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1
Brown, Raquel Monique. "RHOX GENES FUNCTION DURING FOLLICULOGENESIS." OpenSIUC, 2011. https://opensiuc.lib.siu.edu/theses/725.
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Mammalian ovulation is a complex, hormone-dependent developmental program in which several events must take place in an ordered progression to ensure that the oocyte is competent for fertilization. This process requires the coordinated expression of many genes which must be turned on and off in the right place at the right time for proper development of the follicle. While the hormone signals from the brain that initiate ovulation are known, the master control genes which regulate this process are not well known. Homeobox proteins are potential candidates to perform as master regulators. Homeobox proteins are DNA-binding proteins that regulate the transcription of downstream genes and thereby control biological events. We recently identified a new homeobox gene cluster on the mouse X chromosome that are only expressed in reproductive tissues. These reproductive homeobox (Rhox) homeobox genes are expressed in the ovary, placenta, testis, and epididymis, and thus are good candidates to regulate both male and female reproductive tissue development and physiology. Rhox gene expression fell into three categories: Class I exhibited peak expression prior to ovulation (0-8 hours after hCG), Class II were predominantly expressed during ovulation (8-16 hours after hCG), and Class III peaked after ovulation. The slightly overlapping windows of peak Rhox gene expression suggest that these genes may regulate specific events during the ovulatory cycle. The founding member of the cluster, Rhox5, is highly expressed in granulosa cells of pre-ovulatory follicles. We previously reported that Rhox5-null female mice are viable and fertile, suggesting that RHOX5 is either not essential for ovulation, or that one of the other RHOX factors may compensate functionally in granulosa cells. In order to identify potentially redundant RHOX factors, we examined the expression patterns of all 32 Rhox genes using an eCG primed, hCG induced superovulation model, in wild-type, Rhox5-null, and heterozygous littermate mice. Expression levels of Rhox1, exhibited peak expression prior to being hormonal primed, was reduced in the Rhox5-null animal. However, Rhox8 mRNA and protein were reduced at 2h and 4h post hCG, but recovered once the follicles passed the antral stage of development. Conversely, in progesterone receptor knockout mice (PRKO), Rhox8 exhibited normal stimulation by eCG, but failed to reach its peak mRNA level at 8h post-hCG found in WT mice. This suggests a model in which Rhox8 transcription is dependent upon RHOX5 during early folliculogenesis and progesterone during the periovulatory window when RHOX5 normally wanes. Subsequent promoter analysis in granulosa cells revealed essential homeobox binding and progesterone response elements within Rhox8's 5'-flanking region. Transfection of RHOX5 and PGR expression plasmids stimulated, whereas dominant negative and mutant constructs inhibited, Rhox8 promoter activity. At present, the specific impact of misregulation of Rhox5 and Rhox8 during early folliculogenesis is not known. However, follicle counts from serially sectioned ovaries, extirpated from normal cycling animals, indicated that Rhox5-null mice possess ~50% fewer follicles than heterozygous littermates. Loss of RHOX5 in Sertoli cells results in male subfertility characterized by poor germ cell survival due in part to the misregulation of metabolism promoting genes. One of these genes, Ins2, is also stimulated by RHOX5 and RHOX8 in granulosa cells, suggesting impaired insulin signaling may contribute reduced follicle development in Rhox5-null ovaries.
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Fitter, David W. "Function of GOLDEN2-like genes in Arabidopsis." Thesis, University of Oxford, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.393774.
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Sengul, Meryem Senay. "Two Odorant-Binding Protein Genes in Mosquitoes: Comparative Genomics, Expression, and Function." Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/26578.
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Insect Odorant-Binding Proteins (OBPs) are small, water-soluble molecules that solubilize hydrophobic odorant molecules in the sensillum lymph and transport them to their cognate receptors in the olfactory receptor neurons. With the availability of the genome sequence of the African malaria mosquito, Anopheles gambiae, there has been a profound interest in the characterization and functional analyses of Obp genes in order to understand the molecular basis of mosquito host-seeking behavior. However, no direct evidence has been found for specific functions of any mosquito OBPs.
In this study, I describe the comparative genomics and expression analyses on two mosquito Obp genes (Obp1 and Obp7) as well as efforts to determine their functions. Both of these Obp genes were identified in Anopheles stephensi and only Obp7 gene was identified in Anopheles quadriannulatus by screening bacterial artificial chromosome (BAC) libraries of these species. Comparative analyses revealed several interesting features including segments of conserved non-coding sequences (CNSs) that contain potential regulatory elements relevant to olfactory tissue development and blood-feeding.
The expression profiles of these genes were examined in detail in the Asian malaria mosquito An. stephensi. Obp1 and Obp7 transcripts were significantly higher in females than male mosquitoes and they were predominantly found in the antenna, which is the primary olfactory organ of mosquitoes. Twenty-four hours after a blood meal, mRNA levels of these two genes were significantly reduced in the maxillary palp and proboscis, referred to as secondary olfactory organs of mosquitoes. These findings collectively indicate that Obp1 and Obp7 genes in An. stephensi likely function in female olfactory response and may be involved in behaviors related to blood-feeding.
To investigate the function of these Obp genes more directly, a Sindbis virus based expression system is established to knockdown the two Obp gene orthologs in Aedes aegypti. The effective knockdown of Obp1 and Obp7 genes (8 and 100-fold, respectively) is accomplished in female mosquito olfactory tissues. The potential for a systematic analysis of the molecular players involved in mosquito olfaction using this newly developed technique is discussed. Such analysis will provide the foundation for interfering with mosquito host-seeking behavior for the prevention of disease transmission.Ph. D.
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Auburn, Richard Peter. "Screening for genes involved in Drosophila neuromuscular function." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621081.
