---
_id: '15048'
abstract:
- lang: eng
  text: Embryogenesis results from the coordinated activities of different signaling
    pathways controlling cell fate specification and morphogenesis. In vertebrate
    gastrulation, both Nodal and BMP signaling play key roles in germ layer specification
    and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis
    is still insufficiently understood. Here, we took a reductionist approach using
    zebrafish embryonic explants to study the coordination of Nodal and BMP signaling
    for embryo patterning and morphogenesis. We show that Nodal signaling triggers
    explant elongation by inducing mesendodermal progenitors but also suppressing
    BMP signaling activity at the site of mesendoderm induction. Consistent with this,
    ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm
    intercalations, key processes during explant elongation. Translating these ex
    vivo observations to the intact embryo showed that, similar to explants, Nodal
    signaling suppresses the effect of BMP signaling on cell intercalations in the
    dorsal domain, thus allowing robust embryonic axis elongation. These findings
    suggest a dual function of Nodal signaling in embryonic axis elongation by both
    inducing mesendoderm and suppressing BMP effects in the dorsal portion of the
    mesendoderm.
acknowledged_ssus:
- _id: Bio
- _id: LifeSc
acknowledgement: "We thank Patrick Müller for sharing the chordintt250 mutant zebrafish
  line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b
  plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated
  the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro
  and Katherine Rogers and members of the Heisenberg lab for discussions, technical
  advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo
  for discussions. We thank the Imaging and Optics Facility as well as the Life Science
  facility at IST Austria for support with microscopy and fish maintenance.\r\nThis
  work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573
  to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy
  of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience
  and Technology Austria. "
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Alexandra
  full_name: Schauer, Alexandra
  id: 30A536BA-F248-11E8-B48F-1D18A9856A87
  last_name: Schauer
  orcid: 0000-0001-7659-9142
- first_name: Kornelija
  full_name: Pranjic-Ferscha, Kornelija
  id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
  last_name: Pranjic-Ferscha
- first_name: Robert
  full_name: Hauschild, Robert
  id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87
  last_name: Hauschild
  orcid: 0000-0001-9843-3522
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
citation:
  ama: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation
    by Nodal-dependent restriction of BMP signaling. <i>Development</i>. 2024;151(4):1-18.
    doi:<a href="https://doi.org/10.1242/dev.202316">10.1242/dev.202316</a>
  apa: Schauer, A., Pranjic-Ferscha, K., Hauschild, R., &#38; Heisenberg, C.-P. J.
    (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling.
    <i>Development</i>. The Company of Biologists. <a href="https://doi.org/10.1242/dev.202316">https://doi.org/10.1242/dev.202316</a>
  chicago: Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp
    J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.”
    <i>Development</i>. The Company of Biologists, 2024. <a href="https://doi.org/10.1242/dev.202316">https://doi.org/10.1242/dev.202316</a>.
  ieee: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust
    axis elongation by Nodal-dependent restriction of BMP signaling,” <i>Development</i>,
    vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.
  ista: Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis
    elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4),
    1–18.
  mla: Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction
    of BMP Signaling.” <i>Development</i>, vol. 151, no. 4, The Company of Biologists,
    2024, pp. 1–18, doi:<a href="https://doi.org/10.1242/dev.202316">10.1242/dev.202316</a>.
  short: A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development
    151 (2024) 1–18.
date_created: 2024-03-03T23:00:50Z
date_published: 2024-02-01T00:00:00Z
date_updated: 2024-03-04T07:28:25Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
- _id: Bio
doi: 10.1242/dev.202316
ec_funded: 1
file:
- access_level: open_access
  checksum: 6961ea10012bf0d266681f9628bb8f13
  content_type: application/pdf
  creator: dernst
  date_created: 2024-03-04T07:24:43Z
  date_updated: 2024-03-04T07:24:43Z
  file_id: '15050'
  file_name: 2024_Development_Schauer.pdf
  file_size: 14839986
  relation: main_file
  success: 1
file_date_updated: 2024-03-04T07:24:43Z
has_accepted_license: '1'
intvolume: '       151'
issue: '4'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1-18
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742573'
  name: Interaction and feedback between cell mechanics and fate specification in
    vertebrate gastrulation
- _id: 26B1E39C-B435-11E9-9278-68D0E5697425
  grant_number: '25239'
  name: 'Mesendoderm specification in zebrafish: The role of extraembryonic tissues'
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
  record:
  - id: '14926'
    relation: research_data
    status: public
scopus_import: '1'
status: public
title: Robust axis elongation by Nodal-dependent restriction of BMP signaling
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 151
year: '2024'
...
