Discovery and characterization of a transient chaetal gland during the development of Capitella teleta (Sedentaria: Annelida).

Chaetae are among the most extensively studied structures in polychaetes, serving as a defining morphological trait for annelids. Capitella teleta stands out as one of the few established annelid models for developmental and morphological studies, thus receiving significant scholarly attention. In this study, we unveil a previously unnoticed glandular structure associated with chaetae within the larvae of C. teleta. Our investigations demonstrate the absence of comparable structures in the chaetal follicles of adults and juveniles (older than 1 week), as well as during active chaetogenesis, underscoring the transient nature of these glands. This indicates that larval chaetal follicles transform into a gland that later disappears. Utilizing histology and transmission electron microscopy, we characterized these glands. Our findings underscore the diversity of chaetal ultrastructure in annelids and show that, even in well-studied species, novel morphological details can be found. We emphasize the importance of examining various life-history stages to capture such transient morphological features. This work lays a crucial morphological foundation and deepens our understanding of chaetae and chaetogenesis in C. teleta, paving the way for more accurate interpretations of future experimental studies on chaetogenesis in this species.

The cellular 3D printer of a marine bristle worm-chaetogenesis in Platynereis dumerilii (Audouin & Milne Edwards, 1834) (Annelida).

Annelid chaetae are extracellular chitinous structures that are formed in an extracellular epidermal invagination, the chaetal follicle. The basalmost cell of this follicle, the chaetoblast, serves like a 3D-printer as it dynamically shapes the chaeta. During chaetogenesis apical microvilli of the chaetoblast form the template for the chaeta, any structural details result from modulating the microvilli pattern. This study describes this process in detail in the model organism Platynereis dumerilii and clarifies some aspects of chaetogenesis in its close relative Nereis vexillosa, the first annelid in which the ultrastructure of chaetogenesis had been described. Nereid species possess compound chaetae characteristic for numerous subgroups of errant annelids. The distal most section of these chaetae is movable; a hinge connects this part of the chaeta to the shaft. Modulation of the microvilli and differences in their structure, diameter and number of microvilli, and their withdrawal and reappearance determine the shape of these compound chaetae. Chaetal structure and pattern also change during life history. While larvae possess a single type of chaeta (in addition to internal aciculae), juveniles and adults possess two types of chaetae that are replaced by large paddle-shaped chaetae in swimming epitokous stages. Chaetogenesis is a continuous process that lasts during the entire lifespan. The detailed developmental sequence of chaetae and their site of formation are very similar within species and species groups. We expect that similarity results from a conserved gene regulatory network making this an optimal system to test the phylogenetic affinity of taxa and the homology of their chaetae.

Genomic Adaptations to an Endoparasitic Lifestyle in the Morphologically Atypical Crustacean Sacculina carcini (Cirripedia: Rhizocephala).

The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental program, we produced a draft genome sequence for comparison with the genomes of nonparasitic barnacles and characterized the transcriptomes of internal and external tissues. The comparison of clusters of orthologous genes revealed the depletion of multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans. Transcriptomic analyses comparing interna and externa tissues revealed an unexpected variation of gene expression between rootlets sampled around host midgut and thoracic ganglia. Genes associated with lipid uptake were strongly expressed by the internal tissues. We identified candidate genes probably involved in host manipulation (suppression of ecdysis and gonad development) including those encoding crustacean neurohormones and the juvenile hormone binding protein. The evolution of Rhizocephala therefore appears to have involved a rapid turnover of genes (losses and expansions) as well as the fine tuning of gene expression.

Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research.

BACKGROUND: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? QUESTIONS: Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. RESULTS: We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information-a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. CONCLUSIONS: We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences.

Chaetal arrangement and type diversity in two Magelona species (Magelonidae, Annelida) with ultrastructural details of the internal support chaetae.

