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1
Sauers, Daniel J. "Light directed gene patterning using photocaged doxycycline /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 196 p, 2010. http://proquest.umi.com/pqdweb?did=1993328811&sid=6&Fmt=2&clientId=8331&RQT=309&VName=PQD.
2
Mellick, Albert S. Jr, and n/a. "Tissue Specific Gene Expression Patterning and Carcinogenesis." Griffith University. School of Health Science, 2004. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20041102.114313.
Abstract:
Despite significant advances in diagnosis and treatment, breast cancer remains the leading cause of cancer-related deaths in Australian women. Colorectal cancer is the second most common cancer in both males and females; after prostate and breast cancer, respectively, and excluding non-melanocytic skin cancer. Both breast cancer and colorectal cancer follow a common progressive course of illness; presenting (at least initially) with benign symptoms that can be treated by ablation (or removal) of the affected area. Cancer progression is associated with breakdown of tissue barriers (such as basement membranes), leading to the spread of cancer cells (via the vasculature or lymphatic system), and the establishment of secondary metastatic disease at green-field sites. Secondary tumours presenting in the lungs, ovaries, liver, bone, or brain are associated with chronic-debilitating symptoms that are difficult to treat, and will result in death. In the case of breast and colon cancer, effective early therapeutic intervention does have a significant impact upon patient survival. Tumour progression in breast and colon carcinomas is characterised by invasion of the surrounding stroma, and the acquisition of stromal characteristics, by previously epithelial cells. This progression is associated with the expression of extracellular proteases (ECPs) and increased motility. The process of mesenchymal transformation that tumour cells undergo is also referred to as the epithelial to mesenchymal transition (EMT). In general terms the aim of the study, presented in this thesis, was to investigate gene expression in cancer biology; and to characterise changes in breast cancer and colon cancer, with a focus on those genes, and gene products that may play a role in metastasis, including a family of ECPs, the matrix metalloproteinases (MMPs). In our laboratory, we have applied methods in microdissection, differential display polymerase chain reaction amplification (DD-PCR), and array hybridisation analysis to identify gene expression patterns in late stage archival formalin fixed paraffin embedded (FFPE) breast tumour biopsies that may be indicative of the EMT; or the response to the surrounding stroma/interstitium to the presence of the tumour.' The quality of nucleic acid obtainable from FFPE material presents a considerable challenge for gene expression studies. In order to identify tissue specific gene expression patterns, DD-PCR products, amplified from message obtained following segregation of tumour tissue from surrounding stroma, was hybridised to arrayed cDNA libraries created from stromal tumours, or sarcomas. In this way, 21 known genes, or expressed sequence tags (ESTs), were identified. These included the cytoskeletal element and EMT marker, vimentin, the mammary developmental factor and, signal transducer and activator of transcription (STAT)-3, and the cargo selection protein (TIP47). Seventeen genes showed differential expression in either the tumour, or stromal fractions. When applied to transformed breast cancer cell lines (MDA-MB-435 & T47D) DD-array analysis revealed a further 17 genes that were differentially regulated in invasive cells, compared with those displaying a less invasive phenotype. Six of the ESTs identified by DD-PCR array analysis, had no known (or predicted) function. For example, bcaf-2 was identified as the 3'-end of a putative open reading frame (ORF) localised to chromosome 6, while bcaf-10 showed homology with a known ORF. In order to analyse the expression of these bcafs further, a stromal cell culture model, representative of the original osteosarcoma cDNA libraries from which they were obtained, was used. In this model, CD14' (or adherent) peripheral blood mononuclear cells (PBMCs) treated with macrophage colony stimulating factor (M-CSF), can be allowed to differentiate into macrophage-like (ML) cells; while cells treated with M-CSF, and the receptor activator of NF-KB ligand (RANKL) will differentiate into multinucleate osteoclast-like (OCL) multinucleate giant cells. Uniquely, the stromal EST, bcaf-2 was expressed only by RANKL-treated (or OCL) cells. bcaf-2 and other ESTs, identified by DD-PCR analysis (and recently published) are the subject of on going research in our laboratory. The role of RANKL in mammary gland development and bone metastasis suggested that the identification of a RANKL-regulated stromal factor in breast tissue (bcaf-2) was not an artefact. RANKL is a membrane-bound, member of the tumour necrosis factor (TNF)-a cytokine super family. In order to test the hypothesis that RANKL might act as an inflammatory cytokine to regulate clinically significant stromal gene expression in the breast, we employed quantitative real time PCR analysis to examine the relative levels of selected members of a group of metal dependent ECPs, the matrix metalloproteinases (MMPs). RNA was extracted from ML cells and OCL cells, as well as RANK positive breast cancer cell lines (T47D, MDA-MB-435 & MCF-7). When the relative levels of protease mRNA were compared we demonstrated a significant (>20- fold) specific increase in collagenase (collagenase 2lMMP-8 and collagenase 3lMMP-13), and the tissue inhibitor of MMP (TIMP)-2 expression in M-CSF and RANKL treated PBMCs cells. When the assay was applied to RANKL treated breast cancer cell lines (MCF-7, T47D & MDAMB- 231), minor (40-fold) but potentially significant alterations in stromal protease gene expression were observed. The changes observed did not however, support the hypothesis that RANKL might act as an inflammatory cytokine to induce significant alterations in ECP expression in breast cancer cells. To investigate the role of RANKL as a driver of EMT in aberrant breast epithelium, total message (mRNNcDNA) from T47D, MCF-7, MDA-MB-231 cells, and message from the same cell lines treated with RANKL were compared by comparative fluorescent cDNA microarray analysis. Of the 1,700 targets available on the arrays, this study identified 160 that were differentially expressed in RANKL treated cells. The results suggest that RANKL may promote rather than suppress a mammary epithelial phenotype in breast cancer. In fact a putative mesenchymal to epithelial transition (MET) was observed following microscopic analysis, and this finding is the subject of on going research in our laboratory. Sporadic structural alterations in certain mitogenic factors represent important early events in cancer progression, while inherited mutations govern familial susceptibility to disease. In colon cancer, a close link exists between Winglessllnt (WNT) signalling, disease pathology, and the expression of MMPs. To examine the relationship between protease expression and structural genetic alterations in this EMT-linked signalling pathway, and others, we applied combined QPCR analysis of MMP expression and PCR-Single Strand Conformation Analysis (SSCA) to 26 colonic tumours, and patient-matched normal colonic mucosa. In this study, significant correlations between the expression of ECPs, and a key mediator of WNT signalling (p-catenin) were identified. While tumours possessing specific functional mutations in K-Ras, were found to group with phenotypic clustering based on protease gene expression. This result may be due to an interruption of normal interactions between RasIRaf signalling and transforming growth factor (TGF) P signalling, via Sma- and Mad- related protein (SMAD) signalling. These results demonstrate that the already identified link between mutations in kinase signalling, and aspects of gross colon tumour morphology (such as dysplasia) may be due to aberrant MMP expression patterning. The final aim of this research was to utilise methods developed in microdissection and specific Q-PCR analysis, to identify whether tumour-stroma differences in MMP gene expression might be used as markers of disease pathology. Total RNA from tumour, and biopsy-matched adjacent stromal tissue were segregated from 35 FFPE archival breast tumour biopsies. Comparison with stroma identified specific associations between TIMP-2 expression in the stroma and lymph node involvement, as well as stromelysin-3 (MMP-I I ) and TIMP-I expression and calcification of the tumour. Furthermore, a significant correlation was identified in the pattern of gelatinase (gelatinase AIMMP-2 & gelatinaseB1MMP-9) expression; while no significant correlation was identified in tumour-stroma MMP gene expression differences, and tumour grade, or hormone receptor status. These results suggest that coordinated changes within the tumour, and proximal stromal tissues (rather than tissue specific changes per se), regulate pathologically significant changes in breast carcinogenesis. In conclusion, this thesis describes the use of novel techniques in specific and global gene expression analysis that permitted examination of stromal gene expression changes in epithelial tumour progression. Microdissection facilitated localisation of expression to particular tissues, while cell culture models provided material with which to optimise and demonstrate the efficacy of techniques used (where tumour material itself was not abundant). Furthermore, we have identified significant and specific correlations between general stromal protease gene expression changes, a putative mammary epithelial differentiation factor (RANKL), alterations in growth factor signalling, and epithelial tumour pathology in the breast and colon. The combination of techniques developed in this study may assist in improvement of categorisation of tumours in clinical pathology. Specifically, the development of novel grading systems that link underlying molecular genetic changes with changes in tumour pathology. These processes may assist to improve diagnosis and provide more effective patient/tumour-specific drug therapies.
3
Mellick, Albert S. Jr. "Tissue Specific Gene Expression Patterning and Carcinogenesis." Thesis, Griffith University, 2004. http://hdl.handle.net/10072/365189.