---
_id: '14774'
abstract:
- lang: eng
  text: Morphogen gradients impart positional information to cells in a homogenous
    tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act
    as a morphogen during zebrafish gastrulation. However, technical limitations have
    so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation
    of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing
    neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a
    locus. By combining sensitive imaging with single-molecule fluorescence correlation
    spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin,
    propagates by diffusion through the extracellular space and forms a graded distribution
    towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles
    of its downstream targets determines the precise input-output relationship of
    Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters
    the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during
    zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate
    that extracellular diffusion of the protein from the source is crucial for it
    to achieve its morphogenic potential.
acknowledgement: "We thank members of the Brand lab, as well as Justina Stark (Ivo
  Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden,
  Germany) for project-related discussions; Darren Gilmour (University of Zurich),
  Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private
  Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology
  platform, TU Dresden for imaging and image analysis-related support; and Maurizio
  Abbate (Technical support, Arivis) for help with image analysis. We are also grateful
  to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul
  and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft
  (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics
  of Life’ seed grant and by institutional funds from Technische Universitat Dresden
  (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited
  in PMC for immediate release."
article_number: dev201559
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Rohit K
  full_name: Harish, Rohit K
  id: 1bae78aa-ee0e-11ec-9b76-bc42990f409d
  last_name: Harish
- first_name: Mansi
  full_name: Gupta, Mansi
  last_name: Gupta
- first_name: Daniela
  full_name: Zöller, Daniela
  last_name: Zöller
- first_name: Hella
  full_name: Hartmann, Hella
  last_name: Hartmann
- first_name: Ali
  full_name: Gheisari, Ali
  last_name: Gheisari
- first_name: Anja
  full_name: Machate, Anja
  last_name: Machate
- first_name: Stefan
  full_name: Hans, Stefan
  last_name: Hans
- first_name: Michael
  full_name: Brand, Michael
  last_name: Brand
citation:
  ama: Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous
    Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation.
    <i>Development</i>. 2023;150(19). doi:<a href="https://doi.org/10.1242/dev.201559">10.1242/dev.201559</a>
  apa: Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate,
    A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests
    to its role as a morphogen during zebrafish gastrulation. <i>Development</i>.
    The Company of Biologists. <a href="https://doi.org/10.1242/dev.201559">https://doi.org/10.1242/dev.201559</a>
  chicago: Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari,
    Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous
    Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.”
    <i>Development</i>. The Company of Biologists, 2023. <a href="https://doi.org/10.1242/dev.201559">https://doi.org/10.1242/dev.201559</a>.
  ieee: R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient
    attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>,
    vol. 150, no. 19. The Company of Biologists, 2023.
  ista: Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand
    M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role
    as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559.
  mla: Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient
    Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>,
    vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:<a href="https://doi.org/10.1242/dev.201559">10.1242/dev.201559</a>.
  short: R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S.
    Hans, M. Brand, Development 150 (2023).
date_created: 2024-01-10T09:18:54Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2024-01-10T12:45:25Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.201559
external_id:
  isi:
  - '001097449100002'
  pmid:
  - '37665167'
file:
- access_level: open_access
  checksum: 2d6f52dc33260a9b2352b8f28374ba5f
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-10T12:41:13Z
  date_updated: 2024-01-10T12:41:13Z
  file_id: '14790'
  file_name: 2023_Development_Harish.pdf
  file_size: 12836306
  relation: main_file
  success: 1
file_date_updated: 2024-01-10T12:41:13Z
has_accepted_license: '1'
intvolume: '       150'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
status: public
title: Real-time monitoring of an endogenous Fgf8a gradient attests to its role as
  a morphogen during zebrafish gastrulation
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 150
year: '2023'
...