The systematics of Annelida has repeatedly been changed based on morphological data, but more recently established transcriptomic approaches yielded a stable and widely accepted phylogenetic tree, placing Magelonidae and Oweniidae as sister group to all remaining annelids. This led to an increased interest in these groups in terms of morphological traits and their phylogenetic significance. As one of the most characteristic morphological characters of annelids, the chaetae of Magelonidae are well investigated regarding their shape, but phylogenetically relevant aspects like their general arrangement are still poorly studied. Furthermore, some species possess abdominal internal support chaetae that no study has addressed in detail thus far. The chaetal arrangement and position of formative sites were studied in the differently expressed parapodia of the thorax, the ninth chaetiger and the abdomen of Magelona mirabilis and Magelona johnstoni. Our results show that all chaetigers primarily bore one row of chaetae per parapodial ramus, each with a single formative site. We also present the first histological as well as ultrastructural data on the magelonid support chaetae, showing that they represent internal hooded hooks, with which they share a common chaetal sac. Their distribution within Magelonidae, however, still requires a broader examination to evaluate their presence as a convergent or homologous trait.

Ultrastructure of cerebral eyes in Oweniidae and Chaetopteridae (Annelida) - implications for the evolution of eyes in Annelida.

BACKGROUND: Recent phylogenomic studies have revealed a robust, new hypothesis of annelid phylogeny. Most surprisingly, a few early branching lineages formed a basal grade, whereas the majority of taxa were categorized as monophyletic Pleistoannelida. Members of these basal groups show a comparatively simple organization lacking certain characters regarded to be annelid specific. Thus, the evolution of organ systems and the characteristics probably present in the last common annelid ancestor require reevaluation. With respect to light-sensitive organs, a pair of simple larval eyes is regarded as being present in their last common ancestor. However, the evolutionary origin and structure of adult eyes remain obscure. Typically, adult eyes are multicellular pigment cups or pinhole eyes with or without a lens comprising rhabdomeric photoreceptor cells (PRCs) and pigmented supportive cells (PSCs) in converse design. However, in the most basal lineages, eyes are only present in a few taxa, and thus far, their ultrastructure is unknown. RESULTS: Ultrastructural investigations of members of Oweniidae and Chaetopteridae reveal a corresponding design of adult cerebral eyes and PRCs. The eyes in species of these groups are simple pigment spot eyes, either forming a flat patch or embedded in a tube-like invagination. They are part of the epidermis and comprise two cell types, PSCs and rhabdomeric PRCs. Both cell types bear microvilli and one more or less reduced cilium. However, the PRCs showed only a moderate increase in the apical membrane surface in the form of irregularly arranged microvilli intermingling with those of the PSCs; a densely arranged brush border of rhabdomeric microvilli was absent. Additionally, both cell types show certain characteristics elsewhere observable in typical epidermal supportive cells. CONCLUSIONS: These findings shed new light on the evolutionary history of adult eyes in Annelida. Most likely, the adult eye of the annelid stem species was a pair of simple pigment spot eyes with only slightly specialized PSCs and PRCs being an integrative part of the epidermis. As is the case for the nuchal organs, typical pigment cup adult eyes presumably evolved later in the annelid phylogeny, namely, in the stem lineages of Amphinomida and Pleistoannelida.

Getting two birds with one stone: Combining immunohistochemistry and Azan staining in animal morphology.

Classical histological stained sections have the disadvantage that fine structures, like individual neurites, or specific macromolecules, like neurotransmitters cannot be visualized. Due to its highly specific staining of only one target molecule within the cell, the visualization of delicate structures, which would be superimposed by other tissue layers in classical Azan staining, is possible with immunohistochemistry. However, using immunohistological methods not all tissues of a specimen can be visualized at once. In contrast, density specific stains like Azan allow for a whole staining of the tissues. We provide a step by step protocol of how to combine immunohistochemistry and Azan staining in the same serial paraffin sections. The combination of both methods allows for a highly detailed investigation of structures of interest. The spatial detection of the previous, to Azan staining, gained antibody-labeled signal allows for a much better understanding of animal organ systems. By using serial sections, it is possible to create an aligned image stack that is both Azan stained and also antibody-labeled. Thus enabling a correlative approach that bridges traditional histology with immunohistochemistry in animal morphology.

