Perturbation analysis of a multi-morphogen Turing reaction-diffusion stripe patterning system reveals key regulatory interactions.

Periodic patterning is widespread in development and can be modelled by reaction-diffusion (RD) processes. However, minimal two-component RD descriptions are vastly simpler than the multi-molecular events that actually occur and are often hard to relate to real interactions measured experimentally. Addressing these issues, we investigated the periodic striped patterning of the rugae (transverse ridges) in the mammalian oral palate, focusing on multiple previously implicated pathways: FGF, Hh, Wnt and BMP. For each, we experimentally identified spatial patterns of activity and distinct responses of the system to inhibition. Through numerical and analytical approaches, we were able to constrain substantially the number of network structures consistent with the data. Determination of the dynamics of pattern appearance further revealed its initiation by 'activators' FGF and Wnt, and 'inhibitor' Hh, whereas BMP and mesenchyme-specific-FGF signalling were incorporated once stripes were formed. This further limited the number of possible networks. Experimental constraint thus limited the number of possible minimal networks to 154, just 0.004% of the number of possible diffusion-driven instability networks. Together, these studies articulate the principles of multi-morphogen RD patterning and demonstrate the utility of perturbation analysis for constraining RD systems.This article has an associated 'The people behind the papers' interview.

Modelling from the experimental developmental biologists viewpoint.

In this review we consider Reaction-Diffusion as the archetype of a model in developmental biology. We consider its history in relation to experimental work since it was first proposed in 1952 by Turing and revived in the 1970s by Meinhardt. We then discuss the most recent examples of experiments that address this model, including the challenges that remain in capturing the physico-chemical manifestation of the model mechanism in a real developmental system. Finally we discuss the model's current status and use in the experimental community.

Whole population cell analysis of a landmark-rich mammalian epithelium reveals multiple elongation mechanisms.

Tissue elongation is a fundamental component of developing and regenerating systems. Although localised proliferation is an important mechanism for tissue elongation, potentially important contributions of other elongation mechanisms, specifically cell shape change, orientated cell division and cell rearrangement, are rarely considered or quantified, particularly in mammalian systems. Their quantification, together with proliferation, provides a rigorous framework for the analysis of elongation. The mammalian palatal epithelium is a landmark-rich tissue, marked by regularly spaced ridges (rugae), making it an excellent model in which to analyse the contributions of cellular processes to directional tissue growth. We captured confocal stacks of entire fixed mouse palate epithelia throughout the mid-gestation growth period, labelled with membrane, nuclear and cell proliferation markers and segmented all cells (up to ∼20,000 per palate), allowing the quantification of cell shape and proliferation. Using the rugae as landmarks, these measures revealed that the so-called growth zone is a region of proliferation that is intermittently elevated at ruga initiation. The distribution of oriented cell division suggests that it is not a driver of tissue elongation, whereas cell shape analysis revealed that both elongation of cells leaving the growth zone and apico-basal cell rearrangements do contribute significantly to directional growth. Quantitative comparison of elongation processes indicated that proliferation contributes most to elongation at the growth zone, but cell shape change and rearrangement contribute as much as 40% of total elongation. We have demonstrated the utility of an approach to analysing the cellular mechanisms underlying tissue elongation in mammalian tissues. It should be broadly applied to higher-resolution analysis of links between genotypes and malformation phenotypes.

Mapping cellular processes in the mesenchyme during palatal development in the absence of Tbx1 reveals complex proliferation changes and perturbed cell packing and polarity.