---
_id: '12231'
abstract:
- lang: eng
  text: Ventral tail bending, which is transient but pronounced, is found in many
    chordate embryos and constitutes an interesting model of how tissue interactions
    control embryo shape. Here, we identify one key upstream regulator of ventral
    tail bending in embryos of the ascidian Ciona. We show that during the early tailbud
    stages, ventral epidermal cells exhibit a boat-shaped morphology (boat cell) with
    a narrow apical surface where phosphorylated myosin light chain (pMLC) accumulates.
    We further show that interfering with the function of the BMP ligand Admp led
    to pMLC localizing to the basal instead of the apical side of ventral epidermal
    cells and a reduced number of boat cells. Finally, we show that cutting ventral
    epidermal midline cells at their apex using an ultraviolet laser relaxed ventral
    tail bending. Based on these results, we propose a previously unreported function
    for Admp in localizing pMLC to the apical side of ventral epidermal cells, which
    causes the tail to bend ventrally by resisting antero-posterior notochord extension
    at the ventral side of the tail.
acknowledgement: "iona intestinalis adults were provided by Dr Yutaka Satou (Kyoto
  University) and Dr Manabu Yoshida (the University of Tokyo) with support from the
  National Bio-Resource Project of AMED, Japan. We thank Dr Hidehiko Hashimoto and
  Dr Yuji Mizotani for technical information about 1P-myosin antibody staining. We
  thank Dr Kaoru Imai and Dr Yutaka Satou for valuable discussion about Admp and for
  the DNA construct of Bmp2/4 under the Dlx.b upstream sequence. We thank Ms Maki
  Kogure for constructing the FUSION360 of the intercalating epidermal cell.\r\nThis
  work was supported by funding from the Japan Society for the Promotion of Science
  (JP16H01451, JP21H00440). Open Access funding provided by Keio University: Keio
  Gijuku Daigaku."
article_number: dev200215
article_processing_charge: No
article_type: original
author:
- first_name: Yuki S.
  full_name: Kogure, Yuki S.
  last_name: Kogure
- first_name: Hiromochi
  full_name: Muraoka, Hiromochi
  last_name: Muraoka
- first_name: Wataru C.
  full_name: Koizumi, Wataru C.
  last_name: Koizumi
- first_name: Raphaël
  full_name: Gelin-alessi, Raphaël
  last_name: Gelin-alessi
- first_name: Benoit G
  full_name: Godard, Benoit G
  id: 3263621A-F248-11E8-B48F-1D18A9856A87
  last_name: Godard
- first_name: Kotaro
  full_name: Oka, Kotaro
  last_name: Oka
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
- first_name: Kohji
  full_name: Hotta, Kohji
  last_name: Hotta
citation:
  ama: Kogure YS, Muraoka H, Koizumi WC, et al. Admp regulates tail bending by controlling
    ventral epidermal cell polarity via phosphorylated myosin localization in Ciona.
    <i>Development</i>. 2022;149(21). doi:<a href="https://doi.org/10.1242/dev.200215">10.1242/dev.200215</a>
  apa: Kogure, Y. S., Muraoka, H., Koizumi, W. C., Gelin-alessi, R., Godard, B. G.,
    Oka, K., … Hotta, K. (2022). Admp regulates tail bending by controlling ventral
    epidermal cell polarity via phosphorylated myosin localization in Ciona. <i>Development</i>.
    The Company of Biologists. <a href="https://doi.org/10.1242/dev.200215">https://doi.org/10.1242/dev.200215</a>
  chicago: Kogure, Yuki S., Hiromochi Muraoka, Wataru C. Koizumi, Raphaël Gelin-alessi,
    Benoit G Godard, Kotaro Oka, Carl-Philipp J Heisenberg, and Kohji Hotta. “Admp
    Regulates Tail Bending by Controlling Ventral Epidermal Cell Polarity via Phosphorylated
    Myosin Localization in Ciona.” <i>Development</i>. The Company of Biologists,
    2022. <a href="https://doi.org/10.1242/dev.200215">https://doi.org/10.1242/dev.200215</a>.
  ieee: Y. S. Kogure <i>et al.</i>, “Admp regulates tail bending by controlling ventral
    epidermal cell polarity via phosphorylated myosin localization in Ciona,” <i>Development</i>,
    vol. 149, no. 21. The Company of Biologists, 2022.
