Sex and Biology: Broader Impacts Beyond the Binary

What are the implications of misunderstanding sex as a binary, and why is it essential for scientists to incorporate a more expansive view of biological sex in our teaching and research? This roundtable will include many of our symposium speakers, including biologists and intersex advocates, to discuss these topics and visibilize the link between ongoing reification of dyadic sex within scientific communities and the social, political, and medical oppression faced by queer, transgender, and especially intersex communities. As with the symposium as a whole, this conversation is designed to bring together empirical research and implementation of equity, inclusion, and justice principles, which are often siloed into separate rooms and conversations at academic conferences. Given the local and national attacks on the rights of intersex individuals and access to medical care and bodily autonomy, this interdisciplinary discussion is both timely and urgent.

It Takes Two to Tango: Including a Female Perspective in Reproductive Biology

Like many scientific disciplines, the field of reproductive biology is subject to biases in terminology and research foci. For example, females are often described as coy and passive players in reproductive behaviors and are termed "promiscuous" if they engage in extra-pair copulations. Males on the other hand are viewed as actively holding territories and fighting with other males. Males are termed "multiply mating" if they mate with multiple females. Similarly, textbooks often illustrate meiosis as it occurs in males but not females. This edition of Integrative and Comparative Biology (ICB) includes a series of papers that focus on reproduction from the female perspective. These papers represent a subset of the work presented in our symposium and complementary sessions on female reproductive biology. In this round table discussion, we use a question and answer format to leverage the diverse perspectives and voices involved with the symposium in an exploration of theoretical, cultural, pedagogical, and scientific issues related to the study of female biology. We hope this dialog will provide a stepping-stone toward moving reproductive science and teaching to a more inclusive and objective framework.

FluoRender: joint freehand segmentation and visualization for many-channel fluorescence data analysis

Background

Image segmentation and registration techniques have enabled biologists to place large amounts of volume data from fluorescence microscopy, morphed three-dimensionally, onto a common spatial frame. Existing tools built on volume visualization pipelines for single channel or red-green-blue (RGB) channels have become inadequate for the new challenges of fluorescence microscopy. For a three-dimensional atlas of the insect nervous system, hundreds of volume channels are rendered simultaneously, whereas fluorescence intensity values from each channel need to be preserved for versatile adjustment and analysis. Although several existing tools have incorporated support of multichannel data using various strategies, the lack of a flexible design has made true many-channel visualization and analysis unavailable. The most common practice for many-channel volume data presentation is still converting and rendering pseudosurfaces, which are inaccurate for both qualitative and quantitative evaluations.

Results

Here, we present an alternative design strategy that accommodates the visualization and analysis of about 100 volume channels, each of which can be interactively adjusted, selected, and segmented using freehand tools. Our multichannel visualization includes a multilevel streaming pipeline plus a triple-buffer compositing technique. Our method also preserves original fluorescence intensity values on graphics hardware, a crucial feature that allows graphics-processing-unit (GPU)-based processing for interactive data analysis, such as freehand segmentation. We have implemented the design strategies as a thorough restructuring of our original tool, FluoRender.

Conclusion

The redesign of FluoRender not only maintains the existing multichannel capabilities for a greatly extended number of volume channels, but also enables new analysis functions for many-channel data from emerging biomedical-imaging techniques.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1694-9) contains supplementary material, which is available to authorized users.

An overview of burning mouth syndrome for the dermatologist

Burning mouth syndrome is characterized by an idiopathic burning pain affecting the oral mucosa, with no clinically apparent changes. It can present to a variety of health professionals including dermatologists. This article summarizes the important aspects of the condition, including theories of pathogenesis, diagnosis and management.

Evolutionarily conserved morphogenetic movements at the vertebrate head-trunk interface coordinate the transport and assembly of hypopharyngeal structures

The vertebrate head–trunk interface (occipital region) has been heavily remodelled during evolution, and its development is still poorly understood. In extant jawed vertebrates, this region provides muscle precursors for the throat and tongue (hypopharyngeal/hypobranchial/hypoglossal muscle precursors, HMP) that take a stereotype path rostrally along the pharynx and are thought to reach their target sites via active migration. Yet, this projection pattern emerged in jawless vertebrates before the evolution of migratory muscle precursors. This suggests that a so far elusive, more basic transport mechanism must have existed and may still be traceable today.

