Genetic network of the eye in Platyhelminthes: expression and functional analysis of some players during planarian regeneration

Positive selection in cilia-related genes may facilitate deep-sea adaptation of Thermocollonia jamsteci

Deep-sea hydrothermal vents are characterized by high hydrostatic pressure, hypoxia, darkness and toxic substances. However, how organisms adapt to such extreme marine ecosystems remain poorly understood. We hypothesize that adaptive evolution plays an essential role in generating novelty for evolutionary adaptation to the deep-sea environment because adaptive evolution has been found to be critical for species origin and evolution. In this project, the chromosome-level genome of the deep-sea hydrothermal vent gastropod T. jamsteci was constructed for the first time to examine molecular mechanisms of its adaptation to the deep-sea environment. The genome size was large (2.54 Gb), ranking at the top of all species in the Vetigastropoda subclass, driven primarily by the bursts of transposable elements (TEs). The transposition of TEs may also trigger chromosomal changes including both inter-chromosomal fusions and intra-chromosomal activities involving chromosome inversions, rearrangements and fusions, as revealed by comparing the genomes of T. jamsteci and its closely related shallow-sea species Gibbula magus. Innovative changes including the expansion of the ABC transporter gene family that may facilitate detoxification, duplication of genes related to endocytosis, immunity, apoptosis, and anti-apoptotic domains that may help T. jamsteci fight against microbial pathogens, were identified. Furthermore, comparative analysis identified positive selection signals in a large number of genes including the hypoxia up-regulated protein 1, which is a chaperone that may promote adaptation of the T. jamsteci to hypoxic deepsea environments, hox2, Rx2, Pax6 and cilia-related genes BBS1, BBS2, BBS9 and RFX4. Notably, because of the critical importance of cilia and IFT in development, positive selection in cilia-related genes may play a critical role in facilitating T. jamsteci to adapt to the high-pressure deep-sea ecosystem. Results from this study thus revealed important molecular clues that may facilitate further research on the adaptation of molluscs to deep-sea hydrothermal vents.

Schmidtea mediterranea as a Model Organism to Study the Molecular Background of Human Motile Ciliopathies

Cilia and flagella are evolutionarily conserved organelles that form protrusions on the surface of many growth-arrested or differentiated eukaryotic cells. Due to the structural and functional differences, cilia can be roughly classified as motile and non-motile (primary). Genetically determined dysfunction of motile cilia is the basis of primary ciliary dyskinesia (PCD), a heterogeneous ciliopathy affecting respiratory airways, fertility, and laterality. In the face of the still incomplete knowledge of PCD genetics and phenotype-genotype relations in PCD and the spectrum of PCD-like diseases, a continuous search for new causative genes is required. The use of model organisms has been a great part of the advances in understanding molecular mechanisms and the genetic basis of human diseases; the PCD spectrum is not different in this respect. The planarian model (Schmidtea mediterranea) has been intensely used to study regeneration processes, and-in the context of cilia-their evolution, assembly, and role in cell signaling. However, relatively little attention has been paid to the use of this simple and accessible model for studying the genetics of PCD and related diseases. The recent rapid development of the available planarian databases with detailed genomic and functional annotations prompted us to review the potential of the S. mediterranea model for studying human motile ciliopathies.

Planarian nociception: Lessons from a scrunching flatworm

In addition to being studied for their exceptional regeneration abilities, planarians (i.e., flatworms) have also been extensively used in the context of pharmacological experiments during the past century. Many researchers used planarians as a model system for the study of drug abuse because they display high similarities with the nervous system of vertebrates at cellular and molecular levels (e.g., neuronal morphology, neurotransmitter ligands, and receptor function). This research field recently led to the discovery of causal relationships between the expression of Transient Receptor Potential ion channels in planarians and their behavioral responses to noxious stimuli such as heat, cold or pharmacological analogs such as TRP agonists, among others. It has also been shown that some antinociceptive drugs modulate these behaviors. However, among the few authors that tried to implement a full behavior analysis, none reached a consensual use of the terms used to describe planarian gaits yet, nor did they establish a comprehensive description of a potential planarian nociceptive system. The aim of this review is therefore to aggregate the ancient and the most recent evidence for a true nociceptive behavior in planarians. It also highlights the convenience and relevance of this invertebrate model for nociceptive tests and suggests further lines of research. In regards to past pharmacological studies, this review finally discusses the opportunities given by the model to extensively screen for novel antinociceptive drugs.

FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle star Amphiura filiformis

Regeneration as an adult developmental process is in many aspects similar to embryonic development. Although many studies point out similarities and differences, no large-scale, direct and functional comparative analyses between development and regeneration of a specific cell type or structure in one animal exist. Here, we use the brittle star Amphiura filiformis to characterise the role of the FGF signalling pathway during skeletal development in embryos and arm regeneration. In both processes, we find ligands expressed in ectodermal cells that flank underlying skeletal mesenchymal cells, which express the receptors. Perturbation of FGF signalling showed inhibited skeleton formation in both embryogenesis and regeneration, without affecting other key developmental processes. Differential transcriptome analysis finds mostly differentiation genes rather than transcription factors to be downregulated in both contexts. Moreover, comparative gene analysis allowed us to discover brittle star-specific differentiation genes. In conclusion, our results show that the FGF pathway is crucial for skeletogenesis in the brittle star, as in other deuterostomes, and provide evidence for the re-deployment of a developmental gene regulatory module during regeneration.