The 22q11 deletion syndromes represent a spectrum of overlapping conditions including cardiac defects and craniofacial malformations. Amongst the craniofacial anomalies that are seen, cleft of the secondary palate is a common feature. Haploinsufficiency of TBX1 is believed to be a major contributor toward many of the developmental structural anomalies that occur in these syndromes, and targeted deletion of Tbx1 in the mouse reproduces many of these malformations, including cleft palate. However, the cellular basis of this defect is only poorly understood. Here, palatal development in the absence of Tbx1 has been analysed, focusing on cellular properties within the whole mesenchymal volume of the palatal shelves. Novel image analyses and data presentation tools were applied to quantify cell proliferation rates, including regions of elevated as well as reduced proliferation, and cell packing in the mesenchyme. Also, cell orientations (nucleus-Golgi axis) were mapped as a potential marker of directional cell movement. Proliferation differed only subtly between wild-type and mutant until embryonic day (E)15.5 when proliferation in the mutant was significantly lower. Tbx1(-/-) palatal shelves had slightly different cell packing than wild-type, somewhat lower before elevation and higher at E15.5 when the wild-type palate has elevated and fused. Cell orientation is biased towards the shelf distal edge in the mid-palate of wild-type embryos but is essentially random in the Tbx1(-/-) mutant shelves, suggesting that polarised processes such as directed cell rearrangement might be causal for the cleft phenotype. The implications of these findings in the context of further understanding Tbx1 function during palatogenesis and of these methods for the more general analysis of genotype-phenotype functional relationships are discussed.

Nodal signaling establishes a competency window for stochastic cell fate switching.

Specification of the germ layers by Nodal signaling has long been regarded as an archetype of how graded morphogens induce different cell fates. However, this deterministic model cannot explain why only a subset of cells at the early zebrafish embryo margin adopt the endodermal fate, whereas their immediate neighbours, experiencing a similar signaling environment, become mesoderm. Combining pharmacology, quantitative imaging and single cell transcriptomics, we demonstrate that sustained Nodal signaling establishes a bipotential progenitor state from which cells can switch to an endodermal fate or differentiate into mesoderm. Switching is a random event, the likelihood of which is modulated by Fgf signaling. This inherently imprecise mechanism nevertheless leads to robust endoderm formation because of buffering at later stages. Thus, in contrast to previous deterministic models of morphogen action, Nodal signaling establishes a temporal window when cells are competent to undergo a stochastic cell fate switch, rather than determining fate itself.

Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways.

The transcriptional effector SMAD4 is a core component of the TGF-ß family signaling pathways. However, its role in vertebrate embryo development remains unresolved. To address this, we deleted Smad4 in zebrafish and investigated the consequences of this on signaling by the TGF-ß family morphogens, BMPs and Nodal. We demonstrate that in the absence of Smad4, dorsal/ventral embryo patterning is disrupted due to the loss of BMP signaling. However, unexpectedly, Nodal signaling is maintained, but lacks robustness. This Smad4-independent Nodal signaling is sufficient for mesoderm specification, but not for optimal endoderm specification. Furthermore, using Optical Projection Tomography in combination with 3D embryo morphometry, we have generated a BMP morphospace and demonstrate that Smad4 mutants are morphologically indistinguishable from embryos in which BMP signaling has been genetically/pharmacologically perturbed. Smad4 is thus differentially required for signaling by different TGF-ß family ligands, which has implications for diseases where Smad4 is mutated or deleted.

Temporal dynamics in the formation and interpretation of Nodal and BMP morphogen gradients.

One of the most powerful ideas in developmental biology has been that of the morphogen gradient. In the classical view, a signaling molecule is produced at a local source from where it diffuses, resulting in graded levels across the tissue. This gradient provides positional information, with thresholds in the level of the morphogen determining the position of different cell fates. While experimental studies have uncovered numerous potential morphogens in biological systems, it is becoming increasingly apparent that one important feature, not captured in the simple model, is the role of time in both the formation and interpretation of morphogen gradients. We will focus on two members of the transforming growth factor-ß family that are known to play a vital role as morphogens in early vertebrate development: the Nodals and the bone morphogenetic proteins (BMPs). Primarily drawing on the early zebrafish embryo, we will show how recent studies have demonstrated the importance of feedback and other interactions that evolve through time, in shaping morphogen gradients. We will further show how rather than simply reading out levels of a morphogen, the duration of ligand exposure can be a crucial determinant of how cells interpret morphogens, in particular through the unfolding of downstream transcriptional events and in their interactions with other pathways.

Epithelial invagination by a vertical telescoping cell movement in mammalian salivary glands and teeth.

