---
_id: '14502'
abstract:
- lang: eng
  text: A precise quantitative description of the ultrastructural characteristics
    underlying biological mechanisms is often key to their understanding. This is
    particularly true for dynamic extra- and intracellular filamentous assemblies,
    playing a role in cell motility, cell integrity, cytokinesis, tissue formation
    and maintenance. For example, genetic manipulation or modulation of actin regulatory
    proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural
    architecture of actin filament-rich cell peripheral structures, such as lamellipodia
    or filopodia. However, the observed ultrastructural effects often remain subtle
    and require sufficiently large datasets for appropriate quantitative analysis.
    The acquisition of such large datasets has been enabled by recent advances in
    high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates
    the development of complementary approaches to maximize the extraction of relevant
    biological information. We have developed a computational toolbox for the semi-automatic
    quantification of segmented and vectorized fila- mentous networks from pre-processed
    cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple
    experimental conditions. GUI-based components simplify the processing of data
    and allow users to obtain a large number of ultrastructural parameters describing
    filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing
    cryo-ET data of untreated and chemically perturbed branched actin filament networks
    and that of parallel actin filament arrays. In principle, the computational toolbox
    presented here is applicable for data analysis comprising any type of filaments
    in regular (i.e. parallel) or random arrangement. We show that it can ease the
    identification of key differences between experimental groups and facilitate the
    in-depth analysis of ultrastructural data in a time-efficient manner.
author:
- first_name: Georgi A
  full_name: Dimchev, Georgi A
  id: 38C393BE-F248-11E8-B48F-1D18A9856A87
  last_name: Dimchev
  orcid: 0000-0001-8370-6161
- first_name: Behnam
  full_name: Amiri, Behnam
  last_name: Amiri
- first_name: Florian
  full_name: Fäßler, Florian
  id: 404F5528-F248-11E8-B48F-1D18A9856A87
  last_name: Fäßler
  orcid: 0000-0001-7149-769X
- first_name: Martin
  full_name: Falcke, Martin
  last_name: Falcke
- first_name: Florian KM
  full_name: Schur, Florian KM
  id: 48AD8942-F248-11E8-B48F-1D18A9856A87
  last_name: Schur
  orcid: 0000-0003-4790-8078
citation:
  ama: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for
    ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023.
    doi:<a href="https://doi.org/10.15479/AT:ISTA:14502">10.15479/AT:ISTA:14502</a>
  apa: Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2023).
    Computational toolbox for ultrastructural quantitative analysis of filament networks
    in cryo-ET data. Institute of Science and Technology Austria. <a href="https://doi.org/10.15479/AT:ISTA:14502">https://doi.org/10.15479/AT:ISTA:14502</a>
  chicago: Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian
    KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of
    Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria,
    2023. <a href="https://doi.org/10.15479/AT:ISTA:14502">https://doi.org/10.15479/AT:ISTA:14502</a>.
  ieee: G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational
    toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET
    data.” Institute of Science and Technology Austria, 2023.
  ista: Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox
    for ultrastructural quantitative analysis of filament networks in cryo-ET data,
    Institute of Science and Technology Austria, <a href="https://doi.org/10.15479/AT:ISTA:14502">10.15479/AT:ISTA:14502</a>.
  mla: Dimchev, Georgi A., et al. <i>Computational Toolbox for Ultrastructural Quantitative
    Analysis of Filament Networks in Cryo-ET Data</i>. Institute of Science and Technology
    Austria, 2023, doi:<a href="https://doi.org/10.15479/AT:ISTA:14502">10.15479/AT:ISTA:14502</a>.
  short: G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023).
