488 research outputs found
Instantaneous cell migration velocity may be ill-defined
Cell crawling is critical to biological development, homeostasis and disease.
In many cases, cell trajectories are quasi-random-walk. In vitro assays on flat
surfaces often described such quasi-random-walk cell trajectories as
approximations to a solution of a Langevin process. However, experiments show
quasi-diffusive behavior at small timescales, indicating that instantaneous
velocity and velocity autocorrelations are not well-defined. We propose to
characterize mean-squared cell displacement using a modified F\"urth equation
with three temporal and spatial regimes: short- and long-time/range diffusion
and intermediate time/range ballistic motion. This analysis collapses
mean-squared displacements of previously published experimental data onto a
single-parameter family of curves, allowing direct comparison between movement
in different cell types, and between experiments and numerical simulations. Our
method also show that robust cell-motility quantification requires an
experiment with a maximum interval between images of a few percent of the
cell-motion persistence time or less, and a duration of a few
orders-of-magnitude longer than the cell-motion persistence time or more.Comment: 5 pages, plus Supplemental materia
Redes de neurônios
In the last ten years many scientific advances regarding neurons and the way they are interconnected has mad o it possible to study the dynamics of storage and Processing of information in the brain. In particular, the physicist J. J. Hopfield proposed a formal minimalist model to these neural networks reducing the problem to a particular case of a well – defined physical problem – the spin glass. Although the problem à s well defined, its solution is far from being trivial.Here we introduce the problem, describe Hopfield model, with its achievements and limitations, and present our contribution to the description of information storage in neural networks.Na última década várias descobertas em relação a neurônios e á maneira como estão interconectados, formando redes, possibilitaram o estudo da dinâmica do armazenamento e processamento de informação pelo cérebro. Em particular, o fÃsico J. J. Hopfield propôs um modelo formal, minimalista para estas redes neuronais, reduzindo o problema a um caso particular de um sistema fÃsico bem definido - o vidro de spin. Embora o problema esteja bem definido, sua solução está longe de ser trivial.Neste texto nós introduzimos o problema, descrevemos o modelo de Hopfield com seus resultados e limitações e apresentamos nossa contribuição para a descrição do armazenamento da informação em redes de neurônios
Geometrical distribution of Cryptococcus neoformans mediates flower-like biofilm development
Microbial biofilms are highly structured and dynamic communities in which phenotypic diversification allows microorganisms to adapt to different environments under distinct conditions. The environmentally ubiquitous pathogen Cryptococcus neoformans colonizes many niches of the human body and implanted medical devices in the form of biofilms, an important virulence factor. A new approach was used to characterize the underlying geometrical distribution of C. neoformans cells during the adhesion stage of biofilm formation. Geometrical aspects of adhered cells were calculated from the Delaunay triangulation and Voronoi diagramobtained fromscanning electronmicroscopy images (SEM). A correlation between increased biofilm formation and higher ordering of the underlying cell distribution was found. Mature biofilm aggregates were analyzed by applying an adapted protocol developed for ultrastructure visualization of cryptococcal cells by SEM. Flower-like clusters consisting of cells embedded in a dense layer of extracellular matrix were observed as well as distinct levels of spatial organization: adhered cells, clusters of cells and community of clusters. The results add insights into yeast motility during the dispersion stage of biofilm formation. This study highlights the importance of cellular organization for biofilm growth and presents a novel application of the geometrical method of analysis
Shape-velocity correlation defines polarization in migrating cell simulations
Cell migration plays essential roles in development, wound healing, diseases,
and in the maintenance of a complex body. Experiments in collective cell
migration generally measure quantities such as cell displacement and velocity.
The observed short-time diffusion regime for mean square displacement in
single-cell migration experiments on flat surfaces calls into question the
definition of cell velocity and the measurement protocol. Theoretical results
in stochastic modeling for single-cell migration have shown that this fast
diffusive regime is explained by a white noise acting on displacement on the
direction perpendicular to the migrating cell polarization axis (not on
velocity). The prediction is that only the component of velocity parallel to
the polarization axis is a well-defined quantity, with a robust measurement
protocol. Here, we ask whether we can find a definition of a migrating-cell
polarization that is able to predict the cell's subsequent displacement, based
on measurements of its shape. Supported by experimental evidence that cell
nucleus lags behind the cell center of mass in a migrating cell, we propose a
robust parametrization for cell migration where the distance between cell
nucleus and the cell's center of mass defines cell shape polarization. We
tested the proposed methods by applying to a simulation model for
three-dimensional cells performed in the CompuCell3D environment, previously
shown to reproduce biological cells kinematics migrating on a flat surface
Growth laws and self-similar growth regimes of coarsening two-dimensional foams: Transition from dry to wet limits
We study the topology and geometry of two dimensional coarsening foams with
arbitrary liquid fraction. To interpolate between the dry limit described by
von Neumann's law, and the wet limit described by Marqusee equation, the
relevant bubble characteristics are the Plateau border radius and a new
variable, the effective number of sides. We propose an equation for the
individual bubble growth rate as the weighted sum of the growth through
bubble-bubble interfaces and through bubble-Plateau borders interfaces. The
resulting prediction is successfully tested, without adjustable parameter,
using extensive bidimensional Potts model simulations. Simulations also show
that a selfsimilar growth regime is observed at any liquid fraction and
determine how the average size growth exponent, side number distribution and
relative size distribution interpolate between the extreme limits. Applications
include concentrated emulsions, grains in polycrystals and other domains with
coarsening driven by curvature
Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops
PTDC/BIA-MOL/30438/2017 PTDC/MED-OUT/4301/2020 RiboMed 857119 PD/BD/128292/2017 LCF/PR/HP21/52310016 PTDC/BIA-MOL/6624/2020 PTDC/MED-ONC/7864/2020DNA oxidation by ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming. The conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) initiates developmental and cell-type-specific transcriptional programs through mechanisms that include changes in the chromatin structure. Here, we show that the presence of 5hmC in the transcribed gene promotes the annealing of the nascent RNA to the template DNA strand, leading to the formation of an R-loop. Depletion of TET enzymes reduced global R-loops in the absence of gene expression changes, whereas CRISPR-mediated tethering of TET to an active gene promoted the formation of R-loops. The genome-wide distribution of 5hmC and R-loops shows a positive correlation in mouse and human stem cells and overlap in half of all active genes. Moreover, R-loop resolution leads to differential expression of a subset of genes that are involved in crucial events during stem cell proliferation. Altogether, our data reveal that epigenetic reprogramming via TET activity promotes co-transcriptional R-loop formation, disclosing new mechanisms of gene expression regulation.publishersversionpublishe
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