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Andrews, Tallulah. "Clustering genes by function to understand disease phenotypes." Thesis, University of Oxford, 2015. https://ora.ox.ac.uk/objects/uuid:06bfce1f-4ae0-4715-9ee3-290c43ae9b18.
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Developmental disorders including: autism, intellectual disability, and congenital abnormalities are present in 3-8% of live births and display a huge amount of phenotypic and genetic heterogeneity. Traditionally, geneticists have identified individual monogenic diseases among these patients but a majority of patients fail to receive a clinical diagnosis. However, the genomes of these patients frequently harbour large copynumber variants (CNVs) but their interpretation remains challenging. Using pathway analysis I found significant functional associations for 329 individual phenotypes and show that 39% of these could explain the patientsâ multiple co-morbid phenotypes; and multiple associated genes clustered within individual CNVs. I showed there was significantly more such clustering than expected by chance. In addition, the presence of a multiple functionally-related genes is a significant predictor of CNV pathogenicity beyond the presence of known disease genes and size of the CNV. This clustering of functionally-related genes was part of a broader pattern of functional clusters across the human genome. These genome-wide functional clusters showed tissuespecific expression and some evidence of chromatin-domain level regulation. Furthermore, many genome-wide functional clusters were enriched in segmental duplications making them prone to CNV-causing mutations and were frequently seen disrupted in healthy individuals. However, the majority of the time a pathogenic CNV affected the entire functional cluster, where as benign CNVs tended to affect only one or two genes. I also showed that patients with CNVs affecting the same functional cluster are significantly more phenotypically similar to each other than expected even if their CNVs do not affect any of the same genes. Lastly, I considered one of the major limitations in pathway analysis, namely ascertainment biases in functional information due to the prioritization of genes linked to human disease, and show how the modular nature of gene-networks can be used to identify and prioritize understudied genes.
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Lopes, Miguel. "The function of Msx genes in vascular development." Paris 6, 2011. http://www.theses.fr/2011PA066343.
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Une des étapes les plus importantes de la formation de circulatoire système est la mise en place d’un réseau vasculaire. Les vaisseaux sont composés d’une couche endothéliale intérieure et d’une couche murale extérieure (cellules musculaires lisses [VSMCs] pour les artères et les veines ; péricytes pour les capillaires et les veinules). Dans l’embryon de souris, Msx1lacZ et Msx2lacZ sont exprimés dans des VSMCs (vaisseaux intersomitiques et carotide respectivement) et dans quelques cellules endothéliales de l’aorte (Goupille et al. , 2008). Chez l’adulte, Msx1lacZ et Msx2lacZ sont surtout exprimés dans les cellules musculaires lisses des artères périphériques. De plus, Msx1lacZ est aussi exprimé dans les péricytes des capillaires du muscle squelettique. Nous avons inactivé les deux gènes Msx spécifiquement dans des cellules murales en combinant les allèles Msx1lacz, Msx2lox et α-Sm22Cre (Lopes et al. In press). Des analyses de projection tomographique optique ont démontré un excès de bifurcations dans les vaisseaux céphaliques des embryons mutants à E11. 5. Les artères vertébrale et carotide présentent un calibre augmenté, directement associé à une réduction de couverture par les cellules musculaires lisses. Tirant profit d’un nouvel allèle Msx1CreERT2, nous avons démontré, par traçage cellulaire, que l’anomalie initiale concernait une population de précurseurs des VSMCs. Le phénotype anormal est dû à une réduction du signal BMP dans ces précurseurs, qui entraîne la sous-expression des gènes codant pour les métalloprotéase-2 et métalloprotéase-9. Ces deux gènes sont impliqués dans la migration des précurseurs et leur intégration dans la couche murale
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Lind, Johanna. "Memory, genes, and brain imaging : relating the APOE gene to brain function and structure /." Stockholm : Karolinska institutet, 2007. http://diss.kib.ki.se/2007/978-91-7357-110-4/.
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Elstob, Philip Ronald. "Hox gene function and cell identity in Drosphila." Thesis, University College London (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.272353.
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Heinrich, Stefanie May. "Human SP-A- genes, structure, function- and lung diseases." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-138347.
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Cwajna, Mark. "The sequential function of Hox genes in limb development." Thesis, McGill University, 2011. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=96918.
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Loss-of-function experiments have demonstrated that the establishment of the limb architecture relies upon the function of HoxA and HoxD genes, which are required from early limb bud stages onwards. While there is a tight link between Hox genes and skeletal development, Hox function during osteochondrogenesis remains unclear.Without HoxA/D genes there is an early development arrest, resulting in drastic truncation of the limb skeleton. The severity of this mutation made its analysis uninformative regarding the specific function of HoxA/D genes at later stages of limb development. In order to investigate Hox function during later stages of osteochondrogenesis, we generated conditional Hox inactivations in the osteochondrogenic lineage to circumvent the early affect of HoxA/D loss of function.Comparing the ubiquitous Hox deficiency and specific inactivation in limb skeleton progenitors suggests that HoxA/D genes are needed early on for normal bone patterning and also at later stages to support normal bone growth.Des expériences de perte de fonction ont démontré que la mise en place de l'architecture du squelette des membres requière la fonction des gènes HoxA et HoxD. Cependant, le rôle de ces gènes au cours de l'osteochondrogenèse est inconnu. Le but de mon projet de recherche était de définir ce rôle.En absence des gènes HoxA/D, le développement des membres est compromis dès les stades précoces, bien avant le début de l'osteochondrogenèse. Par conséquent, j'ai généré et analysé des inactivations conditionnelles des gènes HoxA/D dans le lignage osteochondrogenic afin d'établir le rôle de ces gènes au cours du développement osseux. Mes résultats montrent que la croissance des os en développement requiert la fonction des gènes HoxA/D dans le lignage osteochodrogénique. De plus, la comparaison entre l'inactivation ubiquitaire et conditionnelle permet de mieux comprendre la contribution précoce et tardif des gènes HoxA/D dans la formation du squelette des membres.
