Dissertations / Theses on the topic 'RUNX'

The Runx family of transcription factors supports cell fate determination, cell cycle regulation, global protein synthesis control, and genetic as well as epigenetic regulation of target genes. Runx1, which is essential for hematopoiesis; Runx2, which is required for osteoblast differentiation; and Runx3, which is involved in neurologic and gut development; are expressed in the growth plate during chondrocyte maturation, and in the chondrocytes of permanent cartilage structures. While Runx2 is known to control genes that contribute to chondrocyte hypertrophy, the functions of Runx1 and Runx3 during chondrogenesis and in cartilage tissue have been less well studied. The goals of this project were to characterize expression of Runx proteins in articular cartilage and differentiating chondrocytes and to determine the contribution of Runx1 to osteoarthritis (OA). Here, the expression pattern of Runx1 and Runx2 was characterized in normal bovine articular cartilage. Runx2 is expressed at higher levels in deep zone chondrocytes, while Runx1 is primarily expressed in superficial zone chondrocytes, which is the single cell layer that lines the surface of articular cartilage. Based on this finding, the hypothesis was tested that Runx1 is involved in osteoarthritis, which is a disease characterized by degradation of articular cartilage and changes in chondrocytes. These studies showed that Runx1 is upregulated in articular cartilage explants in response to mechanical compression. Runx1 was also expressed in chondrocytes found at the periphery of OA lesions in the articular cartilage of mice that underwent an OA-inducing surgery. Runx1 was also upregulated in cartilage explants of human osteoarthritic knees, and IHC data showed that Runx1 is mainly expressed in chondrocyte “clones” characteristic of OA. To ascertain the potential function of the upregulation of Runx1 in these cartilage stress conditions and disease states, the hypothesis was tested that Runx1 is upregulated in very specific chondrocyte populations in response to the cartilage damage in osteoarthritis. These studies addressed the properties of these cells that related to functions in cell growth and differentiation. In both the surface layer of normal articular cartilage, and in OA cartilage, Runx1 expression by IF co-localized with markers of mesenchymal progenitor cells, as well as markers of proliferation Ki-67 and PCNA. This finding indicated that Runx1 is found in a population of cells that represent a proliferative population of mesenchymal progenitor cells in osteoarthritis. To further address Runx1 function and identify downstream targets of Runx proteins, a promoter analysis of genes that are known to be either downregulated or upregulated during chondrocyte maturation was done. These studies found that many of these genes have 1 or more Runx binding sites within 2kb of their transcription start site, indicating that they are potential downstream Runx target genes. Lastly, some preliminary experiments were done to characterize novel roles of Runx proteins in the chondrocyte. Runx proteins have been shown to epigenetically regulate their target genes by remaining bound to them throughout mitosis, “poising” them for transcription upon exit from mitosis. The hypothesis that Runx proteins also function by remaining bound to their target genes throughout mitosis in chondrocytes was tested. It was demonstrated by immunofluorescense imaging of Runx proteins on metaphase chromosomes of ATDC5 cells, that Runx2 remains bound to chromosomes during mitosis. Cell proliferation and hypertrophy are both linked to increases in protein synthesis. Runx factors, which regulate rates of global protein synthesis, are expressed in both proliferating and hypertrophic chondrocytes. Thus, it was hypothesized that Runx proteins regulate rates of global protein synthesis during chondrocyte maturation. These studies showed that the overexpression of Runx proteins in a chondrocyte cell line (ATDC5) did not affect protein synthesis rates or levels of protein synthesis machinery. Additionally, Runx proteins did not affect proliferation rates in this chondrocyte cell line.

The Runx family of transcription factors supports cell fate determination, cell cycle regulation, global protein synthesis control, and genetic as well as epigenetic regulation of target genes. Runx1, which is essential for hematopoiesis; Runx2, which is required for osteoblast differentiation; and Runx3, which is involved in neurologic and gut development; are expressed in the growth plate during chondrocyte maturation, and in the chondrocytes of permanent cartilage structures. While Runx2 is known to control genes that contribute to chondrocyte hypertrophy, the functions of Runx1 and Runx3 during chondrogenesis and in cartilage tissue have been less well studied. The goals of this project were to characterize expression of Runx proteins in articular cartilage and differentiating chondrocytes and to determine the contribution of Runx1 to osteoarthritis (OA). Here, the expression pattern of Runx1 and Runx2 was characterized in normal bovine articular cartilage. Runx2 is expressed at higher levels in deep zone chondrocytes, while Runx1 is primarily expressed in superficial zone chondrocytes, which is the single cell layer that lines the surface of articular cartilage. Based on this finding, the hypothesis was tested that Runx1 is involved in osteoarthritis, which is a disease characterized by degradation of articular cartilage and changes in chondrocytes. These studies showed that Runx1 is upregulated in articular cartilage explants in response to mechanical compression. Runx1 was also expressed in chondrocytes found at the periphery of OA lesions in the articular cartilage of mice that underwent an OA-inducing surgery. Runx1 was also upregulated in cartilage explants of human osteoarthritic knees, and IHC data showed that Runx1 is mainly expressed in chondrocyte “clones” characteristic of OA. To ascertain the potential function of the upregulation of Runx1 in these cartilage stress conditions and disease states, the hypothesis was tested that Runx1 is upregulated in very specific chondrocyte populations in response to the cartilage damage in osteoarthritis. These studies addressed the properties of these cells that related to functions in cell growth and differentiation. In both the surface layer of normal articular cartilage, and in OA cartilage, Runx1 expression by IF co-localized with markers of mesenchymal progenitor cells, as well as markers of proliferation Ki-67 and PCNA. This finding indicated that Runx1 is found in a population of cells that represent a proliferative population of mesenchymal progenitor cells in osteoarthritis. To further address Runx1 function and identify downstream targets of Runx proteins, a promoter analysis of genes that are known to be either downregulated or upregulated during chondrocyte maturation was done. These studies found that many of these genes have 1 or more Runx binding sites within 2kb of their transcription start site, indicating that they are potential downstream Runx target genes. Lastly, some preliminary experiments were done to characterize novel roles of Runx proteins in the chondrocyte. Runx proteins have been shown to epigenetically regulate their target genes by remaining bound to them throughout mitosis, “poising” them for transcription upon exit from mitosis. The hypothesis that Runx proteins also function by remaining bound to their target genes throughout mitosis in chondrocytes was tested. It was demonstrated by immunofluorescense imaging of Runx proteins on metaphase chromosomes of ATDC5 cells, that Runx2 remains bound to chromosomes during mitosis. Cell proliferation and hypertrophy are both linked to increases in protein synthesis. Runx factors, which regulate rates of global protein synthesis, are expressed in both proliferating and hypertrophic chondrocytes. Thus, it was hypothesized that Runx proteins regulate rates of global protein synthesis during chondrocyte maturation. These studies showed that the overexpression of Runx proteins in a chondrocyte cell line (ATDC5) did not affect protein synthesis rates or levels of protein synthesis machinery. Additionally, Runx proteins did not affect proliferation rates in this chondrocyte cell line.

