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720 results on '"Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)"'

1. A longitudinal survey in the wild reveals major shifts in fish host microbiota after parasite infection

Author

Eglantine Mathieu-Begne, Simon Blanchet, Olivier Rey, Eve Toulza, Charlotte Veyssière, Sophie Manzi, Maxim Lefort, Orlane Scelsi, Géraldine Loot, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)

Subjects
Individual survey, host-parasite interaction, coinfection, individual survey, Co-infection, bacteria community, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, metabarcoding, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Metabarcoding, Genetics, Host-parasite interaction, Bacteria community, Ecology, Evolution, Behavior and Systematics, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Recent studies have highlighted associations between diseases and host microbiota. It is yet extremely challenging-especially under natural conditions-to clarify whether the host microbiota promotes future infections, or whether changes in host microbiota result from infections. Nonetheless, deciphering between these two processes is essential for highlighting the role of microbes in disease progression. We longitudinally surveyed, in the wild, the microbiota of individual fish hosts (Leuciscus burdigalensis) both before and after infection by a crustacean ectoparasite (Tracheliastes polycolpus). We found a striking association between parasite infection and the host microbiota composition restricted to the fins the parasite anchored. We clearly demonstrated that infections by the parasite induced a shift in (and did not result from) the host fin microbiota. Fin microbiota further got similar to that of the adult stage, and the free-living infective stage of the parasite during infection with a predominance of the Burkholderiaceae bacteria family. This suggests that Burkholderiaceae bacteria is involved in a co-infection process and possibly facilitate T. polycolpus infection. We reveal novel mechanistic insights for understanding the role of the microbiota in host-parasite interactions, which has implications for predicting the progression of diseases in natural host populations.

Published
2023

2. Electronic Structure and Geometry of the Lowest 2LMCT State of Fe(III) Potential Fluorescent Emitters

Author

Tabea Huss, Isabelle M. Dixon, Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
Inorganic Chemistry, [CHIM]Chemical Sciences, Physical and Theoretical Chemistry
Abstract

International audience; Metal complexes with a 3d6 electron count are emerging as an alternative to 4d6-based photosensitizers, emitters, or photoredox catalysts. In recent years several Fe(II) potential emitters have been proposed, based on strongly donating ligand sets. Those tend to facilitate oxidation to their 3d5 species, whose photophysics is based on low-lying ligand-to-metal charge transfer (LMCT) states. The geometry and electronic structure of 2LMCT states are unveiled in this work.

Published
2023

3. Connectivity among thermal habitats buffers the effects of warm climate on life‐history traits and population dynamics

Author

Félix Pellerin, Elvire Bestion, Laurane Winandy, Lucie Di Gesu, Murielle Richard, Robin Aguilée, Julien Cote, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), and ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011)

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, Population Dynamics, Lizard, Animals, Climate change, Lizards, Habitat fragmentation, Animal Science and Zoology, Dispersal, Experiments, Life History Traits, Ecosystem, Ecology, Evolution, Behavior and Systematics
Abstract

Contemporary climate change affects population dynamics, but its influence varies with landscape structure. It is still unclear whether landscape fragmentation buffers or amplifies the effects of climate on population size and the age and body size of individuals composing these populations. This study aims to investigate the impacts of warm climates on lizard life-history traits and population dynamics in habitats that vary in their connectivity. We monitored common lizard Zootoca vivipara populations for 3 years in an experimental system in which both climatic conditions and connectivity among habitats were simultaneously manipulated. We considered two climatic treatments (i.e. present-day climate and warm climate [+1.4°C than present-day climate]) and two connectivity treatments (i.e. a connected treatment in which individuals could move from one climate to the other and an isolated treatment in which movement between climates was not possible). We monitored survival, reproduction, growth, dispersal, age and body size of each individual in the system as well as population density through time. We found that the influence of warm climates on life-history traits and population dynamics depended on connectivity among thermal habitats. Populations in warm climates were (i) composed of younger individuals only when isolated; (ii) larger in population size only in connected habitats and (iii) composed of larger age-specific individuals independently of the landscape configuration. The connectivity among habitats altered population responses to climate warming likely through asymmetries in the flow and phenotype of dispersers between thermal habitats. Our results demonstrate that landscape fragmentation can drastically change the dynamics and persistence of populations facing climate change.Le changement climatique actuel impacte la dynamique des populations, mais son influence varie avec la structure du paysage. A ce jour, il est difficile de prédire si la fragmentation du paysage réduit ou augmente les effets du réchauffement climatique sur la taille des populations, ainsi que sur l'âge et la taille corporelle des individus qui composent ces populations. Cette étude s'intéresse aux impacts d'un climat plus chaud sur les traits d'histoire de vie et la dynamique de populations vivant dans des habitats qui diffèrent quant à leur niveau de connectivité. Pendant trois ans, nous avons suivi des populations de lézards vivipares Zootoca vivipara au sein d'un dispositif expérimental qui permet de manipuler simultanément les conditions climatiques et le niveau de connectivité entre habitats. Nous avons considéré deux traitements climatiques [i.e., climat actuel et climat chaud (+1.4°C plus chaud que le climat actuel)] et deux traitements de connectivité (i.e., un traitement connecté au sein duquel les individus pouvaient se déplacer d'un climat à un autre, et un traitement isolé au sein duquel les déplacements entre climats n'étaient pas permis). Tout au long de l'expérience, nous avons mesuré la survie, la reproduction, la croissance, la dispersion, l'âge et la taille corporelle de chaque individu ainsi que la densité des populations. Nous avons observé que l'influence du climat chaud sur les traits d'histoire de vie et la dynamique de population dépendait du niveau de connectivité entre habitats. Les populations en climat chaud étaient composées (i) d'individus plus jeunes seulement en habitat isolé, (ii) de plus d'individus uniquement en habitat connecté et (iii) d'individus plus grands à âge égal et ce indépendamment de la configuration du paysage. Nos résultats montrent que le niveau de connectivité entre habitats altère les réponses des populations au réchauffement climatique via une asymétrie dans le flux et le phénotype des dispersants entre climats. Nos résultats démontrent que la fragmentation du paysage peut influencer de façon drastique la dynamique et la persistance des populations face au changement climatique.

Published
2022

4. Chiral spin liquids with projected Gaussian fermionic entangled pair states

Author

Niu, Sen, Li, Jheng-Wei, Chen, Ji-Yao, Poilblanc, Didier, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), PHotonique, ELectronique et Ingénierie QuantiqueS (PHELIQS), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Fermions Fortement Corrélés (LPT) (FFC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Condensed Matter - Strongly Correlated Electrons, Strongly Correlated Electrons (cond-mat.str-el), FOS: Physical sciences, [PHYS.COND.CM-SCE]Physics [physics]/Condensed Matter [cond-mat]/Strongly Correlated Electrons [cond-mat.str-el]
Abstract

International audience; We study the parton construction of chiral spin liquids (CSLs) using projected Gaussian fermionic entangled pair states (GfPEPSs). First, we show that GfPEPSs can represent generic spinless Chern insulators faithfully with finite bond dimensions. Then, by applying the Gutzwiller projection to a bi-layer GfPEPSs, spin-1/2 Abelian and non-Abelian CSLs are obtained for Chern number $C=1$ and $C=2$, respectively. As a consequence of the topological obstruction for GfPEPSs, very weak Gossamer tails are observed in the correlation functions of the fermionic projected entangled pair state (PEPS) ansatze, suggesting that the no-go theorem for chiral PEPS is universal but does not bring any practical limitation. Remarkably, without fine tuning, all topological sectors can be constructed showing the expected number of chiral branches in the respective entanglement spectra, providing a sharp improvement with respect to the known bosonic PEPS approach.

Published
2023

5. A physical noise model for quantum measurements

Author

Loulidi, Faedi, Nechita, Ion, Pellegrini, Clément, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Toulouse UMR5219 (IMT), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
noise, Quantum Physics, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], quantum state, FOS: Physical sciences, measurement theory, Quantum Physics (quant-ph)
Abstract

International audience; In this paper we introduce a novel noise model for quantum measurements motivated by an indirect measurement scheme with faulty preparation. Averaging over random dynamics governing the interaction between the quantum system and a probe, a natural, physical noise model emerges. We compare it to existing noise models (uniform and depolarizing) in the framework of incompatibility robustness. We observe that our model allows for larger compatibility regions for specific classes of measurements.

Published
2023

6. Breaking the chains: extreme value statistics and localization in random spin chains

Author

Colbois, Jeanne, Laflorencie, Nicolas, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Condensed Matter - Strongly Correlated Electrons, Quantum Physics, Statistical Mechanics (cond-mat.stat-mech), Strongly Correlated Electrons (cond-mat.str-el), [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], FOS: Physical sciences, Disordered Systems and Neural Networks (cond-mat.dis-nn), Condensed Matter - Disordered Systems and Neural Networks, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Quantum Physics (quant-ph), Condensed Matter - Statistical Mechanics
Abstract

Despite a very good understanding of single-particle Anderson localization in one-dimensional (1D) disordered systems, many-body effects are still full of surprises, a famous example being the interaction-driven many-body localization (MBL) problem, about which much has been written, and perhaps the best is yet to come. Interestingly enough the non-interacting limit provides a natural playground to study non-trivial multiparticle physics, offering the possibility to test some general mechanisms with very large-scale exact diagonalization simulations. In this work, we first revisit the 1D many-body Anderson insulator through the lens of extreme value theory, focusing on the extreme polarizations of the equivalent spin chain model in a random magnetic field. A many-body-induced chain breaking mechanism is explored numerically, and compared to an analytically solvable toy model. A unified description, from weak to large disorder strengths $W$ emerges, where the disorder-dependent average localization length $\xi(W)$ governs the extreme events leading to chain breaks. In particular, tails of the local magnetization distributions are controlled by $\xi(W)$. Remarkably, we also obtain a quantitative understanding of the full distribution of the extreme polarizations, which is given by a Fr\'echet-type law. In a second part, we explore finite interaction physics and the MBL question. For the available system sizes, we numerically quantify the difference in the extreme value distributions between the interacting problem and the non-interacting Anderson case. Strikingly, we observe a sharp "extreme-statistics transition" as $W$ changes, which may coincide with the MBL transition., Comment: 18 + 6 pages; 13 + 4 figures

Published
2023

7. Resilient infinite randomness criticality for a disordered chain of interacting Majorana fermions

Author

Chepiga, Natalia, Laflorencie, Nicolas, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Condensed Matter - Strongly Correlated Electrons, Quantum Physics, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], Statistical Mechanics (cond-mat.stat-mech), Strongly Correlated Electrons (cond-mat.str-el), FOS: Physical sciences, Disordered Systems and Neural Networks (cond-mat.dis-nn), [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Condensed Matter - Disordered Systems and Neural Networks, Quantum Physics (quant-ph), Condensed Matter - Statistical Mechanics
Abstract

The quantum critical properties of interacting fermions in the presence of disorder are still not fully understood. While it is well known that for Dirac fermions, interactions are irrelevant to the non-interacting infinite randomness fixed point (IRFP), the problem remains largely open in the case of Majorana fermions which further display a much richer disorder-free phase diagram. Here, pushing the limits of DMRG simulations, we carefully examine the ground-state of a Majorana chain with both disorder and interactions. Building on appropriate boundary conditions and key observables such as entanglement, energy gap, and correlations, we strikingly find that the non-interacting Majorana IRFP is very stable against finite interactions, in contrast with previous claims., 5+2 pages, 5+4 figures

Published
2023

8. Classical fully-packed loop model with attractive interactions on the square lattice

Author

Dabholkar, Bhupen, Ran, Xiaoxue, Rong, Junchen, Yan, Zheng, Sreejith, G. J., Meng, Zi Yang, Alet, Fabien, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut des Hautes Études Scientifiques (IHES), and IHES

Subjects
Condensed Matter - Strongly Correlated Electrons, Strongly Correlated Electrons (cond-mat.str-el), Statistical Mechanics (cond-mat.stat-mech), FOS: Physical sciences, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Condensed Matter - Statistical Mechanics
Abstract

We study a classical model of fully-packed loops on the square lattice, which interact through attractive loop segment interactions between opposite sides of plaquettes. This study is motivated by effective models of interacting quantum matter arising in frustrated magnets or Rydberg atom arrays, for which loop degrees of freedom appear at low energy. Through a combination of Monte Carlo simulations and an effective height field theory, we find that the critical point known to occur at infinite temperature gives rise to a high-temperature critical phase with floating exponents. At lower temperature, the system transitions via a Kosterlitz-Thouless phase transition to a nematic phase where lattice rotation symmetry is broken. We discuss consequences for the phase diagram of the quantum loop model on the same lattice., 10+2 pages, 6+3 figures

Published
2023

9. Tensor network variational optimizations for real-time dynamics: application to the time-evolution of spin liquids

Author

Ponnaganti, Ravi Teja, Mambrini, Matthieu, Poilblanc, Didier, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Condensed Matter - Strongly Correlated Electrons, Strongly Correlated Electrons (cond-mat.str-el), Quantum Gases (cond-mat.quant-gas), FOS: Physical sciences, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], Condensed Matter - Quantum Gases
Abstract

Within the Projected Entangled Pair State (PEPS) tensor network formalism, a simple update (SU) method has been used to investigate the time evolution of a two-dimensional U(1) critical spin-1/2 spin liquid under Hamiltonian quench [Phys. Rev. B 106, 195132 (2022)]. Here we introduce two different variational frameworks to describe the time dynamics of SU(2)-symmetric translationally-invariant PEPS, aiming to improve the accuracy. In one approach, after using a Trotter-Suzuki decomposition of the time evolution operator in term of two-site elementary gates, one considers a single bond embedded in an environment approximated by a Corner Transfer Matrix Renormalization Group (CTMRG). A variational update of the two tensors on the bond is performed under the application of the elementary gate and then, after symmetrization of the site tensors, the environment is updated. In the second approach, a cluster optimization is performed on a finite (periodic) cluster, maximizing the overlap of the exact time-evolved state with a symmetric finite-size PEPS ansatz. Observables are then computed on the infinite lattice contracting the infinite-PEPS (iPEPS) by CTMRG. We show that the variational schemes outperform the SU method and remain accurate over a significant time interval before hitting the entanglement barrier. Studying the spectrum of the transfer matrix, we find that the asymptotic correlations are very well preserved under time evolution, including the critical nature of the singlet correlations, as expected from the Lieb-Robinson (LR) bound theorem. Consistently, the system (asymptotic) boundary is found to bedescribed by the same Conformal Field Theory of central charge c = 1 during time evolution. We also compute the time-evolution of the short distance spin-spin correlations and estimate the LR velocity., Comment: Minor revisions have been implemented following the suggestions provided by the referees