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Shoichet, Sarah Althea. "Identification and characterisation of genes involved in cognitive function." [S.l.] : [s.n.], 2004. http://www.diss.fu-berlin.de/2004/218/index.html.
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Winterbottom, Emily Frances. "The Function of Gsx genes in Xenopus primary neurogenesis." Thesis, University of York, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507495.
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Parker, Scott. "The function of the caveolin genes in Caenorhabditis elegans." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615064.
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Knox, Andrea Lesley. "Characterisation of genes that modulate integrin function in Drosophila." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621668.
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Baker, John Summers. "The function of innate immune genes in Crohn's disease." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.560924.
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Crohn's Disease (CD) is a debilitating condition characterised by chronic intermittent intestinal inflammation. More than 90 genetic polymorphisms are associated with CD susceptibility, including several in genes of the innate immune system. Here I present a series of experiments designed to enhance our knowledge of the roles of CD-associated polymorphisms in pathogenesis. Many therapeutic regimens are employed in CD treatment, but patients' responses to treatment and disease progression vary widely. There is great interest in studying whether analysis of patients' genotype at CD-associated polymorphisms can be used to predict their disease course, and guide clinical decision-making. To answer these questions, it is essential to be able routinely and cost- effectively to genotype patients at the full range of known CD-associated polymorphisms. The first project presented here describes the design and initial successful testing of a CD-specific genotyping microarray for use in genotype-phenotype studies. The polymorphism most strongly associated with CD susceptibility is in the pattern recognition receptor NOD2; the remaining experiments presented here study the function of NOD2 in primary human monocyte-derived Dendritic Cells (DCs). First, a microarray study is presented which characterises global transcriptional responses to NOD2 stimulation in DCs. NOD2 stimulation is shown to enhance transcriptional changes induced by Toll-Like Receptor 2 stimulation, and NOD2-mediated transcriptional regulation is shown to be lost in DCs expressing CD-associated NOD2 variants. Second, experiments are presented which describe development of a new protocol for proteomic analysis of post-translational protein modifications, and which identify a number of novel candidate targets of NOD2 signalling in DCs. Finally, a project is presented which demonstrates for the first time that NOD2 stimulation induces autophagy in DCs, in an NF-kB and RIPK2-dependent pathway. CD-associated polymorphisms in NOD2 and ATG 16Ll abolish NOD2-mediated autophagy induction, resulting in impaired bacterial handling and antigen presentation.
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Ma, Lina. "Regulation and function of genes involved in Drosophila ciliogenesis." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5711.
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Proneural proteins are transcription factors of the bHLH family and have a conserved role in directing neurogenesis from invertebrate to mammals. In Drosophila, proneural proteins are required for early developmental specification of precursor cells of sense organs (SOPs). Despite considerable progress having been made in this field, it remains unknown how proneural proteins organise the well-orchestrated process that facilitates each type of SOP to acquire both generic neuronal properties and individual neuronal subtype identity during the progression from specification to differentiation. To approach this question, we investigate the gene regulatory network by proneural protein Ato by means of the microarray analysis. Ato directs the formation of the Drosophila chordotonal organs (Ch), important proprioceptive sense organs (Jarman et al., 1993b). The microarray study generated a list of candidate Ato target genes (Cachero et al., 2011). My PhD project entails the characterisation of two potential Ato target genes arising from this screen: Rfx and dila. To determine their positions in the gene regulatory network, I analysed the regulation and function of these genes. First, I demonstrated that both Rfx and dila are activated during Ch neurogenesis as direct targets of Ato. This was established by characterising their expression patterns, cis-regulation analyses and identifying the potential Ato binding sites by site-directed mutagenesis. RFX is a well-known ciliogenic regulator (Dubruille et al., 2002; El Zein et al., 2009; Swoboda et al., 2000), and its activation by Ato is consistent with Ch neurons having ciliated dendrites. However, the role of dila was completely unknown, but its sequence suggested that it may be involved in neuronal differentiation rather than gene regulation. I generated several dila mutant alleles and demonstrated that dila mutants exhibit severe uncoordination, due to a series of defects in ciliated neurons. These defects were linked to a disruption in the ciliogenesis machinery, particularly in the process known as intraflagellar transport (IFT). dila mutants also display reduced male fertility because of aberrant basal body function, which leads to a disorder in sperm individualisation. Thus DILA is required for the differentiation of all ciliated cells in Drosophila. Visualisation of tagged protein localised DILA to the basal body and transition zone of the sensory cilia. Further analysis revealed the genetic interaction between DILA and UNC (another basal body protein) during ciliogenesis. Taken together I propose that DILA regulates IFT at the base of the cilia in collaboration with UNC. Given that dila is an evolutionarily conserved gene, dila homologues could be candidate genes for human ciliopathies. Rfx is essential for ciliogenesis in both Ch and the external sense (ES) organs, which have distinctive cilia. Despite of this common role of RFX, I discovered that Rfx is expressed differently in Ch and ES lineages, which led me to hypothesise that the difference in Rfx expression modulates ciliogenesis in these two lineages. I obtained preliminary data that support this hypothesis. Overall, my study demonstrates important links between Ato and the regulation of ciliogenesis, which is an important process in Ch neuron differentiation. The data support a model in which Ato controls ciliogenesis both directly (e.g. via activating a ciliary genes like dila) and indirectly (e.g. via regulating the transcriptional factors essential for ciliogenesis, like RFX).
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Hall, Emma Andisi. "Screening for genes involved in cilia formation and function." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/9898.