  ista: Kogure YS, Muraoka H, Koizumi WC, Gelin-alessi R, Godard BG, Oka K, Heisenberg
    C-PJ, Hotta K. 2022. Admp regulates tail bending by controlling ventral epidermal
    cell polarity via phosphorylated myosin localization in Ciona. Development. 149(21),
    dev200215.
  mla: Kogure, Yuki S., et al. “Admp Regulates Tail Bending by Controlling Ventral
    Epidermal Cell Polarity via Phosphorylated Myosin Localization in Ciona.” <i>Development</i>,
    vol. 149, no. 21, dev200215, The Company of Biologists, 2022, doi:<a href="https://doi.org/10.1242/dev.200215">10.1242/dev.200215</a>.
  short: Y.S. Kogure, H. Muraoka, W.C. Koizumi, R. Gelin-alessi, B.G. Godard, K. Oka,
    C.-P.J. Heisenberg, K. Hotta, Development 149 (2022).
date_created: 2023-01-16T09:50:12Z
date_published: 2022-11-01T00:00:00Z
date_updated: 2023-08-04T09:33:24Z
day: '01'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1242/dev.200215
external_id:
  isi:
  - '000903991700002'
  pmid:
  - '36227591'
file:
- access_level: open_access
  checksum: 871b9c58eb79b9e60752de25a46938d6
  content_type: application/pdf
  creator: dernst
  date_created: 2023-01-27T10:36:50Z
  date_updated: 2023-01-27T10:36:50Z
  file_id: '12423'
  file_name: 2022_Development_Kogure.pdf
  file_size: 9160451
  relation: main_file
  success: 1
file_date_updated: 2023-01-27T10:36:50Z
has_accepted_license: '1'
intvolume: '       149'
isi: 1
issue: '21'
keyword:
- Developmental Biology
- Molecular Biology
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Admp regulates tail bending by controlling ventral epidermal cell polarity
  via phosphorylated myosin localization in Ciona
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 149
year: '2022'
...
---
_id: '12245'
abstract:
- lang: eng
  text: MicroRNAs (miRs) have an important role in tuning dynamic gene expression.
    However, the mechanism by which they are quantitatively controlled is unknown.
    We show that the amount of mature miR-9, a key regulator of neuronal development,
    increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize
    the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s
    that produce the same mature miR-9 and show that they are sequentially expressed
    during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on
    to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5
    in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the
    developmental increase of mature miR-9, reduces late neuronal differentiation
    and fails to downregulate Her6 at late stages. Mathematical modelling shows that
    an adaptive network containing Her6 is insensitive to linear increases in miR-9
    but responds to stepwise increases of miR-9. We suggest that a sharp stepwise
    increase of mature miR-9 is created by sequential and additive temporal activation
    of distinct loci. This may be a strategy to overcome adaptation and facilitate
    a transition of Her6 to a new dynamic regime or steady state.
acknowledgement: "We are grateful to Dr Tom Pettini for the advice on smiFISH technique
  and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological
  Services Facility, Bioimaging and Systems Microscopy Facilities of the University
  of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust
  Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award
  (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award
  to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship
  in Basic Science (219992/Z/19/Z). Open Access funding provided by The University
  of Manchester. Deposited in PMC for immediate release."
article_number: dev200474
article_processing_charge: No
article_type: original
author:
- first_name: Ximena
  full_name: Soto, Ximena
  last_name: Soto
- first_name: Joshua
  full_name: Burton, Joshua
  last_name: Burton
- first_name: Cerys S.
  full_name: Manning, Cerys S.
  last_name: Manning
- first_name: Thomas
  full_name: Minchington, Thomas
  id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f
  last_name: Minchington
- first_name: Robert
  full_name: Lea, Robert
  last_name: Lea
- first_name: Jessica
  full_name: Lee, Jessica
  last_name: Lee
- first_name: Jochen
  full_name: Kursawe, Jochen
  last_name: Kursawe
- first_name: Magnus
  full_name: Rattray, Magnus
  last_name: Rattray
- first_name: Nancy
  full_name: Papalopulu, Nancy
  last_name: Papalopulu
citation:
  ama: Soto X, Burton J, Manning CS, et al. Sequential and additive expression of
    miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19).
    doi:<a href="https://doi.org/10.1242/dev.200474">10.1242/dev.200474</a>
  apa: Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., …
    Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors
    control timing of neurogenesis. <i>Development</i>. The Company of Biologists.