A Novel Taxon of Monosegmented Double-Stranded RNA Viruses Endemic to Triclad Flatworms

Freshwater planarians, flatworms from order Tricladida, are experimental models of stem cell biology and tissue regeneration. An aspect of their biology that remains less well studied is their relationship with viruses that may infect them. In this study, we identified a taxon of monosegmented double-stranded RNA (dsRNA) viruses in five planarian species, including the well-characterized model Schmidtea mediterranea Sequences for the S. mediterranea virus (abbreviated SmedTV for S. mediterranea tricladivirus) were found in public transcriptome data from multiple institutions, indicating that SmedTV is prevalent in S. mediterranea lab colonies, though without causing evident disease. The presence of SmedTV in discrete cells was shown through in situ hybridization methods for detecting the viral RNA. SmedTV-staining cells were found to be concentrated in neural structures (eyes and brain) but were also scattered in other worm tissues as well. In contrast, few SmedTV-staining cells were seen in stem cell compartments (also consistent with RNA sequencing data) or early blastema tissue. RNA interference (RNAi) targeted to the SmedTV sequence led to apparent cure of infection, though effects on worm health or behavior were not observed. Efforts to transmit SmedTV horizontally through microinjection were unsuccessful. Based on these findings, we conclude that SmedTV infects S. mediterranea in a persistent manner and undergoes vertical transmission to progeny worms during serial passage in lab colonies. The utility of S. mediterranea as a regeneration model, coupled with the apparent capacity of SmedTV to evade normal host immune/RNAi defenses under standard conditions, argues that further studies are warranted to explore this newly recognized virus-host system.IMPORTANCE Planarians are freshwater flatworms, related more distantly to tapeworms and flukes, and have been developed as models to study the molecular mechanisms of stem cell biology and tissue regeneration. These worms live in aquatic environments, where they are likely to encounter a variety of viruses, bacteria, and eukaryotic organisms with pathogenic potential. How the planarian immune system has evolved to cope with these potential pathogens is not well understood, and only two types of planarian viruses have been described to date. Here, we report discovery and inaugural studies of a novel taxon of dsRNA viruses in five different planarian species. The virus in the best-characterized model species, Schmidtea mediterranea, appears to persist long term in that host while avoiding endogenous antiviral or RNAi mechanisms. The S. mediterranea virus-host system thus seems to offer opportunity for gaining new insights into host defenses and their evolution in an important lab model.

Cognitive Stimulation Induces Differential Gene Expression in Octopus vulgaris: The Key Role of Protocadherins

Octopuses are unique invertebrates, with sophisticated and flexible behaviors controlled by a high degree of brain plasticity, learning, and memory. Moreover, in Octopus vulgaris, it has been demonstrated that animals housed in an enriched environment show adult neurogenesis in specific brain areas. Firstly, we evaluated the optimal acclimatization period needed for an O. vulgaris before starting a cognitive stimulation experiment. Subsequently, we analyzed differential gene expression in specific brain areas in adult animals kept in tested (enriched environment), wild (naturally enriched environment), and control conditions (unenriched environment). We selected and sequenced three protocadherin genes (PCDHs) involved in the development and maintenance of the nervous system; three Pax genes that control cell specification and tissue differentiation; the Elav gene, an earliest marker for neural cells; and the Zic1 gene, involved in early neural formation in the brain. In this paper, we evaluated gene expression levels in O. vulgaris under different cognitive stimulations. Our data shows that Oct-PCDHs genes are upregulated in the learning and lower motor centers in the brain of both tested and wild animals (higher in the latter). Combining these results with our previous studies on O. vulgaris neurogenesis, we proposed that PCDH genes may be involved in adult neurogenesis processes, and related with their cognitive abilities.

The Pax gene family: Highlights from cephalopods

Pax genes play important roles in Metazoan development. Their evolution has been extensively studied but Lophotrochozoa are usually omitted. We addressed the question of Pax paralog diversity in Lophotrochozoa by a thorough review of available databases. The existence of six Pax families (Pax1/9, Pax2/5/8, Pax3/7, Pax4/6, Paxβ, PoxNeuro) was confirmed and the lophotrochozoan Paxβ subfamily was further characterized. Contrary to the pattern reported in chordates, the Pax2/5/8 family is devoid of homeodomain in Lophotrochozoa. Expression patterns of the three main pax classes (pax2/5/8, pax3/7, pax4/6) during Sepia officinalis development showed that Pax roles taken as ancestral and common in metazoans are modified in S. officinalis, most likely due to either the morphological specificities of cephalopods or to their direct development. Some expected expression patterns were missing (e.g. pax6 in the developing retina), and some expressions in unexpected tissues have been found (e.g. pax2/5/8 in dermal tissue and in gills). This study underlines the diversity and functional plasticity of Pax genes and illustrates the difficulty of using probable gene homology as strict indicator of homology between biological structures.

