scholarly journals A defined platform of human peri-gastrulation-like biological fate patterning reveals coordination between Reaction-Diffusion and Positional-Information

2017 ◽  
Author(s):  
Mukul Tewary ◽  
Joel □stblom ◽  
Nika Shakiba ◽  
Peter W. Zandstra
Keyword(s):  
Cell Fate ◽  
Reaction Diffusion ◽  
Positional Information ◽  
Periodic Patterns ◽  
Experimental Conditions ◽  
Radial Gradient ◽  
Biological Fate ◽  
Dependent Cell ◽  
Geometrically Constrained ◽  
High Throughput Assay

AbstractHow position dependent cell fate acquisition occurs during embryogenesis has been a central question in developmental biology. To study this process, we developed a defined, high-throughput assay using BMP4 to induce peri-gastrulation-like fate patterning in geometrically constrained human pluripotent stem cell colonies. We observed that, upon BMP4 treatment, phosphorylated SMAD1 (pSMAD1) activity in the colonies organized into a radial gradient – an observation mechanistically compliant with a BMP4-NOGGIN Reaction-Diffusion (RD) model. Consequent fate acquisition occurred as a function of both the pSMAD1 signaling strength, and induction time – consistent with the Positional-Information (PI) paradigm. Our findings implicate coordination between RD and PI underlying the peri-gastrulation-like fate patterning. This model not only predicts experimental results of perturbing key parameters like colony size, and BMP4 dose, but also identifies experimental conditions that rescue patterning in colonies of sizes that have been reported to be patterning-reticent, and recapitulate RD-like periodic patterns in large colonies.

scholarly journals The periodic coloration in birds forms through a prepattern of somite origin

Science ◽  
2018 ◽  
Vol 361 (6408) ◽  
pp. eaar4777 ◽  
Author(s):  
Nicolas Haupaix ◽  
Camille Curantz ◽  
Richard Bailleul ◽  
Samantha Beck ◽  
Annie Robic ◽  
...  
Keyword(s):  
Expression Profile ◽  
Natural Variation ◽  
Reaction Diffusion ◽  
Positional Information ◽  
Pigment Production ◽  
Periodic Patterns ◽  
Local Dynamics ◽  
Step Process ◽  
Early Developmental ◽  
Dose Dependent

The periodic stripes and spots that often adorn animals’ coats have been largely viewed as self-organizing patterns, forming through dynamics such as Turing’s reaction-diffusion within the developing skin. Whether preexisting positional information also contributes to the periodicity and orientation of these patterns has, however, remained unclear. We used natural variation in colored stripes of juvenile galliform birds to show that stripes form in a two-step process. Autonomous signaling from the somite sets stripe position by forming a composite prepattern marked by the expression profile of agouti. Subsequently, agouti regulates stripe width through dose-dependent control of local pigment production. These results reveal that early developmental landmarks can shape periodic patterns upstream of late local dynamics, and thus constrain their evolution.

scholarly journals Identification of miRNA precursors in the phloem of Cucurbita maxima

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8269 ◽  
Author(s):  
Eugeny Tolstyko ◽  
Alexander Lezzhov ◽  
Andrey Solovyev
Keyword(s):  
Cell Fate ◽  
Positional Information ◽  
Mature Mirnas ◽  
Inorganic Phosphorus ◽  
Pcr Analysis ◽  
Cucurbita Maxima ◽  
Phloem Exudate ◽  
Long Distance ◽  
Long Distance Transport ◽  
Range Cell

