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Article ; Online: Methods for the Study of Apical Constriction During Ascidian Gastrulation.

Fiúza, Ulla-Maj / Lemaire, Patrick

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2438, Page(s) 377–413

Abstract: Gastrulation is the first major morphogenetic event during ascidian embryogenesis. Ascidian gastrulation begins with the invagination of the endodermal progenitors, a two-step process driven by individual cell shape changes of endoderm cells. During the ... ...

Abstract	Gastrulation is the first major morphogenetic event during ascidian embryogenesis. Ascidian gastrulation begins with the invagination of the endodermal progenitors, a two-step process driven by individual cell shape changes of endoderm cells. During the first step, endoderm cells constrict apically, thereby flattening the vegetal side of the embryo. During the second step, endoderm cells shorten along their apicobasal axis and tissue invagination ensues. Individual cell shape changes are mediated by localized actomyosin contractile activity. Here, we describe methods used during ascidian endoderm apical constriction to study myosin activity and cellular morphodynamics with confocal and light sheet microscopy and followed by quantitative image analysis.
MeSH term(s)	Animals ; Constriction ; Endoderm ; Gastrulation ; Morphogenesis ; Urochordata
Language	English
Publishing date	2022-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2035-9_23
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Article ; Online: Mechanical and genetic control of ascidian endoderm invagination during gastrulation.

Fiuza, Ulla-Maj / Lemaire, Patrick

Seminars in cell & developmental biology

2021 Volume 120, Page(s) 108–118

Abstract: Gastrulation is a near universal developmental process of animal embryogenesis, during which dramatic morphogenetic events take place: the mesodermal and endodermal tissues are internalized, the ectoderm spreads to cover the embryo surface, and the ... ...

Abstract	Gastrulation is a near universal developmental process of animal embryogenesis, during which dramatic morphogenetic events take place: the mesodermal and endodermal tissues are internalized, the ectoderm spreads to cover the embryo surface, and the animal body plan and germ layers are established. Morphogenesis during gastrulation has long been considered the result of spatio-temporally localised forces driven by the transcriptional programme of the embryo. Recent work has shown that tissue rheological properties, which define the mechanical response of tissues to internally-generated or external forces, are also important dynamic regulators of gastrulation. Here, we first introduce how embryonic mechanics can be represented, before outlining current knowledge of the mechanical and genetic control of gastrulation in ascidians, invertebrate marine chordates which develop with invariant cell lineages and a solid-like rheological behaviour until the neurula stages. We discuss the potential of these organisms for the experimental and computational whole-embryo characterisation of the mechanisms shaping gastrulation, and how they may inform the more complex tissue internalization strategies used by other model organisms.
MeSH term(s)	Animals ; Endoderm/metabolism ; Gastrulation/genetics ; Urochordata
Language	English
Publishing date	2021-08-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2021.08.001
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Article ; Online: High-resolution line-scan Brillouin microscopy for live imaging of mechanical properties during embryo development.

Bevilacqua, Carlo / Gomez, Juan Manuel / Fiuza, Ulla-Maj / Chan, Chii Jou / Wang, Ling / Hambura, Sebastian / Eguren, Manuel / Ellenberg, Jan / Diz-Muñoz, Alba / Leptin, Maria / Prevedel, Robert

Nature methods

2023 Volume 20, Issue 5, Page(s) 755–760

Abstract: Brillouin microscopy can assess mechanical properties of biological samples in a three-dimensional (3D), all-optical and hence non-contact fashion, but its weak signals often lead to long imaging times and require an illumination dosage harmful for ... ...

Abstract	Brillouin microscopy can assess mechanical properties of biological samples in a three-dimensional (3D), all-optical and hence non-contact fashion, but its weak signals often lead to long imaging times and require an illumination dosage harmful for living organisms. Here, we present a high-resolution line-scanning Brillouin microscope for multiplexed and hence fast 3D imaging of dynamic biological processes with low phototoxicity. The improved background suppression and resolution, in combination with fluorescence light-sheet imaging, enables the visualization of the mechanical properties of cells and tissues over space and time in living organism models such as fruit flies, ascidians and mouse embryos.
MeSH term(s)	Animals ; Mice ; Microscopy/methods ; Embryonic Development ; Drosophila ; Embryo, Nonmammalian ; Imaging, Three-Dimensional/methods
Language	English
Publishing date	2023-03-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-023-01822-1
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Article ; Online: A Nodal/Eph signalling relay drives the transition from apical constriction to apico-basal shortening in ascidian endoderm invagination.

Fiuza, Ulla-Maj / Negishi, Takefumi / Rouan, Alice / Yasuo, Hitoyoshi / Lemaire, Patrick

Development (Cambridge, England)

2020 Volume 147, Issue 15

Abstract: Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of ... ...

