Isolation and expression of a Pax-6 gene in the regenerating and intact Planarian Dugesia(G)tigrina

miR-8b is involved in brain and eye regeneration of Dugesia japonica in head regeneration

MicroRNAs (miRNAs) are a class of evolutionarily conserved small non-coding RNAs that regulate gene expression at the translation level in cell growth, proliferation and differentiation. In addition, some types of miRNAs have been proven to be key modulators of both CNS development and plasticity, such as let-7, miR-9 and miR-124. In this research, we found miR-8b acts as an important regulator involved in brain and eyespot regeneration in Dugesia japonica. miR-8b was highly conserved among species and was abundantly expressed in central nervous system. Here, we detected the expression dynamics of miR-8b by qPCR during the head regeneration of D. japonica. Knockdown miR-8b by anti-MIRs method caused severe defects of eyes and CNS. Our study revealed the evolutionary conserved role of miR-8b in the planarian regeneration process, and further provided more research ideas and available information for planarian miRNAs.

Summary: Most miRNAs in planarians are homologous to humans and other mammals, and may also play a similar regulatory role. Knockdown miR-8b planarian miR-8b induces brain and eyespot defects during head regeneration.

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.

Cleavage modification did not alter blastomere fates during bryozoan evolution

BACKGROUND

Stereotypic cleavage patterns play a crucial role in cell fate determination by precisely positioning early embryonic blastomeres. Although misplaced cell divisions can alter blastomere fates and cause embryonic defects, cleavage patterns have been modified several times during animal evolution. However, it remains unclear how evolutionary changes in cleavage impact the specification of blastomere fates. Here, we analyze the transition from spiral cleavage - a stereotypic pattern remarkably conserved in many protostomes - to a biradial cleavage pattern, which occurred during the evolution of bryozoans.

RESULTS

Using 3D-live imaging time-lapse microscopy (4D-microscopy), we characterize the cell lineage, MAPK signaling, and the expression of 16 developmental genes in the bryozoan Membranipora membranacea. We found that the molecular identity and the fates of early bryozoan blastomeres are similar to the putative homologous blastomeres in spiral-cleaving embryos.

CONCLUSIONS

Our work suggests that bryozoans have retained traits of spiral development, such as the early embryonic fate map, despite the evolution of a novel cleavage geometry. These findings provide additional support that stereotypic cleavage patterns can be modified during evolution without major changes to the molecular identity and fate of embryonic blastomeres.

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.

PAX6: 25th anniversary and more to learn

The DNA-binding transcription factor PAX6 was cloned 25 years ago by multiple teams pursuing identification of human and mouse eye disease causing genes, cloning vertebrate homologues of pattern-forming regulatory genes identified in Drosophila, or abundant eye-specific transcripts. Since its discovery in 1991, genetic, cellular, molecular and evolutionary studies on Pax6 mushroomed in the mid 1990s leading to the transformative thinking regarding the genetic program orchestrating both early and late stages of eye morphogenesis as well as the origin and evolution of diverse visual systems. Since Pax6 is also expressed outside of the eye, namely in the central nervous system and pancreas, a number of important insights into the development and function of these organs have been amassed. In most recent years, genome-wide technologies utilizing massively parallel DNA sequencing have begun to provide unbiased insights into the regulatory hierarchies of specification, determination and differentiation of ocular cells and neurogenesis in general. This review is focused on major advancements in studies on mammalian eye development driven by studies of Pax6 genes in model organisms and future challenges to harness the technology-driven opportunities to reconstruct, step-by-step, the transition from naïve ectoderm, neuroepithelium and periocular mesenchyme/neural crest cells into the three-dimensional architecture of the eye.

Using Drosophila for Studies of Intermediate Filaments

Drosophila melanogaster is a useful organism for determining protein function and modeling human disease. Drosophila offers a rapid generation time and an abundance of genomic resources and genetic tools. Conservation in protein structure, signaling pathways, and developmental processes make studies performed in Drosophila relevant to other species, including humans. Drosophila models have been generated for neurodegenerative diseases, muscular dystrophy, cancer, and many other disorders. Recently, intermediate filament protein diseases have been modeled in Drosophila. These models have revealed novel mechanisms of pathology, illuminated potential new routes of therapy, and make whole organism compound screens feasible. The goal of this chapter is to outline steps to study intermediate filament function and model intermediate filament-associated diseases in Drosophila. The steps are general and can be applied to study the function of almost any protein. The protocols outlined here are for both the novice and experienced Drosophila researcher, allowing the rich developmental and cell biology that Drosophila offers to be applied to studies of intermediate filaments.

