33 Works

Data from: Progressive genome-wide introgression in agricultural Campylobacter coli

Samuel K. Sheppard, Xavier Didelot, Keith A. Jolley, Aaron E. Darling, David J. Kelly, Alison Cody, Frances M. Colles, Norval J.C. Strachan, Iain D. Ogden, Ken Forbes, Nigel P. French, Philip Carter, William G. Miller, Noel D. McCarthy, Robert Owen, Eva Litrup, Michael Egholm, Stephen D. Bentley, Julian Parkhill, Martin C. J. Maiden, Daniel Falush, Jason P. Affourtit, Norval J. C. Strachan, Ben Pascoe & Guillaume Meric
Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been...

Data from: Weekend admission as an independent predictor of mortality: an analysis of Scottish hospital admissions

Adam E. Handel, Sunil V. Patel, Andrew Skingsley, Katrina Bramley, Roma Sobieski & Sreeram V. Ramagopalan
OBJECTIVES: Weekend admissions have been shown to be associated with an increased risk of mortality compared with weekday admissions for many diagnoses. We analysed emergency department admissions within the Scottish National Health Service to investigate whether mortality is increased in case of weekend emergency department admissions. DESIGN: A cohort study. SETTING: Scotland National Health Service (NHS) emergency departments. PARTICIPANTS: 5 271 327 emergency department admissions between 1999 and 2009. We included all patients admitted via...

Data from: Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

Samuel K. Sheppard, Xavier Didelot, Guillaume Meric, Alicia Torralbo, Keith A. Jolley, David J. Kelly, Stephen D. Bentley, Martin C. J. Maiden, Julian Parkhill & Daniel Falush
Genome-wide association studies have the potential to identify causal genetic factors underlying important phenotypes but have rarely been performed in bacteria. We present an association mapping method that takes into account the clonal population structure of bacteria and is applicable to both core and accessory genome variation. Campylobacter is a common cause of human gastroenteritis as a consequence of its proliferation in multiple farm animal species and its transmission via contaminated meat and poultry. We...

Data from: An antibody screen of a Plasmodium vivax antigen library identifies novel merozoite proteins associated with clinical protection

Camila T. França, Jessica B. Hostetler, Sumana Sharma, Michael T. White, Enmoore Lin, Benson Kiniboro, Andreea Waltmann, Andrew W. Darcy, Connie S. Li Wai Suen, Peter Siba, Christopher L. King, Julian C. Rayner, Rick M. Fairhurst, Ivo Mueller & Connie S. N. Li Wai Suen
Background. Elimination of Plasmodium vivax malaria would be greatly facilitated by the development of an effective vaccine. A comprehensive and systematic characterization of antibodies to P. vivax antigens in exposed populations is useful in guiding rational vaccine design. Methodology/Principal Findings. In this study, we investigated antibodies to a large library of P. vivax entire ectodomain merozoite proteins in 2 Asia-Pacific populations, analysing the relationship of antibody levels with markers of current and cumulative malaria exposure,...

Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

Francine Kershaw, Inês Carvalho, Jacqueline Loo, Cristina Pomilla, Peter B. Best, Ken P. Findlay, Salvatore Cerchio, Tim Collins, Marcia H. Engel, Gianna Minton, Peter Ersts, Jaco Barendse, P. G. H. Kotze, Yvette Razafindrakoto, Solange Ngouessono, Michael Meӱer, Meredith Thornton & Howard C. Rosenbaum
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample,...

Data from: Gray matter volume modifications in migraine: a cross-sectional and longitudinal study

Roberta Messina, Maria A. Rocca, Bruno Colombo, Elisabetta Pagani, Andrea Falini, Peter J. Goadsby & Massimo Filippi
Objective. To explore cross-sectional and longitudinal gray matter (GM) volume changes in migraine patients and their association with patients’ clinical characteristics and disease activity. Methods. Brain T2-weighted and 3D T1-weighted scans were acquired from 73 episodic migraineurs and 46 age- and sex-matched non-migraine controls at baseline. Twenty-four migraineurs and 25 controls agreed to be re-examined after a mean follow-up of 4 years. Using a general linear model and SPM12, a whole-brain analysis was performed to...

