---
_id: '12964'
abstract:
- lang: eng
  text: "Pattern formation is of great importance for its contribution across different
    biological behaviours. During developmental processes for example, patterns of
    chemical gradients are\r\nestablished to determine cell fate and complex tissue
    patterns emerge to define structures such\r\nas limbs and vascular networks. Patterns
    are also seen in collectively migrating groups, for\r\ninstance traveling waves
    of density emerging in moving animal flocks as well as collectively migrating
    cells and tissues. To what extent these biological patterns arise spontaneously
    through\r\nthe local interaction of individual constituents or are dictated by
    higher level instructions is\r\nstill an open question however there is evidence
    for the involvement of both types of process.\r\nWhere patterns arise spontaneously
    there is a long standing interest in how far the interplay\r\nof mechanics, e.g.
    force generation and deformation, and chemistry, e.g. gene regulation\r\nand signaling,
    contributes to the behaviour. This is because many systems are able to both\r\nchemically
    regulate mechanical force production and chemically sense mechanical deformation,\r\nforming
    mechano-chemical feedback loops which can potentially become unstable towards\r\nspatio
    and/or temporal patterning.\r\nWe work with experimental collaborators to investigate
    the possibility that this type of\r\ninteraction drives pattern formation in biological
    systems at different scales. We focus first on\r\ntissue-level ERK-density waves
    observed during the wound healing response across different\r\nsystems where many
    previous studies have proposed that patterns depend on polarized cell\r\nmigration
    and arise from a mechanical flocking-like mechanism. By combining theory with\r\nmechanical
    and optogenetic perturbation experiments on in vitro monolayers we instead find\r\nevidence
    for mechanochemical pattern formation involving only scalar bilateral feedbacks\r\nbetween
    ERK signaling and cell contraction. We perform further modeling and experiment\r\nto
    study how this instability couples with polar cell migration in order to produce
    a robust\r\nand efficient wound healing response. In a following chapter we implement
    ERK-density\r\ncoupling and cell migration in a 2D active vertex model to investigate
    the interaction of\r\nERK-density patterning with different tissue rheologies
    and find that the spatio-temporal\r\ndynamics are able to both locally and globally
    fluidize a tissue across the solid-fluid glass\r\ntransition. In a last chapter
    we move towards lower spatial scales in the context of subcellular\r\npatterning
    of the cell cytoskeleton where we investigate the transition between phases of\r\nspatially
    homogeneous temporal oscillations and chaotic spatio-temporal patterning in the\r\ndynamics
    of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton\r\nand
    its activator). Experimental evidence supports an intrinsic chemical oscillator
    which we\r\nencode in a reaction model and couple to a contractile active gel
    description of the cell cortex.\r\nThe model exhibits phases of chemical oscillations
    and contractile spatial patterning which\r\nreproduce many features of the dynamics
    seen in Drosophila oocyte epithelia in vivo. However,\r\nadditional pharmacological
    perturbations to inhibit myosin contractility leaves the role of\r\ncontractile
    instability unclear. We discuss alternative hypotheses and investigate the possibility\r\nof
    reaction-diffusion instability."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Daniel R
  full_name: Boocock, Daniel R
  id: 453AF628-F248-11E8-B48F-1D18A9856A87
  last_name: Boocock
  orcid: 0000-0002-1585-2631
citation:
  ama: Boocock DR. Mechanochemical pattern formation across biological scales. 2023.
    doi:<a href="https://doi.org/10.15479/at:ista:12964">10.15479/at:ista:12964</a>
  apa: Boocock, D. R. (2023). <i>Mechanochemical pattern formation across biological
    scales</i>. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/at:ista:12964">https://doi.org/10.15479/at:ista:12964</a>
  chicago: Boocock, Daniel R. “Mechanochemical Pattern Formation across Biological
    Scales.” Institute of Science and Technology Austria, 2023. <a href="https://doi.org/10.15479/at:ista:12964">https://doi.org/10.15479/at:ista:12964</a>.
  ieee: D. R. Boocock, “Mechanochemical pattern formation across biological scales,”
    Institute of Science and Technology Austria, 2023.
  ista: Boocock DR. 2023. Mechanochemical pattern formation across biological scales.
    Institute of Science and Technology Austria.
  mla: Boocock, Daniel R. <i>Mechanochemical Pattern Formation across Biological Scales</i>.
    Institute of Science and Technology Austria, 2023, doi:<a href="https://doi.org/10.15479/at:ista:12964">10.15479/at:ista:12964</a>.
  short: D.R. Boocock, Mechanochemical Pattern Formation across Biological Scales,
    Institute of Science and Technology Austria, 2023.
date_created: 2023-05-15T14:52:36Z
date_published: 2023-05-17T00:00:00Z
date_updated: 2023-08-04T11:02:40Z
day: '17'
ddc:
- '530'
degree_awarded: PhD
department:
- _id: GradSch
- _id: EdHa
doi: 10.15479/at:ista:12964
ec_funded: 1
file:
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  date_created: 2023-05-17T13:39:54Z
  date_updated: 2023-05-19T07:04:25Z
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  file_size: 40414730
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  date_created: 2023-05-17T13:39:53Z
  date_updated: 2023-05-17T14:35:13Z
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  file_name: thesis_boocock.zip
  file_size: 34338567
  relation: source_file
file_date_updated: 2023-05-19T07:04:25Z
has_accepted_license: '1'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
month: '05'
oa_version: Published Version
page: '146'
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '665385'
  name: International IST Doctoral Program
publication_identifier:
  isbn:
  - 978-3-99078-032-9
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '8602'
    relation: part_of_dissertation
    status: public
status: public
supervisor:
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
title: Mechanochemical pattern formation across biological scales
tmp:
  image: /images/cc_by_nc_sa.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC
    BY-NC-SA 4.0)
  short: CC BY-NC-SA (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...