Here we show for the first time that all occipital tissues participate in well-conserved cell movements. These cell movements are spearheaded by the occipital lateral mesoderm and ectoderm that split into two streams. The rostrally directed stream projects along the floor of the pharynx and reaches as far rostrally as the floor of the mandibular arch and outflow tract of the heart. Notably, this stream leads and engulfs the later emerging HMP, neural crest cells and hypoglossal nerve. When we (i) attempted to redirect hypobranchial/hypoglossal muscle precursors towards various attractants, (ii) placed non-migratory muscle precursors into the occipital environment or (iii) molecularly or (iv) genetically rendered muscle precursors non-migratory, they still followed the trajectory set by the occipital lateral mesoderm and ectoderm. Thus, we have discovered evolutionarily conserved morphogenetic movements, driven by the occipital lateral mesoderm and ectoderm, that ensure cell transport and organ assembly at the head–trunk interface.

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At the vertebrate head–trunk interface, all tissues engage in stereotype cell movements.

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A ventrally–rostrally directed stream of cells leads along the floor of the pharynx to the developing jaw and outflow tract of the heart.

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The cell movements are spearheaded by the lateral mesoderm and surface ectoderm; muscle precursors for throat and tongue muscles (hypopharyngeal muscles); neural crest cells and outgrowing axons of the hypoglossal nerve follow.

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Hypopharyngeal muscle precursors follow the trajectory set by the lateral mesoderm and ectoderm, even when challenged with ectopic attractants or when rendered non-migratory.

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The newly discovered cell movements are the likely ground state for cell transport and organ assembly at the head–trunk interface before actively migrating muscle precursors evolved in “bony” (osteichthyan) vertebrates.

A practical workflow for making anatomical atlases for biological research

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

Retroperitoneal lymph node dissection for metastatic germ cell tumours

INTRODUCTION

In the North Trent Cancer network (NTCN) patients requiring retroperitoneal lymphadenectomy for metastatic testicular cancer have been treated by vascular service since 1990. This paper reviews our experience and considers the case for involvement of vascular surgeons in the management of these tumours.

PATIENTS AND METHODS

Patients referred by the NTCN to the vascular service for retroperitoneal lymphadenectomy between 1990 and 2009 were identified through a germ cell database. Data were supplemented by a review of case notes to record histology, intraoperative and postoperative details.

RESULTS

A total of 64 patients were referred to the vascular service for retroperitoneal lymph node dissection, with a median age of 29 years (16-63 years) and a median follow-up of 4.9 years. Ten patients died: eight from tumour recurrence, one from septicaemia during chemotherapy and one by suicide. Of the 54 who survived, 7 were alive with residual masses and 47 patients were disease-free at the last follow-up. Sixteen patients required vascular procedures: four had aortic repair (fascia), three had aortic replacement (spiral graft), four had inferior vena cava resection, two had iliac artery replacement and two had iliac vein resection.

CONCLUSIONS

Retroperitoneal lymph node dissection often involves mobilisation and/or the resection/replacement of major vessels. We recommend that a vascular surgeon should be a part of testicular germ cell multidisciplinary team.

Heregulin enhances regenerative proliferation in postnatal rat utricular sensory epithelium after ototoxic damage

Hair cell loss due to acoustic and ototoxic damage often leads to hearing and balance impairments. Although a spontaneous event in chicks and lower vertebrates, hair cell replacement occurs at a much lower frequency in mammals presumably due to a very low rate of supporting cell proliferation following injury. We report here that heregulin, a member of the neuregulin family, dramatically enhances proliferation of supporting cells in postnatal rat utricular epithelial sheet cultures after gentamicin treatment, as revealed by bromo-deoxyuridine (BrdU) immunocytochemistry. A dose-dependent study shows that the maximal effects of heregulin are achieved at 3 nM. The mitogenic effects of heregulin are confirmed in utricular whole mount cultures. Autoradiography of the utricular whole mount cultures shows that heregulin also enhances the number of tritiated thymidine-labeled cells within the hair cell layer. TaqMan quantitative RT-PCR analysis and immunocytochemistry reveal that heregulin and its binding receptors (ErbB-2, ErbB-3 and ErbB-4) are expressed in the inner ear sensory epithelium. Of several ligands activating various ErbB receptors, including heregulin, neuregulin-3, beta-cellulin, heparin binding-epidermal growth factor (HB-EGF), transforming growth factor-alpha (TGF-alpha) and EGF, heregulin shows the most potent mitogenic effects on supporting cells. Because neuregulin-3 that signals only through ErbB-4 does not show an effect, these data suggest that activation of the ErbB-2-ErbB-3 heterodimeric complexes, rather than ErbB-4, is critical for the proliferative response in the utricular sensory epithelium. In addition, gentamicin treatment induces an upregulation of heregulin mRNA. Considered together, heregulin may play an important role in hair cell regeneration following ototoxic damage.

