19 Works

Mathematica code from Epidemiological dynamics of bacteriocin competition and antibiotic resistance

Sonja Lehtinen, Nicholas J. Croucher, François Blanquart & Christophe Fraser
Mathematica notebook containing the code to reproduce the results.

Mathematica code from Epidemiological dynamics of bacteriocin competition and antibiotic resistance

Sonja Lehtinen, Nicholas J. Croucher, François Blanquart & Christophe Fraser
Mathematica notebook containing the code to reproduce the results.

Supplementary material from \"Epidemiological dynamics of bacteriocin competition and antibiotic resistance\"

Sonja Lehtinen, Nicholas J. Croucher, François Blanquart & Christophe Fraser
Bacteriocins, toxic peptides involved in the competition between bacterial strains, are extremely diverse. Previous work on bacteriocin dynamics has highlighted the role of non-transitive ‘rock–paper–scissors’ competition in maintaining the coexistence of different bacteriocin profiles. The focus to date has primarily been on bacteriocin interactions at the within-host scale (i.e. within a single bacterial population). Yet in species such as Streptococcus pneumoniae, with relatively short periods of colonization and limited within-host diversity, ecological outcomes are also...

Supplementary material from \"The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA\"

Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, COVID-19 Genomics UK (COG-UK) Consortium & Luca Ferretti
The raw material for viral evolution is provided by intra-host mutations occurring either during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the...

COG-UK authorship list from The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, COVID-19 Genomics UK (COG-UK) Consortium & Luca Ferretti
The raw material for viral evolution is provided by intra-host mutations occurring either during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the...

Supplementary Figures and Table from The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, COVID-19 Genomics UK (COG-UK) Consortium & Luca Ferretti
The raw material for viral evolution is provided by intra-host mutations occurring either during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the...

Supplementary Figures and Table from The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, COVID-19 Genomics UK (COG-UK) Consortium & Luca Ferretti
The raw material for viral evolution is provided by intra-host mutations occurring either during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the...

Data from: Clinical spectrum of STX1B-related epileptic disorders

Stefan Wolking, Patrick May, Davide Mei, Rikke S. Møller, Simona Balestrini, Katherine L. Helbig, Cecilia Desmettre Altuzarra, Nicolas Chatron, Charu Kaiwar, Katharina Stoehr, Peter Widdess-Walsh, Bryce A. Mendelsohn, Adam Numis, Maria R. Cilio, Wim Van Paesschen, Lene L. Svendsen, Stephanie Oates, Elaine Hughes, Sushma Goyal, Kathleen Brown, Margarita Sifuentes Saenz, Thomas Dorn, Hiltrud Muhle, Alistair T. Pagnamenta, Dimitris V. Vavoulis … & Julian Schubert
Objective: The aim of this study was to expand the spectrum of epilepsy syndromes related to STX1B, encoding the presynaptic protein syntaxin-1B, and establish genotype-phenotype correlations by identifying further disease-related variants. Methods: We used next generation sequencing in the framework of research projects and diagnostic testing. Clinical data and EEGs were reviewed, including already published cases. To estimate the pathogenicity of the variants, we used established and newly developed in silico prediction tools. Results: We...

Supporting text and figures from Epidemiological dynamics of bacteriocin competition and antibiotic resistance

Sonja Lehtinen, Nicholas J. Croucher, François Blanquart & Christophe Fraser
Additional text and figures in combined pdf file

COG-UK authorship list from The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, COVID-19 Genomics UK (COG-UK) Consortium & Luca Ferretti
The raw material for viral evolution is provided by intra-host mutations occurring either during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the...

Supplementary material from \"The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA\"

Lele Zhao, Matthew Hall, Mariateresa de Cesare, George MacIntyre-Cockett, Katrina Lythgoe, Christophe Fraser, David Bonsall, Tanya Golubchik, COVID-19 Genomics UK (COG-UK) Consortium & Luca Ferretti
The raw material for viral evolution is provided by intra-host mutations occurring either during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the...

Data from: Stable recombination hotspots in birds

Sonal Singhal, Ellen M. Leffler, Keerthi Sannareddy, Isaac Turner, Oliver Venn, Daniel M. Hooper, Alva I. Strand, Qiye Li, Brian Raney, Christopher N. Balakrishnan, Simon C. Griffith, Gil McVean & Molly Przeworski
The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have...