Published
2023

10. Polytope compatibility: from quantum measurements to magic squares

Author

Bluhm, Andreas, Nechita, Ion, Schmidt, Simon, Calculs algorithmes programmes et preuves (CAPP), Laboratoire d'Informatique de Grenoble (LIG), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre for the Mathematics of Quantum Theory (QMATH), Department of Mathematical Sciences [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), PHC program Star (Applications of randommatrix theory and abstract harmonic analysis to quantum information theory), ANR-20-CE47-0014,ESQuisses,Évolutions Stochastiques Quantiques(2020), ANR-20-CE40-0008,STARS,Espace de trafics et asymptotiques de spectres aléatoires(2020), and European Project

Subjects
Quantum information, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], ION NECHITA, [MATH.MATH-MP]Mathematics [math]/Mathematical Physics [math-ph], matrix convex set, Magic square, Joint measurability, SIMON SCHMIDT, Polytope, Measurement compatibility, ANDREAS BLUHM
Abstract

37 pages, 3 figures; Several central problems in quantum information theory (such as measurement compatibility and quantum steering) can be rephrased as membership in the minimal matrix convex set corresponding to special polytopes (such as the hypercube or its dual). In this article, we generalize this idea and introduce the notion of polytope compatibility, by considering arbitrary polytopes. We find that semiclassical magic squares correspond to Birkhoff polytope compatibility. In general, we prove that polytope compatibility is in one-to-one correspondence with measurement compatibility, when the measurements have some elements in common and the post-processing of the joint measurement is restricted. Finally, we consider how much tuples operators with appropriate joint numerical range have to be scaled in the worst case in order to become polytope compatible and give both analytical sufficient conditions and numerical ones based on linear programming.

Published
2023

11. Data-driven discovery of stochastic dynamical equations of collective motion

Author

Nabeel, Arshed, Jadhav, Vivek, M, Danny Raj, Sire, Clément, Theraulaz, Guy, Escobedo, Ramón, Iyer, Srikanth K., Guttal, Vishwesha, Physique Statistique des Systèmes Complexes (LPT) (PhyStat), Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur la Cognition Animale - UMR5169 (CRCA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Indo-French Centre for the Promotion of Advanced Research (project N°64T4-B), and GT also gratefully acknowledges the Indian Institute of Science for support via Infosys Visiting Chair Professor at the Centre for Ecological Sciences, IISc, Bengaluru.

Subjects
[PHYS]Physics [physics], [SCCO]Cognitive science, Biological Physics (physics.bio-ph), FOS: Biological sciences, FOS: Physical sciences, Physics - Biological Physics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quantitative Biology - Quantitative Methods, Quantitative Methods (q-bio.QM), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; Abstract Coarse-grained descriptions of collective motion of flocking systems are often derived for the macroscopic or the thermodynamic limit. However, many real flocks are small sized (10 to 100 individuals), called the mesoscopic scales, where stochasticity arising from the finite flock sizes is important. Developing mesoscopic scale equations, typically in the form of stochastic differential equations, can be challenging even for the simplest of the collective motion models. Here, we take a novel data-driven equation learning approach to construct the stochastic mesoscopic descriptions of a simple self-propelled particle (SPP) model of collective motion. In our SPP model, a focal individual can interact with k randomly chosen neighbours within an interaction radius. We consider k = 1 (called stochastic pairwise interactions), k = 2 (stochastic ternary interactions), and k equalling all available neighbours within the interaction radius (equivalent to Vicsek-like local averaging). The data-driven mesoscopic equations reveal that the stochastic pairwise interaction model produces a novel form of collective motion driven by a multiplicative noise term (hence termed, noise-induced flocking). In contrast, for higher order interactions (k > 1), including Vicsek-like averaging interactions, yield collective motion driven primarily by the deterministic forces. We find that the relation between the parameters of the mesoscopic equations describing the dynamics and the population size are sensitive to the density and to the interaction radius, exhibiting deviations from mean-field theoretical expectations. We provide semi-analytic arguments potentially explaining these observed deviations. In summary, our study emphasizes the importance of mesoscopic descriptions of flocking systems and demonstrates the potential of the data-driven equation discovery methods for complex systems studies.

Published
2023

12. Investigating the genetic basis of vertebrate dispersal combining <scp>RNA</scp> ‐seq, <scp>RAD</scp> ‐seq and quantitative genetics

Author

Luis M. San‐Jose, Elvire Bestion, Félix Pellerin, Murielle Richard, Lucie Di Gesu, Jordi Salmona, Laurane Winandy, Delphine Legrand, Camille Bonneaud, Olivier Guillaume, Olivier Calvez, Kathryn R. Elmer, Andrey A. Yurchenko, Hans Recknagel, Jean Clobert, Julien Cote, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Centre for Ecology and Conservation, University of Exeter, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), and European Project: ERC-2018-CoG-817779,ECOFEED

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, Genetics, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms that regulate it and link it to other phenotypic aspects in order to form the so-called dispersal syndromes. Here, we comprehensively combined quantitative genetics, genome-wide sequencing and transcriptome sequencing to investigate the genetic basis of natal dispersal in a known ecological and evolutionary model of vertebrate dispersal: the common lizard, Zootoca vivipara. Our study supports the heritability of dispersal in semi-natural populations, with less variation attributable to maternal and natal environment effects. In addition, we found an association between natal dispersal and both variation in the carbonic anhydrase (CA10) gene, and in the expression of several genes (TGFB2, SLC6A4, NOS1) involved in central nervous system functioning. These findings suggest that neurotransmitters (serotonin and nitric oxide) are involved in the regulation of dispersal and shaping dispersal syndromes. Several genes from the circadian clock (CRY2, KCTD21) were also differentially expressed between disperser and resident lizards, supporting that the circadian rhythm, known to be involved in long-distance migration in other taxa, might affect dispersal as well. Since neuronal and circadian pathways are relatively well conserved across vertebrates, our results are likely to be generalisable, and we therefore encourage future studies to further investigate the role of these pathways in shaping dispersal in vertebrates.

Published
2023

13. Bi-orthonormal orbital optimization with a cheap core-electron free three-body correlation factor for Quantum Monte Carlo and Transcorrelation

Author

Ammar, Abdallah, Scemama, Anthony, Giner, Emmanuel, Laboratoire de Chimie et Physique Quantiques Laboratoire (LCPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de chimie théorique (LCT), and Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Chemical Physics (physics.chem-ph), [PHYS]Physics [physics], Physics - Chemical Physics, FOS: Physical sciences
Abstract

We introduce a novel three-body correlation factor that is designed to vanish in the core region around each nucleus and approach a universal two-body correlation factor for valence electrons. The Transcorrelated Hamiltonian is used to optimize the orbitals of a single Slater determinant within a biorthonormal framework. The Slater-Jastrow wave function is optimized on a set of atomic and molecular systems containing both second-row elements and $3d$ transition metal elements. The optimization of the correlation factor and the orbitals, along with increasing the basis set, results in a systematic lowering of the Variational Monte Carlo energy for all systems tested. Importantly, the optimal parameters of the correlation factor obtained for atomic systems are transferable to molecules. Additionally, the present correlation factor is computationally efficient, using a mixed analytical-numerical integration scheme that reduces the costly numerical integration from $\mathbb{R}^6$ to $\mathbb{R}^3$., Comment: 18 pages, 7 figures

Published
2023

14. Lizards from warm and declining populations are born with extremely short telomeres

Author

Andréaz Dupoué, Pauline Blaimont, Frédéric Angelier, Cécile Ribout, David Rozen-Rechels, Murielle Richard, Donald Miles, Pierre de Villemereuil, Alexis Rutschmann, Arnaud Badiane, Fabien Aubret, Olivier Lourdais, Sandrine Meylan, Julien Cote, Jean Clobert, Jean-François Le Galliard, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Rider University, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Ohio University, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), CEREEP-Ecotron Ile de France (UMS 3194), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ANR-13-JSV7-0011,DESTRESS,Dégradation de l'habitat et stress hormonal : combiner théorie physiologique et biologie de la conservation(2013), ANR-17-CE02-0013,AQUATHERM,Rôles de la régulation hydrique et thermique dans les réponses écologiques au changement climatique(2017), European Project: 87779,ECOFEED, European Project, Le Galliard, Jean-François, Jeunes Chercheuses et Jeunes Chercheurs - Dégradation de l'habitat et stress hormonal : combiner théorie physiologique et biologie de la conservation - - DESTRESS2013 - ANR-13-JSV7-0011 - JC - VALID, Rôles de la régulation hydrique et thermique dans les réponses écologiques au changement climatique - - AQUATHERM2017 - ANR-17-CE02-0013 - AAPG2017 - VALID, ECOFEED - ECOFEED - 0000-00-00 - 0000-00-00 - 87779 - VALID, Interreg POCTEFA ECTOPYR - INCOMING, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE)

Subjects
Risk, Aging, Multidisciplinary, [SDE.MCG]Environmental Sciences/Global Changes, Reproduction, aging, Population Dynamics, Lizards, ectotherms, Telomere, telomeres, Extinction, Biological, Global Warming, life-history tradeoffs, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Animals, [SDV.BA.ZV] Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Telomere Shortening, population extinction
Abstract

Aging is the price to pay for acquiring and processing energy through cellular activity and life history productivity. Climate warming can exacerbate the inherent pace of aging, as illustrated by a faster erosion of protective telomere DNA sequences. This biomarker integrates individual pace of life and parental effects through the germline, but whether intra- and intergenerational telomere dynamics underlies population trends remains an open question. Here, we investigated the covariation between life history, telomere length (TL), and extinction risk among three age classes in a cold-adapted ectotherm ( Zootoca vivipara ) facing warming-induced extirpations in its distribution limits. TL followed the same threshold relationships with population extinction risk at birth, maturity, and adulthood, suggesting intergenerational accumulation of accelerated aging rate in declining populations. In dwindling populations, most neonates inherited already short telomeres, suggesting they were born physiologically old and unlikely to reach recruitment. At adulthood, TL further explained females’ reproductive performance, switching from an index of individual quality in stable populations to a biomarker of reproductive costs in those close to extirpation. We compiled these results to propose the aging loop hypothesis and conceptualize how climate-driven telomere shortening in ectotherms may accumulate across generations and generate tipping points before local extirpation.

Published
2023

15. Novel operational index reveals rapid recovery of genetic connectivity in freshwater fish species after riverine restoration

Author

Jérôme G. Prunier, Géraldine Loot, Charlotte Veyssiere, Nicolas Poulet, Simon Blanchet, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Office français de la biodiversité (OFB), Institut de mécanique des fluides de Toulouse (IMFT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)

Subjects
genetic connectivity, genetic monitoring, restoration, potamodromous, Ecology, F INDEX, weirs, [PHYS.MECA.MEFL]Physics [physics]/Mechanics [physics]/Fluid mechanics [physics.class-ph], low-head dams, fish passes, Ecology, Evolution, Behavior and Systematics, dam removal, Nature and Landscape Conservation
Abstract

International audience; Hyperfragmentation of rivers by anthropogenic barriers is a major threat to biodiversity. Restoration policies are being adopted worldwide to mitigate these impacts, particularly those on fish connectivity. We assessed the utility of a novel genetic index of fragmentation, the F INDEX , by monitoring real-time responses of two fish genera to restoration operations at 11 weirs in France. The F INDEX outperformed traditional genetic tools, detecting barriers more efficiently, and thereby improving estimates of recovery of connectivity following restoration. Most weirs had significant impacts on connectivity before restoration, especially the highest and steepest ones. Restoration actions systematically improved genetic connectivity, sometimes completely and in just a few months, with an overall halving of fragmentation levels. Our study demonstrates that current restoration policies are recovering genetic connectivity efficiently, and that practitioners may benefit from the F INDEX as a new operational tool to assess barrier strength for nonmigratory organisms and to plan and monitor riverine restoration.

Published
2023

16. Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates

Author

Lydia Hadjeras, Marie Bouvier, Isabelle Canal, Leonora Poljak, Quentin Morin-Ogier, Carine Froment, Odile Burlet-Schlitz, Lina Hamouche, Laurence Girbal, Muriel Cocaign-Bousquet, Agamemnon J. Carpousis, Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de pharmacologie et de biologie structurale (IPBS), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-13-BSV6-0005,memRNase,Localisation membranaire de la RNase E : rôle dans la maturation, la surveillance et la dégradation des ARNm(2013), ANR-16-CE12-0014,IB-mRND,Biologie integrative de la dégradation des ARN messagers(2016), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010)

Subjects
General Immunology and Microbiology, inner membrane protein, RNase E, General Neuroscience, [SDV]Life Sciences [q-bio], ribosome quality control, RNA degradosome, General Agricultural and Biological Sciences, ribosome assembly, General Biochemistry, Genetics and Molecular Biology
Abstract

RNA processing and degradation shape the transcriptome by generating stable molecules that are necessary for translation (rRNA and tRNA) and by facilitating the turnover of mRNA, which is necessary for the posttranscriptional control of gene expression. In bacteria and the plant chloroplast, RNA degradosomes are multienzyme complexes that process and degrade RNA. In many bacterial species, the endoribonuclease RNase E is the central component of the RNA degradosome. RNase E-based RNA degradosomes are inner membrane proteins in a large family of gram-negative bacteria (β- and γ-Proteobacteria). Until now, the reason for membrane localization was not understood. Here, we show that a mutant strain of Escherichia coli, in which the RNA degradosome is localized to the interior of the cell, has high levels of 20S and 40S particles that are defective intermediates in ribosome assembly. These particles have aberrant protein composition and contain rRNA precursors that have been cleaved by RNase E. After RNase E cleavage, rRNA fragments are degraded to nucleotides by exoribonucleases. In vitro, rRNA in intact ribosomes is resistant to RNase E cleavage, whereas protein-free rRNA is readily degraded. We conclude that RNA degradosomes in the nucleoid of the mutant strain interfere with cotranscriptional ribosome assembly. We propose that membrane-attached RNA degradosomes in wild-type cells control the quality of ribosome assembly after intermediates are released from the nucleoid. That is, the compact structure of mature ribosomes protects rRNA against cleavage by RNase E. Turnover of a proportion of intermediates in ribosome assembly explains slow growth of the mutant strain. Competition between mRNA and rRNA degradation could be the cause of slower mRNA degradation in the mutant strain. We conclude that attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA precursors, thus explaining the reason for conservation of membrane-attached RNA degradosomes throughout the β- and γ-Proteobacteria.

