A planarian nidovirus expands the limits of RNA genome size.

RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is in the 100-300 kb range. This large difference presents a daunting gap for the transition from primordial RNP to contemporary DNA-RNP-based life. Whether or not RNA viruses represent transitional steps towards DNA-based life, studies of larger RNA viruses advance our understanding of the size constraints on RNP entities and the role of genome size in virus adaptation. For example, emergence of the largest previously known RNA genomes (20-34 kb in positive-stranded nidoviruses, including coronaviruses) is associated with the acquisition of a proofreading exoribonuclease (ExoN) encoded in the open reading frame 1b (ORF1b) in a monophyletic subset of nidoviruses. However, apparent constraints on the size of ORF1b, which encodes this and other key replicative enzymes, have been hypothesized to limit further expansion of these viral RNA genomes. Here, we characterize a novel nidovirus (planarian secretory cell nidovirus; PSCNV) whose disproportionately large ORF1b-like region including unannotated domains, and overall 41.1-kb genome, substantially extend the presumed limits on RNA genome size. This genome encodes a predicted 13,556-aa polyprotein in an unconventional single ORF, yet retains canonical nidoviral genome organization and expression, as well as key replicative domains. These domains may include functionally relevant substitutions rarely or never before observed in highly conserved sites of RdRp, NiRAN, ExoN and 3CLpro. Our evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and acquired additional genes, including those typical of large DNA viruses or hosts, e.g. Ankyrin and Fibronectin type II, which might modulate virus-host interactions. PSCNV's greatly expanded genome, proteomic complexity, and unique features-impressive in themselves-attest to the likelihood of still-larger RNA genomes awaiting discovery.

Processing Schmidtea mediterranea for Transmission Electron Microscopy: Classical and Microwave Techniques.

The flatworm Schmidtea mediterranea and related species are emerging model systems in such fields as stem-cell biology, regeneration, and evolutionary biology. Excellent molecular tools have been developed for S. mediterranea, but ultrastructural techniques have received less attention, which is unfortunate, as these methods are necessary to better understand the actual histological, cellular and subcellular features of regeneration and development. Tissue-processing regimens can be quite idiosyncratic for particular species or specimen types-what works for mammalian tissues or cell cultures will not necessarily give good results with freshwater planarians. Here we present detailed, optimized protocols for preparation of S. mediterranea by "standard" chemical fixation, and by a rapid microwave-based technique.

A functional genomics screen in planarians reveals regulators of whole-brain regeneration.

Planarians regenerate all body parts after injury, including the central nervous system (CNS). We capitalized on this distinctive trait and completed a gene expression-guided functional screen to identify factors that regulate diverse aspects of neural regeneration in Schmidtea mediterranea. Our screen revealed molecules that influence neural cell fates, support the formation of a major connective hub, and promote reestablishment of chemosensory behavior. We also identified genes that encode signaling molecules with roles in head regeneration, including some that are produced in a previously uncharacterized parenchymal population of cells. Finally, we explored genes downregulated during planarian regeneration and characterized, for the first time, glial cells in the planarian CNS that respond to injury by repressing several transcripts. Collectively, our studies revealed diverse molecules and cell types that underlie an animal's ability to regenerate its brain.

Preparation of the planarian Schmidtea mediterranea for high-resolution histology and transmission electron microscopy.

The flatworm Schmidtea mediterranea is an emerging model species in fields such as stem cell biology, regeneration and evolutionary biology. Excellent molecular tools have been developed for S. mediterranea, but ultrastructural techniques have received far less attention. Processing specimens for histology and transmission electron microscopy (TEM) is notoriously idiosyncratic for particular species or specimen types. Unfortunately, however, most methods for S. mediterranea described in the literature lack numerous essential details, and those few that do provide them rely on specialized equipment that may not be readily available. Here we present an optimized protocol for ultrastructural preparation of S. mediterranea. The protocol can be completed in 6 d, much of which is 'hands-off' time. To aid with troubleshooting, we also illustrate the major effects of seemingly minor variations in fixative, buffer concentration and dehydration steps. This procedure will be useful for all planarian researchers, particularly those with relatively little experience in tissue processing.

A sex-specific transcription factor controls male identity in a simultaneous hermaphrodite.

