49 Works

Data from: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420

Nicolas Blondiaux, Martin Moune, Matthieu Desroses, Rosangela Frita, Marion Flipo, Vanessa Mathys, Karine Soetaert, Mehdi Kiass, Vincent Delorme, Kamel Djaout, Vincent Trebosc, Christian Kemmer, René Wintjens, Alexandre Wohlkönig, Rudy Antoine, Ludovic Huot, David Hot, Mireia Coscolla, Julia Feldmann, Sebastien Gagneux, Camille Locht, Priscille Brodin, Marc Gitzinger, Benoit Deprez, Nicolas Willand … & Alain R. Baulard
Antibiotic resistance is one of the biggest threats to human health globally. Alarmingly, multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis have now spread worldwide. Some key antituberculosis antibiotics are prodrugs, for which resistance mechanisms are mainly driven by mutations in the bacterial enzymatic pathway required for their bioactivation. We have developed drug-like molecules that activate a cryptic alternative bioactivation pathway of ethionamide in M. tuberculosis, circumventing the classic activation pathway in which resistance mutations have now...

Data from: Identification of a bacterial pathogen associated with Porites white patch syndrome in the Western Indian Ocean

Mathieu G. Séré, Pablo Tortosa, Pascale Chabanet, Jean-Pascal Quod, Michael J. Sweet & Michael H. Schleyer
Porites white patch syndrome (PWPS) is a coral disease recently described in the western Indian Ocean. This study aimed to isolate and identify potential pathogens associated with PWPS utilising both culture and non-culture screening techniques and inoculation trials. A total of 14 bacterial strains (those dominant in disease lesions, absent or rare in healthy tissues and considered potential pathogens in a previous study) were cultured and used to experimentally inoculate otherwise healthy individuals in an...

Data from: Biogeography of Leptospira in wild animal communities inhabiting the insular ecosystem of the western Indian Ocean islands and neighboring Africa

Muriel Dietrich, Yann Gomard, Erwan Lagadec, Beza Ramasindrazana, Gildas Le Minter, Vanina Guernier, Aude Benlali, Gérard Rocamora, Wanda Markotter, Steve M. Goodman, Koussay Dellagi, Pablo Tortosa & Steven M. Goodman
Understanding the processes driving parasite assemblages is particularly important in the context of zoonotic infectious diseases. Leptospirosis is a widespread zoonotic bacterial infection caused by pathogenic species of the genus Leptospira. Despite a wide range of animal hosts, information is still lacking on the factors shaping Leptospira diversity in wild animal communities, especially in regions, such as tropical insular ecosystems, with high host species richness and complex biogeographical patterns. Using a large dataset (34 mammal...

Data from: Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

Alejandro Couce, Larissa Viraphong Caudwell, Christoph Feinauer, Thomas Hindré, Jean-Paul Feugeas, Martin Weigt, Richard E. Lenski, Dominique Schneider & Olivier Tenaillon
Understanding the extreme variation among bacterial genomes remains an unsolved challenge in evolutionary biology, despite long-standing debate about the relative importance of natural selection, mutation, and random drift. A potentially important confounding factor is the variation in mutation rates between lineages and over evolutionary history, which has been documented in several species. Mutation accumulation experiments have shown that hypermutability can erode genomes over short timescales. These results, however, were obtained under conditions of extremely weak...

Data from: Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli

Colin Raeside, Joël Gaffé, Daniel E. Deatherage, Olivier Tenaillon, Adam M. Briska, Ryan N. Ptashkin, Stéphane Cruveiller, Claudine Médigue, Richard E. Lenski, Jeffrey E. Barrick & Dominique Schneider
Large-scale rearrangements may be important in evolution because they can alter chromosome organization and gene expression in ways not possible through point mutations. In a long-term evolution experiment, twelve Escherichia coli populations have been propagated in a glucose-limited environment for over 25 years. We used whole-genome mapping (optical mapping) combined with genome sequencing and PCR analysis to identify the large-scale chromosomal rearrangements in clones from each population after 40,000 generations. A total of 110 rearrangement...

Data from: Electrophoretic mobility confirms reassortment bias among geographic isolates of segmented RNA phages

Samuel L. Díaz-Muñoz, Olivier Tenaillon, Daniel Goldhill, Kristen Brao, Paul E. Turner & Lin Chao
Background: Sex presents evolutionary costs and benefits, leading to the expectation that the amount of genetic exchange should vary in conditions with contrasting cost-benefit equations. Like eukaryotes, viruses also engage in sex, but the rate of genetic exchange is often assumed to be a relatively invariant property of a particular virus. However, the rates of genetic exchange can vary within one type of virus according to geography, as highlighted by phylogeographic studies of cystoviruses. Here...

