Biology subjects

Mulder, B.

Publications and source records attributed to Mulder, B..

6 recordsLinked to original sources

bioRxiv2020

A plausible mechanism for longitudinal lock-in of cortical microtubule array after light-induced reorientation

The light-induced reorientation of the cortical microtubule array in dark-grown A. thaliana hypocotyl cells is a striking example of the dynamical plasticity of the microtubule cytoskeleton. A consensus model, based on katanin-mediated severing at microtubule crossovers, has been developed that successfully describes the onset of the observed switch between a transverse and longitudinal array orientation. However, we currently lack an understanding of why the newly-populated longitudinal array direction remains stable for longer times and re-equilibration effects would tend to drive the system back to a mixed orientation state. Using both simulations and analytical calculations, we show that the assumption of a small orientation-dependent shift in microtubule dynamics is sufficient to explain the long term lock-in of the longitudinal array orientation. Furthermore, we show that the natural alternative hypothesis that there is a selective advantage in severing longitudinal microtubules, is neither necessary nor sufficient to achieve cortical array reorientation, but is able to accelerate this process significantly.

plant biology↗

bioRxiv2019

Reconstitution of basic mitotic spindles in cell-like confinement

Bipolar organization of the mitotic spindle is the result of forces generated by dynamic microtubules and associated proteins in interaction with chromosomes and the cell boundary1-4. Biophysical experiments on isolated spindle components have provided important insights into the force-generating properties of different components5-8, but a quantitative understanding of the force balance that results from their concerted action is lacking. Here we present an experimental platform based on water-in-oil emulsion droplets that allows for the bottom-up reconstitution of basic spindles. We find a typical metaphase organization, where two microtubule asters position symmetrically at moderate distance from the mid-zone, is readily obtained even in the absence of chromosomes. Consistent with simulations, we observe an intrinsic repulsive force between two asters that can be counterbalanced alternatively by cortical pulling forces, anti-parallel microtubule crosslinking, or adjustment of microtubule dynamics, emphasizing the robustness of the system. Adding motor proteins that slide anti-parallel microtubules apart drives the asters to maximum separation, as observed in cells during anaphase9,10. Our platform offers a valuable complementary approach to in vivo experiments where essential mitotic components are typically removed, instead of added, one by one.

cell biology↗

bioRxiv2019

From plasmodesma geometry to effective symplastic permeability through biophysical modelling

Regulation of molecular transport via intercellular channels called plasmodesmata (PDs) is important for both coordinating developmental and environmental responses among neighbouring cells, and isolating (groups of) cells to execute distinct programs. Cell-to-cell mobility of fluorescent molecules and PD dimensions (measured from electron micrographs) are both used as methods to predict PD transport capacity (i.e., effective symplasmic permeability), but often yield very different values. Here, we build a theoretical bridge between both experimental approaches by calculating the effective symplasmic permeability from a geometrical description of individual PDs and considering the flow towards them. We find that a dilated central region has the strongest impact in thick cell walls and that clustering of PDs into pit fields strongly reduces predicted permeabilities. Moreover, our open source multi-level model allows to predict PD dimensions matching measured permeabilities and add a functional interpretation to structural differences observed between PDs in different cell walls.

cell biology↗

bioRxiv2018

Cell boundary confinement sets the size and position of the E. coli chromosome

While the spatiotemporal structure of the genome is crucial to its biological function, many basic questions remain unanswered on the morphology and segregation of chromosomes. Here, we experimentally show in Escherichia coli that spatial confinement plays a dominant role in determining both the chromosome size and position. In non-dividing cells with lengths up to 10 times normal, single chromosomes are observed to expand more than 4 fold in size, an effect only modestly influenced by deletions of various nucleoid-associated proteins. Chromosomes show pronounced internal dynamics but exhibit a robust positioning where single nucleoids reside strictly at mid-cell, while two nucleoids self-organize at [1/4] and [3/4] cell positions. Molecular dynamics simulations of model chromosomes recapitulate these phenomena and indicate that these observations can be attributed to depletion effects induced by cytosolic crowders. These findings highlight boundary confinement as a key causal factor that needs to be considered for understanding chromosome organization.

biophysics↗

bioRxiv2018

A microtubule-based mechanism predicts cell division orientation in plant embryogenesis

Oriented cell divisions are significant in plant morphogenesis because plant cells are embedded in cell walls and cannot relocate. Cell divisions follow various regular orientations, but the underlying mechanisms have not been clarified. We show that cell-shape dependent self-organisation of cortical microtubule arrays is crucial for determining planes of early tissue-generating divisions and forms the basis for robust control of cell division orientation in the embryo. To achieve this, we simulate microtubules on actual cell surface shapes from which we derive a minimal set of three rules for proper array orientation. The first rule captures the effects of cell shape alone on microtubule organisation, the second rule describes the regulation of microtubule stability at cell edges and the third rule includes the differential effect of auxin on local microtubule stability. These rules explain early embryonic division plane orientations and offer a framework for understanding patterned cell divisions in plant morphogenesis.

developmental biology↗

bioRxiv2017

A Framework to Simulate Cortical microtubule Dynamics inArbitrary Shaped Plant Cells

Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells. It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes. This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules. To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed. To date, however, these models have been restricted to 2D planes or geometrically simple surfaces in 3D, which strongly limits their applicability as plant cells display a wide variety of shapes. This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array. Here we describe a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces. This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images. We validate the framework against expected or known results for the spherical and cubical geometry. We then use it to systematically study the individual contributions of global geometry, edge-induced catastrophes and cell face-induced stability to array organization in a cuboidal geometry. Finally, we apply our framework to analyze the highly non-trivial geometry of leaf pavement cells of Nicotiana benthamiana and Hedera helix. We show that our simulations can predict multiple features of the array structure in these cells, revealing, among others, strong constraints on the orientation of division planes.

systems biology↗