(Tissue) P Systems with Vesicles of Multisets

We consider tissue P systems working on vesicles of multisets with the very simple operations of insertion, deletion, and substitution of single objects. With the whole multiset being enclosed in a vesicle, sending it to a target cell can be indicated in those simple rules working on the multiset. As derivation modes we consider the sequential mode, where exactly one rule is applied in a derivation step, and the set maximal mode, where in each derivation step a non-extendable set of rules is applied. With the set maximal mode, computational completeness can already be obtained with tissue P systems having a tree structure, whereas tissue P systems even with an arbitrary communication structure are not computationally complete when working in the sequential mode. Adding polarizations (-1, 0, 1 are sufficient) allows for obtaining computational completeness even for tissue P systems working in the sequential mode.Comment: In Proceedings AFL 2017, arXiv:1708.0622

Matrix of gene expressions in cell populations identified from ISH pictures.

<p>Rows correspond to cell populations and columns to chemical species or other variables. A black square means a species is present or a variable is on in the associated tissue.</p

Genes expressed in the three classical meristematic identities.

<p>Genes expressed in the three classical meristematic identities.</p

Contributions of each gene to the number of models to explore.

<p>Contributions of each gene to the number of models to explore.</p

SAM domains.

<p>A Shoot Apical Meristem is a dome-shaped structure whose zonal cell types (identities) have been depicted in different colors. The Organizing Center (OC), Flank, Peripheral Zone (PZ), Central Zone (CZ) and internal cells are shown in progressively paler shades of green, while an Anlage and Primordium are shown in two shades of brown. Cells in the CZ grow, divide and differentiate into the PZ or an Anlage, which respectively go on to become the flank or a primordium. Each Anlage is generated periodically. In a vegetative meristem, these Anlagen go on to produce primordia that lack their own OC and grow into leaves. Inflorescence meristems produce Anlagen that become floral primordia that do contain their own OCs (colored red).</p

Common representation of the core regulatory network controlling SAM identity.

<p>Nodes represent genes and edges represent regulatory interactions. V-shaped and T-shaped arrow heads respectively denote activation and repression by the regulatory nodes.</p

Interactions found in the 12 networks in the first peak of fitness.

<p>The naming and color scheme are as described for <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005744#pcbi.1005744.g009" target="_blank">Fig 9</a>. This shows the repressions of <i>FD</i> by <i>AP1</i> and of the auxin pathway by <i>TFL1</i> are the most straightforward additions required to make the network consistent with the data. This also shows that some interactions are not required to explain the data, namely <i>FT</i> → <i>AP1</i>, <i>FD</i> → <i>AP1</i> and <i>AP1</i> → <i>SOC1</i>.</p

Counts of the distinct models generated by the GP algorithm, with fitness < −0.18.

<p>Models with the same number have the same fitness value. The approach favors models with lower fitness values, but even at a given fitness value (1a-1c, 3a-3d), not all models are found with the same frequency, suggesting that some may be easier to find than others.</p

Principal components of the variability in the subset of 12 models.

<p>Principal components of the variability in the subset of 12 models.</p

Transitions in mutant plants.

<p>Transitions in mutant plants.</p