Abstract:
Despite significant advances in diagnosis and treatment, breast cancer remains the leading cause of cancer-related deaths in Australian women. Colorectal cancer is the second most common cancer in both males and females; after prostate and breast cancer, respectively, and excluding non-melanocytic skin cancer. Both breast cancer and colorectal cancer follow a common progressive course of illness; presenting (at least initially) with benign symptoms that can be treated by ablation (or removal) of the affected area. Cancer progression is associated with breakdown of tissue barriers (such as basement membranes), leading to the spread of cancer cells (via the vasculature or lymphatic system), and the establishment of secondary metastatic disease at green-field sites. Secondary tumours presenting in the lungs, ovaries, liver, bone, or brain are associated with chronic-debilitating symptoms that are difficult to treat, and will result in death. In the case of breast and colon cancer, effective early therapeutic intervention does have a significant impact upon patient survival. Tumour progression in breast and colon carcinomas is characterised by invasion of the surrounding stroma, and the acquisition of stromal characteristics, by previously epithelial cells. This progression is associated with the expression of extracellular proteases (ECPs) and increased motility. The process of mesenchymal transformation that tumour cells undergo is also referred to as the epithelial to mesenchymal transition (EMT). In general terms the aim of the study, presented in this thesis, was to investigate gene expression in cancer biology; and to characterise changes in breast cancer and colon cancer, with a focus on those genes, and gene products that may play a role in metastasis, including a family of ECPs, the matrix metalloproteinases (MMPs). In our laboratory, we have applied methods in microdissection, differential display polymerase chain reaction amplification (DD-PCR), and array hybridisation analysis to identify gene expression patterns in late stage archival formalin fixed paraffin embedded (FFPE) breast tumour biopsies that may be indicative of the EMT; or the response to the surrounding stroma/interstitium to the presence of the tumour.' The quality of nucleic acid obtainable from FFPE material presents a considerable challenge for gene expression studies. In order to identify tissue specific gene expression patterns, DD-PCR products, amplified from message obtained following segregation of tumour tissue from surrounding stroma, was hybridised to arrayed cDNA libraries created from stromal tumours, or sarcomas. In this way, 21 known genes, or expressed sequence tags (ESTs), were identified. These included the cytoskeletal element and EMT marker, vimentin, the mammary developmental factor and, signal transducer and activator of transcription (STAT)-3, and the cargo selection protein (TIP47). Seventeen genes showed differential expression in either the tumour, or stromal fractions. When applied to transformed breast cancer cell lines (MDA-MB-435 & T47D) DD-array analysis revealed a further 17 genes that were differentially regulated in invasive cells, compared with those displaying a less invasive phenotype. Six of the ESTs identified by DD-PCR array analysis, had no known (or predicted) function. For example, bcaf-2 was identified as the 3'-end of a putative open reading frame (ORF) localised to chromosome 6, while bcaf-10 showed homology with a known ORF. In order to analyse the expression of these bcafs further, a stromal cell culture model, representative of the original osteosarcoma cDNA libraries from which they were obtained, was used. In this model, CD14' (or adherent) peripheral blood mononuclear cells (PBMCs) treated with macrophage colony stimulating factor (M-CSF), can be allowed to differentiate into macrophage-like (ML) cells; while cells treated with M-CSF, and the receptor activator of NF-KB ligand (RANKL) will differentiate into multinucleate osteoclast-like (OCL) multinucleate giant cells. Uniquely, the stromal EST, bcaf-2 was expressed only by RANKL-treated (or OCL) cells. bcaf-2 and other ESTs, identified by DD-PCR analysis (and recently published) are the subject of on going research in our laboratory. The role of RANKL in mammary gland development and bone metastasis suggested that the identification of a RANKL-regulated stromal factor in breast tissue (bcaf-2) was not an artefact. RANKL is a membrane-bound, member of the tumour necrosis factor (TNF)-a cytokine super family. In order to test the hypothesis that RANKL might act as an inflammatory cytokine to regulate clinically significant stromal gene expression in the breast, we employed quantitative real time PCR analysis to examine the relative levels of selected members of a group of metal dependent ECPs, the matrix metalloproteinases (MMPs). RNA was extracted from ML cells and OCL cells, as well as RANK positive breast cancer cell lines (T47D, MDA-MB-435 & MCF-7). When the relative levels of protease mRNA were compared we demonstrated a significant (>20- fold) specific increase in collagenase (collagenase 2lMMP-8 and collagenase 3lMMP-13), and the tissue inhibitor of MMP (TIMP)-2 expression in M-CSF and RANKL treated PBMCs cells. When the assay was applied to RANKL treated breast cancer cell lines (MCF-7, T47D & MDAMB- 231), minor (40-fold) but potentially significant alterations in stromal protease gene expression were observed. The changes observed did not however, support the hypothesis that RANKL might act as an inflammatory cytokine to induce significant alterations in ECP expression in breast cancer cells. To investigate the role of RANKL as a driver of EMT in aberrant breast epithelium, total message (mRNNcDNA) from T47D, MCF-7, MDA-MB-231 cells, and message from the same cell lines treated with RANKL were compared by comparative fluorescent cDNA microarray analysis. Of the 1,700 targets available on the arrays, this study identified 160 that were differentially expressed in RANKL treated cells. The results suggest that RANKL may promote rather than suppress a mammary epithelial phenotype in breast cancer. In fact a putative mesenchymal to epithelial transition (MET) was observed following microscopic analysis, and this finding is the subject of on going research in our laboratory. Sporadic structural alterations in certain mitogenic factors represent important early events in cancer progression, while inherited mutations govern familial susceptibility to disease. In colon cancer, a close link exists between Winglessllnt (WNT) signalling, disease pathology, and the expression of MMPs. To examine the relationship between protease expression and structural genetic alterations in this EMT-linked signalling pathway, and others, we applied combined QPCR
analysis of MMP expression and PCR-Single Strand Conformation Analysis (SSCA) to 26 colonic tumours, and patient-matched normal colonic mucosa. In this study, significant correlations between the expression of ECPs, and a key mediator of WNT signalling (p-catenin) were identified. While tumours possessing specific functional mutations in K-Ras, were found to group with phenotypic clustering based on protease gene expression. This result may be due to an interruption of normal interactions between RasIRaf signalling and transforming growth factor (TGF) P signalling, via Sma- and Mad- related protein (SMAD) signalling. These results demonstrate that the already identified link between mutations in kinase signalling, and aspects of gross colon tumour morphology (such as dysplasia) may be due to aberrant MMP expression patterning. The final aim of this research was to utilise methods developed in microdissection and specific Q-PCR analysis, to identify whether tumour-stroma differences in MMP gene expression might be used as markers of disease pathology. Total RNA from tumour, and biopsy-matched adjacent stromal tissue were segregated from 35 FFPE archival breast tumour biopsies. Comparison with stroma identified specific associations between TIMP-2 expression in the stroma and lymph node involvement, as well as stromelysin-3 (MMP-I I ) and TIMP-I expression and calcification of the tumour. Furthermore, a significant correlation was identified in the pattern of gelatinase (gelatinase AIMMP-2 & gelatinaseB1MMP-9) expression; while no significant correlation was identified in tumour-stroma MMP gene expression differences, and tumour grade, or hormone receptor status. These results suggest that coordinated changes within the tumour, and proximal stromal tissues (rather than tissue specific changes per se), regulate pathologically significant changes in breast carcinogenesis. In conclusion, this thesis describes the use of novel techniques in specific and global gene expression analysis that permitted examination of stromal gene expression changes in epithelial tumour progression. Microdissection facilitated localisation of expression to particular tissues, while cell culture models provided material with which to optimise and demonstrate the efficacy of techniques used (where tumour material itself was not abundant). Furthermore, we have identified significant and specific correlations between general stromal protease gene expression changes, a putative mammary epithelial differentiation factor (RANKL), alterations in growth factor signalling, and epithelial tumour pathology in the breast and colon. The combination of techniques developed in this study may assist in improvement of categorisation of tumours in clinical pathology. Specifically, the development of novel grading systems that link underlying molecular genetic changes with changes in tumour pathology. These processes may assist to improve diagnosis and provide more effective patient/tumour-specific drug therapies.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Health Sciences
Faculty of Health Sciences
Full Text
4
Blader, Patrick. "Analysis of gene expression during early development of the zebrafish, Brachydanio rerio." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282415.
5
Boehm, Christian Reiner. "Gene expression control for synthetic patterning of bacterial populations and plants." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267842.
Abstract:
The development of shape in multicellular organisms has intrigued human minds for millenia. Empowered by modern genetic techniques, molecular biologists are now striving to not only dissect developmental processes, but to exploit their modularity for the design of custom living systems used in bioproduction, remediation, and regenerative medicine. Currently, our capacity to harness this potential is fundamentally limited by a lack of spatiotemporal control over gene expression in multicellular systems. While several synthetic genetic circuits for control of multicellular patterning have been reported, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its fundamental role in biological self-organization. In this thesis, I introduce the first synthetic genetic system implementing population-based AND logic for programmed hierarchical patterning of bacterial populations of Escherichia coli, and address fundamental prerequisites for implementation of an analogous genetic circuit into the emergent multicellular plant model Marchantia polymorpha. In both model systems, I explore the use of bacteriophage T7 RNA polymerase as a gene expression engine to control synthetic patterning across populations of cells. In E. coli, I developed a ratiometric assay of bacteriophage T7 RNA polymerase activity, which I used to systematically characterize different intact and split enzyme variants. I utilized the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. I validated the AND gate-like behavior of this system both in cell suspension and in surface culture. Then, I used the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. To prepare the adaption of bacteriophage T7 RNA polymerase-driven synthetic patterning from the prokaryote E. coli to the eukaryote M. polymorpha, I developed a toolbox of genetic elements for spatial gene expression control in the liverwort: I analyzed codon usage across the transcriptome of M. polymorpha, and used insights gained to design codon-optimized fluorescent reporters successfully expressed from its nuclear and chloroplast genomes. For targeting of bacteriophage T7 RNA polymerase to these cellular compartments, I functionally validated nuclear localization signals and chloroplast transit peptides. For spatiotemporal control of bacteriophage T7 RNA polymerase in M. polymorpha, I characterized spatially restricted and inducible promoters. For facilitated posttranscriptional processing of target transcripts, I functionally validated viral enhancer sequences in M. polymorpha. Taking advantage of this genetic toolbox, I introduced inducible nuclear-targeted bacteriophage T7 RNA polymerase into M. polymorpha. I showed implementation of the bacteriophage T7 RNA polymerase/PT7 expression system accompanied by hypermethylation of its target nuclear transgene. My observations suggest operation of efficient epigenetic gene silencing in M. polymorpha, and guide future efforts in chassis engineering of this multicellular plant model. Furthermore, my results encourage utilization of spatiotemporally controlled bacteriophage T7 RNA polymerase as a targeted silencing system for functional genomic studies and morphogenetic engineering in the liverwort. Taken together, the work presented enhances our capacity for spatiotemporal gene expression control in bacterial populations and plants, facilitating future efforts in synthetic morphogenesis for applications in synthetic biology and metabolic engineering.
6
Jackman, William R. "Segmentation and molecular patterning of the amphioxus hindbrain, pharynx, and somites /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9998038.
Abstract:
Thesis (Ph. D.)--University of Oregon, 2000.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 96-105). Also available for download via the World Wide Web; free to University of Oregon users.
7
Buxton, Paul Graeme. "Embryonic roles for the slug regulatory gene in hindbrain regulation and limb patterning." Thesis, University College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266133.
8
McKnight, Kristen Dawn. "Gene expression profiling reveals novel attributes of the mouse definitive endoderm." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/3431.
Abstract:
Gastrulation is one of the most critical events of embryogenesis, generating the three primary germ layers (definitive endoderm, mesoderm, and ectoderm) and establishing the embryonic body plan. The definitive endoderm, which generates the lungs, liver, pancreas, and digestive tract, has become a tissue of particular interest in recent years. Understanding definitive endoderm formation and patterning will greatly aid progress in the in vitro differentiation of embryonic stem cells to definitive endoderm for use in treatment of diseases such as diabetes and hepatitis as an alternative for whole organ replacement.
