19 Works

Genomics data for the week of February 24-26, 2021


Redox controls RecA protein activity via reversible oxidation of its methionine residues

Benjamin Ezraty, Camille Henry, Frederic Barras, Laurent Loiseau, Alexandra Vergnes, Didier Vertommen, Angela Mérida-Floriano, Sindhu Chitteni-Pattu, Elizabeth Anne Wood, Josep Casadesús & Michael M. Cox
Reactive oxygen species (ROS) cause damage to DNA and proteins. The RecA protein plays a central role in the bacterial response to DNA damage. Here we report that RecA itself is also targeted by ROS. In vivo consequences of RecA oxidation include defects in SOS induction, DNA repair efficiency, and P1 transduction. In vitro, oxidized RecA fails to display ATPase activity, DNA strand exchange capacity and formation of nucleofilaments. Consistently, mass spectrometry analysis of oxidized...

Threatened salmon rely on a rare life history strategy in a warming landscape

Flora Cordoleani, Corey Phillis, Anna Sturrock, Alyssa FitzGerald, George Whitman, Anthony Malkassian, Peter Weber & Rachel Johnson
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams....


Stéphane Ranque

Supplement: Multicenter validated detection of focal cortical dysplasia using deep learning

Ravnoor S Gill, Hyo M Lee, Benoit Caldairou, Seok-Jun Hong, Carmen Barba, Francesco Deleo, Ludovico D’Incerti, Vanessa C Mendes Coelho, Matteo Lenge, Mira Semmelroch, Dewi Schrader, Fabrice Bartolomei, Maxime Guye, Andreas Schulze-Bonhage, Horst Urbach, Kyoo Ho Cho, Fernando Cendes, Renzo Guerrini, Graeme Jackson, R Edward Hogan, Neda Bernasconi & Andrea Bernasconi
Objective. To test the hypothesis that a multicenter-validated computer deep learning algorithm detects MRI-negative focal cortical dysplasia (FCD). Methods. We used clinically acquired 3D T1-weighted and 3D FLAIR MRI of 148 patients (median age, 23 years [range, 2-55]; 47% female) with histologically verified FCD at nine centers to train a deep convolutional neural network (CNN) classifier. Images were initially deemed as MRI-negative in 51% of cases, in whom intracranial EEG determined the focus. For risk...

The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets

Kathryn Stankiewicz, Kate Vasquez Kuntz, Jean-Baptiste Ledoux, Didier Aurelle, Joaquim Garrabou, Yuichi Nakajima, Mikael Dahl, Yuna Zayasu, Sabri Jaziri, Federica Costantini & Iliana Baums
The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the ΔK method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of K and is sensitive to uneven sampling. If this finding holds for empirical datasets, conclusions about the scale of gene flow may have...

Supplementary: Global continental and marine detrital εNd: an updated compilation for use in understanding marine Nd cycling

Suzanne Robinson, Ruza Ivanovic, Tina van de Flierdt, Cecile Blanchet, Kazuyo Tachikawa, Ellen E. Martin, Carys Falko, Trevor Williams, Lauren Gregoire, Yves Plancherel, Catherine Jeandel & Thomas Arsouze
Understanding the role of sediment-water interactions in the oceanic cycling of neodymium (Nd) isotopes is essential for its reliable use as a modern and palaeoceanographic tracer of ocean circulation. However, the exact processes that control Nd cycling in the ocean are poorly defined and require an up-to-date knowledge of the sources, sinks and transformation of this tracer to and within the ocean (e.g. as per the GEOTRACES core mission). We propose a considerable improvement of...