Salt Transiently Inhibits Mitochondrial Energetics in Mononuclear Phagocytes.

BACKGROUND: Dietary high salt (HS) is a leading risk factor for mortality and morbidity. Serum sodium transiently increases postprandially but can also accumulate at sites of inflammation affecting differentiation and function of innate and adaptive immune cells. Here, we focus on how changes in extracellular sodium, mimicking alterations in the circulation and tissues, affect the early metabolic, transcriptional, and functional adaption of human and murine mononuclear phagocytes. METHODS: Using Seahorse technology, pulsed stable isotope-resolved metabolomics, and enzyme activity assays, we characterize the central carbon metabolism and mitochondrial function of human and murine mononuclear phagocytes under HS in vitro. HS as well as pharmacological uncoupling of the electron transport chain under normal salt is used to analyze mitochondrial function on immune cell activation and function (as determined by Escherichiacoli killing and CD4+ T cell migration capacity). In 2 independent clinical studies, we analyze the effect of a HS diet during 2 weeks (URL: http://www.clinicaltrials.gov. Unique identifier: NCT02509962) and short-term salt challenge by a single meal (URL: http://www.clinicaltrials.gov. Unique identifier: NCT04175249) on mitochondrial function of human monocytes in vivo. RESULTS: Extracellular sodium was taken up into the intracellular compartment, followed by the inhibition of mitochondrial respiration in murine and human macrophages. Mechanistically, HS reduces mitochondrial membrane potential, electron transport chain complex II activity, oxygen consumption, and ATP production independently of the polarization status of macrophages. Subsequently, cell activation is altered with improved bactericidal function in HS-treated M1-like macrophages and diminished CD4+ T cell migration in HS-treated M2-like macrophages. Pharmacological uncoupling of the electron transport chain under normal salt phenocopies HS-induced transcriptional changes and bactericidal function of human and murine mononuclear phagocytes. Clinically, also in vivo, rise in plasma sodium concentration within the physiological range reversibly reduces mitochondrial function in human monocytes. In both a 14-day and single meal HS challenge, healthy volunteers displayed a plasma sodium increase of [Formula: see text] and [Formula: see text] respectively, that correlated with decreased monocytic mitochondrial oxygen consumption. CONCLUSIONS: Our data identify the disturbance of mitochondrial respiration as the initial step by which HS mechanistically influences immune cell function. Although these functional changes might help to resolve bacterial infections, a shift toward proinflammation could accelerate inflammatory cardiovascular disease.

Commentary on: "Unravelling the ultrastructure and mineralogical composition of fireworm stinging bristles" by Righi et al. 2020.

In a recent paper published in Zoology, Righi et al. (2020) investigated the chaetae of the venomous fireworm Hermodice carunculata (Amphinomida, Annelida) and revived the hypothesis of venom injection by hollow chaetae. This conclusion reached by Rigihi et al. (2020) contradicts previously published results, and in our opinion, it is also not supported by their data. We propose the idea that broken chaetae cause lesions and unprotected exposure to venomous epidermal mucous. Herein we also provide further data that show the artificial nature of the empty core of the calcareous bristles. We further emphasise that there is no evidence for venom storage within the chaetae. The idea that fireworm's chaetae are equipped with a venom delivery mechanism, analogous to hypodermic needles, must be considered as refuted. We hope our commentary may help future clarification of venom delivery in fireworms.

The anatomy and development of the nervous system in Magelonidae (Annelida) - insights into the evolution of the annelid brain.

