetic molecular machines is frequently drawn from protein motors, which are naturally occurring and ubiquitous. However, despite the fact that rotary motors such as ATP synthase and the bacterial flagellar motor play extremely important roles in nature, very few rotary devices have been constructed using DNA. This paper describes an experimental study of the putative mechanism of a rotary...

Data from: Population genetic structure and secondary symbionts in host-associated populations of the pea aphid complex

Julia Ferrari, Joan A West, Sara Via & H. Charles J. Godfray
Polyphagous insect herbivores experience different selection pressures on their various host plant species. How this affects population divergence and speciation may be influenced by the bacterial endosymbionts that many harbor. Here, we study the population structure and symbiont community of the pea aphid (Acyrthosiphon pisum), which feeds on a range of legume species and is known to form genetically differentiated host-adapted populations. Aphids were collected from eight legume genera in England and Germany. Extensive host...

Data from: A new model for ancient DNA decay based on paleogenomic meta-analysis

Logan Kistler, Roselyn Ware, Oliver Smith, Matthew Collins & Robin G. Allaby
The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for...

Data from: Delimiting tropical mountain ecoregions for conservation

Philip J. Platts, Neil D. Burgess, Roy E. Gereau, Jon C. Lovett, Andrew R. Marshall, Colin J. McClean, Petri K. E. Pellikka, Ruth D. Swetnam & Rob Marchant
Ecological regions aggregate habitats with similar biophysical characteristics within well-defined boundaries, providing spatially consistent platforms for monitoring, managing and forecasting the health of interrelated ecosystems. A major obstacle to the implementation of this approach is imprecise and inconsistent boundary placement. For globally important mountain regions such as the Eastern Arc (Tanzania and Kenya), where qualitative definitions of biophysical affinity are well established, rule-based methods for landform classification provide a straightforward solution to ambiguities in region...

Data from: Parasites and competitors suppress bacterial pathogen synergistically due to evolutionary trade-offs

XiaoFang Wang, Zhong Wei, Mei Li, Xueqi Wang, Anqi Shan, Xinlan Mei, Alexandre Jousset, Qirong Shen, Yangchun Xu & Ville-Petri Friman
Parasites and competitors are important for regulating pathogen densities and subsequent disease dynamics. It is, however, unclear to what extent this is driven by ecological and evolutionary processes. Here we used experimental evolution to study the eco-evolutionary feedbacks between Ralstonia solanacearum bacterial pathogen, Ralstonia-specific phage parasite and Bacillus amyloliquefaciens competitor bacterium in the laboratory and plant rhizosphere. We found that while the phage had a small effect on pathogen densities on its own, it considerably...

Data from: Impact of enrichment conditions on cross-species capture of fresh and degraded DNA

Johanna L. A. Paijmans, Joerns Fickel, Alexandre Courtiol, Michael Hofreiter & Daniel W. Förster
By combining high-throughput sequencing with target-enrichment (“hybridization capture”), researchers are able to obtain molecular data from genomic regions of interest for projects that are otherwise constrained by sample quality (e.g. degraded and contamination-rich samples) or a lack of a priori sequence information (e.g. studies on non-model species). Despite the use of hybridization capture in various fields of research for many years, the impact of enrichment conditions on capture success are not yet thoroughly understood. We...

Data from: The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions

Ben Libberton, Malcolm J. Horsburgh & Michael A. Brockhurst
Recent evidence suggests that interference competition between bacteria shapes the distribution of the opportunistic pathogen Staphylococcus aureus in the lower nasal airway of humans, either by preventing colonization or by driving displacement. This competition within the nasal microbial community would add to known host factors that affect colonization. We tested the role of toxin-mediated interference competition in both structured and unstructured environments, by culturing S. aureus with toxin-producing or nonproducing Staphylococcus epidermidis nasal isolates. Toxin-producing...

Data from: Pre-adapting parasitic phages to a pathogen leads to increased pathogen clearance and lowered resistance evolution with Pseudomonas aeruginosa cystic fibrosis bacterial isolates

Ville-Petri Friman, V-P. Friman, D. Soanes-Brown, P. Sierocinski, A. Buckling, H. K. Johansen, S. Molin & M. Merabishvili
Recent years have seen renewed interest in phage therapy - the use of viruses to specifically kill disease-causing bacteria – because of the alarming rise in antibiotic resistance. However, a major limitation of phage therapy is the ease at with bacteria can evolve resistance to phages. Here we determined if in vitro experimental coevolution can increase the efficiency of phage therapy by limiting the resistance evolution of intermittent and chronic cystic fibrosis Pseudomonas aeruginosa lung...

Data from: Microsatellites for the marsh Fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers

Melanie R. Smee, Yannick Pauchet, Paul Wilkinson, Brian Wee, Michael C. Singer, Richard H. Ffrench-Constant, David J. Hodgson & Alexander S. Mikheyev
BACKGROUND: Until recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of...

Data from: A genetic discontinuity in root-nodulating bacteria of cultivated pea in the Indian trans-Himalayas

Praveen Rahi, Riti Kapoor, J. Peter W. Young & Arvind Gulati
Evolutionary relationships of 120 root-nodulating bacteria isolated from the nodules of Pisum sativum cultivated at 22 different locations of the trans-Himalayan valleys of Lahaul and Spiti in the state of Himachal Pradesh of India were studied using 16S rRNA gene PCR-RFLP, ERIC-PCR, sequencing of 16S rRNA, atpD, recA, nodC and nifH genes, carbon-source utilization pattern (BIOLOG™), and whole-cell fatty acid profiling. The results demonstrated that all isolates belonged to Rhizobium leguminosarum symbiovar viciae (Rlv). Isolates...

Data from: Reframing the evidence base for policy-relevance to increase impact: a case study on forest fragmentation in the oil palm sector

Jennifer M. Lucey, Georgina Palmer, K. Loong Yeong, David P. Edwards, Michael J. M. Senior, Sarah A. Scriven, Glen Reynolds & Jane K. Hill
It is necessary to improve knowledge exchange between scientists and decision-makers so that scientific evidence can be readily accessed to inform policy. To maximise impact of scientific evidence in policy development, the scientific community should engage more fully with decision-makers, building long-term working relationships in order to identify and respond to ‘policy windows’ with science that is reframed for policy-relevance. We illustrate the process and challenges using a case study in which we synthesised evidence...

Data from: Still armed after domestication? Impact of domestication and agronomic selection on silicon defences in cereals

Kimberley J. Simpson, Ruth N. Wade, Mark Rees, Colin P. Osborne & Sue E. Hartley
1. Plant phenotypes reflect trade-offs between competing resource-intensive physiological processes. A shift in resource allocation, away from anti-herbivore defences and towards growth and reproduction, is predicted through plant domestication, such that crops are faster growing and higher yielding than their wild ancestors. These changes are hypothesized to have come at the cost of defence investment, leaving crops ‘disarmed by domestication’. Silicon is the principal anti-herbivore defence in grasses, including many of our most important staple...

Data from: Horizontal transfer of facultative endosymbionts is limited by host relatedness

Piotr Lukasik, Huifang Guo, Margriet Van Asch, Lee M. Henry, H. Charles J. Godfray & Julia Ferrari
Heritable microbial symbionts can have important effects on many aspects of their hosts’ biology. Acquisition of a novel symbiont strain can provide fitness benefits to the host, with significant ecological and evolutionary consequences. We measured barriers to horizontal transmission by artificially transferring facultative symbionts from the grain aphid, Sitobion avenae, and five other aphid species into two clonal genotypes of S. avenae. We found the symbiont Hamiltonella defensa establishes infections more easily following a transfer...

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