date_created: 2023-11-08T19:40:54Z
date_published: 2023-11-21T00:00:00Z
date_updated: 2023-11-21T08:36:02Z
day: '21'
ddc:
- '570'
department:
- _id: FlSc
doi: 10.15479/AT:ISTA:14502
file:
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  creator: fschur
  date_created: 2023-11-08T20:23:07Z
  date_updated: 2023-11-08T20:23:07Z
  file_id: '14503'
  file_name: Computational_Toolbox_v1.2.zip
  file_size: 347641117
  relation: main_file
  success: 1
- access_level: open_access
  checksum: 14db2addbfca61a085ba301ed6f2900b
  content_type: text/plain
  creator: dernst
  date_created: 2023-11-21T08:20:23Z
  date_updated: 2023-11-21T08:20:23Z
  file_id: '14586'
  file_name: Readme.txt
  file_size: 1522
  relation: main_file
  success: 1
file_date_updated: 2023-11-21T08:20:23Z
has_accepted_license: '1'
keyword:
- cryo-electron tomography
- actin cytoskeleton
- toolbox
license: https://choosealicense.com/licenses/agpl-3.0/
month: '11'
oa: 1
project:
- _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A
  grant_number: P33367
  name: Structure and isoform diversity of the Arp2/3 complex
publisher: Institute of Science and Technology Austria
related_material:
  record:
  - id: '10290'
    relation: used_for_analysis_in
    status: public
status: public
title: Computational toolbox for ultrastructural quantitative analysis of filament
  networks in cryo-ET data
tmp:
  legal_code_url: https://www.gnu.org/licenses/agpl-3.0.html
  name: GNU Affero General Public License v3.0
  short: 'GNU AGPLv3  '
type: software
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '7128'
abstract:
- lang: eng
  text: Loss of functional cardiomyocytes is a major determinant of heart failure
    after myocardial infarction. Previous high throughput screening studies have identified
    a few microRNAs (miRNAs) that can induce cardiomyocyte proliferation and stimulate
    cardiac regeneration in mice. Here, we show that all of the most effective of
    these miRNAs activate nuclear localization of the master transcriptional cofactor
    Yes-associated protein (YAP) and induce expression of YAP-responsive genes. In
    particular, miR-199a-3p directly targets two mRNAs coding for proteins impinging
    on the Hippo pathway, the upstream YAP inhibitory kinase TAOK1, and the E3 ubiquitin
    ligase β-TrCP, which leads to YAP degradation. Several of the pro-proliferative
    miRNAs (including miR-199a-3p) also inhibit filamentous actin depolymerization
    by targeting Cofilin2, a process that by itself activates YAP nuclear translocation.
    Thus, activation of YAP and modulation of the actin cytoskeleton are major components
    of the pro-proliferative action of miR-199a-3p and other miRNAs that induce cardiomyocyte
    proliferation.
article_processing_charge: Yes
article_type: original
author:
- first_name: Consuelo
  full_name: Torrini, Consuelo
  last_name: Torrini
- first_name: Ryan J
  full_name: Cubero, Ryan J
  id: 850B2E12-9CD4-11E9-837F-E719E6697425
  last_name: Cubero
  orcid: 0000-0003-0002-1867
- first_name: Ellen
  full_name: Dirkx, Ellen
  last_name: Dirkx
- first_name: Luca
  full_name: Braga, Luca
  last_name: Braga
- first_name: Hashim
  full_name: Ali, Hashim
  last_name: Ali
- first_name: Giulia
  full_name: Prosdocimo, Giulia
  last_name: Prosdocimo
- first_name: Maria Ines
  full_name: Gutierrez, Maria Ines
  last_name: Gutierrez
- first_name: Chiara
  full_name: Collesi, Chiara
  last_name: Collesi
- first_name: Danilo
  full_name: Licastro, Danilo
  last_name: Licastro
- first_name: Lorena
  full_name: Zentilin, Lorena
  last_name: Zentilin
- first_name: Miguel
  full_name: Mano, Miguel
  last_name: Mano
- first_name: Serena
  full_name: Zacchigna, Serena
  last_name: Zacchigna
- first_name: Michele
  full_name: Vendruscolo, Michele
  last_name: Vendruscolo
- first_name: Matteo
  full_name: Marsili, Matteo
  last_name: Marsili
- first_name: Areejit
  full_name: Samal, Areejit
  last_name: Samal
- first_name: Mauro
  full_name: Giacca, Mauro
  last_name: Giacca
citation:
  ama: Torrini C, Cubero RJ, Dirkx E, et al. Common regulatory pathways mediate activity
    of microRNAs inducing cardiomyocyte proliferation. <i>Cell Reports</i>. 2019;27(9):2759-2771.e5.
