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Many questions in developmental biology depend on measuring the position and movement of individual cells within developing embryos. Yet, tools that provide this data are often challenged by high cell density and their accuracy is difficult to measure. Here, we present a three-step procedure to address this problem. Step one is a novel segmentation algorithm based on image derivatives that, in combination with selective post-processing, reliably and automatically segments cell nuclei from images of densely packed tissue. Step two is a quantitative validation using synthetic images to ascertain the efficiency of the algorithm with respect to signal-to-noise ratio and object density. Finally, we propose an original method to generate reliable and experimentally faithful ground truth datasets: Sparse-dense dual-labeled embryo chimeras are used to unambiguously measure segmentation errors within experimental data. Together, the three steps outlined here establish a robust, iterative procedure to fine-tune image analysis algorithms and microscopy settings associated with embryonic 3D image data sets.

D’Arcy Thompson predicted a century ago that animal body shape is conditioned by gravity, but there has been no animal model to study how cellular forces are coordinated to generate body shapes that withstand gravity; the hirame medaka fish mutant, with pronounced body flattening, reveals how the hirame /YAP gene controls gravity-resisting cellular forces to produce complex 3D organs and body shapes. YAP protein gives tissue shape How is tissue tension controlled at the organismal level to maintain body shape and complex three-dimensional structures? Makoto Furutani-Seiki and colleagues describe a medaka fish mutant, hirame ( hir ), with a flattened body. They show that the phenotype is due to reduction of internal forces caused by the absence of YAP protein, part of the Hippo signalling pathway. This striking effect is linked to the control exerted by YAP on actomyosin-mediated tension through the regulation of the RhoGAP GTPase activating protein ARHGAP18. YAP also controls the 3D structure of human cell spheres in this manner in a human cell culture system. Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head 1 . Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force 2 , 3 . Although a century ago D’Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity 4 , there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish ( Oryzias latipes ) mutant, hirame ( hir ), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues.

The extensive use of pharmaceuticals has resulted in the intensive contamination of water bodies. Tetracycline is a type of antibiotic and its potential toxicity is causing environmental concern. The effects of developmental toxicity and the mechanisms of tetracycline on fish embryos are not well understood. Zebrafish embryos are used in this study to investigate the developmental toxicity of this compound. Four hour post-fertilization (hpf) zebrafish embryos are exposed to different concentrations of tetracycline until 96 hpf. The larvae display developmental delay phenotypes, including hatching delay, shorter body length, increased yolk sac area and uninflated swim bladder upon exposure to tetracycline. Delayed yolk sac absorption and swim bladder deficiency at 96 hpf are observed in the zebrafish larvae upon exposure to 20 μg/L of tetracycline. To test whether tetracycline causes oxidative damage and the resulting oxidative stress-induced apoptosis, the generation of reactive oxygen species (ROS), Acridine Orange staining and real time polymerase chain reaction have been performed in this study. The results indicate that tetracycline exposure results in significant increases in ROS production and cell apoptosis, mainly in the tail areas at 96 hpf. The gene expression pattern demonstrates that tetracycline induces ROS which causes apoptosis in the zebrafish larvae, and the results also indicate that caspase-dependent apoptotic pathways may greatly contribute to tetracycline-induced apoptosis in the early-life stages of the zebrafish. In addition, we have investigated the effects of tetracycline on marker genes related to resistance mechanisms and gene regulating drug biotransformation. The results of these gene expression studies indicate that tetracycline could induce zebrafish to resist pharmaceuticals and Cytochrome P450s that are involved in the biotransformation of tetracycline in zebrafish larvae. The overall results indicate that tetracycline can produce oxidative stress and induce apoptosis, which brings about significant developmental delay in zebrafish embryos.