Eco-evolutionary outsiders: establishing in a distantly related neighbourhood delays and reorganizes nutrient recycling

Xu Pan, Mathieu Santonja, Pierre-Emmanuel Courty, Olaf Butenschön, Matty Berg, Phil Murray, Benjamin Yguel, Daphnée Brulé & Andreas Prinzing
Rapid environmental change forces long-lived plants like trees to immigrate into zones still occupied by phylogenetically distantly related species. Does such phylogenetic isolation (PI) change the trees’ ecosystem functioning such as litter decomposition? We studied oaks (Quercus petraea) of low and high PI, reciprocally transplanting their litters to identify effect of aboveground litter quality and belowground decomposer biota. Across 8 and 14 months we quantified decomposition (mass loss, C-loss and N-loss), decomposer biota (Acari, Collembola,...

Is a restricted niche the explanation for species vulnerability? Insights from a large field survey of Astragalus tragacantha L. (Fabaceae)

Alex Baumel, Teddy Baumberger, Pierre-Jean Dumas, Julien Ugo, Laureen Keller, Estelle Dumas, Thierry Tatoni, Lucie Miché, Pascal Mirleau, Isabelle Laffont-Schwob & Laurence Affre
In this study, we examine the realized niche of A. tragacantha in Provence. We focus our fieldwork on habitat characteristics, floristic survey and perform an exhaustive demographic census. We base our analyses on total density and densities of different size stages of A. tragacantha. We delineate its realized ecological niche with the Outlying Mean Index (OMI) multivariate method and estimated the effects of environmental gradients on A. tragacantha populations with the Generalized Joint Attribute Modelling...

Effects of high and low-efficacy therapy in secondary progressive multiple sclerosis

Izanne Roos, Emmanuelle Leray, Romain Casey, Dana Horakova, Eva Havrdova, Guillermo Izquierdo, Sara Eichau, Francesco Patti, Gilles Edan, Marc Debouverie, Jean Pelletier, Serkan Ozakbas, Maria Pia Amato, Pierre Clavelou, Pierre Grammond, Cavit Boz, Katherine Buzzard, Olga Skibina, Jonathan Ciron, Oliver Gerlach, Francois Grand'Maison, Jeannette Lechner-Scott, Charles Malpas, Helmut Butzkueven, Sandra Vukusic … & Tomas Kalincik
Objective: To compare the clinical effectiveness of high- and low-efficacy treatments in patients with recently active and inactive secondary progressive multiple sclerosis (SPMS) after accounting for therapeutic lag. Methods: Patients treated with high- (natalizumab, alemtuzumab, mitoxantrone, ocrelizumab, rituximab, cladribine, fingolimod) or low-efficacy (interferon β, glatiramer acetate, teriflunomide) therapies after SPMS onset were selected from MSBase and OFSEP, two large observational cohorts. Therapeutic lag was estimated for each patient based on their demographic and clinical characteristics....

Raw data for: Biomechanical demands of percussive techniques in the context of early stone toolmaking

Robin Macchi, Guillaume Daver, Michel Brenet, Sandrine Prat, Laurent Hugueville, Sonia Harmand, Jason Lewis & Mathieu Domalain
Recent discoveries in archaeology and palaeoanthropology highlight that stone stool knapping could have emerged first within the genera Australopithecus or Kenyanthropus rather than Homo. To explore the implications of this hypothesis determining the physical demands and motor control needed for performing the percussive movements during the oldest stone toolmaking technology (i.e. Lomekwian) would help. We analysed the joint-angle patterns and muscle activity of a knapping expert using three stone tool replication techniques: unipolar flaking on...


Philippe PAROLA

Complete genomic sequences until May, 2021.

Anthony Levasseur

Data from: High-speed motility originates from cooperatively pushing and pulling flagella bundles in bilophotrichous bacteria

Klaas Bente, Sarah Mohammadinejad, Mohammad A. Charsooghi, Felix Bachmann, Agnese Codutti, Christopher T. Lefèvre, Stefan Klumpp & Damien Faivre
Bacteria propel and change direction by rotating long, helical filaments, called flagella. The number of flagella, their arrangement on the cell body and their sense of rotation hypothetically determine the locomotion characteristics of a species. The movement of the most rapid microorganisms has in particular remained unexplored because of additional experimental limitations. We show that magnetotactic cocci with two flagella bundles on one pole swim faster than 500 μm·s-1 along a double helical path, making...