Evolutionary transitions between hermaphroditic and dioecious reproductive states are found in many groups of animals. To understand such transitions, it is important to characterize diverse modes of sex determination utilized by metazoans. Currently, little is known about how simultaneous hermaphrodites specify and maintain male and female organs in a single individual. Here we show that a sex-specific gene, Smed-dmd-1 encoding a predicted doublesex/male-abnormal-3 (DM) domain transcription factor, is required for specification of male germ cells in a simultaneous hermaphrodite, the planarian Schmidtea mediterranea. dmd-1 has a male-specific role in the maintenance and regeneration of the testes and male accessory reproductive organs. In addition, a homologue of dmd-1 exhibits male-specific expression in Schistosoma mansoni, a derived, dioecious flatworm. These results demonstrate conservation of the role of DM domain genes in sexual development in lophotrochozoans and suggest one means by which modulation of sex-specific pathways can drive the transition from hermaphroditism to dioecy.

Evolution and development of polarized germ cell cysts: new insights from a polychaete worm, Ophryotrocha labronica.

Polarized oogenic cysts are clonal syncytia of germ cells in which some of the sister cells (cystocytes) differentiate not as oocytes, but instead as nurse cells: polyploid cells that support oocyte development. The intricate machinery required to establish and maintain divergent cell fates within a syncytium, and the importance of associated oocyte patterning for subsequent embryonic development, have made polarized cysts valuable subjects of study in developmental and cell biology. Nurse cell/oocyte specification is best understood in insects, particularly Drosophila melanogaster. However, polarized cysts have evolved independently in several other animal phyla. We describe the differentiation of female cystocytes in an annelid worm, the polychaete Ophryotrocha labronica. These worms are remarkable for their elegantly simple cysts, which comprise a single oocyte and nurse cell, making them an appealing complement to insects as subjects of study. To elucidate the process of cystocyte differentiation in O. labronica, we have constructed digital 3D models from electron micrographs of serially sectioned ovarian tissue. These models show that 2-cell cysts arise by fragmentation of larger "parental" cysts, rather than as independent units. The parental cysts vary in size and organization, are produced by asynchronous, indeterminate mitotic divisions of progenitor cystoblasts, and lack fusome-like organizing organelles. All of these characteristics represent key cytological differences from "typical" cyst development in insects like D. melanogaster. In light of such differences and the plasticity of female cyst structure among other animals, we suggest that it is time to reassess common views on the conservation of oogenic cysts and the importance of cysts in animal oogenesis generally.

Development of polarized female germline cysts in the polychaete, Ophryotrocha labronica.

Polarized oogenic cysts are clonal syncytia in which cellular compartments (cystocytes) differentiate as either oocytes or nurse cells-supportive germ cells that transport material to the oocyte through cytoplasmic bridges. Although polarized cysts have evolved independently in several animal phyla, most research on this phenomenon has focused on insects, particularly Drosophila melanogaster. To provide a foundation for comparative studies of cyst polarization, we have examined the coelomic development of polarized cysts in an annelid worm, Ophryotrocha labronica, using a variety of microscopic techniques. This species has elegantly simple cysts, each consisting of two interconnected cells (one oocyte and one nurse cell) free of somatic follicular tissue. These cysts arise from segmental ovaries, but are released to the coelom early in oogenesis, where they carry out most of their development. Although the oocyte remains transcriptionally active through oogenesis, nurse cells in this species are robust biosynthetic factories, with highly polyploid nuclei, enormous nucleoli, numerous mitochondria, and abundant rough endoplasmic reticulum. Ultimately, the nurse cell dumps its cytoplasm into oocyte, detaches, and undergoes programmed cell death. Although in insects, and possibly some polychaetes, the overall polarity of the cyst is linked to the specification of future embryonic axes in the oocyte, in Ophryotrocha this appears not to be the case. Our findings provide a detailed analysis of cyst development, addressing earlier misconceptions in the literature and adding new insights. This foundation shows the potential of Ophryotrocha labronica as a model system for further experimental analysis of nurse cell-oocyte differentiation.

Biolistics for high-throughput transformation and RNA interference in Drosophila melanogaster.