Data from: A comparative survey of the frequency and distribution of polymorphism in the genome of Xenopus tropicalis

Chris Showell, Samantha Carruthers, Amanda Hall, Fernando Pardo-Manuel De Villena, Derek Stemple & Frank L. Conlon
Naturally occurring DNA sequence variation within a species underlies evolutionary adaptation and can give rise to phenotypic changes that provide novel insight into biological questions. This variation exists in laboratory populations just as in wild populations and, in addition to being a source of useful alleles for genetic studies, can impact efforts to identify induced mutations in sequence-based genetic screens. The Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as a model system...

Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Samuel K. Sheppard, Lu Cheng, Guillaume Méric, Caroline P. A. De Haan, Ann-Katrin Llarena, Pekka Marttinen, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Thomas R. Connor, Norval J. C. Strachan, Ken Forbes, Frances M. Colles, Keith A. Jolley, Stephen D. Bentley, Martin C. J. Maiden, Marja-Liisa Hänninen, Julian Parkhill, William P. Hanage & Jukka Corander
Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major...

Data from: Novel R pipeline for analyzing Biolog phenotypic microarray data

Minna Vehkala, Mikhail Shubin, Thomas R. Connor, Nicholas R. Thomson & Jukka Corander
Data produced by Biolog Phenotype MicroArrays are longitudinal measurements of cells’ respiration on distinct substrates. We introduce a three-step pipeline to analyze phenotypic microarray data with novel procedures for grouping, normalization and effect identification. Grouping and normalization are standard problems in the analysis of phenotype microarrays defined as categorizing bacterial responses into active and non-active, and removing systematic errors from the experimental data, respectively. We expand existing solutions by introducing an important assumption that active...

Data from: Biofilm morphotypes and population structure among Staphylococcus epidermidis from commensal and clinical samples

Llinos Harris, Susan Murray, Ben Pascoe, James Bray, Guillaume Meric, Leonardos Magerios, Thomas S. Wilkinson, Rose E. Jeeves, Holger Rohde, Stefan Schwarz, Herminia De Lencastre, Maria Miragaia, Joana Rolo, Rory Bowden, Keith A. Jolley, Martin C. J. Maiden, Dietrich Mack, Samuel Sheppard, Llinos G. Harris, Rose Jeeves & Samuel K. Sheppard
Bacterial species comprise related genotypes that can display divergent phenotypes with important clinical implications. Staphylococcus epidermidis is a common cause of nosocomial infections and, critical to its pathogenesis, is its ability to adhere and form biofilms on surfaces, thereby moderating the effect of the host’s immune response and antibiotics. Commensal S. epidermidis populations are thought to differ from those associated with disease in factors involved in adhesion and biofilm accumulation. We quantified the differences in...

Data from: Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes

Philip Francis Thomsen, Peter Rask Møller, Eva Egelyng Sigsgaard, Steen Wilhelm Knudsen, Ole Ankjær Jørgensen & Eske Willerslev
Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental...

Data from: Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary

Liang Liu, Jin Zhang, Frank E. Rheindt, Fumin Lei, Yanhua Qu, Yu Wang, Yu Zhang, Corwin Sullivan, Wenhui Nie, Jinhuan Wang, Fengtang Yang, Jinping Chen, Scott V. Edwards, Jin Meng & Shaoyuan Wu
The timing of the diversification of placental mammals relative to the Cretaceous–Paleogene (KPg) boundary mass extinction remains highly controversial. In particular, there have been seemingly irreconcilable differences in the dating of the early placental radiation not only between fossil-based and molecular datasets but also among molecular datasets. To help resolve this discrepancy, we performed genome-scale analyses using 4,388 loci from 90 taxa, including representatives of all extant placental orders and transcriptome data from flying lemurs...

