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Spatial Models of Gene Patterns in Plants

Larsson, André LU (2017)
Abstract (Swedish)
Hur utvecklas en växt? Om man studerar växter så upptäcker man ganska snart de många symmetrier och regelbundna former som finns i växtriket. Nya växtorgan såsom löv och blommor bildas ofta i regelbundna mönster, som exempelvis kan ge upphov till de spiraler som kan observeras på en ananas eller kotte. Beroende på frekvensen och
vinklarna mellan de nya organ som skapas, kan olika mönster hos växten uppstå.

Alla nya växtorgan ovan jord skapas först i växtskottet. I mitten av skottet finns en grupp celler, motsvarande djurrikets stamceller, som ännu inte specialiserats. Det är från dessa celler nya växtorgan bildas.

Växtskottets funktion är noga reglerat av ett komplext nätverk av gener. På en cellnivå kan en cells... (More)
Hur utvecklas en växt? Om man studerar växter så upptäcker man ganska snart de många symmetrier och regelbundna former som finns i växtriket. Nya växtorgan såsom löv och blommor bildas ofta i regelbundna mönster, som exempelvis kan ge upphov till de spiraler som kan observeras på en ananas eller kotte. Beroende på frekvensen och
vinklarna mellan de nya organ som skapas, kan olika mönster hos växten uppstå.

Alla nya växtorgan ovan jord skapas först i växtskottet. I mitten av skottet finns en grupp celler, motsvarande djurrikets stamceller, som ännu inte specialiserats. Det är från dessa celler nya växtorgan bildas.

Växtskottets funktion är noga reglerat av ett komplext nätverk av gener. På en cellnivå kan en cells funktion och öde bestämmas av vilka gener som är på eller av. Mikroskopidata har påvisat existensen av rumsliga mönster av olika genuttryck i skottet, nödvändiga för skottets funktion och för skapandet av nya organ. I artiklarna
I, II och III används datormodeller för att undersöka rumsliga mönster av gener i skottet, och hur dessa påverkar skapandet av nya organ.

Även växtens rotsystem är viktig för dess utveckling. Nya celler skapas kontinuerligt i rotspetsen, och bidrar till tillväxten under jord. Bland annat så skapas specialiserade rothårsceller, från vilka rothår växer ut, viktiga för växtens näringsupptag och för förankring av växten i jorden. Bildandet av ett rothår karaktäriseras av att särskilda proteiner (Rho-of-Plant) samlas på platsen där ett rothår senare växer ut. I artiklarna IV och V undersöks modeller för rothårstillväxt, för att förklara uppkomsten av de rumsliga mönster av proteiner som observerats i samband med bildandet av rothår.

Gemensamt för de artiklar som är med i avhandlingen är alltså att de, med hjälp av datormodellering, avser att förklara hur rumsliga mönster av gener och proteiner i växter påverkar hur en växt utvecklas och tar form. Att förstå de molekylära mekanismer som ligger bakom hur en växt utvecklas kan räknas som grundforskning, men i förlängningen kan upptäckter inom detta område ge upphov till nya innovationer inom till exempel jordbruk och skogsindustri. (Less)
Abstract
The growth and development of plants exhibits a striking symmetry, visible in the regular arrangement of leaves and flowers. Plant development is carefully controlled at the molecular level by gene regulatory networks, and the symmetry of plants can be observed also in the molecular patterns of gene expression.

This thesis investigates the molecular basis for spatial patterns of gene expression in plant development with computer models. Understanding the molecular mechanisms for regulating plant development can provide important cues for developing new technologies and methods, improving conditions in agriculture and forest industry.

Papers I, II and III investigates spatial gene patterns important in the creation of new... (More)
The growth and development of plants exhibits a striking symmetry, visible in the regular arrangement of leaves and flowers. Plant development is carefully controlled at the molecular level by gene regulatory networks, and the symmetry of plants can be observed also in the molecular patterns of gene expression.

This thesis investigates the molecular basis for spatial patterns of gene expression in plant development with computer models. Understanding the molecular mechanisms for regulating plant development can provide important cues for developing new technologies and methods, improving conditions in agriculture and forest industry.

