A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of similar to 240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, "preferred terms", and "structural equivalency". We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the "URI table") by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the "Analyzer") to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

Morphology and Anatomy of Stem Mines in Cipocereus minensis (Wender.) Ritter (Cactaceae), an Endemic Species to Eastern Brazil

Plant mines are structures with the form of a cavity caused by consumption of host plant tissue by the insect's miner larvae. Plant mines are more common in leaves, but in Cipocereus minensis, a species in which the leaves are modified spines, the miner activity is restricted to the stem. The aim of this paper was to document the morphological and anatomical differences in the infected and uninfected stems of C. minensis due to the feeding habit of the mining agent. Fresh tissue samples of non-mined and mined young stem of C minensis were collected and examined in transverse sections. We hypothesize that the infection begins following mating when the females scratch the surface of the stem or while they feed on fruits and lay eggs, which subsequently develop into larvae, invading the cactus stem. The insect's miner larvae had mostly consumed the parenchyma tissue towards the center of the stem, and periderm formed along the entire path of the insect. This meristematic tissue or "wound periderm" is a common response for compartmentalization to isolate the damaged tissue, in this case the incubating chamber, in which the eggs will be placed. There were no signs of consumption of vascular tissue in the infested samples, further suggesting a compartmentalized infestation. The nest chamber was found in the stem pith region, with periderm surrounding an insect's miner pupa inside identified as a member of the Cerambycidae. The mining insect depends on a host plant to complete the life cycle; however, the nature of this partnership and the long-term effects of the insect on the plant tissue are unknown. The complex mechanisms by which herbivorous insects control the morphogenesis of the plant host are discussed. We propose that C. minensis has a recognition system to identify insect attack and evaluate the effectiveness of early response triggering compartmentalized defense mechanisms by protecting the injured area with a new layer of periderm.

Aerial organ anatomy of Smilax syphilitica (Smilacaceae)

Smilax L. in Brazil is represented by 32 taxa and it is a taxonomically difficult genus because the plants are dioecious and show wide phenotypic variation. The analysis and use of leaf anatomy characters is recognized as a frequently successful taxonomic method to distinguish between individual taxon, when floral material is absent or minute differences in flowers and foliage exist such as in Smilax. The aim of this study was to characterize the anatomical features of the aerial organs in Smilax syphilitica collected from the Atlantic Rainforest, in Santa Teresa-ES and the Smilax aff syphilitica from the Amazon Rainforest, in Manaus, Brazil. For this, a total of three samples of Smilax were collected per site. Sample leaves and stems were fixed with FAA 50, embedded in historesin, sectioned on a rotary microtome, stained and mounted in synthetic resin. Additionally, histochemical tests were performed and cuticle ornamentation was analyzed with standard scanning electron microscopy. S. syphilitica and S. aff syphilitica differed in cuticle ornamentation, epidermal cell arrangement and wall thickness, stomata type and orientation, calcium oxalate crystal type, and position of stem thorns. Leaf blades of S. syphilitica from the Amazon Rainforest have a network of rounded ridges on both sides, while in S. aff syphilitica, these ridges are parallel and the spaces between them are filled with numerous membranous platelets. Viewed from the front, the epidermal cells of S. syphilitica have sinuous walls (even more pronounced in samples from the Amazon); while in S. aff syphilitica, these cells are also sinuous but elongated in the cross-section of the blade and arranged in parallel. Stomata of S. syphilitica are paracytic, whereas in S. aff syphilitica, are both paracytic and anisocytic, and their polar axes are directed towards the mid-vein. Calcium oxalate crystals in S. syphilitica are prisms, whereas in S. aff syphilitica, crystal sand. Thorns occur in nodes and internodes in S. syphilitica but only in internodes in S. aff syphilitica. These features have proven to be of diagnostic value and may support a separation into two species, but future studies are needed to confirm that S. aff syphilitica is indeed a new taxon. Rev. Biol. Trop. 60(3): 1137-1148. Epub 2012 September 01.

