The caudal fin of zebrafish (danio rerio) is often used to study regeneration thanks to its extraordinary regenerative ability, easy access, and relative simplicity in structure. Branching morphogenesis is observed in many organs, including lungs and salivary glands in mammals, as well as the fin rays in zebrafish and is thought to follow unifying principles. An important developmental gene, sonic hedgehog a (shha), has been shown in other studies to play an essential role in the branch formation. Previous studies in our lab have shown that the transient depletion of the shha-expressing cells following laser ablation of the shha-expressing cells in the regenerating caudal fin results in a delay of fin rays branch formation. In order to study the long-term effect of ablating the shha-expressing cells, I generated a new zebrafish transgenic line (Tg)(2.4shha:CFP-NTR-ABC) to perform a conditional cell ablation using the Metronidazole/Nitroreductase (Mtz/NTR) system. Preliminary data suggest that cell ablation using the Mtz/NTR system is successful in the Tg(2.4shha:CFP-NTR-ABC) embryos. In addition, short-term ablation of the shha-expressing cells through Mtz/NTR system delays branch formation during caudal fin regeneration of the Tg(2.4shha:CFP-NTR-ABC) adult fish. Further work will involve the analysis of the effects of the long-term ablation of the shha-expressing cells and the involvement of other signaling pathways in the ray branching formation during zebrafish caudal fin regeneration. This study can provide insights into understanding of the molecular mechanisms underlying branching morphogenesis in various organs. During the course of the above project, I have observed an organ-wide response to local injury in the zebrafish caudal fin. In this study, I have shown, for the first time, an immediate organ-wide response to partial fin amputation characterized by the damage of blood vessels, nerve fibers and the activation of inflammatory response in the non-amputated tissues. I established that the adult zebrafish caudal fin serves as an excellent model for the study of the organ-wide response to local injury, and such study may provide new insights into the field of regenerative medicine in which stimulating regeneration locally may trigger responses in unintended locations.   Résumé La nageoire caudale du poisson zèbre (danio rerio) est souvent utilisée pour étudier les mécanismes de régénération à cause de son extraordinaire capacité de régénération, son accès facile, et sa relative simplicité structurale. La morphogenèse de branches est observée dans plusieurs organes incluant les poumons et les glandes salivaires chez les mammifères ainsi que les rayons des nageoires du poisson zèbre et est supposée suivre des principes communs. Un important gène de développement, sonic hedgehog a (shha), joue un rôle essentiel dans la formation des branches. Des études précédentes effectuées dans notre laboratoire ont montré que l’absence transitoire des cellules exprimant shha dans des expériences d’ablation au rayon laser induit un délai de la formation des branches dans les rayons au cours de la régénération de la nageoire caudale. Afin d’étudier les effets de l’ablation à long terme des cellules exprimant shha, j’ai fait un nouvelle lignée transgénique de poisson zèbre Tg(2.4shha:CFP-NTR-ABC) pour effectuer une ablation cellulaire conditionnelle à l’aide du système Métronidazole / Nitroréductase (Mtz/NTR). Mes données préliminaires suggèrent que l’ablation cellulaire à l’aide du système Mtz/NTR fonctionne sur les embryons Tg(2.4shha:CFP-NTR-ABC). De plus, l’ablation à court terme des cellules exprimant shha à l’aide du système Mtz/NTR induit un délai de la formation des branches au cours de la régénération des rayons la nageoire caudale des poissons adultes Tg(2.4shha:CFP-NTR-ABC). Des études supplémentaires incluront l’analyse des effets de l’ablation à long terme des cellules exprimant shha et le rôle d’autres cascades de signalisation dans la formation des branches des rayons au cours de la régénération de la nageoire caudale du poisson zèbre. Cette étude pourrait fournir des informations concernant la compréhension des mécanismes moléculaires sous-jacents à la formation de branches dans des organes variés. Au cours de l’étude décrite ci-dessus, j’ai fait l’observation d’une réponse globale de toute la nageoire caudale à une blessure locale. Dans cette étude, j’ai montré pour la première fois, une réponse immédiate et globale après amputation partielle de la nageoire. Cette réponse est caractérisée par des lésions des vaisseaux sanguins, des fibres nerveuses et par l’activation d’une réponse inflammatoire dans les tissus non-amputés. J’ai établi que la nageoire caudale du poisson zèbre adulte est un excellent modèle pour l’étude de la réponse globale d’un organe à une lésion locale. Une telle étude pourrait fournir de nouvelles informations pertinentes à la médecine régénérative qui, en visant à stimuler la régénération de façon locale, peut entraîner des réponses dans des domaines non voulus.

Hedgehog (HH) signaling controls renal development. Mutations in PTC1, the HH receptor, cause cancer in non-renal tissues. We hypothesized that constitutively active HH signaling is deleterious to renal development in mice with PTC1 deficiency targeted to the metanephric mesenchyme (MM)(Rarb2-Cre;Ptc1 loxP/-, termed Ptc1 mutants). Increased HH signaling in MM of mutant mice was confirmed by qRT-PCR for Ptc1. A decrease in NCAM-positive nephrogenic precursors at E13.5 and WT1-positive glomeruli at E18.5 was found. Increased cortical expression of Foxd1 was observed. At E13.5, a cluster of ectopic cells expressing Raldh2, Ptc2 and Bmp4 accumulated at the presumptive uretero-pelvic junction (UPJ). Magnetic resonance imaging demonstrated an increase in pelvic volume. Constitutive expression of GLI3 repressor via the Gli3Δ699 allele in Ptc1 mutants increased nephron number comparable to wild type mice and decreased pelvic volume compared to Ptc1 mutants. Thus repression of HH activity is required for proper nephrogenesis and patterning of the UPJ.