Published
2023

17. Plant litter chemistry drives long‐lasting changes in the catabolic capacities of soil microbial communities

Author

Bourget, Malo, Fanin, Nicolas, Fromin, Nathalie, Hättenschwiler, Stephan, Roumet, Catherine, Shihan, Ammar, Huys, Raoul, Sauvadet, Marie, Freschet, Grégoire, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Ecologie fonctionnelle et biogéochimie des sols et des agro-écosystèmes (UMR Eco&Sols), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
microbial catabolic capacities, leaf litter, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, root litter, soil microbial communities, litter decomposition, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study, legacy effects, litter traits
Abstract

International audience; Although microbial communities play an important role in explaining plant litter decomposition rates, whether and how litter chemistry may alter catabolic capacities of soil microbial communities remains poorly studied.During a 1-year litter decomposition experiment of 12 herbaceous species with contrasting litter chemistry, we examined the effect of plant litter type (roots vs. leaves) and litter chemical traits on the resulting capacity of soil microbial communities to degrade a wide range of carbon substrates of variable complexity (MicroResp™ method).Litter chemistry impacted both the total catabolic activity as well as specific catabolic capacities of microbial communities. In the early stages of litter decomposition total catabolic activity was mainly influenced by the amount of C and N in litter leachates, and litter N, P and Mg, then, later, by lignin concentrations. Some specific catabolic capacities could also be related to litter initial chemistry. Overall, litter trait effects on soil microbial communities decreased over time and the relative importance of traits shifted during the decomposition process.Our results highlight that litter chemistry is a strong driver of catabolic capacities of microbial decomposers and, while its effect fades with time, it remains substantial throughout the litter decomposition process. These long-lasting effects of litter chemistry suggest a persistent control on microbial catabolic capacities in ecosystems with recurrent litter production. Soil microbial catabolic activities were driven by broadly the same chemical traits across leaf and root litters.Synthesis. Such long-lasting effects of litter chemistry on catabolic capacities of microbial communities may represent a substantial indirect driver of the decomposition process. Disentangling the relative importance of this overlooked effect of litter chemistry on decomposition represents the next challenge. We argue that such research line should open ground-breaking perspectives for reconsidering our current understanding of the mechanistic links between litter traits and decomposition rate.

Published
2023

18. Clarifying the effect of biodiversity on productivity in natural ecosystems with longitudinal data and methods for causal inference

Author

Dee, Laura E, Ferraro, Paul J, Severen, Christopher N, Kimmel, Kaitlin A, Borer, Elizabeth T, Byrnes, Jarrett E K, Clark, Adam Thomas, Hautier, Yann, Hector, Andrew, Raynaud, Xavier, Reich, Peter B, Wright, Alexandra J, Arnillas, Carlos A, Davies, Kendi F, MacDougall, Andrew, Mori, Akira S, Smith, Melinda D, Adler, Peter B, Bakker, Jonathan D, Brauman, Kate A, Cowles, Jane, Komatsu, Kimberly, Knops, Johannes M H, McCulley, Rebecca L, Moore, Joslin L, Morgan, John W, Ohlert, Timothy, Power, Sally A, Sullivan, Lauren L, Stevens, Carly, Loreau, Michel, Sub Ecology and Biodiversity, Ecology and Biodiversity, University of Colorado [Boulder], University of Minnesota [Twin Cities] (UMN), University of Minnesota System, University of Massachusetts [Boston] (UMass Boston), University of Massachusetts System (UMASS), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Karl-Franzens-Universität Graz, German Centre for Integrative Biodiversity Research (iDiv), Utrecht University [Utrecht], Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Western Sydney University, University of Michigan System, California State University [Los Angeles] (CAL STATE LA), University of Toronto at Scarborough, Université Saint-Francis-Xavier (CANADA), Yokohama National University, Colorado State University [Fort Collins] (CSU), University of Washington [Seattle], University of Alabama [Tuscaloosa] (UA), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), CEREEP-Ecotron Ile De France (CNRS/ENS UMS 3194), Regional Council of Ile- de-France (DIM Program R2DS I-05-098/R), GoF/ANR’s Investissements d’Avenir program (ANR-11-INBS-0001 AnaEE France, ANR-10-IDEX- 0001-02 PSL), Sub Ecology and Biodiversity, and Ecology and Biodiversity

Subjects
Identification, Multidisciplinary, Ecology, Chemistry(all), Biochemistry, Genetics and Molecular Biology(all), Resistance, General Physics and Astronomy, Instrumental variables, General Chemistry, Biodiversity, Physics and Astronomy(all), Plants, General Biochemistry, Genetics and Molecular Biology, Time, Causality, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Plant diversity, Alter, Biomass, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Guide, In-differences, Ecosystem
Abstract

Causal effects of biodiversity on ecosystem functions can be estimated using experimental or observational designs — designs that pose a tradeoff between drawing credible causal inferences from correlations and drawing generalizable inferences. Here, we develop a design that reduces this tradeoff and revisits the question of how plant species diversity affects productivity. Our design leverages longitudinal data from 43 grasslands in 11 countries and approaches borrowed from fields outside of ecology to draw causal inferences from observational data. Contrary to many prior studies, we estimate that increases in plot-level species richness caused productivity to decline: a 10% increase in richness decreased productivity by 2.4%, 95% CI [−4.1, −0.74]. This contradiction stems from two sources. First, prior observational studies incompletely control for confounding factors. Second, most experiments plant fewer rare and non-native species than exist in nature. Although increases in native, dominant species increased productivity, increases in rare and non-native species decreased productivity, making the average effect negative in our study. By reducing the tradeoff between experimental and observational designs, our study demonstrates how observational studies can complement prior ecological experiments and inform future ones.

Published
2023

19. Plastic responses to warmer climates: a semi-natural experiment on lizard populations

Author

Elvire Bestion, Luis M San-Jose, Lucie Di Gesu, Murielle Richard, Barry Sinervo, Jessica Côte, Olivier Calvez, Olivier Guillaume, Julien Cote, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), ANR-11-INBS-0001,ANAEE-FR,ANAEE-Services(2011), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-12-JSV7-0004,FRADISYN,Populations fragmentées et syndromes dispersants : des gènes à la dynamique des métapopulations(2012), and European Project: ERC-2018-CoG-817779,ECOFEED

Subjects
Thermal physiology, intergenerational effects, climate change, Ectotherm, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, natural selection, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, General Agricultural and Biological Sciences, lizard, phenotypic plasticity, Ecology, Evolution, Behavior and Systematics
Abstract

Facing warming environments, species can exhibit plastic or microevolutionary changes in their thermal physiology to adapt to novel climates. Here, using semi-natural mesocosms, we experimentally investigated over two successive years whether a 2°C-warmer climate produces selective and inter- and intragenerational plastic changes in the thermal traits (preferred temperature and dorsal coloration) of the lizard Zootoca vivipara. In a warmer climate, the dorsal darkness, dorsal contrast, and preferred temperature of adults plastically decreased and covariances between these traits were disrupted. While selection gradients were overall weak, selection gradients for darkness were slightly different between climates and in the opposite direction to plastic changes. Contrary to adults, male juveniles were darker in warmer climates either through plasticity or selection and this effect was strengthened by intergenerational plasticity when juveniles’ mothers also experienced warmer climates. While the plastic changes in adult thermal traits alleviate the immediate overheating costs of warming, its opposite direction to selective gradients and to juveniles’ phenotypic responses may slow down evolutionary shifts toward phenotypes that are better adapted to future climates. Our study demonstrates the importance of considering inter- and intragenerational plasticity along with selective processes to better understand adaptation and population dynamics in light of climate change.

Published
2023

20. TREXIO: A File Format and Library for Quantum Chemistry

Author

Evgeny Posenitskiy, Vijay Gopal Chilkuri, Abdallah Ammar, Michał Hapka, Katarzyna Pernal, Ravindra Shinde, Edgar Josué Landinez Borda, Claudia Filippi, Kosuke Nakano, Otto Kohulák, Sandro Sorella, Pablo de Oliveira Castro, William Jalby, Pablo López Ríos, Ali Alavi, Anthony Scemama, Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques Laboratoire (LCPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Qubit Pharmaceuticals, Systèmes étendus et magnétisme (LCPQ) (SEM), Aix Marseille Université (AMU), University of Warsaw (UW), Łódź University of Technology, Institute for Nanotechnology (MESA+), University of Twente, National Institute for Materials Science (NIMS), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Laboratoire d'Informatique Parallélisme Réseaux Algorithmes Distribués (LI-PaRAD), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Max Planck Institute for Solid State Research, Max-Planck-Gesellschaft, Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), European Project: 952165,H2020,H2020-INFRAEDI-2019-1,Trex(2020), Université Paris-Saclay, Computational Chemical Physics, and MESA+ Institute

Subjects
quantum chemistry, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Chemical Physics (physics.chem-ph), data, Physics - Chemical Physics, physics.chem-ph, 2023 OA procedure, General Physics and Astronomy, quantum chemistry data interoperability, FOS: Physical sciences, interoperability, Physical and Theoretical Chemistry
Abstract

TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and exchanging wave function parameters and matrix elements, making it an important tool for researchers in the field of quantum chemistry. In this work, we present an overview of the TREXIO file format and library. The library consists of a front-end implemented in the C programming language and two different back-ends: a text back-end and a binary back-end utilizing the HDF5 library which enables fast read and write operations. It is compatible with a variety of platforms and has interfaces for the Fortran, Python, and OCaml programming languages. In addition, a suite of tools has been developed to facilitate the use of the TREXIO format and library, including converters for popular quantum chemistry codes and utilities for validating and manipulating data stored in TREXIO files. The simplicity, versatility, and ease of use of TREXIO make it a valuable resource for researchers working with quantum chemistry data., Comment: 13 pages, 2 figures

Published
2023
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21. High redshift constraints on extended logotropic models

Author

Benaoum, Hachemi B, Chavanis, Pierre-Henri, Luongo, Orlando, Muccino, Marco, Quevedo, Hernando, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Logotropic models, Dark energy, Astronomy and Astrophysics, [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph]
Abstract

International audience; A single logotropic fluid, responsible for the existence of the whole dark sector, is here extensively revised at intermediate redshifts. In particular, by investigating possible generalizations that conceptually overcome previous issues of standard logotropic scenarios, we fix bound over classes of logotropic models that exhibit additional terms in the equation of state. Employing σ8 measurements combined with low redshift data sets of Supernovae and Hubble observational data, we show the statistical significance of those extensions and their departure from the standard cosmological model. Evidences against generalized versions of logotropic models are, in particular, prompted. Our outcomes definitively show that any departure from the original logotropic model, including the Anton–Schmidt dark energy, are clearly disfavored at the level of perturbations and/or background cosmology. This indicates that, in order to have a logotropic fluid, plausible generalized versions of it would point out to reduce the complexity of the fluid itself, instead of adding extra terms.

Published
2023

22. The self-gravitating Fermi gas in Newtonian gravity and general relativity

Author

Chavanis, Pierre-Henri, HEP, INSPIRE, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Fermi-Dirac statistics, [PHYS.GRQC] Physics [physics]/General Relativity and Quantum Cosmology [gr-qc], Black holes, Astrophysics::High Energy Astrophysical Phenomena, FOS: Physical sciences, White dwarfs, Dark matter halos, Astrophysics::Cosmology and Extragalactic Astrophysics, General Relativity and Quantum Cosmology (gr-qc), General Relativity and Quantum Cosmology, Neutron stars, [PHYS.GRQC]Physics [physics]/General Relativity and Quantum Cosmology [gr-qc], Astrophysics::Galaxy Astrophysics
Abstract

International audience; We review the history of the self-gravitating Fermi gas in Newtonian gravity and general relativity. We mention applications to white dwarfs, neutron stars and dark matter halos. We describe the nature of instabilities and phase transitions in the self-gravitating Fermi gas as energy (microcanonical ensemble) or temperature (canonical ensemble) is reduced. When $NN_{\rm OV}$, a new turning point appears at an energy $E"_c$ below which the system experiences a gravitational collapse towards a black hole [P.H. Chavanis, G. Alberti, Phys. Lett. B 801, 135155 (2020)]. When $N_{\rm OV}N'_*$, the condensed branch disappears and the instability at $E_c$ directly leads to a black hole. We discuss implications of these results for dark matter halos made of massive neutrinos.