Anatomy and evolution of the mandibular, hyopalatine, and opercular muscles in characiform fishes (Teleostei: Ostariophysi)

The Characiformes are distributed throughout large portions of the freshwaters of Africa and America. About 90% of the almost 2000 characiform species inhabit the American rivers, with their greatest diversity occurring in the Neotropical region. As in most other groups of fishes, the current knowledge about characiform myology is extremely poor. This study presents the results of a survey of the mandibular, hyopalatine, and opercular musculature of 65 species representing all the 18 traditionally recognized characiform families, including the 14 subfamilies and several genera incertae sedis of the Characidae, the most speciose family of the order. The morphological variation of these muscles across the order is documented in detail and the homologies of the characiform adductor mandibulae divisions are clarified. Accordingly, the mistaken nomenclature previously applied to these divisions in some characiform taxa is herein corrected. Contradicting some previous studies, we found that none of the examined characiforms lacks an A3 section of the adductor mandibulae, but instead some taxa have an A3 continuous with A2. Derived myological features are identified as new putative synapomorphies for: the Characoidei; the clade composed of the Alestidae, Characidae, Gasteropelecidae, Cynodontoidea, and Erythrinoidea; the clade Cynodontoidea plus Erythrinoidea; the clade formed by Ctenoluciidae and Erythrinidae; the Serrasalminae; and the Triportheinae. Additionally, new myological data seems to indicate that the Agoniatinae might be more closely related to cynodontoids and erythrinoids than to other characids. (C) 2012 Elsevier GmbH. All rights reserved.

Endoscopic anatomy of the palatovaginal canal (palatosphenoidal canal)

Objectives/Hypothesis: Demonstrate the endoscopic anatomy of the palatovaginal (PV) canal and artery for identification and dissection of the vidian nerve during endoscopic transpterygoid approaches. Evaluate the length of the PV canal and its relation with the vidian nerve. Show that the traditionally known PV canal is a misnomer and should be renamed. Study Design: Experimental study: anatomical and radiological. Methods: Dissection of eight cadaveric heads was performed to demonstrate the endoscopic anatomy of the PV canal. Computed tomography scan analysis of 20 patients was used to evaluate the length of the PV canal, the angle formed between this canal and the vidian nerve, and the distance between the vidian canal and the PV canal. Study of 10 dry skull bases was performed to verify the structures involved in the formation of the PV canal. Results: Anatomic steps and foundations for dissection of the vidian nerve using the PV canal as a landmark were described. The mean length of the PV canal was 7.15 mm. The mean proximal distance between the vidian and the PV canal was 1.95 mm, and the mean distal distance was 4.14 mm. The mean angle between those canals was 48 degrees. The osteology study showed the vaginal process of the sphenoid bone did not contribute to the formation of the PV canal. Conclusions: Our anatomic investigations, radiologic studies, and surgical experience demonstrate the important anatomic relationship of the PV canal with the vidian canal and the relevance of the PV canal as a surgical landmark in endoscopic endonasal transpterygoid approaches. Anatomically, PV canal is a misnomer and should be replaced with palatosphenoidal canal.

Influence of Clinically Invisible, but Optical Coherence Tomography Detected, Optic Disc Margin Anatomy on Neuroretinal Rim Evaluation

PURPOSE. We previously demonstrated that most eyes have regionally variable extensions of Bruch's membrane (BM) inside the clinically identified disc margin (DM) that are clinically and photographically invisible. We studied the impact of these findings on DM- and BM opening (BMO)-derived neuroretinal rim parameters. METHODS. Disc stereo-photography and spectral domain optical coherence tomography (SD-OCT, 24 radial B-scans centered on the optic nerve head) were performed on 30 glaucoma patients and 10 age-matched controls. Photographs were colocalized to SD-OCT data such that the DM and BMO could be visualized in each B-scan. Three parameters were computed: (1) DM-horizontal rim width (HRW), the distance between the DM and internal limiting membrane (ILM) along the DM reference plane; (2) BMO-HRW, the distance between BMO and ILM along the BMO reference plane; and (3) BMO-minimum rim width (MRW), the minimum distance between BMO and ILM. Rank-order correlations of sectors ranked by rim width and spatial concordance measured as angular distances between equivalently ranked sectors were derived. RESULTS. The average DM position was external to BMO in all quadrants, except inferotemporally. There were significant sectoral differences among all three rim parameters. DM- HRW and BMO-HRW sector ranks were better correlated (median rho = 0.84) than DM- HRW and BMO-MRW (median rho = 0.55), or BMO-HRW and BMO-MRW (median rho = 0.60) ranks. Sectors with the narrowest BMO-MRW were infrequently the same as those with the narrowest DM-HRW or BMO-HRW. CONCLUSIONS. BMO-MRW quantifies the neuroretinal rim from a true anatomical outer border and accounts for its variable trajectory at the point of measurement. (Invest Ophthalmol Vis Sci. 2012;53:1852-1860) DOI:10.1167/iovs.11-9309