Epithelial bending is a fundamental process that shapes organs during development. Previously known mechanisms involve cells locally changing shape from columnar to wedge-shaped. Here we report a different mechanism that occurs without cell wedging. In mammalian salivary glands and teeth, we show that initial invagination occurs through coordinated vertical cell movement: cells towards the periphery of the placode move vertically upwards while their more central neighbours move downwards. Movement is achieved by active cell-on-cell migration: outer cells migrate with apical, centripetally polarised leading edge protrusions but remain attached to the basal lamina, depressing more central neighbours to "telescope" the epithelium downwards into underlying mesenchyme. Inhibiting protrusion formation by Arp2/3 protein blocks invagination. FGF and Hedgehog morphogen signals are required, with FGF providing a directional cue. These findings show that epithelial bending can be achieved by a morphogenetic mechanism of coordinated cell rearrangement quite distinct from previously recognised invagination processes.

Comparative gene expression in the heads of Drosophila melanogaster and Tribolium castaneum and the segmental affinity of the Drosophila hypopharyngeal lobes.

Drosophila melanogaster has long played an important role in debates surrounding insect and arthropod head segmentation. It is surprising, therefore, that one important feature of Drosophila head segmentation has remained controversial: namely the position of the boundary between the intercalary and mandibular segments. The Drosophila embryonic head has a pair of structures lying behind the stomodeum known as the hypopharyngeal lobes. Traditionally they have been seen as part of the intercalary segment. More recent work looking at the position of the lobes relative to various marker genes has been somewhat equivocal: segment polarity gene expression has been used to argue for a mandibular affinity of these lobes, while the expression of the anterior-most hox gene labial (lab) has supported an intercalary affinity. We have addressed the question of the segmental affinity of the hypopharyngeal lobes by conducting a detailed comparison of gene expression patterns between Drosophila and the red flour beetle Tribolium castaneum, in which the intercalary segment is unambiguously marked out by lab. We demonstrate that there is a large degree of conservation in gene expression patterns between Drosophila and Tribolium, and this argues against an intercalary segment affinity for the hypopharyngeal lobes. The lobes appear to be largely mandibular in origin, although some gene expression attributed to them appears to be associated with the stomodeum. We propose that the difficulties in interpreting the Drosophila head result from a topological shift in the Drosophila embryonic head, associated with the derived process of head involution.

Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom.

The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.

Long-Range Signaling Activation and Local Inhibition Separate the Mesoderm and Endoderm Lineages.

Specification of the three germ layers by graded Nodal signaling has long been seen as a paradigm for patterning through a single morphogen gradient. However, by exploiting the unique properties of the zebrafish embryo to capture the dynamics of signaling and cell fate allocation, we now demonstrate that Nodal functions in an incoherent feedforward loop, together with Fgf, to determine the pattern of endoderm and mesoderm specification. We show that Nodal induces long-range Fgf signaling while simultaneously inducing the cell-autonomous Fgf signaling inhibitor Dusp4 within the first two cell tiers from the margin. The consequent attenuation of Fgf signaling in these cells allows specification of endoderm progenitors, while the cells further from the margin, which receive Nodal and/or Fgf signaling, are specified as mesoderm. This elegant model demonstrates the necessity of feedforward and feedback interactions between multiple signaling pathways for providing cells with temporal and positional information.

Thick and thin fingers point out Turing waves.

Mouse genetics and computer simulations demonstrate that digit number and width are controlled by a Turing-type mechanism in which distal Hox genes modulate periodicity.

Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate.

We present direct evidence of an activator-inhibitor system in the generation of the regularly spaced transverse ridges of the palate. We show that new ridges, called rugae, that are marked by stripes of expression of Shh (encoding Sonic hedgehog), appear at two growth zones where the space between previously laid rugae increases. However, inter-rugal growth is not absolutely required: new stripes of Shh expression still appeared when growth was inhibited. Furthermore, when a ruga was excised, new Shh expression appeared not at the cut edge but as bifurcating stripes branching from the neighboring stripe of Shh expression, diagnostic of a Turing-type reaction-diffusion mechanism. Genetic and inhibitor experiments identified fibroblast growth factor (FGF) and Shh as components of an activator-inhibitor pair in this system. These findings demonstrate a reaction-diffusion mechanism that is likely to be widely relevant in vertebrate development.