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Laboratoire d’analyse et d’architecture des systèmes

Publications de l'équipe MILE

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35documents trouvés

16314
11/12/2017

Analysis of DNA replication by optical mapping in nanochannels

J.LACROIX, S.PELOFY, MC.BLATCHE, M.J.PILLAIRE, S.HUET, C.CHAPUIS, J.S.HOFFMAN, A.BANCAUD

MILE, I2C, TOUCAN, Rennes

Revue Scientifique : Small, Vol.12, N°43, pp.5963-5970, Décembre 2017, DOI 10.1002/smll.201503795 , N° 16314

Lien : https://hal.archives-ouvertes.fr/hal-01384735

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Abstract

DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.

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17438
08/12/2017

Pore cross-talk in colloidal filtration

O.LIOT, S.AKASH, P.BACCHIN, P.DURU, J.MORRIS, P.JOSEPH

MILE, LGC, IMFT, Levich Institute

Rapport LAAS N°17438, Décembre 2017, 7p.

Lien : https://hal.laas.fr/hal-01651843

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Blockage of pores by particles is found in numerous industrial and natural processes, including filtration and oil extraction. We present experimental results of filtration through a linear array of ten channels with one dimension which is sub-micron. These silicon-glass nanoslits serve as model pores, through which a dilute dispersion of Brownian polystyrene spheres flows. The clog growth rate at fixed differential pressure is shown to systematically increase with the number of saturated (entirely clogged) pores, indicating that there is an interaction or " cross-talk " between the pores. This observation is interpreted using a model proposed here, based on the concept that the residual permeability allows a clog to act as a filter. A clogged pore is thus the source of a local increase of particle concentration adjacent to the pore, which then diffuses towards other pores. This phenomenon, evidenced and modelled here in one dimension, should be at play in two-dimensional membranes.

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17417
05/12/2017

Control of evaporation by geometry in capillary structures. From confined pillar arrays in a gap radial gradient to phyllotaxy-inspired geometry

C.CHEN, P.DURU, P.JOSEPH, S.GEOFFROY, M.PRAT

IMFT, MILE, LMDC

Revue Scientifique : Scientific Reports, Vol.7, N°1, 15110p., Décembre 2017 , N° 17417

Lien : https://hal.laas.fr/hal-01643395

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Abstract

Evaporation is a key phenomenon in the natural environment and in many technological systems involving capillary structures. Understanding the evaporation front dynamics enables the evaporation rate from microfluidic devices and porous media to be finely controlled. Of particular interest is the ability to control the position of the front through suitable design of the capillary structure. Here, we show how to design model capillary structures in microfluidic devices so as to control the drying kinetics. This is achieved by acting on the spatial organization of the constrictions that influence the invasion of the structure by the gas phase. Two types of control are demonstrated. The first is intended to control the sequence of primary invasions through the pore space, while the second aims to control the secondary liquid structures: films, bridges, etc., that can form in the region of pore space invaded by the gas phase. It is shown how the latter can be obtained from phyllotaxy-inspired geometry. Our study thus opens up a route toward the control of the evaporation kinetics by means of tailored capillary structures.

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17427
26/10/2017

Clogging of model pores with brownian particles

O.LIOT, P.BACCHIN, P.DURU, P.JOSEPH, J.MORRIS

MILE, LGC, IMFT, Levich Institute

Manifestation avec acte : International Conference on Miniaturized Systems for Chemistry and Life Sciences ( MicroTas ) 2017 du 22 octobre au 26 octobre 2017, Savannah (USA), Octobre 2017, 2p. , N° 17427