Anatomy and essential oils from aerial organs in three species of Aldama (Asteraceae-Heliantheae) that have a difficult delimitation

Recently, molecular analysis caused the South American Viguiera Kunth species to be transferred to Aldama La Llave. However, the circumscription has not been established for certain of the South American species, including Aldama filifolia (Sch. Bip. ex Baker) E. E. Schill. & Panero, A. linearifolia (Chodat) E. E. Schill. & Panero and A. trichophylla (Dusen) Magenta (comb. nov.), which had previously been treated as synonyms because of their high similarity. Therefore, the present study aimed to evaluate the anatomy of the aerial organs, and the yield and chemical composition of the essential oils from these three species, to determine the differences among them and thereby assist in species distinction. The anatomical analysis identified characteristics unique to each species, which are primarily related to the position and occurrence of secretory structures. Histochemical analysis demonstrated that the glandular trichomes and the canals secrete lipophilic substances, which are characterised by the presence of essential oils. The analysis of these essential oils identified monoterpenes as their major constituent and allowed for the recognition of chemical markers for each species. The anatomical and chemical characteristics identified by the present study confirmed that the studied samples belong to three distinct taxa.

ANATOMY OF NERITINA ZEBRA FROM GUYANA AND BRAZIL (MOLLUSCA: GASTROPODA: NERITIDAE)

Neritina zebra is a common brackish water gastropod living on muddy bottoms with poorly known morphological characters. The morphology, including the variety of colour and pattern of shells, and the anatomy are described. We mainly analyzed the animals collected in the estuary of the Ceara river, Ceara, Brazil, from "Parque Estadual do rio Coco", and specimens from other places deposited in institutional collections, from French Guyana (topotypes) to Sao Paulo. A complete anatomical description is performed, including illustration and discussion ninth concerned to systematics. Amongst the more important anatomical data are: heart diotocardian; kidneys solid; anterior esophagus with pair of ventral esophageal pouches; odontophore with 4 cartilages and 2 horizontal muscles (m6, m6a); males with penis dorsal-right to snout, bearing a terminal papilla; pallial oviduct triaulic, possessing 3 pallial apertures.

Optic Disc Margin Anatomy in Patients with Glaucoma and Normal Controls with Spectral Domain Optical Coherence Tomography

Objective: To characterize optic nerve head (ONH) anatomy related to the clinical optic disc margin with spectral domain-optical coherence tomography (SD-OCT). Design: Cross-sectional study. Participants: Patients with open-angle glaucoma with focal, diffuse, and sclerotic optic disc damage, and age-matched normal controls. Methods: High-resolution radial SD-OCT B-scans centered on the ONH were analyzed at each clock hour. For each scan, the border tissue of Elschnig was classified for obliqueness (internally oblique, externally oblique, or nonoblique) and the presence of Bruch's membrane overhanging the border tissue. Optic disc stereophotographs were co-localized to SD-OCT data with customized software. The frequency with which the disc margin identified in stereophotographs coincided with (1) Bruch's membrane opening (BMO), defined as the innermost edge of Bruch's membrane; (2) Bruch's membrane/border tissue, defined as any aspect of either outside BMO or border tissue; or (3) border tissue, defined as any aspect of border tissue alone, in the B-scans was computed at each clock hour. Main Outcome Measures: The SD-OCT structures coinciding with the disc margin in stereophotographs. Results: There were 30 patients (10 with each type of disc damage) and 10 controls, with a median (range) age of 68.1 (42-86) years and 63.5 (42-77) years, respectively. Although 28 patients (93%) had 2 or more border tissue configurations, the most predominant one was internally oblique, primarily superiorly and nasally, frequently with Bruch's membrane overhang. Externally oblique border tissue was less frequent, observed mostly inferiorly and temporally. In controls, there was predominantly internally oblique configuration around the disc. Although the configurations were not statistically different between patients and controls, they were among the 3 glaucoma groups. At most locations, the SD-OCT structure most frequently identified as the disc margin was some aspect of Bruch's membrane and border tissue external to BMO. Bruch's membrane overhang was regionally present in the majority of patients with glaucoma and controls; however, in most cases it was not visible as the disc margin. Conclusions: The clinically perceived disc margin is most likely not the innermost edge of Bruch's membrane detected by SD-OCT. These findings have important implications for the automated detection of the disc margin and estimates of the neuroretinal rim. Financial Disclosure(s): Proprietary or commercial disclosure may be found after the references. Ophthalmology 2012;119:738-747 (C) 2012 by the American Academy of Ophthalmology.

