High resolution scanning and three-dimensional reconstruction of cellular events in large objects during brain development

Possibilities and limitations of three-dimensional reconstruction and simulation techniques to identify patterns, rhythms and functions of apoptosis in the early developing neural tube

The now classical idea that programmed cell death (apoptosis) contributes to a plethora of developmental processes still has lost nothing of its impact. It is, therefore, important to establish effective three-dimensional (3D) reconstruction as well as simulation techniques to decipher the exact patterns and functions of such apoptotic events. The present study focuses on the question whether and how apoptosis promotes neurulation-associated processes in the spinal cord of Tupaia belangeri (Tupaiidae, Scandentia, Mammalia). Our 3D reconstructions demonstrate that at least two craniocaudal waves of apoptosis consecutively pass through the dorsal spinal cord. The first wave appears to be involved in neural fold fusion and/or in selection processes among premigratory neural crest cells. The second one seems to assist in establishing the dorsal signaling center known as the roof plate. In the hindbrain, in contrast, apoptosis among premigratory neural crest cells progresses craniocaudally but discontinuously, in a segment-specific manner. Unlike apoptosis in the spinal cord, these segment-specific apoptotic events, however, precede later ones that seemingly support neural fold fusion and/or postfusion remodeling. Arguing with Whitehead that biological patterns and rhythms differ in that biological rhythms depend "upon the differences involved in each exhibition of the pattern" (Whitehead in An enquiry concerning the principles of natural knowledge. Cambridge University Press, London, 1919, p. 198) we show that 3D reconstruction and simulation techniques can contribute to distinguish between (static) patterns and (dynamic) rhythms of apoptosis. By deciphering novel patterns and rhythms of developmental apoptosis, our reconstructions help to reconcile seemingly inconsistent earlier findings in chick and mouse embryos, and to create rules for computer simulations.

Pax2/Pax8-defined subdomains and the occurrence of apoptosis in the posterior placodal area of mice

The present work aims to improve our understanding of the causes and functions of apoptosis during the morphogenesis of epibranchial placodes in mice. Schematic maps helped to compare the spatiotemporal sequence of apoptotic events with the protein expression patterns of general (Six1) and specific placodal markers (Pax2, Pax8). Our findings challenge the view that, in mammals, all three epibranchial placodes spring from the original posterior placodal area (PPA) of presomite or early somite embryos. Instead, close-meshed analysis of the Pax2/Pax8 expression patterns demonstrates the stepwise emergence of two subdomains which both belong to the gradually expanding PPA, and which largely give rise to the otic placode and epibranchial placode 1 (anterior subdomain), or to the caudal epibranchial placodes (posterior subdomain). Our observations reinforce previous doubts raised on the PPA progeny of early somite Xenopus embryos (Schlosser and Ahrens, Dev Biol 271:439-466, 2004). They also demonstrate that partly different Pax2/Pax8 codes accompany epibranchial placode development in Xenopus laevis and mice. In mice, interplacodal apoptosis assists in the establishment of the two PPA subdomains and, subsequently, of individualized placodes by predominantly eliminating Six1⁺ placodal precursor cells. Onset of interplacodal and intraplacodal large-scale apoptosis is almost always preceded and/or paralleled by Pax2/Pax8 expression minima in the very same region. Future work will demand the use of knock-out mice and whole embryo culture to experimentally test, whether the combined action of differentially expressed Pax2 and Pax8 genes exerts antiapoptotic effects in the mammalian PPA.

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

Abstract. The longstanding debate on the taxonomic status of Tupaia belangeri (Tupaiidae, Scandentia, Mammalia) has persisted in times of molecular biology and genetics. But way beyond that Tupaia belangeri has turned out to be a valuable and widely accepted animal model for studies in neurobiology, stress research, and virology, among other topics. It is thus a privilege to have the opportunity to provide an overview on selected aspects of neural development and neuroanatomy in Tupaia belangeri on the occasion of this special issue dedicated to Hans-Jürg Kuhn. Firstly, emphasis will be given to the optic system. We report rather "unconventional" findings on the morphogenesis of photoreceptor cells, and on the presence of capillary-contacting neurons in the tree shrew retina. Thereafter, network formation among directionally selective retinal neurons and optic chiasm development are discussed. We then address the main and accessory olfactory systems, the terminal nerve, the pituitary gland, and the cerebellum of Tupaia belangeri. Finally, we demonstrate how innovative 3-D reconstruction techniques helped to decipher and interpret so-far-undescribed, strictly spatiotemporally regulated waves of apoptosis and proliferation which pass through the early developing forebrain and eyes, midbrain and hindbrain, and through the panplacodal primordium which gives rise to all ectodermal placodes. Based on examples, this paper additionally wants to show how findings gained from the reported projects have influenced current neuroembryological and, at least partly, medical research.

