89 research outputs found
Dynamic Behavior in Piezoresponse Force Microscopy
Frequency dependent dynamic behavior in Piezoresponse Force Microscopy (PFM)
implemented on a beam-deflection atomic force microscope (AFM) is analyzed
using a combination of modeling and experimental measurements. The PFM signal
comprises contributions from local electrostatic forces acting on the tip,
distributed forces acting on the cantilever, and three components of the
electromechanical response vector. These interactions result in the bending and
torsion of the cantilever, detected as vertical and lateral PFM signals. The
relative magnitudes of these contributions depend on geometric parameters of
the system, the stiffness and frictional forces of tip-surface junction, and
operation frequencies. The dynamic signal formation mechanism in PFM is
analyzed and conditions for optimal PFM imaging are formulated. The
experimental approach for probing cantilever dynamics using frequency-bias
spectroscopy and deconvolution of electromechanical and electrostatic contrast
is implemented.Comment: 65 pages, 15 figures, high quality version available upon reques
FACT sets a barrier for cell fate reprogramming in Caenorhabditis elegans and human cells
The chromatin regulator FACT (facilitates chromatin transcription) is essential for ensuring stable gene expression by promoting transcription. In a genetic screen using Caenorhabditis elegans, we identified that FACT maintains cell identities and acts as a barrier for transcription factor-mediated cell fate reprogramming. Strikingly, FACT's role as a barrier to cell fate conversion is conserved in humans as we show that FACT depletion enhances reprogramming of fibroblasts. Such activity is unexpected because FACT is known as a positive regulator of gene expression, and previously described reprogramming barriers typically repress gene expression. While FACT depletion in human fibroblasts results in decreased expression of many genes, a number of FACT-occupied genes, including reprogramming-promoting factors, show increased expression upon FACT depletion, suggesting a repressive function of FACT. Our findings identify FACT as a cellular reprogramming barrier in C. elegans and humans, revealing an evolutionarily conserved mechanism for cell fate protection
Elastic interactions of active cells with soft materials
Anchorage-dependent cells collect information on the mechanical properties of
the environment through their contractile machineries and use this information
to position and orient themselves. Since the probing process is anisotropic,
cellular force patterns during active mechanosensing can be modelled as
anisotropic force contraction dipoles. Their build-up depends on the mechanical
properties of the environment, including elastic rigidity and prestrain. In a
finite sized sample, it also depends on sample geometry and boundary conditions
through image strain fields. We discuss the interactions of active cells with
an elastic environment and compare it to the case of physical force dipoles.
Despite marked differences, both cases can be described in the same theoretical
framework. We exactly solve the elastic equations for anisotropic force
contraction dipoles in different geometries (full space, halfspace and sphere)
and with different boundary conditions. These results are then used to predict
optimal position and orientation of mechanosensing cells in soft material.Comment: Revtex, 38 pages, 8 Postscript files included; revised version,
accepted for publication in Phys. Rev.
Quasi Two-dimensional Transfer of Elastic Waves
A theory for multiple scattering of elastic waves is presented in a random
medium bounded by two ideal free surfaces, whose horizontal size is infinite
and whose transverse size is smaller than the mean free path of the waves. This
geometry is relevant for seismic wave propagation in the Earth crust. We derive
a time-dependent, quasi-2D radiative transfer equation, that describes the
coupling of the eigenmodes of the layer (surface Rayleigh waves, SH waves, and
Lamb waves). Expressions are found that relate the small-scale fluctuations to
the life time of the modes and to their coupling rates. We discuss a diffusion
approximation that simplifies the mathematics of this model significantly, and
which should apply at large lapse times. Finally, coherent backscattering is
studied within the quasi-2D radiative transfer equation for different source
and detection configurations.Comment: REVTeX, 36 pages with 10 figures. Submitted to Phys. Rev.
Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos
DNA accessibility of cis-regulatory elements (CREs) dictates transcriptional activity and drives cell differentiation during development. While many genes regulating embryonic development have been identified, the underlying CRE dynamics controlling their expression remain largely uncharacterized. To address this, we produced a multimodal resource and genomic regulatory map for the zebrafish community, which integrates single-cell combinatorial indexing assay for transposase-accessible chromatin with high-throughput sequencing (sci-ATAC-seq) with bulk histone PTMs and Hi-C data to achieve a genome-wide classification of the regulatory architecture determining transcriptional activity in the 24-h post-fertilization (hpf) embryo. We characterized the genome-wide chromatin architecture at bulk and single-cell resolution, applying sci-ATAC-seq on whole 24-hpf stage zebrafish embryos, generating accessibility profiles for ∼23,000 single nuclei. We developed a genome segmentation method, ScregSeg (single-cell regulatory landscape segmentation), for defining regulatory programs, and candidate CREs, specific to one or more cell types. We integrated the ScregSeg output with bulk measurements for histone post-translational modifications and 3D genome organization and identified new regulatory principles between chromatin modalities prevalent during zebrafish development. Sci-ATAC-seq profiling of npas4l/cloche mutant embryos identified novel cellular roles for this hematovascular transcriptional master regulator and suggests an intricate mechanism regulating its expression. Our work defines regulatory architecture and principles in the zebrafish embryo and establishes a resource of cell-type-specific genome-wide regulatory annotations and candidate CREs, providing a valuable open resource for genomics, developmental, molecular, and computational biology
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