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.

Regeneration of the elbow joint in the developing chick embryo recapitulates development

Synovial joints are among the most important structures that give us complex motor abilities as humans. Degenerative joint diseases, such as arthritis, cause loss of normal joint functioning and affect over 40 million people in the USA and approximately 350 million people worldwide. Therapies based on regenerative medicine hold the promise of effectively repairing or replacing damaged joints permanently. Here, for the first time, we introduce a model for synovial joint regeneration utilizing the chick embryo. In this model, a block of tissue that contains the prospective elbow is excised, leaving a window with strips of anterior and posterior tissue intact (window excision, WE). In contrast, we also slice out the same area containing the elbow and the distal piece of the limb is pinned back onto the stump (slice excision, SE). Interestingly, when the elbow is removed via WE, regeneration of the joint takes place, whereas the elbow joint does not regenerate following SE. In order to investigate whether the regeneration response recapitulates the developmental program of forming joints, we used GDF-5 and Autotaxin (Atx) as joint tissue specific markers, and Sox-9 and Col-9 as cartilage markers for in situ hybridization on sections at different time points after WE and SE surgeries. Re-expression of GDF-5 and Atx is observed in the WE samples by 60h after surgery. In contrast, the majority of the samples that underwent SE surgery did not express GDF-5 and Atx. Also, in SE fusion of cartilage elements takes place and the joint interzone does not form. This is indicated by continuous Col-9 expression in SE limbs, whereas Col-9 is downregulated at the joint interzone in the regenerating WE samples. This order and pattern of gene expression observed in regenerates is similar to the development of a joint suggesting that regeneration recapitulates development at the molecular level. This model defines some of the conditions required for inducing joint regeneration in an otherwise nonregenerating environment. This knowledge can be useful for designing new therapeutic approaches for joint loss or for conditions affecting joint integrity in humans.

Sea urchin tube feet are photosensory organs that express a rhabdomeric-like opsin and PAX6

All echinoderms have unique hydraulic structures called tube feet, known for their roles in light sensitivity, respiration, chemoreception and locomotion. In the green sea urchin, the most distal portion of these tube feet contain five ossicles arranged as a light collector with its concave surface facing towards the ambient light. These ossicles are perforated and lined with pigment cells that express a PAX6 protein that is universally involved in the development of eyes and sensory organs in other bilaterians. Polymerase chain reaction (PCR)-based sequencing and real time quantitative PCR (qPCR) also demonstrate the presence and differential expression of a rhabdomeric-like opsin within these tube feet. Morphologically, nerves that could serve to transmit information to the test innervate the tube feet, and the differential expression of opsin transcripts in the tube feet is inversely, and significantly, related to the amount of light that tube feet are exposed to depending on their location on the test. The expression of these genes, the differential expression of opsin based on light exposure and the unique morphological features at the distal portion of the tube foot strongly support the hypothesis that in addition to previously identified functional roles of tube feet they are also photosensory organs that detect and respond to changes in the underwater light field.

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.

Conserved and novel gene expression between regeneration and asexual fission in Nematostella vectensis

Due to work in model systems (e.g., flies and mice), the molecular mechanisms of embryogenesis are known in exquisite detail. However, these organisms are incapable of asexual reproduction and possess limited regenerative abilities. Thus, the mechanisms of alternate developmental trajectories and their relation to embryonic mechanisms remain understudied. Because these developmental trajectories are present in a diverse group of animal phyla spanning the metazoan phylogeny, including cnidarians, annelids, and echinoderms, they are likely to have played a major role in animal evolution. The starlet sea anemone Nematostella vectensis, an emerging model system, undergoes larval development, asexual fission, and complete bi-directional regeneration in the field and laboratory. In order to investigate to what extent embryonic patterning mechanisms are utilized during alternate developmental trajectories, we examined expression of developmental regulatory genes during regeneration and fission. When compared to previously reported embryonic expression patterns, we found that all genes displayed some level of expression consistent with embryogenesis. However, five of seven genes investigated also displayed striking differences in gene expression between one or more developmental trajectory. These results demonstrate that alternate developmental trajectories utilize distinct molecular mechanisms upstream of major developmental regulatory genes such as fox, otx, and Hox-like.

Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence

Gene duplication is a major driver of evolutionary divergence. In most vertebrates a single PAX6 gene encodes a transcription factor required for eye, brain, olfactory system, and pancreas development. In zebrafish, following a postulated whole-genome duplication event in an ancestral teleost, duplicates pax6a and pax6b jointly fulfill these roles. Mapping of the homozygously viable eye mutant sunrise identified a homeodomain missense change in pax6b, leading to loss of target binding. The mild phenotype emphasizes role-sharing between the co-orthologues. Meticulous mapping of isolated BACs identified perturbed synteny relationships around the duplicates. This highlights the functional conservation of pax6 downstream (3') control sequences, which in most vertebrates reside within the introns of a ubiquitously expressed neighbour gene, ELP4, whose pax6a-linked exons have been lost in zebrafish. Reporter transgenic studies in both mouse and zebrafish, combined with analysis of vertebrate sequence conservation, reveal loss and retention of specific cis-regulatory elements, correlating strongly with the diverged expression of co-orthologues, and providing clear evidence for evolution by subfunctionalization.

Dicyema Pax6 and Zic: tool-kit genes in a highly simplified bilaterian

BACKGROUND

Dicyemid mesozoans (Phylum Dicyemida) are simple (8-40-cell) cephalopod endoparasites. They have neither body cavities nor differentiated organs, such as nervous and gastrointestinal systems. Whether dicyemids are intermediate between Protozoa and Metazoa (as represented by their "Mesozoa" classification) or degenerate species of more complex metazoans is controversial. Recent molecular phylogenetic studies suggested that they are simplified bilaterians belonging to the Lophotrochozoa. We cloned two genes developmentally critical in bilaterian animals (Pax6 and Zic), together with housekeeping genes (actin, fructose-bisphosphate aldolase, and ATP synthase beta subunit) from a dicyemid to reveal whether their molecular phylogeny supported the "simplification" hypothesis, and to clarify evolutionary changes in dicyemid gene structure and expression profiles.

RESULTS

Genomic/cDNA sequence analysis showed that 1) the Pax6 molecular phylogeny and Zic intron positions supported the idea of dicyemids as reduced bilaterians; 2) the aa sequences deduced from the five genes were highly divergent; and 3) Dicyema genes contained very short introns of uniform length. In situ hybridization analyses revealed that Zic genes were expressed in hermaphroditic gonads, and Pax6 was expressed weakly throughout the developmental stages of the 2 types of embryo and in the hermaphroditic gonads.

CONCLUSION

The accelerated evolutionary rates and very short and uniform intron may represent a part of Dicyema genomic features. The presence and expression of the two tool-kit genes (Pax6 and Zic) in Dicyema suggests that they can be very versatile genes even required for the highly reduced bilaterian like Dicyema. Dicyemids may be useful models of evolutionary body plan simplification.

Expression of Pax gene family members in the anthozoan cnidarian, Nematostella vectensis

Pax genes are a family of homeodomain transcription factors that have been isolated from protostomes (e.g., eight in Drosophilia) and deuterostomes (e.g., nine in vertebrates) as well as outside the Bilateria, from sponges, a placozoan, and several classes of cnidarians. The genome of an anthozoan cnidarian, the starlet sea anemone, Nematostella vectensis, has been surveyed by both degenerate polymerase chain reaction and in silico for the presence of Pax genes. N. vectensis possesses seven Pax genes, which are orthologous to cnidarian Pax genes (A,B,C, and D) previously identified in another anthozoan, a coral, Acropora millepora. Phylogenetic analyses including data from nonchordate deuterostomes indicates that there were five Pax gene classes in the protostome-deuterostome ancestor, but only three in the cnidarian-bilaterian ancestor, with PaxD class genes lost in medusozoan cnidarians. Pax genes play diverse roles in bilaterians, including eye formation (e.g., Pax6), segmentation (e.g., Pax3/7 class genes), and neural patterning (e.g., Pox-neuro, Pax2/5/8). We show the first expression data for members of all four Pax classes in a single species of cnidarian. N. vectensis Pax genes are expressed in both a cell-type and region-specific manner during embryogenesis, and likely play a role in patterning specific components of the cnidarian ectodermal nerve net. The results of these patterns are discussed with respect to Pax gene evolution in the Bilateria.

Pax6 and eye development in Arthropoda

The arthropod compound eye is one of the three main types of eyes observed in the animal kingdom. Comparison of the eyes seen in Insecta, Crustacea, Myriapoda and Chelicerata reveals considerable variation in terms of overall cell number, cell positioning, and photoreceptor rhabdomeres, yet, molecular data suggest there may be unexpected similarities. We review here the role of Pax6 in eye development and evolution and the relationship of Pax6 with other retinal determination genes and signaling pathways. We then discuss how the study of changes in Pax6 primary structure, in the gene networks controlled by Pax6 and in the relationship of Pax6 with signaling pathways may contribute to our insight into the relative role of conserved molecular-genetic mechanisms and emergence of evolutionary novelty in shaping the ommatidial eyes seen in the Arthropoda.

