828 research outputs found
Robustness of force and stress inference in an epithelial tissue
During morphogenesis, the shape of a tissue emerges from collective cellular
behaviors, which are in part regulated by mechanical and biochemical
interactions between cells. Quantification of force and stress is therefore
necessary to analyze the mechanisms controlling tissue morphogenesis. Recently,
a mechanical measurement method based on force inference from cell shapes and
connectivity has been developed. It is non-invasive, and can provide space-time
maps of force and stress within an epithelial tissue, up to prefactors. We
previously performed a comparative study of three force-inference methods,
which differ in their approach of treating indefiniteness in an inverse problem
between cell shapes and forces. In the present study, to further validate and
compare the three force inference methods, we tested their robustness by
measuring temporal fluctuation of estimated forces. Quantitative data of
cell-level dynamics in a developing tissue suggests that variation of forces
and stress will remain small within a short period of time (minutes).
Here, we showed that cell-junction tensions and global stress inferred by the
Bayesian force inference method varied less with time than those inferred by
the method that estimates only tension. In contrast, the amplitude of temporal
fluctuations of estimated cell pressures differs less between different
methods. Altogether, the present study strengthens the validity and robustness
of the Bayesian force-inference method.Comment: 4 pages, 4 figure
A migrating epithelial monolayer flows like a Maxwell viscoelastic liquid
We perform a bidimensional Stokes experiment in an active cellular material:
an autonomously migrating monolayer of Madin-Darby Canine Kidney (MDCK)
epithelial cells flows around a circular obstacle within a long and narrow
channel, involving an interplay between cell shape changes and neighbour
rearrangements. Based on image analysis of tissue flow and coarse-grained cell
anisotropy, we determine the tissue strain rate, cell deformation and
rearrangement rate fields, which are spatially heterogeneous. We find that the
cell deformation and rearrangement rate fields correlate strongly, which is
compatible with a Maxwell viscoelastic liquid behaviour (and not with a
Kelvin-Voigt viscoelastic solid behaviour). The value of the associated
relaxation time is measured as ~min, is observed to be
independent of obstacle size and division rate, and is increased by inhibiting
myosin activity. In this experiment, the monolayer behaves as a flowing
material with a Weissenberg number close to one which shows that both elastic
and viscous effects can have comparable contributions in the process of
collective cell migration.Comment: 17 pages, 15 figure
Fast determination of coarse grained cell anisotropy and size in epithelial tissue images using Fourier transform
Mechanical strain and stress play a major role in biological processes such
as wound healing or morphogenesis. To assess this role quantitatively, fixed or
live images of tissues are acquired at a cellular precision in large fields of
views. To exploit these data, large numbers of cells have to be analyzed to
extract cell shape anisotropy and cell size. Most frequently, this is performed
through detailed individual cell contour determination, using so-called
segmentation computer programs, complemented if necessary by manual detection
and error corrections. However, a coarse grained and faster technique can be
recommended in at least three situations. First, when detailed information on
individual cell contours is not required, for instance in studies which require
only coarse-grained average information on cell anisotropy. Second, as an
exploratory step to determine whether full segmentation can be potentially
useful. Third, when segmentation is too difficult, for instance due to poor
image quality or too large a cell number. We developed a user-friendly, Fourier
transform-based image analysis pipeline. It is fast (typically cells per
minute with a current laptop computer) and suitable for time, space or ensemble
averages. We validate it on one set of artificial images and on two sets of
fully segmented images, one from a Drosophila pupa and the other from a chicken
embryo; the pipeline results are robust. Perspectives include \textit{in vitro}
tissues, non-biological cellular patterns such as foams, and stacks.Comment: 13 pages; 9 figure
Consultant-2: pre- and post processing of machine learning applications.