L'hématopoïèse est le processus de formation des cellules sanguines différenciées à partir de cellules souches hématopoïétiques. Ce processus est étroitement contrôlé par l'intégration de signaux de développementaux et homéostatiques pour assurer une production équilibrée des différents types de cellules sanguines. Au niveau moléculaire, la régulation de ce processus est médiée par un certain nombre de facteurs de transcription, en particulier par les membres de la famille RUNX. Ainsi, des mutations affectant les membres de cette famille peuvent entrainer une déréglementation du programme de différenciation hématopoïétique et causer des hémopathies, dont des leucémies. D'une manière intrigante, de nombreux régulateurs de la transcription et des voies de signalisation contrôlant le développement des cellules sanguines sont évolutivement conservés des humains à Drosophila melanogaster, qui est donc utilisée comme organisme modèle pour étudier les mécanismes sous-jacents à la spécification des lignages sanguins et au contrôle de l'homéostasie des cellules sanguines. Les membres de la famille Myeloid Leukemia Factor (MLF) ont été impliqués dans l'hématopoïèse et dans la transformation oncogénique des cellules sanguines, mais leur fonction et leur mécanisme d'action moléculaire restent insaisissables. Des travaux précédents chez la Drosophile ont montré que MLF stabilise le facteur de transcription de type RUNX Lozenge (LZ) et contrôle le nombre de cellules sanguines LZ+. Au cours de ma thèse, j'ai cherché à déchiffrer le mécanisme moléculaire d'action de MLF sur Lozenge dans les cellules sanguines. Par une approche protéomique puis par des expériences de co-immunoprécipitation dans les cellules de Drosophile Kc167, nous avons identifié le co-chaperon de type Hsp40 DnaJ-1, et son partenaire le chaperon Hsc70-4, comme deux partenaires de MLF. De façon importante, nous avons montré que l'inhibition de l'expression de DnaJ-1 ou de Hsc70-4 dans les cellules Kc167 induit une réduction du niveau de protéine Lozenge et une diminution de sa capacité à activer la transcription très semblable à celles observées suite à l'inhibition de l'expression de MLF. De plus, la sur-expression de mutants de DnaJ-1 incapables d'activer le chaperon Hsc70-4 entraîne aussi une réduction du niveau de Lozenge et de sa capacité de transactivation et des expériences de coimmunoprécipitation montrent que Lozenge interagit avec MLF, DnaJ-1 et Hsc70-4. Nos résultats suggèrent donc que MLF agit au sein d'un complexe chaperon composé de DnaJ-1 et Hsc70-4 pour contrôler le niveau de Lozenge. En utilisant différents mutants de MLF ou DnaJ-1, nous avons montré que MLF et DnaJ-1 interagissent ensemble et avec Lozenge via des domaines phylogénétiquement conservés. D'autre part, des expériences de GST " pull down " in vitro suggèrent que ces trois protéines peuvent interagir ensemble directement. Nous proposons donc que MLF et DnaJ-1 contrôlent le niveau de protéine Lozenge en interagissant avec elle et en favorisant son repliement et/ou sa solubilité via l'activité chaperon de Hsc70-4. En parallèle, nous avons étudié la fonction de DnaJ-1 in vivo dans le développement des cellules sanguines de la Drosophile. Nos résultats montrent que, comme mlf, la perte de dnaj-1 s'accompagne d'une augmentation de la taille et du nombre des cellules sanguines LZ+, ainsi que d'une hyperactivation de la voie de signalisation Notch dans ces cellules. Nos résultats suggèrent que des hauts niveaux de Lozenge sont nécessaires pour contrôler le nombre et la taille des cellules LZ+ et pour inhiber l'expression de Notch. Nous proposons que le complexe MLF/DnaJ-1 contrôle le développement du lignage LZ+ en régulant le niveau de protéine Lozenge, et ainsi le niveau d'activité de la voie Notch. En conclusion, nos résultats ont mis à jour un lien fonctionnel entre MLF, le co-chaperon de type Hsp40 DnaJ-1 et un facteur de transcription de type RUNX, qui pourrait être conservé dans d'autres espèces
Hematopoiesis is the process of formation of fully differentiated blood cells from hematopoietic stem cells (HSCs). This process is tightly controlled by the integration of developmental and homeostatic signals to ensure the generation of an appropriate number of each blood cell type. At the molecular level, the regulation of this developmental process is mediated by a number of transcription factors, especially by members of the RUNX family, and mutations affecting these factors are at the origin of numerous hemopathies, including leukemia. Intriguingly, many transcriptional regulators and signaling pathways controlling blood cell development are evolutionarily conserved from humans to Drosophila melanogaster. Hence, the fruit fly has become a potent and simplified model to study the mechanisms underlying the specification of blood cell lineages and the regulation of blood cell homeostasis. Members of the Myeloid Leukemia Factor (MLF) family have been implicated in hematopoiesis and in oncogenic blood cell transformation, but their function and molecular mechanism of action remain elusive. Previous work in Drosophila showed that MLF stabilizes the RUNX transcription factor Lozenge (LZ) and controls the number of LZ+ blood cells. During my PhD, I sought to further decipher the molecular mechanism of action of MLF on Lozenge during blood cell development. Using a proteomic approach in Drosophila Kc167 cells, we identified the Hsp40 co-chaperone family member DnaJ-1 and its chaperone partner Hsc70-4 as two partners of MLF. These interactions were confirmed by co-immunoprecipitations and in vitro pull-down assays. Importantly, we found that knocking down DnaJ-1 or Hsc70-4 expression in Kc167 cells caused a reduction in the level of Lozenge protein and a concomitant decrease in Lozenge transactivation activity, which were very similar to those caused by MLF knock-down. Similarly, over-expression of two DnaJ-1 mutants that are unable to stimulate the chaperone activity of Hsc70-4 also decreased Lozenge level and impaired its capacity to activate transcription. These results suggest that MLF could act within a chaperone complex composed of DnaJ-1 and Hsc70-4 to control Lozenge stability and activity. Along that line, we showed by co-immunoprecipitation that Lozenge interacts with MLF, DnaJ-1 and Hsc70-4, respectively. Using various truncated mutants of MLF or DnaJ-1, we showed that MLF and DnaJ-1 interact and together with Lozenge