Published
2023

23. Transcorrelated selected configuration interaction in a bi-orthonormal basis and a cheap three-body correlation factor

Author

Ammar, Abdallah, Scemama, Anthony, Giner, Emmanuel, Laboratoire de Chimie et Physique Quantiques Laboratoire (LCPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques (LCPQ), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Laboratoire de chimie théorique (LCT), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and European Project: 952165,H2020,H2020-INFRAEDI-2019-1,Trex(2020)

Subjects
[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, Chemical Physics (physics.chem-ph), Physics - Chemical Physics, FOS: Physical sciences
Abstract

In this work, we develop a mathematical framework for a Selected Configuration Interaction (SCI) algorithm within a bi-orthogonal basis for transcorrelated (TC) calculations. The bi-orthogonal basis used here serves as the equivalent of the standard Hartree Fock (HF) orbitals. However, within the context of TC, it leads to distinct orbitals for the left and right vectors. Our findings indicate that the use of such a bi-orthogonal basis allows for a proper definition of the frozen core approximation. In contrast, the use of HF orbitals results in bad error cancellations for ionization potentials and atomization energies (AE). Compared to HF orbitals, the optimized bi-orthogonal basis significantly reduces the positive part of the second-order energy (PT2), thereby facilitating the use of standard extrapolation techniques of hermitian SCI. While we did not observe a significant improvement in the convergence of the SCI algorithm, this is largely due to the use in the present work of a simple three-body correlation factor introduced in a recent study. This correlation factor, which depends only on atomic parameters, eliminates the need for re-optimization of the correlation factor for molecular systems, making its use straightforward and user-friendly. Despite the simplicity of this correlation factor, we were able to achieve accurate results on the AE of a series of 14 molecules in a triple-zeta basis. We also successfully broke a double bond until the full dissociation limit while maintaining the size consistency property. This work thus demonstrates the potential of the BiO-TC-SCI approach in handling complex molecular systems.

Published
2023
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24. Revisiting the electronic properties of dislocated graphene sheets

Author

Fernández, Nicolás, Pujol, Pierre, Solís, Mario, Vargas, Teofilo, Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
High Energy Physics - Theory, Condensed Matter - Strongly Correlated Electrons, Condensed Matter - Materials Science, Strongly Correlated Electrons (cond-mat.str-el), High Energy Physics - Theory (hep-th), Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, General Relativity and Quantum Cosmology (gr-qc), [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat], General Relativity and Quantum Cosmology
Abstract

The interplay between topological defects, such as dislocations or disclinations, and the electronic degrees of freedom in graphene has been extensively studied. In the literature, for the study of this kind of problems, it is in general used either a gauge theory or a curved spatial Riemannian geometry approach, where, in the geometric case, the information about the defects is contained in the metric and the spin-connection. However, these topological defects can also be associated to a Riemann-Cartan geometry where curvature and torsion plays an important role. In this article we study the interplay between a wedge dislocations in a planar graphene sheet and the properties of its electronic degrees of freedom. Our approach relies in its relation with elasticity theory through the so called elastic-gauge, where their typical coefficients, as for example the Poisson's ratio, appear directly in the metric, and consequently also in the electronic spectrum., Comment: 6 pages, v2 minor modifications

Published
2023
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25. Urogenital schistosomiasis in three different water access in the Senegal river basin: prevalence and monitoring praziquantel efficacy and re-infection levels

Author

Bruno Senghor, Eglantine Mathieu-Begné, Olivier Rey, Souleymane Doucouré, Doudou Sow, Bocar Diop, Mariama Sène, Jérôme Boissier, Cheikh Sokhna, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), University Gaston Berger, LERSTAD, Saint-Louis, Senegal (UGB), and Gaston Berger University of Saint-Louis

Subjects
S. haematobium, Drug efficacy, Infectious Diseases, School children, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Urinary schistosomiasis, Senegal river basin, S.haematobium, Re-infection, Praziquantel, Senegal
Abstract

Background Urogenital schistosomiasis is a neglected tropical disease most prevalent in sub-Saharan Africa. In the Senegal river basin, the construction of the Diama dam led to an increase and endemicity of schistosomiasis. Since 2009, praziquantel has frequently been used as preventive chemotherapy in the form of mass administration to Senegalese school-aged children without monitoring of the treatment efficacy and the prevalence after re-infection. This study aims to determine the current prevalence of urogenital schistosomiasis (caused by Schistosoma haematobium), the efficacy of praziquantel, and the re-infection rates in children from five villages with different water access. Methods The baseline prevalence of S. haematobium was determined in August 2020 in 777 children between 5 and 11 years old and a single dose of praziquantel (40 mg/kg) was administered to those positive. The efficacy of praziquantel and the re-infection rates were monitored 4 weeks and 7 months after treatment, respectively, in 226 children with a high intensity of infection at baseline. Results At the baseline, prevalence was low among children from the village of Mbane who live close to the Lac de Guiers (38%), moderate among those from the villages of Dioundou and Khodit, which neighbor the Doue river (46%), and very high at Khodit (90.6%) and Guia (91.2%) which mainly use an irrigation canal. After treatment, the observed cure rates confirmed the efficacy of praziquantel. The lowest cure rate (88.5%) was obtained in the village using the irrigation canal, while high cure rates were obtained in those using the lake (96.5%) and the river (98%). However, high egg reduction rates (between 96.7 and 99.7%) were obtained in all the villages. The re-infection was significantly higher in the village using the canal (42.5%) than in the villages accessing the Lac de Guiers (18.3%) and the Doue river (14.8%). Conclusion Praziquantel has an impact on reducing the prevalence and intensity of urogenital schistosomiasis. However, in the Senegal river basin, S. haematobium remains a real health problem for children living in the villages near the irrigation canals, despite regular treatment, while prevalence is declining from those frequenting the river and the Lac de Guiers. Trial registration ClinicalTrials.gov, NCT04635553. Registered 19 November 2020 retrospectively registered, https://www.clinicaltrials.gov/ct2/show/NCT04635553?cntry=SN&draw=2&rank=4

Published
2022

26. Superfluidity vs prethermalisation in a nonlinear Floquet system

Author

S. Mu, N. Macé, J. Gong, C. Miniatura, G. Lemarié, M. Albert, National University of Singapore (NUS), Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), MajuLab (UMI 3654), National University of Singapore (NUS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique de Nice (INPHYNI), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE30-0024,COCOA,Contrôle de systèmes complexes d'atomes froids(2017), ANR-19-CE30-0013,GLADYS,De la nature vitreuse des systèmes quantiques désordonnés(2019), and ANR-18-CE30-0017,MANYLOK,Localisation à N corps avec le Kicked Rotor(2018)

Subjects
Condensed Matter::Quantum Gases, [PHYS.COND.GAS]Physics [physics]/Condensed Matter [cond-mat]/Quantum Gases [cond-mat.quant-gas], Quantum Gases (cond-mat.quant-gas), FOS: Physical sciences, General Physics and Astronomy, Condensed Matter - Quantum Gases, [PHYS.PHYS.PHYS-GEN-PH]Physics [physics]/Physics [physics]/General Physics [physics.gen-ph]
Abstract

We show that superfluidity can be used to prevent thermalisation in a nonlinear Floquet system. Generically, periodic driving boils an interacting system to a featureless infinite temperature state. Fast driving is a known strategy to postpone Floquet heating with a large but always finite boiling time. In contrast, using a nonlinear periodically-driven system on a lattice, we show the existence of a continuous class of initial states which do not thermalise at all. This absence of thermalisation is associated to the existence and persistence of a stable superflow motion., 7 pages, 5 figures, Supplementary material

Published
2022

27. Climate aridity and habitat drive geographical variation in morphology and thermo-hydroregulation strategies of a widespread lizard species

Author

Chloé Chabaud, Matthieu Berroneau, Maud Berroneau, Andréaz Dupoué, Michaël Guillon, Robin Viton, Rodrigo S B Gavira, Jean Clobert, Olivier Lourdais, Jean-François Le Galliard, Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cistude Nature, Chemin du Moulinat, Le Haillan, France, Association Cistude Nature, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), CEREEP-Ecotron Ile de France (UMS 3194), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Le Galliard, Jean-François, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and ANR-17-CE02-0013,AQUATHERM,Rôles de la régulation hydrique et thermique dans les réponses écologiques au changement climatique(2017)

Subjects
[SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, [SDE.MCG]Environmental Sciences/Global Changes, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDV.BA.ZV] Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecology, Evolution, Behavior and Systematics
Abstract

Thermo-hydroregulation strategies involve concurrent changes in functional traits related to energy, water balance and thermoregulation and play a key role in determining life-history traits and population demography of terrestrial ectotherms. Local thermal and hydric conditions should be important drivers of the geographical variation of thermo-hydroregulation strategies, but we lack studies that examine these changes across climatic gradients in different habitat types. Here, we investigated intraspecific variation of morphology and thermo-hydroregulation traits in the widespread European common lizard (Zootoca vivipara louislantzi) across a multidimensional environmental gradient involving independent variation in air temperature and rainfall and differences in habitat features (access to free-standing water and forest cover). We sampled adult males for morphology, resting metabolic rate, total and cutaneous evaporative water loss and thermal preferences in 15 populations from the rear to the leading edge of the distribution across an elevational gradient ranging from sea level to 1750 m. Besides a decrease in adult body size with increasing environmental temperatures, we found little effect of thermal conditions on thermo-hydroregulation strategies. In particular, relict lowland populations from the warm rear edge showed no specific ecophysiological adaptations. Instead, body mass, body condition and resting metabolic rate were positively associated with a rainfall gradient, while forest cover and water access in the habitat throughout the season also influenced cutaneous evaporative water loss. Our study emphasizes the importance of rainfall and habitat features rather than thermal conditions for geographical variation in lizard morphology and physiology.

Published
2022

28. Estimating the entanglement of random multipartite quantum states

Author

Fitter, Khurshed, Lancien, Cecilia, Nechita, Ion, Institut Fourier (IF ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Quantum Physics, model, Probability (math.PR), random, [PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph], matrix model, FOS: Physical sciences, benchmark, [PHYS.QPHY]Physics [physics]/Quantum Physics [quant-ph], FOS: Mathematics, overlap, Quantum Physics (quant-ph), entanglement, Mathematics - Probability, performance
Abstract

International audience; Genuine multipartite entanglement of a given multipartite pure quantum state can be quantified through its geometric measure of entanglement, which, up to logarithms, is simply the maximum overlap of the corresponding unit tensor with product unit tensors, a quantity which is also known as the injective norm of the tensor. Our general goal in this work is to estimate this injective norm for randomly sampled tensors. To this end, we study and compare various algorithms, based either on the widely used alternating least squares method or on a novel normalized gradient descent approach, and suited to either symmetrized or non-symmetrized random tensors. We first benchmark their respective performances on the case of symmetrized real Gaussian tensors, whose asymptotic average injective norm is known analytically. Having established that our proposed normalized gradient descent algorithm generally performs best, we then use it to provide approximate numerical values for the average injective norm of complex Gaussian tensors (i.e.~up to normalization uniformly distributed multipartite pure quantum states), with or without permutation-invariance. Finally, we are also able to estimate the average injective norm of random matrix product states constructed from Gaussian local tensors, with or without translation-invariance. All these results constitute the first numerical estimates on the amount of genuinely multipartite entanglement typically present in various models of random multipartite pure states.

Published
2022

29. Harnessing diversity of Lactococcus lactis from raw goat milk: Design of an indigenous starter for the production of Rocamadour, a French PDO cheese

Author

Christel Couderc, Valérie Laroute, Michèle Coddeville, Marie-Aurore Caillaud, Gwenaelle Jard, Christine Raynaud, Muriel Cocaign-Bousquet, Hélène Tormo, Marie-Line Daveran-Mingot, Ecole d'Ingénieurs de Purpan (INP - PURPAN), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Chimie Agro-Industrielle (CAI), Ecole nationale supérieure des ingénieurs en arts chimiques et technologiques (ENSIACET), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d’Application et de Traitement des AgroRessources [Toulouse] (CRT CATAR), and Région Occitanie 14051124

Subjects
Polyphasic approach, Autochthonous starter, Goats, [SDV]Life Sciences [q-bio], Acetoin, General Medicine, Diacetyl, Phenotypic trait, Microbiology, Genetic diversity, Lactococcus lactis, Milk, Cheese, Lactic acid bacteria, Animals, Selection, Food Science, Multilocus Sequence Typing
Abstract

International audience; Twenty-four strains of Lactococcus lactis isolated from raw goat milk collected in the Rocamadour PDO area were analysed by MLST typing and phenotypic characterisation. The strains were combined to design an indigenous starter for the production of Rocamadour PDO cheese.The strains were divided into three classes based on their technological properties: acidifying and proteolytic strains in class I (12/24 strains), slightly acidifying and non-proteolytic strains in class II (2/24 strains), and non-acidifying and non-proteolytic strains in class III (10/24 strains). Interestingly, all but three strains (21/24) produced diacetyl/acetoin despite not having citrate metabolism genes, as would classically be expected for the production of these aroma compounds.Three strains (EIP07A, EIP13D, and EIP20B) were selected for the indigenous starter based on the following inclusion/exclusion criteria: (i) no negative interactions between included strains, (ii) ability to metabolize lactose and at least one strain with the prtP gene and/or capable of producing diacetyl/acetoin, and (iii) selected strains derived from different farms to maximise genetic and phenotypic diversity.Despite consisting exclusively of L. lactis strains, the designed indigenous starter allowed reproducible cheese production with performances similar to those obtained with an industrial starter and with the sensory qualities expected of Rocamadour PDO cheese. Previous article in issue

Published
2022

30. Plant litter chemistry controls coarse‐textured soil carbon dynamics

Author

Raoul Huys, Vincent Poirier, Malo Y. Bourget, Catherine Roumet, Stephan Hättenschwiler, Nathalie Fromin, Alison D. Munson, Grégoire T. Freschet, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre de recherche cerveau et cognition (CERCO UMR5549), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Centre d'Etude de la Forêt (Faculté de foresterie, de géographie et de géomatique), Université Laval [Québec] (ULaval), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Freschet, Grégoire, Towards a Unified theory of biotic Interactions: the roLe of environmental - - TULIP2010 - ANR-10-LABX-0041 - LABX - VALID, Mediterranean Center for Environment and Biodiversity - - CeMEB2010 - ANR-10-LABX-0004 - LABX - VALID, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Mind & Brain Institut (TMBI), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), and Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE)

