scholarly journals A temporally resolved transcriptome for developing “Keller” explants of the Xenopus laevis dorsal marginal zone

2020 ◽  
Author(s):  
Anneke D. Kakebeen ◽  
Robert Huebner ◽  
Asako Shindo ◽  
Kujin Kwon ◽  
Taejoon Kwon ◽  
...  

AbstractExplanted tissues from vertebrate embryos reliably develop in culture and have provided essential paradigms for understanding embryogenesis, from early embryological investigations of induction, to the extensive study of Xenopus animal caps, to the current studies of mammalian gastruloids. Cultured explants of the Xenopus dorsal marginal zone (“Keller” explants) serve as a central paradigm for studies of convergent extension cell movements, yet we know little about the global patterns of gene expression in these explants. In an effort to more thoroughly develop this important model system, we provide here a time-resolved bulk transcriptome for developing Keller explants.

Development ◽  
1988 ◽  
Vol 103 (1) ◽  
pp. 193-209 ◽  
Author(s):  
R. Keller ◽  
M. Danilchik

We show with time-lapse micrography that narrowing in the circumblastoporal dimension (convergence) and lengthening in the animal-vegetal dimension (extension) of the involuting marginal zone (IMZ) and the noninvoluting marginal zone (NIMZ) are the major tissue movements driving blastopore closure and involution of the IMZ during gastrulation in the South African clawed frog, Xenopus laevis. Analysis of blastopore closure shows that the degree of convergence is uniform from dorsal to ventral sides, whereas the degree of extension is greater on the dorsal side of the gastrula. Explants of the gastrula show simultaneous convergence and extension in the dorsal IMZ and NIMZ. In both regions, convergence and extension are most pronounced at their common boundary, and decrease in both animal and vegetal directions. Convergent extension is autonomous to the IMZ and begins at stage 10.5, after the IMZ has involuted. In contrast, expression of convergent extension in the NIMZ appears to be dependent on basal contact with chordamesoderm or with itself. The degree of extension decreases progressively in lateral and ventral sectors. Isolated ventral sectors show convergence without a corresponding degree of extension, perhaps reflecting the transient convergence and thickening that occurs in this region of the intact embryo. We present a detailed mechanism of how these processes are integrated with others to produce gastrulation. The significance of the regional expression of convergence and extension in Xenopus is discussed and compared to gastrulation in other amphibians.


Development ◽  
1995 ◽  
Vol 121 (10) ◽  
pp. 3131-3140 ◽  
Author(s):  
S.W. Moore ◽  
R.E. Keller ◽  
M.A. Koehl

Physically, the course of morphogenesis is determined by the distribution and timing of force production in the embryo and by the mechanical properties of the tissues on which these forces act. We have miniaturized a standard materials-testing procedure (the stress-relaxation test) to measure the viscoelastic properties of the dorsal involuting marginal zone, prechordal mesoderm, and vegetal endoderm of Xenopus laevis embryos during gastrulation. We focused on the involuting marginal zone, because it undergoes convergent extension (an important and wide-spread morphogenetic process) and drives involution, blastopore closure and elongation of the embryonic axis. We show that the involuting marginal zone stiffens during gastrulation, stiffening is a special property of this region rather than a general property of the whole embryo, stiffening is greater along the anteroposterior axis than the mediolateral axis and changes in the cytoskeleton or extracellular matrix are necessary for stiffening, although changes in cell-cell adhesions or cell-matrix adhesions are not ruled out. These findings provide a baseline of data on which future experiments can be designed and make specific, testable predictions about the roles of the cytoskeleton, extracellular matrix and intercellular adhesion in convergent extension, as well as predictions about the morphogenetic role of convergent extension in early development.


Development ◽  
1988 ◽  
Vol 102 (4) ◽  
pp. 677-686 ◽  
Author(s):  
C.M. Regen ◽  
R.A. Steinhardt

The discovery that lithium treatment at blastula stages can induce axis formation suggested that it might act by respecifying the cytoplasmic rearrangement-generated dorsoventral pattern, so that ventral cells behave like their dorsal counterparts. We have studied the effects of Li+ treatment on the spatial layout of the cell-group movements of gastrulation to see whether this is the case. We find that involution of the chordamesoderm and associated archenteron roof is retarded by Li+, an effect which does not suggest dorsal respecification. However, in both migration of the leading edge mesoderm and convergent extension of the marginal zone, ventral regions clearly do show dorsal-type movement. Because of this, and because of examples where disruption of involution and effects on axis differentiation do not correlate, we propose that failure of involution represents a distinct effect of Li+ involving disruption of mechanical relationships at the blastopore. Thus archenteron formation poorly reflects the dorsoventral pattern. Extension of sandwich explants of the ventral marginal zone is proposed as a reliable quantitative assay for alterations to the dorsoventral pattern.


