Research

Organizing flows to control behavior:

stress feedback

Foraging organisms such as fungi and the slime mold Physarum polycephalum grow as remarkably large networks to explore their environment and find scarce and spatially disjunct resources. The mechanisms used by these organisms to integrate disparate sources of information and regulate their growth and morphological adaptation remain unknown. We study the cytoplasmic flows within the vein networks of P. polycephalum as a mechanism to coordinate behavior and transport signals. We find that the cytoplasmic flows are driven by cross-section contractions of the veins. These contractions form a peristaltic wave. We extend the theoretical concept of peristalsis to a random network and show that transport is maximized when the network comprises a single wavelength of the peristaltic wave. Comparisons of theoretically generated contraction patterns with the patterns exhibited by individuals of P. polycephalum demonstrate that individuals maximize internal flows by adapting patterns of contraction to size, thus optimizing transport throughout an organism. This control of fluid flow may be the key to coordinating growth and behavior, including the dynamic changes in network architecture seen over time in an individual.

Quickguide: Physarum.
Karen Alim, Natalie Andrew and Anne Pringle,
Curr. Biol., 23(24), R1082-R1083 (2013). (PDF) .

Random network peristalsis in Physarum polycephalums organizes fluid flows across an individual.
Karen Alim*, Gabriel Amselem*, François Peaudecerf, Michael P. Brenner and Anne Pringle,
Proc. Natl. Acad. Sci. U.S.A., 110(33), 13306-13311 (2013). (PDF) .

Growth control in plant tissue:

stress feedback

A central question in biology is how cells within a tissue coordinate their growth. We investigated how growth heterogeneity is controlled and what could be its function in the shoot apical meristem of plants. Studying a katanin mutant we provide evidence that katanin-dependent microtubule dynamics increases cell competence to respond to mechanical stress, allowing cells to adapt their growth parameters to that of their neighbors. While this mechanism could mediate growth homeostasis, we surprisingly found that it enhances growth heterogeneity. We generated a model of cell tissue growth exploring the strength of the cell response to mechanical stress. The model shows that mechanical forces may decrease growth variability, even providing a theoretical optimum of homogeneity. However, the model also shows that the existence of large stress feedback, and most clearly for low fluctuations in growth, can on the contrary increase growth variability. Validation of the latter by our growth measurements suggests that, despite the existence of a theoretical optimum where growth is homogeneous, growth in plants is suboptimal to maintain an ability to generate and amplify differential growth during organogenesis.

Regulatory role of cell division rules on tissue growth heterogeneity.
Karen Alim, Olivier Hamant and Arezki Boudaoud,
Front. Plant Sci. 3, 00174 (2012). (PDF) .

Mechanical stress acts via katanin to amplify differences in growth rate between adjacent cells in Arabidopsis.
Magalie Uyttewaal*, Agata Burian*, Karen Alim*, Benoît Landrein, Dorota Borowska-Wykręt, Annick Dedieu, Alexis Peaucelle, Michał Ludynia, Jan Traas, Arezki Boudaoud**, Dorota Kwiatkowska** and Olivier Hamant**,
Cell 149, 439-451 (2012). (PDF) .

Leaf vein initiation during plant development:

vein initiation

Plant cells grow, divide, and differentiate in response to the concentration of the hormone auxin. This hormone has the property that it induces the polar distribution of its own efflux facilitator, PIN, in a cell’s membrane. By this mechanism dynamic patterns of auxin and PIN arise on a multicellular level. This is in many parts of plants the first step to development and growth, such as in the formation of veins in the evolving leaf. During vein initiation auxin flows very localized from outer cell layers into the ground meristem. There it induces the polarization of PIN distribution along a strand of cells. Our work identifies the role of the kinetic processes in auxin and PIN dynamics during this polarization. We deduce quantitative predictions based on rigorous mathematical results that enable the determination of the kinetic parameters in future experiments. Furthermore, our analysis suggests the occurrence of bipolar cells. As bipolar cells lie at the origin of the yet puzzling formation of closed, looped veins, we provide a further understanding of vein formation.

Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 33, 165 (2010). arXiv:1005.3768. (PDF) .

The form of semiflexible polymer rings:

polymer form

The form of semiflexible biopolymers is essential to many biological processes, as for example for the protein target search along a DNA. Also considering biopolymers like actin, microtubules and poly- nucleotides as nano-sized building blocks their conformations are of eminent concern. We study how the shape of semiflexible polymer rings is governed by inherent factors such as flexibility and filament diameter and external constraints like confinement. Especially the topological constraint of a ring, ubiquitously occurring in biological systems, results in astonishingly rich polymer configurations. It is the aim of our work to give an intuitive understanding of polymer shapes by rationalizing conformations observed within Monte Carlo Simulations with straightforward analytic arguments. Thereby we provide tools to estimate the shape of semiflexible polymer rings for the design of nano-technological design and coarse-grained biological modelling.

Confinement induces conformational transition of semiflexible polymer rings to figure eight form.
Katja Ostermeir*, Karen Alim* and Erwin Frey,
Soft Matter 6, 3467-3471 (2010). arXiv:1004.4574. (PDF) .

Buckling of stiff polymer rings in weak spherical confinement.
Katja Ostermeir, Karen Alim and Erwin Frey,
Phys. Rev. E 81, 061802 (2010). arXiv:1003.4267. (PDF) .

Excluded volume effects on semiflexible ring polymers.
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler and Erwin Frey,
Nano Letters 10, 1445-1449 (2010). arXiv:0906.3991. (PDF) .

Fluctuating semiflexible polymer ribbon constrained to a ring.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 24, 185-191 (2007). arXiv:0708.0111. (PDF) .

Shapes of semiflexible polymer rings.
Karen Alim and Erwin Frey,
Phys. Rev. Lett. 99, 198102 (2007). arXiv:q-bio/0703049. (PDF) .