The knowledge acquisition bottleneck in the development of large knowledge-based applications has not yet been resolved. One approach which has been advocated is the systematic use of Machine Learning (ML) techniques. However, ML technology poses difficulties to domain experts and knowledge engineers who are not familiar with it. This paper discusses Consultant-2, a system which makes a first step towards providing system support for a pre- and post-processing methodology where a cyclic process of experiments with an ML tool, its data, data description language and parameters attempts to optimize learning performance. Consultant-2 has been developed to support the use of Machine Learning Toolbox (MLT), an integrated architecture of 10 ML tools, and has evolved from a series of earlier systems. Consultant-0 and Consultant-1 had knowledge only about how to choose an ML algorithm based on the nature of the domain data. Consultant-2 is the most sophisticated. It, additionally, has knowledge about how ML experts and domain experts pre-process domain data before a run with the ML algorithm, and how they further manipulate the data and reset parameters after a run of the selected ML algorithm, to achieve a more acceptable result. How these several KBs were acquired and encoded is described. In fact, this knowledge has been acquired by interacting both with the ML algorithm developers and with domain experts who had been using the MLT toolbox on real-world tasks. A major aim of the MLT project was to enable a domain expert to use the toolbox directly; i.e. without necessarily having to involve either a ML specialist or a knowledge engineer. Consultant's principal goal was to provide specific advice to ease this process
Association mapping reveals gene action and interactions in the determination of flowering time in barley
The interaction between members of a gene network has an important impact on the variation of quantitative traits, and can influence the outcome of phenotype/genotype association studies. Three genes (Ppd-H1, HvCO1, HvFT1) known to play an essential role in the regulation of flowering time under long days in barley were subjected to an analysis of nucleotide diversity in a collection of 220 spring barley accessions. The coding region of Ppd-H1 was highly diverse, while both HvCO1 and HvFT1 showed a rather limited level of diversity. Within all three genes, the extent of linkage disequilibrium was variable, but on average only moderate. Ppd-H1 is strongly associated with flowering time across four environments, showing a difference of five to ten days between the most extreme haplotypes. The association between flowering time and the variation at HvFT1 and HvCO1 was strongly dependent on the haplotype present at Ppd-H1. The interaction between HvCO1 and Ppd-H1 was statistically significant, but this association disappeared when the analysis was corrected for the geographical origin of the accessions. No association existed between flowering time and allelic variation at HvFT1. In contrast to Ppd-H1, functional variation at both HvCO1 and HvFT1 is limited in cultivated barley
Topological and geometrical disorder correlate robustly in two-dimensional foams
A 2D foam can be characterised by its distribution of bubble areas, and of
number of sides. Both distributions have an average and a width (standard
deviation). There are therefore at least two very different ways to
characterise the disorder. The former is a geometrical measurement, while the
latter is purely topological. We discuss the common points and differences
between both quantities. We measure them in a foam which is sheared, so that
bubbles move past each other and the foam is "shuffled" (a notion we discuss).
Both quantities are strongly correlated; in this case (only) it thus becomes
sufficient to use either one or the other to characterize the foam disorder. We
suggest applications to the analysis of other systems, including biological
tissues
Two-dimensional flow of foam around an obstacle: force measurements
A Stokes experiment for foams is proposed. It consists in a two-dimensional
flow of a foam, confined between a water subphase and a top plate, around a
fixed circular obstacle. We present systematic measurements of the drag exerted
by the flowing foam on the obstacle, \emph{versus} various separately
controlled parameters: flow rate, bubble volume, bulk viscosity, obstacle size,
shape and boundary conditions. We separate the drag into two contributions, an
elastic one (yield drag) at vanishing flow rate, and a fluid one (viscous
coefficient) increasing with flow rate. We quantify the influence of each
control parameter on the drag. The results exhibit in particular a power-law
dependence of the drag as a function of the bulk viscosity and the flow rate
with two different exponents. Moreover, we show that the drag decreases with
bubble size, and increases proportionally to the obstacle size. We quantify the
effect of shape through a dimensioned drag coefficient, and we show that the
effect of boundary conditions is small.Comment: 26 pages, 13 figures, resubmitted version to Phys. Rev.
Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage
Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Δl-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley
- …