Sulcus anatomy and diameter in pseudophakic eyes and correlation with biometric data: Evaluation with a 50 MHz ultrasound biomicroscope

PURPOSE: To evaluate the sulcus anatomy and possible correlations between sulcus diameter and white-to-white (WTW) diameter in pseudophakic eyes, data that may be important in the stability of add-on intraocular lenses (IOLs). SETTING: University Eye Hospital, Tuebingen, Germany. DESIGN: Case series. METHODS: In pseudophakic eyes, the axial length (AL) and horizontal WTW were measured by the IOLMaster device. Cross-sectional images were obtained with a 50 MHz ultrasound biomicroscope on the 4 meridians: vertical, horizontal (180 degrees), temporal oblique, and nasal oblique. Sulcus-to-sulcus (STS), angle-to-angle (ATA), and sclera-to-sclera (ScTSc) diameters were measured. The IOL optic diameter (6.0 mm) served as a control. To test reliability, optic measurements were repeated 5 times in a subset of eyes. RESULTS: The vertical ATA and STS diameters were statistically significantly larger than the horizontal diameter (P=.0328 and P=.0216, respectively). There was no statistically significant difference in ScTSc diameters. A weak correlation was found between WTW and horizontal ATA (r = 0.5766, P<.0001) and between WTW and horizontal STS (r = 0.5040, P=.0002). No correlation was found between WTW and horizontal ScTSc (r = 0.2217, P=.1217). CONCLUSIONS: The sulcus anatomy had a vertical oval shape with the vertical meridian being the largest, but it also had variation in the direction of the largest meridian. The WTW measurements showed a weak correlation with STS. In pseudophakic eyes, Soemmerring ring or a bulky haptic may affect the ciliary sulcus anatomy.

Anatomy, phylogeny, and palaeoecology of the basal thalattosuchians (Mesoeucrocodylia) from the Liassic of Central Europe

In the marine Jurassic deposits of Europe, a group of marine crocodilians, the Thalattosuchia, belongs to the frequently found reptiles. Thalattosuchia are widely spread in Central Europe from the Jurassic to Lower Cretaceous, and some taxa are also distributed worldwide. The task of the work was to examine all taxa known from the Liassic of Europe. The most frequently known taxa Steneosaurus bollensis and Pelagosaurus typus are anatomically revised. New discoveries at the skull of Pelagosaurus typus e.g., the fact of a partly paired frontal are described by means of computed tomography investigations. In addition, juvenile specimens of this taxon are studied in detail for the first time. The rarely occurring taxon Platysuchus multiscrobiculatus is anatomically described in detail for the first time. It shows both in the skull and in the postcranial material morphological differences to Steneosaurus bollensis and Pelagosaurus typus. Thus Pl. multiscrobiculatus possesses, e.g., an ilium with a deeper acetabulum and a femur with a distinctly flexed femoral head. A juvenile specimen of Pl. multiscrobiculatus is now discovered and is described in parts for the first time, too. Furthermore, Steneosaurus gracilirostris and Steneosaurus brevior known from Lower Jurassic deposits of England are examined and in parts revised. In this work, Steneosaurs brevior is discovered with one specimen from the Upper Liassic of Holzmaden, Germany for the first time, and provides new evidence for the palaeobiogeographical distribution of the taxon. Because of the high number of investigated specimens, it is possible to study ontogenetic development from juvenile to adult stage in Steneosaurus bollensis, Pelagosaurus typus, and Platysuchus multiscrobiculatus. Biometric data are collected from thalattosuchians and extant crocodilians (e.g. Gavialis gangeticus) to investigate intraspecific variation, ontogenetic development, and taxa differentiation. The skulls of Platysuchus multiscrobiculatus and Steneosaurus bollensis are reconstructed three-dimensionally as wax models. The skull reconstructions form the basis of the jaw muscle restoration of Steneosaurus bollensis in connection with comparative studies at extant crocodilians. By means of functional morphologic analysis of the jaw musculature, the dentition, and the locomotor system of S. bollensis, possible conclusions are drawn for the prey options and the hunting behaviour. To clarify the relationships within the Thalattosuchia, a computer-based cladistic phylogenetic in-group analyse of 25 Thalattosuchia taxa is performed. For the analysis, following Thalattosuchia taxa are studied likewise at original material for comparisons: Metriorhynchus superciliosus, Metriorhynchus hastifer, Metriorhynchus leedsi, Geosaurus gracilis, Geosaurus giganteus, Teleidosaurus calvadosi, Teleidosaurus gaudryi, Teleosaurus cadomensis, Teleosaurus geoffroyi, Steneosaurus priscus, Steneosaurus edwardsi, Steneosaurus heberti, Steneosaurus leedsi, Steneosaurus boutilieri, Steneosaurus megarhinus, Steneosaurus obtusidens, and Machimosaurus hugii. The phylogenetic in-group analyse based on 115 characters, reveals a sister-group relationship of the monophyletic Teleosauridae and monophyletic Metriorhynchidae. Within the groups, some taxa are probably paraphyletic. The taxon Pelagosaurus typus is nested inside the Teleosauridae and not outside or within the Metriorhynchidae, as many authors suggested it so far. Based on these results, a tentative palaeobiogeographical-evolutionary scenario is developed.

