Françoise Argoul

In vivo analysis of local wall stiffness at the shoot apical meristem in Arabidopsis using atomic force microscopy.

Whereas the morphogenesis of developing organisms is relatively well understood at the molecular level, the contribution of the mechanical properties of the cells to shape changes remains largely unknown, mainly because of the lack of quantified biophysical parameters at cellular or subcellular resolution. Here we designed an atomic force microscopy approach to investigate the elastic modulus of the outer cell wall in living shoot apical meristems (SAMs). SAMs are highly organized structures that contain the plant stem cells, and generate all of the aerial organs of the plant. Building on modeling and experimental data, we designed a protocol that is able to measure very local properties, i.e. within 40-100 nm deep into the wall of living meristematic cells. We identified three levels of complexity at the meristem surface, with significant heterogeneity in stiffness at regional, cellular and even subcellular levels. Strikingly, we found that the outer cell wall was much stiffer at the tip of the meristem (5 ± 2 MPa on average), covering the stem cell pool, than on the flanks of the meristem (1.5 ± 0.7 MPa on average). Altogether, these results demonstrate the existence of a multiscale spatialization of the mechanical properties of the meristem surface, in addition to the previously established molecular and cytological zonation of the SAM, correlating with regional growth rate distribution.

Mechanics of the IL2RA gene activation revealed by modeling and atomic force microscopy.

Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static.

TRF2 promotes, remodels and protects telomeric Holliday junctions

The ability of the telomeric DNA‐binding protein, TRF2, to stimulate t‐loop formation while preventing t‐loop deletion is believed to be crucial to maintain telomere integrity in mammals. However, little is known on the molecular mechanisms behind these properties of TRF2. In this report, we show that TRF2 greatly increases the rate of Holliday junction (HJ) formation and blocks the cleavage by various types of HJ resolving activities, including the newly identified human GEN1 protein. By using potassium permanganate probing and differential scanning calorimetry, we reveal that the basic domain of TRF2 induces structural changes to the junction. We propose that TRF2 contributes to t‐loop stabilisation by stimulating HJ formation and by preventing resolvase cleavage. These findings provide novel insights into the interplay between telomere protection and homologous recombination and suggest a general model in which TRF2 maintains telomere integrity by controlling the turnover of HJ at t‐loops and at regressed replication forks.

Analysis of diffuse-layer effects on time-dependent interfacial kinetics

Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139(February 1, 2008)We investigate the subtle effects of diffuse charge on interfacial kinetics by solving the governingequations for ion transport (Nernst-Planck) with realistic boundary conditions representing reactionkinetics (Butler-Volmer) and compact-layer capacitance (Stern) in the asymptotic limit ǫ = λ

In situ probing of interfacial processes in the electrodeposition of copper by confocal Raman microspectroscopy

Confocal Raman microspectroscopy is applied to the in situ probing of interfacial processes in pulsed-current copper electrodeposition. This technique provides time-resolved characterization of the vibrational spectra of sulphate ions whenever in solution or adsorbed on the growing electrode. It also confirms the formation of cuprous oxide in the reduction process as the solution pH is increased by proton reduction. Moreover, when the passage of current is terminated, this technique provides evidence for the recombination of copper ions with copper metal to produce cuprous oxide on the outermost branches of the deposit.

Nucleosome positioning by genomic excluding-energy barriers

Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet in living cells, this organization also results from the action of various external factors like DNA-binding proteins and chromatin remodelers. To decipher the code for intrinsic chromatin organization, there is thus a need for in vitro experiments to bridge the gap between computational models of nucleosome sequence preferences and in vivo nucleosome occupancy data. Here we combine atomic force microscopy in liquid and theoretical modeling to demonstrate that a major sequence signaling in vivo are high-energy barriers that locally inhibit nucleosome formation rather than favorable positioning motifs. We show that these genomic excluding-energy barriers condition the collective assembly of neighboring nucleosomes consistently with equilibrium statistical ordering principles. The analysis of two gene promoter regions in Saccharomyces cerevisiae and the human genome indicates that these genomic barriers direct the intrinsic nucleosome occupancy of regulatory sites, thereby contributing to gene expression regulation.

Experimental evidence for homoclinic chaos in an electrochemical growth process

Abstract Experimental investigations of galvanostatic electrochemical growth processes in steady thin layer electrolytes are reported. For some control parameter values, the measurement of the cell potential versus time provides periodic and aperiodic oscillations. The deterministic character of these potential signals is demonstrated using standard dynamical systems theory tools such as time-delay phase portrait reconstructions, Poincare maps and one-dimensional maps. A transient period-doubling transition is described. The homoclinic nature of the chaotic behavior is emphasized. The origin of the spatio-temporal behavior is discussed in terms of the competition between the electrochemical process (reduction of metallic ions) and the transport processes (migration, diffusion and convection). Analysis of video images shows that the oscillations in growth rate are in phase across the entire cell width (up to 40 mm) and are in phase with the oscillations in the cell potential.

The N-terminal domains of TRF1 and TRF2 regulate their ability to condense telomeric DNA

TRF1 and TRF2 are key proteins in human telomeres, which, despite their similarities, have different behaviors upon DNA binding. Previous work has shown that unlike TRF1, TRF2 condenses telomeric, thus creating consequential negative torsion on the adjacent DNA, a property that is thought to lead to the stimulation of single-strand invasion and was proposed to favor telomeric DNA looping. In this report, we show that these activities, originating from the central TRFH domain of TRF2, are also displayed by the TRFH domain of TRF1 but are repressed in the full-length protein by the presence of an acidic domain at the N-terminus. Strikingly, a similar repression is observed on TRF2 through the binding of a TERRA-like RNA molecule to the N-terminus of TRF2. Phylogenetic and biochemical studies suggest that the N-terminal domains of TRF proteins originate from a gradual extension of the coding sequences of a duplicated ancestral gene with a consequential progressive alteration of the biochemical properties of these proteins. Overall, these data suggest that the N-termini of TRF1 and TRF2 have evolved to finely regulate their ability to condense DNA.

BEYOND CLASSICAL MULTIFRACTAL ANALYSIS USING WAVELETS: UNCOVERING A MULTIPLICATIVE PROCESS HIDDEN IN THE GEOMETRICAL COMPLEXITY OF DIFFUSION LIMITED AGGREGATES

We emphasize the wavelet transform as a very promising tool for solving the inverse fractal problem. We show that a dynamical system which leaves invariant a fractal object can be Uncovered from the space-scale arrangement of its wavelet transform modulus maxima. We illustrate our theoretical considerations on pedagogical examples including Bernoulli invariant measures of linear and nonlinear expanding Markov maps as well as the invariant measure of period-doubling dynamical systems at the onset of chaos. We apply this wavelet based technique to analyze the fractal properties of DLA azimuthal Cantor sets defined by intersecting the inner frozen region of large mass off-lattice DLA clusters with a circle. This study clearly reveals the existence of an underlying multiplicative process that is likely to account for the Fibonacci structural ordering recently discovered in the apparently disordered arborescent DLA morphology. The statistical relevance of the golden mean arithmetic to the fractal hierarchy of the DLA azimuthal Cantor sets is demonstrated.

High-resolution surface-plasmon imaging in air and in water: V(z) curve and operating conditions

We present what are believed to be the first images obtained with a far-field high-resolution scanning surface-plasmon microscope in an aqueous medium. Measurements of V(z), the output response of the microscope, versus defocus z give a signature of the surface-plasmon propagation. V(z) is strongly conditioned by the laser beam diameter and the objectives numerical aperture, and we show how the operating mode (in air and in water) must be chosen to maximize the surface-plasmon field and to minimize diffraction (edge) effects.