Distinct expression patterns of notch family receptors and ligands during development of the mammalian inner ear

The cochlea and vestibular structures of the inner ear labyrinth develop from the otic capsule via step-wise regional and cell fate specification. Each inner ear structure contains a sensory epithelium, composed of hair cells, the mechanosensory transducers, and supporting cells. We examined the spatio-temporal expression of genes in the Notch signaling pathway, Notch receptors (Notch1-4) and two ligands, Jagged1 and Delta1, in the developing mammalian inner ear. Our results show that Notch1 and Jagged1 are first expressed in the otic vesicle, likely involved in differentiation of the VIIIth nerve ganglion neurons, and subsequently within the inner ear sensory epithelia, temporally coincident with initial hair cell differentiation. Notch1 expression is specific to hair cells and Jagged1 to supporting cells. Their expression persists into adult. Notch2, Notch3, Notch4, and Delta1 are excluded from the inner ear epithelia. These data support the hypothesis that Notch signaling is involved in hair cell differentiation during inner ear morphogenesis.

Establishment of conditionally immortalized rat utricular epithelial cell lines using a retrovirus-mediated gene transfer technique

Supporting cells in the inner ear sensory epithelium are most likely hair cell progenitors. In an effort to establish an in vitro model system of hair cell differentiation, we developed immortalized epithelial cell lines by transferring the tsA58 allele of the SV40 large T antigen oncogene into neonatal rat utricular supporting cells using a retrovirus. The established cell lines have been stably maintained continuously for more than 25 passages and display many features similar to primary supporting cells. They grow in patches and assume a polygonal morphology. Immunocytochemical characterization of the established cell lines reveals that these cells can be labeled by epithelial cell markers, but not by fibroblast, glial or neuronal markers. The immortalized cells grow rapidly in serum medium at permissive temperature, but the majority cease proliferation when cultured in serum free medium at non-permissive temperature. These cells respond to mitogenic growth factors including bFGF, EGF and TGF-alpha and express growth factor receptors in a manner similar to the primary supporting cells. Furthermore, we find that the cells undergo a morphological differentiation when cultured in serum free medium at non-permissive temperature in the presence of bFGF. Under these conditions, the cells shrink in size, become elongated, and express early hair cell markers such as calretinin and calmodulin. The utricular epithelial cell line we have established may potentially provide an invaluable system for studying hair cell differentiation and regeneration.

Mammalian myosin I alpha is concentrated near the plasma membrane in nerve growth cones

To determine if unconventional myosins play a role in nerve outgrowth, antibodies specific for rat brain derived mammalian myosin I alpha (MMI alpha) were used to label cultured rat superior cervical ganglion nerve cells. Observations were made at both the light and electron microscopic level of resolution using preparative procedures designed to enhance the ability to precisely determine the relationship between antibody label and cellular structures in order to map the distribution and structural association of this myosin. Immunofluorescence showed that MMI alpha has a punctate distribution throughout the nerve cell body, neurites, and growth cones. In growth cones, MMI alpha staining is sometimes elevated in thin peripheral regions of high actin content at the leading edge. Immunoelectron microscopy using colloidal gold conjugated antibodies showed that in growth cones MMI alpha is absent from membranous organelles and is concentrated primarily in the cell cortex adjacent to the cell membrane. The cortical label is equally distributed between upper and lower membranes. The plasma membrane association of the MMI alpha label persists under conditions in which the actin cytoskeleton is perturbed or removed, suggesting a direct association between a fraction of MMI alpha and the plasma membrane. MMI alpha label is also associated with the non-cortical actin cytoskeleton. Partial disruption of the actin cytoskeleton using cytochalasin B causes redistribution of only a subset of MMI alpha label. These data suggest a complex relationship between MMI alpha, the actin cytoskeleton, and the plasma membrane in the growth cone. In contrast to its localization in the growth cone, in neuronal cell bodies MMI alpha is also associated with tubulovesicular structures. This suggests that at this location MMI alpha may either act as an organelle motor or is passively transported to the plasma membrane on vesicles.

