25 research outputs found

    Emergence of Small-World Anatomical Networks in Self-Organizing Clustered Neuronal Cultures

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    In vitro primary cultures of dissociated invertebrate neurons from locust ganglia are used to experimentally investigate the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. At all the different stages of the culture's development, identification of neurons' and neurites' location by means of a dedicated software allows to ultimately extract an adjacency matrix from each image of the culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main network's characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graph's micro- and meso-scale properties emerge. Finally, we identify the main physical processes ruling the culture's morphological transformations, and embed them into a simplified growth model qualitatively reproducing the overall set of experimental observations

    Small RNAs Reflect Grandparental Environments in Apomictic Dandelion

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    Plants can show long-term effects of environmental stresses and in some cases a stress “memory” has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation

    Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans

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    Summary Evidence from animal studies and human famines suggests that starvation may affect the health of the progeny of famished individuals. However, it is not clear whether starvation affects only immediate offspring or has lasting effects; it is also unclear how such epigenetic information is inherited. Small RNA-induced gene silencing can persist over several generations via transgenerationally inherited small RNA molecules in C. elegans, but all known transgenerational silencing responses are directed against foreign DNA introduced into the organism. We found that starvation-induced developmental arrest, a natural and drastic environmental change, leads to the generation of small RNAs that are inherited through at least three consecutive generations. These small, endogenous, transgenerationally transmitted RNAs target genes with roles in nutrition. We defined genes that are essential for this multigenerational effect. Moreover, we show that the F3 offspring of starved animals show an increased lifespan, corroborating the notion of a transgenerational memory of past conditions

    An Arabidopsis natural epiallele maintained by a feed-forward silencing loop between histone and DNA

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    The extent of epigenetic variation is currently well documented, but the number of natural epialleles described so far remains very limited. Determining the relevance of epigenetic changes for natural variation is an important question of research that we investigate by isolating natural epialleles segregating in Arabidopsis recombinant populations. We previously described a genetic incompatibility among Arabidopsis strains based on the silencing of a gene involved in fitness. Here, we isolated a new epiallele resulting from the silencing of a transfer-RNA editing gene in an Arabidopsis accession from the Netherlands ( Nok-1). Crosses with the reference accession Col-0 show a complete incompatibility between this epiallele and another locus localized on a different chromosome. We demonstrate that conversion of an unmethylated version of this allele occurs in hybrids, associated with modifications of small RNA populations. These epialleles can also spontaneously revert within the population. Furthermore, we bring evidence that neither METHYLTRANSFERASE 1, maintaining methylation at CGs, nor components of RNA-directed DNA methylation, are key factors for the transmission of the epiallele over generations. This depends only on the self-reinforcing loop between CHROMOMETHYLASE 3 and KRYPTONITE, involving DNA methylated in the CHG context and histone H3 lysine 9 methylation. Our findings reveal a predominant role of this loop in maintaining a natural epiallele

    Degree distribution and degree-degree correlation.

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    <p>(A) Cumulative node degree distributions on a semi-log scale for the state of the same culture at DIVs 3, 6, 7, and 12 (see legend for the symbol coding). Solid lines correspond to the best exponential fitting , with the mean degrees at DIV 3, 6, 7, and 12 respectively. (B) Degree correlation exponent (blue circles) measuring the network assortativity and the corresponding Pearson coefficient (red squares). Both quantities are averaged for the set of 6 cultures at each day of measure (DIV) and error bars represent the sem.</p

    Density of the network as a function of culture age.

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    <p>(A) Mean number of nodes (blue circles), including neurons and clusters of neurons, and links connecting them (red squares), calculated for the 6 cultures vs. age (DIV). Inset: the link density (green triangles) quantifies the actual number of links divided by that of an all-to-all configuration [, being the number of connected nodes at each age]. (B) Log-linear plot of the mean number of nodes having at least one connection (blue circles), of the mean size of the giant connected component (red squares) and of the second largest connected component (green triangles). In all plots, error bars stand for the standard errors of the mean (sem).</p

    Extraction of the adjacency matrix defining the neural network connectivity.

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    <p>(A) Image cut taken from a 6 DIV culture and (B) the layer on top showing the identification of neurons and clusters of neurons (red), neurites connecting them (green) and neurite branching points (blue). (C) Mapping of the neuronal network into a graph where blue dots represent the nodes and green lines the links of the graph.</p

    Growth model.

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    <p>(A) Schematic representation of how cells get connected. At DIV 0, 4 cells of radius are located at random positions. The first iteration of the algorithm, DIV 1, assigns to each cell a disk of radius (green shade). At the next iteration, DIV 2, the disk's growth rate decreases, , and a link between two cells is established when their disks intersect (DIV 3). This process continues until steps. (B) Force diagram explaining cell migration and clustering. Tension forces , , and are acting on the central cluster composed of two cells, whose vector sum (red arrow) exceeds the adhesion to the substrate (green arrow). As a result, a new equilibrium state is produced with new tension forces , , and , being the central cluster pulled in the direction of the net force approaching the largest cluster.</p

    Network clustering and shortest path properties as a function of culture age.

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    <p>(A) Absolute values of the clustering coefficient (blue circles, left axis) and mean path length (red squares, right axis) normalized to the size of the largest cluster. (B) Semi-log plot of normalized values of and with respect to the expected values for an equivalent random network having the same number of nodes and links and preserving the degree distribution: (blue circles) and (red squares). The average path length is also compared to the value for a regular lattice as (green triangles) with , being the average connectivity and the size of the largest connected component. (C) Local (upper plot) and global (lower plot) efficiency as a function of culture age and compared to their respective values for the random graphs of the null model (see text for an explanation). All quantities are averaged for the set of 6 cultures at each day of measure (DIV). As in the Caption of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085828#pone-0085828-g003" target="_blank">Fig. 3</a>, error bars represent the standard errors of the mean (sem).</p
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