Gene targeting studies have demonstrated a critical role for the Nodal signaling pathway and the forkhead transcription factors Foxh1 and Foxa2 in specification of a group of cells referred to as the anterior primitive streak (APS). However, the transcriptional targets of Foxh1 and/or Foxa2 other than Nodal that regulate specification of this group of cells are currently unknown. Fate mapping and lineage tracing experiments have shown the APS to be the source of the definitive endoderm. However, many questions regarding specification and patterning of the definitive endoderm remain. The study of this tissue has been hampered by the lack of genetic markers specific for the definitive endoderm as many of the current markers, including Cerl, Foxa2, and Sox17, are also expressed in the visceral endoderm, an extraembryonic tissue.
To further investigate the role of Foxh1 in specification of the anterior primitive streak and to address the lack of genetic markers for the definitive endoderm we performed expression profiling on post-implantation mouse embryos using Affymetrix™ GeneChips®. From this analysis we identified and characterized a novel marker of the mouse definitive endoderm. Examination of this, and other, novel endoderm markers in Foxh1 and Foxa2 deficient mouse embryos revealed that contrary to current models of definitive endoderm formation, we find some definitive endoderm is formed in these mutants. Specifically, specification of the midgut and hindgut definitive endoderm is largely unaffected, while foregut formation is severely affected. These results suggest that the formation of the midgut and hindgut definitive endoderm populations is independent of the anterior primitive streak and separate from the foregut definitive endoderm. This represents a major insight into the mechanisms regulating endoderm formation and patterning.
9
Yamamoto, Mako. "The transformation suppressor gene Reck is required for postaxial patterning in mouse forelimbs." Kyoto University, 2012. http://hdl.handle.net/2433/158062.
10
Hidalgo-Downing, Alicia. "Molecular cloning of patched and analysis of its role in intrasegmental patterning in D. melanogaster." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.258158.
11
Ash, David Michael Dobens Leonard L. "A dominant negative allele of the bunched gene blocks bunched function during tissue patterning." Diss., UMK access, 2004.
Abstract:
Thesis (M.S.)--School of Biological Sciences. University of Missouri--Kansas City, 2004."A thesis in cellular and molecular biology." Typescript. Advisor: Leonard L. Dobens. Vita. Title from "catalog record" of the print edition Description based on contents viewed Feb. 22, 2006. Includes bibliographical references (leaves 51-58). Online version of the print edition.
12
Fernandes, Jolene Sabrina Rothenberg Ellen V. Sternberg Paul W. "Dissection of gene regulatory networks underlying patterning and morphogenesis in the C. elegans vulva /." Diss., Pasadena, Calif. : California Institute of Technology, 2007. http://resolver.caltech.edu/CaltechETD:etd-05242007-164706.
13
Nulsen, Candice Renee. "The development and evolution of arthropod appendages: Modulations of a limb patterning gene network." Diss., The University of Arizona, 2000. http://hdl.handle.net/10150/289164.
Abstract:
A quick visual survey of the animal world around us reveals a wide array of morphological diversity, yet it is currently not known how such great diversity may have arisen in evolution. The recent emergence of molecular and developmental data from the field of developmental genetics, including genes, gene expression patterns, and most recently entire genomes, have provided a new set of characters to add in the analysis of animal evolution. One morphological character that displays a wide range of diversity is the appendage. Within the arthropods in particular, limbs vary in their size, shape and number along the body axis, providing an excellent experimental model to study how these changes have come about in evolution. The work in this dissertation uses comparative gene expression patterns to address how an arthropod limb patterning network has been modified to produce different limb morphologies. Over the past several decades, data from the field of Drosophila developmental genetics have aided our understanding of how the fly limb is patterned. Yet, Drosophila is a highly derived insect with an unbranched limb that undergoes a complete metamorphosis. I was interested in learning whether other arthropods displaying different modes of development as well as branched limbs use a similar molecular mechanism to Drosophila in the development and patterning of their limbs. The first arthropod examined was Triops, a branchiopod crustacean with a highly branched and fused limb type. Although some of the genes in the Drosophila limb patterning network appear to be conserved in this animal, the space and time in which they are expressed are different from what we observe in Drosophila. In the second species examined, the grasshopper, Schistocerca americana, again the components of the limb patterning gene network are conserved but the expression patterns are different. It appears that in the grasshopper, downstream genes involved in patterning the P/D axis are conserved in expression and perhaps function, but early in development, there is a dramatic change in the expression of one of the more upstream, dorsal components, a gene called decapentaplegic ( dpp), and it is correlated with the absence of imaginal discs. (Abstract shortened by UMI.)
14
Crease, Devanand John. "Gene induction and patterning in the early Xenopus embryo by molecules with long range activity." Thesis, University of Cambridge, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624106.
15
Andreu, Cervera Abraham. "Role of the ciliopathy gene Ftm/Rpgrip1l and primary cilia in forebrain patterning and morphogenesis." Electronic Thesis or Diss., Sorbonne université, 2018. http://www.theses.fr/2018SORUS223.
Abstract:
Les cils primaires sont essentiels au développement du système nerveux central. Chez la souris, ils jouent un rôle essentiel dans l’organisation de la moelle épinière et du télencéphale via la régulation de la signalisation Hedgehog/Gli. Cependant, malgré la perturbation fréquente de cette voie de signalisation dans les malformations du cerveau antérieur chez l'homme, le rôle des cils primaires dans la morphogenèse du cerveau antérieur a été peu étudié en dehors du télencéphale. Pendant mon doctorat, j’ai étudié le développement du diencéphale, de l’hypothalamus et des yeux chez des souris mutantes pour le gène de ciliopathie Ftm/Rgprip1l. En fin de gestation, les fœtus Ftm-/- présentent une anophtalmie, une réduction de l'hypothalamus ventral et une désorganisation du diencéphale. Chez les embryons Ftm-/-, l'expression de Sonic hedgehog (Shh) est perdue dans le cerveau antérieur ventral, mais maintenue dans la zona limitans intrathalamica (ZLI), l'organisateur diencéphalique. Dans le diencéphale, l'activité de Gli est atténuée dans les régions adjacentes à la ZLI, mais montre un niveau de base plus élevé dans les autres régions. Nos données révèlent un rôle complexe des cils dans le développement du diencéphale, de l'hypothalamus et des yeux via le contrôle régional du ratio entre les formes activatrices et répressives des facteurs de transcription Gli. Ils sont en faveur d’un examen plus approfondi des anomalies du cerveau antérieur dans les ciliopathies sévères et de la recherche de gènes de ciliopathie comme modificateurs dans d'autres maladies humaines présentant des anomalies du cerveau antérieurPrimary cilia are essential for central nervous system development. In the mouse, they play a critical role in patterning the spinal cord and telencephalon via the regulation of Hedgehog/Gli signaling. However, despite the frequent disruption of this signaling pathway in human forebrain malformations, the role of primary cilia in forebrain morphogenesis has been little investigated outside the telencephalon. Here we studied development of the diencephalon, hypothalamus and eyes in mutant mice in which the Ftm/Rgprip1l ciliopathy gene is disrupted. At the end of gestation, Ftm-/- fetuses displayed anophthalmia, a reduction of the ventral hypothalamus and a disorganization of diencephalic nuclei and axonal tracts. In Ftm-/- embryos, we found that the ventral forebrain structures and the rostral thalamus were missing. Optic vesicles formed but lacked the optic cups. We analyzed the molecular causes of these defects. In Ftm-/- embryos, Sonic hedgehog (Shh) expression was lost in the ventral forebrain but maintained in the zona limitans intrathalamica (ZLI), the mid-diencephalic organizer. In the diencephalon, Gli activity was dampened in regions adjacent to the Shh-expressing ZLI but displayed a higher Hh-independent ground level in the other regions. Our data uncover a complex role of cilia in development of the diencephalon, hypothalamus and eyes via the region-specific control of the ratio of activator and repressor forms of the Gli transcription factors. They call for a closer examination of forebrain defects in severe ciliopathies and for a search for ciliopathy genes as modifiers in other human conditions with forebrain defects
16
Van, Leen Eric. "On the morphogenesis of the D. melanogaster pupa : a study on gene patterning and tissue folding." Electronic Thesis or Diss., Sorbonne université, 2020. http://www.theses.fr/2020SORUS387.
Abstract:
Au cours du développement, la coordination des comportements cellulaires est essentielle à la formation d’organes complexes et fonctionnels. L’analyse de ces processus cellulaire est essentielle pour comprendre comment les tissues se forment au cours du développement. Pour ce faire, il est tout d’abord primordial d’identifier les gènes dont l’expression est corrélée avec chacun de ces processus cellulaires. Avec pour modèle la formation de l’épithélium dorsal (le notum) de la pupe de drosophile, mon travail de thèse a visé à identifier les mécanismes moléculaires qui gouvernent la régulation spatiale de la morphogenèse de l’échelle cellulaire à l’échelle de l’organisme. Dans un premier temps, j’ai mis en œuvre une analyse de transcriptomique spatiale qui m’a permis d’identifier de nouveaux gènes impliqués dans la morphogenèse du notum. Dans un second temps, j’ai développé un microscope confocal rotatif avec l’aide de la plateforme d’imagerie de l’Institut Curie. En appliquant cette nouvelle méthode au cours du développement de la pupe jusqu’au stade adulte, j’ai pu observer la morphogenèse de l’aile et du notum de manière simultanée. J’ai ainsi identifié un nouveau mouvement morphogénétique du notum entre 45-50 hAPF qui semble indépendant de la morphogenèse de l’aile dans le temps et dans l’espace. Enfin j’ai montré que ce mouvement est contrôlée par l’expression de sérine-protéases qui libèrent l’attachement de l’épithélium à la cuticule. Ce travail de thèse représente un apport important à une compréhension fine et intégrée de la régulation de la morphogenèse et de la coordination des dynamiques cellulaires au cours du développementIn order to achieve complex shapes during development, multicellular organisms need to coordinate cellular behaviors to form complex and functional organs. Identifying genes that are expressed in patterns that correlate with cellular processes is therefore primordial. Using the dorsal epithelium (the notum) of drosophila pupa as a model, my thesis aimed at uncovering the molecular mechanisms which control the spatial regulation of morphogenesis at the cell and tissue scale. First, I developed spatial transcriptomics which enabled the identification of new expression patterns involved in notum morphogenesis. Second, I developed, in collaboration with the imaging platform of Institut Curie, Rotating Sample Confocal Microscopy. Using this technique, I was able to simultaneously observe the morphogenesis of the notum, hinge and wing blade. This enabled the discovery of a new morphogenetic movement in the notum between 45-50hAPF. My results suggest that this extensive folding and elongation of the notum is independent of folding in the wing. Furthermore, I demonstrated that the expression of serine proteases regulate the attachment of the tissue to the cuticle which triggers the onset of the folding and determines the final shape of the tissue. Overall, this work increases our understanding of the spatial regulation of morphogenesis and contributes to the knowledge on how the extracellular matrix can regulate tissue shape
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Goea, Laura Elena. "Regulatory interactions involved in pronephros development and patterning." Electronic Thesis or Diss., Sorbonne université, 2018. http://www.theses.fr/2018SORUS576.