Comparison of the ability of freeze etch and freeze substitution to preserve actin filament structure

In order to test the ability of freeze substitution to accurately preserve the ultrastructure of the actin component of the cytoskeleton, the structure of rotary shadowed actin filaments was compared following preparation by glutaraldehyde fixation and freeze etch or freeze substitution. Freeze substituted actin filaments were further processed by either etching away frozen organic solvent or critical-point-drying before rotary shadowing. Comparison of filament diameters showed no significant difference between actin filaments that were directly etched and those that were freeze substituted and then etched. However, freeze substituted and then critical-point-dried filaments were significantly larger in diameter than filaments that were directly etched in water. The long pitch (right-handed) two start helix was not affected by the different methods of preparation. However, the left-handed "genetic" helical repeat that was prominent in actin filaments prepared by freeze etch was more difficult to detect in freeze substituted specimen, especially following critical-point-drying. Although the organization and distribution of actin filaments in extracted cells was similar in both freeze substituted and freeze etched specimens, there were some detectable differences. In cells that were freeze substituted and then critical-point-dried, filaments appeared to intersect at greater angles and seemed more "taut." These results suggest that freeze substitution can preserve the overall morphology of actin filaments, but some chemical or physical modification of macromolecular surface structure may occur during the substitution process and these changes may be further exaggerated by subsequent processing steps.

Nerve growth cone lamellipodia contain two populations of actin filaments that differ in organization and polarity

The organization and polarity of actin filaments in neuronal growth cones was studied with negative stain and freeze-etch EM using a permeabilization protocol that caused little detectable change in morphology when cultured nerve growth cones were observed by video-enhanced differential interference contrast microscopy. The lamellipodial actin cytoskeleton was composed of two distinct subpopulations: a population of 40-100-nm-wide filament bundles radiated from the leading edge, and a second population of branching short filaments filled the volume between the dorsal and ventral membrane surfaces. Together, the two populations formed the three-dimensional structural network seen within expanding lamellipodia. Interaction of the actin filaments with the ventral membrane surface occurred along the length of the filaments via membrane associated proteins. The long bundled filament population was primarily involved in these interactions. The filament tips of either population appeared to interact with the membrane only at the leading edge; this interaction was mediated by a globular Triton-insoluble material. Actin filament polarity was determined by decoration with myosin S1 or heavy meromyosin. Previous reports have suggested that the polarity of the actin filaments in motile cells is uniform, with the barbed ends toward the leading edge. We observed that the actin filament polarity within growth cone lamellipodia is not uniform; although the predominant orientation was with the barbed end toward the leading edge (47-56%), 22-25% of the filaments had the opposite orientation with their pointed ends toward the leading edge, and 19-31% ran parallel to the leading edge. The two actin filament populations display distinct polarity profiles: the longer filaments appear to be oriented predominantly with their barbed ends toward the leading edge, whereas the short filaments appear to be randomly oriented. The different length, organization and polarity of the two filament populations suggest that they differ in stability and function. The population of bundled long filaments, which appeared to be more ventrally located and in contact with membrane proteins, may be more stable than the population of short branched filaments. The location, organization, and polarity of the long bundled filaments suggest that they may be necessary for the expansion of lamellipodia and for the production of tension mediated by receptors to substrate adhesion molecules.

Isolation and molecular characterization of a highly polymorphic centromeric tandem repeat in the family Falconidae

An abundant tandem repeat has been cloned from genomic DNA of the merlin (Falco columbarius). The cloned sequence is 174 bp in length, and maps by in situ hybridization to the centromeric regions of several of the large chromosomes within the merlin karyotype. Complementary sequences have been identified within a variety of falcon species; these sequences are either absent or in very low copy number in the family Accipitridae. The cloned merlin repeat reveals highly polymorphic restriction patterns in the peregrine falcon (Falco peregrinus). These polymorphisms, which have been shown to be stably inherited within a family of captive peregrines, can be used to differentiate the Greenland and Argentina populations of this endangered raptor species.