Subjects
priming effect, [SDE] Environmental Sciences, decomposition, Ecology, carbon saturation, Plant Science, Carbon cycle, mineralassociated organic matter, litter traits, plant litter, soil organic matter, [SDE]Environmental Sciences, Ecology, Evolution, Behavior and Systematics, particulate organic matter
Abstract

International audience; As soils store more carbon (C) than the Earth’s atmosphere and terrestrial biomass together, the balance between soil C uptake in the form of soil organic matter and release as CO2 upon its decomposition is a critical determinant in the global C cycle regulating our planet’s climate. Although plant litter is the predominant source of C fuelling both soil C build-up and losses, the issue of how litter chemistry influences this balance remains unresolved.As a contribution to solving that issue, we traced the fate of C during near-complete decomposition of 13C-labelled leaf and root litters from 12 plant species in a coarse-textured soil. We separated the soil organic carbon (SOC) into mineral-associated organic matter (MAOM) and particulate organic matter (POM) pools, and investigated how 14 litter chemical traits affected novel SOC formation and native SOC mineralization (i.e., the priming effect) in these soil fractions.We observed an overall net increase in SOC due to the addition of litter, which was stronger for root than for leaf litters. The presumed stable MAOM-C pool underwent both substantial stabilisation and mineralization, whereas the presumably less stable POM-C pool showed substantial stabilisation and reduced mineralization. Overall, the initial increase in soil C mineralization was fully counterbalanced by a later decrease in native soil C mineralization. POM-C formation as well as MAOM-C formation and mineralization were positively related to the initial litter lignin concentration and negatively to that of the nitrogen leachates, whereas the opposite was observed for POM-C mineralization.Synthesis. Our results highlight the importance of litter chemical traits for SOC formation, and stabilisation, destabilisation, and mineralization. In our coarse-textured soil, the amount of MAOM-C did not change despite large C fluxes through this pool. The litter chemical traits that drove these processes differed from those frequently reported for fine-textured soils far from mineral-associated C saturation. To account for these discrepancies, we propose an integrative perspective in which litter quality and soil texture interactively control soil C fluxes by modulating several SOC stabilisation and destabilisation mechanisms. Irrespective, our results open new critical perspectives for managing soil C pools globally

Published
2022

31. The influence of native populations’ genetic history on the reconstruction of invasion routes: the case of a highly invasive aquatic species

Author

Thomas Brazier, Emira Cherif, Jean-François Martin, André Gilles, Simon Blanchet, Yahui Zhao, Marine Combe, R. J. Scott McCairns, Rodolphe E. Gozlan, Dynamique et durabilité des écosystèmes : de la source à l’océan (DECOD), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institute of Zoology, Chinese Academy of Sciences [Beijing], This study is part of the project GENESIS (ANR-13-ADAP-0005) supported by the Agence Nationale de la Recherche. S.B. was co-funded by the project PROBIS (Biodiversa) and E.C. was funded by an IRD postdoctoral fellowship. R.E.G., A.G., J.F.M. and S.B. received funding for this research from ANR Bioadapt., ANR-13-ADAP-0005,GENESIS,Le rôle de la diversité génétique et de la plasticité phénotypique dans l'adaptation aux changements environmentaux: Une analyse génomique de l'invasion biologique(2013), and ANR-21-LCV3-0003,BioAdapt,BioAdapt, une plateforme pour l'amélioration génétique de plantes cultivées aux stress abiotiques(2021)

Subjects
Invasion pathways, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Population modeling, Ecology, Approximate bayesian computation, Aquatic biological invasion, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Population genomics, Ecology, Evolution, Behavior and Systematics, Demographic inference
Abstract

Data availability: All sequencing data (GBS reads) are publicly-available under the BioProject ID PRJNA799666. The original genetic data yielded by genotyping (in vcf format), additional metadata (e.g. geographical coordinates) and all scripts necessary to reproduce the results presented in the paper are available in a publicly-available Github repository: https://github.com/ThomasBrazier/PseudorasboraGENESIS. Data are available from the authors upon reasonable request.This study has been conducted in accordance with the relevant animal or human ethics approvals.; International audience; Insufficient data on the origins of the first introduced propagule and the initial stages of invasion complicate the reconstruction of a species' invasion history. Phylogeography of the native area profoundly shapes the genomic patterns of the propagules on which subsequent demographic processes of the invasion are based. Thus, a better understanding of this aspect helps to disentangle native and invasive histories. Here, we used genomic data together with clustering methods, explicit admixture tests combined with ABC models and Machine Learning algorithms, to compare patterns of genetic structure and gene flow of native and introduced populations, and infer the most likely invasion pathways of the highly invasive freshwater fish Pseudorasbora parva. This species is the vector of a novel lethal fungal-like pathogen (Sphaerothecum destruens) that is responsible for the decline of several fish species in Europe. We found that the current genetic structuring in the native range of P. parva has been shaped by waves of gene flow from populations in southern and northern China. Furthermore, our results strongly suggest that the genetic diversity of invasive populations results from recurrent global invasion pathways of admixed native populations. Our study also illustrates how the combination of admixture tests, ABC and Machine Learning can be used to detect high-resolution demographic signatures and reconstruct an integrative biological invasion history.

Published
2022

32. Record of the Pyrenean climate since the last interglacial by two stalagmites from Moulis Cave (Ariège, S. France)

Author

Perrin, Christine, Latapie, Lilian, Honiat, Charlotte, Prestimonaco, Laurent, Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Fond Feder, IUS, and European Project

Subjects
[SDE]Environmental Sciences, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences
Abstract

International audience

Published
2022

33. Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development

Author

Claudia Bartoli, Stéphane Boivin, Marta Marchetti, Carine Gris, Virginie Gasciolli, Mégane Gaston, Marie‐Christine Auriac, Frédéric Debellé, Ludovic Cottret, Aurélien Carlier, Catherine Masson‐Boivin, Marc Lepetit, Benoit Lefebvre, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Plateforme TRI FR-AIB, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), INRAE Department of Plant Health and Environment (SPE), IDEX UNITI, Grant/Award Number: RHIZOWHEAT, ANR-18-EURE-0019,TULIP-GSR,The Toulouse-Perpignan(2018), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-16-CE20-0021,GRaSP,Caractérisation du déterminisme génétique du choix du partenaire symbiotique pour une amélioration de la symbiose fixatrice d'azote chez le pois(2016), ANR-16-CE20-0025,WHEATSYM,ROLES DES SIGNAUX MICROBIENS LCO/CO ET DE LEURS RECEPTEURS DE PLANTES DANS DES INTERACTIONS BENEFIQUES ENTRE MONOCOTYLEDONES ET MICROORGANISMES DU SOL(2016), SEGUIN, Nathalie, The Toulouse-Perpignan - - TULIP-GSR2018 - ANR-18-EURE-0019 - EURE - VALID, Towards a Unified theory of biotic Interactions: the roLe of environmental - - TULIP2010 - ANR-10-LABX-0041 - LABX - VALID, Caractérisation du déterminisme génétique du choix du partenaire symbiotique pour une amélioration de la symbiose fixatrice d'azote chez le pois - - GRaSP2016 - ANR-16-CE20-0021 - AAPG2016 - VALID, ROLES DES SIGNAUX MICROBIENS LCO/CO ET DE LEURS RECEPTEURS DE PLANTES DANS DES INTERACTIONS BENEFIQUES ENTRE MONOCOTYLEDONES ET MICROORGANISMES DU SOL - - WHEATSYM2016 - ANR-16-CE20-0025 - AAPG2016 - VALID, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), and Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences, Rhizobium leguminosarum, Bacteria, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Microbiology, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Endophytes, Symbiosis, Root Nodules, Plant, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Ecology, Evolution, Behavior and Systematics, Triticum, Phylogeny, Rhizobium
Abstract

International audience; Although rhizobia that establish a nitrogen-fixing symbiosis with legumes are also known to promote growth in non-legumes, studies on rhizobial associations with wheat roots are scarce. We searched for Rhizobium leguminosarum symbiovar viciae (Rlv) strains naturally competent to endophytically colonize wheat roots. We isolated 20 strains from surface-sterilized wheat roots and found a low diversity of Rlv compared to that observed in the Rlv species complex. We tested the ability of a subset of these Rlv for wheat root colonization when co-inoculated with other Rlv. Only a few strains, including those isolated from wheat roots, and one strain isolated from pea nodules, were efficient in colonizing roots in co-inoculation conditions, while all the strains tested in single strain inoculation conditions were found to colonize the surface and interior of roots. Furthermore, Rlv strains isolated from wheat roots were able to stimulate root development and early arbuscular mycorrhizal fungi colonization. These responses were strain and host genotype dependent. Our results suggest that wheat can be an alternative host for Rlv; nevertheless, there is a strong competition between Rlv strains for wheat root colonization. In addition, we showed that Rlv are endophytic wheat root bacteria with potential ability to modify wheat development.

Published
2022

34. Pathogen-derived mechanical cues potentiate the spatio-temporal implementation of plant defense

Author

Ophélie Léger, Frédérick Garcia, Mehdi Khafif, Sebastien Carrere, Nathalie Leblanc-Fournier, Aroune Duclos, Vincent Tournat, Eric Badel, Marie Didelon, Aurélie Le Ru, Sylvain Raffaele, Adelin Barbacci, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Plateforme TRI FR-AIB, Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Toulouse Réseau Imagerie-Genotoul ( TRI-Genotoul), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), INRAE plant health department grant, and European Project: 336808,EC:FP7:ERC,ERC-2013-StG,VARIWHIM(2013)

Subjects
Mechanotransduction, Physiology, Arabidopsis, Plant Science, Microtubules, Mechanotransduction, Cellular, General Biochemistry, Genetics and Molecular Biology, Plant immunity Mechanoperception Mechanotransduction Microtubules Plant-pathogen interactions Quantitative disease resistance, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Structural Biology, Gene Expression Regulation, Plant, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Immunity, Ecology, Evolution, Behavior and Systematics, Plant Diseases, Plant-pathogen interactions, Quantitative disease resistance, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Plants, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Mechanoperception, Cues, General Agricultural and Biological Sciences, Developmental Biology, Biotechnology, Signal Transduction
Abstract

Background The ongoing adaptation of plants to their environment is the basis for their survival. In this adaptation, mechanoperception of gravity and local curvature plays a role of prime importance in finely regulating growth and ensuring a dynamic balance preventing buckling. However, the abiotic environment is not the exclusive cause of mechanical stimuli. Biotic interactions between plants and microorganisms also involve physical forces and potentially mechanoperception. Whether pathogens trigger mechanoperception in plants and the impact of mechanotransduction on the regulation of plant defense remains however elusive. Results Here, we found that the perception of pathogen-derived mechanical cues by microtubules potentiates the spatio-temporal implementation of plant immunity to fungus. By combining biomechanics modeling and image analysis of the post-invasion stage, we reveal that fungal colonization releases plant cell wall-born tension locally, causing fluctuations of tensile stress in walls of healthy cells distant from the infection site. In healthy cells, the pathogen-derived mechanical cues guide the reorganization of mechanosensing cortical microtubules (CMT). The anisotropic patterning of CMTs is required for the regulation of immunity-related genes in distal cells. The CMT-mediated mechanotransduction of pathogen-derived cues increases Arabidopsis disease resistance by 40% when challenged with the fungus Sclerotinia sclerotiorum. Conclusions CMT anisotropic patterning triggered by pathogen-derived mechanical cues activates the implementation of early plant defense in cells distant from the infection site. We propose that the mechano-signaling triggered immunity (MTI) complements the molecular signals involved in pattern and effector-triggered immunity.

Published
2022

35. Maternal and personal information mediates the use of social cues about predation risk

Author

José Martín, Julien Cote, Delphine Legrand, Michèle Huet, Staffan Jacob, Christine Ducamp, Marion Lemoine, Laurane Winandy, Lucie Di Gesu, Fondation Fyssen, Agence Nationale de la Recherche (France), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), and ANR-12-JSV7-0004,FRADISYN,Populations fragmentées et syndromes dispersants : des gènes à la dynamique des métapopulations(2012)

Subjects
[SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0106 biological sciences, Transgenerational plasticity, Maternal stress, Disturbance cues, Conspecific attraction, Foundation (evidence), Biology, Social cue, 010603 evolutionary biology, 01 natural sciences, Antipredator behaviour, Predation, 010601 ecology, Work (electrical), Inadvertent social information, Animal Science and Zoology, Private information, Social psychology, Personally identifiable information, Private information retrieval, Ecology, Evolution, Behavior and Systematics
Abstract

Organisms can gain information about predation risks from their parents, their own personal experience, and their conspecifics and adjust their behavior to alleviate these risks. These different sources of information can, however, provide conflicting information due to spatial and temporal variation of the environment. This raises the question of how these cues are integrated to produce adaptive antipredator behavior. We investigated how common lizards (Zootoca vivipara) adjust the use of conspecific cues about predation risk depending on whether the information is maternally or personally acquired. We experimentally manipulated the presence of predator scent in gestating mothers and their offspring in a full-crossed design. We then tested the consequences for social information use by monitoring offspring social response to conspecifics previously exposed to predator cues or not. Lizards were more attracted to the scent of conspecifics having experienced predation cues when they had themselves no personal information about predation risk. In contrast, they were more repulsed by conspecific scent when they had personally obtained information about predation risk. However, the addition of maternal information about predation risk canceled out this interactive effect between personal and social information: lizards were slightly more attracted to conspecific scent when these two sources of information about predation risk were in agreement. A chemical analysis of lizard scent revealed that exposure to predator cues modified the chemical composition of lizard scents, a change that might underlie lizards’ use of social information. Our results highlight the importance of considering multiple sources of information while studying antipredator defenses., L.W. was supported by the Fyssen Foundation Post-Doctoral Fellowship and J.C. by an ANR-12-JSV7-0004-01. This work was supported by an “Investissements d’avenir” programme from the Agence Nationale de la Recherche number ANR-11- INBS-0001 Ana EE-Services.