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Cilia are small microtubule based structures found on the surface of almost all mammalian cells, enclosed in a highly specialised extension of the cell membrane. Components of several key developmental signalling pathways, in particular Hedgehog (Hh) signalling, are enriched in cilia and cells with mutations in cilia structure show aberrant signalling, suggesting cilia act as “antennae” to focus these signalling cascades. A spectrum of human diseases, termed ciliopathies, are caused by problems in cilia formation or cilia function, which display wide ranging phenotypes from embryonic lethality to retinal degeneration, polydactyly to cystic kidneys. Despite recent advances in the understanding of the essential roles cilia play in mammalian development, exactly how these complex structures are put together, how they carry out their diverse functions, and how they are regulated is not well understood. In this thesis, I describe a screen for genes involved in cilia formation and function. While optimising ciliogenesis and immunofluorescence protocols for the screen, the phenotypes of two ciliary mutant cell lines were analysed. Wdr35yet/yet and Dync2h1pol/pol mouse lines were identified in an ENU screen for genes involved in early development, and shown to have gross phenotypes similar to other ciliary mutants (Mill et al. 2011). Intraflagellar transport (IFT) is the active transport of proteins up and down the ciliary axoneme. Dync2h1 is a retrograde IFT motor component, whereas Wdr35 is part of the retrograde IFT-A complex. In this thesis, the cellular phenotypes of mouse embryonic fibroblasts derived from these mutants are described, showing that despite the fact both genes are thought to be involved in retrograde IFT, they show distinct ciliary phenotypes, suggesting novel roles for Wdr35 in mouse ciliogenesis. An siRNA screen was carried out in mouse fibroblasts to identify genes involved in (i) cilia formation, assayed by immunofluorescence for ciliary markers, and (ii) cilia function, assayed by activity of a Hh responsive luciferase transgene as an indirect readout of ciliary function. Although scalable, I initially screened a small test set of thirty-six putative cilia candidates, identified by cross species transcriptomic analysis. We identified several possible hits, many of which were in the ciliome database but also importantly, several genes with no known link to ciliogenesis. Repeats, correlation of phenotype to knockdown efficiencies and localisation studies validated two hits, Ccdc63 and Azi1. Ccdc63 is a novel coiled-coil gene with no previous link to ciliogenesis; the phenotype for this gene was analysed in real time using fluorescently tagged ciliary markers. A second hit, Azi1, was followed up in more detail. The reduction in ciliogenesis upon Azi1 knockdown was confirmed with separate siRNAs, and was rescued by overexpressing siRNA insensitive Azi1-GFP, confirming the phenotype is not due to off-target effects of the siRNAs. Azi1 gene trap mutant mice were generated and confirmed to be null mutations. Surprisingly, the mice survive, showing Azi1 is not essential for mammalian ciliogenesis. However, mutant males are infertile, with highly reduced sperm count and sperm abnormalities indicative of an arrest at Stage IX of spermiogenesis, when the flagellum, a highly specialised motile cilium, forms. The small number of sperm that do get to the epididymus are immotile. We suggest Azi1 is essential to in the formation of the sperm flagella and male fertility.
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Chen, Sheau-Hu. "Structure-function relationships in the arginine repressor." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360195.
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Youngson, Neil Alexander. "Characterisation, epigenetic regulation and genome function of the imprinted mouse Rtl1 gene and related genes." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614915.
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Freland, Sofia. "Lymphoid development and function in MHC class I deficient mice /." Stockholm, 1999. http://diss.kib.ki.se/1999/91-628-3714-1/.
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Crawford, Allison Clare. "Evolution and function of cellulase genes in Australian freshwater crayfish." Queensland University of Technology, 2006. http://eprints.qut.edu.au/16274/.
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The most abundant organic compound produced by plants is cellulose, however it has long been accepted that animals do not secrete the hydrolytic enzymes required for its degradation, but rely instead on cellulases produced by symbiotic microbes. The recent discovery of an endogenous cDNA transcript encoding a putative GHF9 endoglucanase in the parastacid crayfish Cherax quadricarinatus (Byrne et al., 1999) suggests that similar cellulase genes may have been inherited by a range of crustacean taxa. In this study, the evolutionary history of the C. quadricarinatus endoglucanase gene and the presence of additional GHF9 genes in other decapod species were investigated. The activity of endoglucanase and endoxylanase enzymes within several cultured decapod species were also compared. The evolutionary history of the C. quadricarinatus endoglucanase gene was assessed by comparing intron/exon structure with that of other invertebrate and plant GHF9 genes. The coding region of the gene was found to be interrupted by eleven introns ranging in size from 102-902 bp, the position of which was largely conserved in both termite and abalone GHF9 genes. These structural similarities suggest GHF9 genes in crustaceans and other invertebrate taxa share a common ancestry. In addition, two introns were observed to share similar positions in plant GHF9 genes, which indicates this enzyme class may have been present in ancient eukaryote organisms. The presence of GHF9 genes in C. quadricarinatus and various other decapod species was then explored via degenerate primer PCR. Two distinct GHF9 gene fragments were determined for C. quadricarinatus and several other Cherax and Euastacus parastacid freshwater crayfish species, and a single GHF9 gene fragment was also determined for the palaemonid freshwater prawn Macrobrachium lar. Phylogenetic analyses of these fragments confirmed the presence of two endoglucanase genes within the Parastacidae, termed EG-1 and EG-2. The duplication event that produced these two genes appears to have occurred prior to the evolution of freshwater crayfish. In addition, EG-2 genes appear to have duplicated more recently within the Cherax lineage. The presence of multiple GHF9 endoglucanase enzymes within the digestive tract of some decapod species may enable more efficient processing of cellulose substrates present in dietary plant material. Endoglucanase and endoxylanase enzyme activities were compared in several parastacid crayfish and penaeid prawn species using dye-linked substrates. Endoglucanase activity levels were higher in crayfish compared with prawn species, which corresponds with the known dietary preferences of these taxa. Endoglucanase temperature and pH profiles were found to be very similar for all species examined, with optimum activity occurring at 60°C and pH 5.0. These results suggest endoglucanase activity in penaeid prawns may also be derived from endogenous sources. Additional in vitro studies further demonstrated crayfish and prawn species liberate comparable amounts of glucose from carboxymethyl-cellulose, which indicates both taxa may utilise cellulose substrates as a source of energy. Endoxylanase temperature and pH profiles were also similar for all crayfish species examined, with optimal activity occurring at 50°C and pH 5.0. These results suggest xylanase activity in crayfish may originate from endogenous enzymes, although it is unclear whether this activity is derived from GHF9 enzymes or a different xylanase enzyme class. In contrast, no endoxylanase activity was detected in the three prawn species examined. Together, these findings suggest a wide range of decapod crustacean species may possess endogenous GHF9 endoglucanase genes and enzymes. Endoglucanases may be secreted by various decapod species in order to digest soluble or amorphous cellulose substrates present in consumed plant material. Further biochemical studies may confirm the presence and functional attributes of additional endoglucanase genes and enzymes in decapods, which may ultimately assist in the design of optimal plant based crustacean aquaculture feeds.