Apoptosis and proliferation in the trigeminal placode

The neurogenic trigeminal placode develops from the crescent-shaped panplacodal primordium which delineates the neural plate anteriorly. We show that, in Tupaia belangeri, the trigeminal placode is represented by a field of focal ectodermal thickenings which over time changes positions from as far rostral as the level of the forebrain to as far caudal as opposite rhombomere 3. Delamination proceeds rostrocaudally from the ectoderm adjacent to the rostral midbrain, and contributes neurons to the trigeminal ganglion as well as to the ciliary ganglion/oculomotor complex. Proliferative events are centered on the field prior to the peak of delamination. They are preceded, paralleled and, finally, outnumbered by apoptotic events which proceed rostrocaudally from non-delaminating to delaminating parts of the field. Apoptosis persists upon regression of the placode, thereby exhibiting a massive “wedge” of apoptotic cells which includes the postulated position of the “ventrolateral postoptic placode” (Lee et al. in Dev Biol 263:176–190, 2003), merges with groups of lens-associated apoptotic cells, and disappears upon lens detachment. In conjunction with earlier work (Washausen et al. in Dev Biol 278:86–102, 2005) our findings suggest that apoptosis contributes repeatedly to the disintegration of the panplacodal primordium, to the elimination of subsets of premigratory placodal neuroblasts, and to the regression of placodes.

Automatic registration of serial sections of mouse lymph node by using Image-Reg

The first step towards the three-dimensional (3D) reconstruction of histological structures from serial sectioned tissue blocks is the proper alignment of microscope image sequences. We have accomplished an automatic rigid registration program, named Image-Reg, to align serial sections from mouse lymph node and Peyer's patch. Our approach is based on the calculation of the pixel-correlation of objects in adjacent images. The registration process is mainly divided into two steps. Once the foreground images have been segmented from the original images, the first step (primary alignment) is performed on the binary images of segmented objects; this process includes rotation by using the moments and translation through the X, Y axes by using the centroid. In the second step, the matching error of two binary images is calculated and the registration results are refined through multi-scale iterations. In order to test the registration performance, Image-Reg has been applied to an image and its transformed (rotated) version and subsequently to an image sequence of three serial sections of mouse lymph node. In addition, to compare our algorithm with other registration methods, three other approaches, viz. manual registration with Reconstruct, semi-automatic landmark registration with Image-Pro Plus and the automatic phase-correlation method with Image-Pro Plus, have also been applied to these three sections. The performance of our program has been also tested on other two-image data sets. These include: (a) two light microscopic images acquired by the automatic microscope (stitched with other software); (b) two images fluorescent images acquired by confocal microscopy (tiled with other software). Our proposed approach provides a fast and accurate linear alignment of serial image sequences for the 3D reconstruction of tissues and organs.

Diversity in mammalian chiasmatic architecture: ipsilateral axons are deflected at glial arches in the prechiasmatic optic nerve of the eutherian Tupaia belangeri

Permanent ipsilaterally projecting axons approach the chiasmatic midline in rodents but are confined to lateral parts of the optic chiasm in marsupials. Hence, principally different mechanisms were thought to underlie axon pathway choice in eutherian (placental) and marsupial mammals. First evidence of diversity in eutherian chiasmatic architecture came from studies in the newborn and adult tree shrew Tupaia belangeri (Jeffery et al. [1998] J. Comp. Neurol. 390:183-193). Here, as in marsupials, ipsilaterally projecting axons do not approach the midline. The present study aims to clarify how the developing tree shrew chiasm is organized, how glial cells are arranged therein, and the extent to which the tree shrew chiasm is similar to that of marsupials or other eutherians. By using routinely stained serial sections as well as immunohistochemistry with antibodies against glial fibrillary acidic protein, vimentin, and medium-molecular-weight neurofilament protein, we investigated chiasm formation from embryonic day 18 (E18) to birth (E43). From E22 onward, ipsilaterally projecting axons diverged from contralaterally projecting axons in prechiasmatic parts of the optic nerve. They made sharp turns when arriving at glial arches found at the transition from the optic nerve to the chiasm. Thus, during the ingrowth period of axons, Tupaia belangeri and marsupials have specialized glial arrays in common, which probably help to deflect ipsilaterally projecting axons to lateral parts of the chiasm. Our observations provide new evidence of diversity in eutherian chiasmatic architecture and identify Tupaia belangeri as an appropriate animal model for studies on the mechanisms underlying axon guidance in the developing chiasm of higher primates.