    <a href="https://doi.org/10.1242/dev.200474">https://doi.org/10.1242/dev.200474</a>
  chicago: Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert
    Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential
    and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>.
    The Company of Biologists, 2022. <a href="https://doi.org/10.1242/dev.200474">https://doi.org/10.1242/dev.200474</a>.
  ieee: X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors
    control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. The Company
    of Biologists, 2022.
  ista: Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray
    M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors
    control timing of neurogenesis. Development. 149(19), dev200474.
  mla: Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors
    Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474,
    The Company of Biologists, 2022, doi:<a href="https://doi.org/10.1242/dev.200474">10.1242/dev.200474</a>.
  short: X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe,
    M. Rattray, N. Papalopulu, Development 149 (2022).
date_created: 2023-01-16T09:53:17Z
date_published: 2022-10-01T00:00:00Z
date_updated: 2023-08-04T09:41:08Z
day: '01'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.200474
external_id:
  isi:
  - '000918161000003'
  pmid:
  - '36189829'
file:
- access_level: open_access
  checksum: d7c29b74e9e4032308228cc704a30e88
  content_type: application/pdf
  creator: dernst
  date_created: 2023-01-30T08:35:44Z
  date_updated: 2023-01-30T08:35:44Z
  file_id: '12438'
  file_name: 2022_Development_Soto.pdf
  file_size: 9348839
  relation: main_file
  success: 1
file_date_updated: 2023-01-30T08:35:44Z
has_accepted_license: '1'
intvolume: '       149'
isi: 1
issue: '19'
keyword:
- Developmental Biology
- Molecular Biology
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
related_material:
  link:
  - relation: software
    url: ' https://github.com/burtonjosh/StepwiseMir9'
scopus_import: '1'
status: public
title: Sequential and additive expression of miR-9 precursors control timing of neurogenesis
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 149
year: '2022'
...
---
_id: '9226'
abstract:
- lang: eng
  text: 'Half a century after Lewis Wolpert''s seminal conceptual advance on how cellular
    fates distribute in space, we provide a brief historical perspective on how the
    concept of positional information emerged and influenced the field of developmental
    biology and beyond. We focus on a modern interpretation of this concept in terms
    of information theory, largely centered on its application to cell specification
    in the early Drosophila embryo. We argue that a true physical variable (position)
    is encoded in local concentrations of patterning molecules, that this mapping
    is stochastic, and that the processes by which positions and corresponding cell
    fates are determined based on these concentrations need to take such stochasticity
    into account. With this approach, we shift the focus from biological mechanisms,
    molecules, genes and pathways to quantitative systems-level questions: where does
    positional information reside, how it is transformed and accessed during development,
    and what fundamental limits it is subject to?'
acknowledgement: This work was supported in part by the National Science Foundation,
  through the Center for the Physics of Biological Function (PHY-1734030), by the
  National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen
  Forschung (FWF P28844). Deposited in PMC for release after 12 months.
article_number: dev176065
article_processing_charge: No
article_type: original
author:
- first_name: Gašper
  full_name: Tkačik, Gašper
  id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
  last_name: Tkačik
  orcid: 0000-0002-6699-1455
- first_name: Thomas
  full_name: Gregor, Thomas
  last_name: Gregor
citation:
  ama: Tkačik G, Gregor T. The many bits of positional information. <i>Development</i>.
    2021;148(2). doi:<a href="https://doi.org/10.1242/dev.176065">10.1242/dev.176065</a>
  apa: Tkačik, G., &#38; Gregor, T. (2021). The many bits of positional information.
    <i>Development</i>. The Company of Biologists. <a href="https://doi.org/10.1242/dev.176065">https://doi.org/10.1242/dev.176065</a>
  chicago: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.”
    <i>Development</i>. The Company of Biologists, 2021. <a href="https://doi.org/10.1242/dev.176065">https://doi.org/10.1242/dev.176065</a>.
  ieee: G. Tkačik and T. Gregor, “The many bits of positional information,” <i>Development</i>,
    vol. 148, no. 2. The Company of Biologists, 2021.
  ista: Tkačik G, Gregor T. 2021. The many bits of positional information. Development.
