Model System In Developmental Biology Research Articles

The Mediterranean mussel Mytilus galloprovincialis: a novel model for developmental studies in mollusks.

A model organism in developmental biology is defined by its experimental amenability and by resources created for the model system by the scientific community. For the most powerful invertebrate models, the combination of both has already yielded a thorough understanding of developmental processes. However, the number of developmental model systems is still limited, and their phylogenetic distribution heavily biased. Members of one of the largest animal lineages, the Spiralia, for example, have long been neglected. In order to remedy this shortcoming, we have produced a detailed developmental transcriptome for the bivalve mollusk Mytilus galloprovincialis, and have expanded the list of experimental protocols available for this species. Our high-quality transcriptome allowed us to identify transcriptomic signatures of developmental progression and to perform a first comparison with another bivalve mollusk: the Pacific oyster Crassostrea gigas. To allow co-labelling studies, we optimized and combined protocols for immunohistochemistry and hybridization chain reaction to create high-resolution co-expression maps of developmental genes. The resources and protocols described here represent an enormous boost for the establishment of Mytilus galloprovincialis as an alternative model system in developmental biology.

The Biological Robots Are Coming! But Note They Have Been Here for ∼3.5 Billion Years

The Biological Robots Are Coming! But Note They Have Been Here for ∼3.5 Billion Years

A gene regulatory network for cell fate specification in Ciona embryos.

Ascidian embryos are used as a model system in developmental biology due to their unique properties, including their invariant cell division patterns, being comprised of a small number of cells and tissues, the feasibility of their experimental manipulation, and their simple and compact genome. These properties have provided an opportunity for examining the gene regulatory network at the single cell resolution and at a genome-wide scale. This article summarizes when and where each regulatory gene is expressed in early ascidian embryos, and the extent to which the gene regulatory network explains each gene expression.

Report of the Fifth Zebrafish Research Conference of China.

The fifth zebrafish research conference of China was held from October 29 to November 1, 2017, at Wuzhen, China, a beautiful small town that is close to Shanghai. The organizing committee, composed of Tao P. Zhong, Ruilin Zhang, Jie He, Xu Wang, Weijun Pan, Ying Cao, Yao Zu, Qiu Jiang, and Jiulin Du, organized enthusiastically and successfully the 4-day meeting. A total of 646 attendees from 110 academic and corporate institutions, mainly from China and also United States, Germany, Sweden, Singapore, Taiwan, and Japan, presented and discussed their recent research progresses. The packed meeting program included keynote and plenary presentations, concurrent oral talks, and poster sessions. The meeting also invited established investigators to present their research achievements in the fields of development and genetics using other model systems. The conference was a great success and revealed how important the zebrafish has become as a model system for developmental biology, functional genomics, tissue regeneration, and biomedicine.

Single transcript imaging to assay gene expression in wholemount Drosophila melanogaster tissues

Single molecule Fluorescence in situ Hybridization (smFISH) for mRNA provides a powerful quantitative handle on expression from endogenous gene loci. While the method has been widely applied in cells in culture, applications to primary tissue samples remain fewer, and often use involved cryosectioning. Even apart from quantitative access to absolute transcript counts in specific tissue volumes, many other advantages of smFISH can be envisaged in tissue samples. Primary among these are the ability to report on subtle differences in expression among different cell types within a tissue, and the ability to correlate the expression from different target genes. Here, we present a modified method of smFISH applicable on various primary wholemount tissues from the fruit fly Drosophila melanogaster, and show the efficacy of the method in a variety of larval and adult tissue, and embryos. We also combine smFISH in tissue with immunofluorescence to demonstrate the possibility of capturing transcriptional and translational aspects of gene expression in the same tissue. Given the widespread use of Drosophila melanogaster as a model system in Developmental Biology and Genetics, such methods are likely to be of wide interest and could yield rich information about gene expression in tissues from this organism.