Abstract:
Les vertébrés ont développé des mécanismes variés de contrôle de l’expression des gènes au cours du développement et de la croissance de l’organisme. La régulation transcriptionnelle joue un rôle central dans l’établissement des réseaux de régulation génique qui sous-tendent l’organogenèse. Le rein des vertébrés s’établit en formant trois structures successives de complexité croissante au cours du développement : le pronéphros, le mésonéphros et le métanéphros. Chez l’amphibien Xenopus laevis, le pronéphros est constitué d’une seule paire de néphrons de grande taille et constitue le rein fonctionnel du têtard. Il est subdivisé en trois domaines distincts : le glomus, unité de filtration du sang ; le tubule, lieu de réabsorption des solutés et d’excrétion des déchets, et le tubule collecteur qui débouche dans le cloaque pour évacuer l’urine. Le tubule pronéphrique présente une segmentation structurale et fonctionnelle comme en témoigne l'expression différentielle de gènes codant différents transporteurs membranaires. Cette segmentation est similaire à celle observée pour le néphron des mammifères. La simplicité d’organisation du pronéphros, associée aux avantages expérimentaux de l’embryon de xénope, en fait un excellent modèle pour l’étude des réseaux gèniques impliqués dans le développement rénal des vertébrés. Les facteurs de transcription Pax2/Pax8 sont des régulateurs majeurs du développement rénal des vertébrés. De nombreux travaux réalisés chez la souris, le poissson zèbre et le xénope ont montré qu’ils étaient requis pour la spécification du lignage rénal, l’induction du du métanéphros, la ramification du bourgeon urétéral et la néphrogenèse. Toutefois, les mécanismes par lesquels Pax2/Pax8 contrôlent ces processus sont encore mal connus; en particulier, leurs gènes cibles ne sont que très partiellement identifiés. Chez le xénope, la perte de fonction de Pax8 conduit à une absence totale de tubule pronéphrique en raison d’un défaut de formation du champ pronéhrique. Ayant pour objectif d’identifier le réseau de régulation génique qui gouverne la mise en place du champ pronéphrique, nous avons entrepris une analyse transcriptomique afin de déterminer les cibles de Pax8 impliqués dans la spécification rénale. Nous montrons que les gènes hnf1b, evi1 et mnx1, tous trois codant pour des facteurs de transcription, sont régulés par Pax8. L’initiation de leur expression dans le champ pronéphrique au stade neurula est dépendante de Pax8. En utilisant une approche bioinformatique basée sur la conservation des séquences génomiques au cours de l’évolution, nous avons identifié une séquence conservée de 300 paires de bases (CNS1) localisée en amont du gène hnf1b portant un site de liaison à Pax8. En utilisant des tests de transactivation de gène rapporteur dans différentes lignées cellulaires et dans l’embryon, nous avons montré que cette séquence répond à Pax8 aussi bien dans un contexte de surexpression que dans le cas d’une expression endogène de Pax8. La mutation du site de liaison à Pax8 dans la séquence annule l’augmentation de l’activité du gène rapporteur. Ces résultats permettent de proposer que Pax8 régule l’expression de hnf1b dans le champ pronéphrique en se fixant à la séquence régulatrice CNS1. L’analyse détaillée et comparée des patrons d’expression de hnf1b, evi1 et mnx1 montrent qu’ils sont exprimés dans des domaines spécifiques du champ pronéphrique qui exprime Pax8. Afin de révéler l’existence de régulations croisées potentielles entre ces gènes, des expériences de gain et de perte de fonction ont été réalisées. La seule régulation mise en évidence est celle de evi1 par mnx1. Au total, nos résultats constituent une première étape dans l’identification du réseau de régulation génique à l’oeuvre dans la spécification du destin rénal chez les vertébrésVertebrate organisms have evolved various mechanisms to control the spatial and temporal patterns of gene expression during growth, differentiation and development. It has become increasingly obvious that the regulatory frameworks are highly dependent on the transcriptional regulation in metazoan organism. The vertebrate kidney develops as three spatially and temporally distinct excretory systems with increasing complexity: the pronephros, the mesonephros, and, finally, the adult kidney or the metanephros (Saxen, 1987). In amphibians, the pronephros is the functional kidney of the tadpole. In Xenopus laevis, it includes a pair of single, large, non-integrated nephron, on each side of the embryo. It can be subdivided into three distinct domains: the glomus, where the blood is filtered into the coelomic cavity, the tubules, where selective re-absorption and secretion is taking place, and the connecting tubule, which carries the waste the cloaca. The pronephric kidney is segmented into distinct domains of the mammalian nephron, as evidenced by the differential expression of several membrane transporter genes (Raciti et al., 2008; Zhou and Vize, 2004). In addition, the Xenopus renal primordium represents a unique system to study gene network organization due to its relative simplicity and the increasing number of genetic regulators identified as necessary for its development.In vertebrates, the transcription factors Pax8 and Pax2 are crucial regulators of kidney development. A large set of studies performed in mouse, zebrafish and Xenopus have demonstrated their requirement for the establishment of the renal lineage, along with metanephric kidney induction, branching morphogenesis and nephron differentiation. Yet, the mechanisms by which they operate and the genes they regulate are still elusive. In Xenopus, loss of Pax8 leads to a complete absence of pronephric tubule, due to a defect in kidney field organization. In an attempt to identify Pax8 downstream targets during renal specification, we compared the microarray screen profiles of Pax8-deficient pronephric cells to the wildtype’s and identified several deregulated genes, including hnf1b, evi1 and mnx1. Morpholino-mediated knockdown experiments evidenced that Pax8 has indeed an essential role in the onset of evi1 and mnx1 expression and is sufficient to activate evi1 expression in ectodermal animal cap cells, as previously shown for hnf1b. Using in silico approaches, we identified an evolutionary conserved non-coding sequence (CNS1) located ~30kb upstream hnf1b gene locus, encompassing a putative Pax8 recognition motif (BS1). Electrophoretic mobility shift assay (EMSA) confirmed that this novel CNS1 directly interacts with Pax8. Using transfection assays in several kidney-derived cell lines, we demonstrate that luciferase activity driven by CNS1 was strongly up-regulated in response to either endogenous or exogenously added Pax8 and that this up-regulation is dependent on the presence of an intact Pax8-binding site. These findings suggest that Pax8 may regulate hnf1b1 expression through specific binding to the hnf1b CNS1, which may clarify the potential mechanism of Pax8 and hnf1b in nephrogenesis. Gene expression profile analysis revealed that evi1, hnf1b and mnx1 are expressed in a subset of the pax8 domain and in a specific region of the pronephric field in accordance with their known role in nephron patterning. We explored the potential cross-regulation between these transcription factors since it could contribute to establish their expression domain. Loss and gain-of-function experiments point to a genetic regulation between mnx1 and evi1, while no relationship can be observed between the other members. We view our results as a start toward building an eventually larger network of interactions between numerous directly and indirectly regulated molecular pathways that mediate specification and patterning of renal cells
18
Karam, Sana. "Mechanisms of pattern formation in the developing cerebellum : role for Eph receptor gene family /." Thesis, Connect to this title online; UW restricted, 2001. http://hdl.handle.net/1773/10557.
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Pahari, Shankar, and University of Lethbridge Faculty of Arts and Science. "The arabidopsis gene Grassy, is required for auxin transport and patterning of leaf vein, shoot and root." Thesis, Lethbridge, Alta. : University of Lethbridge, Faculty of Arts and Science, 2008, 2008. http://hdl.handle.net/10133/670.
Abstract:
Auxin controls a range of growth related characteristics by a mechanism
dependent upon polar auxin transport. We have identified a leaf vein patterning mutant
that shows a simple first leaf vein pattern. The veins are often non-meeting and form
somewhat parallel to one another. The leaves are narrow and pointed so that the overall
leaf phenotype is reminiscent of grass leaves; hence the mutant name grassy (gsy). A
range of shoot and root characteristics are also altered in gsy plants. Compared to wild
type, gsy plants have shorter primary roots with reduced numbers of lateral roots and
increased numbers of longer root hairs. Upon gravitropic stimulation, the root tip bends
slightly away from the normal vector. As well, gsy plants produce an inflorescence with
altered internode elongation and branching pattern. The intensity of the auxin responsive
reporter gene DR5::GUS is unchanged in both roots and developing leaves of gsy,
however, it shows subtle differences to the wild type DR5:GUS expression pattern.
Finally, gsy leaf and root phenotypes are more sensitive to low doses of the auxin efflux
inhibitor NPA and external auxin 2, 4-D. We suggest that this overall pattern is
consistent with defects in auxin transport.xii, 76 leaves : ill. ; 29 cm.
20
Ng, Medard Hein Tsoeng. "Genetic and molecular analyses of nubbin, a gene involved in proximal-distal patterning of the Drosophila wing." Thesis, Open University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309862.
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Heppert, Jennifer K. "Evolution of TOO MANY MOUTHS and stomatal patterning mechanisms in the monocot Dioscorea bulbifera." Honors in the Major Thesis, University of Central Florida, 2009. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1273.
Abstract:
This item is only available in print in the UCF Libraries. If this is your Honors Thesis, you can help us make it available online for use by researchers around the world by following the instructions on the distribution consent form at http://library.ucf.edu/Systems/DigitalInitiatives/DigitalCollections/InternetDistributionConsentAgreementForm.pdf You may also contact the project coordinator, Kerri Bottorff, at kerri.bottorff@ucf.edu for more information.Bachelors
Sciences
Biology
22
Brannon, Mark K. "Wnt pathway-mediated transcriptional regulation of the Xenopus dorsoanterior organizing gene siamois /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/9256.