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Lynch, Michael David. "Genomics tools for elucidating the function of trait conferring genes." Diss., Connect to online resource, 2005. http://wwwlib.umi.com/cr/colorado/fullcit?p3190382.
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Elhaddad, Nagat S. A. Ali. "The function of guard cell expressed genes in Arabidopsis thaliana." Thesis, University of Sheffield, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.575133.
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Guard cells play an essential role in controlling stomatal aperture and respond to many stimuli including changes in the concentration of CO2, light and phytohormones such as ABA. In this project, the function of Arabidopsis genes identified by a microarray screen, as being potentially expressed in guard cells was studied. Two genes encoding an Arabidopsis protein kinase APKla, and a putative pectinesterase AP Ea and their closely related genes AP K 1 band AP Eb respectively were studied. GUS reporter gene fusions were constructed for each gene and expressed in Arabidopsis to investigate expression patterns. The results indicated relatively high guard cell expression for at least three of the genes (APKla. APKlb and APEa). Homozygous knockout mutant plants were identified for each gene of the four guard cell target genes by RT-PCR of T-DNA insertion lines. Putative overexpressing plant lines were created by placing three of the genes (AP KI a, AP K 1 band AP Eb) under the control of the CaMV 355 promoter in transgenic plants. Several physiological techniques were applied to the knockout and over-expressing plant lines to assess whether each gene product had a function in stomatal aperture control or stomatal development. Stomatal conductances were measured using Infra Red Gas Analysis (IRGA) to investigate mutant responses to different light intensities. This suggested an impairment in apkl a and APKl b knockout mutants in stomatal response to light-induced opening. Photosynthetic rate and Ci were measured for apk l a and apklb knockout mutants and no differences to wild-type values were observed. Stomatal indices and densities were examined and no significant differences were found in kinase knockout mutants and over-expressing plants. Stomatal aperture responses of kinase and pectinesterase mutants and putative over-expressers to light. ABA and CO2 were measured in leaf epidermal strip bioassay experiments. The kinase knockout m utants and putative over-expressers had reduced their stomatal apertures in response to light-induced stomatal opening and showed no differences to controls in dark induced-stomatal closure experiments (apart from APKlaOE which had enhanced dark-induced closure). But the kinase knockout mutants also showed reduced stomatal opening responses to C02 free air. A variety of responses to ABA-inhibition of stomatal opening and CO2-induced closure were exhibited by the kinase mutants and putative over-expressers. Relative water content (RWC) was significantly higher in droughted kinase knockout mutant plants perhaps because of their reduced stomatal opening. It is therefore possible that the AP K 1 a and AP K I b genes may useful in produces drought tolerance plants. Pectinesterase knockout mutants and putative over-expresser lines also had reduced stomatal apertures following exposure to light and no differences to wild-type were obtained following dark adaptation (apart from APEbOE). apea-l, apeb-l and apeb- 2 exhibited insensitivity to ABA and C02 since they maintained larger stomatal apertures than controls following exposure to ABA and ambient CO2• Droughted apea mutant plants had significantly lower relative water content perhaps because of their ABA and CO2 insensitivity, whereas no significant differences were noticed between apeb mutants and control plants. Stomatal indices and densities were examined and apea and apeb stomatal densities were similar to control when plants were grown under ambient CO2 but apea mutant plants had higher stomatal densities when grown under either low or elevated C02.
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Moses, Daniel. "Regulatory Elements, Protein Function and Evolution of the Actinodin Genes." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/26216.
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Small fibrils termed actinotrichia are involved with the growth and structure of the fin fold during fin development in fish. The actinodin (and) genes are required for actinotrichia formation, and the loss of these genes from the genomes of tetrapods has been implicated in the tetrapod-specific loss of actinotrichia, loss of a fin fold and the concurrent evolution of paired fins into limbs. This study focuses on the function of the and genes and their role in actinotrichia formation. The results reveal cis-acting regulatory elements required for and1 expression in the fin epithelium. Furthermore, it is shown that the And proteins display similarities to the secreted signaling molecule, Ecrg4, implying a possible role in cell differentiation during fin fold development. In the final section of this report, I use a genomic analysis to show that the and genes were lost from otherwise well-conserved syntenic loci in fish and tetrapod genomes. These results suggest possible causes for the evolutionary loss of and genes and the associated developmental changes that may have permitted fin to limb evolution.
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Shearman, C. A. "Structure, function and regulation of nodulation genes of Rhizobium leguminosarum." Thesis, University of East Anglia, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.376087.
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Speight, Richard Alan. "The structure, function and regulation of mycobacterial porin-encoding genes." Thesis, University College London (University of London), 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367873.
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Ruggiu, Matteo. "The function of DAZL and RBM, two candidate fertility genes." Thesis, Open University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.300014.
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Choi, Yong-Jin. "Function of commissureless and related genes in drosophila neural development." The Ohio State University, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=osu1054558823.