66 Unexpected Protein Dynamics During the Oocyte-to-Embryo Transition in Mice: a Mass Spectrometry and RNA Sequencing Tandem Study

The development of a zygote from fertilization through implantation is orchestrated by a series of changes in gene expression at the RNA and protein levels. In mice, the hexagonal-shaped free ribosomes that translate mRNAs into proteins are rare during cleavage and only become abundant at the morula-blastocyst stage. Thus, how well can we understand development by an analysis of transcripts as proxy for the proteins? This question led us to combine mass spectrometry with RNA sequencing, with a long-term aim to illuminate the functional interconnection between transcriptome, proteome, and morphogenetic transitions in mouse embryos. To obtain cellular material in sufficient numbers for a proteomic approach, we recovered B6C3F1 × CD1 fertilized oocytes in vivo after ovarian stimulation, and cultured them in KSOM(aa) medium under 5% CO2 in air. We collected unfertilized oocytes and embryos from 6 pre-implantation developmental stages (pronuclear oocyte, 2-cell embryo, 4-cell embryo, 8-cell embryo, advanced morula, and blastocyst) in triplicates (600 oocytes or embryos per replicate). The protein lysates of these samples were added with equimolar amounts of isotopically labelled F9 embryonal carcinoma cells, resulting in light/heavy (L/H) protein mixtures. These were analysed using LTQ Orbitrap (Thermo Fisher Scientific, Waltham, MA, USA) and Q-Exactive (Thermo Fisher Scientific) instruments to yield L/H ratios for each measured protein, which were compared to transcript levels measured by RNA sequencing using an Illumina HiSEqn 2500 platform (100 oocytes or embryos per replicate; Illumina Inc., San Diego, CA, USA). All statistical analyses were performed in R (https://www.r-project.org/). Collectively, 6976 proteins were detected in at least the F9 cells (precondition for quantifying the L/H ratios in oocytes or embryos). In particular, 4991 proteins were detected in all developmental stages, and 1893 proteins were detected in all replicates. Spearman correlation analysis of each stage relative to unfertilized oocyte revealed distinct proteome and transcriptome developmental profiles. Furthermore, hierarchical clustering of the proteomes identified 2 main clusters (cluster 1: oocyte to 16-cell embryo; cluster 2: blastocyst), which are different from the well-known clusters of the transcriptomes (cluster 1: oocyte to 2-cell embryo; cluster 2: 4-cell embryo to blastocyst). Functional analysis of the genes that are differently expressed across adjacent stages highlighted the developmental roles of DNA damage response and Wnt signalling among the proteins and metabolism and translation among the RNAs. Our data provide new insight into the regulation of the transition from the differentiated oocyte into the embryo, highlighting the different gene identities and different biological processes featured by the proteins that change quantitatively across consecutive developmental stages, compared with mRNAs. The status of the mouse as model system in developmental biology is enriched with a protein dimension, and caution is called for in the use of transcript dynamics as proxy for protein dynamics.

Natural products and morphogenic activity of γ-Proteobacteria associated with the marine hydroid polyp Hydractinia echinata

Illumina 16S rRNA gene sequencing was used to profile the associated bacterial community of the marine hydroid Hydractinia echinata, a long-standing model system in developmental biology. 56 associated bacteria were isolated and evaluated for their antimicrobial activity. Three strains were selected for further in-depth chemical analysis leading to the identification of 17 natural products. Several γ-Proteobacteria were found to induce settlement of the motile larvae, but only six isolates induced the metamorphosis to the primary polyp stage within 24h. Our study paves the way to better understand how bacterial partners contribute to protection, homeostasis and propagation of the hydroid polyp.

Limb development: a paradigm of gene regulation.

The limb is a commonly used model system for developmental biology. Given the need for precise control of complex signalling pathways to achieve proper patterning, the limb is also becoming a model system for gene regulation studies. Recent developments in genomic technologies have enabled the genome-wide identification of regulatory elements that control limb development, yielding insights into the determination of limb morphology and forelimb versus hindlimb identity. The modulation of regulatory interactions - for example, through the modification of regulatory sequences or chromatin architecture - can lead to morphological evolution, acquired regeneration capacity or limb malformations in diverse species, including humans.

Development and epithelial organisation of muscle cells in the sea anemone Nematostella vectensis.