through their conserved MLF homology domain (MHD) and C-terminal region, respectively. Furthermore, in vitro GST pull-down assays suggested that the interactions between MLF, DnaJ-1 and Lozenge are direct. Thus, we propose that MLF and DnaJ-1 control Lozenge protein level by interacting with it and by promoting its folding and/or solubility via the Hsc70 chaperone machinery. In parallel, we assessed DnaJ-1 function in Drosophila blood cells in vivo using a null allele of dnaj-1 generated by CRISPR/Cas9 technique. We found that, like mlf, dnaj-1 mutation leads to an increase in the number and size of LZ+ blood cells, as well as to an over-activation of the Notch signaling pathway in these cells. Moreover, our data suggested that high levels of active Lozenge are required to control the number and size of LZ+ blood cells, and to down-regulate Notch expression. We propose that the MLF/DnaJ-1 complex controls LZ+ blood cell development in vivo by regulating Lozenge protein level/activity and thereby Notch pathway activation. In sum, our results establish a functional link between MLF, the Hsp40 co-chaperone DnaJ-1 and the RUNX transcription factor Lozenge, which could be conserved in other species

La maladie FPD/AML (thrombopénie familiale avec prédisposition aux leucémies aiguës myéloïdes) est due à des anomalies constitutives de RUNX1, facteur de transcription indispensable à l'hématopoïèse définitive. Dans un premier travail, nous avons proposé un nouveau moyen diagnostique des altérations de RUNX1. La myosine MYH10, normalement réprimée par RUNX1 au cours de la mégacaryopoïèse, persiste dans les plaquettes de patients FPD/AML contrairement aux patients atteints d'autres thrombopénies constitutionnelles, à l'exception des patients Paris-Trousseau. Ce nouvel outil diagnostique peut permettre également d'identifier des mutations acquises de RUNX1 dans la leucémie myélomonocytaire chronique. Nous avons ensuite modélisé la maladie FPD/AML en dérivant des cellules souches pluripotentes induites (iPSC) à partir de fibroblastes de plusieurs patients FPD/AML, porteurs de différentes anomalies de RUNX1. Nous avons reproduit les phénotypes observés chez les patients avec des défauts de génération du compartiment mégacaryocytaire et de plaquettogenèse pour toutes les lignées ; et une amplification du compartiment granulo-monocytaire uniquement avec les lignées porteuses de la mutation prédisposant à la leucémie. Nous avons mis en évidence, pour la première fois, un défaut de génération du compartiment érythrocytaire primitif embryonnaire. Ces résultats ont été confirmés en utilisant une lignée de cellules souches embryonnaires transduite par un shARN dirigé contre RUNX1. Notre modèle est donc validé, et pourra être utilisé dans le futur pour identifier de nouveaux mécanismes impliqués dans la mégacaryopoïèse et dans la leucémogenèse
FPD/AML (familial platelet disorder with predisposition to acute myeloid leukemia) results from constitutive alterations of RUNX1, a hematopoietic transcription factor essential to definitive hematopoiesis. In the first part of our work, we proposed a new diagnostic test to detect RUNX1 alterations. We showed that MYH10, which is regulated negatively by RUNX1 during megakaryopoiesis, persisted in platelets from FPD/AML patients. MYHIO persistence was not detected in platelets from patients with other constitutional thrombocytopenia, except from patients with Paris-Trousseau syndrome. This new test could be used also to detect RUNX1 alterations in acquired haematological disorders like chronic myelomonocytic leukemia. In a second work, we generated induced pluripotent stem cells (iPSC) from fibroblasts of FPD/AML patients with different RUNX1 alterations, in order to model the pathology. We reproduced the phenotype already described in patients with defect in megakaryocytic lineage whatever RUNX1 alterations and increase in granulo-monocytic compartment only with the mutation which predisposes to leukemia. We highlighted for the first time that RUNX1 is necessary also for erythroid lineage. We confirmed these results after RUNX1 knock down in an embryonic stem cell line. In conclusion we validated our model and now we can use it to study the mechanisms leading to dysmegakaryopoiesis and predisposition to leukemia in FPD/AML patients

Runt related transcription factors (Runx) play an important role in mammalian development by regulating the expression of key genes involved in cell proliferation, differentiation and growth. The work described in this thesis details the mechanisms by which the activity of two members of this family are regulated in human cells. Chapter One provides a brief introduction of Runx transcription factors. Chapter Two describes the regulation of Runx2 protein by the PI3 kinase/Akt pathway in human breast cancer cells. The PI3 kinase/Akt pathway is one of the major signal transduction pathways through which growth factors influence cell proliferation and survival. It is also one of the most frequently dysregulated pathways in human cancers. We identify Runx2 protein, a key regulator of breast cancer invasion as a novel substrate of Akt kinase and map residues of Runx2 that are phosphorylated by Akt in breast cancer cells. Our results show that phosphorylation by Akt increases the binding of Runx2 protein to its target gene promoters and we identify the phosphorylation events that enhance DNA binding of Runx2. Our work establishes Runx2 protein as a critical effecter downstream of Akt that regulates breast cancer invasion. In Chapter Three we describe the subnuclear localization of the tumor suppressor protein Runx3 during interphase and mitosis. We find that similar to other Runx family members, Runx3 protein resides in nuclear matrix associated foci during interphase. We delineate a subnuclear targeting signal that directs Runx3 to these nuclear matrix associated foci. Our work establishes that this association of Runx3 protein with the nuclear matrix plays a vital role in regulating its transcriptional activity. Chromatin immunoprecipitation results show that Runx3 occupies rRNA promoters during interphase. We also find that Runx3 remains associated with chromosomes during mitosis and localizes with nucleolar organizing regions (NORs), reflecting an interaction with epigenetic potential. This thesis provides novel insights into various mechanisms by which cells regulate the activity of Runx proteins.