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 Trichoplax PaxB Gene: A Putative Proto-PaxA/B/C Gene Predating the Origin of Nerve and Sensory Cells

Pax genes play key regulatory roles in embryonic and sensory organ development in metazoans but their evolution and ancestral functions remain widely unresolved. We have isolated a Pax gene from Placozoa, beside Porifera the only metazoan phylum that completely lacks nerve and sensory cells or organs. These simplest known metazoans also lack any kind of symmetry, organs, extracellular matrix, basal lamina, muscle cells, and main body axis. The isolated Pax gene from Trichoplax adhaerens harbors a paired domain, an octapeptide, and a full-length homeodomain. It displays structural features not only of PaxB and Pax2/5/8-like genes but also of PaxC and Pax6 genes. Conserved splice sites between Placozoa, Cnidaria, and triploblasts, mark the ancient origin of intron structures. Phylogenetic analyses demonstrate that the Trichoplax PaxB gene, TriPaxB, is basal not only to all other known PaxB genes but also to PaxA and PaxC genes and their relatives in triploblasts (namely Pax2/5/8, Pax4/6, and Poxneuro). TriPaxB is expressed in distinct cell patches near the outer edge of the animal body, where undifferentiated and possibly multipotent cells are found. This expression pattern indicates a developmental role in cell-type specification and/or differentiation, probably in specifying-determining fiber cells, which are regarded as proto-neural/muscle cells in Trichoplax. While PaxB, Pax2/5/8, and Pax6 genes have been linked to nerve cell and sensory system/organ development in virtually all animals investigated so far, our study suggests that Pax genes predate the origin of nerve and sensory cells.

Cloning and functional analysis of ascidian Mitf in vivo: insights into the origin of vertebrate pigment cells

The microphthalmia-associated transcription factor (Mitf) is a basic-helix-loop-helix-leucine zipper (bHLH-ZIP) transcription factor essential for the development and function of all melanin-producing pigment cells in vertebrates. To elucidate the evolutionary history of Mitf and the antiquity of its association with pigment cells, we have isolated and characterized HrMitf, a sole member of the Mitf-TFE bHLH-ZIP subfamily in the ascidian Halocynthia roretzi. Maternal HrMitf mRNA is detected in the fertilized egg and in the animal hemisphere from 4-cell stage through the gastrula stage. From the neurula through the early tailbud stage, HrMitf is preferentially expressed in the pigment-lineage cells that express the lineage-specific melanogenesis genes tyrosinase (HrTyr) and Tyrp. Overexpression of HrMitf induced ectopic expression of HrTyr enzyme activity in mesenchymal cells where the same enzyme activity was induced by overexpression of HrPax3/7, suggesting that a part(s) of the Pax3-Mitf-tyrosinase gene regulatory cascade seen in vertebrate melanocytes is operative during ascidian embryogenesis. We also show HrMitf and mouse Mitf-A, a Mitf isoform abundantly expressed in pigmented epithelial cells, share similar functional characteristics. These results suggest antiquity of the association of the Mitf-TFE subfamily with pigment cells and may support the idea that acquisition of multiple promoters (isoforms) by an ancestral Mitf gene has allowed the evolution of multiple pigment cell types.

Regeneration and gene regulation in planarians

Planarians can regenerate using a pluripotent stem cell system. This phenomenon provides a unique opportunity to understand gene regulation in the process of differentiation from pluripotent stem cells. Recent studies have made significant advances in our understanding of the pluripotent stem cell system in this model. In particular, a gene knockdown method by RNA interference enabled great progress in identifying genes involved in regeneration and stem cell regulation.

The Eye Specification Network in Drosophila

One of the most exciting revelations in retinal biology is the realization that the molecules and mechanisms that regulate eye development have been conserved in all seeing animals including such diverse organisms as the fruit fly, mouse and man. The emerging commonality among mechanisms used in eye development allows for the use of model systems such as the fruit fly, Drosophila melanogaster, to provide key insights into the development and diseases of the mammalian eye. Eye specification in Drosophila is controlled, in part, by the concerted activities of eight nuclear proteins and several signal transduction cascades that together form a tightly woven regulatory network. Loss of function mutations in several components lead to the complete derailment of eye development while ectopic expression of threse genes in non-retinal tissues can direct the fates of these tissues towards eye formation. Here we will describe what is currently known about this remarkable regulatory cassettee highlight some of the outstanding questions that still need to be answered.