Labels strengthen motor learning of new tools

Francois Foerster
These scripts and datasets correspond to the behavioural data of the study "Labels strengthen motor learning of new tools". Participants learnt how to manipulate novel tools either associated with a name (ie. a label). Results show that adding a label to a novel tool reinforces the learning of the tool use throughout practice (SuccessTask script). Moreover, the label influence the participants' ability to move or use the tool (ReactionTimes script).

Data from: An ultrasound image-based dynamic fusion modeling method for predicting the quantitative impact of in vivo liver motion on intraoperative HIFU therapies: investigations in a porcine model

William Apoutou N'Djin, Jean-Yves Chapelon & David Melodelima
Organ motion is a key component in the treatment of abdominal tumors by High Intensity Focused Ultrasound (HIFU), since it may influence the safety, efficacy and treatment time. Here we report the development in a porcine model of an Ultrasound (US) image-based dynamic fusion modeling method for predicting the effect of in vivo motion on intraoperative HIFU treatments performed in the liver in conjunction with surgery. A speckle tracking method was used on US images...

Data from: Long-term outcome in neuroZika: when biological diagnosis matters

Annie Lannuzel, Jean-Louis Fergé, Quentin Lobjois, Aissatou Signate, Benoit Rozé, Benoit Tressières, Yoann Madec, Pascale Poullain, Cécile Herrmann, Fatiha Najioullah, Eavan McGovern, Anne-Charlotte Savidan, Ruddy Valentino, Sébastien Breurec, Raymond Césaire, Etienne Hirsch, Pierre-Marie Lledo, Guillaume Thiery, André Cabié, Françoise Lazarini & Emmanuel Roze
Objectives: To characterize the full spectrum, relative frequency and prognosis of the neurological manifestations in Zika virus (ZIKV) postnatal infection. Methods: We conducted an observational study in consecutive ZIKV-infected patients presenting with neurological manifestations during the French West Indies 2016 outbreak. Results: Eighty-seven patients, including 6 children, were enrolled. Ninety-five percent of all cases required hospitalization. Guillain-Barré syndrome was the most frequent manifestation (46.0%) followed by encephalitis or encephalomyelitis (20.7%), isolated single or multiple cranial...

Data from: Pattern of polyphenol intake and the long-term risk of dementia in older persons

Sophie Lefèvre-Arbogast, David Gaudout, Julien Bensalem, Luc Letenneur, Jean-François Dartigues, Boris P. Hejblum, Catherine Féart, Cécile Delcourt & Cécilia Samieri
Objective: To investigate the optimal combination of dietary polyphenols associated with the long-term risk of dementia in a large prospective French cohort of older persons, the Three-City (3C) Study. Methods: We included 1,329 non-demented older adults from the 3C Study with assessment of intake of 26 polyphenol subclasses and followed for 12 years for dementia. Using Partial Least Square for Cox models, we identified a pattern of polyphenol intake associated with dementia risk. Results: The...

IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Jessika Consuegra, Joël Gaffé, Richard E. Lenski, Thomas Hindre, Jeffrey E. Barrick, Olivier Tenaillon & Dominique Schneider
The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017)...

Data from: Perinatal exposure to glyphosate and a glyphosate-based herbicide affect spermatogenesis in mice

Thu Ha Pham, Lohann Derian, Christine Kervarrec, Pierre-Yves Kernanec, Bernard Jégou, Fatima Smagulova & Aurore Gely-Pernot
Glyphosate is the most widely used herbicide in the world. Several studies have investigated the effects of glyphosate and glyphosate-based-herbicides (GBHs) on male reproduction, but there is still little and conflicting evidence for its toxicity. In this study, we analyzed the effects of glyphosate, alone or in formula, on the male reproductive system. Pregnant mice were treated from E10.5 to 20 days postpartum (dpp) by adding glyphosate or a GBH (Roundup® 3 Plus) to their...

Data from: Detecting adaptive convergent amino acid evolution

Carine Rey, Vincent Lanore, Philippe Veber, Laurent Guéguen, Nicolas Lartillot, Marie Sémon & Bastien Boussau
In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed...

Data from: Screening test for neutralizing antibodies against yellow fever virus, based on a flavivirus pseudotype

Séverine Mercier-Delarue, Christine Durier, Nathalie Colin De Verdière, Jean-Dominique Poveda, VIncent Meiffrédy, Maria Dolores Fernandez Garcia, Stephane Lastère, Raymond Césaire, Jean-Claude Manuggera, Jean-Michel Molina, Ali Amara & François Simon
Given the possibility of yellow fever virus reintroduction in epidemiologically receptive geographic areas, the risk of vaccine supply disruption is a serious issue. New strategies to reduce the doses of injected vaccines should be evaluated very carefully in terms of immunogenicity. The plaque reduction test for the determination of neutralizing antibodies (PRNT) is particularly time-consuming and requires the use of a confinement laboratory. We have developed a new test based on the use of a...