RUNX2 belongs to the RUNT domain family of transcription factors of which three have been identified in humans (RUNX1, RUNX2 and RUNX3). RUNX proteins are vital for metazoan development and participate in the regulation of cellular differentiation and cell cycle progression (Coffman, 2003). RUNX2 is required for proper bone formation by driving the differentiation of osteoblasts from mesenchymal progenitors during development (Ducy et al, 1997; Komori et al, 1997; Otto et al, 1997). RUNX2 is also vital for chondrocyte maturation by promoting the differentiation of chondrocytes to the hypertrophic phenotype (Enomoto et al, 2000). The consequences of completely disrupting the RUNX2 locus in mice provided compelling and conclusive evidence for the biological importance of RUNX2 where knockout mice died shortly after birth with a complete lack of bone formation (Komori et al, 1997; Otto et al, 1997). A further indication of the requisite role of RUNX2 in skeletal development was the discovery that RUNX2 haploinsufficiency in humans and mice caused the skeletal syndrome Cleidocranial Dysplasia (CCD) (Mundlos et al, 1997; Lee et al, 1997). A unique feature of RUNX2 is the consecutive polyglutamine and polyalanine tracts (Q/A domain). Mutations causing CCD have been observed in the Q/A domain of RUNX2 (Mundlos et al, 1997). The Q/A domain is an essential part of RUNX2 and participates in transactivation function (Thirunavukkarasu et al, 1998). Previous genotyping studies conducted in our laboratory identified several rare RUNX2 Q/A variants in addition to a frequently occurring 18 base pair deletion of the polyalanine tract termed the 11Ala allele. Analysis of serum parameters in 78 Osteoarthritis patients revealed the 11Ala allele was associated with significantly decreased osteocalcin. Furthermore, analysis of 11Ala allele frequencies within a Geelong Osteoporosis Study (GOS) fracture cohort and an appropriate age matched control group revealed the 11Ala allele was significantly overrepresented in fracture cases indicating an association with increased fracture risk. To further investigate the 11Ala allele and rare Q/A variants, 747 DNA samples from the Southeast Queensland bone study were genotyped using PCR and PAGE. The experiment served two purposes: 1) to detect additional rare Q/A variants to enrich the population of already identified mutants and 2) have an independent assessment of the effect of the 11Ala allele on fracture to either support or refute our previous observation which indicated the 11Ala allele was associated with an increased risk of fracture in the GOS. From the 747 samples genotyped, 665 were WT, 76 were heterozygous for the 11Ala allele, 5 were homozygous for the 11Ala allele and 1 was heterozygous for a rare 21 bp deletion of the polyglutamine tract. Chi-square analysis of RUNX2 genotype distributions within fracture and non-fracture groups in the Southeast Queensland bone study revealed that individuals that carried at least one copy of the 11Ala allele were enriched in the fracture group (p = 0.16, OR = 1.712). The OR of 1.712 was of similar magnitude to the OR observed in the GOS case-control investigation (OR = 1.9) providing support for the original study. Monte-Carlo simulations were used to combine the results from the GOS and the Southeast Queensland bone study. The simulations were conducted with 10000 iterations and demonstrated that the maximum probability of obtaining both study results by chance was less than 5 times in two hundred (p < 0.025) suggesting that the 11Ala allele of RUNX2 was associated with an increased fracture risk. The second element of the research involved the analysis of rare RUNX2 Q/A variants identified from multiple epidemiological studies of bone. Q/A repeat variants were derived from four populations: the GOS, an Aberdeen cohort, CAIFOS and a Sydney twin study. Collectively, a total of 20 rare glutamine and one alanine variants were identified from 4361 subjects. All RUNX2 Q/A variants were heterozygous for a mutant allele and a wild type allele. Analysis of incident fracture during a five year follow up period in the CAIFOS revealed that Q-variants (n = 8) were significantly more likely to have fractured compared to non-carriers (p = 0.026, OR 4.932 95% CI 1.2 to 20.1). Bone density data as measured by quantitative ultrasound was available for CAIFOS. Analysis of BUA and SOS Z-scores revealed that Q-repeat variants had significantly lower BUA (p = 0.031, mean Z-score of -0.79) and a trend for lower SOS (p = 0.190, mean Z-score of -0.69). BMD data was available for all four populations. To normalize the data across the four studies, FN BMD data was converted into Z-scores and the effect of the Q/A variants on BMD was analysed using a one sample approach. The analysis revealed Q/A variants had significantly lower FN BMD (p = 0.0003) presenting with a 0.65 SD decrease. Quantitative transactivation analysis was conducted on RUNX2 proteins harbouring rare glutamine mutations and the 11Ala allele. RUNX2 proteins containing a glutamine deletion (16Q), a glutamine insertion (30Q) and the 11Ala allele were overexpressed in NIH3T3 and HEK293 cells and their ability to transactivate a known target promoter was assessed. The 16Q and 30Q had significantly decreased reporter activity compared to WT in NIH3T3 cells (p = 0.002 and 0.016, for 16Q and 30Q, respectively). In contrast 11Ala RUNX2 did not show significantly different promoter activation potential (p = 0.54). Similar results were obtained in HEK293 cells where both the 16Q and 30Q RUNX2 displayed decreased reporter activity (p=0.007 and 0.066 for 16Q and 30Q respectively) whereas the 11Ala allele had no material effect on RUNX2 function (p = 0.20). The RUNX2 gene target reporter assay provided evidence to suggest that variation within the glutamine tract of RUNX2 was capable of altering the ability of RUNX2 to activate a known target promoter. In contrast, the 11Ala allele showed no variation in RUNX2 activity. The third feature of the research served the purpose of identifying potential RUNX2 gene targets with particular emphasis on discovering genes cooperatively regulated by RUNX2 and the powerful bone promoting agent BMP2. The experiment was conducted by creating stably transfected NIH3T3 cells lines overexpressing RUNX2 or BMP2 or both RUNX2 and BMP2. Microarray analysis revealed very few genes were differentially regulated between standard NIH3T3 cells and cells overexpressing RUNX2. The results were confirmed via RT-PCR analysis which demonstrated that the known RUNX2 gene targets Osteocalcin and Matrix Metalloproteinase-13 were modestly induced 2.5 fold (p = 0.00017) and 2.1 fold (p = 0.002) respectively in addition to identifying only two genes (IGF-II and SCYA11) that were differentially regulated greater than 10 fold. IGF-II and SYCA11 were significantly down-regulated 27.6 fold (p = 1.95 x 10-6) and 