Plant development and responses to environmental cues largely depend on mobile signals including microRNAs (miRNAs) required for post-transcriptional silencing of specific genes. Short-range cell-to-cell transport of miRNA in developing tissues and organs is involved in transferring positional information essential for determining cell fate. Among other RNA species, miRNAs are found in the phloem sap. Long-distance transport of miRNA via the phloem takes a part in regulation of physiological responses to changing environmental conditions. As shown for regulation of inorganic phosphorus and sulfate homeostasis, mature miRNAs rather than miRNAs precursors are transported in the phloem as signaling molecules. Here, a bioinformatics analysis of transcriptomic data for Cucurbita maxima phloem exudate RNAs was carried out to elucidate whether miRNA precursors could also be present in the phloem. We demonstrated that the phloem transcriptome contained a subset of C. maxima pri-miRNAs that differed from a subset of pri-miRNA sequences abundant in a leaf transcriptome. Differential accumulation of pri-miRNA was confirmed by PCR analysis of C. maxima phloem exudate and leaf RNA samples. Therefore, the presented data indicate that a number of C. maxima pri-miRNAs are selectively recruited to the phloem translocation pathway. This conclusion was validated by inter-species grafting experiments, in which C. maxima pri-miR319a was found to be transported across the graft union via the phloem, confirming the presence of pri-miR319a in sieve elements and showing that phloem miRNA precursors could play a role in long-distance signaling in plants.

scholarly journals Successive specification of Drosophila neuroblasts NB 6-4 and NB 7-3 depends on interaction of the segment polarity genes wingless, gooseberry and naked cuticle

Development ◽  
2001 ◽  
Vol 128 (17) ◽  
pp. 3253-3261 ◽  
Author(s):  
Nirupama Deshpande ◽  
Rainer Dittrich ◽  
Gerhard M. Technau ◽  
Joachim Urban
Keyword(s):  
Cell Fate ◽  
Cell Lineage ◽  
Positional Information ◽  
Dorsoventral Patterning ◽  
Expression Domain ◽  
Direct Role ◽  
Segment Polarity Genes ◽  
Segment Polarity ◽  
Unique Identity

The Drosophila central nervous system derives from neural precursor cells, the neuroblasts (NBs), which are born from the neuroectoderm by the process of delamination. Each NB has a unique identity, which is revealed by the production of a characteristic cell lineage and a specific set of molecular markers it expresses. These NBs delaminate at different but reproducible time points during neurogenesis (S1-S5) and it has been shown for early delaminating NBs (S1/S2) that their identities depend on positional information conferred by segment polarity genes and dorsoventral patterning genes. We have studied mechanisms leading to the fate specification of a set of late delaminating neuroblasts, NB 6-4 and NB 7-3, both of which arise from the engrailed (en) expression domain, with NB 6-4 delaminating first. In contrast to former reports, we did not find any evidence for a direct role of hedgehog in the process of NB 7-3 specification. Instead, we present evidence to show that the interplay of the segmentation genes naked cuticle (nkd) and gooseberry (gsb), both of which are targets of wingless (wg) activity, leads to differential commitment to NB 6-4 and NB 7-3 cell fate. In the absence of either nkd or gsb, one NB fate is replaced by the other. However, the temporal sequence of delamination is maintained, suggesting that formation and specification of these two NBs are under independent control.

Genes that control dorsoventral polarity affect gene expression along the anteroposterior axis of the Drosophila embryo

Development ◽  
1987 ◽  
Vol 99 (3) ◽  
pp. 327-332 ◽  
Author(s):  
S.B. Carroll ◽  
G.M. Winslow ◽  
V.J. Twombly ◽  
M.P. Scott
Keyword(s):  
Gene Expression ◽  
Cell Fate ◽  
Maternal Effect ◽  
Positional Information ◽  
Drosophila Embryo ◽  
Dorsoventral Polarity ◽  
Anteroposterior Axis ◽  
Positional Marker ◽  
Control Pattern ◽  
The Relationship

At least 13 genes control the establishment of dorsoventral polarity in the Drosophila embryo and more than 30 genes control the anteroposterior pattern of body segments. Each group of genes is thought to control pattern formation along one body axis, independently of the other group. We have used the expression of the fushi tarazu (ftz) segmentation gene as a positional marker to investigate the relationship between the dorsoventral and anteroposterior axes. The ftz gene is normally expressed in seven transverse stripes. Changes in the striped pattern in embryos mutant for other genes (or progeny of females homozygous for maternal-effect mutations) can reveal alterations of cell fate resulting from such mutations. We show that in the absence of any of ten maternal-effect dorsoventral polarity gene functions, the characteristic stripes of ftz protein are altered. Normally there is a difference between ftz stripe spacing on the dorsal and ventral sides of the embryo; in dorsalized mutant embryos the ftz stripes appear to be altered so that dorsal-type spacing occurs on all sides of the embryo. These results indicate that cells respond to dorsoventral positional information in establishing early patterns of gene expression along the anteroposterior axis and that there may be more significant interactions between the different axes of positional information than previously determined.