Cyclostomes, the living jawless vertebrates including hagfishes and lampreys, represent the most basal lineage of vertebrates. Although the monophyly of cyclostomes has been supported by recent molecular analyses, the phenotypic traits of hagfishes, especially the lack of some vertebrate-defining features and the reported endodermal origin of the adenohypophysis, have been interpreted as hagfishes exhibiting a more ancestral state than those of all other vertebrates. Furthermore, the adult anatomy of hagfishes cannot be compared easily with that of lampreys. Here we describe the craniofacial development of a series of staged hagfish embryos, which shows that their adenohypophysis arises ectodermally, consistent with the molecular phylogenetic data. This finding also allowed us to identify a pan-cyclostome pattern, one not shared by jawed vertebrates. Comparative analyses indicated that many of the hagfish-specific traits can be explained by changes secondarily introduced into the hagfish lineage. We also propose a possibility that the pan-cyclostome pattern may reflect the ancestral programme for the craniofacial development of all living vertebrates. An analysis of staged hagfish embryos shows that the hagfish adenohypophysis is ectodermal in origin, revealing it to be a developmental quirk unique to hagfishes that was hitherto misleading; from this and other observations a ‘pan-cyclostome’ developmental pattern is derived, indicating that it was primitive for all vertebrates. The face of early vertebrate evolution The hagfish is the most primitive extant vertebrate. Its anatomy and development hold clues to understanding the evolution of that most enigmatic of structures, the vertebrate head. Hagfish embryos are notoriously hard to obtain, but a few years ago Shigeru Kuratani and colleagues managed to prepare some, and — for the first time since 1899 — significant work on hagfish embryology began. This paper presents the first detailed report on the craniofacial development of a hagfish species, Eptatretus burgeri . The authors identify an embryonic development pattern shared only by the jawless lampreys and hagfish that may have been primitive for all vertebrates.

One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. The conservation of embryonic development across species is of great interest in evolutionary biology. Here, using transcriptome analysis, the authors show that the pharyngula stage of development—in mid-embryogenesis—is conserved between mice, chickens, frogs and zebrafish.

As the use of nanoparticles (NPs) is increasing, the potential toxicity and behavior of NPs in living systems need to be better understood. Our goal was to evaluate the developmental toxicity and bio-distribution of two different sizes of fluorescently-labeled SiO2 NPs, 25 and 115 nm, with neutral surface charge or with different surface functionalization, rendering them positively or negatively charged, in order to predict the effect of NPs in humans. We performed a zebrafish embryo toxicity test (ZFET) by exposing the embryos to SiO2 NPs starting from six hours post fertilization (hpf). Survival rate, hatching time, and gross morphological changes were assessed at 12, 24, 36, 48, 60, and 72 hpf. We evaluated the effect of NPs on angiogenesis by counting the number of sub-intestinal vessels between the second and seventh intersegmental vessels and gene expression analysis of vascular endothelial growth factor (VEGF) and VEGF receptors at 72 hpf. SiO2 NPs did not show any adverse effects on survival rate, hatching time, gross morphology, or physiological angiogenesis. We found that SiO2 NPs were trapped by the chorion up until to the hatching stage. After chemical removal of the chorion (dechorionation), positively surface-charged SiO2 NPs (25 nm) significantly reduced the survival rate of the fish compared to the control group. These results indicate that zebrafish chorion acts as a physical barrier against SiO2 NPs, and removing the chorions in ZFET might be necessary for evaluation of toxicity of NPs.

How genetic programs generate cell-intrinsic forces to shape embryos is actively studied, but less so how tissue-scale physical forces impact morphogenesis. Here we address the role of the latter during axis extension, using Drosophila germband extension (GBE) as a model. We found previously that cells elongate in the anteroposterior (AP) axis in the extending germband, suggesting that an extrinsic tensile force contributed to body axis extension. Here we further characterized the AP cell elongation patterns during GBE, by tracking cells and quantifying their apical cell deformation over time. AP cell elongation forms a gradient culminating at the posterior of the embryo, consistent with an AP-oriented tensile force propagating from there. To identify the morphogenetic movements that could be the source of this extrinsic force, we mapped gastrulation movements temporally using light sheet microscopy to image whole Drosophila embryos. We found that both mesoderm and endoderm invaginations are synchronous with the onset of GBE. The AP cell elongation gradient remains when mesoderm invagination is blocked but is abolished in the absence of endoderm invagination. This suggested that endoderm invagination is the source of the tensile force. We next looked for evidence of this force in a simplified system without polarized cell intercalation, in acellular embryos. Using Particle Image Velocimetry, we identify posteriorwards Myosin II flows towards the presumptive posterior endoderm, which still undergoes apical constriction in acellular embryos as in wildtype. We probed this posterior region using laser ablation and showed that tension is increased in the AP orientation, compared to dorsoventral orientation or to either orientations more anteriorly in the embryo. We propose that apical constriction leading to endoderm invagination is the source of the extrinsic force contributing to germband extension. This highlights the importance of physical interactions between tissues during morphogenesis.