    148(2), dev176065.
  mla: Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.”
    <i>Development</i>, vol. 148, no. 2, dev176065, The Company of Biologists, 2021,
    doi:<a href="https://doi.org/10.1242/dev.176065">10.1242/dev.176065</a>.
  short: G. Tkačik, T. Gregor, Development 148 (2021).
date_created: 2021-03-07T23:01:25Z
date_published: 2021-02-01T00:00:00Z
date_updated: 2023-08-07T13:57:30Z
day: '01'
department:
- _id: GaTk
doi: 10.1242/dev.176065
external_id:
  isi:
  - '000613906000007'
  pmid:
  - '33526425'
intvolume: '       148'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1242/dev.176065
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P28844-B27
  name: Biophysics of information processing in gene regulation
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: The many bits of positional information
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 148
year: '2021'
...
---
_id: '7165'
abstract:
- lang: eng
  text: Cell division, movement and differentiation contribute to pattern formation
    in developing tissues. This is the case in the vertebrate neural tube, in which
    neurons differentiate in a characteristic pattern from a highly dynamic proliferating
    pseudostratified epithelium. To investigate how progenitor proliferation and differentiation
    affect cell arrangement and growth of the neural tube, we used experimental measurements
    to develop a mechanical model of the apical surface of the neuroepithelium that
    incorporates the effect of interkinetic nuclear movement and spatially varying
    rates of neuronal differentiation. Simulations predict that tissue growth and
    the shape of lineage-related clones of cells differ with the rate of differentiation.
    Growth is isotropic in regions of high differentiation, but dorsoventrally biased
    in regions of low differentiation. This is consistent with experimental observations.
    The absence of directional signalling in the simulations indicates that global
    mechanical constraints are sufficient to explain the observed differences in anisotropy.
    This provides insight into how the tissue growth rate affects cell dynamics and
    growth anisotropy and opens up possibilities to study the coupling between mechanics,
    pattern formation and growth in the neural tube.
article_number: dev176297
article_processing_charge: No
article_type: original
author:
- first_name: Pilar
  full_name: Guerrero, Pilar
  last_name: Guerrero
- first_name: Ruben
  full_name: Perez-Carrasco, Ruben
  last_name: Perez-Carrasco
- first_name: Marcin P
  full_name: Zagórski, Marcin P
  id: 343DA0DC-F248-11E8-B48F-1D18A9856A87
  last_name: Zagórski
  orcid: 0000-0001-7896-7762
- first_name: David
  full_name: Page, David
  last_name: Page
- first_name: Anna
  full_name: Kicheva, Anna
  id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
  last_name: Kicheva
  orcid: 0000-0003-4509-4998
- first_name: James
  full_name: Briscoe, James
  last_name: Briscoe
- first_name: Karen M.
  full_name: Page, Karen M.
  last_name: Page
citation:
  ama: Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation
    influences progenitor arrangement in the vertebrate neuroepithelium. <i>Development</i>.
    2019;146(23). doi:<a href="https://doi.org/10.1242/dev.176297">10.1242/dev.176297</a>
  apa: Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe,
    J., &#38; Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement
    in the vertebrate neuroepithelium. <i>Development</i>. The Company of Biologists.
    <a href="https://doi.org/10.1242/dev.176297">https://doi.org/10.1242/dev.176297</a>
  chicago: Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna
    Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences
    Progenitor Arrangement in the Vertebrate Neuroepithelium.” <i>Development</i>.
    The Company of Biologists, 2019. <a href="https://doi.org/10.1242/dev.176297">https://doi.org/10.1242/dev.176297</a>.
  ieee: P. Guerrero <i>et al.</i>, “Neuronal differentiation influences progenitor
    arrangement in the vertebrate neuroepithelium,” <i>Development</i>, vol. 146,
    no. 23. The Company of Biologists, 2019.
  ista: Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page
    KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate
    neuroepithelium. Development. 146(23), dev176297.
  mla: Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement
    in the Vertebrate Neuroepithelium.” <i>Development</i>, vol. 146, no. 23, dev176297,
    The Company of Biologists, 2019, doi:<a href="https://doi.org/10.1242/dev.176297">10.1242/dev.176297</a>.
