Dorsal hindbrain ablation results in rerouting of neural crest migration and changes in gene expression, but normal hyoid development

Our previous studies have shown that hindbrain neural tube cells can regulate to form neural crest cells for a limited time after neural fold removal (Scherson, T., Serbedzija, G., Fraser, S. E. and Bronner-Fraser, M. (1993). Development 188, 1049-1061; Sechrist, J., Nieto, M. A., Zamanian, R. T. and Bronner-Fraser, M. (1995). Development 121, 4103-4115). In the present study, we ablated the dorsal hindbrain at later stages to examine possible alterations in migratory behavior and/or gene expression in neural crest populations rostral and caudal to the operated region. The results were compared with those obtained by misdirecting neural crest cells via rhombomere rotation. Following surgical ablation of dorsal r5 and r6 prior to the 10 somite stage, r4 neural crest cells migrate along normal pathways toward the second branchial arch. Similarly, r7 neural crest cells migrate primarily to the fourth branchial arch. When analogous ablations are performed at the 10- 12 somite stage, however, a marked increase in the numbers of DiI/Hoxa-3-positive cells from r7 are observed within the third branchial arch. In addition, some DiI-labeled r4 cells migrate into the depleted hindbrain region and the third branchial arch. During their migration, a subset of these r4 cells up-regulate Hoxa-3, a transcript they do not normally express. Krox20 transcript levels were augmented after ablation in a population of neural crest cells migrating from r4, caudal r3 and rostral r3. Long-term survivors of bilateral ablations possess normal neural crest-derived cartilage of the hyoid complex, suggesting that misrouted r4 and r7 cells contribute to cranial derivatives appropriate for their new location. In contrast, misdirecting of the neural crest by rostrocaudal rotation of r4 through r6 results in a reduction of Hoxa-3 expression in the third branchial arch and corresponding deficits in third arch-derived structures of the hyoid apparatus. These results demonstrate that neural crest/tube progenitors in the hindbrain can compensate by altering migratory trajectories and patterns of gene expression when the adjacent neural crest is removed, but fail to compensate appropriately when the existing neural crest is misrouted by neural tube rotation

Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI

We present an archetypal set of three-dimensional digital atlases of the quail embryo based on microscopic magnetic resonance imaging (µMRI). The atlases are composed of three modules: (1) images of fixed ex ovo quail, ranging in age from embryonic day 5 to 10 (e05 to e10); (2) a coarsely delineated anatomical atlas of the µMRI data; and (3) an organ system–based hierarchical graph linked to the anatomical delineations. The atlas is designed to be accessed using SHIVA, a free Java application. The atlas is extensible and can contain other types of information including anatomical, physiological, and functional descriptors. It can also be linked to online resources and references. This digital atlas provides a framework to place various data types, such as gene expression and cell migration data, within the normal three-dimensional anatomy of the developing quail embryo. This provides a method for the analysis and examination of the spatial relationships among the different types of information within the context of the entire embryo

MBAT: A scalable informatics system for unifying digital atlasing workflows

Abstract Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

Cambrian Small Bilaterian Fossils from 40 to 55 Million Years Before the Cambrian

Ten phosphatized specimens of a small (<180 micrometers) animal displaying clear bilaterian features have been recovered from the Doushantuo Formation, China, dating from 40 to 55 million years before the Cambrian. Seen in sections, this animal (Vernanimalcula guizhouena gen. et sp. nov.) had paired coeloms extending the length of the gut; paired external pits that could be sense organs; bilateral, anterior-posterior organization; a ventrally directed anterior mouth with thick walled pharynx; and a triploblastic structure. The structural complexity is that of an adult rather than a larval form. These fossils provide the first evidence confirming the phylogenetic inference that Bilateria arose well before the Cambrian

Digital Atlasing and Standardization in the Mouse Brain

Computer Systems, Imagery and Medi

Quail developmental atlas 2007

This movie displays an archetypal online digital atlas of the quail embryo based on microscopic magnetic resonance imaging. The atlas is composed of two modules: (1) images of fixed in ovo and ex ovo embryos E6 to E12 days and (2) a grossly annotated atlas of E6, E7, E8, and E9 quail with anatomical structures delineatedComponente Curricular::Educação Superior::Ciências Biológicas::Morfologi

A Critical Period for Conversion of Ectodermal Cells to a Neural Crest Fate

Previously, we found that interactions between neural and nonneural ectoderm can generate neural crest cells, with both the ectodermal and the neuroepithelial cells contributing to induced population (M. A. J. Selleck and M. Bronner-Fraser, 1995, Development 121, 525–538). To further characterize the ability of ectodermal cells to form neural crest, we have challenged their normal fate by transplanting them into the neural tube. To ensure that the ectoderm was from nonneural regions, we utilized extraembryonic ectoderm (the proamnion) and transplanted it into the presumptive midbrain of 1.5-day-old chick embryos. We observed that the grafted ectoderm has the capacity to adopt a neural crest fate, responding within a few hours of surgery by turning on neural crest markers HNK-1 and Slug. However, the competence of the ectoderm to respond to neural crest-inducing signals is time limited, declining rapidly in donors older than the 10-somite stage. Similarly, the inductive capacity of the host midbrain declines in a time-dependent fashion. Our results show that extraembryonic ectoderm has the capacity to form neural crest cells given proper inducing signals, expressing both morphological and molecular markers characteristic of neural crest cells

MRI in Developmental Biology and the Construction of Developmental Atlases

Microscopic magnetic resonance imaging (μMRI) is a noninvasive, nonoptical imaging modality that allows the entire volume of opaque specimens to be imaged. Because μMRI is not a destructive method, biologists are afforded anatomically unperturbed imagery of embryonic development and the ability to observe morphogenetic movements deep within optically inaccessible embryos. Compared with optical methods, μMRI data acquisition is slow, and image resolution is very low. This might suggest that μMRI is not viable for developmental studies. In this article, we discuss when μMRI is an appropriate imaging modality and how it has contributed to a richer understanding of embryonic development by allowing direct observation of dynamic processes in optically inaccessible regions of unperturbed embryos. We close the article with a discussion of μMRI for the construction of digital anatomical developmental atlases and how such atlases can be used

Three-Dimensional Digital Mouse Atlas Using High-Resolution MRI

We present an archetypal digital atlas of the mouse embryo based on microscopic magnetic resonance imaging. The atlas is composed of three modules: (1) images of fixed embryos 6 to 15.5 days postconception (dpc) [Theiler Stages (TS) 8 to 24]; (2) an annotated atlas of the anterior portion of a 13.5 dpc (TS 22) mouse with anatomical structures delineated and linked to explanatory files; and (3) three-dimensional renderings of the entire 13.5 dpc embryo and specific organ systems. The explanatory files include brief descriptions of the structure at each volume element in the image and links to 3D reconstructions, allowing visualization of the shape of the isolated structures. These files can also contain or be linked to other types of information and data including detailed anatomical and physiological information about structures with pointers to online references, relationships between structures, temporal characteristics (cell lineage patterns, size, and shape changes), and gene expression patterns (both spatial and temporal). As an example, we have “painted” in the expression pattern of Dlx5/Dlx6 genes. This digital atlas provides a means to put specific data within the context of normal specimen anatomy, to analyze the information in 3D, and to examine relationships between different types of information