Annual killifish adapted to life in seasonally ephemeral water-bodies exhibit desiccation resistant eggs that can undergo diapause, a period of developmental arrest, enabling them to traverse the otherwise inhospitable dry season. Environmental cues that potentially indicate the season can govern whether eggs enter a stage of diapause mid-way through development or skip this diapause and instead undergo direct development. We report, based on construction of a supermatrix phylogenetic tree of the order Cyprinodontiformes and a battery of comparative analyses, that the ability to produce diapause eggs evolved independently at least six times within African and South American killifish. We then show in species representative of these lineages that embryos entering diapause display significant reduction in development of the cranial region and circulatory system relative to direct-developing embryos. This divergence along alternative developmental pathways begins mid-way through development, well before diapause is entered, during a period of purported maximum developmental constraint (the phylotypic period). Finally, we show that entering diapause is accompanied by a dramatic reduction in metabolic rate and concomitant increase in long-term embryo survival. Morphological divergence during the phylotypic period thus allows embryos undergoing diapause to conserve energy by shunting resources away from energetically costly organs thereby increasing survival chances in an environment that necessitates remaining dormant, buried in the soil and surrounded by an eggshell for much of the year. Our results indicate that adaptation to seasonal aquatic environments in annual killifish imposes strong selection during the embryo stage leading to marked diversification during this otherwise conserved period of vertebrate development.

Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge. It improves the 3D imaging ability of SPIM in resolving complex structures and optimizes SPIM live imaging performance by using a real-time adjustable tiling light sheet and creating a flexible compromise between spatial and temporal resolution. We demonstrate the 3D live imaging ability of TLS-SPIM by imaging cellular and subcellular behaviours in live C. elegans and zebrafish embryos, and show how TLS-SPIM can facilitate cell biology research in multicellular specimens by studying left-right symmetry breaking behaviour of C. elegans embryos. Selective plane illumination microscopy (SPIM) is capable of high-resolution, high-speed 3D imaging of single cells, but application to multicellular samples is challenging. Here the authors develop tiling light sheet SPIM to image large multicellular specimens in 3D with subcellular resolution.

As an adaptive reproductive strategy to their habitat, the majority of freshwater bivalve lineages incubate their larvae in the adults’ gills. The Unionida (pearly mussels) with up to 1000 living species worldwide, are widely accepted as key components of modern freshwater ecosystems. Furthermore, they are unique amongst other freshwater bivalves because their larvae, after finishing maternal incubation, must also parasitize fish to complete their embryonic development and dispersal. Here, we report fossil evidence of a functional freshwater bivalve reproductive system in Margaritifera valdensis , a unionoid from the iconic Lower Cretaceous Iguanodon locality on the Isle of Wight, southern England. We document four interconnected bioelements of their gill anatomy: gill supports, interlamellar junctions within the gill demibranchs, mineral concretions, and fossilized gill soft tissue. Moreover, diverse developmental stages of brooded embryos and larvae are identified. These data reveal larval incubation within modified gills and evidence a calcium source for their shell formation. These highlight a key evolutionary innovation that facilitated the Mesozoic diversification of unionoid bivalves in calcium-deficient freshwater habitats. Our findings provide the first fossil evidence that by the Early Cretaceous this successful brooding adaptation in freshwater unionoid bivalves developed, providing a significant clue to understanding the evolution and general role of bivalves’ gill anatomy in their function for reproduction.