23
Behesti, Isfahani Hourinaz. "An analysis of the regulation of dorso-ventral patterning and T-box gene function in early eye development." Thesis, University College London (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.433906.
24
Wallbank, Richard William Roy. "Structure and function of the regulatory regions of pannier, a gene involved in the bristle patterning of Drosophilidae." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610369.
25
Sjödal, My. "Specification of the lens and olfactory placodes and dorsoventral patterning of the telencephalon /." Umeå : Univ, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1347.
26
Wahl, Jacquelyn Marie Bell. "Genetics of merle patterning in the domestic dog and gene transcript profiling and immunobiology of dermatomyositis in the shetland sheepdog." Thesis, [College Station, Tex. : Texas A&M University, 2008. http://hdl.handle.net/1969.1/ETD-TAMU-2840.
27
Persson, Madelen. "The role of transcriptional repression in Shh signalling and patterning of the ventral neural tube /." Stockholm : Karolinska institutet, 2004. http://diss.kib.ki.se/2004/91-7349-834-3/.
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Aragón, Manresa Ferran. "The role of vHnf1 and Fgf Signaling in the caudal Hindbrain Patterning." Doctoral thesis, Universitat Pompeu Fabra, 2008. http://hdl.handle.net/10803/7147.
Abstract:
Durant els primers estadis del desenvolupament embrionari dels metazous els teixits embrionaris son progressivament regionalitzats fins que adquireixen destins específics. En els vertebrats, el tub neural, que és el primordi del sistema nerviós central, es tempranament regionalitzat en el seu eix antero-posterior i queda dividit en les tres vesícules cerebrals i la medul·la espinal. La vesícula cerebral més posterior rep el nom de rombencèfal. En el rombencèfal un següent estadi de regionalització condueix cap a una organització en una serie de segments anomenats rombomers. Aquesta organització primària serveix de patró per les estructures que es van generant en el rombencèfal. A part d'unitats morfològiques els rombomers també son compartiments que observen restricció del llinatge cel·lular i expressen combinacions específiques de gens que els hi confereixen una identitat posicional. L'assoliment d'una identitat posicional per part de cadascun dels rombomers implica un procés jeràrquic i gradual en el qual intervenen tota una serie de factors de transcripció de tipus Hox i no Hox així com diferents molècules de senyalitzacióvHnf1 es un dels primers factors de transcripció expressats en el rombencèfal. En aquest projecte s'ha estudiat el paper de vHnf1 així com la implicació de la senyalització FGF en la regionalització del rombencèfal caudal del embrió de pollet. Els resultats mostren que vHnf1 s'expressa tempranament en el rombencèfal amb un límit rostral d'expressió coincident amb la frontera prospectiva entre els rombomers 4 i 5. Experiments de sobrexpressió mostren que vHnf1 es capaç de conferir caràcter caudal a rombomers rostrals tot induint Krox20 in MafB i reprimint Hoxb1 a r4. Les induccions de Krox20 i MafB resultaren ésser dependents de la senyalització per FGFs. Sorprenentment, els nostres resultats també mostren que vHnf1 indueix fortament la expressió de Fgf3. És més, anàlisis per RT-PCRs semiquantitatives demostraren que aquesta inducció es molt ràpida suggerint que Fgf3 és directament regulat per vHnf1. En aquest projecte també es presenta l'anàlisi dels perfils d'expressió d'alguns gens del grup de "sinexpressió" dels FGFs en el rombencéfal caudal. Finalment es determina que la senyalització FGF funciona a través de la via intracel·lular Ras-MAPK en el procés de regionalització del rombencéfal caudal sense implicació de la via PI3K-Akt.
Aquests resultats ofereixen nova informació sobre els mecanismes moleculars implicats en la regionalització del rombencèfal caudal en vertebrats. De manera interessant aquests resultats posen de manifest certes diferencies en els mecanismes de regulació que operen en la regionalització del rombencéfal de diferents especies.
During early embryonic development of chordates, the hindbrain, which is the caudalmost brain vesicle, is transiently organized along the AP axis in a series of segments called rhombomeres (r). This segmental organization serves as scaffold for several structures that develop within the hindbrain in repeated patterns. Each rhombomere has a molecular identity given by a specific combination of gene expression. Rhombomeric identity is the result of a progressively refined patterning that involves the interplay of different cell signaling pathways and rhombomere-specific transcription factors.
In the present project the role of vHnf1, one of the earliest transcription factors expressed in the hindbrain, and its interplay with FGF signaling has been analyzed during the chick embryo development. The results show that vHnf1 is very early expressed in the chick neuroepithelium with a sharp boundary of expression coinciding with the presumptive r4/r5 interrhombomeric boundary. Gain-of-function experiments demonstrated that vHnf1 is able to confer partial caudal character to rostral rhombomeres through the mediation of FGF signaling. We also analyzed the expression of genes of the FGF synexpression group in the caudal hindbrain. Finally, we determined that the role of FGF signaling in regulating the caudal rhombomeric markers Krox20 and MafB is mediated through the Ras-ERK1/2 intracellular pathway.
The results of this project provide new information about the molecular mechanisms involved in patterning the vertebrate caudal hindbrain. Interestingly, while requirement of vHnf1 and FGF signaling for caudal hindbrain patterning is an evolutionary conserved feature, the ways by which FGF signals are regulated during this process differ across species.
29
Chen, Hui-Min. "A More Accessible Drosophila Genome to Study Fly CNS Development: A Dissertation." eScholarship@UMMS, 2015. http://escholarship.umassmed.edu/gsbs_diss/758.
Abstract:
Understanding the complex mechanisms to assemble a functional brain demands sophisticated experimental designs. Drosophila melanogaster, a model organism equipped with powerful genetic tools and evolutionarily conserved developmental programs, is ideal for such mechanistic studies. Valuable insights were learned from research in Drosophila ventral nerve cord, such as spatial patterning, temporal coding, and lineage diversification. However, the blueprint of Drosophila cerebrum development remains largely unknown.
Neural progenitor cells, called neuroblasts (NBs), serially and stereotypically produce neurons and glia in the Drosophila cerebrum. Neuroblasts inherit specific sets of early patterning genes, which likely determine their individual identities when neuroblasts delaminate from neuroectoderm. Unique neuroblasts may hence acquire the abilities to differentially interpret the temporal codes and deposit characteristic progeny lineages. We believe resolving this age-old speculation requires a tracing system that links patterning genes to neuroblasts and corresponding lineages, and further allows specific manipulations.
Using modern transgenic systems, one can immortalize transient NB gene expressions into continual labeling of their offspring. Having a collection of knockin drivers that capture endogenous gene expression patterns would open the door for tracing specific NBs and their progenies based on the combinatorial expression of various early patterning genes. Anticipating the need for a high throughput gene targeting system, we created Golic+ (gene targeting during oogenesis with lethality inhibitor and CRISPR/Cas “plus”), which features efficient homologous recombination in cystoblasts and a lethality selection for easy targeting candidate recovery. Using Golic+, we successfully generated T2AGal4 knock-ins for 6 representative early patterning genes, including lab, unpg, hkb, vnd, ind, and msh. They faithfully recapitulated the expression patterns of the targeted genes. After preserving initial NB expressions by triggering irreversible genetic labeling, we revealed the lineages founded by the NBs expressing a particular early patterning gene.
Identifying the neuroblasts and lineages that express a particular early patterning gene should elucidate the genetic origin of neuroblast diversity. We believe such an effort will lead to a deeper understanding of brain development and evolution.
30
Barbosa, Spinola Carla Maria. "Characterization of the use of AAVs as tools for in utero gene delivery and implications for the study of role of Sonic Hedgehog signaling in the differentiation and patterning of the cochlear epithelium." Electronic Thesis or Diss., Sorbonne université, 2023. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2023SORUS408.pdf.