DNA-binding characteristics of cnidarian Pax-C and Pax-B proteins in vivo and in vitro: no simple relationship with the Pax-6 and Pax-2/5/8 classes

Cnidarians are the simplest animals in which distinct eyes are present. We have previously suggested that cnidarian Pax-Cam might represent a precursor of the Pax-6 class. Here we show that when expressed in Drosophila imaginal discs, Pax-Cam chimeric proteins containing the C-terminal region of EY were capable of eye induction and driving expression of a reporter gene under the control of a known EY target (the sine oculis gene). Whilst these results are consistent with a Pax-6-like function for Pax-Cam, in band shift experiments we were unable to distinguish the DNA-binding behaviour of the Pax-Cam Paired domain from that of a second Acropora Pax protein, Pax-Bam. The ability of a Pax-Bam/EY chimera to also induce eye formation in leg imaginal discs, together with the in vitro data, cast doubt on previously assumed direct relationships between cnidarian Pax genes and the Pax-6 and Pax-2/5/8 classes of bilateral animals.

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.

Pax6 in the sepiolid squid Euprymna scolopes: evidence for a role in eye, sensory organ and brain development

The cloning of a Pax6 orthologue from the sepiolid squid Euprymna scolopes and its developmental expression pattern are described. The data are consistent with the presence of a single gene encoding a protein with highly conserved DNA-binding paired and homeodomains. A detailed expression analysis by in situ hybridization and immunodetection revealed Pax6 mRNA and protein with predominantly nuclear localization in the developing eye, olfactory organ, brain lobes (optic lobe, olfactory lobe, peduncle lobe, superior frontal lobe and dorsal basal lobe), arms and mantle, suggestive of a role in eye, brain, and sensory organ development.

Eye regeneration at the molecular age

Eye tissues such as the lens and the retina possess remarkable regenerative abilities. In amphibians, a complete lens can be regenerated after lentectomy. The process is a classic example of transdifferentiation of one cell type to another. Likewise, retina can be regenerated, but the strategy used to replace the damaged retina differs, depending on the animal system and the age of the animal. Retina can be regenerated by transdifferentiation or by the use of stem cells. In this review, we present a synthesis on the regenerative capacity of eye tissues in different animals with emphasis on the strategy and the molecules involved. In addition, we stress the place of this field at the molecular age and the importance of the recent technologic advances.

Conserved and divergent functions of Drosophila atonal, amphibian, and mammalian Ath5 genes

Insect and vertebrate eyes differ in their formation, cellular composition, neural connectivity, and visual function. Despite this diversity, Drosophila atona and its vertebrate Ortholog in the eye, Ath5, each regulate determination of the first retinal neuron class-R8 photo-receptors and retinal ganglion cells (RGCs)-in their respective organisms. We have performed a cross-species functional comparison of these genes. In ato mutant Drosophila, ectopic Xenopus Ath5 (Xath5) rescues photoreceptor cell development comparably with atonaI. In contrast, mouse Ath5 (Math5) induces formation of very few ommatidia, and most of these lack R8 cells. In the developing frog eye, ectopic atonal, like Xath5, promotes the differentiation RGCs. Despite strong conservation of atonaI, Xath5, and Math5 structure and shared function, other factors must contribute to the species specificity of retinal neuron determination. These observations suggest that the atonaI family may occupy a position in a gene hierarchy where differences in gene regulation or function can be correlated with evolutionary diversity of eye development.

Regeneration in planarians and other worms: New findings, new tools, and new perspectives

Molecular biology, recombinant DNA techniques, and new methods of cell lineage have reignited the interest of planarians and other worms (mainly annelids and nemerteans) as invertebrate model systems of regeneration. Here, the mean results produced in the last five years are reviewed, an update of the genes and molecules involved in planarian regeneration is provided, and a new morphallactic-epimorphic model of pattern formation is suggested. Moreover, and most importantly, we highlight the new strides brought upon by genomic/proteomic analyses, RNA interference (RNAi) to inactivate gene function, and Bromodeoxyuridine (BrdU) cell labelling. The raising hope to obtain transformed neoblasts and transgenic planarians is also stressed. Altogether, such approaches will eventually lead to solve the long-standing open questions on regeneration which still baffles us. Finally, we warn against overlooking the evident links between regeneration processes and those controlling the daily wear and tear of tissues and cells. Both processes act, at least in planarians, upon a unique stem-cell endowed with an unrivaled developmental potential in the animal kingdom-the neoblast. This cell could be considered the forebear and a model system for stem-cell analysis.