Papers I, II and III investigates spatial gene patterns important in the creation of new plant organs such as leaves and flowers. In Paper I, signalling of the plant hormone auxin is investigated, a key player in the initiation of new plant organs. For Paper I, we developed a model, closely connected to the experimental data, explaining how the depletion of auxin can stabilize the distribution of auxin in a novel plant mutant. For Paper II, we developed a model connecting the radial patterning of the plant shoot to a model for generating peaks of auxin marking new plant organs. With this model, it was shown how the radial patterning of the shoot can restrict the initiation of new organs to a ring of cells around the meristem. Paper III investigates models for creating a mutually exclusive patterning including a gap, observed in the radial patterning of the genes KANADI and REVOLUTA in the shoot. By investigating a collection of different model interactions, we found that diffusion was required to facilitate a mutually exclusive patterning including a gap. We then mapped this result onto a biological network including the genes REVOLUTA, KANADI and diffusing microRNAs, and continued to develop an integrated model describing how the radial patterning affect the dynamics of organ initiation.

Papers IV and V investigate models for the initiation of root hairs. Prior to root hair outgrowth, the root hair cells become polarized with a local patch of Rho-of-Plant proteins appearing at one end of the cell. In Paper IV, a molecular model for creating such a patch of Rho-of-Plants proteins is investigated in relation to models of mechanical stresses in root hair cells. Paper V investigates the molecular model of root hair initiation in more detail, demarcating regions of patterning, and extending the single cell model to a root hair cell file, explaining the distant polarization of root hair cells in the root. (Less)
Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Associate Professor Fleck, Christian, Wageningen University and Research, Wageningen, The Netherlands
organization
publishing date
type
Thesis
publication status
published
subject
keywords
computational morphodynamics, gene regulation, spatial models, plants, development, auxin, meristem, Fysicumarkivet A:2017:Larsson
pages
227 pages
publisher
Lund University, Faculty of Science, Department of Astronomy and Theoretical Physics
defense location
Lecture hall F, Department of Physics, Sölvegatan 14, Lund
defense date
2017-06-22 10:15
ISBN
978-91-7753-339-9
978-91-7753-338-2
language
English
LU publication?
yes
id
ad65c745-aa0d-4441-be72-70a2072aa037
date added to LUP
2017-05-28 14:50:39
date last changed
2018-04-17 09:17:39
@phdthesis{ad65c745-aa0d-4441-be72-70a2072aa037,
  abstract     = {The growth and development of plants exhibits a striking symmetry, visible in the regular arrangement of leaves and flowers. Plant development is carefully controlled at the molecular level by gene regulatory networks, and the symmetry of plants can be observed also in the molecular patterns of gene expression.<br/><br/>This thesis investigates the molecular basis for spatial patterns of gene expression in plant development with computer models. Understanding the molecular mechanisms for regulating plant development can provide important cues for developing new technologies and methods, improving conditions in agriculture and forest industry.<br/><br/>Papers I, II and III investigates spatial gene patterns important in the creation of new plant organs such as leaves and flowers. In Paper I, signalling of the plant hormone auxin is investigated, a key player in the initiation of new plant organs. For Paper I, we developed a model, closely connected to the experimental data, explaining how the depletion of auxin can stabilize the distribution of auxin in a novel plant mutant. For Paper II, we developed a model connecting the radial patterning of the plant shoot to a model for generating peaks of auxin marking new plant organs. With this model, it was shown how the radial patterning of the shoot can restrict the initiation of new organs to a ring of cells around the meristem. Paper III investigates models for creating a mutually exclusive patterning including a gap, observed in the radial patterning of the genes KANADI and REVOLUTA in the shoot. By investigating a collection of different model interactions, we found that diffusion was required to facilitate a mutually exclusive patterning including a gap. We then mapped this result onto a biological network including the genes REVOLUTA, KANADI and diffusing microRNAs, and continued to develop an integrated model describing how the radial patterning affect the dynamics of organ initiation.<br/><br/>Papers IV and V investigate models for the initiation of root hairs. Prior to root hair outgrowth, the root hair cells become polarized with a local patch of Rho-of-Plant proteins appearing at one end of the cell. In Paper IV, a molecular model for creating such a patch of Rho-of-Plants proteins is investigated in relation to models of mechanical stresses in root hair cells. Paper V investigates the molecular model of root hair initiation in more detail, demarcating regions of patterning, and extending the single cell model to a root hair cell file, explaining the distant polarization of root hair cells in the root.},
  author       = {Larsson, André},
  isbn         = {978-91-7753-339-9},
  keyword      = {computational morphodynamics,gene regulation,spatial models,plants,development,auxin,meristem,Fysicumarkivet A:2017:Larsson},
  language     = {eng},
  pages        = {227},
  publisher    = {Lund University, Faculty of Science, Department of Astronomy and Theoretical Physics},
  school       = {Lund University},
  title        = {Spatial Models of Gene Patterns in Plants},
  year         = {2017},
}