    doi:<a href="https://doi.org/10.1016/j.celrep.2019.05.005">10.1016/j.celrep.2019.05.005</a>
  apa: Torrini, C., Cubero, R. J., Dirkx, E., Braga, L., Ali, H., Prosdocimo, G.,
    … Giacca, M. (2019). Common regulatory pathways mediate activity of microRNAs
    inducing cardiomyocyte proliferation. <i>Cell Reports</i>. Elsevier. <a href="https://doi.org/10.1016/j.celrep.2019.05.005">https://doi.org/10.1016/j.celrep.2019.05.005</a>
  chicago: Torrini, Consuelo, Ryan J Cubero, Ellen Dirkx, Luca Braga, Hashim Ali,
    Giulia Prosdocimo, Maria Ines Gutierrez, et al. “Common Regulatory Pathways Mediate
    Activity of MicroRNAs Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>.
    Elsevier, 2019. <a href="https://doi.org/10.1016/j.celrep.2019.05.005">https://doi.org/10.1016/j.celrep.2019.05.005</a>.
  ieee: C. Torrini <i>et al.</i>, “Common regulatory pathways mediate activity of
    microRNAs inducing cardiomyocyte proliferation,” <i>Cell Reports</i>, vol. 27,
    no. 9. Elsevier, p. 2759–2771.e5, 2019.
  ista: Torrini C, Cubero RJ, Dirkx E, Braga L, Ali H, Prosdocimo G, Gutierrez MI,
    Collesi C, Licastro D, Zentilin L, Mano M, Zacchigna S, Vendruscolo M, Marsili
    M, Samal A, Giacca M. 2019. Common regulatory pathways mediate activity of microRNAs
    inducing cardiomyocyte proliferation. Cell Reports. 27(9), 2759–2771.e5.
  mla: Torrini, Consuelo, et al. “Common Regulatory Pathways Mediate Activity of MicroRNAs
    Inducing Cardiomyocyte Proliferation.” <i>Cell Reports</i>, vol. 27, no. 9, Elsevier,
    2019, p. 2759–2771.e5, doi:<a href="https://doi.org/10.1016/j.celrep.2019.05.005">10.1016/j.celrep.2019.05.005</a>.
  short: C. Torrini, R.J. Cubero, E. Dirkx, L. Braga, H. Ali, G. Prosdocimo, M.I.
    Gutierrez, C. Collesi, D. Licastro, L. Zentilin, M. Mano, S. Zacchigna, M. Vendruscolo,
    M. Marsili, A. Samal, M. Giacca, Cell Reports 27 (2019) 2759–2771.e5.
date_created: 2019-11-26T22:30:07Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2021-01-12T08:11:56Z
day: '28'
ddc:
- '576'
doi: 10.1016/j.celrep.2019.05.005
extern: '1'
external_id:
  pmid:
  - '31141697'
file:
- access_level: open_access
  checksum: c5d855d07263bfec718673385d0ea2d7
  content_type: application/pdf
  creator: rcubero
  date_created: 2019-11-26T22:30:43Z
  date_updated: 2020-07-14T12:47:50Z
  file_id: '7129'
  file_name: torrini_cellreports_2019.pdf
  file_size: 4650750
  relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: '        27'
issue: '9'
keyword:
- cardiomyocyte
- cell cycle
- Cofilin2
- cytoskeleton
- Hippo
- microRNA
- regeneration
- YAP
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 2759-2771.e5
pmid: 1
publication: Cell Reports
publication_identifier:
  issn:
  - 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Common regulatory pathways mediate activity of microRNAs inducing cardiomyocyte
  proliferation
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
year: '2019'
...