Published
2021

36. Characterization of a small tRNA-binding protein that interacts with the archaeal proteasome complex

Author

Gaëlle Hogrel, Laura Marino‐Puertas, Sébastien Laurent, Ziad Ibrahim, Jacques Covès, Eric Girard, Frank Gabel, Daphna Fenel, Marie‐Claire Daugeron, Béatrice Clouet‐d'Orval, Tamara Basta, Didier Flament, Bruno Franzetti, University of St Andrews. School of Biology, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Grenoble Instruct-ERIC Centre, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-18-CE11-0018,PROTE-IN,Réseau d'interaction du proteasome archéen: vers la démonstration d'un lien entre la fonction du protéasome et le contrôle qualité des ARNs(2018), and ANR-16-CE12-0016,CASPAR,Rôle Physiologique des Ribonucléases de type ß-CASP dans le Métabolisme des ARN chez les Archées(2016)

Subjects
Proteomics, Proteasome Endopeptidase Complex, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], ribosome-associated quality control, QH301 Biology, Archaeal Proteins, NDAS, QH426 Genetics, Crystallography, X-Ray, Microbiology, Archaea, protein-protein interaction, QH301, proteasome, RNA, Transfer, OB-fold, tRNA binding, Carrier Proteins, QH426, Molecular Biology
Abstract

Authors acknowledge financial support from the French Agence Nationale de la Recherche (grant [ANR-18-CE11-0018-01] to B.F. and [ANR-16-CE12-0016-01] to B.C.O). This work used the platforms of the Grenoble Instruct-ERIC Centre (ISBG: UMS3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10-INBS-05-02) and GRAL, a project of the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003) within the Grenoble Partnership for Structural Biology. The IBS Electron Microscope facility is supported by the Auvergne Rhône-Alpes Region, the Fonds Feder, the Fondation pour la Recherche Médicale and GIS-IBiSA. The proteasome system allows the elimination of functional or structurally impaired proteins. This includes the degradation of nascent peptides. In Archaea, how the proteasome complex interacts with the translational machinery remains to be described. Here, we characterised a small orphan protein, Q9UZY3 (Uniprot ID) conserved in Thermococcales. The protein was identified in native pull-down experiments using the proteasome regulatory complex (PAN) as bait. X-ray crystallography and SAXS experiments revealed that the protein is monomeric and adopts a β-barrel core structure with an Oligonucleotide/oligosaccharide-Binding (OB) fold, typically found in translation elongation factors. Mobility shift experiment showed that Q9UZY3 displays tRNA binding properties. Pull-downs, co-immunoprecipitation and ITC studies revealed that Q9UZY3 interacts in vitro with PAN. Native pull-downs and proteomic analysis using different versions of Q9UZY3 showed that the protein interacts with the assembled PAN-20S proteasome machinery in Pyrococcus abyssi cellular extracts. The protein was therefore named Pbp11, for Proteasome Binding Protein of 11 kDa. Interestingly, the interaction network of Pbp11 also includes ribosomal proteins, tRNA processing enzymes and exosome subunits dependent on Pbp11's N-terminal domain that was found to be essential for tRNA binding. Together these data suggest that Pbp11 participates in an interface between the proteasome and the translational machinery. Publisher PDF

Published
2022

37. A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation

Author

S. Cohen, A. Guenolé, I. Lazar, A. Marnef, T. Clouaire, D. V. Vernekar, N. Puget, V. Rocher, C. Arnould, M. Aguirrebengoa, M. Genais, N. Firmin, R. A. Shamanna, R. Mourad, V. A. Bohr, V. Borde, G. Legube, Unité de biologie moléculaire, cellulaire et du développement - UMR5077 (MCD), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Dynamique de l'information génétique : bases fondamentales et cancer (DIG CANCER), Institut Curie [Paris]-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Institutes of Health [Bethesda] (NIH), ANR-15-CE11-0011,Resolve,Mecanisme de résolution des intermédiaires de recombinaison méiotique de la levure à la souris(2015), ANR-18-CE12-0018,CreaDiv,Mécanisme de la recombinaison mitotique et méiotique(2018), ANR-21-CE12-0033,SMART,Analyse en molécule unique des évènements de recombinaison homologue(2021), ANR-18-CE12-0015,REPAIRCHROM,Analyse multi-échelle des mécanismes précoces de remodelage de la chromatine au niveau des dommages dans l'ADN(2018), ANR-14-CE10-0002,DIvA,Fonction de la chromatine dans la réparation des DSBs.(2014), ANR-10-EQPX-0003,ICGex,Equipement de biologie intégrative du cancer pour une médecine personnalisée(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), and European Project: 647344,H2020,ERC-2014-CoG,DIvA(2015)

Subjects
congenital, hereditary, and neonatal diseases and abnormalities, DNA Repair, [SDV]Life Sciences [q-bio], 1.1 Normal biological development and functioning, General Physics and Astronomy, Double-strand DNA breaks, General Biochemistry, Genetics and Molecular Biology, Double-Stranded, Rare Diseases, Underpinning research, Genetics, Humans, DNA Breaks, Double-Stranded, Cancer, Multidisciplinary, RecQ Helicases, DNA Breaks, nutritional and metabolic diseases, Recombinational DNA Repair, General Chemistry, DNA, Chromatin, enzymes and coenzymes (carbohydrates), RNA, Generic health relevance
Abstract

Transcriptionally active loci are particularly prone to breakage and mounting evidence suggests that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncover a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we find that BLM promotes cell death. We report that upon excessive RNA:DNA hybrid accumulation, DNA synthesis is enhanced at DSBs, in a manner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs.

Published
2022

38. Nuclear HMGB1 protects from nonalcoholic fatty liver disease through negative regulation of liver X receptor

Author

Jean Personnaz, Enzo Piccolo, Alizée Dortignac, Jason S. Iacovoni, Jérôme Mariette, Vincent Rocher, Arnaud Polizzi, Aurélie Batut, Simon Deleruyelle, Lucas Bourdens, Océane Delos, Lucie Combes-Soia, Romain Paccoud, Elsa Moreau, Frédéric Martins, Thomas Clouaire, Fadila Benhamed, Alexandra Montagner, Walter Wahli, Robert F. Schwabe, Armelle Yart, Isabelle Castan-Laurell, Justine Bertrand-Michel, Odile Burlet-Schiltz, Catherine Postic, Pierre-Damien Denechaud, Cédric Moro, Gaelle Legube, Chih-Hao Lee, Hervé Guillou, Philippe Valet, Cédric Dray, Jean-Philippe Pradère, Institut des Maladies Métaboliques et Casdiovasculaires (UPS/Inserm U1297 - I2MC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Geroscience and rejuvenation research center (RESTORE), Université de Toulouse (UT)-Université de Toulouse (UT)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SIAAP - Direction du Développement et de la Prospective, SIAAP, Toxicologie Intégrative & Métabolisme (ToxAlim-TIM), ToxAlim (ToxAlim), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Ecole d'Ingénieurs de Purpan (INP - PURPAN), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de pharmacologie et de biologie structurale (IPBS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Unité de biologie moléculaire, cellulaire et du développement - UMR5077 (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Center for Integrative Genomics - Institute of Bioinformatics, Génopode (CIG), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL)-Université de Lausanne = University of Lausanne (UNIL), Lee Kong Chian School of Medicine, Nanyang Technological University [Singapour], Columbia University [New York], MetaToul FluxoMet (TBI-MetaToul), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Harvard T.H. Chan School of Public Health, This study was supported by grants from INSERM, Paul Sabatier University, the Agence Nationale de la Recherche (ANR-17-CE14-0016, to J.-P.P.), and the Région Occitanie and Association Française d’Etude et de Recherche sur l’Obésité (to J.-P.P.). J.P. was supported by a scholarship from Paul Sabatier University. E.P. was supported by a scholarship from Agence Nationale de la Recherche (ANR-17-CE14-0016). R.P. was supported by a scholarship from Région Midi-Pyrénées-INSERM (no. 15050341). O.B.-S. and L.C.-S. and the proteomic facility were supported, in part, by the Région Occitanie, European funds (Fonds Européens de Développement Régional, FEDER), Toulouse Métropole, and the French Ministry of Research with the Investissement d’Avenir Infrastructures Nationales en Biologie et Santé program (ProFI, Proteomics French Infrastructure project, ANR-10-INBS-08), ANR-17-CE14-0016,HOLISTic,Rôle de la protéine HMGB1 au cours du stress metabolique(2017), and Lee Kong Chian School of Medicine (LKCMedicine)

Subjects
Fatty Liver, Multidisciplinary, [SDV]Life Sciences [q-bio], Medicine [Science], chemical and pharmacologic phenomena, Lipid Metabolisms
Abstract

Dysregulations of lipid metabolism in the liver may trigger steatosis progression, leading to potentially severe clinical consequences such as nonalcoholic fatty liver diseases (NAFLDs). Molecular mechanisms underlying liver lipogenesis are very complex and fine-tuned by chromatin dynamics and multiple key transcription factors. Here, we demonstrate that the nuclear factor HMGB1 acts as a strong repressor of liver lipogenesis. Mice with liver-specific Hmgb1 deficiency display exacerbated liver steatosis, while Hmgb1-overexpressing mice exhibited a protection from fatty liver progression when subjected to nutritional stress. Global transcriptome and functional analysis revealed that the deletion of Hmgb1 gene enhances LXRα and PPARγ activity. HMGB1 repression is not mediated through nucleosome landscape reorganization but rather via a preferential DNA occupation in a region carrying genes regulated by LXRα and PPARγ. Together, these findings suggest that hepatocellular HMGB1 protects from liver steatosis development. HMGB1 may constitute a new attractive option to therapeutically target the LXRα-PPARγ axis during NAFLD. Published version This study was supported by grants from INSERM, Paul Sabatier University, the Agence Nationale de la Recherche (ANR-17-CE14-0016, to J.-P.P.), and the Région Occitanie and Association Française d’Etude et de Recherche sur l’Obésité (to J.-P.P.). J.P. was supported by a scholarship from Paul Sabatier University. E.P. was supported by a scholarship from Agence Nationale de la Recherche (ANR-17-CE14-0016). R.P. was supported by a scholarship from Région Midi-Pyrénées-INSERM (no. 15050341). O.B.-S. and L.C.-S. and the proteomic facility were supported, in part, by the Région Occitanie, European funds (Fonds Européens de Développement Régional, FEDER), Toulouse Métropole, and the French Ministry of Research with the Investissement d’Avenir Infrastructures Nationales en Biologie et Santé program (ProFI, Proteomics French Infrastructure project, ANR-10-INBS-08).

Published
2022

39. Condensin positioning at telomeres by Taz1 promotes telomere disjunction in anaphase

Author

Léonard Colin, Céline Reyes, Julien Berthezene, Laetitia Maestroni, Laurent Modolo, Esther Toselli, Nicolas Chanard, Stephane Schaak, Olivier Cuvier, Yannick Gachet, Stéphane Coulon, Pascal Bernard, Sylvie Tournier, Laboratoire de biologie et modélisation de la cellule (LBMC UMR 5239), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de biologie moléculaire, cellulaire et du développement - UMR5077 (MCD), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Bernard, Pascal, École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], macromolecular substances
Abstract

The localization of condensin along chromosome arms is crucial for chromosome segregation in anaphase. Condensin is also enriched at telomeres but how and for what function remains elusive. Here we show that Taz1, the main component of the Shelterin complex that ensures telomeric functions, acts as a positioning device to enrich condensin at telomeres in fission yeast. High condensin occupancy at telomeres is needed for their full disjunction in anaphase. Consistent with a cis-acting process, condensin drives telomere separation independently of the decatenation activity of Topoisomerase II also required for chromosome arm separation. Our results reveal a cis-acting pathway that enriches condensin at telomeres to promote their separation during mitosis.One-Sentence SummaryThe telomeric protein Taz1 promotes the accumulation of condensin at telomeres that drives their disjunction in anaphase.

Published
2022

40. Transcriptomic Adjustments in a Freshwater Ectoparasite Reveal the Role of Molecular Plasticity for Parasite Host Shift

Author

Eglantine Mathieu-Bégné, Simon Blanchet, Guillaume Mitta, Clément Le Potier, Géraldine Loot, Olivier Rey, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), and ANR-11-JSV7-0010,INCLIMPAR,Les effets du changement climatique sur les parasites : une étude prédictive intégrée(2011)

Subjects
Fresh Water, rapid adaptation, host shift, plasticity, gene expression, parasite specificity, emerging parasites, Host-Parasite Interactions, Fish Diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Parasites, Transcriptome, Genetics (clinical), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

International audience; A parasite’s lifestyle is characterized by a critical dependency on its host for feeding, shelter and/or reproduction. The ability of parasites to exploit new host species can reduce the risk associated with host dependency. The number of host species that can be infected by parasites strongly affects their ecological and evolutionary dynamics along with their pathogenic effects on host communities. However, little is known about the processes and the pathways permitting parasites to successfully infect alternative host species, a process known as host shift. Here, we tested whether molecular plasticity changes in gene expression and in molecular pathways could favor host shift in parasites. Focusing on an invasive parasite, Tracheliastes polycolpus, infecting freshwater fish, we conducted a transcriptomic study to compare gene expression in parasites infecting their main host species and two alternative host species. We found 120 significant differentially expressed genes (DEGs) between parasites infecting the different host species. A total of 90% of the DEGs were identified between parasites using the main host species and those using the two alternative host species. Only a few significant DEGs (seven) were identified when comparing parasites from the two alternative host species. Molecular pathways enriched in DEGs and associated with the use of alternative host species were related to cellular machinery, energetic metabolism, muscle activity and oxidative stress. This study strongly suggests that molecular plasticity is an important mechanism sustaining the parasite’s ability to infect alternative hosts.

