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- Landberg, Katarina, et al.
(författare)
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The Moss Physcomitrella patens Reproductive Organ Development Is Highly Organized, Affected by the Two SHI/STY Genes and by the Level of Active Auxin in the SHI/STY Expression Domain
- 2013
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 1532-2548 .- 0032-0889. ; 162:3, s. 1406-1419
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Tidskriftsartikel (refereegranskat)abstract
- In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3(pro):GUS and PpPINA(pro): GFP-GUS, and the auxin-conjugating transgene PpSHI2(pro):IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.
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2. |
- Daher, Firas Bou, et al.
(författare)
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Anisotropic growth is achieved through the additive mechanical effect of material anisotropy and elastic asymmetry
- 2018
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Ingår i: eLife. - 2050-084X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Fast directional growth is a necessity for the young seedling; after germination, it needs to quickly penetrate the soil to begin its autotrophic life. In most dicot plants, this rapid escape is due to the anisotropic elongation of the hypocotyl, the columnar organ between the root and the shoot meristems. Anisotropic growth is common in plant organs and is canonically attributed to cell wall anisotropy produced by oriented cellulose fibers. Recently, a mechanism based on asymmetric pectin-based cell wall elasticity has been proposed. Here we present a harmonizing model for anisotropic growth control in the dark-grown Arabidopsis thaliana hypocotyl: basic anisotropic information is provided by cellulose orientation) and additive anisotropic information is provided by pectin-based elastic asymmetry in the epidermis. We quantitatively show that hypocotyl elongation is anisotropic starting at germination. We present experimental evidence for pectin biochemical differences and wall mechanics providing important growth regulation in the hypocotyl. Lastly, our in silico modelling experiments indicate an additive collaboration between pectin biochemistry and cellulose orientation in promoting anisotropic growth.
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3. |
- Bozorg, Behruz, et al.
(författare)
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A continuous growth model for plant tissue
- 2016
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Ingår i: Physical Biology. - : IOP Publishing. - 1478-3975. ; 13:6, s. 065002-065002
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Tidskriftsartikel (refereegranskat)abstract
- Morphogenesis in plants and animals involves large irreversible deformations. In plants, the response of the cell wall material to internal and external forces is determined by its mechanical properties. An appropriate model for plant tissue growth must include key features such as anisotropic and heterogeneous elasticity and cell dependent evaluation of mechanical variables such as turgor pressure, stress and strain. In addition, a growth model needs to cope with cell divisions as a necessary part of the growth process. Here we develop such a growth model, which is capable of employing not only mechanical signals but also morphogen signals for regulating growth. The model is based on a continuous equation for updating the resting configuration of the tissue. Simultaneously, material properties can be updated at a different time scale. We test the stability of our model by measuring convergence of growth results for a tissue under the same mechanical and material conditions but with different spatial discretization. The model is able to maintain a strain field in the tissue during re-meshing, which is of particular importance for modeling cell division. We confirm the accuracy of our estimations in two and three-dimensional simulations, and show that residual stresses are less prominent if strain or stress is included as input signal to growth. The approach results in a model implementation that can be used to compare different growth hypotheses, while keeping residual stresses and other mechanical variables updated and available for feeding back to the growth and material properties.
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5. |
- Gibson, Cameron, et al.
(författare)
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Mean-field theory approach to three-dimensional nematic phase transitions in microtubules
- 2023
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Ingår i: Physical Review E. - 2470-0045. ; 108:6
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Tidskriftsartikel (refereegranskat)abstract
- Microtubules are dynamic intracellular fibers that have been observed experimentally to undergo spontaneous self-alignment. We formulate a three-dimensional (3D) mean-field theory model to analyze the nematic phase transition of microtubules growing and interacting within a 3D space, then make a comparison with computational simulations. We identify a control parameter Geff and predict a unique critical value Geff=1.56 for which a phase transition can occur. Furthermore, we show both analytically and using simulations that this predicted critical value does not depend on the presence of zippering. The mean-field theory developed here provides an analytical estimate of microtubule patterning characteristics without running time-consuming simulations and is a step towards bridging scales from microtubule behavior to multicellular simulations.