10.1 fold (p = 0.0002) respectively. The results provided support for the notion that RUNX2 on its own was not sufficient for optimal gene expression and required the presence of additional factors. To discover genes cooperatively regulated by RUNX2 and BMP2, microarray gene expression analysis was performed on standard NIH3T3 cells and NIH3T3 cells stably transfected with both RUNX2 and BMP2. Comparison of the gene expression profiles revealed the presence of a large number of differentially regulated genes. Four genes EHOX, CCL9, CSF2 and OSF-1 were chosen to be further characterized via RT-PCR. Sequential RT-PCR analysis on cDNA derived from control cells and cells stably transfected with either RUNX2, BMP2 or both RUNX2/BMP2 revealed that EHOX and CSF2 were cooperatively induced by RUNX2 and BMP2 whereas CCL9 and OSF-1 were suppressed by BMP2. The overexpression of both RUNX2 and BMP2 in NIH3T3 fibroblasts provided a powerful model upon which to discover potential RUNX2 gene targets and also identify genes synergistically regulated by BMP2 and RUNX2. The fourth element of the research investigated the role of RUNX2 in the ascorbic acid mediated induction of MMP-13 mRNA. The study was carried out using NIH3T3 cell lines stably transfected with BMP2, RUNX2 and both BMP2 and RUNX2. The cell lines were grown to confluence and subsequently cultured for a further 12 days in standard media or in media supplemented with AA. RT-PCR analysis was used to assess MMP-13 mRNA expression. The RT-PCR results demonstrated that AA was not sufficient for inducing MMP-13 mRNA in NIH3T3 cells. In contrast RUNX2 significantly induced MMP-13 levels 85 fold in the absence of AA (p = 0.0055) and upregulated MMP-13 mRNA levels 254 fold in the presence of AA (p = 0.0017). The results demonstrated that RUNX2 was essential for the AA mediated induction of MMP-13 mRNA in NIH3T3 cells. The effect of BMP2 on MMP-13 expression was also investigated. BMP2 induced MMP-13 mRNA transcripts a modest 3.8 fold in the presence of AA (p = 0.0027). When both RUNX2 and BMP2 were overexpressed in the presence of AA, MMP-13 mRNA levels were induced a massive 4026 fold (p = 8.7 x 10-4) compared to control cells. The investigation revealed that RUNX2 was an essential factor for the AA mediated induction of MMP-13 and that RUNX2 and BMP2 functionally cooperated to regulate MMP-13 mRNA levels.

RUNX2 belongs to the RUNT domain family of transcription factors of which three have been identified in humans (RUNX1, RUNX2 and RUNX3). RUNX proteins are vital for metazoan development and participate in the regulation of cellular differentiation and cell cycle progression (Coffman, 2003). RUNX2 is required for proper bone formation by driving the differentiation of osteoblasts from mesenchymal progenitors during development (Ducy et al, 1997; Komori et al, 1997; Otto et al, 1997). RUNX2 is also vital for chondrocyte maturation by promoting the differentiation of chondrocytes to the hypertrophic phenotype (Enomoto et al, 2000). The consequences of completely disrupting the RUNX2 locus in mice provided compelling and conclusive evidence for the biological importance of RUNX2 where knockout mice died shortly after birth with a complete lack of bone formation (Komori et al, 1997; Otto et al, 1997). A further indication of the requisite role of RUNX2 in skeletal development was the discovery that RUNX2 haploinsufficiency in humans and mice caused the skeletal syndrome Cleidocranial Dysplasia (CCD) (Mundlos et al, 1997; Lee et al, 1997). A unique feature of RUNX2 is the consecutive polyglutamine and polyalanine tracts (Q/A domain). Mutations causing CCD have been observed in the Q/A domain of RUNX2 (Mundlos et al, 1997). The Q/A domain is an essential part of RUNX2 and participates in transactivation function (Thirunavukkarasu et al, 1998). Previous genotyping studies conducted in our laboratory identified several rare RUNX2 Q/A variants in addition to a frequently occurring 18 base pair deletion of the polyalanine tract termed the 11Ala allele. Analysis of serum parameters in 78 Osteoarthritis patients revealed the 11Ala allele was associated with significantly decreased osteocalcin. Furthermore, analysis of 11Ala allele frequencies within a Geelong Osteoporosis Study (GOS) fracture cohort and an appropriate age matched control group revealed the 11Ala allele was significantly overrepresented in fracture cases indicating an association with increased fracture risk. To further investigate the 11Ala allele and rare Q/A variants, 747 DNA samples from the Southeast Queensland bone study were genotyped using PCR and PAGE. The experiment served two purposes: 1) to detect additional rare Q/A variants to enrich the population of already identified mutants and 2) have an independent assessment of the effect of the 11Ala allele on fracture to either support or refute our previous observation which indicated the 11Ala allele was associated with an increased risk of fracture in the GOS. From the 747 samples genotyped, 665 were WT, 76 were heterozygous for the 11Ala allele, 5 were homozygous for the 11Ala allele and 1 was heterozygous for a rare 21 bp deletion of the polyglutamine tract. Chi-square analysis of RUNX2 genotype distributions within fracture and non-fracture groups in the Southeast Queensland bone study revealed that individuals that carried at least one copy of the 11Ala allele were enriched in the fracture group (p = 0.16, OR = 1.712). The OR of 1.712 was of similar magnitude to the OR observed in the GOS case-control investigation (OR = 1.9) providing support for the original study. Monte-Carlo simulations were used to combine the results from the GOS and the Southeast Queensland bone study. The simulations were conducted with 10000 iterations and demonstrated that the maximum probability of obtaining both study results by chance was less than 5 times in two hundred (p < 0.025) suggesting that the 11Ala allele of RUNX2 was associated with an increased fracture risk. The second element of the research involved the analysis of rare RUNX2 Q/A variants identified from multiple epidemiological studies of bone. Q/A repeat variants were derived from four populations: the GOS, an Aberdeen cohort, CAIFOS and a Sydney twin study. Collectively, a total of 20 rare glutamine and one alanine variants were identified from 4361 subjects. All RUNX2 Q/A variants were heterozygous for a mutant allele and a wild type allele. Analysis of incident fracture during a five year follow up period in the CAIFOS revealed that Q-variants (n = 8) were significantly more likely to have fractured compared to non-carriers (p = 0.026, OR 4.932 95% CI 1.2 to 20.1). Bone density data as measured by quantitative ultrasound was available for CAIFOS. Analysis of BUA and SOS Z-scores revealed that Q-repeat variants had significantly lower BUA (p = 0.031, mean Z-score of -0.79) and a trend for lower SOS (p = 0.190, mean Z-score of -0.69). BMD data was available for all four populations. To normalize the data across the four studies, FN BMD data was converted into Z-scores and the effect of the Q/A variants on BMD was analysed using a one sample approach. The analysis revealed Q/A variants had significantly lower FN BMD (p = 0.0003) presenting with a 0.65 SD decrease. Quantitative transactivation analysis was conducted on RUNX2 proteins harbouring rare glutamine mutations and the 11Ala allele. RUNX2 proteins containing a glutamine deletion (16Q), a glutamine insertion (30Q) and the 11Ala allele were overexpressed in NIH3T3 and HEK293 cells and their ability to transactivate a known target promoter was assessed. The 16Q and 30Q had significantly decreased reporter activity compared to WT in NIH3T3 cells (p = 0.002 and 0.016, for 16Q and 30Q, respectively). In contrast 11Ala RUNX2 did not show significantly different promoter activation potential (p = 0.54). Similar results were obtained in HEK293 cells where both the 16Q and 30Q RUNX2 displayed decreased reporter activity (p=0.007 and 0.066 for 16Q and 30Q respectively) whereas the 11Ala allele had no material effect on RUNX2 function (p = 0.20). The RUNX2 gene target reporter assay provided evidence to suggest that variation within the glutamine tract of RUNX2 was capable of altering the ability of RUNX2 to activate a known target promoter. In contrast, the 11Ala allele showed no variation in RUNX2 activity. The third feature of the research served the purpose of identifying potential RUNX2 gene targets with particular emphasis on discovering genes cooperatively regulated by RUNX2 and the powerful bone promoting agent BMP2. The experiment was conducted by creating stably transfected NIH3T3 cells lines overexpressing RUNX2 or BMP2 or both RUNX2 and BMP2. Microarray analysis revealed very few genes were differentially regulated between standard NIH3T3 cells and cells overexpressing RUNX2. The results were confirmed via RT-PCR analysis which demonstrated that the known RUNX2 gene targets Osteocalcin and Matrix Metalloproteinase-13 were modestly induced 2.5 fold (p = 0.00017) and 2.1 fold (p = 0.002) respectively in addition to identifying only two genes (IGF-II and SCYA11) that were differentially regulated greater than 10 fold. IGF-II and SYCA11 were significantly down-regulated 27.6 fold (p = 1.95 x 10-6) and 10.1 fold (p = 0.0002) respectively. The results provided support for the notion that RUNX2 on its own was not sufficient for optimal gene expression and required the presence of additional factors. To discover genes cooperatively regulated by RUNX2 and BMP2, microarray gene expression analysis was performed on standard NIH3T3 cells and NIH3T3 cells stably transfected with both RUNX2 and BMP2. Comparison of the gene expression profiles revealed the presence of a large number of differentially regulated genes. Four genes EHOX, CCL9, CSF2 and OSF-1 were chosen to be further characterized via RT-PCR. Sequential RT-PCR analysis on cDNA derived from control cells and cells stably transfected with either RUNX2, BMP2 or both RUNX2/BMP2 revealed that EHOX and CSF2 were cooperatively induced by RUNX2 and BMP2 whereas CCL9 and OSF-1 were suppressed by BMP2. The overexpression of both RUNX2 and BMP2 in NIH3T3 fibroblasts provided a powerful model upon which to discover potential RUNX2 gene targets and also identify genes synergistically regulated by BMP2 and RUNX2. The fourth element of the research investigated the role of RUNX2 in the ascorbic acid mediated induction of MMP-13 mRNA. The study was carried out using NIH3T3 cell lines stably transfected with BMP2, RUNX2 and both BMP2 and RUNX2. The cell lines were grown to confluence and subsequently cultured for a further 12 days in standard media or in media supplemented with AA. RT-PCR analysis was used to assess MMP-13 mRNA expression. The RT-PCR results demonstrated that AA was not sufficient for inducing MMP-13 mRNA in NIH3T3 cells. In contrast RUNX2 significantly induced MMP-13 levels 85 fold in the absence of AA (p = 0.0055) and upregulated MMP-13 mRNA levels 254 fold in the presence of AA (p = 0.0017). The results demonstrated that RUNX2 was essential for the AA mediated induction of MMP-13 mRNA in NIH3T3 cells. The effect of BMP2 on MMP-13 expression was also investigated. BMP2 induced MMP-13 mRNA transcripts a modest 3.8 fold in the presence of AA (p = 0.0027). When both RUNX2 and BMP2 were overexpressed in the presence of AA, MMP-13 mRNA levels were induced a massive 4026 fold (p = 8.7 x 10-4) compared to control cells. The investigation revealed that RUNX2 was an essential factor for the AA mediated induction of MMP-13 and that RUNX2 and BMP2 functionally cooperated to regulate MMP-13 mRNA levels.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Medical Science
Faculty of Health
Full Text

Prostate cancer is the most prevalent malignant neoplasia affecting men over 65 years of age. While prostate carcinoma is considered mostly curable when confined to the prostatic capsule, more aggressive forms have a predilection to metastasise to the bone. Increased expression of RUNX2 in primary tumours has been proposed to promote bone metastasis due to its critical role in bone regulation. However a role in tumour development and progression remains to be elucidated for RUNX2, or its β-subunit, CBFb. This thesis examines a role for RUNX2 during prostate cancer progression and defines a novel role for CBFβ and the RUNX-associated transcriptional repressor, ETO in prostate development and tumorigenesis. ETO was differentially expressed during prostate development and tumorigenesis, in vivo. Additionally, in vitro, ETO protein expression was confirmed in all prostate cancer cell subtypes, with high expression associated with aggressive, metastatic prostate cancer cells. Manipulation of ETO in vitro demonstrated a requirement for ETO in the growth and invasion of human prostate cancer cells. Subsequent examination of these cells in subcutaneous xenograft models revealed a requirement for ETO in aggressive tumour growth in vivo. Examination of CBFβ in vivo, demonstrated its differential expression during prostate development and tumorigenesis. CBFβ knockdown in an aggressive prostate cancer cell line demonstrated that CBFβ expression was required for growth and invasion in vitro and delayed tumour growth following in vivo xenograft examination. RUNX2 was shown to promote increased cell growth and invasion in human prostate cancer cells in vitro. Subsequent in vivo examination of a non-aggressive prostate cancer cell line following forced RUNX2 expression demonstrated decreased primary tumour growth but was associated with increased metastasis. These data provide a new role for ETO and CBFβ in prostate development and tumorigenesis and a novel role for RUNX2 in the phenotypic shift associated with metastatic prostate cancer.