Published
2022
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41. Herbivory on the pedunculate oak along an urbanization gradient in Europe : Effects of impervious surface, local tree cover, and insect feeding guild

Author

Elena Valdés‐Correcher, Anna Popova, Andrea Galmán, Andreas Prinzing, Andrey V. Selikhovkin, Andy G. Howe, Anna Mrazova, Anne‐Maïmiti Dulaurent, Arndt Hampe, Ayco Jerome Michel Tack, Christophe Bouget, Daniela Lupaștean, Deborah Harvey, Dmitry L. Musolin, Gábor L. Lövei, Giada Centenaro, Inge Van Halder, Jonas Hagge, Jovan Dobrosavljević, Juha‐Matti Pitkänen, Julia Koricheva, Katerina Sam, Luc Barbaro, Manuela Branco, Marco Ferrante, Maria Faticov, Markéta Tahadlová, Martin Gossner, Maxime Cauchoix, Michał Bogdziewicz, Mihai‐Leonard Duduman, Mikhail V. Kozlov, Mona C. Bjoern, Nikita A. Mamaev, Pilar Fernandez‐Conradi, Rebecca L. Thomas, Ross Wetherbee, Samantha Green, Slobodan Milanović, Xoaquín Moreira, Yannick Mellerin, Yasmine Kadiri, Bastien Castagneyrol, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Martin-Luther-University Halle-Wittenberg, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Saint Petersburg University (SPBU), University of Copenhagen = Københavns Universitet (UCPH), University of South Bohemia, Agro-écologie, Hydrogéochimie, Milieux et Ressources (AGHYLE), UniLaSalle, Stockholm University, Groupement d'Interêt Public Ecosystèmes Forestiers GIP ECOFOR (GIP ECOFOR ), University Stefan cel Mare of Suceava (USU), Royal Holloway [University of London] (RHUL), St Petersburg State University (SPbU), Aarhus University [Aarhus], Georg-August-University = Georg-August-Universität Göttingen, University of Belgrade [Belgrade], Natural Resources Institute Finland (LUKE), University of London [London], Czech Academy of Sciences [Prague] (CAS), Centre d'Ecologie et des Sciences de la COnservation (CESCO), Muséum national d'Histoire naturelle (MNHN)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Dynamiques et écologie des paysages agriforestiers (DYNAFOR), École nationale supérieure agronomique de Toulouse (ENSAT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade de Lisboa = University of Lisbon (ULISBOA), Institut Fédéral de Recherches sur la Forêt, la Neige et le Paysage (WSL), Institut Fédéral de Recherches [Suisse], Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Turku, IT University of Copenhagen (ITU), Ecologie des Forêts Méditerranéennes (URFM), Norwegian University of Life Sciences (NMBU), Coventry University, Mision Biologica de Galicia (MBG), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), ANR‐10‐LABX‐45, Agence Nationale de la Recherche, Fondation BNP Paribas, ANR-10-LABX-0045,COTE,COntinental To coastal Ecosystems: evolution, adaptability and governance(2010), Agence Nationale de la Recherche (France), BNP Paribas Foundation, Valdés-Correcher, Elena, Sam, Katerina, Ferrante, Marco, Bogdziewicz, Michał, Castagneyrol, Bastien, Research Centre for Ecological Change, and Department of Agricultural Sciences

Subjects
impervious surface, local canopy cover, insect herbivory, DIVERSITY, PLANT DEFENSES, HEAT, LEAF HERBIVORY, URBAN, Insect Herbivory, Leaf Miners, citizen science, Impervious Surface, Local Canopy Cover, leaf gallers, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Leaf Gallers, GLOBAL PATTERNS, Ecology, LANDSCAPE CONTEXT, Citizen Science, fungi, FOREST, Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss, 1181 Ecology, evolutionary biology, ABUNDANCE, leaf miners, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quercus robur, TOP-DOWN
Abstract

14 páginas, 3 figuras, Urbanization is an important driver of the diversity and abundance of tree-associated insect herbivores, but its consequences for insect herbivory are poorly understood. A likely source of variability among studies is the insufficient consideration of intra-urban variability in forest cover. With the help of citizen scientists, we investigated the independent and interactive effects of local canopy cover and percentage of impervious surface on insect herbivory in the pedunculate oak (Quercus robur L.) throughout most of its geographic range in Europe. We found that the damage caused by chewing insect herbivores as well as the incidence of leaf-mining and gall-inducing herbivores consistently decreased with increasing impervious surface around focal oaks. Herbivory by chewing herbivores increased with increasing forest cover, regardless of impervious surface. In contrast, an increase in local canopy cover buffered the negative effect of impervious surface on leaf miners and strengthened its effect on gall inducers. These results show that-just like in non-urban areas-plant-herbivore interactions in cities are structured by a complex set of interacting factors. This highlights that local habitat characteristics within cities have the potential to attenuate or modify the effect of impervious surfaces on biotic interactions., This study was carried out with financial support from the French National Research Agency (ANR) in the frame of the Investments for the Future Programme, within the Cluster of Excellence COTE (Continental To coastal Ecosystems: evolution, adaptability, and governance) (ANR-10-LABX-45) and was further funded by the BNP Paribas Foundation as part of its Climate & Biodiversity Initiative the citizen science project Tree Bodyguards. The authors warmly thank all the young European citizens and their teachers who made this study possible. They also thank the professional scientists who kindly agreed to participate in this study: Alexander Kozel (Belarusian State Technological University and American Psychological Association), Andreas Schuldt (Forest Nature Conservation, Georg-August-University Göttingen, Göttingen, German), Aurélien Sallé (Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, Université d'Orléans), Chloe Mendiondo and Claire Colliaux (Department of Agroecology, Aarhus University, Flakkebjerg Research Centre, DK-4200 Slagelse, Denmark), György Csóka (Department of Forest Protection, NARIC Forest Research Institute, Mátrafüred, Hungary), Lars Opgennoorth (Biodiversity and Conservation Biology, Ecological Genetics, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland), Laurent Augusto (INRAE, Bordeaux Sciences Agro), Marija Popović (Faculty of Forestry, University of Belgrade, Belgrade, Serbia), Mickael Pihain (Research Unit “Ecosystèmes, Biodiversité, Evolution”, University of Rennes 1/CNRS, 35042 Rennes, France), Olivier Bouriaud (Applied Ecology Laboratory, Forestry Faculty, “Ștefan cel Mare, University of Suceava, Suceava, Romania), Stefan K. Müller (Freie evangelische Schule Lörrach), Tomas Roslin (Department of Ecology; Swedish University of Agricultural Sciences), Valentin Queloz (Forest Entomology, Swiss Federal Research Institute WSL), and Vojtech Lanta (Institute of Botany CAS, Dukelská 135, 37901 Třeboň, Czech Republic). They also thank Michael Scherer-Lorenzen (Geobotany, Faculty of Biology, University of Freiburg) for the help during the coordination of the research.

Published
2022

42. Force-generating apoptotic cells orchestrate avian neural tube bending

Author

Daniela Roellig, Sophie Theis, Amsha Proag, Guillaume Allio, Bertrand Bénazéraf, Jérôme Gros, Magali Suzanne, Unité de biologie moléculaire, cellulaire et du développement - UMR5077 (MCD), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Morphogénie Logiciels, Institut Pasteur [Paris] (IP), M.S.’s lab is supported by grants from the European Research Council (ERC) under the European Union Horizon 2020 research and innovation program (grant number EPAF: 648001), from the Institut National de la Santé et de la Recherche Médicale (Inserm, Plan cancer 2014–2019), and from the association Toulouse Cancer Santé (TCS, ApoMacImaging: 171441). S.T. had a CIFRE fellowship from the ANRT and now has a fellowship from the Fondation pour la Recherche Médicale (FRM). The transgenic quail lines used in this project were generated thanks to the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) and ERC grant agreement no: 337635 to J.G., We thank Eric Theveneau, Alice Davy, Corinne Benassayag, and Bruno Monier for their constructive comments on the manuscript., European Project: 648001,H2020,ERC-2014-CoG,EPAF(2015), and European Project: 337635,EC:FP7:ERC,ERC-2013-StG,LIMBCELLDYNAMICS(2014)

Subjects
quail/chicken, Neural Tube, [SDV]Life Sciences [q-bio], nucleus fragmentation, apoptosis, morphogenesis, neural tube closure, Cell Biology, General Biochemistry, Genetics and Molecular Biology, Epithelium, epithelium folding, mechanical forces, Animals, Molecular Biology, Neurulation, Developmental Biology
Abstract

International audience; Apoptosis plays an important role in morphogenesis, and the notion that apoptotic cells can impact their surroundings came to light recently. However, how this applies to vertebrate morphogenesis remains unknown. Here, we use the formation of the neural tube to determine how apoptosis contributes to morphogenesis in vertebrates. Neural tube closure defects have been reported when apoptosis is impaired in vertebrates, although the cellular mechanisms involved are unknown. Using avian embryos, we found that apoptotic cells generate an apico-basal force before being extruded from the neuro-epithelium. This force, which relies on a contractile actomyosin cable that extends along the apico-basal axis of the cell, drives nuclear fragmentation and influences the neighboring tissue. Together with the morphological defects observed when apoptosis is prevented, these data strongly suggest that the neuroepithelium keeps track of the mechanical impact of apoptotic cells and that the apoptotic forces, cumulatively, contribute actively to neural tube bending.

Published
2022

43. Lipo-chitooligosaccharides as regulatory signals of fungal growth and development

Author

Candice L. Swift, Arthur QuyManh Maes, Nancy P. Keller, Cristobal Carrera Carriel, Kevin Garcia, Guillaume Bécard, Joanna Tannous, Quanita J. Choudhury, Jean-Michel Ané, Michelle A. O’Malley, Junko Maeda, Jin Woo Bok, Michelle Keller-Pearson, Tomás Allen Rush, Patricia Jargeat, Virginie Puech-Pagès, Sylvain Cottaz, Michael R. Sussman, Fabienne Maillet, Jeniel E. Nett, Adeline Bascaules, Jessy Labbé, Kevin R. Cope, Alexandra Haouy, Bailey Kleven, Véréna Poinsot, Chad J. Johnson, Sébastien Fort, Corinne Lefort, Devanshi Khokhani, Fort, Sébastien, University of Wisconsin-Madison, Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Metatoul - Agromix, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions moléculaires et réactivité chimique et photochimique (IMRCP), Institut de Chimie de Toulouse (ICT-FR 2599), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), South Dakota State University (SDSTATE), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), The University of Tennessee [Knoxville], University of Georgia [USA], University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Centre de Recherches sur les Macromolécules Végétales (CERMAV), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Université Fédérale Toulouse Midi-Pyrénées, Interactions Microbiennes dans la Rhizosphère et les Racines, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-MetaToul-MetaboHUB, Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut de Chimie de Toulouse (ICT-FR 2599), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of California [Santa Barbara] (UCSB), University of California, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), MetaToul Agromix, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-MetaboHUB-MetaToul, MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-MetaboHUB-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Fluides, Energie, Réacteurs, Matériaux et Transferts (FERMAT), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), BIBAC - Chimie analytique et interactions biomolécules - matière molle biomimétique (BIBAC), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie de Toulouse (ICT), Université de Toulouse (UT), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)

Subjects
0301 basic medicine, Hypha, Science, General Physics and Astronomy, Oligosaccharides, Chitin, 02 engineering and technology, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Microbiology, Microbial ecology, 03 medical and health sciences, Fungal biology, Pseudohyphal growth, Symbiosis, Ascomycota, Mycorrhizae, Spore germination, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Cellular microbiology, Fungal ecology, lcsh:Science, [SDV.BBM.BC] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Chitosan, Multidisciplinary, Ecology, Phylum, Basidiomycota, Fatty Acids, fungi, Fungi, General Chemistry, Spores, Fungal, 021001 nanoscience & nanotechnology, biology.organism_classification, [SDV.MP.MYC] Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Spore, 030104 developmental biology, lcsh:Q, 0210 nano-technology, Bacteria, Rhizobium, Signal Transduction
Abstract

Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by rhizobial bacteria that trigger the nodulation process in legumes, and by some fungi that also establish symbiotic relationships with plants, notably the arbuscular and ecto mycorrhizal fungi. Here, we show that many other fungi also produce LCOs. We tested 59 species representing most fungal phyla, and found that 53 species produce LCOs that can be detected by functional assays and/or by mass spectroscopy. LCO treatment affects spore germination, branching of hyphae, pseudohyphal growth, and transcription in non-symbiotic fungi from the Ascomycete and Basidiomycete phyla. Our findings suggest that LCO production is common among fungi, and LCOs may function as signals regulating fungal growth and development., Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by certain bacteria and fungi that establish symbiotic relationships with plants. Here, the authors show that LCOs are produced also by many other, non-symbiotic fungi, and regulate fungal growth and development.