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7. |
- Heisler, Marcus, et al.
(författare)
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Computer modeling of plant development
- 2006
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Ingår i: Journal of Plant Growth Regulation. - : Springer Science and Business Media LLC. - 0721-7595 .- 1435-8107. ; 25, s. 267-269
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Tidskriftsartikel (refereegranskat)
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8. |
- Heisler, Marcus G., et al.
(författare)
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Modelling meristem development in plants
- 2007
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Ingår i: Current Opinion in Plant Biology. - : Elsevier BV. - 1369-5266. ; 10:1, s. 92-97
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Forskningsöversikt (refereegranskat)abstract
- Meristems continually supply new cells for post-embryonic plant development and coordinate the initiation of new organs, such as leaves and flowers. Meristem function is regulated by a large and interconnected dynamic system that includes transcription networks, intercellular protein signalling, polarized transport of hormones and a constantly changing cellular topology. Mathematical modelling, in which the dynamics of a system are simulated using explicitly defined interactions, can serve as a powerful tool for examining the expected behaviour of such a system given our present knowledge and assumptions. Modelling can also help to investigate new hypotheses in silico both to validate ideas and to obtain inspiration for new experiments. Several recent studies have used new molecular data together with modelling and computational techniques to investigate meristem function.
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9. |
- Heisler, Marcus, et al.
(författare)
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Modeling auxin transport and plant development
- 2006
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Ingår i: Journal of Plant Growth Regulation. - : Springer Science and Business Media LLC. - 0721-7595 .- 1435-8107. ; 25, s. 302-312
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Tidskriftsartikel (refereegranskat)abstract
- The plant hormone auxin plays a critical role in plant development. Central to its function is its distribution in plant tissues, which is, in turn, largely shaped by intercellular polar transport processes. Auxin transport relies on diffusive uptake as well as carrier-mediated transport via influx and efflux carriers. Mathematical models have been used to both refine our theoretical understanding of these processes and to test new hypotheses regarding the localization of efflux carriers to understand auxin patterning at the tissue level. Here we review models for auxin transport and how they have been applied to patterning processes, including the elaboration of plant vasculature and primordium positioning. Second, we investigate the possible role of auxin influx carriers such as AUX1 in patterning auxin in the shoot meristem. We find that AUX1 and its relatives are likely to play a crucial role in maintaining high auxin levels in the meristem epidermis. We also show that auxin influx carriers may play an important role in stabilizing auxin distribution patterns generated by auxin-gradient type models for phyllotaxis.
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10. |
- Jönsson, Henrik, et al.
(författare)
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An approximate maximum likelihood approach, applied to phylogenetic trees
- 2003
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Ingår i: Journal of Computational Biology. - 1557-8666. ; 10:5, s. 737-749
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Tidskriftsartikel (refereegranskat)abstract
- A novel type of approximation scheme to the maximum likelihood (ML) approach is presented and discussed in the context of phylogenetic tree reconstruction from aligned DNA sequences. It is based on a parameterized approximation to the conditional distribution of hidden variables (related, e.g., to the sequences of unobserved branch point ancestors) given the observed data. A modified likelihood, based on the extended data, is then maximized with respect to the parameters of the model as well as to those involved in the approximation. With a suitable form of the approximations the proposed method allows for simpler updating of the parameters, at the cost of an increased parameter count and a slight decrease in performance. The method is tested on phylogenetic tree reconstruction from artificially generated sequences, and its performance is compared to that of ML, showing that the approach is competitive for reasonably similar sequences. The method is also applied to real DNA sequences from primates, yielding a result consistent with those obtained by other standard algorithms.
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