Warm range margin of boreal bryophytes and lichens not directly limited by temperatures

Caroline Greiser, Johan Ehrlén, Miska Luoto, Eric Meineri, Sonia Merinero, Benny Willman & Kristoffer Hylander
1. Species at their warm range margin are potentially threatened by higher temperatures, but may persist in microrefugia. Whether such microsites occur due to more suitable microclimate or due to lower biotic pressure from e.g. competitive species, is still not fully resolved. 2. We examined whether boreal bryophytes and lichens show signs of direct climate limitation, i.e. whether they perform better in cold and/or humid microclimates at their warm range margin. We transplanted a moss,...

Triangular Regulation of Cucurbit[8]uril 1:1 Complexes

Sébastien Combes, Khoa Truong Tran, Hakim Karoui, David Bardelang, MEHMET MENAF AYHAN, Olivier Ouari, Antal Rockenbauer, Alain Tonetto, Valérie Monnier, Laurence Charles, Roselyne Rosas, Stéphane Viel, Didier Siri, Paul Tordo, Sylvain Clair & Ruibing Wang
Triangular shapes have inspired scientists over time and are common in nature, such as the flower petals of oxalis triangularis, the triangular faces of tetrahedrite crystals, and the icosahedron faces of virus capsids. Supramolecular chemistry has enabled the construction of triangular assemblies, many of which possess functional features. Among these structures, cucurbiturils have been used to build supramolecular triangles, and we recently reported paramagnetic cucurbit[8]uril (CB[8]) triangles, but the reasons for their formation remain unclear....

Prey and predator density-dependent interactions under different water volumes

Ross Cuthbert, Tatenda Dalu, Ryan Wasserman, Arnaud Sentis, Olaf Weyl, William Froneman, Amanda Callaghan & Jaimie Dick
Predation is a critical ecological process that directly and indirectly mediates population stabilities, as well as ecosystem structure and function. The strength of interactions between predators and prey may be mediated by multiple density-dependences concerning numbers of predators and prey. In temporary wetland ecosystems in particular, fluctuating water volumes may alter predation rates through differing search space and prey encounters rates. Using a functional response approach, we examined the influence of predator and prey densities...

Individual high-quality reads (dd-RADsequencing) from: Genomic signatures of clonality in the deep water kelp Laminaria rodriguezii

Lauric Reynes & Didier Aurelle
The development of population genomic approaches in non-model species allows for renewed studies of the impact of reproductive systems and genetic drift on population diversity. Here, we investigate the genomic signatures of partial clonality in the deep water kelp Laminaria rodriguezii, known to reproduce by both sexual and asexual means. We compared these results with the species Laminaria digitata, a closely related species that differs by different traits, in particular its reproductive mode (no clonal...

Effects of cucurbit[n]uril (n = 7, 8, 10) hosts on the formation and stabilization of a naphthalenediimide (NDI) radical anion

Xiran Zhao, Fengbo Liu, Zhiyong Zhao, Hakim Karoui, David Bardelang, Olivier Ouari & Simin Liu
The binding interactions of a NDI diammonium dichloride salt with cucurbit[n]uril (CB[n], n = 7,8, 10) and the formation process of a NDI radical anion upon photoexcitation of the NDI derivative in the presence of a CB[n] host have been investigated.

Registration Year

  • 2021

Resource Types

  • Dataset


  • Aix-Marseille University
  • Méditerranée Infection Foundation
  • University of Rennes 1
  • University of Seville
  • Institut de Chimie Radicalaire
  • Marseille Public University Hospital System
  • VU University Amsterdam
  • South African Institute for Aquatic Biodiversity
  • Dokuz Eylül University
  • University of Newcastle Australia