4 results on '"Vroomans, Renske M.A."'
Search Results
2. Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening : Plant Systems Biology
- Author
-
Li, Xin-Ran, Vroomans, Renske M.A., Fox, Samantha, Grieneisen, Verônica A., Østergaard, Lars, Marée, Athanasius F.M., and Institute of Biotechnology
- Subjects
polar auxin transport ,fungi ,mathematical modeling ,food and beverages ,1182 Biochemistry, cell and molecular biology ,heterocyclic compounds ,fruit development ,auxin ,1183 Plant biology, microbiology, virology ,systems biology of patterning - Abstract
The phytohormone auxin is implied in steering various developmental decisions during plant morphogenesis in a concentration-dependent manner. Auxin maxima have been shown to maintain meristematic activity, for example, of the root apical meristem, and position new sites of outgrowth, such as during lateral root initiation and phyllotaxis. More recently, it has been demonstrated that sites of auxin minima also provide positional information. In the developing Arabidopsis fruit, auxin minima are required for correct differentiation of the valve margin. It remains unclear, however, how this auxin minimum is generated and maintained. Here, we employ a systems biology approach to model auxin transport based on experimental observations. This allows us to determine the minimal requirements for its establishment. Our simulations reveal that two alternative processes—which we coin “flux-barrier” and “flux-passage”—are both able to generate an auxin minimum, but under different parameter settings. Both models are in principle able to yield similar auxin profiles but present qualitatively distinct patterns of auxin flux. The models were tested by tissue-specific inducible ablation, revealing that the auxin minimum in the fruit is most likely generated by a flux-passage process. Model predictions were further supported through 3D PIN localization imaging and implementing experimentally observed transporter localization. Through such an experimental–modeling cycle, we predict how the auxin minimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal.
- Published
- 2019
3. Modelling asymmetric somitogenesis: Deciphering the mechanisms behind species differences
- Author
-
Vroomans, Renske M.A., ten Tusscher, Kirsten H.W.J., Sub Theoretical Biology, Theoretical Biology and Bioinformatics, Sub Theoretical Biology, and Theoretical Biology and Bioinformatics
- Subjects
0301 basic medicine ,Determination front ,animal cell ,Mesoderm ,Mice ,somite ,Somitogenesis ,vertebrate ,zebra fish ,Zebrafish ,Genetics ,biology ,article ,Vertebrate ,Clock and wavefront model ,Gene Expression Regulation, Developmental ,medicine.anatomical_structure ,Somites ,priority journal ,Vertebrates ,Presomitic mesoderm ,Segmentation clock ,Algorithms ,signal transduction ,Fibroblast Growth Factor 8 ,phenotype ,chicken ,Embryonic Development ,embryo ,Tretinoin ,Models, Biological ,animal tissue ,03 medical and health sciences ,developmental biology ,FGF8 ,Species Specificity ,biology.animal ,fibroblast growth factor ,medicine ,Paraxial mesoderm ,Animals ,controlled study ,Molecular Biology ,reproducibility ,Left-right signalling ,mouse ,Body Patterning ,nonhuman ,species difference ,embryo development ,Cell Biology ,biology.organism_classification ,molecular dynamics ,Somite ,030104 developmental biology ,Computational modelling ,Evolutionary biology ,Developmental biology ,Chickens ,embryo pattern formation ,mathematical model - Abstract
Somitogenesis is one of the major hallmarks of bilateral symmetry in vertebrates. This symmetry is lost when retinoic acid (RA) signalling is inhibited, allowing the left-right determination pathway to influence somitogenesis. In all three studied vertebrate model species, zebrafish, chicken and mouse, the frequency of somite formation becomes asymmetric, with slower gene expression oscillations driving somitogenesis on the right side. Still, intriguingly, the resulting left-right asymmetric phenotypes differ significantly between these model species. While somitogenesis is generally considered as functionally equivalent among different vertebrates, substantial differences exist in the subset of oscillating genes between different vertebrate species. Variation also appears to exist in the way oscillations cease and somite boundaries become patterned. In addition, in absence of RA, the FGF8 gradient thought to constitute the determination wavefront becomes asymmetric in zebrafish and mouse, extending more anteriorly to the right, while remaining symmetric in chicken. Here we use a computational modelling approach to decipher the causes underlying species differences in asymmetric somitogenesis. Specifically, we investigate to what extent differences can be explained from observed differences in FGF asymmetry and whether differences in somite determination dynamics may also be involved. We demonstrate that a simple clock-and-wavefront model incorporating the observed left-right differences in somitogenesis frequency readily reproduces asymmetric somitogenesis in chicken. However, incorporating asymmetry in FGF signalling was insufficient to robustly reproduce mouse or zebrafish asymmetry phenotypes. In order to explain these phenoptypes we needed to extend the basic model, incorporating species-specific details of the somitogenesis determination mechanism. Our results thus demonstrate that a combination of differences in FGF dynamics and somite determination cause species differences in asymmetric somitogenesis. In addition,they highlight the power of using computational models as well as studying left-right asymmetry to obtain more insight in somitogenesis.
- Published
- 2017
4. Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening.
- Author
-
Li, Xin-Ran, Vroomans, Renske M.A., Fox, Samantha, Grieneisen, Verônica A., Østergaard, Lars, and Marée, Athanasius F.M.
- Abstract
The phytohormone auxin is implied in steering various developmental decisions during plant morphogenesis in a concentration-dependent manner. Auxin maxima have been shown to maintain meristematic activity, for example, of the root apical meristem, and position new sites of outgrowth, such as during lateral root initiation and phyllotaxis. More recently, it has been demonstrated that sites of auxin minima also provide positional information. In the developing Arabidopsis fruit, auxin minima are required for correct differentiation of the valve margin. It remains unclear, however, how this auxin minimum is generated and maintained. Here, we employ a systems biology approach to model auxin transport based on experimental observations. This allows us to determine the minimal requirements for its establishment. Our simulations reveal that two alternative processes—which we coin "flux-barrier" and "flux-passage"—are both able to generate an auxin minimum, but under different parameter settings. Both models are in principle able to yield similar auxin profiles but present qualitatively distinct patterns of auxin flux. The models were tested by tissue-specific inducible ablation, revealing that the auxin minimum in the fruit is most likely generated by a flux-passage process. Model predictions were further supported through 3D PIN localization imaging and implementing experimentally observed transporter localization. Through such an experimental–modeling cycle, we predict how the auxin minimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal. We investigate the mechanism leading to a spatially confined auxin minimum required for Arabidopsis fruit opening and seed dispersal. Our experiment–modeling cycle reveals a counterintuitive mechanism of its formation: efflux activity creates an auxin minimum strip that is accompanied by high auxin fluxes crossing it perpendicularly. This dynamical process can be associated with the maturation of the fruit. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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