Published
2020

44. Intracellular Positioning Systems Limit the Entropic Eviction of Secondary Replicons Toward the Nucleoid Edges in Bacterial Cells

Author

Dauverd -Girault, Julie, Planchenault, Charlène, Pons, Marine, Schiavon, Caroline, Siguier, Patricia, Rech, Jérôme, Guynet, Catherine, Dauverd-Girault, Julie, Cury, Jean, Rocha, Eduardo, Junier, Ivan, Cornet, François, Espéli, Olivier, espeli, olivier, Appel à projets générique - Génèse et maintenance des chromosomes secondaire bactériens - - MAGISBAC2014 - ANR-14-CE10-0007 - Appel à projets générique - VALID, Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires - UMR5100 (LMGM), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications Grenoble - UMR 5525 (TIMC-IMAG), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Institut Jean Roger, This work as funded by ANR ANR-14-CE10-0007-01 to OE, FC and ER by the CNRS PICS initiative to OE and IJ and by the Foundation ARC (PJA 20171206119) to OE, ANR-14-CE10-0007,MAGISBAC,Génèse et maintenance des chromosomes secondaire bactériens(2014), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie et génétique moléculaires (LMGM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL), Génétique des Interactions macromoléculaires, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génomique et Évolution des Microorganismes (TIMC-GEM ), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC ), IMAG-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-IMAG-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Biologie Computationnelle et Modélisation (TIMC-BCM ), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, chemistry.chemical_compound, 0302 clinical medicine, Plasmid, Structural Biology, Chromosome Segregation, chromosome, Replicon, 0303 health sciences, Chromosomes, Bacterial, partition, segregation, Cell biology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, MESH: DNA, Circular, polymer unmixing, DNA, Circular, Intracellular, Plasmids, DNA, Bacterial, MESH: Chromosomes, Bacterial, signal transduction and intracellular signaling Keywords: plasmid, MESH: Biological Transport, MESH: Chromosome Segregation, MESH: Replicon, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Bacterial genome size, Biology, MESH: Enterobacteriaceae, 03 medical and health sciences, Enterobacteriaceae, trafficking, MESH: Plasmids, plasmid, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Nucleoid, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Molecular Biology, 030304 developmental biology, spatiotemporal organization, Chromosome, Biological Transport, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biochemical phenomena, metabolism, and nutrition, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Section/Category: Sorting, chemistry, Cytoplasm, bacteria, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030217 neurology & neurosurgery, DNA
Abstract

International audience; Bacterial genomes, organized intracellularly as nucleoids, are composed of a main chromosome coexisting with different types of secondary replicons. Secondary replicons are major drivers of 16 bacterial adaptation by gene exchange. They are highly diverse in type and size, ranging from less than 2 to more than 1000 kb, and must integrate with bacterial physiology, including to the nucleoid dynamics, to limit detrimental costs leading to their counter-selection. We show that large DNA circles, whether from a natural plasmid or excised from the chromosome tend to localize in a dynamic manner in a zone separating the nucleoid from the cytoplasm at the edge of the nucleoid.This localization is in good agreement with in silico simulations of DNA circles in the nucleoid volume. Subcellular positioning systems counteract this tendency, allowing replicons to enter the nucleoid space. In enterobacteria, these systems are found in replicons above 25 kb, defining the limit with small randomly segregated plasmids. Larger replicons carry at least one of the three described family of systems, ParAB, ParRM and StbA. Replicons above 180 kb all carry a ParAB system, suggesting this system is specifically required in the cases of large replicons. Simulations demonstrated that replicon size profoundly affects localization, compaction and dynamics of DNA circles in the nucleoid volume. The present work suggests that presence of partition systems on the larger plasmids or chromids is not only due to selection for accurate segregation but also to counteract their unmixing with the chromosome and consequent exclusion from the nucleoid.

Published
2020

45. Identification of Bipotential Blood Cell/Nephrocyte Progenitors in Drosophila: Another Route for Generating Blood Progenitors

Author

Ismaël Morin-Poulard, Manon Destalminil-Letourneau, Laetitia Bataillé, Jean-Louis Frendo, Gaëlle Lebreton, Nathalie Vanzo, Michèle Crozatier, Unité de biologie moléculaire, cellulaire et du développement - UMR5077 (MCD), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Geroscience and rejuvenation research center (RESTORE), Université de Toulouse (UT)-Université de Toulouse (UT)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HAL UR1, Admin, Association pour La Recherche sur le Cancer, Ligue Contre le Cancer, Fondation pour la Recherche Médicale, and Centre National de La Recherche Scientifique

Subjects
Klf15, QH301-705.5, [SDV]Life Sciences [q-bio], fungi, Cell Biology, lymph gland ontogeny, hematopoiesis, [SDV] Life Sciences [q-bio], [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, blood bi-potent progenitor, nephrocyte, Drosophila, Biology (General), Developmental Biology
Abstract

The Drosophila lymph gland is the larval hematopoietic organ and is aligned along the anterior part of the cardiovascular system, composed of cardiac cells, that form the cardiac tube and its associated pericardial cells or nephrocytes. By the end of embryogenesis the lymph gland is composed of a single pair of lobes. Two additional pairs of posterior lobes develop during larval development to contribute to the mature lymph gland. In this study we describe the ontogeny of lymph gland posterior lobes during larval development and identify the genetic basis of the process. By lineage tracing we show here that each posterior lobe originates from three embryonic pericardial cells, thus establishing a bivalent blood cell/nephrocyte potential for a subset of embryonic pericardial cells. The posterior lobes of L3 larvae posterior lobes are composed of heterogeneous blood progenitors and their diversity is progressively built during larval development. We further establish that in larvae, homeotic genes and the transcription factor Klf15 regulate the choice between blood cell and nephrocyte fates. Our data underline the sequential production of blood cell progenitors during larval development.

Published
2022

46. Environmental variation drives the decoupling of leaf and root traits within species along an elevation gradient

Author

Weemstra, Monique, Roumet, Catherine, Cruz-Maldonado, Nereyda, Anthelme, Fabien, Stokes, Alexia, Freschet, Grégoire, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and ANR-16-CE03-0009,ECOPICS,Services écosystémiques souterrains produits par les communautés végétales le long de gradients altitudinaux en France et au Mexique(2016)

Subjects
leaf traits, Climate, fungi, food and beverages, Plant Science, Original Articles, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Environment, Plants, Plant Roots, Plant Leaves, Soil, root traits, Phenotype, intraspecific trait variation, trait correlations, elevation gradient, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, trait covariation
Abstract

Background and Aims Plant performance is enhanced by balancing above- and below-ground resource uptake through the intraspecific adjustment of leaf and root traits. It is assumed that these organ adjustments are at least partly coordinated, so that analogous leaf and root traits broadly covary. Understanding the extent of such intraspecific leaf–root trait covariation would strongly contribute to our understanding of how plants match above- and below-ground resource use strategies as their environment changes, but comprehensive studies are lacking. Methods We measured analogous leaf and root traits from 11 species, as well as climate, soil and vegetation properties along a 1000-m elevation gradient in the French Alps. We determined how traits varied along the gradient, to what extent this variation was determined by the way different traits respond to environmental cues acting at different spatial scales (i.e. within and between elevations), and whether trait pairs covaried within species. Key Results Leaf and root trait patterns strongly diverged: across the 11 species along the gradient, intraspecific leaf trait patterns were largely consistent, whereas root trait patterns were highly idiosyncratic. We also observed that, when compared with leaves, intraspecific variation was greater in root traits, due to the strong effects of the local environment (i.e. at the same elevation), while landscape-level effects (i.e. at different elevations) were minor. Overall, intraspecific trait correlations between analogous leaf and root traits were nearly absent. Conclusions Our study suggests that environmental gradients at the landscape level, as well as local heterogeneity in soil properties, are the drivers of a strong decoupling between analogous leaf and root traits within species. This decoupling of plant resource acquisition strategies highlights how plants can exhibit diverse whole-plant acclimation strategies to modify above- and below-ground resource uptake, improving their resilience to environmental change.

Published
2022

47. Planification de la séquence « Éviter-Réduire-Compenser » à l'échelle du paysage : quel apport de la modélisation des réseaux écologiques à la mise en œuvre des sites naturels de compensation ?

Author

Padilla, Brian, Tarabon, Simon, Moulherat, Sylvain, Boileau, Jules, Soret, Marie, Papet, Guillaume, Bergès, L., Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Ubiquiste, TerrOïko, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Territoires, Environnement, Télédétection et Information Spatiale (UMR TETIS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Politique publique, Réseau écologique, [SDE.MCG]Environmental Sciences/Global Changes, Modélisation paysagère, [SDE]Environmental Sciences, Préservation de l’environnement, Réglementation environnementale, Compensation écologique, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Aménagement du territoire
Abstract

National audience; In recent years, several teams of researchers have developed methodological frameworks and specific modeling tools to take into account the dynamic dimension of biodiversity in environmental assessments. Today, these developing approaches are still little used in France. However, as the authors of this paper illustrate, recent work has shown their interest and relevance in all phases of projects, from preliminary reflections to design, both at the scale of operations and that of territorial planning.; Plusieurs équipes de chercheurs ont développé ces dernières années des cadres méthodologiques et des outils de modélisation spécifiques permettant de prendre en compte la dimension dynamique de la biodiversité dans les évaluations environnementales. Aujourd’hui, ces approches en développement sont encore peu utilisées en France. Cependant, comme l’illustrent les auteurs de cet article, de récents travaux ont montré leur intérêt et leur pertinence à toutes les phases des projets, des réflexions préliminaires à la conception, tant à l’échelle des opérations qu'à celle de la planification territoriale.

Published
2022

48. Human–nature connectedness as a pathway to sustainability: A global meta‐analysis

Author

Barragan‐jason, Gladys, de Mazancourt, Claire, Parmesan, Camille, Singer, Michael, Loreau, Michel, Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Texas at Austin [Austin], Plymouth University, ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), and European Project: 666971,H2020,ERC-2014-ADG,BIOSTASES(2015)

Subjects
meta-analysis, human–nature connectedness, environmental education, [SDE]Environmental Sciences, nature conservation, proenvironmental behavior, human health, sustainability, nature-based solutions, people and nature, human-nature connectedness
Abstract

International audience; Internationally agreed sustainability goals are being missed. Here, we conduct global meta-analyses to assess how the extent to which humans see themselves as part of nature—known as human–nature connectedness (HNC)—can be used as a leverage point to reach sustainability. A meta-analysis of 147 correlational studies shows that individuals with high HNC had more pronature behaviours and were significantly healthier than those with low HNC. A meta-analysis of 59 experimental studies shows significant increases in HNC after manipulations involving contact with nature and mindfulness practices. Surprisingly, this same meta-analysis finds no significant effect of environmental education on HNC. Thus, HNC is positively linked to mind-sets that value sustainability and behaviours that enhance it. Further, we argue that HNC can be enhanced by targeted practices, and we identify those most likely to succeed. Our results suggest that enhancing HNC, via promotion of targeted practices, can improve sustainability and should be integrated into conservation policy.

Published
2022

49. IL-2 and IL-15 drive intrathymic development of distinct periphery-seeding CD4(+)Foxp3(+) regulatory T lymphocytes

Author

Cécile Apert, Ariel O. Galindo-Albarrán, Sarah Castan, Claire Detraves, Héloise Michaud, Nicola McJannett, Bart Haegeman, Simon Fillatreau, Bernard Malissen, Georg Holländer, Saulius Žuklys, Jérémy C. Santamaria, Olivier P. Joffre, Paola Romagnoli, Joost P. M. van Meerwijk, Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Station d'Ecologie Théorique et Expérimentale (SETE), Centre National de la Recherche Scientifique (CNRS)-Fédération de Recherche Agrobiosciences, Interactions et Biodiversité (FR AIB), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre d'Immunophénomique (CIPHE), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Basel (Unibas), University of Oxford, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), and ANR-10-INBS-0007,PHENOMIN,INFRASTRUCTURE NATIONALE EN PHENOGENOMIQUE SOURIS(2010)

Subjects
thymus, T lymphocyte, regulatory T cell (T reg), immunopathology, cytokines, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, Immunology, T lymphocytes, Immunology and Allergy, regulatory T cells
Abstract

Development of Foxp3-expressing regulatory T-lymphocytes (Treg) in the thymus is controlled by signals delivered in T-cell precursors via the TCR, co-stimulatory receptors, and cytokine receptors. In absence of IL-2, IL-15 or their receptors, fewer Treg apparently develop in the thymus. However, it was recently shown that a substantial part of thymic Treg are cells that had recirculated from the periphery back to the thymus, troubling interpretation of these results. We therefore reassessed the involvement of IL-2 and IL-15 in the development of Treg, taking into account Treg-recirculation. At the age of three weeks, when in wt and IL-15-deficient (but not in IL-2-deficient) mice substantial amounts of recirculating Treg are present in the thymus, we found similarly reduced proportions of newly developed Treg in absence of IL-2 or IL-15, and in absence of both cytokines even less Treg developed. In neonates, when practically no recirculating Treg were found in the thymus, the absence of IL-2 led to substantially more reduced Treg-development than deficiency in IL-15. IL-2 but not IL-15 modulated the CD25, GITR, OX40, and CD73-phenotypes of the thymus-egress-competent and periphery-seeding Treg-population. Interestingly, IL-2 and IL-15 also modulated the TCR-repertoire expressed by developing Treg. Upon transfer into Treg-less Foxp3(sf) mice, newly developed Treg from IL-2- (and to a much lesser extent IL-15-) deficient mice suppressed immunopathology less efficiently than wt Treg. Taken together, our results firmly establish important non-redundant quantitative and qualitative roles for IL-2 and, to a lesser extent, IL-15 in intrathymic Treg-development., Frontiers in Immunology, 13, ISSN:1664-3224

Published
2022
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50. Simulating chiral spin liquids with projected entangled-pair states

Author

Juraj Hasik, Maarten Van Damme, Didier Poilblanc, Laurens Vanderstraeten, Quantum Condensed Matter Theory (ITFA, IoP, FNWI), Laboratoire de Physique Théorique (LPT), Institut de Recherche sur les Systèmes Atomiques et Moléculaires Complexes (IRSAMC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Condensed Matter - Strongly Correlated Electrons, Physics and Astronomy, Strongly Correlated Electrons (cond-mat.str-el), General Physics and Astronomy, FOS: Physical sciences, [PHYS.COND]Physics [physics]/Condensed Matter [cond-mat]
Abstract

Doubts have been raised on the representation of chiral spin liquids exhibiting topological order in terms of projected entangled pair states (PEPSs). Here, starting from a simple spin-1/2 chiral frustrated Heisenberg model, we show that a faithful representation of the chiral spin liquid phase is in fact possible in terms of a generic PEPS upon variational optimization. We find a perfectly chiral gapless edge mode and a rapid decay of correlation functions at short distances consistent with a bulk gap, concomitant with a gossamer long-range tail originating from a PEPS bulk-edge correspondence. For increasing bond dimension, (i) the rapid decrease of spurious features -- SU(2) symmetry breaking and long-range tails in correlations -- together with (ii) a faster convergence of the ground state energy as compared to state-of-the-art cylinder matrix-product state simulations involving far more variational parameters, prove the fundamental relevance of the PEPS ansatz for simulating systems with chiral topological order., Comment: 8 pages, 6 figures, source code available at https://github.com/jurajHasik/peps-torch

Published
2022
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