BACKGROUND: The annelid anterior central nervous system is often described to consist of a dorsal prostomial brain, consisting of several commissures and connected to the ventral ganglionic nerve cord via circumesophageal connectives. In the light of current molecular phylogenies, our assumptions on the primary design of the nervous system in Annelida has to be reconsidered. For that purpose we provide a detailed investigation of the adult nervous system of Magelonidae - a putatively basally branching annelid family - and studied early stages of the development of the latter. RESULTS: Our comparative investigation using an integrative morphological approach shows that the nervous system of Magelonidae is located inside the epidermis. The brain is composed of an anterior compact neuropil and posteriorly encircles the prostomial coelomic cavities. From the brain two lateral medullary cords branch off which fuse caudally. Prominent brain structures such as nuchal organs, ganglia or mushroom bodies are absent and the entire nervous system is medullary. Our investigations also contradict previous investigations and present an updated view on established assumptions and descriptions. CONCLUSION: The comprehensive dataset presented herein enables a detailed investigation of the magelonid anterior central nervous system for the first time. The data reveal that early in annelid evolution complexity of brains and anterior sensory structures rises. Polymorphic neurons in clusters and distinct brain parts, as well as lateral organs - all of which are not present in outgroup taxa and in the putative magelonid sister group Oweniidae - already evolved in Magelonidae. Commissures inside the brain, ganglia and nuchal organs, however, most likely evolved in the stem lineage of Amphinomidae + Sipuncula and Pleistoannelida (Errantia+ Sedentaria). The investigation demonstrates the necessity to continuously question established descriptions and interpretations of earlier publications and the need for transparent datasets. Our results also hint towards a stronger inclusion of larval morphology and developmental investigations in order to understand adult morphological features, not only in Annelida.

The central nervous system of Oweniidae (Annelida) and its implications for the structure of the ancestral annelid brain.

BACKGROUND: Recent phylogenomic analyses congruently reveal a basal clade which consists of Oweniidae and Mageloniidae as sister group to the remaining Annelida. These results indicate that the last common ancestor of Annelida was a tube-dwelling organism. They also challenge traditional evolutionary hypotheses of different organ systems, among them the nervous system. In textbooks the central nervous system is described as consisting of a ganglionic ventral nervous system and a dorsally located brain with different tracts that connect certain parts of the brain to each other. Only limited information on the fine structure, however, is available for Oweniidae, which constitute the sister group (possibly together with Magelonidae) to all remaining annelids. RESULTS: The brain of Oweniidae is ring- shaped and basiepidermal. Ganglia, higher brain centers or complex sensory organs do not exist; instead the central nervous system is medullary. Posterior to the brain the ventral medullary cord arises directly from the ventral region of the brain in Myriowenia sp. while in Owenia fusiformis two medullary cords arise perpendicular to the brain ring, extend caudally and fuse posterior. The central nervous system is composed of a central neuropil and surrounding somata of the neurons. According to ultrastructural and histological data only one type of neuron is present in the central nervous system. CONCLUSION: The central nervous system of Oweniidae is the simplest in terms of enlargement of the dorsal part of the brain and neuron distribution found among Annelida. Our investigation suggests that neither ganglia nor commissures inside the brain neuropil or clusters of polymorphic neurons were present in the annelid stem species. These structures evolved later within Annelida, most likely in the stem lineage of Amphinomidae, Sipuncula and Pleistoannelida. Palps were supposedly present in the last common ancestor of annelids and innervated by two nerves originating in the dorsal part of the brain. A broader comparison with species of each major spiralian clade shows the medullary nervous system to be a common feature and thus possibly representing the ancestral state of the spiralian nervous system. Moreover, ganglia and clusters of polymorphic neurons seemingly evolved independently in the compared taxa of Spiralia and Annelida.

Convergent evolution of the ladder-like ventral nerve cord in Annelida.