Abstract:
La cochlée est l'organe sensoriel auditif des mammifères. Il s'agit d'un long organe spiralé qui décompose les sons complexes en ses fréquences distinctes analysées à différentes positions le long de son axe longitudinal. Cette organisation de la cochlée en fonction de la fréquence tient à ses propriétés morphologiques et mécaniques qui varient progressivement le long de son axe longitudinal, également appelé axe basal-apical. Des études antérieures ont montré que la voie de signalisation Sonic Hedgehog (Shh) contrôle l'établissement de l'axe basal-apical de la cochlée, sa taille, et la différenciation de ses cellules sensorielles auditives. Cependant, les périodes pendant lesquelles Shh contrôle ces processus distincts au cours du développement embryonnaire ne sont pas bien définies. On ne sait pas non plus comment les gradations morphologiques apparaissent le long de l'axe basal-apical de la cochlée, ni comment la signalisation Shh contribue à ces processus. Mon projet de thèse s'inscrit dans le cadre de ces questions et mes objectifs étaient (i) de caractériser l'activité de la voie Shh dans l'épithélium neurosensoriel cochléaire en développement et (ii) de développer des outils pour manipuler l'expression génique, temporellement et spatialement, dans la cochlée en développement, pendant les stades de développement embryonnaire de la souris, en mettant principalement l'accent sur la signalisation Shh. Pour caractériser l'activité de signalisation de Shh, j'ai d'abord imagé des cochlées entières prélevées aux stades embryonnaires E13.5 et E14.5 et exprimant le gène rapporteur de Gli Tg(GBS-GFP). Mais l’absence de signal GFP spécifique dans l'épithélium suggère que la signalisation de Shh pourrait être trop faible pour être détectée par cette approche. J'ai ensuite réalisé un RNAscope sur des sections de tête entière d'embryons (de E12.5 à E15.5), en utilisant des sondes ciblant les composants de la voie Shh (Gli1-3, Patched1 et Sonic Hedgehog). Globalement, ces gènes sont exprimés dans l'épithélium sensoriel et les tissus environnants. Notons que Patched1 présente une expression graduelle, avec une expression maximale à l'apex cochléaire à des stades plus avancés (E15.5), près de la source connue de Shh dans le ganglion spiral, ce qui suggère une modulation de la signalisation de Shh par l'épithélium. Parallèlement, j'ai caractérisé le taux de transduction de deux vecteurs viraux adéno-associés (AAV), AAV-PHP.eB et AAV-DJ, aux stades embryonnaires, leur transduction élevée des cellules de l’épithélium sensoriel n’étant connue qu’aux stades postnataux. J’ai mis au point la procédure chirurgicale permettant de réaliser des injections in utero dans l'oreille interne, à partir de 13.5. En quantifiant le taux de transduction de l'AAV-PHP.eB à 48h, 72h et ~5 jours après l'injection, j'ai trouvé des taux de transduction comparables dans les oreilles droite et gauche, un taux de transduction plus élevé à la base qu'à l'apex de la cochlée, et globalement, un taux de transduction plus élevé ~5 jours après injection. Quant à l'AAV-DJ, la transduction n'était efficace que lorsque l'injection était réalisée après E15.5. Ces résultats suggèrent que l'efficacité de transduction de ces vecteurs viraux augmente parallèlement à la maturation des cellules de la base vers l'apex, et qu’au moins 3 jours sont nécessaires pour une forte expression de la GFP. Mon travail a révélé l'expression des principaux composants de la voie Shh dans l'épithélium neurosensoriel en développement de E12.5 à E15.5. Il a également établi les fenêtres temporelles permettant une transduction efficace des cellules cochléaires par les sérotypes AAV-PHP.eB et AAV-DJ. Cette approche virale semble adaptée à la manipulation de l'expression des gènes à partir des stades embryonnaires tardifs. Pour les stades embryonnaires plus précoces, d'autres approches conditionnelles devraient être envisagées, y compris d'autres vecteurs viraux ou la génétique (système CreERT2 -lox)The cochlea is the auditory sensory organ of mammals. It is a long spiral-shaped organ that decomposes complex sounds into distinct frequency components analyzed at different positions along its longitudinal axis (length). This frequency-position organization of the cochlea is supported by its morphological and mechanical properties that gradually vary along its longitudinal axis, also called basal-to-apical axis. Past studies showed that the Sonic Hedgehog (Shh) signaling pathway controls the establishment of the basal-to-apical axis of the cochlea, its size, and the differentiation of its auditory sensory cells. Yet, the time windows during which Shh controls these distinct processes during embryonic development are not well defined. It’s also not clear how morphological gradations arise along the basal-to-apical axis of the cochlea, and how Shh signaling contributes to these processes. My thesis project falls within the scope of these questions, and my objectives were (i) to characterize the activity of the Shh pathway within the developing cochlear neurosensory epithelium and (ii) to develop tools to manipulate gene expression temporally and spatially in the developing cochlea, at embryonic stages, with a primary focus on Shh signaling. To characterize Shh signaling activity, I first imaged whole mount cochlea expressing the Gli-reporter gene Tg(GBS-GFP) at embryonic days E13.5 and E14.5, but I couldn’t detect any specific GFP signal within the epithelium, suggesting that Shh signaling might be too low to be detected by this approach. Yet some GFP positive cells were present in the underlying mesenchyme. I next performed RNAscope in sections of whole head embryos (from E12.5 to E15.5), using probes targeting Shh pathway components (Gli transcription factors, Patched1 receptor, and Sonic Hedgehog). Overall, these genes are expressed in the sensory epithelium and surrounding tissues. Remarkably, Patched1 shows a graded expression, with highest expression at the cochlear apex at later stages (E15.5), nearest to the known spiral ganglion source of Shh, suggesting a modulation of Shh signaling by the epithelium. In parallel, I characterized two adeno-associated viral (AAV) vectors as tools for manipulating gene expression in the developing sensory epithelia of the inner ear. The AAV-PHP.eB and AAV-DJ serotypes were known to transduce sensory cells and supporting cells, respectively, with a high efficiency at postnatal stages, but their transduction rate was not characterized at embryonic stages. My first challenge was to develop the surgical procedure and practice to routinely perform in utero injections into the inner ear, from E13.5. By quantifying the transduction rate of AAV-PHP.eB at 48h, 72h and ~5 days post-injection, I found comparable transduction rates in the right and left inner ears, a higher transduction rate at the base than at the apex of the cochlea, and overall, a higher transduction rate at ~5 days post-injection. Injecting AAV-PHP.eB later at E14.5 also increased the transduction rate. As for AAV-DJ, the transduction was efficient only when the injection was performed after E15.5. These results suggest that the transduction efficiency of these viral vectors increases parallel to the maturation of cells from the base to the apex. In addition, more than 3 days are necessary to obtain a high expression of the reporter gene. My work revealed the expression pattern of the major Shh-pathway components within the developing neurosensory epithelium from E12.5 to E15.5. My work also established the temporal windows suitable for an efficient transduction of cochlear cell by the AAV-PHP.eB and AAV-DJ serotypes. This viral approach appears suited for manipulating gene expression from late embryonic stages on. For earlier embryonic stages, other conditional approaches should be considered including other viral vectors or genetics (CreERT2 -lox system)
31
John, Alphy. "Propriétés subcellulaires et dynamique à l'échelle de l'embryon gouvernant la morphogenèse." Electronic Thesis or Diss., Université Côte d'Azur, 2021. http://theses.univ-cotedazur.fr/2021COAZ6017.
Abstract:
La morphogenèse est le processus de remodelage du zygote, la cellule œuf fécondée, qui permet d’obtenir la forme finale de l’animal. Chez l’embryon, les combinaisons de profils d’expression génique déterminent les axes de symétrie du corps et établissent les coordonnées spatiotemporelles de spécification des cellules. Ces profils affectent aussi l’organisation des composants du cytosquelette pour réguler la morphogenèse des tissus. Tandis qu’un travail important a été réalisé pour comprendre comment les motifs d’expression génique antéro-postérieur (AP) et dorso-ventral (DV) contrôlent indépendamment la morphogenèse, on en sait toujours peu sur l’impact du croisement de ces motifs. Nous utilisons l’embryon de drosophile comme modèle et nous concentrons sur le processus de repliement tissulaire, un processus vital pour l’animal. Des anomalies de repliement peuvent en effet altérer la neurulation chez les vertébrés et la gastrulation chez l’ensemble des animaux organisés en trois feuillets primordiaux. Les études passées ont montré qu’un réseau d’actomyosine, couvrant la surface médiale-apicale des futures cellules mésodermiques, et sous le contrôle du motif d’expression génique DV, joue un rôle clé dans l’invagination du mésoderme. Néanmoins, les preuves expérimentales et théoriques ont plaidé contre la constriction apicale comme seul mécanisme responsable de l’invagination. Dans cette étude, j’ai mis à jour un réseau jonctionnel sous contrôle des profils d’expression génique AP et DV. Ce réseau contractile génère une tension le long de l’axe apico-basal des cellules et dans le plan du tissu, initiant l’intercalation des cellules à 10-15 μm à l’intérieur de l’épithélium mésodermique. Les forces latérales dans les cellules mésodermiques semblent jouer un rôle à la fois dans l’extension du mésoderme et dans l’invagination. Pour conclure, à travers l’implémentation de microscopie à feuillet de lumière 4D, d’ablation infrarouge femtoseconde pour perturber le cytosquelette et d’optogénétique pour contrôler synthétiquement la morphologie tissulaire, ce travail montre sous un jour nouveau l’origine et les fonctions d’un mécanisme inédit responsable de l’élongation et du repliement coordonnés du tissuMorphogenesis is the process of reshaping single-cell zygotes to the final form of a developed animal. Embryonic gene patterning systems determine the body axes and lay down the spatiotemporal specification coordinates for cells. Gene patterning systems also affect the organization of cytoskeletal components in order to drive tissue morphogenesis. While much work was done to understand how AP and DV patterning independently control morphogenesis, little is known on how cross-patterning functions. We use the Drosophila embryo as a model system and focus on the process of tissue folding, a process that is vital for the animal since folding defects can impair neurulation in vertebrates and gastrulation in all animals which are organized into the three germ layers. Past work has shown that an actomyosin meshwork spanning the apical-medial side of prospective mesoderm cells and under the control of the embryo DV patterning plays a key role in mesoderm invagination. Nevertheless, both experimental and theoretical pieces of evidence have argued against apical constriction being the sole mechanism driving invagination. In this study, I have uncovered a lateral cell junctional network under the control of both AP and DV patterning. This contractile network generates tension along the apical-basal axis and within the tissue plane, 10-15 μm inside the mesoderm epithelium initiating lateral cell intercalation. Lateral forces in mesoderm cells seem to play a multivalent role in both driving mesoderm extension and invagination. Finally, by implementing 4D multi-view light-sheet imaging, infra-red femtosecond ablation to perturb the cytoskeleton, and optogenetics to synthetically control tissue morphology, this work shines new light on the origin and functions of a novel mechanism responsible for coordinated tissue elongation and folding
32
Moreno, González Eduardo. "Characterization of the Hox patterning genes in acoel flatworms." Doctoral thesis, Universitat de Barcelona, 2010. http://hdl.handle.net/10803/1909.
Abstract:
One of the main issues in animal evolution deal with the transition from radial organisms (Cnidaria and Ctnenophora), with only one axis of symmetry, the Oral-Aboral (OA) axis, to bilateral organism (Bilateria), bearing two orthogonal body axes, the Antero-posterior (AP) and the Dorso-ventral (DV) axis.Finding the extant bilateral organism closest to the bilaterian ancestor is the first and necessary step to open new ways of analysis. Recent molecular phylogenies have convincingly shown that the acoel flatworms, traditionally classified within the turbellarian Platyhelminthes, are the sister group of the remaining Bilateria, branching out before the common ancestor of protostomes, and deuterostomes.
Hox and ParaHox genes encode for transcriptional regulators involved in the control the AP body axis in all bilateral animals. Hox genes are usually organized in clusters in Bilateria, which have been originated by means of several gene tandem duplications from an original ProtoHox gene. In addition, Hox genes show a collinear correspondence between gene order within the cluster and the body levels at which these genes are expressed.
On the contrary, in the phylogenetic sister group of Bilateria, the Cnidaria, Hox genes are not linked in a single cluster and do not seem to play a similar role for patterning the OA axis.
Since it is still unclear when in the evolutionary history of bilaterians the Hox system first conferred positional identity along the AP-axis, the comparative study of the patterning genes Hox and ParaHox in acoel flatworms, could be crucial to understand the origin of the Hox-ParaHox axial patterning system and how the morphological transition from radial to bilateral animals took place.