With twelve Drosophila genomes now sequenced, there is a growing need to develop higher-throughput methods for identifying the functions of the many newly identified genes. Genetic transformation and RNA interference are two technologies that have been used extensively to facilitate gene-function studies in Drosophila melanogaster, to introduce genes or block the expression of endogenous genes, respectively. Both of these technologies typically require the delivery of nucleic acids into developing insect embryos, and virtually all studies to date have relied on microinjection as the DNA delivery method of choice. In this study, we describe the use of biolistics as a higher-throughput method of nucleic acid delivery. By bombarding dechorionated D. melanogaster embryos with 1 microm gold beads coated with P-element or piggyBac transformation vectors, we observed transformation frequencies (3-4%) that are comparable to those achieved using microinjection methods, but in only a fraction of the time required for the DNA delivery. Biolistic delivery of double-stranded RNA (dsRNA) specific to a beta-glucuronidase (gus) transgene resulted in a significant (71%) reduction in gus transcripts in embryos and the RNA interference (RNAi) persisted through two successive larval molts, albeit at reduced levels. DsRNAs specific to four essential genes were delivered to embryos and resulted in arrested development and phenotypes that closely match that of null mutations. These results suggest that biolistic delivery of dsRNA into embryos could be adapted for high throughput RNAi screens of early Drosophila developmental genes.

Muscle formation during embryogenesis of the polychaete Ophryotrocha diadema (Dorvilleidae) - new insights into annelid muscle patterns.

BACKGROUND: The standard textbook information that annelid musculature consists of oligochaete-like outer circular and inner longitudinal muscle-layers has recently been called into question by observations of a variety of complex muscle systems in numerous polychaete taxa. To clarify the ancestral muscle arrangement in this taxon, we compared myogenetic patterns during embryogenesis of Ophryotrocha diadema with available data on oligochaete and polychaete myogenesis. This work addresses the conflicting views on the ground pattern of annelids, and adds to our knowledge of the evolution of lophotrochozoan taxa. RESULTS: Somatic musculature in Ophryotrocha diadema can be classified into the trunk, prostomial/peristomial, and parapodial muscle complexes. The trunk muscles comprise strong bilateral pairs of distinct dorsal and ventral longitudinal strands. The latter are the first to differentiate during myogenesis. They originate within the peristomium and grow posteriorly through the continuous addition of myocytes. Later, the longitudinal muscles also expand anteriorly and form a complex arrangement of prostomial muscles. Four embryonic parapodia differentiate in an anterior-to-posterior progression, significantly contributing to the somatic musculature. Several diagonal and transverse muscles are present dorsally. Some of the latter are situated external to the longitudinal muscles, which implies they are homologous to the circular muscles of oligochaetes. These circular fibers are only weakly developed, and do not appear to form complete muscle circles. CONCLUSION: Comparison of embryonic muscle patterns showed distinct similarities between myogenetic processes in Ophryotrocha diadema and those of oligochaete species, which allows us to relate the diverse adult muscle arrangements of these annelid taxa to each other. These findings provide significant clues for the interpretation of evolutionary changes in annelid musculature.

Redox-active metals in commercial preparations of lipopolysaccharide: implications for studies of cellular responses to bacterial products.

The mechanisms by which lipopolysaccharide (LPS) activates cells have been the subject of intense investigation for many years. Whereas much information on this process has been collected for mammalian species, little is known about the signalling path-ways operative in other animals. One general mode of cellular activation that has been recently pro-posed for pathways independent of the primary mammalian LPS receptor, CD14, involves reactive oxygen species (ROS) as intermediates in LPS-induced signalling pathways. Therefore, we used 2',7'-dichlorodihydrofluorescein, a fluorogenic probe of redox activity, to examine LPS-induced oxidative responses of a macrophage-like cell line from the rainbow trout, RTS11. Lipopolysaccharide dose-dependently increased oxidation of this probe by RTS11 cells, and a variety of other cell lines. This process was inhibited by catalase, superoxide dismutase and NG-methylarginine citrate, an inhibitor of nitric oxide synthases, suggesting the involvement of a diverse assortment of cellular ROS. More careful dissection of this phenomenon led us to conclude that the increase in oxidation was, in fact, due almost entirely to metals, particularly copper, in some LPS preparations, which is something to consider when experimenting with LPS.