Temporal regulation of planarian eye regeneration

While tissue regeneration is typically studied using standard injury models, in nature injuries vary greatly in the amount and location of tissues lost. Planarians have the unique ability to regenerate from many different injuries (including from tiny fragments with no brain), allowing us to study the effects of different injuries on regeneration timelines. We followed the timing of regeneration for one organ, the eye, after multiple injury types that involved tissue loss (single‐ and double‐eye ablation, and decapitation) in Schmidtea mediterranea. Our data reveal that the timing of regeneration remained constant despite changing injury parameters. Optic tissue regrowth, nerve re‐innervation, and functional recovery were similar between injury types (even when the animal was simultaneously regrowing its brain). Changes in metabolic rate (i.e., starving vs. fed regenerates) also had no effect on regeneration timelines. In addition, our data suggest there may exist a role for optic nerve degeneration following eye ablation. Our results suggest that the temporal regulation of planarian eye regeneration is tightly controlled and resistant to variations in injury type.

Differential expression of retinal determination genes in the principal and secondary eyes of Cupiennius salei Keyserling (1877)

BACKGROUND

Transcription factors that determine retinal development seem to be conserved in different phyla throughout the animal kingdom. In most representatives, however, only a few of the involved transcription factors have been sampled and many animal groups remain understudied. In order to fill in the gaps for the chelicerate group of arthropods, we tested the expression pattern of the candidate genes involved in the eye development in the embryo of the wandering spider Cupiennius salei. One main objective was to profile the molecular development of the eyes and to search for possible variation among eye subtype differentiation. A second aim was to form a basis for comparative studies in order to elucidate evolutionary pathways in eye development.

RESULTS

We screened the spider embryonic transcriptome for retina determination gene candidates and discovered that all except one of the retinal determination genes have been duplicated. Gene expression analysis shows that the two orthologs of all the genes have different expression patterns. The genes are mainly expressed in the developing optic neuropiles of the eyes (lateral furrow, mushroom body, arcuate body) in earlier stages of development (160 to 220 h after egg laying). Later in development (180 to 280 h after egg laying), there is differential expression of the genes in disparate eye vesicles; for example, Cs-otxa is expressed only in posterior-lateral eye vesicles, Cs-otxb, Cs-six1a, and Cs-six3b in all three secondary eye vesicles, Cs-pax6a only in principal eye vesicles, Cs-six1b in posterior-median, and posterior-lateral eye vesicles, and Cs-six3a in lateral and principal eye vesicles.

CONCLUSIONS

Principle eye development shows pax6a (ey) expression, suggesting pax6 dependence, although secondary eyes develop independently of pax6 genes and show differential expression of several retinal determination genes. Comparing this with the other arthropods suggests that pax6-dependent median eye development is a ground pattern of eye development in this group and that the ocelli of insects, the median eyes of chelicerates, and nauplius eyes can be homologised. The expression pattern of the investigated genes makes it possible to distinguish between secondary eyes and principal eyes. Differences of gene expression among the different lateral eyes indicate disparate function combined with genetic drift.

Novel monoclonal antibodies to study tissue regeneration in planarians

Background

Planarians are an attractive model organism for studying stem cell-based regeneration due to their ability to replace all of their tissues from a population of adult stem cells. The molecular toolkit for planarian studies currently includes the ability to study gene function using RNA interference (RNAi) and observe gene expression via in situ hybridizations. However, there are few antibodies available to visualize protein expression, which would greatly enhance analysis of RNAi experiments as well as allow further characterization of planarian cell populations using immunocytochemistry and other immunological techniques. Thus, additional, easy-to-use, and widely available monoclonal antibodies would be advantageous to study regeneration in planarians.

Results

We have created seven monoclonal antibodies by inoculating mice with formaldehyde-fixed cells isolated from dissociated 3-day regeneration blastemas. These monoclonal antibodies can be used to label muscle fibers, axonal projections in the central and peripheral nervous systems, two populations of intestinal cells, ciliated cells, a subset of neoblast progeny, and discrete cells within the central nervous system as well as the regeneration blastema. We have tested these antibodies using eight variations of a formaldehyde-based fixation protocol and determined reliable protocols for immunolabeling whole planarians with each antibody. We found that labeling efficiency for each antibody varies greatly depending on the addition or removal of tissue processing steps that are used for in situ hybridization or immunolabeling techniques. Our experiments show that a subset of the antibodies can be used alongside markers commonly used in planarian research, including anti-SYNAPSIN and anti-SMEDWI, or following whole-mount in situ hybridization experiments.

Conclusions

The monoclonal antibodies described in this paper will be a valuable resource for planarian research. These antibodies have the potential to be used to better understand planarian biology and to characterize phenotypes following RNAi experiments. In addition, we present alterations to fixation protocols and demonstrate how these changes can increase the labeling efficiencies of antibodies used to stain whole planarians.