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Norman, Dennis. "Comparison of structure and function of lipoprotein receptors." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340596.
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Eriksson, Jonas. "Genetic and Genomic Studies in Chicken : Assigning Function to Vertebrate Genes." Doctoral thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-162597.
Full textAbstract:
A major challenge in the post-genomic era is to understand how genome sequence variants (genotype) give rise to the enormous diversity observed in terms of morphology, physiology and behavior (phenotype) among living organisms. Domestic animals—with their tremendous phenotypic variation—are excellent model organisms for determining the relationships between genotype and phenotype. In this thesis, I describe the utilization of the chicken, in combination with modern genetic and genomic approaches, in developing our understanding of the genetic mechanisms underlying phenotypic variation. These studies provide novel information on the genetics behind variation in carotenoid- and melanin-based pigmentation—observed in many organisms—and also cast light on the genetic basis of chicken domestication. In paper I, we report that the yellow skin phenotype—observed in most commercial chickens—is caused by one or several tissue-specific mutations altering the expression of beta-carotene oxygenase 2 (BCO2 or BCDO2) in skin. In addition, we present the first conclusive evidence of a hybrid origin of the domestic chicken, since the allele causing yellow skin most likely originates from the grey jungle fowl (Gallus sonneratii) and not from the previously described sole ancestor, the red jungle fowl (Gallus gallus). In paper II, we detect a number of loci that were likely important during the domestication process of chicken and the later specialization into meat (broiler) and egg (layer) producing lines. One of the major findings was that worldwide, almost all domestic chickens carry a missense mutation in TSHR (thyroid stimulating hormone receptor) in a position that is completely conserved amongst vertebrates. We speculate that this “domestication-mutation” has played an important role in the transformation of the wild red jungle fowl ancestor into the modern domestic chicken. In paper III, we demonstrate that the dilution of red (pheomelanin) pigmentation—observed in the plumage of the Inhibitor of Gold chicken—is caused by a frame-shift mutation in the catechol-O-methyltransferase domain containing 1 (COMTD1) gene. The production and regulation of pheomelanin is poorly understood and this discovery advances our current knowledge of this pathway.
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Ertel, Adam M. T̈ozeren Aydin. "Annotation and function of switch-like genes in health and disease /." Philadelphia, Pa. : Drexel University, 2008. http://hdl.handle.net/1860/2813.
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Tate, Alison Winifred. "Identification of genes encoding proteins implicated in peroxisomal function and disease." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.625073.
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Guo, Qian. "THE FUNCTION OF Socs GENES IN DROSOPHILA DEVELOPMENT AND SIGNALING PATHWAYS." UKnowledge, 2007. http://uknowledge.uky.edu/gradschool_theses/466.
Full textAbstract:
The duration and intensity of the JAK/stat signaling must be tightly regulated to prevent excessive transcriptional response and to reset the pathway to receive additional signals. Socs are the largest class of these regulators in mammals. Eight Socs genes have been found in mammals. CIS, and SOCS1-3, the canonical Socs, are transcriptionally activated by and down-regulate the JAK signaling. Socs4-7, the non-canonical Socs, are less studied and their relationship with the JAK/STAT pathway has not been well established. The Drosophila genome encodes three non-canonical Socs homologues, Socs16D, Socs36E, and Socs44A. Expression of Socs36E is controlled by the JAK pathway and misexpression causes phenotypes similar to that from reduction of JAK in both ovary and wing, which may make it functionally more similar to the canonical Socs. Expression of Socs44A is not controlled by the JAK pathway and misexpression causes JAK mutant phenotypes in wing but not in ovary. Imprecise excision mutants of the three Socs genes have been generated by us and have no visible phenotypes. The mutants of Socs36E and Socs44A significantly enhance the tumor formation in hopTum-l mutant, a gain-of-function mutation of the JAK/STAT pathway. The function of Drosophila Socs will be further studied with different strategies.
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Zhou, Wenhua. "Targeting G-quadruplex DNA in promoters of cardiac function-related genes." Thesis, Imperial College London, 2012. http://hdl.handle.net/10044/1/9695.
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G-quadruplexes (G4) are four-stranded DNA secondary structures, which are involved in a diverse range of biological processes. Although the anti-cancer potential of G4s in promoters of oncogenes has been thoroughly investigated, the functions of promoter G4s in non-cancer-related genes are not well understood. The aims of this thesis are (i) to investigate the biological importance of promoter G4s in cardiac function-related genes, and (ii) to explore the feasibility and potential of multitargeting strategy at the single gene level. These aims have been achieved by revealing the prevalence of G4s in TRRs (transcription regulatory regions) of cardiac function-related genes via bioinformatics approaches, and then investigating potential biological significance of G4s in promoters of human MEF2D and TnIc genes via a combination of biophysical, molecular, and cell biology approaches. By using bioinformatics approaches, TRRs of cardiac function-related genes were found to be enriched by potential G4-forming sequences. According to these results, G4s from the promoters of human MEF2D and TnIc were chosen and subjected to biophysical characterisations in solution. By using EMSA, DMS footprinting, CD and smFRET spectroscopy, the formation, thermodynamic stability, and unfolding kinetics of MEF2D and TnIc G4s were investigated. Briefly, in 100 mM K+, the MEF2DG4 can adopt a hybrid of very stable parallel/anti-parallel G4(s), while the TnIc MNSG4 and -80G4 are able to adopt anti-parallel and parallel structures, respectively, with comparable stability as compared to other oncogene G4s. Subsequently, cooperative regulatory roles of TnIc G4s as enhancers once stabilised by a G4-binding ligand (di-copper complex) were observed in vitro mainly by dual luciferase reporter assays in HEK293 cells. Three possible G4-mediated mechanisms have been proposed. This work provides the first indication about the biological significance of promoter G4s in cardiac function-related genes, and the feasibility to target multiple G4s at the single gene level.