IntroductionNematostella vectensis, a member of the cnidarian class Anthozoa, has been established as a promising model system in developmental biology, but while information about the genetic regulation of embryonic development is rapidly increasing, little is known about the cellular organization of the various cell types in the adult. Here, we studied the anatomy and development of the muscular system of N. vectensis to obtain further insights into the evolution of muscle cells.ResultsThe muscular system of N. vectensis is comprised of five distinct muscle groups, which are differentiated into a tentacle and a body column system. Both systems house longitudinal as well as circular portions. With the exception of the ectodermal tentacle longitudinal muscle, all muscle groups are of endodermal origin. The shape and epithelial organization of muscle cells vary considerably between different muscle groups. Ring muscle cells are formed as epitheliomuscular cells in which the myofilaments are housed in the basal part of the cell, while the apical part is connected to neighboring cells by apical cell-cell junctions. In the longitudinal muscles of the column, the muscular part at the basal side is connected to the apical part by a long and narrow cytoplasmic bridge. The organization of these cells, however, remains epitheliomuscular. A third type of muscle cell is represented in the longitudinal muscle of the tentacle. Using transgenic animals we show that the apical cell-cell junctions are lost during differentiation, resulting in a detachment of the muscle cells to a basiepithelial position. These muscle cells are still located within the epithelium and outside of the basal matrix, therefore constituting basiepithelial myocytes. We demonstrate that all muscle cells, including the longitudinal basiepithelial muscle cells of the tentacle, initially differentiate from regular epithelial cells before they alter their epithelial organisation.ConclusionsA wide range of different muscle cell morphologies can already be found in a single animal. This suggests how a transition from an epithelially organized muscle system to a mesenchymal could have occurred. Our study on N. vectensis provides new insights into the organisation of a muscle system in a non-bilaterian organism.

Assembly of Imaging Chambers and High-Resolution Imaging of Early Chick Embryos

The chick embryo is a classical model system for developmental biology. Its flat disk morphology exemplifies the amniote embryos from reptiles, birds, and most mammals (including humans). It is also particularly amenable to manipulation and culture both in vitro and in ovo. As a consequence, studies with this system have been important for promoting our understanding of cell and tissue movements, lineages, inductive processes, and cell fate decisions. In recent years, imaging techniques have been devised that allow these questions to be studied at the cellular level at late neurulation and segmentation stages. Modern improvements to imaging techniques now allow direct visualization of molecular interactions and cellular events and are likely to be instrumental in linking these processes to whole tissue and embryo morphogenesis. Here, we describe a method for high-resolution (confocal or multiphoton) time-lapse imaging of chick embryos at stages spanning pregastrulation to early neurulation. We give detailed instructions for assembling the specialized imaging chambers required for this procedure.

Chick Embryo Culture and Electroporation

Important events in embryonic development such as gastrulation, neurulation, and cranial neural crest development occur in ectodermal tissues during vertebrate embryonic development. Although the chicken embryo is a well-established model system in developmental biology, problems of accessibility of the ectoderm for experimental manipulation and an inability to generate gene knockouts previously impeded studies of gene regulation and key processes during chicken gastrulation and neurulation. The technique of in ovo electroporation permits genetic manipulation and provides a powerful animal model. However, the problem of accessibility to the ectoderm in ovo requires an ex ovo whole-embryo culture approach combined with electroporation. This unit provides convenient and reproducible whole-embryo ex ovo culture and electroporation protocols. These chicken embryo culture protocols can be used not only for gene regulatory experiments, but also for time-lapse imaging of the dynamics of early vertebrate development.

The Genome of the Western Clawed Frog Xenopus tropicalis

The western clawed frog Xenopus tropicalis is an important model for vertebrate development that combines experimental advantages of the African clawed frog Xenopus laevis with more tractable genetics. Here we present a draft genome sequence assembly of X. tropicalis. This genome encodes more than 20,000 protein-coding genes, including orthologs of at least 1700 human disease genes. Over 1 million expressed sequence tags validated the annotation. More than one-third of the genome consists of transposable elements, with unusually prevalent DNA transposons. Like that of other tetrapods, the genome of X. tropicalis contains gene deserts enriched for conserved noncoding elements. The genome exhibits substantial shared synteny with human and chicken over major parts of large chromosomes, broken by lineage-specific chromosome fusions and fissions, mainly in the mammalian lineage.

Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis

The starlet sea anemone, Nematostella vectensis, is a basal metazoan organism that has recently emerged as an important model system in developmental biology and evolutionary genomics. StellaBase, the Nematostella Genomics Database (http://stellabase.org), was developed in 2005 as a resource to support the Nematostella research community. Recently, it has become apparent that Nematostella may be a particularly useful system for studying (i) microevolutionary variation in natural populations, and (ii) the functional evolution of human disease genes. We have developed two new databases that will foster such studies: StellaBase Disease (http://stellabase.org/disease) is a relational database that houses 155 904 invertebrate homologous isoforms of human disease genes from four leading genomic model systems (fly, worm, yeast and Nematostella), including 14 874 predicted genes from the sea anemone itself. StellaBase SNP (http://stellabase.org/SNP) is a relational database that describes the location and underlying type of mutation for 20 063 single nucleotide polymorphisms.

Embryon d'oursin et séquençage du génome de l'espèce S. purpuratus : quels apports à l'étude du cycle cellulaire ?

Sea urchin is a classical research model system in developmental biology; moreover, the external fertilization and growth of embryos, their rapid division cycle, their transparency and the accessibility of these embryos to molecular visualization methods, made them good specimens to analyze the regulatory mechanisms of cell division. These features as well as the phylogenetic position of sea urchin, close to vertebrates but in an outgroup within the deuterostomes, led scientists working on this model to sequence the genome of the species S. purpuratus. The genome contains a full repertoire of cell cycle control genes. A comparison of this toolkit with those from vertebrates, nematodes, drosophila, as well as tunicates, provides new insight into the evolution of cell cycle control. While some gene subtypes have undergone lineage-specific expansions in vertebrates (i.e. cyclins, mitotic kinases,...), others seem to be lost in vertebrates, for instance the novel cyclin B identified in S. purpuratus. On the other hand, some genes which were previously thought to be vertebrate innovations, are also found in sea urchins (i.e. MCM9). To note is also the absence of cell cycle inhibitors of the INK type, which are apparently confined to vertebrates. The uncovered genomic repertoire of cell-cycle regulators will thus provide molecular tools that should further enhance future research on cell cycle control and developmental regulation in this model.

Aggression and vasotocin are associated with dominant–subordinate relationships in zebrafish

Agonistic interactions are present throughout the animal kingdom as well as in humans. In this report, we present a model system to study neurological correlates of dominant–subordinate relationships. Zebrafish, Danio rerio, has been used as a model system for developmental biology for decades. We propose here that it is also an excellent model for studying social behavior. Adult male zebrafish were separated for 5 days and then pairs were formed and allowed to interact for 5 days. Under these conditions, aggression is prevalent and dominant–subordinate relationships are quickly established. Dominant behavior is characterized by a repeated pattern of chasing and biting, whereas subordinates engage in retreats. By day 5, the dominant–subordinate relationship was firmly established and there were differences in behavior over time. Chases, bites and retreats were all less frequent on day 5 of the social interaction than on day 1. Arginine vasotocin is the teleostean homologue of arginine vasopressin, a neuropeptide whose expression has been linked to aggression and social position in mammals. Immunohistochemistry indicated differences in vasotocin staining between dominant and subordinate individuals. Dominant individuals express vasotocin in one to three pairs of large cells in the magnocellular preoptic area whereas subordinate individuals express vasotocin in 7–11 pairs of small cells in the parvocellular preoptic area. These results suggest that the vasotocinergic system may play a role in shaping dominant–subordinate relationships and agonistic behavior in this model organism.