Electronic supplementary material

The online version of this article (doi:10.1186/s12861-014-0050-9) contains supplementary material, which is available to authorized users.

A molecular wound response program associated with regeneration initiation in planarians

Planarians are capable of regenerating any missing body part and present an attractive system for molecular investigation of regeneration initiation. The gene activation program that occurs at planarian wounds to coordinate regenerative responses remains unknown. We identified a large set of wound-induced genes during regeneration initiation in planarians. Two waves of wound-induced gene expression occurred in differentiated tissues. The first wave includes conserved immediate early genes. Many second-wave genes encode conserved patterning factors required for proper regeneration. Genes of both classes were generally induced by wounding, indicating that a common initial gene expression program is triggered regardless of missing tissue identity. Planarian regeneration uses a population of regenerative cells (neoblasts), including pluripotent stem cells. A class of wound-induced genes was activated directly within neoblasts, including the Runx transcription factor-encoding runt-1 gene. runt-1 was required for specifying different cell types during regeneration, promoting heterogeneity in neoblasts near wounds. Wound-induced gene expression in neoblasts, including that of runt-1, required SRF (serum response factor) and sos-1. Taken together, these data connect wound sensation to the activation of specific cell type regeneration programs in neoblasts. Most planarian wound-induced genes are conserved across metazoans, and identified genes and mechanisms should be important broadly for understanding wound signaling and regeneration initiation.

The cell biology of schistosomes: a window on the evolution of the early metazoa

This review of schistosome cell biology has a dual purpose; its intent is to alert two separate research communities to the activities of the other. Schistosomes are by far and away the best-characterised platyhelminths, due to their medical and economic importance, but seem to be almost totally ignored by researchers on the free-living lower metazoans. Equally, in their enthusiasm for the parasitic way of life, schistosome researchers seldom pay attention to the work on free-living animals that could inform their molecular investigations. The publication of transcriptomes and/or genomes for Schistosoma mansoni and Schistosoma japonicum, the sponge Archimedon, the cnidarians Nematostella and Hydra and the planarian Schmidtea provide the raw material for comparisons. Apart from interrogation of the databases for molecular similarities, there have been differences in technical approach to these lower metazoans; widespread application of whole mount in situ hybridisation to Schmidtea contrasts with the application of targeted proteomics to schistosomes. Using schistosome cell biology as the template, the key topics of cell adhesion, development, signalling pathways, nerve and muscle, and epithelia, are reviewed, where possible interspersing comparisons with the sponge, cnidarian and planarian data. The biggest jump in the evolution of cellular capabilities appears to be in the transition from a diploblast to triploblast level of organisation associated with development of a mobile and plastic body form.

OTX2 and CRX rescue overlapping and photoreceptor-specific functions in the Drosophila eye

BACKGROUND

Otd-related transcription factors are evolutionarily conserved to control anterior patterning and neurogenesis. In humans, two such factors, OTX2 and CRX, are expressed in all photoreceptors from early specification through adulthood and associate with several photoreceptor-specific retinopathies. It is not well understood how these factors function independently vs. redundantly, or how specific mutations lead to different disease outcomes. It is also unclear how OTX1 and OTX2 functionally overlap during other aspects of neurogenesis and ocular development. Drosophila encodes a single Otd factor that has multiple functions during eye development. Using the Drosophila eye as a model, we tested the ability of the human OTX1, OTX2, and CRX genes, as well as several disease-associated CRX alleles, to rescue the different functions of Otd.

RESULTS

Our results indicate the following: OTX2 and CRX display overlapping, yet distinct subfunctions of Otd during photoreceptor differentiation; CRX disease alleles can be functionally distinguished based on their rescue properties; and all three factors are able to rescue rhabdomeric photoreceptor morphogenesis.

CONCLUSIONS

Our findings have important implications for understanding how Otx proteins have subfunctionalized during evolution, and cement Drosophila as an effective tool to unravel the molecular bases of photoreceptor pathogenesis.

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

Background

Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system.

Results

In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function.

Conclusions

We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.

Melanopsin-mediated light-sensing in amphioxus: a glimpse of the microvillar photoreceptor lineage within the deuterostomia

The two fundamental lineages of photoreceptor cells, microvillar and ciliary, were long thought to be a prerogative of invertebrate and vertebrate organisms, respectively. However evidence of their ancient origin, preceding the divergence of these two branches of metazoa, suggests instead that they should be ubiquitously distributed. Melanopsin-expressing 'circadian' light receptors may represent the remnants of the microvillar photo- receptors amongst vertebrates, but they lack the characteristic architecture of this lineage, and much remains to be clarified about their signaling mechanisms. Hesse and Joseph cells of the neuronal tube of amphioxus (Branchiostoma fl.)-the most basal chordate extant-turn out to be depolarizing primary microvillar photoreceptors, that generate a melanopsin-initiated, PLC-dependent response to light, mobilizing internal Ca and increasing a membrane conductance selective to Na and Ca ions. As such, they represent a canonical instance of invertebrate-like visual cells in the chordate phylum.