Data from: Tempo and mode of genome evolution in a 50,000-generation experiment

Olivier Tenaillon, Jeffrey E. Barrick, Noah Ribeck, Daniel E. Deatherage, Jeffrey L. Blanchard, Aurko Dasgupta, Gabriel C. Wu, Sébastien Wielgoss, Stéphane Cruveiller, Claudine Médigue, Dominique Schneider & Richard E. Lenski
Adaptation by natural selection depends on the rates, effects and interactions of many mutations, making it difficult to determine what proportion of mutations in an evolving lineage are beneficial. Here we analysed 264 complete genomes from 12 Escherichia coli populations to characterize their dynamics over 50,000 generations. The populations that retained the ancestral mutation rate support a model in which most fixed mutations are beneficial, the fraction of beneficial mutations declines as fitness rises, and...

Data from: Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli

Jessica Plucain, Thomas Hindré, Mickaël Le Gac, Olivier Tenaillon, Stéphane Cruveiller, Claudine Médigue, Nicholas Leiby, William R. Harcombe, Christopher J. Marx, Richard E. Lenski & Dominique Schneider
Ecological opportunities promote population divergence into coexisting lineages. However, the genetic mechanisms that enable new lineages to exploit these opportunities are poorly understood except in cases of single mutations. We examined how two Escherichia coli lineages diverged from their common ancestor at the outset of a long-term coexistence. By sequencing genomes and reconstructing the genetic history of one lineage, we showed that three mutations together were sufficient to produce the frequency-dependent fitness effects that allowed...

Data from: Phylogeny of seven Bulinus species originating from endemic areas in three African countries, in relation to the human blood fluke Schistosoma haematobium

Rima Zein-Eddine, Félicité Flore Djuikwo-Teukeng, Mustafa Al-Jawhari, Bruno Senghor, Tine Huyse & Gilles Dreyfuss
Background: Snails species belonging to the genus Bulinus (Planorbidae) serve as intermediate host for flukes belonging to the genus Schistosoma (Digenea, Platyhelminthes). Despite its importance in the transmission of these parasites, the evolutionary history of this genus is still obscure. In the present study, we used the partial mitochondrial cytochrome oxidase subunit I (cox1) gene, and the nuclear ribosomal ITS, 18S and 28S genes to investigate the haplotype diversity and phylogeny of seven Bulinus species...

Data from: Asthma-like symptoms in homeless children in the Greater Paris area in 2013: prevalence, associated factors and utilization of healthcare services in the ENFAMS survey

Delphine Lefeuvre, Marie-Christine Delmas, Christophe Marguet, Pierre Chauvin & Stéphanie Vandentorren
Asthma remains poorly studied in homeless children. We sought to estimate the prevalence of asthma-like symptoms (ALS) and to identify the factors associated with ALS and healthcare service utilisation. Materials and Methods: A cross-sectional survey of a random sample of sheltered homeless families was conducted by interviewing 801 parents of children (0–12 years) in 17 languages. ALS were defined as wheezing or night cough without fever during the previous year. Poisson regression models with robust...

Data from: Risks of 23 specific malformations associated with prenatal exposure to ten antiepileptic drugs

Pierre-Olivier Blotière, Fanny Raguideau, Alain Weill, Elisabeth Elefant, Isabelle Perthus, Véronique Goulet, Florence Rouget, Mahmoud Zureik, Joël Coste & Rosemary Dray-Spira
Objective: To assess the association between exposure to monotherapy with 10 different antiepileptic drugs (AED) during the first two months of pregnancy and the risk of 23 major congenital malformations (MCMs). Methods: This nationwide cohort study, based on the French healthcare databases, included all pregnancies&[ge]20 weeks and ending between January 2011 and March 2015. Women were considered to be exposed when an AED had been dispensed between one month before and two months after the...

Data from: Evaluation of exposure to effervescent drugs in a large health check-up population in France: a cross-sectional study

Germain Perrin, Sarah Berdot, Frédérique Thomas, Bruno Pannier, Nicolas Danchin, Pierre Durieux & Brigitte Sabatier
OBJECTIVES: The relationship between high dietary sodium intake and hypertension is well established. Some drugs are associated with high-sodium content, particularly effervescent tablets (ETs). Despite a possible cardiovascular risk associated with the use of such drugs, observational data describing exposure to ETs in ambulatory subjects are lacking. The aim of this study was to estimate the prevalence of exposure to ETs, and to highlight factors associated with this exposure, in a large French health check-up...