Biology and pathology of the invertebrate eye

Although this article is not a comprehensive review of ocular biology and disease across the millions of invertebrate species, it is hoped that it highlights the surprising gene homologies that influence ocular development despite the dramatic differences in resulting ocular development and final morphology. In the same way that ocular anatomy and physiology is undergirded by similarities in the genetic foundation of the eye, it is to be expected that eye disease in invertebrates, as it is studied in more depth, will show substantial homologies with the eye disease of the vertebrates that veterinary ophthalmologists are more used to treating.

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

Planarians are the free-living members (order Tricladida) of the phylum Platyhelminthes. They are triploblastic, acoelomate, unsegmented and located at the base of the Lophotrochozoa clade. Besides their huge regenerative capacity, planarians have simple eyes, considered similar to the prototypic eye suggested by Charles Darwin in his book 'On the Origin of Species'. The conserved genetic network that determines the initial steps of eye development across metazoans supports a monophyletic origin of the various eye types present in the animal kingdom. Here we summarise the pattern of expression of certain genes involved in the eye network that have been isolated in planarians, such as Otx, Pax-6, Six, Rax and opsin. We describe the effects of RNA interference-mediated loss of function on eye regeneration. Finally, we discuss the relevance of these findings for the evolution of the eye gene network.

The genetic network of prototypic planarian eye regeneration is Pax6 independent

We report the presence of two Pax6-related genes, Pax6A and Pax6B, which are highly conserved in two planarian species Dugesia japonica and Girardia tigrina (Platyhelminthes, Tricladida). Pax6A is more similar to other Pax6 proteins than Pax6B, which is the most divergent Pax6 described so far. The planarian Pax6 homologs do not show any clear orthology to the Drosophila duplicated Pax6 genes, eyeless and twin of eyeless, which suggests an independent Pax6 duplication in a triclad or platyhelminth ancestor. Pax6A is expressed in the central nervous system of intact planarians, labeling a subset of cells of both cephalic ganglia and nerve cords, and is activated during cephalic regeneration. Pax6B follows a similar pattern, but shows a lower level of expression. Pax6A and Pax6B transcripts are detected in visual cells only at the ultrastructural level, probably because a limited amount of transcripts is present in these cells. Inactivation of both Pax6A and Pax6B by RNA-mediated gene interference (RNAi) inhibits neither eye regeneration nor eye maintenance, suggesting that the genetic network that controls this process is not triggered by Pax6 in planarians.

Development of pigment-cup eyes in the polychaetePlatynereis dumeriliiand evolutionary conservation of larval eyes in Bilateria

The role of Pax6 in eye development in insects and vertebrates supports the view that their eyes evolved from simple pigment-cup ocelli present in their last common ancestors (Urbilateria). The cerebral eyes in errant polychaetes represent prototype invertebrate pigment-cup ocelli and thus resemble the presumed ancestral eyes. We have analysed expression of conserved eye specification genes in the early development of larval and adult pigment-cup eyes in Platynereis dumerilii (Polychaeta, Annelida, Lophotrochozoa). Both larval and adult eyes form in close vicinity of the optic anlagen on both sides of the developing brain ganglia. While pax6 is expressed in the larval, but not in the developing, adult eyes, expression of six1/2 from trochophora stages onwards specifically outlines the optic anlagen and thus covers both the developing larval and adult eyes. Using Platynereis rhabdomeric opsin as differentiation marker, we show that the first pair of adult eye photoreceptor cells is detected within bilateral clusters that transitorily express ath, the Platynereis atonal orthologue, thus resembling proneural sensory clusters. Our data indicate that – similar to insects, but different from the vertebrates – polychaete six1/2 expression outlines the entire visual system from early developmental stages onwards and ath-positive clusters generate the first photoreceptor cells to appear. We propose that pax6-, six1/2- and ath-positive larval eyes, as found in today’s trochophora, were present already in Urbilateria.

