---
_id: '6371'
abstract:
- lang: eng
  text: "Decades of studies have revealed the mechanisms of gene regulation in molecular
    detail. We make use of such well-described regulatory systems to explore how the
    molecular mechanisms of protein-protein and protein-DNA interactions shape the
    dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics
    of protein-DNA binding determines the potential of regulatory networks to evolve
    and adapt, which can be captured using a simple mathematical model. \r\nii) The
    evolution of regulatory connections can lead to a significant amount of crosstalk
    between binding proteins. We explore the effect of crosstalk on gene expression
    from a target promoter, which seems to be modulated through binding competition
    at non-specific DNA sites. \r\niii) We investigate how the very same biophysical
    characteristics as in i) can generate significant fitness costs for cells through
    global crosstalk, meaning non-specific DNA binding across the genomic background.
    \r\niv) Binding competition between proteins at a target promoter is a prevailing
    regulatory feature due to the prevalence of co-regulation at bacterial promoters.
    However, the dynamics of these systems are not always straightforward to determine
    even if the molecular mechanisms of regulation are known. A detailed model of
    the biophysical interactions reveals that interference between the regulatory
    proteins can constitute a new, generic form of system memory that records the
    history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics
    of protein-DNA binding can be harnessed to investigate the principles that shape
    and ultimately limit cellular gene regulation. These results provide a basis for
    studies of higher-level functionality, which arises from the underlying regulation.
    \  \r\n"
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Claudia
  full_name: Igler, Claudia
  id: 46613666-F248-11E8-B48F-1D18A9856A87
  last_name: Igler
citation:
  ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription
    factor binding shapes gene regulation. 2019. doi:<a href="https://doi.org/10.15479/AT:ISTA:6371">10.15479/AT:ISTA:6371</a>
  apa: Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics
    of transcription factor binding shapes gene regulation</i>. Institute of Science
    and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:6371">https://doi.org/10.15479/AT:ISTA:6371</a>
  chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics
    of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science
    and Technology Austria, 2019. <a href="https://doi.org/10.15479/AT:ISTA:6371">https://doi.org/10.15479/AT:ISTA:6371</a>.
  ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription
    factor binding shapes gene regulation,” Institute of Science and Technology Austria,
    2019.
  ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of
    transcription factor binding shapes gene regulation. Institute of Science and
    Technology Austria.
  mla: Igler, Claudia. <i>On the Nature of Gene Regulatory Design - The Biophysics
    of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science
    and Technology Austria, 2019, doi:<a href="https://doi.org/10.15479/AT:ISTA:6371">10.15479/AT:ISTA:6371</a>.
  short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription
    Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria,
    2019.
date_created: 2019-05-03T11:55:51Z
date_published: 2019-05-03T00:00:00Z
date_updated: 2024-02-21T13:45:52Z
day: '03'
ddc:
- '576'
- '579'
degree_awarded: PhD
department:
- _id: CaGu
doi: 10.15479/AT:ISTA:6371
file:
- access_level: open_access
  checksum: c0085d47c58c9cbcab1b0a783480f6da
  content_type: application/pdf
  creator: cigler
  date_created: 2019-05-03T11:54:52Z
  date_updated: 2021-02-11T11:17:13Z
  embargo: 2020-05-02
  file_id: '6373'
  file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf
  file_size: 12597663
  relation: main_file
- access_level: closed
  checksum: 2eac954de1c8bbf7e6fb35ed0221ae8c
  content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
  creator: cigler
  date_created: 2019-05-03T11:54:54Z
  date_updated: 2020-07-14T12:47:28Z
  embargo_to: open_access
  file_id: '6374'
  file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx
  file_size: 34644426
  relation: source_file
file_date_updated: 2021-02-11T11:17:13Z
has_accepted_license: '1'
keyword:
- gene regulation
- biophysics
- transcription factor binding
- bacteria
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: '152'
project:
- _id: 251EE76E-B435-11E9-9278-68D0E5697425
  grant_number: '24573'
  name: Design principles underlying genetic switch architecture (DOC Fellowship)
publication_identifier:
  issn:
  - 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '67'
    relation: part_of_dissertation
    status: public
  - id: '5585'
    relation: popular_science
    status: public
status: public
supervisor:
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
title: On the nature of gene regulatory design - The biophysics of transcription factor
  binding shapes gene regulation
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6354'
abstract:
- lang: eng
  text: Blood platelets are critical for hemostasis and thrombosis, but also play
    diverse roles during immune responses. We have recently reported that platelets
    migrate at sites of infection in vitro and in vivo. Importantly, platelets use
    their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing
    efficient intravascular bacterial trapping. Here, we describe a method that allows
    analyzing platelet migration in vitro, focusing on their ability to collect bacteria
    and trap bacteria under flow.