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Croucher, Adam. "Investigating the expression and function of meiotic genes in human tumours." Thesis, University of Sheffield, 2012. http://etheses.whiterose.ac.uk/2751/.
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Abu, El-Madg Mohammed El-Sayed Rizk. "The function and regulation of chick Ebf genes in somite development." Thesis, Royal Veterinary College (University of London), 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.522148.
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Millar, Lorna Anne. "Diversity and function of the lipooligosaccharide biosynthesis genes from Campylobacter jejuni." Thesis, University of Leicester, 2003. http://hdl.handle.net/2381/30348.
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The enteric pathogen, Campylobacter jejuni, produces a range of LOS structures, however, the precise functions of LOS molecules in infection are largely undetermined. LOS structural diversity is known to arise from variation in LOS biosynthesis gene content and gene sequence. In determining the extent of LOS biosynthesis gene content variation in a group of mainly clinical C. jejuni isolates, in this study two new clusters of LOS biosynthesis genes have been identified. The C. jejuni LOS core can also undergo phase variation due to the presence of GC homopolymeric tracts in the protein coding sequence of biosynthesis genes in the cluster. Therefore, the variation in homopolymeric tract length was investigated in five genes including those in the LOS biosynthesis cluster. Many bacteria are known to vary LPS or LOS structure in response to different environment stimuli. Following the identification of a number of promoters in the LOS core biosynthesis cluster, promoter activity was measured following growth under several different conditions. Although promoter expression did not vary extensively with the different environmental stimuli, less LOS was extracted from cell grown under iron-limitation. The other aim of this work was to investigate LOS biosynthesis gene function. The genes waaF and lpxL are involved in core and lipid A biosynthesis respectively. Mutation of both genes had a substantial effect on LOS core structure and preliminary studies indicate both genes are important for adhesion and invasion of human intestinal cells. The deletion of several genes from the general protein glycosylation pathway also led to the truncation of the LOS core, indicating overlap between the two carbohydrate biosynthesis pathways.
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Béve, Jenny. "Structure and function of the yeast mediator tail domain /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-599-2/.
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Linardopoulou, Elena. "Structure, function and evolution of human subtelomeres /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/8120.
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Schweighoffer, Edina. "The role of Syk protein tyrosine kinase in B cell development and function." Thesis, Open University, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.250493.
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Stevanin, Tania Maria. "Bacterial flavohaemoglobins : physiological function and responses to nitrosative stress." Thesis, University of Sheffield, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.340137.
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Weicksel, Steven E. "hox Gene Regulation and Function During Zebrafish Embryogenesis: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/692.
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Hox genes encode a conserved family of homeodomain containing transcription factors essential for metazoan development. The establishment of overlapping Hox expression domains specifies tissue identities along the anterior-posterior axis during early embryogenesis and is regulated by chromatin architecture and retinoic acid (RA). Here we present the role nucleosome positioning plays in hox activation during embryogenesis. Using four stages of early embryo development, we map nucleosome positions at 37 zebrafish hox promoters. We find nucleosome arrangement to be progressive, taking place over several stages independent of RA. This progressive change in nucleosome arrangement on invariant sequence suggests that trans-factors play an important role in organizing nucleosomes. To further test the role of trans-factors, we created hoxb1b and hoxb1a mutants to determine if the loss of either protein effected nucleosome positions at the promoter of a known target, hoxb1a. Characterization of these mutations identified hindbrain segmentation defects similar to targeted deletions of mouse orthologs Hoxa1 and Hoxb1 and zebrafish hoxb1b and hoxb1a morpholino (MO) loss-of-function experiments. However, we also identified differences in hindbrain segmentation as well as phenotypes in facial motor neuron migration and reticulospinal neuron formation not previously observed in the MO experiments. Finally, we find that nucleosomes at the hoxb1a promoter are positioned differently in hoxb1b-/- embryos compared to wild-type. Together, our data provides new insight into the roles of hoxb1b and hoxb1a in zebrafish hindbrain segmentation and reticulospinal neuron formation and indicates that nucleosome positioning at hox promoters is dynamic, depending on sequence specific factors such as Hox proteins.
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Weicksel, Steven E. "hox Gene Regulation and Function During Zebrafish Embryogenesis: A Dissertation." eScholarship@UMMS, 2010. http://escholarship.umassmed.edu/gsbs_diss/692.
Full textAbstract:
Hox genes encode a conserved family of homeodomain containing transcription factors essential for metazoan development. The establishment of overlapping Hox expression domains specifies tissue identities along the anterior-posterior axis during early embryogenesis and is regulated by chromatin architecture and retinoic acid (RA). Here we present the role nucleosome positioning plays in hox activation during embryogenesis. Using four stages of early embryo development, we map nucleosome positions at 37 zebrafish hox promoters. We find nucleosome arrangement to be progressive, taking place over several stages independent of RA. This progressive change in nucleosome arrangement on invariant sequence suggests that trans-factors play an important role in organizing nucleosomes. To further test the role of trans-factors, we created hoxb1b and hoxb1a mutants to determine if the loss of either protein effected nucleosome positions at the promoter of a known target, hoxb1a. Characterization of these mutations identified hindbrain segmentation defects similar to targeted deletions of mouse orthologs Hoxa1 and Hoxb1 and zebrafish hoxb1b and hoxb1a morpholino (MO) loss-of-function experiments. However, we also identified differences in hindbrain segmentation as well as phenotypes in facial motor neuron migration and reticulospinal neuron formation not previously observed in the MO experiments. Finally, we find that nucleosomes at the hoxb1a promoter are positioned differently in hoxb1b-/- embryos compared to wild-type. Together, our data provides new insight into the roles of hoxb1b and hoxb1a in zebrafish hindbrain segmentation and reticulospinal neuron formation and indicates that nucleosome positioning at hox promoters is dynamic, depending on sequence specific factors such as Hox proteins.