Conservation of Pax 6 function and upstream activation by Notch signaling in eye development of frogs and flies

Loss of Pax 6 function leads to an eyeless phenotype in both mammals and insects, and ectopic expression of both the Drosophila and the mouse gene leads to the induction of ectopic eyes in Drosophila, which suggested to us that Pax 6 might be a universal master control gene for eye morphogenesis. Here, we report the reciprocal experiment in which the RNAs of the Drosophila Pax 6 homologs, eyeless and twin of eyeless, are transferred into a vertebrate embryo; i.e., early Xenopus embryos at the 2- and 16-cell stages. In both cases, ectopic eye structures are formed. To understand the genetic program specifying eye morphogenesis, we have analyzed the regulatory mechanisms of Pax 6 expression that initiates eye development. Previously, we have demonstrated that Notch signaling regulates the expression of eyeless and twin of eyeless in Drosophila. Here, we show that in Xenopus, activation of Notch signaling also induces eye-related gene expression, including Pax 6, in isolated animal caps. In Xenopus embryos, the activation of Notch signaling causes eye duplications and proximal eye defects, which are also induced by overexpression of eyeless and twin of eyeless. These findings indicate that the gene regulatory cascade is similar in vertebrates and invertebrates.

Reconstructing the eyes of Urbilateria

The shared roles of Pax6 and Six homologues in the eye development of various bilaterians suggest that Urbilateria, the common ancestors of all Bilateria, already possessed some simple form of eyes. Here, we re-address the homology of bilaterian cerebral eyes at the level of eye anatomy, of eye-constituting cell types and of phototransductory molecules. The most widespread eye type found in Bilateria are the larval pigment-cup eyes located to the left and right of the apical organ in primary, ciliary larvae of Protostomia and Deuterostomia. They can be as simple as comprising a single pigment cell and a single photoreceptor cell in inverse orientation. Another more elaborate type of cerebral pigment-cup eyes with an everse arrangement of photoreceptor cells is found in adult Protostomia. Both inverse larval and everse adult eyes employ rhabdomeric photoreceptor cells and thus differ from the chordate cerebral eyes with ciliary photoreceptors. This is highly significant because on the molecular level we find that for phototransduction rhabdomeric versus ciliary photoreceptor cells employ divergent rhodopsins and non-orthologous G-proteins, rhodopsin kinases and arrestins. Our comparison supports homology of cerebral eyes in Protostomia; it challenges, however, homology of chordate and non-chordate cerebral eyes that employ photoreceptor cells with non-orthologous phototransductory cascades.

Isolation of Cladonema Pax-B genes and studies of the DNA-binding properties of cnidarian Pax paired domains

Pax genes encode nuclear transcription factors that are involved in developmental control. They contain a conserved DNA-binding domain, the paired domain. The DNA-binding specificity of paired domains is directly related to the gene regulation function of Pax proteins. Pax genes were previously divided into five groups on the basis of a phylogenetic analysis of paired domains. In this study, two highly similar cnidarian Pax-B genes from Cladonema californicum, a jellyfish with eyes, were found and sequenced. In an effort to understand the function of the cnidarian Pax genes isolated in this and a previous study, we characterized the consensus DNA sequences bound by the cnidarian paired domains using a PCR-based method and electrophoretic mobility shift assays. The consensus DNA sequences obtained are very similar to those bound by mammalian Pax proteins. Comparison of known consensus sequences indicates that they are all partially palindromic, but this characteristic is most prominent in cnidarians, which suggests that the DNA sequences bound by the ancestral paired domain could have been palindromic. Also, cnidarian paired domains, like those of Pax-2/5/8, possess a broader binding specificity than other paired domains, which implies that the common ancestor of Pax-2/5/8 and Pax-4/6 paired domains could also have had a similar broad DNA-binding specificity. Thus far, a definitive Pax-6 gene has not been found in several cnidarian species examined, which is consistent with a later origin of the Pax-6 gene and raises two possibilities: the Pax genes of cnidarians are multifunctional and control two or more developmental pathways, including eye development, or they use a Pax-independent pathway for eye development. Whether this pathway does exist and is unique to cnidarians or it whether it represents a true master control under which Pax-6 was later included remains to be determined.

Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences

Insight into the origin and early evolution of the animal phyla requires an understanding of how animal groups are related to one another. Thus, we set out to explore animal phylogeny by analyzing with maximum parsimony 138 morphological characters from 40 metazoan groups, and 304 18S rDNA sequences, both separately and together. Both types of data agree that arthropods are not closely related to annelids: the former group with nematodes and other molting animals (Ecdysozoa), and the latter group with molluscs and other taxa with spiral cleavage. Furthermore, neither brachiopods nor chaetognaths group with deuterostomes; brachiopods are allied with the molluscs and annelids (Lophotrochozoa), whereas chaetognaths are allied with the ecdysozoans. The major discordance between the two types of data concerns the rooting of the bilaterians, and the bilaterian sister-taxon. Morphology suggests that the root is between deuterostomes and protostomes, with ctenophores the bilaterian sister-group, whereas 18S rDNA suggests that the root is within the Lophotrochozoa with acoel flatworms and gnathostomulids as basal bilaterians, and with cnidarians the bilaterian sister-group. We suggest that this basal position of acoels and gnathostomulids is artifactal because for 1,000 replicate phylogenetic analyses with one random sequence as outgroup, the majority root with an acoel flatworm or gnathostomulid as the basal ingroup lineage. When these problematic taxa are eliminated from the matrix, the combined analysis suggests that the root lies between the deuterostomes and protostomes, and Ctenophora is the bilaterian sister-group. We suggest that because chaetognaths and lophophorates, taxa traditionally allied with deuterostomes, occupy basal positions within their respective protostomian clades, deuterostomy most likely represents a suite of characters plesiomorphic for bilaterians.

