Laboratory :
Author :
Revue :
Year :

Foam as a self-assembling amorphous photonic band gap material
View ORCID ProfileJoshua Ricouvier, Patrick Tabeling, and Pavel Yazhgur
Phys. Fluids - 116 (19) 9202-9207 - - 2019
We show that slightly polydisperse disordered 2D foams can be used as a self-assembled template for isotropic photonic band gap (PBG) materials for transverse electric (TE) polarization. Calculations based on in-house experimental and simulated foam structures demonstrate that, at sufficient refractive index contrast, a dry foam organization with threefold nodes and long slender Plateau borders is especially advantageous to open a large PBG. A transition from dry to wet foam structure rapidly closes the PBG mainly by formation of bigger fourfold nodes, filling the PBG with defect modes. By tuning the foam area fraction, we find an optimal quantity of dielectric material, which maximizes the PBG in experimental systems. The obtained results have a potential to be extended to 3D foams to produce a next generation of self-assembled disordered PBG materials, enabling fabrication of cheap and scalable photonic devices.
Recent insights into the genotype–phenotype relationship from massively parallel genetic assays
Harry Kemble Philippe Nghe Olivier Tenaillon
Nature Physics - 9 12 - - 2019
With the molecular revolution in Biology, a mechanistic understanding of the genotype–phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep mutational scanning assays, capable of scoring comprehensive libraries of genotypes for fitness and a variety of phenotypes in massively parallel fashion. The resulting empirical genotype–fitness maps pave the way to predictive models, potentially accelerating our ability to anticipate the behaviour of pathogen and cancerous cell populations from sequencing data. Besides from cellular fitness, phenotypes of direct application in industry (e.g. enzyme activity) and medicine (e.g. antibody binding) can be quantified and even selected directly by these assays. This review discusses the technological basis of and recent developments in massively parallel genetics, along with the trends it is uncovering in the genotype–phenotype relationship (distribution of mutation effects, epistasis), their possible mechanistic bases and future directions for advancing towards the goal of predictive genetics.
Large scale control and programming of gene expression using CRISPR.
Deyell M, Ameta S, Nghe P
Semin Cell Dev Biol. - S1084-9521(18 30110-1 - doi: 10.1016/j.semcdb.2019.05.013 - 2019
The control of gene expression in cells and organisms allows to unveil gene to function relationships and to reprogram biological responses. Several systems, such as Zinc fingers, TALE (Transcription activator-like effectors), and siRNAs (small-interfering RNAs), have been exploited to achieve this. However, recent advances in Clustered Regularly Interspaced Short Palindromic Repeats and Cas9 (CRISPR-Cas9) have overshadowed them due to high specificity, compatibility with many different organisms, and design flexibility. In this review we summarize state-of-the art for CRISPR-Cas9 technology for large scale gene perturbation studies, including single gene and multiple genes knock-out, knock-down, knock-up libraries, and their associated screening assays. We feature in particular the combination of these methods with single-cell transcriptomics approaches. Finally, we highlight the application of CRISPR-Cas9 systems in building synthetic circuits that can be interfaced with gene networks to control cellular states.
Fibrin-Targeted Polymerized Shell Microbubbles as Potential Theranostic Agents for Surgical Adhesions
Catherine A. Gormley, Benjamin J. Keenan, Jo Ann Buczek-Thomas,† Amanda C. S. N. Pessoa, Jiang Xu, Fabrice Monti, Patrick Tabeling, R. Glynn Holt, Jon O. Nagy, and Joyce Y. Wong
Langmuir - 35(31) 10061–10067 - doi: 10.1021/acs.langmuir.8b03692 - 2019
The development of new therapies for surgical adhesions has proven to be difficult as there is no consistently effective way to assess treatment efficacy in clinical trials without performing a second surgery, which can result in additional adhesions. We have developed lipid microbubble formulations that use a short peptide sequence, CREKA, to target fibrin, the molecule that forms nascent adhesions. These targeted polymerized shell microbubbles (PSMs) are designed to allow ultrasound imaging of early adhesions for diagnostic purposes and for evaluating the success of potential treatments in clinical trials while acting as a possible treatment. In this study, we show that CREKA-targeted microbubbles preferentially bind fibrin over fibrinogen and are stable for long periods of time (~48 h), that these bound microbubbles can be visualized by ultrasound, and that neither these lipid-based bubbles nor their diagnostic-ultrasound-induced vibrations damage mesothelial cells in vitro. Moreover, these bubbles show the potential to identify adhesionlike fibrin formations and may hold promise in blocking or breaking up fibrin formations in vivo.

Deposition kinetics of bi- and tridisperse colloidal suspensions in microchannels under the van der Waals regime
Cesare M. Cejas, Lucrezia Maini, Fabrice Montia and Patrick Tabeling
Soft Matter - 15 7438-7447 - - 2019
We investigate the kinetics of irreversible adsorption under the van der Waals regime, i.e. weakly Brownian polydisperse colloidal suspensions injected into shallow microchannels at high ionic strengths, where each suspension is represented by populations of particles with different particle sizes. We find that each population size of the particle in the suspension can be treated independently using an analytical solution based on the advection–diffusion equation and that the distribution of the adsorbed particles along the channel axis behaves according to a power law. The experimental measurements agree with Langevin simulations and are well accounted for by theory valid in the van der Waals regime. Operating in the van der Waals regime permits the present study to confirm the use of microfluidics as an effective in situ method to measure the Hamaker constant of particles under aqueous conditions.

