Schematic illustration of the network self-organization at three different instants of the automata generations.

<p>(A) DIV 3, (B) DIV 6, and (C) DIV 12. Simulation parameters: , , and .</p

Degree distribution and degree-degree correlation.

<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

Extraction of the adjacency matrix defining the neural network connectivity.

<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

Density of the network as a function of culture age.

<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

Growth model.

<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

Culture development of locust frontal ganglion neurons into clustered networks.

<p>(A) After 3 DIV, completely dissociated neurons had already started growing neuronal processes with continuous branching. The area outlined in (b) is enlarged in B. (C) Same area as in (B) but at 6 DIV. At this stage, neurons and small clusters of neurons are already densely connected and form a complex network. At the same stage, branched neurites (pointed by the black arrow) that failed to contact neighboring neurons start to retract. (D) Migration of neurons due to the tension along neurites leads to the formation of large neuronal clusters and of thicker bundles of neurites. For a better visualization, the area outlined in (e) is enlarged in E.</p

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

<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

Comparison between model and experiment.

<p>Legends in each panel clarifies on the topological quantities measured in experiments (dashed curves), and the corresponding trends of the simulated networks (solid curves). Simulation parameters are the same as in the caption of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0085828#pone-0085828-g007" target="_blank">Fig. 7</a>, and each point is the ensemble average over 50 independent runs of the growth algorithm.</p

Expression profiles of <i>TAD3-1</i> alleles in Col-0 x Nok-1 hybrids determined by pyrosequencing.

<p>Expression profiles of <i>TAD3-1</i> alleles in Col-0 x Nok-1 hybrids determined by pyrosequencing.</p

Sequence length distribution of the small RNAs over the <i>TAD3-1</i> locus.

<p>sRNA reads were counted in three different genomic regions: the first one (Chr5: 8,446,240–8,447,463) comprises two transposons upstream of <i>TAD3-1</i>, the second includes the promoter of <i>TAD3-1</i> (Chr5: 8,447,463–8,447,954) and the last one corresponds to the <i>TAD3-1</i> gene (Chr5: 8,447,954–8,451,218). Transposable elements are depicted in orange and <i>TAD3-1</i> in grey. Counts are given in reads per million of mapped reads. The precise distribution of sRNA reads is described in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006551#pgen.1006551.s011" target="_blank">S11 Fig</a>.</p