In this Thesis, we report on the cloning, genomic arrangement, and expression domains of Hox genes in the acoel species Symsagittifera roscoffensis. Three Hox genes were detected: one from each of the major groups of Hox genes, which are anterior, central, and posterior, named SrHox1, SrHox5 and SrHoxPost respectively. All acoel species studied to date contain the same minimal complement of three Hox genes and one Cdx ParaHox gene, suggesting that the last common bilaterian ancestor (or Urbilateria) had a simple Hox gene complement, composed of only 3 or 4 genes.
In bacterial artificial chromosome cloning, sequencing, and chromosomal fluorescence in situ hybridization, Hox genes were not observed as being clustered in a unique genomic region in S. roscoffensis. Nevertheless, despite its dispersion within the genome, Hox genes are expressed in nested domains along the AP axis in the juvenile worm. The basic set of Hox genes in acoels and their coarse nested spatial deployment might be the first indicators of the role of Hox genes in the evolution of bilateral symmetry and AP positional identity from a hypothetical radial ancestor.
In order to understand how the AP axis has been established over evolutionary time, the execution of functional analyses is essential. With this purpose, we have performed the knockdown of the posterior Hox, IpHoxPost, during the postembryonic development, regeneration and adulthood of the acoel species Isodiametra pulchra, using RNA interference technologies.
The analysis has been done for the first time in acoels, and we demonstrate that the functions of this gene are restricted to the posterior region of the animal, within the muscular and neural tissues. We conclude, therefore, that the posterior Hox genes were used to specify and maintain defined anatomical regions within the AP axis of animals since the beginning of bilaterian evolution.
"Caracterización de los genes Hox en el acelo Symsagittifera roscoffensis"
TEXTO:
Los genes Hox codifican factores de transcripción que regionalizan el eje antero-posterior durante el desarrollo embrionario en todos los animales bilaterales estudiados.
Los animales radiales (cnidarios y ctenóforos) poseen genes Hox, pero estos no desempeñan un rol similar al de sus homólogos en Bilateria, por lo que el sistema de regionalización Hox puede ser considerado una innovación de los Bilateria.
Recientes análisis filogenéticos han demostrado que Acoelomorpha (acelos y nemertodermátidos), un grupo de gusanos clasificados tradicionalmente como platelmintos, divergieron antes del último antecesor común de protóstomos y deuteróstomos.
En consecuencia, representan el grupo de organismos bilaterales idóneo para estudiar la evolución del sistema Hox entre cnidarios y bilaterales. Por este motivo, el objetivo principal de esta tesis ha sido analizar el sistema Hox en acelos.
Encontramos un complemento simple de 3 genes Hox en las 2 especies de acelos estudiadas: Symsagittifera roscoffensis e Isodiametra pulchra. Estos genes no están ligados en el genoma de S. roscoffensis pero se expresan de forma colinear durante el desarrollo postembrionario, lo que representa el primer ejemplo de expresión colinear de genes Hox en Bilateria, indicando que la colinearidad estuvo presente en el ancestro de todos los Bilateria.
Las funciones del Hox posterior fueron analizadas mediante RNA de interferencia en I. pulcra. El fenotipo knockdown indica que IpHoxPost está implicado en la regulación del establecimiento de las estructuras morfológicas en la parte posterior, especialmente de los músculos bucales y los situados alrededor de los aparatos copuladores; así como en el proceso de maduración de los huevos y la proliferación celular. Esto indica que el rol del Hox posterior en la regulación del desarrollo y diversificación del mesodermo postembrionario y la musculatura ha surgido tempranamente durante la evolución de los Bilateria.
33
de, Sousa Nunes Rita Matos Dias. "Search for endoderm genes involved in early patterning of vertebrates." Thesis, University College London (University of London), 2004. http://discovery.ucl.ac.uk/1446642/.
Abstract:
In addition to giving rise to the gut, the endoderm plays a crucial role in embryonic axis determination. The murine extra-embryonic endoderm is thought to provide an early positional cue defining the antero-posterior axis of the embryo. The axial mesendoderm, which emanates from the gastrula organizer, populates the midline of the embryo and patterns it in all three axes. Later, maintenance and refinement of the antero-posterior axis of the brain requires the embryonic endoderm (reviewed in Martinez-Barbera and Beddington, 2001). Genes expressed in the endoderm are responsible for imparting it with its patterning properties. It is therefore useful to identify the expression profile of the endoderm. To this end, a cDNA library was made from 7.5 days post-coitum mouse endoderm (Harrison et al., 1995). Many clones from this library were sequenced and constitute a set of expression sequence tags (ESTs). I screened these ESTs in silico for non- essential molecules whose role in embryonic patterning had not been determined. I then screened clones obeying these criteria by whole-mount in situ hybridisation on 6.5 - 9.5 dpc mouse embryos. Restricted expression was displayed by 18% of the clones (from the total of my work and that of two other students). The restricted expression patterns encountered are presented. One of the restricted genes I encountered in the mouse in situ hybridisation screen was that encoding the serum and glucocorticoid-regulated kinase (Sgk). I was very interested in the expression pattern of Sgk since it was asymmetric in the visceral endoderm at the onset of gastrulation. Sgk expression presented other interesting features, such as being exclusively expressed in angioblasts at 9.5 dpc. I constructed a targeting vector in order to analyse Sgk function in mouse by a loss-of-function approach. I targeted embryonic stem (ES) cells with this construct and recovered neomycin-resistant clones. One of these is possibly a clone where homologous recombination took place at the Sgk locus. I cloned zebrafish orthologues of some of the restrictedly expressed endoderm genes. I functionally screened these genes in zebrafish by a loss-of-function approach, using antisense morpholino oligonucleotides (MOs). I uncovered several molecules required for proper early embryonic development, one of which I studied in more detail. This was Nop seven-associated protein 2 (Nsa2), a eukaryotic protein involved in ribosome biogenesis (Harnpicharnchai et al., 2001). Zebrafish nsa2 morphants have slowed epiboly and early patterning defects. Furthermore, nsa2 morphant cells gradually die by apoptosis. A smaller embryo develops from surviving nsa2 morphant cells during the first day of development, after which presumably all cells die. The phenotype of nsa2 zebrafish morphants is analogous to that of morphants for the ribosomal proteins RpL19 and RpS5, which when mutated in fly cause the Minute phenotype. I describe the zebrafish Minute phenotype and hypothesize that nsa2 is likely to be a Minute.
34
Kolm, Peggy J. (Peggy Jeannette). "Patterning of the posterior neurectoderm by labial-like Hox genes and retinoids." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/43468.
35
James, Karen Elizabeth. "The role of Ras in dorsoventral patterning and morphogenesis, and the developmental mechanism of eggshell evolution in Drosophila /." Thesis, Connect to this title online; UW restricted, 2002. http://hdl.handle.net/1773/10298.
36
Haddon, Catherine. "The development of the Zebrafish ear and a quest for genes involved in sensory patterning." Thesis, Open University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363972.
37
Gremski, Kristina. "Gynoecium patterning in Arabidopsis thaliana control of transmitting tract development by the HECATE genes /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3221292.
Abstract:
Thesis (Ph. D.)--University of California, San Diego, 2006.Title from first page of PDF file (viewed September 8, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
38
Sakamoto, Susumu. "Id genes are required for morphogenesis and cellular patterning in the developing mammalian cochlea." Kyoto University, 2020. http://hdl.handle.net/2433/253482.
39
Raciti, Marilena. "Reprogramming fibroblasts to neural-stem-like cells by structured overexpression of pallial patterning genes." Doctoral thesis, SISSA, 2012. http://hdl.handle.net/20.500.11767/3924.
Abstract:
In this study, we assayed the capability of four genes implicated in embryonic specification of the cortico-cerebral field, Foxg1, Pax6, Emx2 and Lhx2, to reprogramm mouse embryonic fibroblasts toward neural identities. Lentivirus-mediated, TetON-dependent overexpression of Pax6 and Foxg1 transgenes specifically activated the neural stem cell (NSC) reporter Sox1-EGFP in a substantial fraction of engineered cells. The efficiency of this process was enhanced up to ten times by simultaneous inactivation of Trp53 and co-administration of a specific drug mix inhibiting HDACs, H3K27-HMTase and H3K4m2-demethylase. Remarkably, a fraction of the reprogrammed population expressed other NSC markers and retained its new identity, even upon transgenes switching off. When transferred into a pro-differentiative environment, Pax6/Foxg1-overexpressing cells activated the neuronal marker Tau-EGFP. Frequency of Tau-EGFP cells was almost doubled upon delayed delivery of Emx2 and Lhx2 transgenes. A further improvement of the neuron-like cells output was achieved by tonic inhibition of BMP and TGFb pathways. These Tau-EGFP cells showed a negative resting potential and displayed active electric responses, following injection of depolarizing currents.
40
FRANCHINI, EMANUELA. "ROLE OF ALOG FAMILY GENES IN INFLORESCENCE PATTERNING IN ORYZA SATIVA AND ARABIDOPSIS THALIANA." Doctoral thesis, Università degli Studi di Milano, 2020. http://hdl.handle.net/2434/714283.
Abstract:
Inflorescence architecture is a key agronomical trait that determines fruit and seed yield.
Understanding the genetic basis of inflorescence architecture will not only contribute to elucidate crop evolution/domestication mechanisms but also improve crop grain yield.
Flowering plants develop different types of inflorescences, such as racemes in Arabidopsis and panicles in rice. The architecture is established during the early stages of reproductive development and it is determined by the activity of different meristem types and by the timing of the transition between indeterminate meristems to determinate ones.
Inflorescence development is finely regulated by a genetic network that includes meristem identity genes and genes that regulate their expression; many genes are already known but others have still to be characterized to provide insight into how this complex process is controlled.
Transcriptomic analysis performed in rice and in Arabidopsis through laser microdissection of different meristematic tissues highlighted differentially expressed genes belonging to the ALOG family suggesting their role in inflorescence patterning.
We focus on G1L1, G1L2, and G1L5 of rice and on LSH1, LSH3, and LSH4 of Arabidopsis. G1L5 is already known to be a major regulator of inflorescence architecture, whereas LSH3 and LSH4 seem to have a role in meristem maintenance and organogenesis. Their expression profiles were analyzed by qRT-PCR and RNA in situ hybridization experiments using meristematic tissues from both species. We are also generating single and double/triple K.O mutants in different combinations by CRISPR-Cas9 genome editing technology to have a better understanding of their role in inflorescence patterning.