acknowledgement: ' FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project
  41/16 (F.G.)'
article_number: e3018
author:
- first_name: Shuxia
  full_name: Fan, Shuxia
  last_name: Fan
- first_name: Michael
  full_name: Lorenz, Michael
  last_name: Lorenz
- first_name: Steffen
  full_name: Massberg, Steffen
  last_name: Massberg
- first_name: Florian R
  full_name: Gärtner, Florian R
  id: 397A88EE-F248-11E8-B48F-1D18A9856A87
  last_name: Gärtner
  orcid: 0000-0001-6120-3723
citation:
  ama: Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping
    assay under flow. <i>Bio-Protocol</i>. 2018;8(18). doi:<a href="https://doi.org/10.21769/bioprotoc.3018">10.21769/bioprotoc.3018</a>
  apa: Fan, S., Lorenz, M., Massberg, S., &#38; Gärtner, F. R. (2018). Platelet migration
    and bacterial trapping assay under flow. <i>Bio-Protocol</i>. Bio-Protocol. <a
    href="https://doi.org/10.21769/bioprotoc.3018">https://doi.org/10.21769/bioprotoc.3018</a>
  chicago: Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet
    Migration and Bacterial Trapping Assay under Flow.” <i>Bio-Protocol</i>. Bio-Protocol,
    2018. <a href="https://doi.org/10.21769/bioprotoc.3018">https://doi.org/10.21769/bioprotoc.3018</a>.
  ieee: S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and
    bacterial trapping assay under flow,” <i>Bio-Protocol</i>, vol. 8, no. 18. Bio-Protocol,
    2018.
  ista: Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial
    trapping assay under flow. Bio-Protocol. 8(18), e3018.
  mla: Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under
    Flow.” <i>Bio-Protocol</i>, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:<a
    href="https://doi.org/10.21769/bioprotoc.3018">10.21769/bioprotoc.3018</a>.
  short: S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).
date_created: 2019-04-29T09:40:33Z
date_published: 2018-09-20T00:00:00Z
date_updated: 2021-01-12T08:07:12Z
day: '20'
ddc:
- '570'
department:
- _id: MiSi
doi: 10.21769/bioprotoc.3018
ec_funded: 1
file:
- access_level: open_access
  checksum: d4588377e789da7f360b553ae02c5119
  content_type: application/pdf
  creator: dernst
  date_created: 2019-04-30T08:04:33Z
  date_updated: 2020-07-14T12:47:28Z
  file_id: '6360'
  file_name: 2018_BioProtocol_Fan.pdf
  file_size: 2928337
  relation: main_file
file_date_updated: 2020-07-14T12:47:28Z
has_accepted_license: '1'
intvolume: '         8'
issue: '18'
keyword:
- Platelets
- Cell migration
- Bacteria
- Shear flow
- Fibrinogen
- E. coli
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
project:
- _id: 260AA4E2-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '747687'
  name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells
publication: Bio-Protocol
publication_identifier:
  issn:
  - 2331-8325
publication_status: published
publisher: Bio-Protocol
quality_controlled: '1'
status: public
title: Platelet migration and bacterial trapping assay under flow
tmp:
  image: /images/cc_by.png
  legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
  name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
  short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2018'
...