Eye evolution: common use and independent recruitment of genetic components

Animal eyes can vary in complexity ranging from a single photoreceptor cell shaded by a pigment cell to elaborate arrays of these basic units, which allow image formation in compound eyes of insects or camera-type eyes of vertebrates. The evolution of the eye requires involvement of several distinct components-photoreceptors, screening pigment and genes orchestrating their proper temporal and spatial organization. Analysis of particular genetic and biochemical components shows that many evolutionary processes have participated in eye evolution. Multiple examples of co-option of crystallins, Galpha protein subunits and screening pigments contrast with the conserved role of opsins and a set of transcription factors governing eye development in distantly related animal phyla. The direct regulation of essential photoreceptor genes by these factors suggests that this regulatory relationship might have been already established in the ancestral photoreceptor cell.

The evolution of cell types in animals: emerging principles from molecular studies

Cell types are fundamental units of multicellular life but their evolution is obscure. How did the first cell types emerge and become distinct in animal evolution? What were the sets of cell types that existed at important evolutionary nodes that represent eumetazoan or bilaterian ancestors? How did these ancient cell types diversify further during the evolution of organ systems in the descending evolutionary lines? The recent advent of cell type molecular fingerprinting has yielded initial insights into the evolutionary interrelationships of cell types between remote animal phyla and has allowed us to define some first principles of cell type diversification in animal evolution.

The planarian nanos-like gene Smednos is expressed in germline and eye precursor cells during development and regeneration

Planarians are highly regenerative organisms with the ability to remake all their cell types, including the germ cells. The germ cells have been suggested to arise from totipotent neoblasts through epigenetic mechanisms. Nanos is a zinc-finger protein with a widely conserved role in the maintenance of germ cell identity. In this work, we describe the expression of a planarian nanos-like gene Smednos in two kinds of precursor cells namely, primordial germ cells and eye precursor cells, during both development and regeneration of the planarian Schmidtea mediterranea. In sexual planarians, Smednos is expressed in presumptive male primordial germ cells of embryos from stage 8 of embryogenesis and throughout development of the male gonads and in the female primordial germ cells of the ovary. Thus, upon hatching, juvenile planarians do possess primordial germ cells. In the asexual strain, Smednos is expressed in presumptive male and female primordial germ cells. During regeneration, Smednos expression is maintained in the primordial germ cells, and new clusters of Smednos-positive cells appear in the regenerated tissue. Remarkably, during the final stages of development (stage 8 of embryogenesis) and during regeneration of the planarian eye, Smednos is expressed in cells surrounding the differentiating eye cells, possibly corresponding to eye precursor cells. Our results suggest that similar genetic mechanisms might be used to control the differentiation of precursor cells during development and regeneration in planarians.

Ancient mechanisms of visual sense organ development based on comparison of the gene networks controlling larval eye, ocellus, and compound eye specification in Drosophila

Key mechanisms of development are strongly constrained, and hence often shared in the formation of highly diversified homologous organs. This diagnostic is applied to uncovering ancient gene activities in the control of visual sense organ development by comparing the gene networks, which regulate larval eye, ocellus and compound eye specification in Drosophila. The comparison reveals a suite of shared aspects that are likely to predate the diversification of arthropod visual sense organs and, consistent with this, have notable similarities in the developing vertebrate visual system: (I) Pax-6 genes participate in the patterning of primordia of complex visual organs. (II) Primordium determination and differentiation depends on formation of a transcription factor complex that contains the products of the selector genes Eyes absent and Sine oculis. (III) The TGF-beta signaling factor Decapentaplegic exerts transcriptional activation of eyes absent and sine oculis. (IV) Canonical Wnt signaling contributes to primordium patterning by repression of eyes absent and sine oculis. (V) Initiation of determination and differentiation is controlled by hedgehog signaling. (VI) Egfr signaling drives retinal cell fate specification. (VII) The proneural transcription factor atonal regulates photoreceptor specification. (VII) The zinc finger gene glass regulates photoreceptor specification and differentiation.

The ascidian homolog of the vertebrate homeobox gene Rx is essential for ocellus development and function

The tadpole larvae prosencephalon of the ascidian Ciona intestinalis contains a single large ventricle, along the inner walls of which lie two sensory organs: the otolith (a gravity-sensing organ) and the ocellus (a photo-sensing organ composed of a single cup-shaped pigment cell, about 20 photoreceptor cells, and three lens cells). Comparison has been drawn between the morphology and physiology of photoreceptor cells in the ascidian ocellus and the vertebrate eye. The development of vertebrate and invertebrate eyes requires the activity of several conserved genes and it is regulated by precise expression patterns and cell fate decisions common to several species. We have isolated a Ciona homeobox gene (Ci-Rx) that belongs to the paired-like class of homeobox genes. Rx genes have been identified from a variety of organisms and have been demonstrated to have a role in vertebrate eye formation. Ci-Rx is expressed in the anterior neural plate in the middle tailbud stage and subsequently in the larval stage in the sensory vesicle around the ocellus. Loss of Ci-Rx function leads to an ocellus-less phenotype that shows a loss of photosensitive swimming behavior, suggesting the important role played by Ci-Rx in basal chordate photoreceptor cell differentiation and ocellus formation. Furthermore, studies on Ci-Rx regulatory elements electroporated into Ciona embryos using LacZ or GFP as reporter genes indicate the presence of Ci-Rx in pigment cells, photoreceptors, and neurons surrounding the sensory vesicle. In Ci-Rx knocked-down larvae, neither basal swimming activity nor shadow responses develop. Thus, Rx has a role not only in pigment cells and photoreceptor formation but also in the correct development of the neuronal circuit that controls larval photosensitivity and swimming behavior. The results suggest that a Ci-Rx "retinal" territory exists, which consists of pigment cells, photoreceptors, and neurons involved in transducing the photoreceptor signals.