Abstract	Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin network. First, endoderm precursors constrict their apex. Second, they shorten apico-basally, while retaining small apical surfaces, thereby causing invagination. The mechanisms that prevent endoderm cell division, trigger the transition between step 1 and step 2, and drive apico-basal shortening have remained elusive. Here, we demonstrate a conserved role for Nodal and Eph signalling during invagination in two distantly related ascidian species,
MeSH term(s)	Animals ; Ciona intestinalis/embryology ; Endoderm/cytology ; Endoderm/embryology ; Gastrulation/physiology ; Nodal Protein/metabolism ; Receptor, EphA1/metabolism
Chemical Substances	Nodal Protein ; Receptor, EphA1 (EC 2.7.10.1)
Language	English
Publishing date	2020-08-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.186965
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Article ; Online: MorphoSeq: Full Single-Cell Transcriptome Dynamics Up to Gastrulation in a Chordate.

Sladitschek, Hanna L / Fiuza, Ulla-Maj / Pavlinic, Dinko / Benes, Vladimir / Hufnagel, Lars / Neveu, Pierre A

Cell

2020 Volume 181, Issue 4, Page(s) 922–935.e21

Abstract: Single-cell RNA sequencing (scRNA-seq) provides a leap forward in resolving cellular diversity and developmental trajectories but fails to comprehensively delineate the spatial organization and precise cellular makeup of individual embryos. Here, we ... ...

Abstract	Single-cell RNA sequencing (scRNA-seq) provides a leap forward in resolving cellular diversity and developmental trajectories but fails to comprehensively delineate the spatial organization and precise cellular makeup of individual embryos. Here, we reconstruct from scRNA-seq and light sheet imaging data a canonical digital embryo that captures the genome-wide gene expression trajectory of every single cell at every cell division in the 18 lineages up to gastrulation in the ascidian Phallusia mammillata. By using high-coverage scRNA-seq, we devise a computational framework that stratifies single cells of individual embryos into cell types without prior knowledge. Unbiased transcriptome data analysis mapped each cell's physical position and lineage history, yielding the complete history of gene expression at the genome-wide level for every single cell in a developing embryo. A comparison of individual embryos reveals both extensive reproducibility between symmetric embryo sides and a large inter-embryonic variability due to small differences in embryogenesis timing.
MeSH term(s)	Animals ; Cell Lineage/genetics ; Chordata/genetics ; Computational Biology/methods ; Gastrulation/genetics ; Gene Expression Profiling/methods ; Gene Expression Regulation, Developmental/genetics ; Reproducibility of Results ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Transcriptome/genetics ; Urochordata/genetics
Language	English
Publishing date	2020-04-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2020.03.055
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Zs.A 1167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Contact area-dependent cell communication and the morphological invariance of ascidian embryogenesis.

Guignard, Léo / Fiúza, Ulla-Maj / Leggio, Bruno / Laussu, Julien / Faure, Emmanuel / Michelin, Gaël / Biasuz, Kilian / Hufnagel, Lars / Malandain, Grégoire / Godin, Christophe / Lemaire, Patrick

Science (New York, N.Y.)

2020 Volume 369, Issue 6500

Abstract: Marine invertebrate ascidians display embryonic reproducibility: Their early embryonic cell lineages are considered invariant and are conserved between distantly related species, despite rapid genomic divergence. Here, we address the drivers of this ... ...

Abstract	Marine invertebrate ascidians display embryonic reproducibility: Their early embryonic cell lineages are considered invariant and are conserved between distantly related species, despite rapid genomic divergence. Here, we address the drivers of this reproducibility. We used light-sheet imaging and automated cell segmentation and tracking procedures to systematically quantify the behavior of individual cells every 2 minutes during
MeSH term(s)	Animals ; Cell Communication ; Cell Division ; Cell Tracking ; Reproduction ; Urochordata/cytology ; Urochordata/embryology
Language	English
Publishing date	2020-07-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aar5663
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Article: Cell and molecular biology of Notch.

Fiúza, Ulla-Maj / Arias, Alfonso Martinez

The Journal of endocrinology

2007 Volume 194, Issue 3, Page(s) 459–474

Abstract: Notch signalling is a cell-cell communication process, which allows the establishment of patterns of gene expression and differentiation, regulates binary cell fate choice and the maintenance of stem cell populations. So far, the data published has ... ...

