Growth patterns in Onychophora (velvet worms): lack of a localised posterior proliferation zone

<p>Abstract</p> <p>Background</p> <p>During embryonic development of segmented animals, body segments are thought to arise from the so-called "posterior growth zone" and the occurrence of this "zone" has been used to support the homology of segmentation between arthropods, annelids, and vertebrates. However, the term "posterior growth zone" is used ambiguously in the literature, mostly referring to a region of increased proliferation at the posterior end of the embryo. To determine whether such a localised posterior proliferation zone is an ancestral feature of Panarthropoda (Onychophora + Tardigrada + Arthropoda), we examined cell division patterns in embryos of Onychophora.</p> <p>Results</p> <p>Using in vivo incorporation of the DNA replication marker BrdU (5-bromo-2'-deoxyuridine) and anti-phospho-histone H3 immunolabelling, we found that a localised posterior region of proliferating cells does not occur at any developmental stage in onychophoran embryos. This contrasts with a localised pattern of cell divisions at the posterior end of annelid embryos, which we used as a positive control. Based on our data, we present a mathematical model, which challenges the paradigm that a localised posterior proliferation zone is necessary for segment patterning in short germ developing arthropods.</p> <p>Conclusions</p> <p>Our findings suggest that a posterior proliferation zone was absent in the last common ancestor of Onychophora and Arthropoda. By comparing our data from Onychophora with those from annelids, arthropods, and chordates, we suggest that the occurrence of a "posterior growth zone" currently cannot be used to support the homology of segmentation between these three animal groups.</p

Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology

Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., 'object', 'fiat object part', 'object aggregate') must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them.By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: 'fiat object part aggregate' and 'object with fiat object part aggregate'. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity.We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our result, however, depends on the premise that all material entities are organized according to a constitutive granularity

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

Ultrastructure and phylogenetic significance of the transitory nephridia in Dendrobaena veneta and Tubifex sp. (Annelida: Clitellata)

Titel, Inhaltsverzeichnis 1 Einleitung 1 2 Material und Methoden 6 3 Ergebnisse 10 4 Diskussion 51 5 Zusammenfassung 70 6 Absract 72 7 Literatur 74 8 Anhang 83Frühe Entwicklungsstadien der Tubificidae, Lumbriculidae und Lumbricidae weisen ein Paar transitorischer Nephridien auf, die mit der Ausbildung der segmentalen Metanephridien degenerieren. Die frühe ontogenetische Entwicklung und die Lage der Organe deuten auf eine Homologie mit den in Larvalstadien von Polychaeten und Mollusken auftretenden Head Kidneys hin. Damit ist zu erwarten, dass ultrastrukturelle Merkmale dieser Organe Hinweise auf die phylogenetische Einordnung der Clitellaten innerhalb der Anneliden liefern. In der vorliegenden Arbeit wurde die Entwicklung und Ultrastruktur der transitorischen Nephridien von Dendrobaena veneta (Clitellata, Lumbricidae) und Tubifex sp. (Clitellata, Tubificidae) untersucht. Bei D. veneta bilden die Nephridien schlaufenförmige Kanäle, die in der primären Leibeshöhle zwischen Darmanlage und Epidermis verlaufen. An ihrem proximalen Ende besitzt jedes Nephridium ein offenes Nephrostom. Der Kanal des rechten Nephridiums besteht aus zwei multiciliär bewimperten Zellen, einer Nephrostomzelle und einer Kanalzelle. Beide Zellen umfassen etwa die Hälfte des schlaufenförmigen Kanals. Der Kanal und das Nephrostom des linken Nephridiums werden von nur einer Zelle gebildet. In jüngeren Entwicklungsstadien befinden sich die Nephrostomata der transitorischen Nephridien in einer von Darmanlage und ektomesodermalem Gewebe umgebenen primären Leibeshöhle. Von ventrocaudal grenzt zusätzlich das Mesoderm der Keimstreifen an diesen Hohlraum. Im untersuchten älteren Stadium münden die Nephrostomata in ein den Pharynx ringförmig umgebendes peristoiales Coelom. Die Coelothelien dieses Coelomraumes entstehen aus Ektomesoderm und frontalen Anteilen des Keimstreifenmesoderms. Distal schließt sich bei beiden Nephridien eine von invaginierten Epidermiszellen gebildete Blase an den Kanal an. Bei Tubifex sp. werden beide transitorischen Nephridien von einer Nephrostomzelle und einer Kanalzelle gebildet. Die Nephrostomata der transitorischen Nephridien öffnen sich jeweils in eine dorsolateral der Pharynxanlage gelegene primäre Leibeshöhle, die von der Darmanlage und ektomesodermalen Zellen begrenzt wird. Jedes Nephridium mündet über einen von der Kanalzelle gebildeten intraepidermalen Nephroporus aus, eine epidermale Blase tritt nicht auf. Anhand der ultrastrukturellen Daten kann für das Grundmuster der Clitellaten ein Paar transitorischer Nephridien angenommen werden, die jeweils aus zwei multiciliären Zellen bestehen. Die Nephridien weisen jeweils ein offenes Nephrostom auf. Die Lage der Nephrostomata und die Struktur der primären Leibeshöhlen bei Tubifex sp. und im jüngeren Stadium von D. veneta zeigen, dass das peristomiale Coelom von ektomesodermalem Gewebe und frontalen Anteilen des Mesoderms der Keimstreifen gebildet wird. Dementsprechend lassen sich die transitorischen Nephridien eindeutig einem vor den segmentalen Coelomräumen gelegenem Kopfbereich zuordnen. Der Aufbau der Nephridien aus wenigen Zellen ist ein weiteres Merkmal, das die Hypothese einer Homologie zu den Head Kidneys von Polychaeten und Mollusken stützt. Head Kidneys mit einem offenen Nephrostom treten innerhalb der Polychaeten bei Vertretern der Spionidae auf, die, wie Clitellaten, eine ontogenetisch frühzeitige Entwicklung des peristomialen Coeloms aufweisen. Die Ergebnisse dieser Arbeit deuten darauf hin, dass die Schwestergruppe der Clitellaten innerhalb von Taxa zu suchen ist, die eine ähnlich frühzeitige Entwicklung des Kopfmesoderms aufweisen.Developmental stages of Tubificidae, Lumbriculidae and Lumbricidae possess one pair of transitory nephridia that degenerate when the anteriormost segmental nephridia are formed. The early occurence of the organs and their position in the presumptive head area suggest that they are homologous to the head kidneys in the larvae of polychaetes and molluscs. Therefore, it can be expected that ultrastructural data of the transitory nephridia provide information about the phylogenetic position of the Clitellata within annelids. In this study the ultrastructure and development of the transitory nephridia is investigated in Tubifex sp. (Clitellata, Tubificidae) and Dendrobaena veneta (Clitellata, Lumbricidae). In D. veneta the transitory nephridia form loop-like ducts, which are situated in the primary body cavity between gut rudiment and epidermis. Each nephridium shows a small nephrostom at its proximal end. The right transitory nephridium consists of two multiciliary cells, one nephrostom and one duct cell. Both cells form about one half of the loop-like duct. The nephrostom and duct of the left nephridium is formed by one cell only. In early developmental stages the nephrostomes are situated in a primary body cavity that is surrounded by cells of the gut rudiment and ectomesodermal tissue. Additionally, the frontal part of the germ band mesoderm provides the ventrocaudal boundary of the cavity. In the older investigated stage the nephrostomes open into a peristomial coelom that completely encircles the pharynx. Its coelomic lining can be traced back to ectomesoderm and the frontal parts of the germ band mesoderm. Distally, each nephridial duct is connected to a bladder that is formed by invaginated epidermal cells. In Tubifex sp. both transitory nephridia consist of a nephrostome cell and a duct cell. The nephrostomes of the transitory nephridia open into primary body cavities, which are situated dorsolaterally to each side of the pharynx rudiment. The body cavities are bordered by cells of the gut anlage and ectomesoderm. The external opening of each nephridium is formed by the duct cell that distally pierces the epidermis. An epidermal bladder is lacking. Due to the ultrastructural data, it can be assumed that one pair of transitory nephridia belong to the ground pattern of the Clitellata. The nephridia consist of two multiciliar cells and possess open nephrostomes. The position of the nephrostomes and the structure of the primary body cavities in Tubifex sp. and the younger stage of D. veneta shows, that the peristomial coelom develops from ectomesodermal tissue and frontal parts of the germ band mesoderm. Thus, the transitory nephridia can clearly be assigned to a head region in front of the segmental coelomic cavities. The composition of the nephridia by only two cells further support the hypothesis of a homology to the head kidneys of polychaetes and molluscs. Within the Polychaeta, head kidneys with open nephrostomes occur in developmental stages of some spionid species which show a precocious development of the peristomial coelom. The ultrastructural and developmental data in the investigated "oligochaete species suggest that the sistergroup of the Clitellata can be expected within taxa with a similar early development of the presumptive head mesoderm

