The stable states of the network.

<p>The activity of each node is given for each of the three attractors (SOX9, RUNX2 and None).</p

The model’s chondrocyte gene network.

<p>Every box represents a gene, its protein or in some cases a complex of them. The interactions are represented by red and black lines if they are inhibitory and stimulatory, respectively. Blue boxes denote growth factors, green boxes are transcription factors, yellow boxes do not belong to either category. Reproduced from [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162052#pone.0162052.ref028" target="_blank">28</a>].</p

The effect of perturbations in the SOX9 attractor.

<p>For each node, the average outcomes for three times a hundred perturbations are shown in this Fig The colour code indicates the attractor the system settled in after perturbation. Nodes at maximal value are excluded for overactivation and nodes with zero activity are excluded for knockout.</p

Influence of overactivation of WNT and/or BMP on attractor canalisation.

<p>Model 1 is the network as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162052#pone.0162052.g001" target="_blank">Fig 1</a>. Model 2 is the network where the interaction BMP →MEF2C (slow) was replaced by the interaction WNT→MEF2C (slow). In model 3, the interaction BMP →MEF2C (slow) was removed, leaving only RUNX2 to regulate expression of MEF2C mRNA. For each model, the relative size of the attractors basins of RUNX2 and SOX9, and ‘None’ attractors is shown for the overactivation of WNT and/or BMP.</p

Predicted effect on the overexpression and knockout of the network’s genes using Monte Carlo analysis.

<p>Overview of changes in the size of attractor basins upon perturbation of the nodes. Both overexpression (first three columns) and knockout (last three columns) are shown. Each column is colour-coded, up regulation effects are green and down regulation effects are red. For instance, the first row for the first column indicates that WNT overexpression results in an increase (green) of the attractor basin of the RUNX2 attractor. Different shades of the colours indicate the intensity of the change. No change is indicated by white.</p

Markov Chain representation of the network.

<p>Circles represent steady states and the edges transitions between them. The corresponding transition probability is given for each edge.</p

Gene expression for DLX5, MEF2C, RUNX2, SOX9 and control genes.

<p>A. Fold changes in expression of RUNX2, SOX9, DLX5, MEF2C, AXIN2 and ID1 are shown for different time points in the WNT, BMP and WNT/BMP conditions. Error bars indicate the standard deviation. The results were analysed by paired t-tests (corrected for multiple testing using the Benjamini-Hochberg procedure). *: p < 0,05. **: p < 0,01.</p

Effect of knockout on OA disease model.

<p><i>The first and second column contain the effect of a knockout in the attractor basin</i>. <i>We check whether a knockout (either through the use of a small molecule inhibitor or by a genetic KO) indeed confers protection to OA</i>, <i>indicated as ‘protective’</i>. <i>Sometimes a knockout is seen to aggravate symptoms</i>, <i>indicated as ‘reverse’</i>. <i>Finally</i>, <i>cases where no knockout was found</i>, <i>are marked by ‘absent’</i>. <i>Sometimes indirect support</i>, <i>namely that the protein’s constitutive activation entails hypertrophy</i>, <i>is found</i>. <i>Papers indicating this are referenced after the ‘absent’ tag</i>. <i>For SMAD7</i>, <i>one study found increased Smad7 expression was accompanied by a reduction in osteophyte formation</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162052#pone.0162052.ref067" target="_blank">67</a>]. *<i>In the network model</i>, <i>an insulation of GSK in the destruction complex from cytosolic GSK is assumed</i>. <i>In the case of a knockout this would not hold</i>. <i>Hence a double mutant</i>, <i>with a knockout of both destruction complex (DC) and GSK</i>, <i>constitutes a more appropriate simulation</i>.</p

Oxygen-Dependent Lipid Profiles of Three-Dimensional Cultured Human Chondrocytes Revealed by MALDI-MSI

Articular cartilage is exposed to a gradient of oxygen levels ranging from 5% at the surface to 1% in the deepest layers. While most cartilage research is performed in supraphysiological oxygen levels (19–21%), culturing chondrocytes under hypoxic oxygen levels (≤8%) promotes the chondrogenic phenotype. Exposure of cells to various oxygen levels alters their lipid metabolism, but detailed studies examining how hypoxia affects lipid metabolism in chondrocytes are lacking. To better understand the chondrocyte’s behavior in response to oxygen, we cultured 3D pellets of human primary chondrocytes in normoxia (20% oxygen) and hypoxia (2.5% oxygen) and employed matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) in order to characterize the lipid profiles and their spatial distribution. In this work we show that chondrocytes cultured in hypoxia and normoxia can be differentiated by their lipid profiles. Among other species, phosphatidylglycerol species were increased in normoxic pellets, whereas phosphatidylinositol species were the most prominent lipids in hypoxic pellets. Moreover, spatial mapping revealed that phospahtidylglyycerol species were less prominent in the center of pellets where the oxygen level is lower. Additional analysis revealed a higher abundance of the mitochondrial-specific lipids, cardiolipins, in normoxic conditions. In conclusion MALDI-MSI described specific lipid profiles that could be used as sensors of oxygen level changes and may especially be relevant for retaining the chondrogenic phenotype, which has important implications for the treatment of bone and cartilage diseases

Model_and_data.zip

Additional File for the paper "Modelling with ANIMO:<div>between Fuzzy Logic and Differential Equations" published in BMC Systems Biology.</div><div>See the ReadMe.txt file for information on how to use the models and data with Cytoscape and ANIMO.</div