Phylogenetic relationships and historical biogeography of tribes and genera in the subfamily Nymphalinae (Lepidoptera: Nymphalidae)

We infer for the first time the phylogenetic relationships of genera and tribes in the ecologically and evolutionarily well-studied subfamily Nymphalinae using DNA sequence data from three genes: 1450 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 1077 bp of elongation factor 1-alpha (EF1-α) and 400–403 bp of wingless (both in the nuclear genome). We explore the influence of each gene region on the support given to each node of the most parsimonious tree derived from a combined analysis of all three genes using Partitioned Bremer Support. We also explore the influence of assuming equal weights for all characters in the combined analysis by investigating the stability of clades to different transition/transversion weighting schemes. We find many strongly supported and stable clades in the Nymphalinae. We are also able to identify ‘rogue’ taxa whose positions are weakly supported (the different gene regions are in conflict with each other) and unstable. Our main conclusions are: (1) the tribe Coeini as currently constituted is untenable, and Smyrna, Colobura and Tigridia are part of Nymphalini; (2) ‘Kallimini’ is paraphyletic with regard to Melitaeini and should be split into three tribes: Kallimini s.s., Junoniini and Victorinini; (3) Junoniini, Victorinini, Melitaeini and the newly circumscribed Nymphalini are strongly supported monophyletic groups, and (4) Precis and Junonia are not synonymous or even sister groups. The species Junonia coenia, a model system in developmental biology, clearly belongs in the genus Junonia. A dispersal-vicariance analysis suggests that dispersal has had a major effect on the distributions of extant species, and three biotic regions are identified as being centres of diversification of three major clades: the Palaearctic for the Nymphalis-group, the Afrotropics for Junoniini and the Nearctic for Melitaeini.

The circuitry of a master switch: Myod and the regulation of skeletal muscle gene transcription

The expression of Myod is sufficient to convert a fibroblast to a skeletal muscle cell, and, as such, is a model system in developmental biology for studying how a single initiating event can orchestrate a highly complex and predictable response. Recent findings indicate that Myod functions in an instructive chromatin context and directly regulates genes that are expressed throughout the myogenic program, achieving promoter-specific regulation of its own binding and activity through a feed-forward mechanism. These studies are beginning to merge our understanding of how lineage-specific information is encoded in chromatin with how master regulatory factors drive programs of cell differentiation.

The Chick: A Great Model System Becomes Even Greater

The chick embryo has a long and distinguished history as a major model system in developmental biology and has also contributed major concepts to immunology, genetics, virology, cancer, and cell biology. Now, it has become even more powerful thanks to several new technologies: in vivo electroporation (allowing gain- and loss-of-function in vivo in a time- and space-controlled way), embryonic stem (ES) cells, novel methods for transgenesis, and the completion of the first draft of the sequence of its genome along with many new resources to access this information. In combination with classical techniques such as grafting and lineage tracing, the chicken is now one of the most versatile experimental systems available.

Development of the nervus terminalis: Origin and migration

The origin of the nervus terminalis is one of the least well understood developmental events involved in generating the cranial ganglia of the forebrain in vertebrate animals. This cranial nerve forms at the formidable interface of the anteriormost limits of migrating cranial neural crest cells, the terminal end of the neural tube and the differentiating olfactory and adenohypophyseal placodes. The complex cellular interactions that give rise to the various structures associated with the sensory placode (olfactory) and endocrine placode (adenohypophysis) surround and engulf this enigmatic cranial nerve. The tortured history of nervus terminalis development (see von Bartheld, this issue, pages 13-24) reflects the lack of consensus on the origin (or origins), as well as the experimental difficulties in uncovering the origin, of the nervus terminalis. Recent technical advances have allowed us to make headway in understanding the origin(s) of this nerve. The emergence of the externally fertilized zebrafish embryo as a model system for developmental biology and genetics has shed new light on this century-old problem. Coupled with new developmental models are techniques that allow us to trace lineage, visualize gene expression, and genetically ablate cells, adding to our experimental tools with which to follow up on studies provided by our scientific predecessors. Through these techniques, a picture is emerging in which the origin of at least a subset of the nervus terminalis cells lies in the cranial neural crest. In this review, the data surrounding this finding will be discussed in light of recent findings on neural crest and placode origins.

A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing

In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21,121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization.