[Show abstract][Hide abstract] ABSTRACT: Modern microscopical methods like µCT, FIB, and cLSM have almost replaced traditional histology in the comparative study of animal anatomy. The main advantage of these modern methods is the provision of volume data that represent anatomical structures in their original arrangement and thus enable automated image processing for anatomical 3D reconstruction.
Histology on the other hand provides a higher resolution at cellular level and profoundly eases unambiguous interpretation of the data due to differential, tissue specific stains. .Yet, the use of serial section histology for 3D reconstruction underlay three drawbacks: 1) Image data must be acquired section by section and transformed into an aligned image stack. 2) Structure labeling in terms of segmentation of images cannot be automated. 3) High resolution image stacks comprise several gigabytes of data and thus are difficult to handle by software for processing and publication. The latter impedes sharing of original data sets and enforces researchers to rely on morphological descriptions and diagnoses provided by others. Here we present a standardized work flow for serial section histology to circumvent these difficulties. In short, we use a semi-automated microscope to acquire high resolution image data. The images are collected into a stack and aligned semi-automatically. The subsequent conversion of the image data into small tiles allows manual segmentation at any level of resolution. The data are finally deposited in the database MorphDBase where they can be accessed freely by other researchers. A survey in brain morphology of diverse bilaterian taxa demonstrates that this work flow fastens serial section histology dramatically and results in comparable, openly accessible and well-documented research data.
[Show abstract][Hide abstract] ABSTRACT: 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.
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.
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.
PLoS ONE 12/2012; 7(12):e48603. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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.
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.
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.
PLoS ONE 01/2012; 7(1):e30004. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Recent molecular analyses consistently resolve the “spoon worms” (Echiura) as a subgroup of the Annelida, but their closest
relatives among annelids still remain unclear. Since the adult morphology of echiurans yields limited insight into their ancestry,
we focused on characters of their larval anatomy to contribute to this discussion. Electron microscopical studies of the larval
protonephridia (so-called head kidneys) of the echiuran species Thalassema
thalassemum revealed distinct correspondences to character states in serpulid polychaetes, although a close relationship between Echiura
and Serpulidae is not supported by any phylogenetic analysis. The larval head kidneys of T. thalassemum consist of only two cells, a terminal cell and a duct cell. The terminal cell forms a tuft of six cilia projecting into the
lumen of the terminal cell. The cilia are devoid of circumciliary microvilli. A filter structure is formed by two to three
layers of elongate microvilli that surround the lumen of the terminal cell in a tubular manner. A thin layer of extracellular
matrix (ECM) encloses the outer microvilli of the tubular structure. The tips of the microvilli project into the lumen of
the adjacent duct cell but are not directly connected to it. However, mechanic coupling is facilitated by the surrounding
ECM and abundant hemidesmosomes. The distal end of the multiciliary duct cell forms the external opening of the nephridium;
a specialized nephropore cell is absent. Apart from the multiciliarity of the duct cell, details of the head kidneys in T. thalassemum reveal no support for the current assumption that Echiura is closely related to Capitellida and/or Terebelliformia. Available
data for other echiuran species, however, suggest that the head kidneys of T. thalassemum show a derived state within Echiura.
[Show abstract][Hide abstract] ABSTRACT: 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.
PLoS ONE 04/2011; 6(4):e18794. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 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.
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.
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.
[Show abstract][Hide abstract] ABSTRACT: The Ecdysozoa-hypothesis on the origin of arthropods questions the homology of segmentation in arthropods, onychophorans,
and annelids. The implication of convergent gain of metamery in these groups seems to conflict particularly with the correspondence
in the development of serial coelomic cavities and metanephridia. Ultrastructural studies of the mesoderm development in Onychophora
revealed that main correspondence with the state in annelids concerns the involvement of epithelial lining cells of the embryonic
coelomic cavities in the formation of the visceral and somatic musculature. The significance of this correspondence, however,
remained unclear as comparable data on the state in arthropods were still missing. Developmental studies on selected representatives
covering all major arthropod subgroups aim to fill in this gap. Data were raised by a combination of transmission electron
microscopy and fluorescent stainings of the muscular system and nuclei for the anostracan crustacean Artemia salina. In this species, putative transitory coelomic cavities proved to be absent in all trunk segments. In the second antennal
and second maxillary segments small, compact nephridial anlagen develop into a sacculus and excretory duct. The sacculus originates
from the terminal cells of the nephridial duct, which is formed in advance. The lumen of the sacculus is inconspicuous in
its earliest functional stage and later enlarges to a bulb; it accordingly represents no remnant of any primarily large coelomic
cavity. The muscular system is entirely formed prior to and independent of coelomic or nephridial anlagen. Visceral and somatic
mesoderm already separate in the caudal body region. Transitory segmental clusters of mesodermal cells are composed of somatic
cells only and accordingly represent no “somites”. Our observations overall do not provide any support for the homology of
coelomic cavities in annelids and arthropods.
[Show abstract][Hide abstract] ABSTRACT: In early developmental stages of Erpobdella octoculata two pairs of transitory nephridia occur which degenerate during the formation of the body segments. Because in the ground
pattern of Annelida the first nephridia formed during ontogenesis are protonephridia, it can be assumed that the transitory
nephridia of E. octoculata are homologous to the larval protonephridia (head kidneys) of Polychaeta. To test this hypothesis two cryptolarvae of E. octoculata were investigated ultrastructurally. Both pairs of transitory nephridia are serially arranged to either side of the midgut
vestigium. Each organ consists of a coiled duct that opens separately to the exterior by an intraepidermal nephridiopore cell.
The duct is percellular and formed by seventeen cells. Adluminal adherens and septate junctions connect all duct cells; the
most proximal duct cell completely encloses the terminal end of the duct lumen. A filtration structure characteristic for
protonephridia is lacking. Additionally, the entire organ lacks an inner ciliation. Morphologically and ultrastructurally
the transitory nephridia of E. octoculata show far reaching congruencies with the segmental metanephridia in different species of the Hirudinea. These congruencies
support the assumption that formation of transitory nephridia and definitive metanephridia in Hirudinea depends on the same
genetic information. The same inherited information is assumed to cause the development of larval head kidneys and subsequently
formed nephridia in different species of the Polychaeta. Thus, the presumed identical fate of a segmentally repeated nephridial
anlage supports the hypothesis of a homology between the transitory nephridia in Hirudinea species and the protonephridial
head kidneys in the ground pattern of the Polychaeta. We, therefore, assume that functional constraints lead to a modification
of the protonephridial head kidneys in Hirudinea and explain ultrastructural differences between the transitory nephridia
in Hirudinea and the protonephridia in Polychaeta.