  short: P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe,
    K.M. Page, Development 146 (2019).
date_created: 2019-12-10T14:39:50Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2023-09-06T11:26:36Z
day: '04'
ddc:
- '570'
department:
- _id: AnKi
doi: 10.1242/dev.176297
ec_funded: 1
external_id:
  isi:
  - '000507575700004'
  pmid:
  - '31784457'
file:
- access_level: open_access
  checksum: b6533c37dc8fbd803ffeca216e0a8b8a
  content_type: application/pdf
  creator: dernst
  date_created: 2019-12-13T07:34:06Z
  date_updated: 2020-07-14T12:47:50Z
  file_id: '7177'
  file_name: 2019_Development_Guerrero.pdf
  file_size: 7797881
  relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
intvolume: '       146'
isi: 1
issue: '23'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: B6FC0238-B512-11E9-945C-1524E6697425
  call_identifier: H2020
  grant_number: '680037'
  name: Coordination of Patterning And Growth In the Spinal Cord
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Neuronal differentiation influences progenitor arrangement in the vertebrate
  neuroepithelium
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 146
year: '2019'
...
---
_id: '7404'
abstract:
- lang: eng
  text: The formation of neuronal dendrite branches is fundamental for the wiring
    and function of the nervous system. Indeed, dendrite branching enhances the coverage
    of the neuron's receptive field and modulates the initial processing of incoming
    stimuli. Complex dendrite patterns are achieved in vivo through a dynamic process
    of de novo branch formation, branch extension and retraction. The first step towards
    branch formation is the generation of a dynamic filopodium-like branchlet. The
    mechanisms underlying the initiation of dendrite branchlets are therefore crucial
    to the shaping of dendrites. Through in vivo time-lapse imaging of the subcellular
    localization of actin during the process of branching of Drosophila larva sensory
    neurons, combined with genetic analysis and electron tomography, we have identified
    the Actin-related protein (Arp) 2/3 complex as the major actin nucleator involved
    in the initiation of dendrite branchlet formation, under the control of the activator
    WAVE and of the small GTPase Rac1. Transient recruitment of an Arp2/3 component
    marks the site of branchlet initiation in vivo. These data position the activation
    of Arp2/3 as an early hub for the initiation of branchlet formation.
article_number: dev171397
article_processing_charge: No
article_type: original
author:
- first_name: Tomke
  full_name: Stürner, Tomke
  last_name: Stürner
- first_name: Anastasia
  full_name: Tatarnikova, Anastasia
  last_name: Tatarnikova
- first_name: Jan
  full_name: Müller, Jan
  id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D
  last_name: Müller
- first_name: Barbara
  full_name: Schaffran, Barbara
  last_name: Schaffran
- first_name: Hermann
  full_name: Cuntz, Hermann
  last_name: Cuntz
- first_name: Yun
  full_name: Zhang, Yun
  last_name: Zhang
- first_name: Maria
  full_name: Nemethova, Maria
  id: 34E27F1C-F248-11E8-B48F-1D18A9856A87
  last_name: Nemethova
- first_name: Sven
  full_name: Bogdan, Sven
  last_name: Bogdan
- first_name: Vic
  full_name: Small, Vic
  last_name: Small
- first_name: Gaia
  full_name: Tavosanis, Gaia
  last_name: Tavosanis
citation:
  ama: Stürner T, Tatarnikova A, Müller J, et al. Transient localization of the Arp2/3
    complex initiates neuronal dendrite branching in vivo. <i>Development</i>. 2019;146(7).
    doi:<a href="https://doi.org/10.1242/dev.171397">10.1242/dev.171397</a>
  apa: Stürner, T., Tatarnikova, A., Müller, J., Schaffran, B., Cuntz, H., Zhang,
    Y., … Tavosanis, G. (2019). Transient localization of the Arp2/3 complex initiates
    neuronal dendrite branching in vivo. <i>Development</i>. The Company of Biologists.
    <a href="https://doi.org/10.1242/dev.171397">https://doi.org/10.1242/dev.171397</a>
  chicago: Stürner, Tomke, Anastasia Tatarnikova, Jan Müller, Barbara Schaffran, Hermann
    Cuntz, Yun Zhang, Maria Nemethova, Sven Bogdan, Vic Small, and Gaia Tavosanis.
