Summary How sexually dimorphic gonads are generated is a fundamental question at the interface of developmental and evolutionary biology [1–3]. In C. elegans, sexual dimorphism in gonad form and function largely originates in different apportionment of roles to three “regulatory cells” of the somatic gonad primordium in young larvae. Their essential roles include leading gonad arm outgrowth, serving as the germline niche, connecting to epithelial openings, and organizing reproductive organ development. The development and function of the regulatory cells in both sexes requires the basic Helix-Loop-Helix (bHLH) transcription factor HLH-2, the sole ortholog of the E proteins mammalian E2A and Drosophila Daughterless [4–8], yet how they adopt different fates to execute their different roles has been unknown. Here, we show that each regulatory cell expresses a distinct complement of bHLH-encoding genes--and therefore distinct HLH-2:bHLH dimers--and formulate a “bHLH code” hypothesis for regulatory cell identity. We support this hypothesis by showing that the bHLH gene complement is both necessary and sufficient to confer particular regulatory cell fates. Strikingly, prospective regulatory cells can be directly reprogrammed into other regulatory cell types simply by loss or ectopic expression of bHLH genes, and male-to-female and female-to-male transformations indicate that the code is instructive for sexual dimorphism. The “bHLH code” appears to be embedded in a bow-tie regulatory architecture [9,10], wherein sexual, positional, temporal, and lineage inputs connect through bHLH genes to diverse outputs for terminal features, and provides a plausible mechanism for the evolutionary plasticity of gonad form seen in nematodes [11–15].
Background Intercellular communication by the hedgehog cell signaling pathway is necessary for tooth development throughout the vertebrates, but it remains unclear which specific developmental signals control cell behavior at different stages of odontogenesis. To address this issue, we have manipulated hedgehog activity during zebrafish tooth development and visualized the results using confocal microscopy. Results We first established that reporter lines for dlx2b, fli1, NF-κB, and prdm1a are markers for specific subsets of tooth germ tissues. We then blocked hedgehog signaling with cyclopamine and observed a reduction or elimination of the cranial neural crest derived dental papilla, which normally contains the cells that later give rise to dentin-producing odontoblasts. Upon further investigation we observed that the dental papilla begins to form and then regresses in the absence of hedgehog signaling, through a mechanism unrelated to cell proliferation or apoptosis. We also found evidence of an isometric reduction in tooth size that correlates with the time of earliest hedgehog inhibition. Conclusions We hypothesize that these results reveal a previously uncharacterized function of hedgehog signaling during tooth morphogenesis, regulating the number of cells in the dental papilla and thereby controlling tooth size.
Developmental Dynamics provides a focus for communication among developmental biologists who study the progressive and dynamic emergence of form and function during embryonic development. The journal is an international forum for the exchange of novel and substantive information on mechanisms that control development. We seek manuscripts presenting work done at all levels of biological organization, ranging from the molecular to the organismal, using both animal and plant model systems, and we welcome studies that advance our understanding of the developmental basis of human disease. Developmental Dynamics is fully compliant with current open access policies of major funding agencies including those of the NIH, HHMI, and Wellcome Trust. In addition, all of our content is open access one year after publication, and more than 30% of our content-including all reviews, special issues, primers, and highlights-is open access immediately upon publication. Developmental Dynamics reviews and publishes rapidly: averaging 3 weeks from submission to decision, 4-6 weeks to online publication after acceptance, and 90 days to print publication. There are no page or color charges, and the length of the articles (and the number of figures and references included) are limited only by what is required to tell a novel and significant scientific story.
Objective: To validate and demonstrate the clinical discovery utility of a novel patient-mediated, medical record collection and data extraction platform developed to improve access and utilization of real-world clinical data. Methods: Clinical variables were extracted from the medical records of consented patients with metastatic breast cancer. To validate the extracted data, case report forms completed using the structured data output of the platform were compared to manual chart review for 50 patients. To demonstrate the platform's clinical discovery utility, we assessed associations between time to distant metastasis (TDM) and tumor histology, molecular type, and germline BRCA status in the platform-extracted data of 194 patients. Results: The platform-extracted data had 97.6% precision (91.98%-100% by variable type) and 81.48% recall (58.15%-95.00% by variable type) compared to manual chart review. In our discovery cohort, the shortest TDM was significantly associated with metaplastic (739.0 days) and inflammatory histologies (1,005.8 days), HR-/HER2- molecular types (1,187.4 days), and positive BRCA status (1,042.5 days) as compared to other histologies, molecular types, and negative BRCA status, respectively. Multivariable analyses did not produce statistically significant results, but the average TDMs are reported. Discussion: The platform-extracted clinical data are precise and comprehensive. The data can generate clinically-relevant insights. Conclusion: The structured real-world data produced by a patient-mediated, medical record-extraction platform are reliable and can power clinical discovery. Keywords: data accuracy; electronic health records; real-world data; real-world evidence
Much remains to be learned about how cis-regulatory elements such as enhancers function, especially during vertebrate organ development. To increase knowledge in this area, we have examined the cis-regulation of the transcription factor dlx2b during zebrafish larval tooth formation. We have created a GFP knock-in line that replicates dlx2b expression during tooth development and have also isolated a minimal enhancer of dlx2b (MTE1) sufficient for activating most of the tooth germ expression pattern. We have found that four evolutionarily conserved predicted transcription factor binding sites are required for the function of this minimal enhancer in both contexts. When the conserved sequences are mutated in a transgene it eliminates the activity of the enhancer and when they are deleted at the dlx2b locus it causes a dramatic alteration in the expression pattern. We hypothesize that disabling this enhancer at the dlx2b locus may be enabling other nearby cis-regulatory elements to take control of the promoter. These experiments reveal details of how cis-regulatory elements are working to control gene expression during organogenesis and highlight how much remains to be learned by empirical studies of gene regulation.
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