Arthropod evolution: Same Hox genes, different body plans

AbstractSurveys of Hox genes in various arthropods and related phyla demonstrate that extensive duplication and diversification of Hox genes occurred long before the appearance of overt sdoctopicegmental diversity in arthropod body plans

The multifaceted role of nerves in animal regeneration

International audienceThe discovery that the nervous system plays a critical role in salamander limb regeneration, in 1823, provided the first mechanistic insights into regenerative phenomena and stimulated a long quest for molecular regulators. A role for nerves in the context of regeneration has been suggested for most vertebrate and invertebrate groups, thus offering a possible shared mechanism for the regulation of regenerative processes among animals. Methodological differences and technical limitations, especially in invertebrate groups, have so far hampered broad comparisons and the search for common principles on the role of nerves. This review considers both old and recent work in this topic and provides a broad perspective on the roles of nerves during regeneration. Nerves are found consistently to have important roles in regeneration, but their mode of action varies across species. The ongoing technological developments in a broad range of invertebrate models are now paving the way for the discovery of the shared and unique roles of nerves in animal regeneration

MicroRNAs Act as Cofactors in Bicoid-Mediated Translational Repression

SummaryNoncoding RNAs have recently emerged as important regulators of mRNA translation and turnover [1, 2]. Nevertheless, we largely ignore how their function integrates with protein-mediated translational regulation. We focus on Bicoid, a key patterning molecule in Drosophila, which inhibits the translation of caudal in the anterior part of the embryo [3, 4]. Previous work showed that Bicoid recruits the cap-binding protein d4EHP on the caudal mRNA to repress translation [5]. Here we show that miR-2 family microRNAs are essential cofactors in the repression of caudal. Using an in vivo sensor, we demonstrate that Bicoid acts through a 63 nt response element in the caudal 3′ UTR that includes a single miR-2 target site. Mutating that site abolishes Bicoid-mediated repression, and this effect can be partly reversed by expressing a microRNA with compensatory changes that restore binding to the mutated target. Four predicted Bicoid splice isoforms are capable of caudal repression, including two that lack the d4EHP interaction domain; all four isoforms require the microRNA target for repression. The synergy between Bicoid and microRNAs appears to have evolved recently in the context of the drosophilid caudal BRE. The discovery that microRNAs play an essential role in Bicoid-mediated translational repression opens up new perspectives on Bicoid’s function and evolution

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

International audienceCell lineages provide the framework for understanding how cell fates are decided during development. Describing cell lineages in most organisms is challenging; even a fruit fly larva has~50,000 cells and a small mammal has >1 billion cells. Recently, the idea of applying CRISPR to induce mutations during development, to be used as heritable markers for lineage reconstruction, has been proposed by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated. Here, we use computer simulations to estimate the performance of these approaches under different conditions. We incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters-variable cell division rates, skewed mutational outcomes, target dropouts and different sequencing strategies. Our approach reveals the limitations of published CRISPR recorders, and indicates how future implementations can be optimised

Functionality of the GAL4/UAS system in Tribolium requires the use of endogenous core promoters

<p>Abstract</p> <p>Background</p> <p>The red flour beetle <it>Tribolium castaneum </it>has developed into an insect model system second only to <it>Drosophila</it>. Moreover, as a coleopteran it represents the most species-rich metazoan taxon which also includes many pest species. The genetic toolbox for <it>Tribolium </it>research has expanded in the past years but spatio-temporally controlled misexpression of genes has not been possible so far.</p> <p>Results</p> <p>Here we report the establishment of the GAL4/UAS binary expression system in <it>Tribolium castaneum</it>. Both GAL4Δ and GAL4VP16 driven by the endogenous heat shock inducible promoter of the <it>Tribolium hsp68 </it>gene are efficient in activating reporter gene expression under the control of the Upstream Activating Sequence (UAS). UAS driven ubiquitous tGFP fluorescence was observed in embryos within four hours after activation while <it>in-situ </it>hybridization against tGFP revealed expression already after two hours. The response is quick in relation to the duration of embryonic development in <it>Tribolium </it>- 72 hours with segmentation being completed after 24 hours - which makes the study of early embryonic processes possible using this system. By comparing the efficiency of constructs based on <it>Tribolium, Drosophila</it>, and artificial core promoters, respectively, we find that the use of endogenous core promoters is essential for high-level expression of transgenic constructs.</p> <p>Conclusions</p> <p>With the established GAL4/UAS binary expression system, ectopic misexpression approaches are now feasible in <it>Tribolium</it>. Our results support the contention that high-level transgene expression usually requires endogenous regulatory sequences, including endogenous core promoters in <it>Tribolium </it>and probably also other model systems.</p

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source. DOI: http://dx.doi.org/10.7554/eLife.20062.00

The crustacean Parhyale

International audienceParhyale hawaiensis comes from tropical intertidal shores and mangroves. In research, it is used to explore topics ranging from embryonic development and regeneration, to tidal rhythms and environmental pollution

Development: A deep breath for endocrine organ evolution

Developmental biologists have made surprising discoveries on the evolutionary origins of cell types, organs and body plans. Now, an elegant study in Drosophila raises interesting questions about the origin of two major endocrine organs of insects. © 2014 Elsevier Ltd.Peer Reviewe

Tracking cell lineages in 3D by incremental deep learning

International audienceDeep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently lack a unified user interface. We present ELEPHANT, an interactive platform for 3D cell tracking that addresses these challenges by taking an incremental approach to deep learning. ELEPHANT provides an interface that seamlessly integrates cell track annotation, deep learning, prediction, and proofreading. This enables users to implement cycles of incremental learning starting from a few annotated nuclei. Successive prediction-validation cycles enrich the training data, leading to rapid improvements in tracking performance. We test the software's performance against state-of-the-art methods and track lineages spanning the entire course of leg regeneration in a crustacean over 1 week (504 timepoints). ELEPHANT yields accurate, fully-validated cell lineages with a modest investment in time and effort

The crustacean model Parhyale hawaiensis

International audienceArthropods are the most abundant and diverse animals on earth. Among them, pancrustaceans are an ancient and morphologically diverse group, comprising a wide range of aquatic and semi-aquatic crustaceans as well as the insects, which emerged from crustacean ancestors to colonize most terrestrial habitats. Within insects, Drosophila stands out as one of the most powerful animal models, making major contributions to our understanding of development, physiology and behavior. Given these attributes, crustaceans provide a fertile ground for exploring biological diversity through comparative studies. However, beyond insects, few crustaceans are developed sufficiently as experimental models to enable such studies. The marine amphipod Parhyale hawaiensis is currently the best established crustacean system, offering year-round accessibility to developmental stages, transgenic tools, genomic resources, and established genetics and imaging approaches. The Parhyale research community is small but diverse, investigating the evolution of development, regeneration, aspects of sensory biology, chronobiology, bioprocessing and ecotoxicology