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Waddell, Scott. "Analysis of human p53 function in fission yeast : a no-hybrids approach." Thesis, Institute of Cancer Research (University Of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244024.
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Heidari, Mansour. "Investigation of the molecular function of the nuclear oncoprotein HOX11 in human t-cell leukaemia." Murdoch University, 2003. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20060815.123509.
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HOXll, the prototypical member of the HOXll family (HOX11, HOXllLl and HOXllL2) was originally discovered as a transcriptional regulator aberrantly expressed in tumours with an immature T-cell phenotype (T-ALL) as a result of
specific chromosomal translocations involving T-cell receptor loci. Subsequently, it was revealed that HOXll is required for normal spleen development since newborn
Hoxll-/- mice exhibit asplenia. In both its normal and abnormal roles, HOXll has been postulated to function by binding regulatory elements within specific target genes
to control gene transcription. However, very few genomic targets of HOX11 have been identified and little is known about its mode of action. In this study, we sought to
further understand the role of HOX11 in controlling differentiation and cell growth by 1) determining the identity of genomic sequences that are directly bound by HOXll and 2) determining the identity of proteins which exist within HOXll-containing nuclear complexes.
To identify direct HOXll target sequences, a whole genome PCR-based screening method was employed using immobilised recombinant HOXll that had first been expressed as a biologically active GST fusion protein. Using this approach, restriction enzyme-cleaved human genomic DNA was selected for high-affinity HOXll binding sites. Unexpectedly, almost all clones isolated contained sequences derived from satellite 2 DNA that, together with related satellite 3 DNA, is found on most chromosomes at transcriptionally inactive pericentromeric heterochromatin. The specific binding of HOXl1 to satellite 2 DNA was verified by bandshift assays using
both recombinant HOXll protein and nuclear extract derived from the T-ALL cell line, ALL-SIL. DNA-protein complexes containing HOX11 were identified by their ablation upon addition of HOXl1 antibody.
To confirm that HOXll associates with pericentromeric heterochromatin in vivo, HOXll was characterised in terms of its nuclear localisation during interphase in
unsynchronised leukaemic T-cells (ALL-SIL) harbouring a translocation involving the HOXll locus. Using indirect immunofluorescence and confocal microscopy, HOXll
antibody produced a punctate pattern of staining in the nucleus with discrete areas of dense staining superimposed on a diffuse distribution of HOXll protein. By dual staining, the bright HOXll foci correlated with centromeres since they overlapped with signals detected by an antibody specific for the centromeric protein CENP-B. Further evidence for a direct interaction of HOXll with satellite 2 DNA was provided by chromatin immunoprecipitation assay. In the presence of HOXll antibody, DNA fragments containing satellite 2 sequences were irnmunoprecipitated from sheared, cross-linked ALL-SIL chromatin but not from chromatin isolated from the HOXll-negative T-cell line PER-1 17. Finally, using a combination of immunoprecipitation with HOXll antibody, gel electrophoresis and mass peptide fingerprinting, a set of nuclear proteins were identified as potential HOXll interactors which are known to either localise to centromeric regions or act as regulators of gene expression. Together, these results implicate HOXl 1 in a functional interaction with centromeric heterochromatin,
which may be a key feature of this oncoprotein in terms of both its T-cell transformation and transcriptional regulatory functions.
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Hill, Christopher G. "Studies in microrna function and gene dysregulation in ovarian cancer." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53086.
Full textAbstract:
Ovarian cancer results from the dysregulation, in normal ovarian epithelial cells, of genes responsible for the control of critical biological processes. Since their discovery 20 years ago, microRNAs have increasingly been implicated in that dysregulation due to their role mediating gene expression; changes in microRNA expression levels in cancer have been linked with tumor growth, proliferation and metastasis. Their imputed involvement in cancer has led to the possibility of their use as biomarkers and to their potential clinical use.
Using mRNA and microRNA microarray analysis to compare human gene expression in normal ovarian surface epithelial (OSE) cells and epithelial ovarian cancer (EOC) cells, we explored the interactions between microRNAs and genes. First, we validated in silico predictions of microRNA targets by comparing them with in vitro evidence after exogenous microRNA transfection. We found that pairs of microRNAs with identical 7-nt (nucleotide) seed regions shared 88% of their predicted targets and 55% of their in vitro targets, confirming the importance of the seed as a targeting mechanism. But more importantly, we found that even a single nucleotide change in the seed region can result in a significant shift in the set of targeted genes, implying strong functional conservation of the seeds and their corresponding binding sites.
Next, we discovered a 3-element network motif which explains the upregulation of nearly 800 genes in ovarian cancer which, as predicted microRNA targets, might be expected to be down- regulated. This model shows that, under certain circumstances, repressor genes which are down- regulated in cancer can apparently override the repressive effects of microRNAs, resulting in the upregulation of predicted microRNA targets.
Finally, we developed a phenomenological network model, based on the Pearson correlation of microarray gene expression data, to identify subnetworks dysregulated in cell cycle and apoptosis. While our methodology reported many genes previously associated with ovarian cancer, it significantly suggested potentially oncogenic genes for further investigation. This network model can easily be extended to identify dysregulated genes in other cancers.
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Sutton, Amelia Louise Maple. "The regulation and function of 1,25-dihydroxyvitamin D₃-induced genes in osteoblasts." Connect to text online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=case1121820822.
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Hvidsten, Torgeir R. "Predicting Function of Genes and Proteins from Sequence, Structure and Expression Data." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4490.
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Choudhury, Anuradha. "The regulation and function of DLX genes in the first branchial arch." Thesis, King's College London (University of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420629.
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Qiao, Tong. "The expression and function of spatially regulated genes in the zebrafish embryo." Thesis, King's College London (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301140.
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