Data from: Changing landscapes of Southeast Asia and rodent-borne diseases: decreased diversity but increased transmission risks

Serge Morand, Kim Blasdell, Frédéric Bordes, Philippe Buchy, Bernard Carcy, Kittipong Chaisiri, Yannick Chaval, Julien Claude, Jean-François Cosson, Marc Desquesnes, Sathaporn Jittapalapong, Tawisa Jiyipong, Anamika Karnchanabanthoen, Pumhom Pornpan, Jean-Marc Rolain & Annelise Tran
The reduction in biodiversity through land use changes due to urbanization and agricultural intensification, appears linked to major epidemiological changes in many human diseases. Increasing disease risks and the emergence of novel pathogens appear to result from increased contact between wildlife, domesticated animals and humans. We investigate how increasing human domination of the environment may favor generalist and synanthropic rodent species and affect the diversity and prevalence of rodent-borne pathogens in Southeast Asia, a hotspot...

Data from: The temporal dynamics and infectiousness of subpatent Plasmodium falciparum infections in relation to parasite density

Hannah C. Slater, Amanda Ross, Ingrid Felger, Natalie E. Hofmann, Leanne Robinson, Jackie Cook, Bronner P. Gonçalves, Anders Björkman, Andre Lin Ouedraogo, Ulrika Morris, Mwinyi Msellem, Cristian Koepfli, Ivo Mueller, Fitsum Tadesse, Endalamaw Gadisa, Smita Das, Gonzalo Domingo, Melissa Kapulu, Janet Midega, Seth Owusu-Agyei, Cécile Nabet, Renaud Piarroux, Ogobara Doumbo, Safiatou Niare Doumbo, Kwadwo Koram … & Lucy C. Okell
Malaria infections occurring below the limit of detection of standard diagnostics are common in all endemic settings. However, key questions remain surrounding their contribution to sustaining transmission and whether they need to be detected and targeted to achieve malaria elimination. In this study we analyse a range of malaria datasets to quantify the density, detectability, course of infection and infectiousness of subpatent infections. Asymptomatically infected individuals have lower parasite densities on average in low transmission...

Genotype count for all coding variants in type I IFN genes investigated in 659 life-threatening COVID-19 patients and 534 asymptomatic/mild infected controls

Aurélie Cobat
Clinical outcome upon infection with SARS-CoV-2 ranges from silent infection to lethal COVID-19. We have found an enrichment in rare variants predicted to be loss-of-function (LOF) at the 13 human loci known to govern TLR3- and IRF7-dependent type I interferon (IFN) immunity to influenza virus, in 659 patients with life-threatening COVID-19 pneumonia, relative to 534 subjects with asymptomatic or benign infection. By testing these and other rare variants at these 13 loci, we experimentally define...

Data from: Convergent evolution of sperm gigantism and the developmental origins of sperm size variability in Caenorhabditis nematodes

Anne Vielle, Nicolas Callemeyn-Torre, Clotilde Gimond, Nausicaa Poullet, Jeremy C. Gray, Asher D. Cutter & Christian Braendle
Sperm cells provide essential, if usually diminutive, ingredients to successful sexual reproduction. Despite this conserved function, sperm competition and coevolution with female traits can drive spectacular morphological change in these cells. Here, we characterize four repeated instances of convergent evolution of sperm gigantism in Caenorhabditis nematodes using phylogenetic comparative methods on 26 species. Species at the extreme end of the 50-fold range of sperm-cell volumes across the genus have sperm capable of comprising up to...

Data from: Immune checkpoint inhibitor–related myositis and myocarditis in patients with cancer

Mehdi Touat, Thierry Maisonobe, Samuel Knauss, Omar Ben Hadj Salem, Baptiste Hervier, Karine Auré, Tali-Anne Szwebel, Nora Kramkimel, Claire Lethrosne, Jean-Frédéric Bruch, Pauline Laly, Jacques Cadranel, Nicolas Weiss, Anthony Béhin, Yves Allenbach, Olivier Benveniste, Timothée Lenglet, Dimitri Psimaras, Werner Stenzel & Sarah Léonard-Louis
Objective: To report the clinicopathological features and outcome of myositis in patients treated with immune checkpoint inhibitors (irMyositis). Methods: We retrospectively analyzed patients diagnosed with irMyositis in tertiary centers in Paris, France, and Berlin, Germany, from January 2015, to July 2017. Main outcomes were clinical manifestations and muscle histology, which included MHC-I, C5b-9, CD3, CD4, CD8, CD20, CD68, PD-1, PD-L1 and PD-L2 immunohistochemical stains. Results: Ten patients with metastatic cancer were included; median age was...

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  • Inserm
  • French National Centre for Scientific Research
  • Michigan State University
  • The University of Texas at Austin
  • Paris Descartes University
  • Grenoble Alpes University
  • Charité
  • King's College London
  • Sorbonne University
  • University of Lille