BACKGROUND: A median, segmented, annelid nerve cord has repeatedly been compared to the arthropod and vertebrate nerve cords and became the most used textbook representation of the annelid nervous system. Recent phylogenomic analyses, however, challenge the hypothesis that a subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a paired serial chain of ganglia and somata-free connectives represents either a plesiomorphic or a typical condition in annelids. RESULTS: Using a comparative approach by combining phylogenomic analyses with morphological methods (immunohistochemistry and CLSM, histology and TEM), we compiled a comprehensive dataset to reconstruct the evolution of the annelid VNC. Our phylogenomic analyses generally support previous topologies. However, the so far hard-to-place Apistobranchidae and Psammodrilidae are now incorporated among the basally branching annelids with high support. Based on this topology we reconstruct an intraepidermal VNC as the ancestral state in Annelida. Thus, a subepidermal ladder-like nerve cord clearly represents a derived condition. CONCLUSIONS: Based on the presented data, a ladder-like appearance of the ventral nerve cord evolved repeatedly, and independently of the transition from an intraepidermal to a subepidermal cord during annelid evolution. Our investigations thereby propose an alternative set of neuroanatomical characteristics for the last common ancestor of Annelida or perhaps even Spiralia.

Early evolution of radial glial cells in Bilateria.

Bilaterians usually possess a central nervous system, composed of neurons and supportive cells called glial cells. Whereas neuronal cells are highly comparable in all these animals, glial cells apparently differ, and in deuterostomes, radial glial cells are found. These particular secretory glial cells may represent the archetype of all (macro) glial cells and have not been reported from protostomes so far. This has caused controversial discussions of whether glial cells represent a homologous bilaterian characteristic or whether they (and thus, centralized nervous systems) evolved convergently in the two main clades of bilaterians. By using histology, transmission electron microscopy, immunolabelling and whole-mount in situ hybridization, we show here that protostomes also possess radial glia-like cells, which are very likely to be homologous to those of deuterostomes. Moreover, our antibody staining indicates that the secretory character of radial glial cells is maintained throughout their various evolutionary adaptations. This implies an early evolution of radial glial cells in the last common ancestor of Protostomia and Deuterostomia. Furthermore, it suggests that an intraepidermal nervous system-composed of sensory cells, neurons and radial glial cells-was probably the plesiomorphic condition in the bilaterian ancestor.

Getting to the root of fireworms' stinging chaetae-chaetal arrangement and ultrastructure of Eurythoe complanata (Pallas, 1766) (Amphinomida).

Amphinomid species are since long known to cause urtication upon contact with the human skin. Since it has been reported that amphinomid chaetae are hollow, it has repeatedly been suggested that poison is injected upon epidermal contact. To test predictions for the structural correlate of such a stinging device we studied the structure and formation of chaetae in the fireworm Eurythoe complanata (Amphinomida). Neither the structure of the chaetae nor their formation and their position within the parapodium provide evidence for their function as hollow needles to inject poison. The chaetae even turned out to be not hollow, but containing calcareous depositions. The latter most likely cause artificial ruptures of delicate chitin lamellae in the inner of the chaeta when treated with acidic fixatives. Inorganic calcium compounds harden the chaetae and make them brittle so that they break easily. Additional information on the structure of the chaetal sac, the site of formation and the acicula do not contradict the position of the Amphinomida within Annelida as revealed by phylogenomic studies.

Structure, function and cell dynamics during chaetogenesis of abdominal uncini in Sabellaria alveolata (Sabellariidae, Annelida).

