Université PSL



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Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism
Laboratoire Physique des biomolécules - T. Lionnet, M. M. Spiering, S. J. Benkovic, D. Bensimon and V. Croquette
Proc. Nat. Acad. Sci. USA - 104(50) :19790–95 - DOI:10.1073/pnas.0709793104 - 2007
Helicases are enzymes that couple ATP hydrolysis to the unwinding of double-stranded (ds) nucleic acids. The bacteriophage T4 helicase (gp41) is a hexameric helicase that promotes DNA replication within a highly coordinated protein complex termed the replisome. Despite recent progress, the gp41 unwinding mechanism and regulatory interactions within the replisome remain unclear. Here we use a single tethered DNA hairpin as a real-time reporter of gp41-mediated dsDNA unwinding and single-stranded (ss) DNA translocation with 3-base pair (bp) resolution. Although gp41 translocates on ssDNA as fast as the in vivo replication fork (approximate to 400 bp/s), its unwinding rate extrapolated to zero force is much slower (approximate to 30 bp/s). Together, our results have two implications: first, gp41 unwinds DNA through a passive mechanism; second, this weak helicase cannot efficiently unwind the T4 genome alone. Our results suggest that important regulations occur within the replisome to achieve rapid and processive replication.
Highly Parallel Mix-and-Match Fabrication of Nanopillar Arrays Integrated in Microfluidic Channels for Long DNA Molecule Separation
Laboratoire Pôle Microfluidique - J. Shi, A. P. Fang, L. Malaquin, A. Pepin, D. Decanini, J. L. Viovy and Y. Chen
Applied Physics Letters - 91(15) :153114 - DOI:153114 10.1063/1.2793616 - 2007
We report on a mix-and-match method based on a combination of soft UV nanoimprint lithography, contact optical lithography, and reactive-ion-etch techniques, which is applicable for high throughput manufacturing of nanostructure integrated microfluidic devices. We demonstrate the integration of high density and high aspect ratio nanopillars into microfluidic channels as electrophoresis sieving matrices. As a result, ? DNA and T4 DNA can be separated within a few minutes. By changing the pattern design, the device could be used for separation of other types of molecules.
Microcontact Printing of Living Bacteria Arrays with Cellular Resolution
Laboratoire Pôle Microfluidique - L. P. Xu, L. Robert, O. Y. Qi, F. Taddei, Y. Chen, A.B. Lindner, D. Baigl
Nano Lett. - 7(7) :2068-72 - DOI:10.1021/nl070983z - 2007
Arrays of living bacteria were printed on agarose substrate with cellular resolution using elastomeric stamps with a high aspect ratio generated by reverse in situ lithography (RISL). The printed bacteria reproduced the original stamp patterns with high fidelity and continued growing as in bulk culture. This methodology provides a simple route to any desired bacterial spatial 2D distribution and may be applied to screening as well as to studies of bacteria phenotypic variability, population dynamics, and ecosystem evolution.
Online preconcentration using monoliths in electrochromatography capillary format and microchips
Laboratoire Sciences Analytiques Bioanalytiques et Miniaturisation - V. Augustin, G. Proczek, J. Dugay, S. Descroix, M.C. Hennion
J. Sep. Sci. - 30(17) :2858-65 - PMID:17973277 - 2007
Online preconcentration and separation of analytes using an in situ photopolymerized hexyl acrylate-based monolith stationary phase was evaluated using electrochromatography in capillary format and microchip. The band broadening occurring during the preconcentration process by frontal electrochromatography and during the desorption process by elution electrochromatography was studied. The hexyl acrylate-based monolith provides high retention for neutral analytes allowing the handling of large sample volumes and its structure allows rapid mass transfer, thus reducing the band broadening. For moderately polar analytes such as mono-chlorophenols that are slightly retained in water, it was shown that enrichment factors up to 3500 can be obtained by a hydrodynamic injection of several bed volumes for 120 min under 0.8 MPa with a decrease in efficiency of 50% and a decrease of 30% for the resolution between 2- and 3-chlorophenol. An 8 min preconcentration time allows enrichment factors above 100 for polyaromatic hydrocarbons. The interest of these monoliths when synthesized in microchip is also demonstrated. A 200-fold enrichment was easily obtained for PAHs with only 1 min as preconcentration time, without decrease in efficiency.