The data so far obtained demonstrate the role of G1L1 and G1L2 in inflorescence branching and spikelet number determination and we also propose a role for G1L2 in root development. Furthermore, LSH1 seems to be involved in meristem maintenance and organ differentiation, and LSH3 in stem elongation. We propose the hypothesis that LSH1, LSH3, and LSH4 play a redundant function in inflorescence development.
41
Fetter, Karl Christian. "Natural Selection For Disease Resistance In Hybrid Poplars Targets Stomatal Patterning Traits And Regulatory Genes." ScholarWorks @ UVM, 2019. https://scholarworks.uvm.edu/graddis/1162.
Abstract:
The evolution of disease resistance in plants occurs within a framework of interacting
phenotypes, balancing natural selection for life-history traits along a continuum of
fast-growing and poorly defended, or slow-growing and well-defended lifestyles. Plant
populations connected by gene flow are physiologically limited to evolving along a
single axis of the spectrum of the growth-defense trade-off, and strong local selection
can purge phenotypic variance from a population or species, making it difficult to
detect variation linked to the trade-off. Hybridization between two species that have
evolved different growth-defense trade-off optima can reveal trade-offs hidden in either
species by introducing phenotypic and genetic variance. Here, I investigated the
phenotypic and genetic basis for variation of disease resistance in a set of naturally
formed hybrid poplars.
The focal species of this dissertation were the balsam poplar (Populus balsamifera),
black balsam poplar (P. trichocarpa), narrowleaf cottonwood (P. angustifolia), and
eastern cottonwood (P. deltoides). Vegetative cuttings of samples were collected from
natural populations and clonally replicated in a common garden. Ecophysiology and
stomata traits, and the severity of poplar leaf rust disease (Melampsora medusae)
were collected. To overcome the methodological bottleneck of manually phenotyping
stomata density for thousands of cuticle micrographs, I developed a publicly available
tool to automatically identify and count stomata. To identify stomata, a deep con-
volutional neural network was trained on over 4,000 cuticle images of over 700 plant
species. The neural network had an accuracy of 94.2% when applied to new cuticle
images and phenotyped hundreds of micrographs in a matter of minutes.
To understand how disease severity, stomata, and ecophysiology traits changed
as a result of hybridization, statistical models were fit that included the expected
proportion of the genome from either parental species in a hybrid. These models in-
dicated that the ratio of stomata on the upper surface of the leaf to the total number
of stomata was strongly linked to disease, was highly heritable, and wass sensitive
to hybridization. I further investigated the genomic basis of stomata-linked disease
variation by performing an association genetic analysis that explicitly incorporated
admixture. Positive selection in genes involved in guard cell regulation, immune sys-
tem negative regulation, detoxification, lipid biosynthesis, and cell wall homeostasis
were identified.
Together, my dissertation incorporated advances in image-based phenotyping with
evolutionary theory, directed at understanding how disease frequency changes when
hybridization alters the genomes of a population.
42
MILLER, LEIGH-ANNE DEBORAH. "SPATIAL-TEMPORAL EXPRESSION OF SONIC HEDGEHOG REGULATES GROWTH, PATTERNING AND BRANCHING MORPHOGENESIS OF THE EMBRYONIC MOUSE LUNG." University of Cincinnati / OhioLINK, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1070490268.
43
Allan, Deborah M. "Retinoic acid and mouse development : identification of retinoic acid receptor target genes involved in axial patterning." Thesis, McGill University, 2001. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=38451.
Abstract:
Retinoic acid (RA), the major biologically active form of vitamin A, is required for normal development of the mouse embryo. In particular, RA is necessary for the correct anteroposterior specification of the embryonic axis. Exposure to RA at certain stages of development leads to premature truncation of the vertebral column, accompanied by spina bifida. In contrast, embryos that are homozygous null for RARgamma do not exhibit these defects, indicating that this receptor specifically mediates this teratogenic effect. Differential display PCR and suppression subtractive hybridization were employed using the RARgamma null embryos in an attempt to identify downstream targets that may be involved in the formation of these abnormalities. As a result of this process, a full-length cDNA molecule encoding a novel member of the aldo-keto reductase family (AKR1A4) was cloned. Although RA does not regulate the expression of this gene, its developmental expression pattern and substrate specificity suggests a potential role for this enzyme in the protection of certain rapidly growing embryonic structures from harmful metabolites.A precise level of RA signaling is also required for proper specification of vertebral identity. Exposure to excess RA during the early stages of gastrulation results in posterior homeotic transformations of several vertebrae. These transformations are correlated with shifts in the anterior boundaries of Hox expression. In contrast, the loss of functional RARs leads to anterior vertebral transformations. Although retinoic acid response elements have been identified in Hox promoters, it is likely that RA regulates the expression of some Hox genes through intermediary factors. Cdx1 is a homeobox-containing transcription factor that influences vertebral patterning in a manner similar to RARs, and is directly regulated by RA in the mouse embryo. Analysis of an allelic series of RARgamma/Cdx1 null mutant mice demonstrated that Cdx1 and RARgamma act synergistically to pattern certain cervical vertebrae. In addition, Cdx1 is required for the full effect of RA treatment on the vertebral column. However, Cdx1 does not mediate all of the effects of RARgamma as the incidence of a thoracic to cervical vertebral transformation is significantly higher in RARgamma/Cdx1 double mutants as compared to either single null mouse.
44
Wu, Shan. "The roles of OVATE and other elongation genes in regulating proximal-distal patterning of tomato fruit." The Ohio State University, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=osu1437586702.
45
Puli, Oorvashi Roy G. "Defective proventriculus (Dve), a Novel Role in Dorsal-Ventral Patterning of the Drosophila Eye." University of Dayton / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=dayton1406732166.
46
Newton, J. Michael 1969. "Molecular studies of two genes, Agouti andextension, which determine pigment production and patterning in the domestic dog." Diss., The University of Arizona, 1998. http://hdl.handle.net/10150/282613.
Abstract:
Most of our current knowledge about mammalian pigmentation and pigment synthesis has come from the mouse. Despite the wealth of information still to be gained from the mouse system, more could be learned by extending mouse genetics into other mammals. An attractive model for pigmentation studies is the domestic dog. The wide variety of pigment patterns in the many breeds provide a deep source for molecular and genetic investigation. The studies presented here include molecular characterization of two genes which play important roles in the pigmentation and pigment patterning of domestic dogs. These results are supported by comparison with similar results from the mouse and other mammalian species. The two genes studied here are the melanocyte receptor for α-MSH, encoded by the extension locus, and the functional antagonist of this receptor, the agouti protein, encoded by the agouti locus. Studies in the mouse system have demonstrated that the α-MSH receptor is required for the production of black pigment (eumelanin) and that the action of the agouti protein is to cause a switch from the synthesis of black pigment to the production of yellow pigment (pheomelanin). Various alleles at the extension locus result in varying amounts of black pigment synthesis by melanocytes in the hair follicle. Molecular characterization of these alleles has identified missense mutations which alter receptor activity and correlate with changes in coat color. In the studies presented here I have identified sequence changes in the gene for the α-MSH receptor in domestic dogs. These changes include four missense mutations which correlate with the dominantly inherited coat color of certain breeds as well as a truncation in the receptor protein which correlates with the recessive yellow coat color. The key regulator of mammalian coat color patterning is the agouti locus. Regional and temporal patterns of agouti expression in the mouse correlate with the production of yellow pigment. Here I present evidence that the domestic dog also expresses agouti and that its expression correlates with pheomelanogenesis. Furthermore, I provide evidence that gene regulatory elements which control the ventral-specific expression of the agouti gene are conserved between canines and mice.
47
Pei, Zhenglei. "The role of Gsx homeobox genes in the specification and differentiation of mouse lateral ganglionic eminence progenitors." University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1298324694.
48
Choy, Siu Wah. "Characterization of a transcriptional repressor complex and mab-21 interacting genes in male sensory ray patterning of C. elegans /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202006%20CHOY.
49
Siemanowski, Janna [Verfasser], Gregor [Akademischer Betreuer] Bucher, and Roland [Akademischer Betreuer] Dosch. "Identification and analysis of novel insect head patterning genes / Janna Siemanowski. Gutachter: Gregor Bucher ; Roland Dosch. Betreuer: Gregor Bucher." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://d-nb.info/1076911498/34.
50
Horng, Sam H. "Identification and functional characterization of two patterning genes, Zic4 and Ten_m3, in topographic map formation of the visual pathway." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/58371.
Abstract:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, February 2010.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 114-123).
A central feature of visual pathway development is its organization into retinotopic maps. The developmental process by which these maps form involves a transition from early patterning cues to arrays of axonal guidance factors allowing the relative order of retinotopic axons to be preserved. Mechanisms linking patterning molecules of early development to topographic wiring and subsequent functional responses are not well understood. In this thesis, I performed a microarray screen comparing gene expression in early visual and auditory regions of the thalamus in order to identify early patterning candidates with a potential role in visual pathway differentiation. Among the candidates enriched in the visual thalamus, the transcription factor, Zic4, was found to be expressed in gradients of the developing retina, lateral geniculate nucleus (LGN) and primary visual cortex (V 1). Mice lacking Zic4 exhibited a deficit in eye-specific patterning to the thalamus that was complementary to the phenotype seen in mice lacking Tenm3, a type II homophilic transmembrane receptor and transcriptional regulator. Using intrinsic signal optical imaging techniques, I characterized the functional properties of primary visual cortical retinotopic maps in Zic4 and Ten_m3 null mice and identified complementary changes in the ipsilateral representation of V1, as well as evidence for eye-specific mismatch in the cortical binocular zone. Additionally, complementary positional shifts in VI were found in these mutants identifying a bidirectional modulation of mapping mechanisms in the visual pathway.
(cont.) In order to test whether Zic4 and Ten_m3 interact in serial or parallel pathways, I analyzed the retinogeniculate and cortical maps in the combination mutant. The Ten_m3/Zic4 double null mouse exhibited a partial rescue of retinogeniculate mapping and a complete reversal of the cortical changes found in either mutant alone, suggesting that the two genes interact to modulate common downstream effectors in opposite directions. In sum, this thesis presents a gene microarray screen used to identify Zic4 as a novel visual patterning gene, characterizes its loss-of-function phenotype on retinotopic mapping in the thalamus and cortex, and studies its antagonistic interaction with Ten_m3, another visual pathway patterning gene with a complementary loss-of-function phenotype.
by Sam H. Horng.
Ph.D.