Breast cancer is the third most common cause of cancer death in the UK, accountable for more than 11000 deaths in 2010 alone (www.cancerresearchuk. org). Developmental pathways commonly required for normal development are often hijacked during tumour progression, so a better understanding of mammary gland development is necessary to fully understand the roots of breast cancer. The Runx gene family are known to be important regulators of development in different lineages. In particular RUNX1 and RUNX2 have been widely studied in the context of haematopoiesis and osteogenesis respectively, but their role in epithelial tissue is much less well understood. In this thesis a role for RUNX1 and RUNX2 in mammary development and breast cancer has been identified. The first part of this study is focused on characterizing the expression and function of the Runx genes in the mammary epithelium. RUNX1 and RUNX2 protein levels fluctuate during embryonic and adult mammary development, and an in vivo conditional knockout strategy shows that both genes are important for maintenance of mammary epithelium homeostasis. Moreover, combined loss of RUNX1 and RUNX2 significantly perturbs the normal mammary architecture with an expansion of the basal population in vivo and the appearance of preneoplastic lesions in aged mammary glands. An exciting new role for RUNX2 in mammary stem cells has also been revealed showing that RUNX2 is important for the regenerative potential of mammary epithelial cells in vitro. Evidence is also presented to indicate that RUNX2 could be linked to regulation of quiescence and Wnt signalling in the stem cell compartment and during transformation. Finally, the role of these genes in breast cancer is discussed demonstrating involvement of RUNX1 and RUNX2 specifically in the triple negative (ER-PR-HER2-) subtype. In particular, for the first time, RUNX1 is revealed as an independent prognostic indicator correlating with poor prognosis in triple negative tumours. Meanwhile, evidence from various mouse models demonstrates that RUNX2 may be specifically involved in the squamous metaplastic form of this disease.

To elucidate mechanisms involved in the regulation of a number of mammalian cell differentiation events, studies were performed to characterize the transcriptional repression functions of the Groucho/TLEs, Hairy and Enhancer of split (Hes), and Runt-related (RUNX) protein families. These proteins have been shown to have overlapping or antagonistic roles in a number of cell differentiation processes, in both Drosophila and mammals. More specifically, the aim was to elucidate mechanisms by which Hes and RUNX-mediated transcriptional control is modulated, with respect to their interactions with each other and the Groucho/TLE proteins.
It is shown here that mammalian Hes1 requires TLEs to repress gene expression, similar to the requirement Drosophila Hes proteins have for Groucho. It is shown further that TLEs also interact with mammalian RUNX proteins and inhibit RUNX's ability to transactivate gene expression. In contrast, Hes1 also physically associates with RUNX and enhances RUNX-mediated transactivation. These results, together with our additional finding that RUNX can inhibit Hes1-mediated transcriptional repression, suggest for the first time that RUNX and Hes1 proteins regulate each other's transcriptional functions.
This thesis also shows that Hes1 can be found in a discreet nuclear subcompartment involved in the regulation of gene expression, termed the nuclear matrix. Nuclear matrix binding is mediated by the same Hes1 C-terminal domain that acts as a binding site for Groucho/TLEs, which also localize to the nuclear matrix and are required for Hes1-mediated transcriptional repression. Both the nuclear matrix association and transcription repression activity of Hes1 are inhibited by deletion of its C-terminal region, indicating that Groucho/TLEs act as transcriptional corepressors for Hes1.
Together, the material presented in this thesis suggests that Hes1 and RUNX proteins interact with each other to modulate gene expression in the development of a number of tissues.

In the UK, 12,000 patients die from metastatic breast cancer annually. There is therefore an urgent need to identify the molecules that cause metastasis. Recent work has revealed a role for the RUNX family of transcription factors in the development of metastatic breast cancer. The RUNX proteins form active transcription factor complexes when bound by the heterodimeric partner CBFβ to regulate the expression of metastatic genes. Previous work from our laboratory has demonstrated that knockdown of CBFβ resulted in a decreased invasion capacity of the metastatic breast cancer cell line MDA-MB-231. Three-dimensional culture of MDA-MB-231 cells revealed that loss of CBFβ induces a mesenchymal to epithelial transition (MET). The aim of this project was to determine the role of the RUNX/CBFβ complex in maintaining the mesenchymal phenotype of metastatic breast cancer cells. The data presented show that the phenotype changes were accompanied by changes in EMT marker-gene expression, including Snai2, MMP9, and MMP13. Induction of CBFβ in the CBFβ-knockdown cells remarkably restored both the invasive capacity and the mesenchymal phenotype. Further analysis revealed that maintenance of the mesenchymal phenotype was dependent upon both CBFβ-partner proteins, RUNX1 and RUNX2. Taken together the data presented in this thesis demonstrate that RUNX/CBFβ complexes drive the epithelial to mesenchymal transition (EMT) in breast cancer cells. These findings are likely to be important in the development of potential therapies to inhibit the metastatic spread of breast cancer.