Time-course analysis of mouse serum proteome changes following exposure of the skin to ionizing radiation
Laboratoire Spectrométrie de masse biologique et protéomique - Guipaud O, Holler V, Buard V, Tarlet G, Royer N, Vinh J, Benderitter M.
Proteomics - 7(21) :3992-4002 - PMID:17960731 - 2007
Radiation-induced lesion outcomes of normal tissues are difficult to predict. In particular, radiotherapy or local exposure to a radioactive source by accident can trigger strong injury to the skin. The finding of biomarkers is of fundamental relevance for the prediction of lesion apparition and its evolution, and for the settlement of therapeutic strategies. In order to study radiation-induced cutaneous lesions, we developed a mouse model in which the dorsal skin was selectively exposed to ionizing radiation (IR). 2-D difference gel electrophoresis (2-D DIGE) coupled with MS was used to investigate proteins altered in expression and/or PTM in serum. Proteome changes were monitored from 1 day to 1 month postirradiation, at a dose of 40 Gy, in this specific model developing reproducible clinical symptoms ranging from erythema to skin ulceration with wound healing. About 60 proteins (including some isoforms and likely post-translational variants), representing 20 different proteins, that exhibited significant and reproducible kinetic expression changes, were identified using MS and database searches. Several proteins, down- or up-regulated from day one, could prove to be good candidates to prognosticate the evolution of a skin lesion such as necrosis. In addition, we observed shifts in pI of several spot trains, revealing potential PTM changes, which could also serve as indicators of irradiation or as predictors of lesion severity.
Polyadenylation of a functional mRNA controls gene expression in Escherichia coli
Laboratoire Spectrométrie de masse biologique et protéomique - Joanny G, Le Derout J, Bréchemier-Baey D, Labas V, Vinh J, Régnier P, Hajnsdorf E.
Nucleic Acids Res. - 35(8) :2494-502 - PMID:17395638 - 2007
Although usually implicated in the stabilization of mRNAs in eukaryotes, polyadenylation was initially shown to destabilize RNA in bacteria. All the data are consistent with polyadenylation being part of a quality control process targeting folded RNA fragments and non-functional RNA molecules to degradation. We report here an example in Escherichia coli, where polyadenylation directly controls the level of expression of a gene by modulating the stability of a functional transcript. Inactivation of poly(A)polymerase I causes overexpression of glucosamine-6-phosphate synthase (GlmS) and both the accumulation and stabilization of the glmS transcript. Moreover, we show that the glmS mRNA results from the processing of the glmU-glmS cotranscript by RNase E. Interestingly, the glmU-glmS cotranscript and the mRNA fragment encoding GlmU only slightly accumulated in the absence of poly(A)polymerase, suggesting that the endonucleolytically generated glmS mRNA harbouring a 5' monophosphate and a 3' stable hairpin is highly susceptible to poly(A)-dependent degradation.
In vivo electrochemical detection of nitric oxide in tumor-bearing mice
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Griveau S., Dumezy C, Seguin J., Chabot GG. Scherman D., Bedioui F.
Anal. Chem. - 79(3) :1030-3 - PMID:17263331 - 2007
Interest in elucidating the mechanisms of action of various classes of anticancer agents and exploring the pathways of the induced-nitric oxide (NO) release provides an impetus to conceive a better designed approach to locally detect NO in tumors, in vivo. We report here on the first use of an electrochemical sensor that allows the in vivo detection of NO in tumor-bearing mice. In a first step, we performed the electrochemical characterization of a stable electroactive probe, K4Fe(CN)6, directly injected into the liquid microenvironment especially created around the electrode in the tumor. Second, the ability of the inserted electrode system to detect the presence of NO itself in the tumoral tissue was achieved by using the chemically modified Pt/Ir electrode as NO sensor and two NO donor molecules: diethylammonium (Z)-1-(N,N-diethylamino)diazen-1-ium 1,2-diolate (DEA-NONOate) and (Z)-1-[N-(2-aminopropyl)-N-(2-ammonio propyl)amino]diazen-1-ium 1,2-diolate (PAPA-NONOate). These two NO donor molecules allowed proving the electrochemical detection of (i) directly injected exogenous NO phosphate buffer solution into the tumor (decomposed DEA-NONOate) and (ii) biomimetically induced endogeneous release of NO in the tumoral tissue, upon injection of PAPA-NONOate into the tumor. This approach could be applied to the in vivo study of candidate anticancer drugs acting on the NO pathways.
Frontal analysis capillary electrophoresis hyphenated to electrospray ionization mass spectrometry for the characterization of the antithrombin/heparin pentasaccharide complex
Laboratoire Synthèse Electrochimie Imagerie et Systèmes Analytiques - Fermas S, Gonnet F, Varenne A, Gareil P, Daniel R.
Anal. Chem. - 79(13) :4987-93 - PMID:17536781 - 2007
The interaction of proteins with polysaccharides represents a major and challenging topic in glycobiology, since such complexes mediate fundamental biological mechanisms. A new strategy based on the hyphenation of frontal analysis capillary electrophoresis (FACE) with electrospray ionization mass spectrometry (ESIMS) is reported for the characterization of protein/carbohydrate complexes. While most of the previously reported CE-MS experiments were performed using capillary electrophoresis in zone format, we report for the first time CE-MS experiments in which CE was performed in frontal analysis (FACE-MS). We showed that the frontal mode offered a better sensitivity than zone mode and was well suited for the CE-MS coupling. This FACE-MS coupling was applied to the analysis of the complex between antithrombin and the sulfated pentasaccharide reproducing the antithrombin-binding sequence in heparin. The mixture of coincubated antithrombin and heparin pentasaccharide was continuously injected into the capillary, and the electrophoretic separation of the free and bound forms of the protein was achieved. The intact noncovalent complex antithrombin/heparin pentasaccharide was detected on-line by ESIMS in positive ionization mode and in nondenaturing sheath liquid conditions. The complex stoichiometry was determined from the mass measurement of the complex. In addition, the characterization of the sulfated pentasaccharide ligand dissociated from the complex was performed in negative ionization mode using a denaturing sheath liquid, allowing the determination of its molecular mass and sulfation features. This FACE-ESIMS strategy opens the way to ligand fishing experiments performed on heterogeneous carbohydrate mixtures and subsequent characterization of specifically bound carbohydrates.
Stable Modification of PDMS surface properties by plasma polymerization: Application to the formation of double emulsions in microfluidic systems
Laboratoire Procédés - Plasmas - Microsystèmes - Vanessa Barbier, Michaël Tatoulian, Hong Li, Farzaneh Arefi-Khonsari ,Armand Ajdari and Patrick Tabeling
Langmuir - 22(12) :5230-2 - DOI:10.1021/la053289c - 2006
We describe a method based on plasma polymerization for the modification and control of the surface properties of poly(dimethylsiloxane) (PDMS) surfaces. By depositing plasma polymerized acrylic acid coatings on PDMS, we succeeded to fabricate stable (several days) hydrophilic and patterned hydrophobic/hydrophilic surfaces. We used this approach to generate direct and (for the first time in this material) double emulsions in PDMS microchannels.
A conductive hydrogel based on alginate and carbon nanotubes for probing microbial electroactivity
- Léopold Mottet, Domitille Le Cornec, Jean-Marc Noël, Frédéric Kanoufi, Brigitte Delord, Philippe Poulin, Jérôme Bibettea and Nicolas Bremond
- 14 1434-1441 - 10.1039/C7SM01929G -
Some bacteria can act as catalysts to oxidize (or reduce) organic or inorganic matter with the potential of generating electrical current. Despite their high value for sustainable energy, organic compound production and bioremediation, a tool to probe the natural biodiversity and to select most efficient microbes is still lacking. Compartmentalized cell culture is an ideal strategy for achieving such a goal but the appropriate compartment allowing cell growth and electron exchange must be tailored. Here, we develop a conductive composite hydrogel made of a double network of alginate and carbon nanotubes. Homogeneous mixing of carbon nanotubes within the polyelectrolyte is obtained by a surfactant assisted dispersion followed by a desorption step for triggering electrical conductivity. Dripping the mixture in a gelling bath through simple extrusion or a double one allows the formation of either plain hydrogel beads or liquid core hydrogel capsules. The process is shown to be compatible with the bacterial culture (Geobacter sulfurreducens). Bacteria can indeed colonize the outer wall of plain beads or the inner wall of the conductive capsules' shell that function as an anode from which electrons produced by the cells are collected.

414 publications.