The power of regeneration and the stem-cell kingdom: freshwater planarians (Platyhelminthes)

The great powers of regeneration shown by freshwater planarians, capable of regenerating a complete organism from any tiny body fragment, have attracted the interest of scientists throughout history. In 1814, Dalyell concluded that planarians could "almost be called immortal under the edge of the knife". Equally impressive is the developmental plasticity of these platyhelminthes, including continuous growth and fission (asexual reproduction) in well-fed organisms, and shrinkage (degrowth) during prolonged starvation. The source of their morphological plasticity and regenerative capability is a stable population of totipotent stem cells--"neoblasts"; this is the only cell type in the adult that has mitotic activity and differentiates into all cell types. This cellular feature is unique to planarians in the Bilateria clade. Over the last fifteen years, molecular studies have begun to reveal the role of developmental genes in regeneration, although it would be premature to propose a molecular model for planarian regeneration. Genomic and proteomic data are essential in answering some of the fundamental questions concerning this remarkable morphological plasticity. Such information should also pave the way to understanding the genetic pathways associated with metazoan somatic stem-cell regulation and pattern formation.

Expression of FoxE4 and Rx Visualizes the Timing and Dynamics of Critical Processes Taking Place during Initial Stages of Vertebrate Eye Development

Several transcription factors have a critical function during initial stages of vertebrate eye formation. In this paper, we discuss the role of the Rx subfamily of homeobox-containing genes in retinal development, and the role of the Foxe3 and FoxE4 subfamily of forkhead box-containing genes in lens development. Rx genes are expressed in the initial stages of retinal development and they play a critical role in eye formation. Elimination of Rx function in mice results in lack of eye formation. Abnormal eye development observed in the mouse mutation eyeless (ey1), the medakatemperature-sensitive mutation eyeless (el), and the zebrafish mutation chokh are caused by abnormal regulation or function of Rx genes. In humans, a mutation in Rx leads to anophthalmia. In contrast, Foxe3 and FoxE4 genes are expressed in the lens and they play an essential role in its formation. Mutations in the Foxe3 gene are the cause of the mouse mutation dysgenetic lens (dyl) and in humans, mutation in FOXE3 leads to anterior segment dysgenesis and cataracts. Since Rx and FoxE4 are expressed in the earliest stages of retina and lens development, their expression visualizes the timing and dynamics of the crucial processes that comprise eye formation. In this paper we present a model of eye development based on the expression pattern of these two genes.

The embryonic development of the triclad Schmidtea polychroa

Triclad flatworms are well studied for their regenerative properties, yet little is known about their embryonic development. We here describe the embryonic development of the triclaty 120d Schmidtea polychroa, using histological and immunocytochemical analysis of whole-mount preparations and sections. During early cleavage (stage 1), yolk cells fuse and enclose the zygote into a syncytium. The zygote divides into blastomeres that dissociate and migrate into the syncytium. During stage 2, a subset of blastomeres differentiate into a transient embryonic epidermis that surrounds the yolk syncytium, and an embryonic pharynx. Other blastomeres divide as a scattered population of cells in the syncytium. During stage 3, the embryonic pharynx imbibes external yolk cells and a gastric cavity is formed in the center of the syncytium. The syncytial yolk and the blastomeres contained within it are compressed into a thin peripheral rind. From a location close to the embryonic pharynx, which defines the posterior pole, bilaterally symmetric ventral nerve cord pioneers extend forward. Stage 4 is characterized by massive proliferation of embryonic cells. Large yolk-filled cells lining the syncytium form the gastrodermis. During stage 5 the external syncytial yolk mantle is resorbed and the embryonic cells contained within differentiate into an irregular scaffold of muscle and nerve cells. Epidermal cells differentiate and replace the transient embryonic epidermis. Through stages 6-8, the embryo adopts its worm-like shape, and loosely scattered populations of differentiating cells consolidate into structurally defined organs. Our analysis reveals a picture of S. polychroa embryogenesis that resembles the morphogenetic events underlying regeneration.