2008 ◽  
Vol 182 (6) ◽  
pp. 1073-1082 ◽  
Author(s):  
Gun-Hwa Kim ◽  
Jung-Hyun Her ◽  
Jin-Kwan Han

The single-pass transmembrane protein Ryk (atypical receptor related tyrosine kinase) functions as a Wnt receptor. However, Ryk's correlation with Wnt/Frizzled (Fz) signaling is poorly understood. Here, we report that Ryk regulates Xenopus laevis convergent extension (CE) movements via the β-arrestin 2 (βarr2)-dependent endocytic process triggered by noncanonical Wnt signaling. During X. laevis gastrulation, βarr2-mediated endocytosis of Fz7 and dishevelled (Dvl/Dsh) actually occurs in the dorsal marginal zone tissues, which actively participate in noncanonical Wnt signaling. Noncanonical Wnt11/Fz7-mediated endocytosis of Dsh requires the cell-membrane protein Ryk. Ryk interacts with both Wnt11 and βarr2, cooperates with Fz7 to mediate Wnt11-stimulated endocytosis of Dsh, and signals the noncanonical Wnt pathway in CE movements. Conversely, depletion of Ryk and Wnt11 prevents Dsh endocytosis in dorsal marginal zone tissues. Our study suggests that Ryk functions as an essential regulator for noncanonical Wnt/Fz-mediated endocytosis in the regulation of X. laevis CE movements.


Author(s):  
Olga Lazareva ◽  
Jan Baumbach ◽  
Markus List ◽  
David B Blumenthal

Abstract In network and systems medicine, active module identification methods (AMIMs) are widely used for discovering candidate molecular disease mechanisms. To this end, AMIMs combine network analysis algorithms with molecular profiling data, most commonly, by projecting gene expression data onto generic protein–protein interaction (PPI) networks. Although active module identification has led to various novel insights into complex diseases, there is increasing awareness in the field that the combination of gene expression data and PPI network is problematic because up-to-date PPI networks have a very small diameter and are subject to both technical and literature bias. In this paper, we report the results of an extensive study where we analyzed for the first time whether widely used AMIMs really benefit from using PPI networks. Our results clearly show that, except for the recently proposed AMIM DOMINO, the tested AMIMs do not produce biologically more meaningful candidate disease modules on widely used PPI networks than on random networks with the same node degrees. AMIMs hence mainly learn from the node degrees and mostly fail to exploit the biological knowledge encoded in the edges of the PPI networks. This has far-reaching consequences for the field of active module identification. In particular, we suggest that novel algorithms are needed which overcome the degree bias of most existing AMIMs and/or work with customized, context-specific networks instead of generic PPI networks.


2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xiaoxiang Hu ◽  
Xiaolei Liu ◽  
Chen Li ◽  
Yulu Zhang ◽  
Chengyao Li ◽  
...  

Abstract Background Parasites of the genus Trichinella are the pathogenic agents of trichinellosis, which is a widespread and severe foodborne parasitic disease. Trichinella spiralis resides primarily in mammalian skeletal muscle cells. After invading the cells of the host organism, T. spiralis must elude or invalidate the host’s innate and adaptive immune responses to survive. It is necessary to characterize the pathogenesis of trichinellosis to help to prevent the occurrence and further progression of this disease. The aims of this study were to elucidate the mechanisms of nurse cell formation, pathogenesis and immune evasion of T. spiralis, to provide valuable information for further research investigating the basic cell biology of Trichinella-infected muscle cells and the interaction between T. spiralis and its host. Methods We performed transcriptome profiling by RNA sequencing to identify global changes at 1, 3, 7, 10 and 15 days post-infection (dpi) in gene expression in the diaphragm after the parasite entered and persisted within the murine myocytes; the mice were infected by intravenous injection of newborn larvae. Gene expression analysis was based on the alignment results. Differentially expressed genes (DEGs) were identified based on their expression levels in various samples, and functional annotation and enrichment analysis were performed. Results The most extensive and dynamic gene expression responses in host diaphragms were observed during early infection (1 dpi). The number of DEGs and genes annotated in the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases decreased significantly in the infected mice compared to the uninfected mice at 3 and 7 dpi, suddenly increased sharply at 10 dpi, and then decreased to a lower level at 15 dpi, similar to that observed at 3 and 7 dpi. The massive initial reaction of the murine muscle cells to Trichinella infection steadied in the later stages of infection, with little additional changes detected for the remaining duration of the studied process. Although there were hundreds of DEGs at each time point, only 11 genes were consistently up- or downregulated at all 5 time points. Conclusions The gene expression patterns identified in this study can be employed to characterize the coordinated response of T. spiralis-infected myocytes in a time-resolved manner. This comprehensive dataset presents a distinct and sensitive picture of the interaction between host and parasite during intracellular infection, which can help to elucidate how pathogens evade host defenses and coordinate the biological functions of host cells to survive in the mammalian environment.


2013 ◽  
Vol 304 (3) ◽  
pp. R177-R188 ◽  
Author(s):  
Wendi S. Neckameyer ◽  
Kathryn J. Argue

Numerous studies have detailed the extensive conservation of developmental signaling pathways between the model system, Drosophila melanogaster, and mammalian models, but researchers have also profited from the unique and highly tractable genetic tools available in this system to address critical questions in physiology. In this review, we have described contributions that Drosophila researchers have made to mathematical dynamics of pattern formation, cardiac pathologies, the way in which pain circuits are integrated to elicit responses from sensation, as well as the ways in which gene expression can modulate diverse behaviors and shed light on human cognitive disorders. The broad and diverse array of contributions from Drosophila underscore its translational relevance to modeling human disease.


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