Hedgehog (Hh) signalling from the notochord induces the slow muscle cell fate in the adaxial cells of the developing zebrafish embryo. Slow muscle formation is disrupted in zebrafish ??you-type?? mutants resulting in U-shaped somites. In many you-type mutants, genes encoding components of the Hh signalling pathway are mutated. scube2, a gene not previously known to be involved in Hh signalling, is disrupted in the you-type mutant ??you??. you mutants are deficient in several Hh dependent cell types and show decreased expression of Hh target genes. The Scube (signal peptide-CUB domain-EGF-related) family of proteins act as secreted glycoproteins or cell-surface proteins and are thought to be involved in protein-protein interactions and ligand binding. At the protein level, the Scube family resembles the endocytic receptor Cubilin. Cubilin is known to interact with another endocytic receptor Megalin, which can function as an endocytic receptor for Sonic Hedgehog (SHH) in vitro. Megalin endocytosis of Shh may be an important part of the Hh signal transduction pathway. An anti-Scube2 antibody was developed during this work to investigate the intracellular localization pattern of Scube2 and facilitate the identification of potential Scube2 binding partner(s). In addition, this work identified and characterized two homologs of scube2 in zebrafish, scube 1 and scube 3. The high level of similarity amongst the Scube family of proteins and the weak phenotype of the you mutant suggested scube1 and scube3 might also be involved in slow muscle development. Loss of function experiments performed by antisense morpholino knockdown of scube1 and scube3 in the you mutant decreases the expression of Hh target genes to levels seen in embryos lacking Hh signalling and dramatically enhances the loss of slow muscle fibres compared to you mutants alone. Thus, injecting both scube1 and scube3 morpholinos into you blocks Hh signalling and these embryos fail to develop slow muscle. Inhibition of the three partially redundant scube genes inhibits Hh signalling in zebrafish embryos, thereby demonstrating the essential requirement for scube gene function in the Hh signalling pathway.

Adult haematopoiesis occurs in the context of a supportive stromal cell niche. The bone marrow, spleen and thymus all contain specific, but relatively poorly defined, stromal cells, which are important for maintenance of quiescence and directed differentiation. Even less is known about the haematopoietic niche during haematopoietic development. The formation of red blood cells (erythropoiesis) occurs during haematopoiesis, and is also controlled by a variety of stromal cells. This thesis examined the visceral endoderm, a group of cells that surrounds the developing epiblast and is required for primitive erythropoiesis (early blood production). We attempted to determine which factors in the visceral endoderm were responsible for induction of primitive erythropoiesis, and whether they would be useful as blood induction factors in embryonic stem cell differentiation. Thus, I attempted to immortalise the visceral endoderm using an immortalising agent (SV40Tag), driven off of a previously identified visceral endoderm gene, Indian hedgehog. We modified a bacterial artificial chromosome so that SV40Tag was driven off of the Indian hedgehog gene. The modified bacterial artificial chromosome was used in both pronuclear injections of mouse blastocysts and the electroporation of embryonic stem cells. After neither attempt produced a visceral endoderm cell line, we examined a visceral endoderm-like cell line, END2, for the presence of the blood inducing factors. We demonstrated the ability of END2 conditioned media to apparently increase expression of blood transcripts in differentiating embryonic cells indicating the presence of blood inducing factors. Expression profiles of END2 cells were compared to a previously completed embryonic stem cell differentiation profile to identify enriched genes. Two genes, angiopoietin-like 7 and Bc064033, were tested for an ability to induce blood in differentiating embryonic stem cells. When neither protein was capable of inducing blood, the END2 cells were examined for the presence of other known blood inducing factors and similarity to in vivo visceral endoderm. The END2 cells were found to produce bone morphogenetic protein 4, a potent inducer of blood in embryonic stem cell differentiation, which complicated the search for additional factors. Examination of END2 cells also indicated a lack of visceral endoderm markers such as alpha fetoprotein, indicating that the END2 cells may not be as visceral endoderm-like as expected from the current literature. The previously identified Indian hedgehog gene was also examined for its blood induction abilities in vivo. Indian hedgehog knockout mice were examined for the effect gene removal had on both primitive and definitive erythropoiesis. Levels of primitive erythrocytes were unaffected in the Indian hedgehog knockout mice, but levels of definitive erythrocytes were found to be significantly decreased. Further examination of Indian hedgehog knockout fetal livers also showed that they had decreased numbers of haematopoietic stem cells. The haematopoietic stem cells were fully capable when cultured and generated appropriate numbers of progenitor cells, indicating a non-intrinsic cause for this defect. Levels of hedgehog target genes that are usually highest in the stromal compartment were also found to be most significantly decreased in Indian hedgehog knockout fetal livers. Another hedgehog gene, desert hedgehog, was also shown to be expressed in the fetal liver and may act with Indian hedgehog to regulate stromal production in the fetal liver.

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Thesis (Ph. D.)--University of Alabama at Birmingham, 2008. / Title from first page of PDF file (viewed June 10, 2008). Includes bibliographical references.

Dissertation (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Vita. Bibliography: p.146

Dissertation (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Vita. Bibliography: p.124-150

Dissertation (Ph.D.) --University of Texas Graduate School of Biomedical Sciences at San Antonio, 2008. / Vita. Includes bibliographical references.

Thesis (Ph.D.)--University of Alabama at Birmingham, 2009. / Title from PDF title page (viewed on July 14, 2010). Includes bibliographical references.