Bridging a Gap in Metabarcoding Research: The ASV Table Registry

Metabarcoding is a tool to routinely identify species in environmental mass-samples and thereby analyze their species composition. Using metabarcoding techniques outperforms the traditional species identification by human experts in amount, speed and quality when well curated reference data are available.Therefore, metabarcoding can be seen as the future standard method for all biological research areas where species occurrence and distribution is in question, e.g., ecological research or monitoring projects (Porter and Hajibabaei 2018).A common outcome of metabarcoding research are Amplicon Sequence Variant tables (ASV, Callahan et al. 2017). These tables combine the extracted sequences of all sampling plots with the occurrences of each sequence within a single plot. To identify the species, each sequence is searched in one or more reference databases that hold sequences and their known taxon identifications (e.g., Barcode Of Life Data system (BOLD) or the German Barcode of Life library (GBOL)). The sequence searches utilise tools like BLAST, BOLD identification engine, or vsearch. Found taxa and their taxonomy are added to the ASV tables as taxon assignments.The number and precision of taxon assignments will increase with the growth of available sequences and quality of identifications in reference databases over time (Weigand et al. 2019). The introduction of new marker sequences and improvements in search tools will further enhance the taxon assignments. Thus, the taxon assignments in ASV tables are subject to change. Projects with the aim of building up species inventories on a large scale (GBOL) or monitoring programs, like the Automated Multisensor Stations for Monitoring of BioDiversity (Wägele et al. 2022), quickly produce data sets with thousands of sequences at numerous locations.Currently, most ASV tables are stored as supplements to publications or in private repositories. This makes analysis across multiple research projects difficult and error prone as sequences and their taxon assignments are often not accessible. Efforts, like the European Bioinformatics Institute metagenomics with Mgnify serve the needs for uploading and annotating environmental DNA samples (Mitchell et al. 2017), but a registry for ASV tables with complete data life cycles is lacking.To fill this gap, we develop an ASV Table Registry as part of the German Barcode of Life III - Dark Taxa project. This allows users to:register ASV tables and sequencesupload and manage ASV tables with versioningpublish ASV tables with DOIssearch by sequences, taxa, and occurrence dataretrieve API-based dataassign taxonomic names with various tools and reference databaseskeep track of the applied search methods and parametersThe data life cycle of the uploaded ASV tables consists of several draft versions (each re-annotation with the identification pipeline creates a new draft version) and eventually a published version with a DOI. New draft versions can be created from the published version, then re-annotated and published again. The tracking of former taxon assignments allows researchers to re-evaluate data of former studies, compare them, and add new results. The ASV Table Registry developed here aims to make ASV tables FAIR (Findable, Accessible, Interoperable, and Reusable) and to foster the shared use in research projects.Future development focuses on the incorporation of the MIxS standard (Yilmaz et al. 2011) and on submission of the published data to International Nucleotide Sequence Database Collaboration (INSDC) using established dataflows from the German Federation for Biological Data (GFBio) and NFDI4biodiversity.The ASV data portal is accessible at: https://bolgermany.de/metabarcoding; the source code at: https://gitlab.leibniz-lib.de/GBOL/asv-table-registry