Lien : https://hal.laas.fr/hal-01644282

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Abstract

Pore clogging with Brownian particles is of wide interest in filtration processes. We perform experiments where model sub-micrometric pores are clogged using a Brownian suspension. We study the influence of the ionic strength on the clog formation dynamics. The erosion/drag force competition is also studied using a crossflow in the inlet channel. The way the clogs disintegrate after the clogging process provides some information about their structure, which can be composed of two or three " layers " – labile or not. INTRODUCTION This paper reports new results about model pores clogging with strongly Brownian particles. The accumulation of particles in a porous media is a complex process which involves DLVO, steric and hydrodynamic interactions. The clogging phenomenon may occur in inkjet printers or numerous other applications such as water filtration through a membrane. While the fouling of a membrane at the macroscopic scale is well understood, the investigations at the pore scale are still at their beginning [1]. Very recent works have used model microchannels to study the effect of different parameters, such as ionic strength or Péclet number (advection/diffusion competition) on the clogging of pores at the micrometer scale [2-4]. The sub-micron dimensions are still unexplored in spite of strong specificities (Brownian motion, system size comparable to scales of interaction), and relevance (0.2 µm being a typical industrial pore size). In this context, we study the clogging/unclogging of silicon-glass channels with Brownian particles. We focus particularly on the influence of ionic strength and the building/erosion processes using a crossflow imposed in the inlet microchannel.

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17366
16/10/2017

Capturing chromosome structural properties from their spatial and temporal fluctuations

A.BANCAUD, O.GADAL, K.BYSTRICKY

MILE, LBME

Ouvrage (contribution) : Epigenetics and Systems Biology, Elsevier, N°ISBN 9780128030752, Octobre 2017, Chapter 12, pp.239-263 , N° 17366

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Abstract

Epigenetics and Systems Biology highlights the need for collaboration between experiments and theoretical modeling that is required for successful application of systems biology in epigenetics studies. This book breaks down the obstacles which exist between systems biology and epigenetics researchers due to information barriers and segmented research, giving real-life examples of successful combinations of systems biology and epigenetics experiments. Each section covers one type of modeling and one set of epigenetic questions on which said models have been successfully applied. In addition, the book highlights how modeling and systems biology relate to studies of RNA, DNA, and genome instability, mechanisms of DNA damage signaling and repair, and the effect of the environment on genome stability.

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17333
28/09/2017

Real-time chromatin dynamics at the single gene level during transcription activation

T.GERMIER, S.KOCANOVA, N.WALTHER, A.BANCAUD, H.A.SHABAN, H.SELLOU, A.Z.POLITI, J.ELLENBERG, F.GALLARDO, K.BYSTRICKY

LBME, EMBL, MILE

Rapport LAAS N°17333, Septembre 2017, 30p.

Lien : https://hal.laas.fr/hal-01587450

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Abstract

Genome dynamics relate to regulation of gene expression, the most fundamental process in biology. Yet we still do not know whether the very process of transcription drives spatial organization and chromatin conformation at specific gene loci. To address this issue, we have optimized the ANCHOR/ParB DNA labeling system for real-time imaging and quantitative analysis of the dynamics of a single-copy transgene in human cells. Transcription of the transgene under the control of the endogenous Cyclin D1 promoter was induced by addition of 17beta-estradiol. Motion of the ANCHOR3-tagged DNA locus was recorded in the same cell prior to and during appearance of nascent mRNA visualized using the MS2 system. We found that transcription initiation resulted in rapid confinement of the mRNA-producing gene. The confinement was maintained even upon inhibition of pol2 elongation. It did not occur when recruitment of pol2 or transcription initiation was blocked by anti-estrogens or Triptolide. These results suggest that preinitiation complex formation and concomitant reorganization of the chromatin domain constrains freedom of movement of an induced gene's promoter within minutes. Confined diffusion reflects assembly of functional protein hubs and DNA processing during the rate-limiting steps of transcription.

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17159
19/09/2017

Integration of tunable liquid crystal microcells on 1.55um photodetector arrays using nanoimprint technology

B.SADANI, B.BOISNARD, C.LEVALLOIS, C.PARANTHOEN, S.BOUCHOULE, L.DUPONT, T.CAMPS, J.B.DOUCET, V.BARDINAL

MICA, MILE, INSA Rennes, C2N, TEAM

Manifestation avec acte : International Conference on Micro and Nano Engineering ( MNE ) 2017 du 19 septembre au 22 septembre 2017, Braga (Portugal), Septembre 2017, 1p. , N° 17159

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Associating the voltage-dependent birefringence of liquid crystals to III-V materials constitutes a promising way for the fabrication of widely tunable optical devices needed for future compact communications systems and optical sensors. In this work, liquid crystal microcells are efficiently integrated on 1.55μm photodiode arrays owing to the use of a nanoimprint setup for surface relief alignment grating fabrication and for liquid-crystal microcell sealing. Fabricated devices present a tuning range of 106nm for only 14V applied and without any current consumption.