BACKGROUND: Dynamic apical microvilli of a single cell, called the chaetoblast, inside an ectodermal invagination form the template of annelid chaetae. Changes in the pattern of microvilli are frozen in time by release of chitin, such that the structure of the definitive chaeta reflects its formation. Cellular interactions during chaetogenesis also influence the structure of the chaeta. Analysing chaetogenesis allows for testing hypotheses on the homology of certain chaetal types. We used this approach to test whether the unusual uncini in Sabellaria alveolata are homologous to apparently similar uncini in other annelid taxa. RESULTS: Our study reveals unexpected details of sabellariid uncini, which mechanically reinforce the neuropodia enabling their use as paddles. The final structure of the chaeta is caused by pulses of microvilli formation and dynamic interaction between the chaetoblast and adjoining follicle cells. Cell dynamics during chaetogenesis of the uncini in Sabellaria alveolata exceeds by far that reported in previous studies on the formation of this type of chaetae. CONCLUSION: Despite the superficial similarity of uncini in sabellariids and other annelids, differences in structure and details of formation do not support the homology of this type of chaetae. Chaetogenesis of sabellariid uncini involves unexpected microvilli and cell dynamics, and provides evidence that interactions between cells play a larger role in chaetogenesis than previously expected. In addition to their function as anchors, uncini in Sabellaridae stabilize the paddle-shaped notopodia, as each uncinus possesses a long, thin rod that extends deeply into the notopodium. The rods of all uncini in a single row form a bundle inside the notopodium that additionally serves as a muscle attachment site and thus have a similar function to the inner chaeta (acicula) of errant polychaetes (Aciculata).

Observations and Experiments on the Biology and Life History of Riseriellus occultus (Heteronemertea: Lineidae).

Studies on the biology and life history of nemerteans are scarce, mostly because these animals are nocturnal. In order to broaden the knowledge base on the life history of nemerteans as a prerequisite for comparative analyses, we studied a population of Riseriellus occultus (Heteronemertea: Lineidae) inhabiting the rocky intertidal in southern Brittany near Concarneau (France) for more than 10 years. Our studies show that R. occultus is an iteroparous, perennial species exclusively inhabiting rocky shore crevices that result from onionskin weathering of the granite. From September through October R. occultus reproduces by external fertilization and develops via a planktonic pilidium larva, which, under laboratory conditions, metamorphoses after about six weeks. Adults of R. occultus are nocturnal macrophagous predators that preferentially feed on the gastropods Gibbula umbilicalis and Patella species, but also consume the bivalve Mytilus edulis. Since R. occultus devours the snail inside the shell, we fixed individuals while feeding, and serially sectioned them. Reconstruction of the sections shows that R. occultus swallows the entire soft body and finally detaches the columellar muscle from the shell. Estimates on the density of R. occultus inside the rock crevices provide evidence for clustered distribution and locally high abundance on the rocky shore. These data strongly suggest that R. occultus affects the structure of the rocky shore gastropod community. Although our data are still fragmentary with respect to the ecology of this species and its role in the local food web, our knowledge has grown to such extent that R. occultus can now be regarded as one of the few well characterized nemertean species.

Homology and evolution of the chaetae in Echiura (Annelida).

Echiura is traditionally regarded as a small phylum of unsegmented spiralian worms. Molecular analyses, however, provide unquestionable evidence that Echiura are derived annelids that lost segmentation. Like annelids, echiurans possess chaetae, a single ventral pair in all species and one or two additional caudal hemi-circles of chaetae in two subgroups, but their evolutionary origin and affiliation to annelid chaetae are unresolved. Since annelids possess segmental pairs of dorsal (notopodial) and ventral (neuropodial) chaetae that are arranged in a row, the ventral chaetae in Echiura either represent a single or a paired neuropodial group of chaetae, while the caudal circle may represent fused rows of chaetae. In annelids, chaetogenesis is generally restricted to the ventral part of the notopodial chaetal sac and to the dorsal part of the neuropodial chaetal sac. We used the exact position of the chaetal formation site in the echiuran species, Thalassema thalassemum (Pallas, 1766) and Echiurus echiurus (Pallas, 1767), to test different hypotheses of the evolution of echiurid chaetae. As in annelids, a single chaetoblast is responsible for chaetogenesis in both species. Each chaeta of the ventral pair arises from its own chaetal sac and possesses a lateral formation site, evidencing that the pair of ventral chaetae in Echiura is homologous to a pair of neuropodia that fused on the ventral side, while the notopodia were reduced. Both caudal hemi-circles of chaetae in Echiurus echiurus are composed of several individual chaetal sacs, each with its own formative site. This finding argues against a homology of these hemi-circles of chaetae and annelids' rows of chaetae and leads to the hypothesis that the caudal chaetal rings evolved once within the Echiura by multiplication of ventral chaetae.