Droplet generation at Hele-Shaw microfluidic T-junction
I. Chakraborty, J. Ricouvier, P. Yazghur, P. Tabeling, A. Leshansky
Phys. Fluids - 31(2) 22010 - DOI: 10.1063/1.5086808 - 2019
Liquid Crystal ordering of DNA Dickerson Dodecamer duplexes with different 5’- Phosphate terminations
Marco Todisco Gregory P. Smith Tommaso Pietro Fraccia
Molecular Crystals and Liquid Crystals - 683(1) 69-80 - DOI: 10.1080/15421406.2019.1581706 - 2019
The onset of liquid crystal (LC) phases in concentrated aqueous solutions of DNA oligomers crucially depends on the end-to-end interaction between the DNA duplexes, which can be provided by the aromatic stacking of the terminal base-pairs or by the pairing of complementary dangling-ends. Here we investigated the LC behavior of three blunt-end 12-base-long DNA duplexes synthesized with hydroxyl, phosphate and triphosphate 5’-termini. We experimentally characterized the concentration-temperature phase diagrams and we quantitatively estimated the end-to-end stacking free energy, by comparing the empirical data with the predictions of coarse-grained linear aggregation models. The preservation of LC ordering, even in presence of the bulky and highly charged triphosphate group, indicates that attractive stacking interactions are still present and capable of induce linear aggregation of the DNA duplexes. This finding strengthens the potential role of chromonic like self-assembly for the prebiotic formation of linear polymeric nucleic acids.
Sign epistasis caused by hierarchy within signalling cascades.
Nghe P, Kogenaru M, Tans SJ.
Nat Commun - 9(1) 1451. - doi: 10.1038/s41467-018-03644-8 - 2018
Sign epistasis is a central evolutionary constraint, but its causal factors remain difficult to predict. Here we use the notion of parameterised optima to explain epistasis within a signalling cascade, and test these predictions in Escherichia coli. We show that sign epistasis arises from the benefit of tuning phenotypic parameters of cascade genes with respect to each other, rather than from their complex and incompletely known genetic bases. Specifically, sign epistasis requires only that the optimal phenotypic parameters of one gene depend on the phenotypic parameters of another, independent of other details, such as activating or repressing nature, position within the cascade, intra-genic pleiotropy or genotype. Mutational effects change sign more readily in downstream genes, indicating that optimising downstream genes is more constrained. The findings show that sign epistasis results from the inherent upstream-downstream hierarchy between signalling cascade genes, and can be addressed without exhaustive genotypic mapping.
Coupled catabolism and anabolism in autocatalytic RNA sets.
Arsène S, Ameta S, Lehman N, Griffiths AD, Nghe P.
Nucleic Acids Res. - 46(18) 9660-9666 - doi: 10.1093/nar/gky598. - 2018
The ability to process molecules available in the environment into useable building blocks characterizes catabolism in contemporary cells and was probably critical for the initiation of life. Here we show that a catabolic process in collectively autocatalytic sets of RNAs allows diversified substrates to be assimilated. We modify fragments of the Azoarcus group I intron and find that the system is able to restore the original native fragments by a multi-step reaction pathway. This allows in turn the formation of catalysts by an anabolic process, eventually leading to the accumulation of ribozymes. These results demonstrate that rudimentary self-reproducing RNA systems based on recombination possess an inherent capacity to assimilate an expanded repertoire of chemical resources and suggest that coupled catabolism and anabolism could have arisen at a very early stage in primordial living systems.
Roughness of oxide glass subcritical fracture surfaces
Gael Pallares , Frederic Lechenault, Matthieu George, Elisabeth Bouchaud, Cédric Ottina, Cindy L. Rountree, Matteo Ciccotti ,
Phys. Chem. - 101 (3) 1279-1288 - DOI : 10.1111/jace.15262 - 2018
An original setup combining a very stable loading stage, an atomic force microscope and an environmental chamber, allows to obtain very stable sub-critical fracture propagation in oxide glasses under controlled environment, and subsequently to finely characterize the nanometric roughness properties of the crack surfaces. The analysis of the surface roughness is conducted both in terms of the classical root mean square roughness to compare with the literature, and in terms of more physically adequate indicators related to the self-affine nature of the fracture surfaces. Due to the comparable nanometric scale of the surface roughness, the AFM tip size and the instrumental noise, a special care is devoted to the statistical evaluation of the metrologic properties. The 2 roughness amplitude of several oxide glasses was shown to decrease as a function of the stress intensity factor, to be quite insensitive to the relative humidity and to increase with the degree of heterogeneity of the glass. The results are discussed in terms of several modeling arguments concerning the coupling between crack propagation, material's heterogeneity, crack tip plastic deformation and water diffusion at the crack tip. A synthetic new model is presented combining the predictions of a model by Wiederhorn et al. [1] on the effect of the material's heterogeneity on the crack tip stresses with the self-affine nature of the fracture surfaces.


- For any publication having received the support of the IPGG (presence in the IPGG premises, use of the IPGG technological platform, collaboration between IPGG teams, linked to an IPGG doctoral or postdoctoral grant, or use of the common spaces), you must indicate the following sentence : "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.) ".

- For any publication of results obtained through the use of equipment purchased by the Equipex IPGG, you must add the following coding: "ANR-10-EQPX-34".

65 publications.