Clemonsrandall6481

In the era of molecular biology, identification of cells and even tissues mostly relies on the presence of fluorescent tags, or of "marker gene" expression. We list a number of caveats and present a protocol for embedding, sectioning, and staining semithin plastic sections. The method is neither new nor innovative, but is meant to revive skills that tend to get lost.This easy-to-use and inexpensive protocol (1) yields high-resolution images in transmitted and polarized light, (2) can be utilized simultaneously for transmission electron microscopy, and (3) is applicable to any type of material (wild type, morphants, mutants, transgenic, or pharmacologically treated animals as well as all of their controls), provided the sample size is kept under a limit. Thus, we hope to encourage researchers to use microanatomy and histology to complement molecular studies investigating, e.g., gene function.Ex vivo explant models are a valuable tool for analyzing organ and tissue morphogenesis, providing the opportunity to manipulate and interrogate specific cellular and/or molecular pathways that may not be possible using conventional methods in vivo. The mandible primordia is a remarkably self-organizing structure that has the ability to develop cartilage, bone, teeth, epithelial tissue, and the tongue when grown in culture ex vivo and closely mimics the development of these structures in vivo. Here we describe a robust protocol for the culture of mandibular explants using serum-free, chemically defined culture media. We also describe methods for manipulating mandible and/or Meckel's cartilage development by implantation of agarose beads soaked in various molecular factors to augment mandible development, as well as methods for Alcian blue staining of Meckel's cartilage and immunohistochemistry. This culture method can also be adapted for other molecular analyses, including addition of small-molecule inhibitors and/or growth factors to the culture media, as well as culturing explants from genetically modified mice.Tissue-engineered scaffolds have been identified as appropriate templates for bone regeneration, especially complex geometries seen in craniofacial defects. Here we describe the general fabrication and modification of hydrogels, cryogels, and electrospun scaffolds. These scaffolds offer a variety of templates for facilitating bone growth and regeneration in craniofacial applications.The culture of human cranial suture cells, including their osteoblasts, is an important asset to developmental and molecular biologists to allow study the molecular biology ex vivo. The use of cell cultures by bone biologists to investigate pathological bone formation has been well established (Marie et al. Vitro Cell Dev Biol 25373-380, 1989), and the use of cell culture techniques was subsequently applied to investigate craniosynostosis (Marie. J Bone Miner Res 9(12)1847-1850, 1994). Cell cultures from fused, fusing, and fused cranial sutures allow comparative studies of cellular behavior from sutures with pathological craniosynostosis and those with unaffected sutures (Coussens et al. J Cell Physiol 218(1)183-191, 2009; Coussens et al. Differentiation 76(5)531-545, 2008).In addition to using this limited human resource for primary investigations, these human cell studies may be targeted to complement and help verify the findings of investigative studies undertaken using the more readily accessible animal cranial sutures. It is important, however, to remember that there may be critical differences in the animal genome which could impact on cellular function.This chapter describes the techniques for human suture cell culture and storage which have been used successfully since 2005 in the craniosynostosis laboratories in Adelaide.Intercellular signaling drives human development, but there is a paucity of in vitro models that recapitulate important tissue architecture while remaining operationally simple and scalable. As an example, formation of the upper lip and palate requires the orchestrated proliferation and fusion of embryonic facial growth centers and is dependent on paracrine epithelial-mesenchymal signaling through multiple pathways including the Sonic Hedgehog (SHH), transforming growth factor-beta (Tgf-β), bone morphogenic protein (BMP), and epidermal growth factor (EGF) pathways. We have developed a robust, throughput-compatible microphysiological system to model intercellular signaling including epithelial-mesenchymal interactions that is useful for studying both normal and abnormal orofacial development. We describe the construction and operation of an engineered microplate created using CNC micromilling of 96-well microtiter plates capable of containing up to 20 epithelial-mesenchymal microtissues. A dense three-dimensional mesenchyme is created by embedding cells (O9-1, 3T3) in a biomimetic hydrogel. An epithelial layer is then overlayed on the microtissue by loading cells in engineered microchannels that flank the microtissue. The result is an engineering epithelial-mesenchymal interface that is both on and perpendicular to the imaging plane making it suitable for high-content imaging and analysis. The resulting microtissues and device are compatible with diverse analytical techniques including fluorescent and luminescent cell health and enzymatic reporter assays, gene expression analyses, and protein staining. This tractable model and approach promise to shed light on critical processes in intercellular signaling events in orofacial development and beyond.Histochemical analysis is an indispensable technique in the field of biology used routinely to characterize pathologies of interest throughout the system. This chapter provides the craniofacial biologist with an introduction to tissue harvesting, embedding, and sectioning as well as a toolkit of useful stains for stromal/mesenchymal tissues including bone and