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- Pour toute publication de résultats ayant reçu l’aide de l’IPGG (présence dans les locaux de l’IPGG, passage sur la plateforme technologique de l’IPGG, collaboration inter équipes IPGG, lié à une bourse doctorale ou postdoctorale IPGG, ou encore utilisation des espaces communs), il vous faut indiquer  cette phrase « Ce travail a été réalisé avec le soutien du laboratoire d’excellence Institut Pierre-Gilles de Gennes (programme Investissements d’avenir ANR-10-IDEX-0001-02 PSL et ANR-10-LABX-31). » / « This work has received the support of "Institut Pierre-Gilles de Gennes" (laboratoire d’excellence, “Investissements d’avenir” program ANR-10-IDEX-0001-02 PSL and ANR-10-LABX-31.). ».

- Pour toute publication de résultats obtenu via l'utilisation d’un équipement acheté par l’Equipex IPGG, il vous faut ajouter  la codification suivante : « ANR-10-EQPX-34 ».

Impact of the Oil Matrix on Anionic and Nonionic Surfactant Separation Using Ultra-High-Performance Liquid Chromatography Hyphenated to High-Resolution Mass Spectrometry
Alizée Dufour, Didier Thiébaut, Matthieu Loriau, Leticia Ligiero, and Jérôme Vial
American Chemical Society - 34(11) 13943–13953 - doi.org/10.1016/j.jchromb.2020.122518 - 2020
For the first time, to our knowledge, anionic and nonionic surfactants were analyzed in an oil matrix by ultra-high-performance liquid chromatography hyphenated to high-resolution mass spectrometry (UHPLC-HRMS). The feasibility of this analysis was studied using synthetic mixtures of surfactants prepared in water (quality controls), binary THF/toluene 50/50 v/v (surfactant + THF/toluene), and binary THF/toluene containing 1 and 10% crude oil (Crude1% and Crude10%). These compositions were chosen in order to be as close as possible to petroleum related samples to be investigated in the future. Analyses were carried out by UHPLC methods using both reverse phase and anion-exchange mechanisms with a mixed mode column. Despite the complexity of the oil matrix and the presence of organic solvents used for dilution, the retention times of the surfactants were not affected whatever the concentration of crude oil present in the sample. Nevertheless, a significant matrix effect caused a loss of signal when the concentration of oil reached 10% in mass. For the analysis of samples with this crude oil concentration range, it would be advisable to dilute the sample.




Meta population structure and the evolutionary transition to multicellularity
Caroline J. Rose Katrin Hammerschmidt Yuriy Pichugin Paul B. Rainey
First published - 23(9) 1380-1390 - doi.org/10.1111/ele.13570 - 2020
The evolutionary transition to multicellularity has occurred on numerous occasions, but transitions to complex life forms are rare. Here, using experimental bacterial populations as proxies for nascent multicellular organisms, we manipulate ecological factors shaping the evolution of groups. Groups were propagated under regimes requiring reproduction via a life cycle replete with developmental and dispersal (propagule) phases, but in one treatment lineages never mixed, whereas in a second treatment, cells from different lineages experienced intense competition during the dispersal phase. The latter treatment favoured traits promoting cell growth at the expense of traits underlying group fitness – a finding that is supported by results from a mathematical model. Our results show that the transition to multicellularity benefits from ecological conditions that maintain discreteness not just of the group (soma) phase, but also of the dispersal (germline) phase.

Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet‐associated Pseudomonas in Oxford and Auckland
Xue‐Xian Zhang,corresponding author, Stephen R. Ritchie, Hao Chang, Dawn L. Arnold, Robert W. Jackson, and Paul B. Rainey
Ecol Evol - 10(12) 5963–5975 - doi: 10.1002/ece3.6334 - 2020
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.


METHOD FOR MANIPULATING THE EVOLUTION OF COLLECTIVES OF SELF-REPLICATING ENTITIES AND VARIATION BETWEEN COLLECTIVES OF SELF-REPLICATING ENTITIES
Paul RAINEY Jérôme BIBETTE Jean BAUDRY Nicolas BREMOND Laurent BOITARD Jairo GARNICA Denis COTTINET
My Science Work - - - 2020
The present invention relates to a method for manipulating the evolution of collectives of self-replicating entities and/or variation between collectives of self-replicating entities, in a high throughput droplet milli-fluidic system.
Experimental manipulation of selfish genetic elements links genes to microbial community function
Steven D. Quistad, Guilhem Doulcier and Paul B. Rainey
Philosophical Transactions of the Royal Society - - doi.org/10.1098/rstb.2019.0681 - 2020
Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function.