Regeneration as an evolutionary variable

Regeneration poses a distinctive set of problems for evolutionary biologists, but there has been little substantive progress since these issues were clearly outlined in the monograph of T. H. Morgan (1901). The champions at regeneration among vertebrates are the urodele amphibians such as the newt, and we tend to regard urodele regeneration as an exceptional attribute. The ability to regenerate large sections of the body plan is widespread in metazoan phylogeny, although it is not universal. It is striking that in phylogenetic contexts where regeneration occurs, closely related species are observed which do not possess this ability. It is a challenge to reconcile such variation between species with a conventional selective interpretation of regeneration. The critical hypothesis from phylogenetic analysis is that regeneration is a basic, primordial attribute of metazoans rather than a mechanism which has evolved independently in a variety of contexts. In order to explain its absence in closely related species, it is postulated to be lost secondarily for reasons which are not understood. Our approach to this question is to compare a differentiated newt cell with its mammalian counterpart in respect of the plasticity of differentiation.

Regulatory evolution and the origin of the bilaterians

The adult body plan of bilaterians is achieved by imposing regional specifications on pluripotential cells. The establishment of spatial domains is governed in part by regulating expression of transcription factors. The key to understanding bilaterian evolution is contingent on our understanding of how the regulation of these transcription factors influenced bilaterian stem-group evolution.

Searching for the prototypic eye genetic network: Sine oculis is essential for eye regeneration in planarians

We have identified a sine oculis gene in the planarian Girardia tigrina (Platyhelminthes; Turbellaria; Tricladida). The planarian sine oculis gene (Gtso) encodes a protein with a sine oculis (Six) domain and a homeodomain that shares significant sequence similarity with so proteins assigned to the Six-2 gene family. Gtso is expressed as a single transcript in both regenerating and fully developed eyes. Whole-mount in situ hybridization studies show exclusive expression in photoreceptor cells. Loss of function of Gtso by RNA interference during planarian regeneration inhibits eye regeneration completely. Gtso is also essential for maintenance of the differentiated state of photoreceptor cells. These results, combined with the previously demonstrated expression of Pax-6 in planarian eyes, suggest that the same basic gene regulatory circuit required for eye development in Drosophila and mouse is used in the prototypic eye spots of platyhelminthes and, therefore, is truly conserved during evolution.

Developmental patterning genes and their conserved functions: from model organisms to humans

Molecular and genetic evidence accumulated during the past 20 years in the field of developmental biology indicates that different animals possess many common genetic systems for embryonic patterning. In this review we describe the conserved functions of such developmental patterning genes and their relevance for human pathological conditions. Special attention is given to the Hox genetic system, involved in establishing cell identities along the anterior-posterior axis of all higher metazoans. We also describe other conserved genetic systems, such as the involvement of Pax6 genes in eye development and the role of Nkx2.5-type proteins in heart development. Finally, we outline some fascinating problems at the forefront of the studies of developmental patterning genes and show how knowledge obtained from model genetic organisms such as Drosophila helps to explain normal human morphogenesis and the genetic basis of some birth defects.

A conserved blueprint for the eye?

Although the eyes of all organisms have a common function, visual perception, their structures and developmental mechanisms are quite diverse. Recent research on eye development in Drosophila has identified a set of putative transcription factors required for the earliest step of eye development, specification of the field of cells that will give rise to the eye. These factors appear to act in a hierarchy, although cross-regulation may amplify the eye fate decision or promote progression to the next step. Surprisingly, homologous proteins are also involved in vertebrate eye development, suggesting that this regulatory network was present in a primitive common ancestor and that it has been adapted to control visual organ formation in multiple species. The identification of genes acting upstream and downstream of these transcription factors will contribute to our understanding of the establishment of a developmental field, as well as of the divergence of regulatory pathways controlling the formation of eye structures.