Data from: The global compendium of Aedes aegypti and Ae. albopictus occurrence

Moritz U. G. Kraemer, Marianne E. Sinka, Kirsten A. Duda, Adrian Mylne, Freya M. Shearer, Oliver J. Brady, Janey P. Messina, Christopher M. Barker, Chester G. Moore, Roberta G. Carvalho, Giovanini E. Coelho, Wim Van Bortel, Guy Hendrickx, Francis Schaffner, G. R. William Wint, Iqbal R. F. Elyazar, Hwa-Jen Teng & Simon I. Hay
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN ANOTHER PUBLICATION. PLEASE SEE http://dx.doi.org/10.7554/eLife.08347. Aedes aegypti and Ae. albopictus are the main vectors transmitting dengue and chikungunya viruses. Despite being pathogens of global public health importance, knowledge of their vectors’ global distribution remains patchy and sparse. A global geographic database of known occurrences of Ae. aegypti and Ae. albopictus between 1960 and 2014 was compiled. Herein we present the database, which comprises occurrence data linked...

Data from: A global bionomic database for the dominant vectors of human malaria

N. Claire Massey, Gala Garrod, Antoinette Wiebe, Andrew J. Henry, Zhi Huang, Catherine L. Moyes & Marianne E. Sinka
Anopheles mosquitoes were first recognised as the transmitters of human malaria in the late 19th Century and have been subject to a huge amount of research ever since. Yet there is still much that is unknown regarding the ecology, behaviour (collectively ‘bionomics’) and sometimes even the identity of many of the world’s most prominent disease vectors, much less the within-species variation in their bionomics. Whilst malaria elimination remains an ambitious goal, it is becoming increasingly...

Data from: Zika virus in the Americas: early epidemiological and genetic findings

Nuno Rodrigues Faria, Raimunda Do Socorro Da Silva Azevedo, Moritz U. G. Kraemer, Renato Souza, Mariana Sequetin Cunha, Sarah C. Hill, Julien Thezé, Michael B. Bonsall, Thomas A. Bowden, Ilona Rissanen, Iray Maria Rocco, Juliana Silva Nogueira, Adriana Yurika Maeda, Fernanda Giseli Da Silva Vasami, Fernando Luiz De Lima Macedo, Akemi Suzuki, Sueli Guerreiro Rodrigues, Ana Cecilia Ribeiro Cruz, Bruno Tardeli Diniz, Daniele Barbosa De Almeida Medeiros, Daniela Sueli Guerreiro Rodrigues, Alice Louize Nunes Queiroz, Eliana Vieira Pinto Da Silva, Daniele Freitas Henriques, Elisabeth Salbe Travassos Da Rosa … & Pedro F. C. Vasconcelos
Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015 and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. Using next generation sequencing we generated seven Brazilian ZIKV genomes, sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Phylogenetic and molecular clock analyses show...

Data from: Displayed trees do not determine distinguishability under the network multispecies coalescent

Sha Zhu & James H. Degnan
Recent work in estimating species relationships from gene trees has included inferring networks assuming that past hybridization has occurred between species. Probabilistic models using the multispecies coalescent can be used in this framework for likelihood-based inference of both network topologies and parameters, including branch lengths and hybridization parameters. A difficulty for such methods is that it is not always clear whether, or to what extent, networks are identifiable-that is whether there could be two distinct...

HIV-1 fusion is disrupted by addition of deoxygluose and is rescued with addition of cholesterol

Sergi Padilla-Parra
There has been resurgence in determining the role of host metabolism in viral infection yet deciphering how the metabolic state of single cells affects viral entry and fusion remains unknown. Here, we have developed a novel assay multiplexing genetically-encoded biosensors with single virus tracking (SVT) to evaluate the influence of global metabolic processes on the success rate of virus entry in single cells. We found that cells with a lower ATP:ADP ratio prior to virus...

Supporting text and figures from Epidemiological dynamics of bacteriocin competition and antibiotic resistance

Sonja Lehtinen, Nicholas J. Croucher, François Blanquart & Christophe Fraser
Additional text and figures in combined pdf file

Supplementary material from \"Epidemiological dynamics of bacteriocin competition and antibiotic resistance\"

Sonja Lehtinen, Nicholas J. Croucher, François Blanquart & Christophe Fraser
Bacteriocins, toxic peptides involved in the competition between bacterial strains, are extremely diverse. Previous work on bacteriocin dynamics has highlighted the role of non-transitive ‘rock–paper–scissors’ competition in maintaining the coexistence of different bacteriocin profiles. The focus to date has primarily been on bacteriocin interactions at the within-host scale (i.e. within a single bacterial population). Yet in species such as Streptococcus pneumoniae, with relatively short periods of colonization and limited within-host diversity, ecological outcomes are also...

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