Surface imaging microscopy using an ultramiller for large volume 3D reconstruction of wax- and resin-embedded tissues

Three-dimensional reconstruction of large tissue volumes using histological thin sections poses difficulties because of registration of sections, section distortion, and the possibility of incomplete data set collection due to section loss. We have constructed an integrated surface imaging system that successfully addresses these problems. Embedded tissue is mounted on a high precision XYZ stage and the upper surface is iteratively: (i) stained to provide an effective optical section, (ii) imaged using a digital camera, and (iii) removed with an ultramiller. This approach provides for the reconstruction of high-quality 3D images by inherently preserving image registration, eliminates section distortion, thus removing the need for complex realignment and correction, and also ensures full capture of all image planes. The system has the capacity to acquire images of tissue structure with voxel sizes from 0.5 to 50 mum over dimensions ranging from micrometers to tens of millimeters. The ultramiller enables large samples to be imaged by reliably removing tissue over their full extent. The ability to visualize key features of 3D tissue structure across such a range of scale and resolution will facilitate the development of a greater understanding of the relationship between structure and function. This understanding is essential for better analyses of the structural changes associated with different disease states, and the development of structure-based computer models of biological function.

Serial sectioning and three-dimensional reconstruction of mouse Peyer's patch

Peyer's patches (PPs) are typical gut-associated lymphoid tissues that are located along the wall of the small intestine and that serve as the major sites for generation of immunity to intestinal antigens. Their unique micro-organization is crucial for the generation of the immune response. Although many studies have been reported on the functional anatomy of PP, most investigations have relied on the random sampling of these organs, a procedure that is insufficient for the systemic scanning of the whole tissue or organ. By combining a variety of methods, we have accomplished 3D reconstructions of Peyer's patch. The complex reconstruction procedure includes several steps. First, the PP are serially sectioned at a thickness of 10 microm with a cryostat; (b) the serial sections are stained with haematoxylin-eosin; (c) multiple images from the PP are acquired with an automatic microscope and stitched together with Image Pro Plus to generate a composite image for the whole organ; (d) the serial images are reconstructed with Image J, Reconstruct and 3D Studio Max. The combinational approaches that we present here should be of value when extrapolated to the reconstruction of other tissues or organs. Moreover, the 3D model that we have created and our stereological analysis should be extremely helpful for further in vivo microscopic studies of PP with respect to the immune response.

Use of Autostitch for automatic stitching of microscope images

Image stitching is the process of combining multiple images to produce a panorama or larger image. In many biomedical studies, including those of cancer and infection, the use of this approach is highly desirable in order to acquire large areas of certain structures or whole sections, while retaining microscopic resolution. In this study, we describe the application of Autostitch, viz. software that is normally used for the generation of panoramas in photography, in the seamless stitching of microscope images. First, we tested this software on image sets manually acquired by normal light microscopy and compared the performance with a manual stitching approach performed with Paint Shop Pro. Secondly, this software was applied to an image stack acquired by an automatic microscope. The stitching results were then compared with that generated by a self-programmed rectangular tiling macro integrated in Image J. Thirdly, this program was applied in the image stitching of images from electron microscopy. Thus, the automatic stitching program described here may find applications in convenient image stitching and virtual microscopy in the biomedical research.

Apoptosis and proliferation in developing, mature, and regressing epibranchial placodes

Epibranchial placodes and rhombencephalic neural crest provide precursor cells for the geniculate, petrosal, and nodose ganglia. In chick embryos and in Tupaia belangeri, apoptosis in rhombomeres 3 and 5 helps to select premigratory precursor cells and to segregate crest cell streams derived from the even-numbered rhombomeres. Much less is known about the patterns and functions of apoptosis in epibranchial placodes. We found that, in Tupaia belangeri, combined anlagen of the otic placode and epibranchial placode 1 transiently share a primordial low grade thickening with post-otic epibranchial placodes. Three-dimensional reconstructions reveal complementary, spatially, and temporally regulated apoptotic and proliferative events that demarcate the otic placode and epibranchial placode 1, and help to individualize three pairs of epibranchial placodes in a rostrocaudal sequence. Later, rostrocaudal waves of proliferation and apoptosis extend from dorsal to ventral parts of the placodes, paralleled by the dorsoventral progression of precursor cell delamination. These findings suggest a role for apoptosis during the process of neuroblast generation in the epibranchial placodes. Finally, apoptosis eliminates remnants of the placodes in the presence of late invading macrophages.