scholarly journals Notch-mediated lateral inhibition regulates proneural wave propagation when combined with EGF-mediated reaction diffusion

2016 ◽  
Vol 113 (35) ◽  
pp. E5153-E5162 ◽  
Author(s):  
Makoto Sato ◽  
Tetsuo Yasugi ◽  
Yoshiaki Minami ◽  
Takashi Miura ◽  
Masaharu Nagayama
Keyword(s):  
Notch Signaling ◽  
Cell Fate ◽  
Lateral Inhibition ◽  
Feedback Loop ◽  
Reaction Diffusion ◽  
Signaling Systems ◽  
Visual Center ◽  
Salt And Pepper ◽  
Egf Signaling

Notch-mediated lateral inhibition regulates binary cell fate choice, resulting in salt and pepper patterns during various developmental processes. However, how Notch signaling behaves in combination with other signaling systems remains elusive. The wave of differentiation in the Drosophila visual center or “proneural wave” accompanies Notch activity that is propagated without the formation of a salt and pepper pattern, implying that Notch does not form a feedback loop of lateral inhibition during this process. However, mathematical modeling and genetic analysis clearly showed that Notch-mediated lateral inhibition is implemented within the proneural wave. Because partial reduction in EGF signaling causes the formation of the salt and pepper pattern, it is most likely that EGF diffusion cancels salt and pepper pattern formation in silico and in vivo. Moreover, the combination of Notch-mediated lateral inhibition and EGF-mediated reaction diffusion enables a function of Notch signaling that regulates propagation of the wave of differentiation.

scholarly journals Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Djihad Hadjadj ◽  
Thomas Denecker ◽  
Eva Guérin ◽  
Su-Jung Kim ◽  
Fabien Fauchereau ◽  
...  
Keyword(s):  
Dna Replication ◽  
Cell Fate ◽  
Web Application ◽  
Timing Analysis ◽  
Mutant Cell ◽  
Replication Timing ◽  
Experimental Conditions ◽  
Replication Process ◽  
Time Required ◽  
Dna Replication Timing

Abstract DNA replication must be faithful and follow a well-defined spatiotemporal program closely linked to transcriptional activity, epigenomic marks, intranuclear structures, mutation rate and cell fate determination. Among the readouts of the spatiotemporal program of DNA replication, replication timing analyses require not only complex and time-consuming experimental procedures, but also skills in bioinformatics. We developed a dedicated Shiny interactive web application, the START-R (Simple Tool for the Analysis of the Replication Timing based on R) suite, which analyzes DNA replication timing in a given organism with high-throughput data. It reduces the time required for generating and analyzing simultaneously data from several samples. It automatically detects different types of timing regions and identifies significant differences between two experimental conditions in ∼15 min. In conclusion, START-R suite allows quick, efficient and easier analyses of DNA replication timing for all organisms. This novel approach can be used by every biologist. It is now simpler to use this method in order to understand, for example, whether ‘a favorite gene or protein’ has an impact on replication process or, indirectly, on genomic organization (as Hi-C experiments), by comparing the replication timing profiles between wild-type and mutant cell lines.

scholarly journals The histone demethylase UTX enables RB-dependent cell fate control

2010 ◽  
Vol 24 (4) ◽  
pp. 327-332 ◽  
Author(s):  
J. K. Wang ◽  
M.-C. Tsai ◽  
G. Poulin ◽  
A. S. Adler ◽  
S. Chen ◽  
...  
Keyword(s):  
Cell Fate ◽  
Histone Demethylase ◽  
Fate Control ◽  
Dependent Cell ◽  
Cell Fate Control
Sign in / Sign up

Export Citation Format

Share Document