Toward a dynamical understanding of microbial communities
Paul B. Rainey and Steven D. Quistad
Philosophical Transactions of the Royal Society - - doi.org/10.1098/rstb.2019.0248 - 2020
The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry.




Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity
Guilhem Doulcier, Amaury Lambert, Silvia De Monte, Paul B Rainey
EcologyEvolutionary Biology - - DOI: 10.7554/eLife.53433 - 2020
Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.





Ecological scaffolding and the evolution of individuality
Andrew J. Black, Pierrick Bourrat & Paul B. Rainey
Nature Ecology & Evolution - 4 426–436 - doi.org/10.1038/s41559-019-1086-9 - 2020
Evolutionary transitions in individuality are central to the emergence of biological complexity. Recent experiments provide glimpses of processes underpinning the transition from single cells to multicellular life and draw attention to the critical role of ecology. Here, we emphasize this ecological dimension and argue that its current absence from theoretical frameworks hampers development of general explanatory solutions. Using mechanistic mathematical models, we show how a minimal ecological structure comprising patchily distributed resources and between-patch dispersal can scaffold Darwinian-like properties on collectives of cells. This scaffolding causes cells to participate directly in the process of evolution by natural selection as if they were members of multicellular collectives, with collectives participating in a death–birth process arising from the interplay between the timing of dispersal events and the rate of resource use by cells. When this timescale is sufficiently long and new collectives are founded by single cells, collectives experience conditions that favour evolution of a reproductive division of labour. Together our simple model makes explicit key events in the major evolutionary transition to multicellularity. It also makes predictions concerning the life history of certain pathogens and serves as an ecological recipe for experimental realization of evolutionary transitions.






Liquid Crystal Coacervates Composed of Short Double-Stranded DNA and Cationic Peptides
Tommaso P. Fraccia and Tony Z. Jia
ACS Nano - 14, 11 15071–15082 - doi.org/10.1021/acsnano.0c05083 - 2020
Phase separation of nucleic acids and proteins is a ubiquitous phenomenon regulating subcellular compartment structure and function. While complex coacervation of flexible single-stranded nucleic acids is broadly investigated, coacervation of double-stranded DNA (dsDNA) is less studied because of its propensity to generate solid precipitates. Here, we reverse this perspective by showing that short dsDNA and poly-l-lysine coacervates can escape precipitation while displaying a surprisingly complex phase diagram, including the full set of liquid crystal (LC) mesophases observed to date in bulk dsDNA. Short dsDNA supramolecular aggregation and packing in the dense coacervate phase are the main parameters regulating the global LC-coacervate phase behavior. LC-coacervate structure was characterized upon variations in temperature and monovalent salt, DNA, and peptide concentrations, which allow continuous reversible transitions between all accessible phases. A deeper understanding of LC-coacervates can gain insights to decipher structures and phase transition mechanisms within biomolecular condensates, to design stimuli-responsive multiphase synthetic compartments with different degrees of order and to exploit self-assembly driven cooperative prebiotic evolution of nucleic acids and peptides.
Elasticity and Viscosity of DNA Liquid Crystals
Liana Lucchetti, Tommaso P. Fraccia, Giovanni Nava, Taras TurivTaras Turiv Advanced Materials and Liquid Crystal Institute, Chemical Physics Interdisciplinary Program, Kent State University, Kent, Ohio 44242, United States More by Taras Turiv , Fabrizio
ACS Nano - 9, 7 1034–1039 - doi.org/10.1021/acsmacrolett.0c00394 - 2020
Concentrated solutions of blunt-ended DNA oligomer duplexes self-assemble in living polymers and order into lyotropic nematic liquid crystal phase. Using the optical torque provided by three distinct illumination geometries, we induce independent splay, twist, and bend deformations of the DNA nematic and measure the corresponding elastic coefficients K1, K2, and K3, and viscosities ηsplay, ηtwist, and ηbend. We find the viscoelasticity of the system to be remarkably soft, as the viscoelastic coefficients are smaller than in other lyotropic liquid crystals. We find K1 > K3 > K2, in agreement with the elasticity of the nematic phase of flexible polymers, and ηbend > ηsplay > ηtwist a behavior that is nonconventional in the context of chromonic, polymeric, and thermotropic liquid crystals, indicating a possible role of the weakness and reversibility of the DNA aggregates.

635 publications.