The embryonic development of the flatworm Macrostomum sp

Macrostomid flatworms represent a group of basal bilaterians with primitive developmental and morphological characteristics. The species Macrostomum sp., raised under laboratory conditions, has a short generation time of about 2-3 weeks and produces a large number of eggs year round. Using live observation, histology, electron microscopy and immunohistochemistry we have carried out a developmental analysis of Macrostomum sp. Cleavage (stages 1-2) of this species follows a modified spiral pattern and results in a solid embryonic primordium surrounded by an external yolk layer. During stage 3, cells at the anterior and lateral periphery of the embryo evolve into the somatic primordium which gives rise to the body wall and nervous system. Cells in the center form the large yolk-rich gut primordium. During stage 4, the brain primordium and the pharynx primordium appear as symmetric densities anterior-ventrally within the somatic primordium. Organ differentiation commences during stage 5 when the neurons of the brain primordium extend axons that form a central neuropile, and the outer cell layer of the somatic primordium turns into a ciliated epidermal epithelium. Cilia also appear in the lumen of the pharynx primordium, in the protonephridial system and, slightly later, in the lumen of the gut. Ultrastructurally, these differentiating cells show the hallmarks of platyhelminth epithelia, with a pronounced apical assembly of microfilaments (terminal web) inserting at the zonula adherens, and a wide band of septate junctions underneath the zonula. Terminal web and zonula adherens are particularly well observed in the epidermis. During stage 6, the somatic primordium extends around the surface dorsally and ventrally to form a complete body wall. Muscle precursors extend myofilaments that are organized into a highly regular orthogonal network of circular, diagonal and longitudinal fibers. Neurons of the brain primordium differentiate a commissural neuropile that extends a single pair of ventro-lateral nerve trunks (the main longitudinal cords) posteriorly. The primordial pharynx lumen fuses with the ventral epidermis anteriorly and the gut posteriorly, thereby generating a continuous digestive tract. The embryo adopts its final shape during stages 7 and 8, characterized by the morphallactic lengthening of the body into a U-shaped form and the condensation of the nervous system.

Djeyes absent ( Djeya ) controls prototypic planarian eye regeneration by cooperating with the transcription factor Djsix-1

A conserved network of nuclear proteins is crucial to eye formation in both vertebrates and invertebrates. The finding that freshwater planarians can regenerate eyes without the contribution of Pax6 suggests that alternative combinations of regulatory elements may control the morphogenesis of the prototypic planarian eye. To further dissect the molecular events controlling eye regeneration in planarians, we investigated the role of eyes absent (Djeya) and six-1 (Djsix-1) genes in Dugesia japonica. These genes are expressed in both regenerating eyes and in differentiated photoreceptors of intact adults. Through RNAi studies, we show that Djsix-1 and Djeya are both critical for the regeneration of normal eyes in planarians and genetically cooperate in vivo to establish correct eye cell differentiation. We further demonstrate that the genetic interaction is mediated by physical interaction between the evolutionarily conserved domains of these two proteins. These data indicate that planarians use cooperatively Djsix-1 and Djeya for the proper specification of photoreceptors, implicating that the mechanism involving their evolutionarily conserved domains can be very ancient. Finally, both Djsix-1 and Djeya double-stranded RNA are substantially more effective at producing no-eye phenotypes in the second round of regeneration. This is probably due to the significant plasticity of the planarian model system, based on the presence of a stable population of totipotent stem cells, which ensure the rapid cell turnover of all differentiated cell types.

Morphological and Functional Recovery of the Planarian Photosensing System during Head Regeneration

When exposed to light, planarians display a distinctive light avoidance behavior known as negative phototaxis. Such behavior is temporarily suppressed when animals are decapitated, and it is restored once the animals regenerate their heads. Head regeneration and the simple but reproducible phototactic response of planarians provides an opportunity to study the association between neuronal differentiation and the establishment of behavior in a simple, experimentally tractable metazoan. We have devised a phototaxis assay system to analyze light response recovery during head regeneration and determined that light evasion is markedly re-established 5 days after amputation. Immunohistological and in situ hybridization studies indicate that the photoreceptors and optic nerve connections to the brain begin by the fourth day of cephalic regeneration. To experimentally manipulate the light response recovery, we performed gene knockdown analysis using RNA interference (RNAi) on two genes (1020HH and eye53) previously reported to be expressed at 5 days after amputation and in the dorso-medial region of the brain (where the optic nerves project). Although RNAi failed to produce morphological defects in either the brain or the visual neurons, the recovery of the phototactic response normally observed in 5-day regenerates was significantly suppressed. The data suggest that 1020HH and eye53 may be involved in the functional recovery and maintenance of the visual system, and that the phototaxis assay presented here can be used to reliably quantify the negative phototactic behavior of planarians.