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/PRICIPAL 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

Using Semantics for morphological Descriptions in Morph•D•Base

Providing data in a semantically structured format has become the gold standard in data science. However, a significant amount of data is still provided as unstructured text - either because it is legacy data or because adequate tools for storing and disseminating data in a semantically structured format are still missing. We have developed a description module for Morph∙D∙Base, a semantic knowledge base for taxonomic and morphologic data, that enables users to generate highly standardized and formalized descriptions of anatomical entities using free text and ontology-based descriptions. The main organizational backbone of a description in Morph∙D∙Base is a partonomy, to which the user adds all the anatomical entities of the specimen that they want to describe. Each element of this partonomy is an instance of an ontology class and can be further described in two different ways: as semantically enriched free-text description that is annotated with terms from ontologies, and semantically through defined input forms with a wide range of ontology-terms to choose from. To facilitate the integration of the free text into a semantic context, text can be automatically annotated using jAnnotator, a javascript library that uses about 700 ontologies with more than 8.5 million classes of the National Center for Biomedical Ontology (NCBO) bioportal. Users get to choose from suggested class definitions and link them to terms in the text, resulting in a semantic markup of the text. This markup may also include labels of elements that the user already added to the partonomy. Anatomical entities marked in the text can be added to the partonomy as new elements that can subsequently be described semantically using the input forms. Each free text together with its semantic annotations is stored following the W3C Web Annotation Data Model standard (https://www.w3.org/TR/annotation-model). The whole description with the annotated free text and the formalized semantic descriptions for each element of the partonomy are saved in the tuplestore of Morph∙D∙Base. The demonstration is targeted at developers and users of data portals and will give an insight to the semantic Morph∙D∙Base knowledge base (https://proto.morphdbase.de) and jAnnotator (http://git.morphdbase.de/christian/jAnnotator)

Entry Life-Cycle with automatic Change-History & Provenance Tracking in collaborative Semantic Web Content Management Systems as implemented in SOCCOMAS

SOCCOMAS is a ready-to-use Semantic Ontology-Controlled Content Management System (http://escience.biowikifarm.net/wiki/SOCCOMAS). Each web content management system (WCMS) run by SOCCOMAS is controlled by a set of ontologies and an accompanying Java-based middleware with the data housed in a Jena tuple store. The ontologies describe the behavior of the WCMS, including all of its input forms, input controls, data schemes and workflow processes (Fig. 1). Data is organized into different types of data entries, which represent collections of data referring to a particular material entity, for instance an individual specimen. SOCCOMAS implements a suite of general processes, which can be used to manage and organize all data entry types. One category of processes manages the life-cycle of a data entry, including all required for changing between the following possible entry states: current draft version; backup draft version; recycle bin draft version; deleted draft version; current published version; previously published version. The processes also allow a user to create a revised draft based on the current published version. Another category of processes automatically tracks the overall provenance (i.e. creator, authors, creation and publication date, contributers, relation between different versions, etc.) for each particular data entry. Additionally, on a significantly finer level of granularity, SOCCOMAS also tracks in a detailed change-history log all changes made to a particular data record at the level of individual input fields. All information (data, provenance metadata, change-history metadata) is stored based on Resource Description Framework (RDF) compliant data schemes into different named graphs (i.e. a URI under which triple statements are stored in the tuple store). All recorded information can be accessed through a SPARQL endpoint. All data entries are Linked Open Data and thus provide access to an HTML representation of the data for visualization in a web-browser or as a machine-readable RDF file. The ontology-controlled design of SOCCOMAS allows administrators to easily customize already existing templates for input forms of data entries, define new templates for new types of data entries, and define underlying RDF-compliant data schemes and apply them to each relevant input field. SOCCOMAS provides an engine for running and developing semantic WCMSs, where only ontology editing, but no middleware and front end programming, are required for adapting the WCMS to one's own specific requirements

Definitions of the basic types of material entity of the Basic Formal Ontology (BFO version 1.1).

<p>Definitions of the basic types of material entity of the Basic Formal Ontology (BFO version 1.1).</p