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17376
01/09/2017

DNA grafting and arrangement on oxide surfaces for self-assembly of Al and CuO nanoparticles

T.CALAIS, D.BOURRIER, A.BANCAUD, Y.J.CHABAL, A.ESTEVE, C.ROSSI

NEO, TEAM, MILE, University of Texas

Revue Scientifique : Langmuir, Septembre 2017, DOI 10.1021/acs.langmuir.7b02159 , N° 17376

Lien : https://hal.laas.fr/hal-01613194

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DNA-directed assembly of nano-objects as a means to manufacture advanced nanomaterial architectures has been the subject of many studies. However, most applications have dealt with noble metals as there are fundamental difficulties to work with other materials. In this work, we propose a generic and systematic approach for functionalizing and characterizing oxide surfaces with single-stranded DNA oligonucleotides. This protocol is applied to aluminum and copper oxide nanoparticles due to their great interest for the fabrication of highly energetic heterogeneous nanocomposites. The surface densities of streptavidin and biotinylated DNA oligonucleotides are precisely quantified combining atomic absorption spectroscopy with conventional dynamic light scattering and fluorimetry, and maximized to provide a basis for understanding the grafting mechanism. First, the streptavidin coverage is consistently below 20% of the total surface for both nanoparticles. Second, direct and unspecific grafting of DNA single strands onto Al and CuO nanoparticles largely dominates the overall functionalization process:

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17241
01/08/2017

Quasi-static drainage in a network of nanoslits of non-uniform depth designed by grayscale laser lithography

A.NAILLON, H.MASSADI, R.COURSON, J.BEKHIT, L.SEVENO, P.F.CALMON, M.PRAT, P.JOSEPH

MILE, TEAM, IMFT

Revue Scientifique : Microfluidics and Nanofluidics, Vol.21, N°8, 131p., Août 2017 , N° 17241

Lien : https://hal.laas.fr/hal-01566417

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A method is reported to fabricate silicon-glass nanofluidic chips with non-uniform channel depths in the range 20-500 nm and micrometer resolution in width. The process is based on grayscale laser lithography to structure photoresist in 2.5 dimensions in a single step, followed by a reactive ion etching to transfer the resist depth profile into silicon. It can be easily integrated in a complete process flow chart. The method is used to fabricate a network of interconnected slits of non-uniform depth, a geometry mimicking a nanoporous medium. The network is then used to perform a pressure step controlled drainage experiment, i.e. the immiscible displacement of a wetting fluid (liquid water) by a non-wetting one (nitrogen). The drainage patterns are analyzed by comparison with simulations based on the invasion percolation algorithm. The results indicate that slow drainage in the considered nanofluidic system well corresponds to the classical capillary fingering regime.

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17124
01/07/2017

A MEMS approcach to determine the biochemical oxygen demand (BOD) of wastewaters

L.RECOULES, A.MIGAOU, X.DOLLAT, G.THOUAND, A.M.GUE, A.BOUKABACHE

MILE, I2C, Nantes

Revue Scientifique : Journal of Micromechanics and Microengineering, Vol.27, N°7, 075018p., Juillet 2017 , N° 17124

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A MEMS approach to obtain an efficient tool for the evaluation of the biochemical oxygen demand (BOD) of wastewaters is introduced. Its operating principle is based on the measurement of oxygen concentration in water samples containing organic pollutants and specific bacteria. The microsystem has been designed to perform multiple and parallel measurements in a poly-wells microfluidic device. The monitoring of the bacterial activity is ensured by optical sensors incorporated in each well of the fluidic network. By using an optode sensor, it is hereby demonstrated that this approach is efficient to measure organic pollutants by testing different Luria Bertani buffer dilutions. These results also show that it is possible to reduce the duration of measurements from 5 d (BOD5) of the standard approach to few hours, typically 3 h–5 h.

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