Flatworm asexual multiplication implicates stem cells and regeneration

The phenomenon of asexual multiplication is rare in the animal kingdom, but it occurs in all main flatworm taxa. In the present paper, we review data regarding the presence of different forms of asexual multiplication in flatworms and argue that the presence of a population of totipotent or pluripotent stem cells, "neoblasts", is a primitive feature of decisive importance for the developing potential of flatworms. Next we present information on the role of stem cells in fission, head regeneration, and pharynx regeneration of planarians. Furthermore, the tracing of neoblasts in lower flatworms and cestodes is presented, and the results indicating heterogeneity of the neoblast pool are discussed. Finally, the mode by which the neoblasts are stimulated to divide, migrate, and differentiate and the nature of the interactions are discussed. We focus on (i) biogenic amines and neuropeptides, (ii) the role of neuropeptides in the early stage of regeneration, (iii) the evidence for the influences of growth factors and nitric oxide, and (iv) the influence of weak electromagnetic fields. We discuss the pattern in which a gradient system of morphogens and (or) a hierarchical system of inductions is expressed in development.

Transgenic planarian lines obtained by electroporation using transposon-derived vectors and an eye-specific GFP marker

To generate transgenic planarians we used a set of versatile vectors for animal transgenesis based on the promiscuous transposons, mariner, Hermes and piggyBac, and a universal enhanced GFP (EGFP) marker system with three Pax6 dimeric binding sites, the 3xP3-EGFP developed by Berghammer et al. [Berghammer, A. J., Klinger, M. & Wimmer, E. A. (1999) Nature 402, 370-371]. This marker is expressed specifically in the eyes of various arthropod taxa. Upon microinjection into the parenchyma of adult planarians and subsequent electroporation, these vectors transpose efficiently into the planarian genome. One of the cell types transformed are the totipotent "neoblast" stem cells present in the adults, representing 30% of total cells. The neoblast represents a unique cell type with the capacity to proliferate and to differentiate into all somatic cell types as well as into germ cells. All three transposon vectors have high transformation efficiency, but only Hermes and piggyBac show stable integration. The mariner vector is frequently lost presumably because of the presence of active mariner-type transposons in the genome of the Girardia tigrina. Transformed animals are mosaics containing both transformed and untransformed neoblasts. These differentiate to form EGFP-positive and -negative photoreceptor cells. Such mosaicism is maintained through several cycles of regeneration induced by decapitation or asexual reproduction. Transformed neoblasts also contribute to the germ line, and can give rise to pure transgenic planarian lines in which EGFP is expressed in all photoreceptor cells after sexual reproduction. The presence of the transgenes was confirmed by PCR, plasmid rescue assay, inverse PCR, and Southern blotting. Our results with the 3xP3-EGFP marker confirm the presence of Pax6 activity in the differentiated photoreceptor cells of planarian eyes. Transgenesis will be an important tool to dissect developmental molecular mechanisms in planarian regeneration, development and stem cell biology, and may also be an entry point to analyze the biology of parasitic Platyhelminthes.

Drosophila retinal homeobox (drx) is not required for establishment of the visual system, but is required for brain and clypeus development

The possibility that mechanisms of retinal determination may be similar between vertebrates and Drosophila has been supported by the observations that Pax6/eyeless genes are necessary and sufficient for retinal development. These studies suggest that the function of other gene families, operating during early eye development, might also be conserved. One candidate is the retinal homeobox (Rx) family of transcription factors. Vertebrate Rx is expressed in the prospective eye and forebrain and is required for eye morphogenesis, retinal precursor appearance, and normal forebrain development, indicating that it is an essential regulator of early eye and brain formation. Here, we test the hypothesis that Drosophila Rx (drx) is required for adult and larval eye development. We have isolated a drx null allele and demonstrate that the mutant compound eye and larval visual system is not detectably abnormal. However, we find that drx is required for development of a central brain structure, the ellipsoid body, suggesting that Rx function in the brain may be conserved. Finally, we characterize a novel anterior head phenotype and demonstrate that drx is required for clypeus development. Thus, our data suggest that drx may be required for the regulation of genes involved in brain morphogenesis and clypeus precursor development. We propose that differences in insect and vertebrate eye development may be explained by changes in gene regulation and/or the tissue of origin for eye precursor cells.

Planarian Gtsix3, a member of the Six/so gene family, is expressed in brain branches but not in eye cells

Six/sine oculis (Six/so) class genes, with representatives in vertebrates and invertebrates, include members with key developmental roles in the anterior part of the central nervous system (CNS) and eye. Having characterized the role of the first planarian gene of the Six/so family in eye development, we attempted to identify novel genes of this family related to the platyhelminth eye genetic network. We isolated a new Six/so gene in the planarian Girardia tigrina, Gtsix-3, which belongs to the Six3/6 class. Whole mount in situ hybridization revealed Gtsix3 expression in a stripe surrounding the cephalic ganglia in adults. This spatial pattern corresponds to the cephalic branches, the nerve cells that connect the CNS with the marginal sensory organs located continuously at the edge of the head. During head regeneration, Gtsix-3 shows delayed activation compared to other head genes, with an initial two spot pattern that later evolves to a continuous lateral expression in the new regenerated cephalic ganglia with a final reduction to the adult pattern. However, Gtsix-3 is not activated in tail regeneration and no eye expression is observed at any regenerative stage. These findings provide a new marker for the developing anterior nervous system and evidence the complexity of planarian brain.