Data from: Is predictability salient? A study of attentional capture by auditory patterns

Rosy Southwell, Anna Baumann, Cécile Gal, Nicolas Barascud, Karl Friston & Maria Chait
In this series of behavioural and electroencephalography (EEG) experiments, we investigate the extent to which repeating patterns of sounds capture attention. Work in the visual domain has revealed attentional capture by statistically predictable stimuli, consistent with predictive coding accounts which suggest that attention is drawn to sensory regularities. Here, stimuli comprised rapid sequences of tone pips, arranged in regular (REG) or random (RAND) patterns. EEG data demonstrate that the brain rapidly recognizes predictable patterns manifested...

Data from: Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution

Aude Gilabert, Thomas D. Otto, Gavin G. Rutledge, Blaise Franzon, Benjamin Ollomo, Céline Arnathau, Patrick Durand, Nancy D. Moukodoum, Alain-Prince Okouga, Barthélémy Ngoubangoye, Boris Makanga, Larson Boundenga, Christophe Paupy, François Renaud, Franck Prugnolle & Virginie Rougeron
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, Plasmodium vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long and short read sequence technologies two new P. vivax-like reference...

Data from: Assessing the complex architecture of polygenic traits in diverged yeast populations

Francisco A Cubillos, Eleonora Billi, Enikö Zörgö, Leopold Parts, Patrick Fargier, Stig Omholt, Anders Blomberg, Jonas Warringer, Edward J Louis & Gianni Liti
Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is to identify the causative variants driving phenotypic variation. Recently the baker’s yeast, Saccharomyces cerevisiae has emerged as a powerful model for dissecting complex traits. However, past studies using a laboratory strain were unable to reveal the complete architecture of polygenic traits. Here, we present a linkage study using 576 recombinant strains obtained from...

Data from: First circumglobal assessment of Southern Hemisphere humpback whale mitochondrial genetic variation and implications for management

Howard C. Rosenbaum, Francine Kershaw, Martin Mendez, Cristina Pomilla, Matthew S. Leslie, Ken P. Findlay, Peter B. Best, Timothy Collins, Michel Vely, Marcia H. Engel, Robert Baldwin, Gianna Minton, Michael Meyer, Lillian Florez-Gonzalez, M. Michael Poole, Nan Hauser, Claire Garrigue, Muriel Brasseur, John Bannister, Megan Anderson, Carlos Olavarria & C. Scott Baker
The description of genetic population structure over a species’ geographic range can provide insights into its evolutionary history and also support effective management efforts. Assessments for globally distributed species are rare, however, requiring significant international coordination and collaboration. The global distribution of demographically discrete populations for the humpback whale Megaptera novaeangliae is not fully known, hampering the definition of appropriate management units. Here, we present the first circumglobal assessment of mitochondrial genetic population structure across...

Data from: No evidence for maintenance of a sympatric Heliconius species barrier by chromosomal inversions

John W. Davey, Sarah L. Barker, Pasi M. Rastas, Ana Pinharanda, Simon H. Martin, Richard Durbin, W. Owen McMillan, Richard M. Merrill & Chris D. Jiggins
Mechanisms that suppress recombination are known to help maintain species barriers by preventing the breakup of coadapted gene combinations. The sympatric butterfly species Heliconius melpomene and Heliconius cydno are separated by many strong barriers, but the species still hybridize infrequently in the wild, and around 40% of the genome is influenced by introgression. We tested the hypothesis that genetic barriers between the species are maintained by inversions or other mechanisms that reduce between-species recombination rate....

Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell & Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and...

Data from: Formin is associated with left-right asymmetry in the pond snail and the frog

Angus Davison, Gary S. McDowell, Jennifer M. Holden, Harriet F. Johnson, Georgios D. Koutsovoulos, M. Maureen Liu, Paco Hulpiau, Frans Van Roy, Christopher M. Wade, Ruby Banerjee, Fengtang Yang, Satoshi Chiba, John W. Davey, Daniel J. Jackson, Michael Levin & Mark L. Blaxter
While components of the pathway that establishes left-right asymmetry have been identified in diverse animals, from vertebrates to flies, it is striking that the genes involved in the first symmetry-breaking step remain wholly unknown in the most obviously chiral animals, the gastropod snails. Previously, research on snails was used to show that left-right signaling of Nodal, downstream of symmetry breaking, may be an ancestral feature of the Bilateria. Here, we report that a disabling mutation...

Data from: Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

Christopher E. Laumer, Harald Gruber-Vodicka, Michael G. Hadfield, Vicki B. Pearse, Ana Riesgo, John C. Marioni & Gonzalo Giribet
The phylogenetic placement of the morphologically simple placozoans is crucial to understanding the evolution of complex animal traits. Here, we examine the influence of adding new genomes from placozoans to a large dataset designed to study the deepest splits in the animal phylogeny. Using site-heterogeneous substitution models, we show that it is possible to obtain strong support, in both amino acid and reduced-alphabet matrices, for either a sister-group relationship between Cnidaria and Placozoa, or for...

Data from: Two-phase importance sampling for inference about transmission trees

Elina Numminen, Claire Chewapreecha, Jukka Sirén, Claudia Turner, Paul Turner, Stephen D. Bentley, Jukka Corander & J. Siren
There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary...

Data from: The kinetochore prevents centromere-proximal crossover recombination during meiosis

Nadine Vincenten, Lisa-Marie Kuhl, Isabel Lam, Ashwini Oke, Alastair R. W. Kerr, Andreas Hochwagen, Jennifer C. Fung, Scott Keeney, Gerben Vader & Adèle L. Marston
During meiosis, crossover recombination is essential to link homologous chromosomes and drive 22 faithful chromosome segregation. Crossover recombination is non-random across the genome, 23 and centromere-proximal crossovers are associated with an increased risk of aneuploidy, 24 including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub- 25 complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers 26 in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the 27...

Data from: Genome-wide meta-analysis of sciatica in Finnish population

Susanna Lemmelä, Svetlana Solovieva, Rahman Shiri, Christian Benner, Markku Heliövaara, Johannes Kettunen, Verneri Anttila, Samuli Ripatti, Markus Perola, Ilkka Seppälä, Markus Juonala, Mika Kähönen, Veikko Salomaa, Jorma Viikari, Olli Raitakari, Terho Lehtimäki, Aarno Palotie, Eira Viikari-Juntula, Kirsti Husgafvel-Pursiainen, Olli T. Raitakari & Eira Viikari-Juntura
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291...

Data from: The perceptual shaping of anticipatory actions

Giovanni Maffei, Ivan Herreros, Marti Sanchez-Fibla, Karl J. Friston & Paul F.M.J. Verschure
Humans display anticipatory motor responses to minimize the adverse effects of predictable perturbations. A widely accepted explanation for this behavior relies on the notion of an inverse model that, learning from motor errors, anticipates corrective responses. Here, we propose and validate the alternative hypothesis that anticipatory control can be realized through a cascade of purely sensory predictions that drive the motor system, reflecting the causal sequence of the perceptual events preceding the error. We compare...

Data from: Galcanezumab in chronic migraine: the randomized, double-blind, placebo-controlled REGAIN study

Holland C. Detke, Peter J. Goadsby, Shufang Wang, Deborah I. Friedman, Katherine J. Selzler & Sheena K. Aurora
Objective: To evaluate the efficacy and safety of galcanezumab, a humanized monoclonal antibody that selectively binds to calcitonin gene-related peptide (CGRP), in the preventive treatment of chronic migraine. Methods: REGAIN was a Phase 3 study with a 3-month double-blind, placebo-controlled treatment phase and a 9-month open-label extension. Eligible patients 18-65 years of age with chronic migraine were randomized 2:1:1 to monthly subcutaneous injections of placebo (n = 558), galcanezumab 120 mg (with a 240-mg loading...

Registration Year

  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
  • 2010

Resource Types

  • Dataset


  • Wellcome Trust
  • University of Cambridge
  • University of Edinburgh
  • University of Helsinki
  • University of Oxford
  • Swansea University
  • Mahidol University
  • Ghent University
  • University of Pretoria
  • Columbia University