    “Transient Localization of the Arp2/3 Complex Initiates Neuronal Dendrite Branching
    in Vivo.” <i>Development</i>. The Company of Biologists, 2019. <a href="https://doi.org/10.1242/dev.171397">https://doi.org/10.1242/dev.171397</a>.
  ieee: T. Stürner <i>et al.</i>, “Transient localization of the Arp2/3 complex initiates
    neuronal dendrite branching in vivo,” <i>Development</i>, vol. 146, no. 7. The
    Company of Biologists, 2019.
  ista: Stürner T, Tatarnikova A, Müller J, Schaffran B, Cuntz H, Zhang Y, Nemethova
    M, Bogdan S, Small V, Tavosanis G. 2019. Transient localization of the Arp2/3
    complex initiates neuronal dendrite branching in vivo. Development. 146(7), dev171397.
  mla: Stürner, Tomke, et al. “Transient Localization of the Arp2/3 Complex Initiates
    Neuronal Dendrite Branching in Vivo.” <i>Development</i>, vol. 146, no. 7, dev171397,
    The Company of Biologists, 2019, doi:<a href="https://doi.org/10.1242/dev.171397">10.1242/dev.171397</a>.
  short: T. Stürner, A. Tatarnikova, J. Müller, B. Schaffran, H. Cuntz, Y. Zhang,
    M. Nemethova, S. Bogdan, V. Small, G. Tavosanis, Development 146 (2019).
date_created: 2020-01-29T16:27:10Z
date_published: 2019-04-04T00:00:00Z
date_updated: 2023-09-07T14:47:00Z
day: '04'
department:
- _id: MiSi
doi: 10.1242/dev.171397
external_id:
  isi:
  - '000464583200006'
  pmid:
  - '30910826'
intvolume: '       146'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1242/dev.171397
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transient localization of the Arp2/3 complex initiates neuronal dendrite branching
  in vivo
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 146
year: '2019'
...
---
_id: '9524'
abstract:
- lang: eng
  text: Cytosine methylation is the most common covalent modification of DNA in eukaryotes.
    DNA methylation has an important role in many aspects of biology, including development
    and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive
    restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies.
    Combining these techniques with DNA microarrays and high-throughput sequencing
    has made the mapping of DNA methylation feasible on a genome-wide scale. Here
    we discuss recent developments and future directions for identifying and mapping
    methylation, in an effort to help colleagues to identify the approaches that best
    serve their research interests.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
- first_name: Steven
  full_name: Henikoff, Steven
  last_name: Henikoff
citation:
  ama: Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns.
    <i>Development</i>. 2007;134(22):3959-3965. doi:<a href="https://doi.org/10.1242/dev.001131">10.1242/dev.001131</a>
  apa: Zilberman, D., &#38; Henikoff, S. (2007). Genome-wide analysis of DNA methylation
    patterns. <i>Development</i>. The Company of Biologists. <a href="https://doi.org/10.1242/dev.001131">https://doi.org/10.1242/dev.001131</a>
  chicago: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
    Patterns.” <i>Development</i>. The Company of Biologists, 2007. <a href="https://doi.org/10.1242/dev.001131">https://doi.org/10.1242/dev.001131</a>.
  ieee: D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,”
    <i>Development</i>, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965,
    2007.
  ista: Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns.
    Development. 134(22), 3959–3965.
  mla: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
    Patterns.” <i>Development</i>, vol. 134, no. 22, The Company of Biologists, 2007,
    pp. 3959–65, doi:<a href="https://doi.org/10.1242/dev.001131">10.1242/dev.001131</a>.
  short: D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.
date_created: 2021-06-08T06:29:50Z
date_published: 2007-11-15T00:00:00Z
date_updated: 2021-12-14T08:57:58Z
day: '15'
department:
- _id: DaZi
doi: 10.1242/dev.001131
extern: '1'
external_id:
  pmid:
  - '17928417'
intvolume: '       134'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1242/dev.001131
month: '11'
oa: 1
oa_version: Published Version
page: 3959-3965
pmid: 1
publication: Development
publication_identifier:
  eissn:
  - 1477-9129
  issn:
  - 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of DNA methylation patterns
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 134
year: '2007'
...