Re-evaluation and in silico annotation of the Tupaia herpesvirus proteins

Herpesviruses represent an exceptionally suitable model to analyze evolutionary old pathogens, their competency to adapt to existing and changing molecular niches in host species, and the modulation of the gene content and function to comply with the requirements of life. The basis for numerous studies dealing with these questions are reliable statements about the gene content of herpesviral genomes and the functions of viral proteins. The recent determination of the coding strategy of the chimpanzee cytomegalovirus genome and the re-evaluation of the gene content of the human cytomegalovirus genome made it also necessary to restructure the putative transcription map of the Tupaia herpesvirus (THV) genome. Twenty-three THV-specific ORFs formerly predicted to be coding for viral proteins were deleted from the THV transcription map resulting in a gene layout that is now characterized by the presence of conserved genes in the genome center, that probably reflect the genome structure of common herpesviral ancestors, and species-specific genes at the termini. The conserved regions in the THV genome are characterized by high G + C contents between 60% and 80%, a high CpG dinucleotide frequency, and the presence of densely packed putative CpG islands. The genome termini seem to provide the requirements of large scale rearrangements and complements of the gene content to adapt to new environmental demands. With the help of the recently designed method of dictionary-driven, pattern-based protein annotation it was possible to assign putative functions to almost all potential THV proteins, e.g. 123 were found to be putative membrane or secreted proteins, putative signal domains were identified in 69, and 29 proteins were predicted to be glycosylated. The present study adds new aspects to the knowledge about the precise gene composition of herpesvirus genomes and viral protein functions that are of exceptional importance for studies dealing with the phylogeny, the evolution, vaccine vector development, virus-host interactions, pathogenesis and the determination of protein functions of herpesviruses.

Molecular anatomy of Tupaia (tree shrew) adenovirus genome; evolution of viral genes and viral phylogeny

Adenoviruses are globally spread and infect species in all five taxons of vertebrates. Outstanding attention is focused on adenoviruses because of their transformation potential, their possible usability as vectors in gene therapy and their applicability in studies dealing with, e.g. cell cycle control, DNA replication, transcription, splicing, virus-host interactions, apoptosis, and viral evolution. The accumulation of genetic data provides the basis for the increase of our knowledge about adenoviruses. The Tupaia adenovirus (TAV) infects members of the genus Tupaiidae that are frequently used as laboratory animals in behavior research dealing with questions about biological and molecular processes of stress in mammals, in neurobiological and physiological studies, and as model organisms for human hepatitis B and C virus infections. In the present study the TAV genome underwent an extensive analysis including determination of codon usage, CG depletion, gene content, gene arrangement, potential splice sites, and phylogeny. The TAV genome has a length of 33,501 bp with a G+C content of 49.96%. The genome termini show a strong CG depletion that could be due to methylation of these genome regions during the viral replication cycle. The analysis of the coding capacity of the complete TAV genome resulted in the identification of 109 open reading frames (ORFs), of which 38 were predicted to be real viral genes. TAV was classified within the genus Mastadenovirus characterized by typical gene content, arrangement, and homology values of 29 conserved ORFs. Phylogenetic trees show that TAV is part of a separate evolutionary lineage and no mastadenovirus species can be considered as the most related. In contrast to other mastadenoviruses a direct ancestor of TAV captured a DUT gene from its mammalian host, presumably controlling local dUTP levels during replication and enhance viral replication in non-dividing host tissues. Furthermore, TAV possesses a second DNA-binding protein gene, that is likely to play a role in the determination of the host range. In view of these data it is conceivable that TAV underwent evolutionary adaptations to its biological environment resulting in the formation of special genomic components that provided TAV with the ability to expand its host range during viral evolution.

Use of "reference series" to realign histological serial sections for three-dimensional reconstructions of the positions of cellular events in the developing brain

The present study demonstrates how, predominantly by external fiducials, histological serial sections used to reconstruct patterns of individually marked cellular events in large organs or whole embryos can be realigned with the help of "reference series". Resin-embedded embryos were cut at 1 microm and consecutive sections were alternately placed on two sets of slides. For cytological diagnosis and acquisition of embryonic contours, stained sections of the first series, termed "working series", were scanned with the x 100 objective using "Huge Image", a recently established image acquisition system. For acquisition of the contours of the resin block, adjacent unstained sections of the second series, termed "reference series", were scanned with the x 5 objective. Thereafter, "hybrid sections" were created which combined vectorized embryonic contours and cellular events taken from the working series with vectorized block contours taken from the reference series. For realignment, consecutive "hybrid sections" were matched by best-fit of the block contours. Stacks of realigned "hybrid sections" were shaped like truncated pyramids and, thus, reflected repeated "trimming" of the resin block during the sectioning procedure. Among 266 "hybrid sections" at intervals of 8 microm, needed to reconstruct the brain of a 15-day-old embryo of Tupaia belangeri (Scandentia), internal fiducials were required five times for realigning a total of six adjacent truncated pyramids. Application of this method provided realistic reconstructions of the positions of apoptotic cells in the entire developing brain without the need of secondary introduction of external fiducials.