Demonstration of pelvic anatomy by modified midline transection that maintains intact internal pelvic organs

Gross dissection for demonstrating anatomy of the human pelvis has traditionally involved one of two approaches, each with advantages and disadvantages. Classic hemisection in the median plane through the pelvic ring transects the visceral organs but maintains two symmetric pelvic halves. An alternative paramedial transection compromises one side of the bony pelvis but leaves the internal organs intact. The authors propose a modified technique that combines advantages of both classical dissections. This novel approach involves dividing the pubic symphysis and sacrum in the median plane after shifting all internal organs to one side. The hemipelvis without internal organs is immediately available for further dissection of the lower limb. The hemipelvis with intact internal organs is ideal for showing the complex spatial relationships of the pelvic organs and vessels relative to the intact pelvic floor.

Monte Carlo Dose Calculation on Deforming Anatomy

This article presents the implementation and validation of a dose calculation approach for deforming anatomical objects. Deformation is represented by deformation vector fields leading to deformed voxel grids representing the different deformation scenarios. Particle transport in the resulting deformed voxels is handled through the approximation of voxel surfaces by triangles in the geometry implementation of the Swiss Monte Carlo Plan framework. The focus lies on the validation methodology which uses computational phantoms representing the same physical object through regular and irregular voxel grids. These phantoms are chosen such that the new implementation for a deformed voxel grid can be compared directly with an established dose calculation algorithm for regular grids. Furthermore, separate validation of the aspects voxel geometry and the density changes resulting from deformation is achieved through suitable design of the validation phantom. We show that equivalent results are obtained with the proposed method and that no statistically significant errors are introduced through the implementation for irregular voxel geometries. This enables the use of the presented and validated implementation for further investigations of dose calculation on deforming anatomy.

Teat anatomy affects requirements for udder preparation in Mediterranean buffaloes

The present study was conducted to assess the interrelation between teat anatomy and machine milking in dairy buffaloes raised in Switzerland. A 3-min pre-stimulation induced milk ejection before cluster attachment in most cases and caused an optimal milk removal during machine milking. In an additional experiment, longitudinal cross-section ultrasound was obtained before and after a 3-min pre-stimulation. Teat wall thickness, teat diameter, cisternal diameter and teat canal length were evaluated. It was observed that 3-min pre-stimulation dramatically reduced teat canal length whereas all the other anatomical parameters remained unchanged. The vacuum needed to open the teat canal was also measured before and after a 3-min pre-stimulation by using a special teat cup with only the mouthpiece of the liner remaining on the top of the teat cup (no liner, no pulsation). Without pre-stimulation but after wetting the teat canal by stripping one squirt of milk out of the teat, no milk could be withdrawn with a vacuum up to 39 kPa. However, after pre-stimulation, milk flow occurred in all buffaloes at a vacuum between 16 and 38 kPa. In the last experiment, the teat tissue was examined in slaughtered buffaloes and compared with teat tissue of cows. No difference was noted in histological sections and teat canal length was similar in cows and buffaloes. Proximal to the teat canal, the teat did not pass into an open cistern but the lumen was collapsed. In conclusion, buffaloes need to be well pre-stimulated because the tissue above the teat canal provides additional teat closure before milk ejection. Therefore, milk can only be obtained after pre-stimulation.