Abstract	Notch signalling is a cell-cell communication process, which allows the establishment of patterns of gene expression and differentiation, regulates binary cell fate choice and the maintenance of stem cell populations. So far, the data published has elucidated the main players in the Notch signalling pathway. However, its regulatory mechanisms are exhibiting an increasing complexity which could account for the multitude of roles it has during development and in adult organisms. In this review, we will describe the multiple roles of Notch and how various factors can regulate Notch signalling.
MeSH term(s)	Animals ; Calcium-Binding Proteins/metabolism ; Cell Differentiation/physiology ; Drosophila/metabolism ; Drosophila Proteins ; Embryonic Structures/metabolism ; Endocrine System/embryology ; Endocrine System/metabolism ; Gene Expression Regulation, Developmental ; Humans ; Intercellular Signaling Peptides and Proteins/metabolism ; Intracellular Signaling Peptides and Proteins ; Jagged-1 Protein ; Membrane Proteins/metabolism ; Receptors, Notch/genetics ; Receptors, Notch/metabolism ; Serrate-Jagged Proteins ; Signal Transduction/physiology
Chemical Substances	Calcium-Binding Proteins ; Drosophila Proteins ; Intercellular Signaling Peptides and Proteins ; Intracellular Signaling Peptides and Proteins ; Jagged-1 Protein ; Membrane Proteins ; Receptors, Notch ; Ser protein, Drosophila ; Serrate-Jagged Proteins ; delta protein
Language	English
Publishing date	2007-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	3028-4
ISSN	1479-6805 ; 0022-0795
ISSN (online)	1479-6805
ISSN	0022-0795
DOI	10.1677/JOE-07-0242
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Article: Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians

Madgwick, Alicia / Marta Silvia Magri / Christelle Dantec / Damien Gailly / Ulla-Maj Fiuza / Léo Guignard / Sabrina Hettinger / Jose Luis Gomez-Skarmeta / Patrick Lemaire

Developmental biology. 2019 Apr. 15, v. 448, no. 2

2019

Abstract: Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species ... ...

Abstract	Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages.Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns.We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of “shadow” enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.
Keywords	Ciona ; ancestry ; chromatin ; data collection ; eggs ; electroporation ; embryogenesis ; evolution ; morphogenesis ; regulator genes ; regulatory sequences ; transcription (genetics) ; transcription initiation site
Language	English
Dates of publication	2019-0415
Size	p. 71-87.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2019.01.003
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Article ; Online: Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians.

Madgwick, Alicia / Magri, Marta Silvia / Dantec, Christelle / Gailly, Damien / Fiuza, Ulla-Maj / Guignard, Léo / Hettinger, Sabrina / Gomez-Skarmeta, Jose Luis / Lemaire, Patrick

Developmental biology

2019 Volume 448, Issue 2, Page(s) 71–87

Abstract	Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.
MeSH term(s)	Animals ; Base Sequence ; Body Patterning/genetics ; Chromatin/genetics ; Ciona/embryology ; Ciona/genetics ; Conserved Sequence/genetics ; Embryo, Nonmammalian/metabolism ; Embryonic Development/genetics ; Enhancer Elements, Genetic ; Evolution, Molecular ; Gastrula/embryology ; Gene Expression Regulation, Developmental ; Genetic Variation ; Regulatory Sequences, Nucleic Acid/genetics ; Species Specificity ; Time Factors ; Urochordata/embryology ; Urochordata/genetics
Chemical Substances	Chromatin
Language	English
Publishing date	2019-01-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1114-9
ISSN	1095-564X ; 0012-1606
ISSN (online)	1095-564X
ISSN	0012-1606
DOI	10.1016/j.ydbio.2019.01.003
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Article ; Online: Mechanisms of ligand-mediated inhibition in Notch signaling activity in Drosophila.

Fiuza, Ulla-Maj / Klein, Thomas / Martinez Arias, Alfonso / Hayward, Penelope

Developmental dynamics : an official publication of the American Association of Anatomists

2010 Volume 239, Issue 3, Page(s) 798–805

Abstract: The transmembrane proteins Delta and Serrate act as ligands for the signaling receptor Notch. In addition to this activating role, Delta and Serrate can also inhibit Notch signaling activity. This inhibitory effect is concentration-dependent and appears ... ...

Abstract	The transmembrane proteins Delta and Serrate act as ligands for the signaling receptor Notch. In addition to this activating role, Delta and Serrate can also inhibit Notch signaling activity. This inhibitory effect is concentration-dependent and appears to be evolutionarily conserved. In characterizing the underlying cellular mechanisms of the ligand inhibitory effect, we can confirm that ligand-mediated inhibition of Notch signaling can occur as a cell autonomous process (cis-inhibition) and that ligand-mediated inhibition prevents a step in Notch signaling activation early enough to suppress Notch ectodomain shedding.
MeSH term(s)	Animals ; Cell Culture Techniques ; Coculture Techniques ; Crosses, Genetic ; Drosophila melanogaster/metabolism ; Endocytosis ; Gene Expression Regulation, Developmental ; Genes, Reporter ; Ligands ; RNA Interference ; Receptors, Notch/antagonists & inhibitors ; Receptors, Notch/metabolism ; Signal Transduction ; Transfection
Chemical Substances	Ligands ; Receptors, Notch
Language	English
Publishing date	2010-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1102541-4
ISSN	1097-0177 ; 1058-8388
ISSN (online)	1097-0177
ISSN	1058-8388
DOI	10.1002/dvdy.22207
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