Effective image visualization for publications – a workflow using open access tools and concepts

Schmied, Christopher; Jambor, Helena

doi:10.12688/f1000research.27140.2

Cited by 12 publications

(8 citation statements)

References 39 publications

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“…For microscopy images, we only performed minimal linear intensity adjustments in microscopy images to improve their contrast and brightness 38 . We created illustrations and assembled the final figure plates using Inkscape v1.2.2 39 .…”

Section: Data Visualization and Figure Assemblymentioning

confidence: 99%

Patterned embryonic invagination evolved in response to mechanical instability

Vellutini

Cuenca

Krishna

et al. 2023

Preprint

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The cephalic furrow is a deep epithelial fold that demarcates the head–trunk boundary of fly embryos during gastrulation. It forms under strict genetic control using active cellular mechanisms and follows an invariant morphogenetic sequence. But unlike other embryonic invaginations, the cells that invaginate in the cephalic furrow do not give rise to any precursor tissues or larval traits. The cephalic furrow is transient and unfolds leaving no trace. For these reasons, its function during development has remained elusive. Here we show that the cephalic furrow plays a mechanical role duringDrosophilagastrulation. By live-imaging mutant embryos, we find that without the cephalic furrow, ectopic folds appear around the head–trunk interface indicating that the epithelial stability has been compromised. Usingin vivoperturbations andin silicosimulations, we demonstrate that ectopic folding in cephalic furrow mutants occurs due to the concomitant formation of mitotic domains and extension of the germ band. These events increase the tissue strain in the head–trunk interface giving rise to mechanical instabilities. Further, we show by simulations that an early pre-patterned invagination can effectively prevent the build-up of compressive stresses by retaining epithelial tissue out-of-plane before other morphogenetic movements take place. Our findings suggest the cephalic furrow absorbs compressive stresses at the head–trunk boundary during fly gastrulation, and raise the hypothesis that mechanical forces may have played a role in the evolution of the cephalic furrow.

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Section: Data Visualization and Figure Assemblymentioning

confidence: 99%

Patterned embryonic invagination evolved in response to mechanical instability

Vellutini

Cuenca

Krishna

et al. 2023

Preprint

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“…Unless otherwise stated, all images of embryos are maximum intensity projections of confocal z -stacks of the upper half of the embryo. Fiji was used to adjust image brightness and contrast, in accordance with guidelines presented by Schmied and Jambor (2020). Image gamma was adjusted to 0.1 for all opa transcript stains, due to the extremely bright transcriptional foci.…”

Section: Extraction Of Quantitative Expression Tracesmentioning

confidence: 99%

A timer gene network is spatially regulated by the terminal system in theDrosophilaembryo

Clark

Battistara

Benton

2022

Preprint

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In insects, patterning of the anteroposterior axis relies on exquisite coordination of segmentation gene expression in space and time. And yet, there is also wide variation across species in the timing of segmentation and the geometry of the embryonic fate map. The majority of described species exhibit sequential segmentation during posterior growth. Other species, such as the fly Drosophila melanogaster, specify almost all of their segments simultaneously prior to gastrulation. The dynamics of both sequential segmentation and simultaneous segmentation correlate with the spatiotemporal expression of the "timer" genes caudal, Dichaete and odd-paired, which are expressed sequentially within segmenting tissues. These genes have critical roles in the development of many species; however, even in the extensively studied Drosophila embryo, the regulatory interactions responsible for shaping their expression remain poorly understood. In particular, it is not known whether the timer genes cross-regulate each other, nor why they are differentially expressed between the broad region of the blastoderm that gives rise to the gnathal, thoracic and abdominal segments and the small posterior region that gives rise to the embryonic terminalia. In this work, we investigated these questions using multiplexed fluorescent in situ hybridisation and high resolution confocal imaging of wild-type and mutant Drosophila embryos. First, we re-examined segmentation gene expression in the posterior of the embryo, and discovered that two parasegment-like boundaries are generated sequentially from the terminal region during germband extension and posterior growth. Next, we found that caudal, Dichaete, and odd-paired dynamically cross-regulate each other, and also that they are differentially spatially regulated by the posterior terminal genes. Finally, we formalised the regulatory network we inferred from our data as a logical computational model. Our model qualitatively recapitulated both wild-type development and the mutant phenotypes we had examined. Our findings resolve a decades-long ambiguity over the number of segments formed during Drosophila embryogenesis. In addition, they reveal how dynamic spatial inputs from an extrinsic signalling centre modulate the intrinsic dynamics of a gene regulatory network to generate an essential developmental pattern.

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“…Unless otherwise stated, all images of embryos are maximum projections of confocal Z-stacks. Fiji was also used to adjust image brightness and contrast, and to rotate, crop and reslice images where necessary, in accordance with guidelines presented by Schmied and Jambor (2021). Fixed intensity values were applied for qualitative comparisons of signal intensity between images.…”

Section: Image Processing and Figure Assemblymentioning

confidence: 99%

The neuroblast timer gene nubbin exhibits functional redundancy with gap genes to regulate segment identity in Tribolium

2021

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The neuroblast timer genes hunchback, Krüppel, nubbin, and castor are expressed in temporal sequence in neural stem cells, and in corresponding spatial sequence along the Drosophila blastoderm. As canonical gap genes, hunchback and Krüppel play a crucial role in insect segmentation, but the roles of nubbin and castor in this process remain ambiguous. We have investigated the expression and functions of nubbin and castor during segmentation in the beetle Tribolium. We show that Tc-hunchback, Tc-Krüppel, Tc-nubbin and Tc-castor are expressed sequentially in the segment addition zone, and that Tc-nubbin regulates segment identity redundantly with two previously described gap/gap-like genes, Tc-giant and Tc-knirps. Simultaneous knockdown of Tc-nubbin, Tc-giant and Tc-knirps results in the formation of ectopic legs on abdominal segments. This homeotic transformation is caused by loss of abdominal Hox gene expression, likely due to expanded Tc-Krüppel expression. Our findings support the theory that the neuroblast timer series was co-opted for use in insect segment patterning, and contribute to our growing understanding of the evolution and function of the gap gene network outside of Drosophila.

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Effective image visualization for publications – a workflow using open access tools and concepts

Cited by 12 publications

References 39 publications

Patterned embryonic invagination evolved in response to mechanical instability

Patterned embryonic invagination evolved in response to mechanical instability

A timer gene network is spatially regulated by the terminal system in theDrosophilaembryo

The neuroblast timer gene nubbin exhibits functional redundancy with gap genes to regulate segment identity in Tribolium

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