The nervous systems of basally branching nemertea (palaeonemertea).

In recent years, a lot of studies have been published dealing with the anatomy of the nervous system in different spiralian species. The only nemertean species investigated in this context probably shows derived characters and thus the conditions found there are not useful in inferring the relationship between nemerteans and other spiralian taxa. Ingroup relationships within Nemertea are still unclear, but there is some agreement that the palaeonemerteans form a basal, paraphyletic grade. Thus, palaeonemertean species are likely the most informative when comparing with other invertebrate groups. We therefore analyzed the nervous system of several palaeonemertean species by combining histology and immunostaining. 3D reconstructions based on the aligned slices were performed to get an overall impression of the central nervous system, and immunohistochemistry was chosen to reveal fine structures and to be able to compare the data with recently published results. The insights presented here permit a first attempt to reconstruct the primary organization of the nemertean nervous system. This comparative analysis allows substantiating homology hypotheses for nerves of the peripheral nervous system. This study also provides evidence that the nemertean brain primarily consists of two lobes connected by a strong ventral commissure and one to several dorsal commissures. During nemertean evolution, the brain underwent continuous compartmentalization into a pair of dorsal and ventral lobes interconnected by commissures and lateral tracts. Given that this conclusion can be corroborated by cladistic analyses, nemerteans should share a common ancestor with spiralians that primarily have a simple brain consisting of paired medullary, frontally commissurized and reinforced cords. Such an organization resembles the situation found in presumably basally branching annelids or mollusks.

Fiat or bona fide boundary--a matter of granular perspective.

BACKGROUND: Distinguishing bona fide (i.e. natural) and fiat (i.e. artificial) physical boundaries plays a key role for distinguishing natural from artificial material entities and is thus relevant to any scientific formal foundational top-level ontology, as for instance the Basic Formal Ontology (BFO). In BFO, the distinction is essential for demarcating two foundational categories of material entity: object and fiat object part. The commonly used basis for demarcating bona fide from fiat boundary refers to two criteria: (i) intrinsic qualities of the boundary bearers (i.e. spatial/physical discontinuity, qualitative heterogeneity) and (ii) mind-independent existence of the boundary. The resulting distinction of bona fide and fiat boundaries is considered to be categorial and exhaustive. METHODOLOGY/PRINCIPAL FINDINGS: By Referring to various examples from biology, we demonstrate that the hitherto used distinction of boundaries is not categorial: (i) spatial/physical discontinuity is a matter of scale and the differentiation of bona fide and fiat boundaries is thus granularity-dependent, and (ii) this differentiation is not absolute, but comes in degrees. By reducing the demarcation criteria to mind-independence and by also considering dispositions and historical relations of the bearers of boundaries, instead of only considering their spatio-structural properties, we demonstrate with various examples that spatio-structurally fiat boundaries can nevertheless be mind-independent and in this sense bona fide. CONCLUSIONS/SIGNIFICANCE: We argue that the ontological status of a given boundary is perspective-dependent and that the strictly spatio-structural demarcation criteria follow a static perspective that is ignorant of causality and the dynamics of reality. Based on a distinction of several ontologically independent perspectives, we suggest different types of boundaries and corresponding material entities, including boundaries based on function (locomotion, physiology, ecology, development, reproduction) and common history (development, heredity, evolution). We argue that for each perspective one can differentiate respective bona fide from fiat boundaries.

Accommodating ontologies to biological reality--top-level categories of cumulative-constitutively organized material entities.

BACKGROUND: The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. 'object', 'fiat object part', 'object aggregate') must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. METHODOLOGY/PRINCIPAL FINDINGS: Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for 'portion of matter' as another material building block. This implies the necessity for further extending BFO by 'portion of matter' as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. CONCLUSIONS/SIGNIFICANCE: We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle.