Passive microrheology of soft materials with atomic force microscopy: A wavelet-based spectral analysis

International audienceCompared to active microrheology where a known force or modulation is periodically imposed to a soft material, passive microrheology relies on the spectral analysis of the spontaneous motion of tracers inherent or external to the material. Passive microrheology studies of soft or living materials with atomic force microscopy (AFM) cantilever tips are rather rare because, in the spectral densities, the rheological response of the materials is hardly distinguishable from other sources of random or periodic perturbations. To circumvent this difficulty, we propose here a wavelet-based decomposition of AFM cantilever tip fluctuations and we show that when applying this multi-scale method to soft polymer layers and to living myoblasts, the structural damping exponents of these soft materials can be retrieved. Local stiffness and internal friction of soft materials (passive or active such as living cells) have lately been addressed at the nanoscale thanks to the development of pico-to nano-Newton force sensing systems and of nanome-ter resolution position detection devices. 1 Atomic force mi-croscopy (AFM) is one of these methods, where a sharply tipped flexible cantilever is indented inside a material to extract its local viscoelasticity from the shift and spreading of the cantilever spectral resonance modes. 2–4 However, these estimations are limited to rather narrow frequency bands surrounding the cantilever resonance modes or their higher harmonics. Spectral decomposition of cantilever fluctuations in contact with soft living tissues in the low frequency range has more rarely been explored. The few attempts which can be found in the literature were performed with small amplitude harmonic excitations (50 nm) of the sample position driven by a piezo-translator, in the 0.1 to 100 Hz frequency range, for a small and finite number of frequencies. 5,6 Whereas passive (driven by thermal fluctuations) microrheology has been performed for the past two decades by a variety of techniques capturing micro-probe spatial fluctuations , 7 it has not been applied yet to AFM cantilever fluctuations. The limitation of AFM-based passive rheology in the low frequency range comes from the mixing of the background vibrations of the liquid chamber with the cantilever fluctuations given by the rheological response of the material which are difficult to disentangle by standard FFT-based spectral averaging methods. In this work, we show that in quasi-stationary situations, these limitations can be circumvented using a wavelet-based spectral analysis of micro-cantilever fluctuations under passive excitation. Two experimental applications to passive polymer layers and living adherent myoblast cells are reported. Based on the generalized Stokes-Einstein relation (GSER) and associated generalizing assumptions, 8 passive microrheology of soft materials enables the extraction of the frequency-dependent complex modulus GðxÞ which is common to a large class of soft materials (foams, emulsions, slur-ries, and cells). 9–11 The observed scaling laws are explained by a characteristic structural disorder and the metastability of these materials which are embodied under the name of " soft glassy materials " or structural damping model. 12 Their complex shear modulus behaves a

Power-law and log-normal avalanche size statistics in random growth processes

ACKNOWLEDGMENTS We thank J.P. Bouchaud for constructive comments. We acknowledge financial support from the Agence Nationale de la Recherche (ANR grant number ANR-18- CE45-0012-01) and from the French Research Ministry (MESR) (contract No. 2017-SG-D-09) and from ENS Lyon for SP PhD funding. FJPR acknowledges financial support from the Carnegie Trust.Peer reviewedPostprin

In vivo Study of the Histone Chaperone Activity of Nucleolin by FRAP

Nucleolin is a major nucleolar protein involved in various aspects of ribosome biogenesis such as regulation of polymerase I transcription, pre-RNA maturation, and ribosome assembly. Nucleolin is also present in the nucleoplasm suggesting that its functions are not restricted to nucleoli. Nucleolin possesses, in vitro, chromatin co-remodeler and histone chaperone activities which could explain numerous functions of nucleolin related to the regulation of gene expression. The goal of this report was to investigate the consequences of nucleolin depletion on the dynamics of histones in live cells. Changes in histone dynamics occurring in nucleolin silenced cells were measured by FRAP experiments on eGFP-tagged histones (H2B, H4, and macroH2A). We found that nuclear histone dynamics was impacted in nucleolin silenced cells; in particular we measured higher fluorescence recovery kinetics for macroH2A and H2B but not for H4. Interestingly, we showed that nucleolin depletion also impacted the dissociation constant rate of H2B and H4. Thus, in live cells, nucleolin could play a role in chromatin accessibility by its histone chaperone and co-remodeling activities

Structural organization of human replication timing domains

AbstractRecent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U-shaped MRT domains bordered by “master” replication origins specified by a localized (∼200–300kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina-associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties

Multifractal Desynchronization of the Cardiac Excitable Cell Network During Atrial Fibrillation. II. Modeling

In a companion paper (I. Multifractal analysis of clinical data), we used a wavelet-based multiscale analysis to reveal and quantify the multifractal intermittent nature of the cardiac impulse energy in the low frequency range ≲ 2Hz during atrial fibrillation (AF). It demarcated two distinct areas within the coronary sinus (CS) with regionally stable multifractal spectra likely corresponding to different anatomical substrates. The electrical activity also showed no sign of the kind of temporal correlations typical of cascading processes across scales, thereby indicating that the multifractal scaling is carried by variations in the large amplitude oscillations of the recorded bipolar electric potential. In the present study, to account for these observations, we explore the role of the kinetics of gap junction channels (GJCs), in dynamically creating a new kind of imbalance between depolarizing and repolarizing currents. We propose a one-dimensional (1D) spatial model of a denervated myocardium, where the coupling of cardiac cells fails to synchronize the network of cardiac cells because of abnormal transjunctional capacitive charging of GJCs. We show that this non-ohmic nonlinear conduction 1D modeling accounts quantitatively well for the “multifractal random noise” dynamics of the electrical activity experimentally recorded in the left atrial posterior wall area. We further demonstrate that the multifractal properties of the numerical impulse energy are robust to changes in the model parameters

Evolutionary comparisons reveal a positional switch for spindle pole oscillations in Caenorhabditis embryos.

International audienceDuring the first embryonic division in Caenorhabditis elegans, the mitotic spindle is pulled toward the posterior pole of the cell and undergoes vigorous transverse oscillations. We identified variations in spindle trajectories by analyzing the outwardly similar one-cell stage embryo of its close relative Caenorhabditis briggsae. Compared with C. elegans, C. briggsae embryos exhibit an anterior shifting of nuclei in prophase and reduced anaphase spindle oscillations. By combining physical perturbations and mutant analysis in both species, we show that differences can be explained by interspecies changes in the regulation of the cortical Gα-GPR-LIN-5 complex. However, we found that in both species (1) a conserved positional switch controls the onset of spindle oscillations, (2) GPR posterior localization may set this positional switch, and (3) the maximum amplitude of spindle oscillations is determined by the time spent in the oscillating phase. By investigating microevolution of a subcellular process, we identify new mechanisms that are instrumental to decipher spindle positioning

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

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