cartilage. Techniques are tailored to decalcified, paraffin-embedded mouse tissue; however, these methods are applicable under a broad range of conditions.Embryonic morphogenesis is strictly dependent on tight spatiotemporal control of developmental gene expression, which is typically achieved through the concerted activity of multiple enhancers driving cell type-specific expression of a target gene. Mammalian genomes are organized in topologically associated domains, providing a preferred environment and framework for interactions between transcriptional enhancers and gene promoters. While epigenomic profiling and three-dimensional chromatin conformation capture have significantly increased the accuracy of identifying enhancers, assessment of subregional enhancer activities via transgenic reporter assays in mice remains the gold standard for assigning enhancer activity in vivo. Once this activity is defined, the ideal method to explore the functional necessity of a transcriptional enhancer and its contribution to target gene dosage and morphological or physiological processes is deletion of the enhancer sequence from the mouse genome. Here we present detailed protocols for efficient introduction of enhancer-reporter transgenes and CRISPR-mediated genomic deletions into the mouse genome, including a step-by-step guide for pronuclear microinjection of fertilized mouse eggs. We provide instructions for the assembly and genomic integration of enhancer-reporter cassettes that have been used for validation of thousands of putative enhancer sequences accessible through the VISTA enhancer browser, including a recently published method for robust site-directed transgenesis at the H11 safe-harbor locus. Galunisertib Together, these methods enable rapid and large-scale assessment of enhancer activities and sequence variants in mice, which is essential to understand mammalian genome function and genetic diseases.X-ray micro-computed tomography (micro-CT) imaging has important applications in microarchitecture analysis of cortical and trabecular bone structure. While standardized protocols exist for micro-CT-based microarchitecture assessment of long bones, specific protocols need to be developed for different types of skull bones taking into account differences in embryogenesis, organization, development, and growth compared to the rest of the body. This chapter describes the general principles of bone microarchitecture analysis of murine craniofacial skeleton to accommodate for morphological variations in different regions of interest.Craniofacial phenomics has opened up numerous opportunities to correlate genetic and epigenetic factors to craniofacial phenotypes in order to improve our understanding of growth and development in health and disease. Three-dimensional (3D) imaging has played a key role in advancing craniofacial phenomics by facilitating highly sensitive and specific characterizations of craniofacial and dental morphology. Here we describe the use of micro-computed tomography (micro-CT) to image the murine craniofacial complex, followed by surface reconstruction for traditional morphometric analyses. We also describe the application of geometric morphometrics, based on Generalized Procrustes Analysis, for use in human premolars. These principles are interchangeable between various vertebrate species, and between various surface imaging techniques (including micro-CT and 3D surface scanners), offering a high level of versatility and precision for extensive phenotyping of the entire craniofacial complex.Danio rerio (zebrafish), traditionally used in forward genetic screens, has in the last decade become a popular model for reverse genetic studies with the introduction of TALENS, zinc finger nucleases, and CRISPR/Cas9. Unexpectedly, homozygous frameshift mutations generated by these tools frequently result in phenotypes that are less penetrant than those seen in embryos injected with antisense morpholino oligonucleotides targeting the same gene. One explanation for the difference is that some frameshift mutations result in nonsense-mediated decay of the gene transcript, a process which can induce expression of homologous genes. This form of genetic compensation, called transcriptional adaptation, does not occur when the mutant allele results in no RNA transcripts being produced from the targeted gene. Such RNA-less mutants can be generated by deleting a gene's promoter using a pair of guide RNAs and Cas9 protein. Here, we present a protocol and use it to generate alleles of arhgap29b and slc41a1 that lack detectable zygotic transcription. In the case of the arhgap29b mutant, an emerging phenotype did not segregate with the promoter deletion mutation, highlighting the potential for off-target mutagenesis with these tools. In summary, this chapter describes a method to generate zebrafish mutants that avoid a form of genetic compensation that occurs in many frameshift mutants.Single-cell RNA-sequencing technologies have revolutionized the way that researchers can interrogate cellular relationships and the level of detail by which tissue architecture can be characterized. Multiple cell capturing methods have been developed that, when coupled to next-generation sequencing, can yield cell-to-cell specific information regarding gene expression profiles. One of the commonalities between all of the cell capturing techniques to succeed is the necessity to submit samples with a high cell viability. In addition, these cells should have undergone minimal processing to limit induced stress responses so that their transcriptomes, when sequenced, closely reflect their transcriptomes in vivo at the time of isolation. Below we present a streamlined protocol to isolate fresh cells from tissues in vivo. We also share extensive notes to highlight considerations researchers should take into account before beginning their cell isolation protocol.