Objetivo: No atual trabalho propomo-nos a avaliar morfometricamente possíveis alterações na reparação óssea alveolar pós-exodontia de ratos tratados com Meloxicam, um anti-inflamatório inibidor preferencial da cicloxigenase 2 (COX-2) e correlacionar com a expressão temporal da COX-2 e do fator de transcrição 2 com domínio Runt (Runx-2) associada com a diferenciação de células da linhagem osteoblástica. Material e Métodos: A exodontia do incisivo superior direito foi realizada em 120 ratos Wistar, divididos em grupo controle (n = 60) - animais tratados com injeção intraperitoneal de 0,1 ml de solução salina 0,9% diariamente e grupo tratado (n = 60) animais tratados com injeção de Meloxicam na dose de 3mg/kg de massa corporal, diariamente, ambos durante 7 dias. O volume total do alvéolo (VtA) e do tecido ósseo (VtO), o número de células imunomarcadas/mm² (Nm) para COX-2 e Runx-2 e a expressão protéica por Western blotting (WB) da COX-2 e RUNX-2 foram avaliados nos períodos 3, 7, 10, 14, 21 e 30 dias póscirurgias. Resultados: No grupo tratado o VtA manteve-se constante até os 21 dias, enquanto que no controle foi 0,272 vezes menor em relação aos 3 dias decorrente da maior atividade osteoclástica. Porém, aos 14 dias, no grupo tratado o VtO foi 0,337 vezes menor em relação ao controle decorrente da inibição parcial da transmigração de células inflamatórias responsáveis pela degradação do coágulo e da angiogênese, ocasionando um retardo na formação dos tecidos de granulação/conjuntivo, na diferenciação das células osteoblásticas e na formação/remodelação do tecido ósseo, e consequentemente no reparo ósseo alveolar. A imunomarcação para COX-2 foi observada em diversos tipos celulares, como fibroblastos, células endoteliais, células inflamatórias, osteoblastos e osteócitos. O Nm para COX-2 não apresentou diferenças estatísticas significantes entre os grupos no intervalo de 3 e 21 dias pós-cirurgia, enquanto que, a expressão protéica pelo WB foi em média 0,232 vezes menor no grupo tratado em relação ao controle. Por outro lado, a imunomarcação para Runx-2 foi mais expressiva em osteoblastos e osteócitos e raramente em fibroblastos. O Nm para Runx-2 no grupo tratado durante todo período experimental foi em média 0,256 vezes menor em relação ao controle, sendo o mesmo observado para a expressão protéica pelo WB. Conclusão: Dentro dos limites da atual pesquisa, a aplicação do Meloxicam por um curto período de tempo atrasa temporariamente o processo inicial de reparo ósseo alveolar diminuindo a expressão das proteínas COX-2 e RUNX-2.
Objective: To evaluate morphometrically possible changes in post-extraction alveolar bone healing in rats treated with Meloxicam, a selective anti-inflammatory inhibitor of cyclooxygenase (COX-2) and to correlate it with the temporal expression of COX-2 and transcription factor 2 with Runt domain (Runx-2) associated with differentiation of osteoblastic lineage cells. Material and Methods: The extraction of the right upper incisor was made in 120 male Wistar rats, divided into control group (n=60) - animals treated with an intraperitoneal injection of 0,1 ml of 0,9% NaCl solution daily for 7 days and the treated group (n=60) - animals treated with injection of 3mg/kg of body weight of Meloxicam 0.9% NaCl solution daily for 7 days. The total alveolar volume (VtA), total bone tissue volume (VtO), number of immunohistochemically positive cells/mm² (Nm) for COX-2 and RUNX-2 and the Western blotting (WB) COX-2 and RUNX-2 protein expressions were evaluated after 3, 7, 10, 14, 21 and 30 days after the surgeries. Results: In the treated group the VtA remained constant until the 21st day, while in the control group at the same day the value was 0,272 times lower compared to the 3 days period, due to the higher osteoclastic activity. However, at 14 days the VtO was 0,337 times lower in the treated group compared to the control due to the partial inhibition of the transmigration of inflammatory cells responsible for the degradation of the clot and angiogenesis, causing a delay in the formation of granulation/connective tissues, differentiation of osteoblastic cells and in bone tissue formation/remodeling, and consequently in the alveolar bone repair. The immunostaining for COX-2 was observed in various cell types, such as fibroblasts, endothelial cells, inflammatory cells, osteoblasts and osteocytes. The Nm for COX-2 showed no statistical differences between groups from the 3rd to the 21st day, while the WB protein expression was on average 0,232 times lower in the treated group compared to the control. On the other hand, the immunostaining for Runx-2 was more expressive in osteoblasts and osteocytes and rarely in fibroblasts. The Nm for Runx-2 on the treated group was, during the whole experimental period, on average 0,256 times smaller than in the control. The same difference was observed in the protein expression by WB. Conclusion: Within the limits of the present study, its was concluded that the application of Meloxicam daily for 7 days causes a temporary delay in the alveolar bone repair decreasing the expression of proteins COX-2 and RUNX-2.

The family of runt related transcription factors (RUNX/Cbfa/AML/PEBP2) are essential for cellular differentiation and fetal development. RUNX factors are distributed throughout the nucleus in punctate foci that are associated with the nuclear matrix/scaffold and generally correspond with sites of active transcription. Truncations of RUNX proteins that eliminate the C-terminus including a 31-amino acid segment designated the nuclear matrix targeting signal (NMTS) lose nuclear matrix association and result in lethal hematopoietic (RUNX1) and skeletal (RUNX2) phenotypes in mice. These findings suggest that the targeting of RUNX factors to subnuclear foci may mediate the formation of multimeric regulatory complexes and contribute to transcriptional control. In this study, we hypothesized that RUNX transcription factors may dynamically move through the nucleus and associate with subnuclear domains in a C-terminal dependent mechanism to regulate transcription. Therefore, we investigated the subnuclear distribution and mobility of RUNX transcription factors in living cells using enhanced green fluorescent protein (EGFP) fused to RUNX proteins. The RUNX C-terminus was demonstrated to be necessary for the dynamic association of RUNX with stable subnuclear domains. Time-lapse fluorescence microscopy showed that RUNX1 and RUNX2 localize to punctate foci that remain stationary in the nuclear space in living cells. By measuring fluorescence recovery after photobleaching, both RUNX1 and RUNX2 were found to dynamically and rapidly associate with these subnuclear foci with a half-time of recovery in the ten-second time scale. A large immobile fraction of RUNX1 and RUNX2 proteins was observed in the photobleaching experiments, which suggests that this fraction of RUNX1 and RUNX2 proteins are immobilized through the C-terminal domain by interacting with the nuclear architecture. Truncation of the C-terminus of RUNX2, which removes the NMTS as well as several co-regulatory protein interaction domains, increases the mobility of RUNX2 by at least an order of magnitude, resulting in a half-time of recovery equivalent to that of EGFP alone. Contributions of the NMTS sequence to the subnuclear distribution and mobility of RUNX2 were further assessed by creating point mutations in the NMTS of RUNX2 fused to EGFP. The results show that these point mutations decrease, but do not abolish, association with the nuclear matrix compared to wild-type EGFP-RUNX2. Three patterns of subnuclear distribution were similarly observed in living cells for both NMTS mutants and wild-type RUNX2. Furthermore, the NMTS mutations showed no measurable effect on the mobility of RUNX2. However, the mobility of RUNX proteins in each of the different subnuclear distributions observed in living cells were significantly different from each other. The punctate distribution appears to correlate with higher fluorescence intensity, suggesting that the protein concentration in the cell may have an effect on the formation or size of the foci. These findings suggest that the entire NMTS and/or the co-regulatory protein interaction domains may be necessary to immobilize RUNX2 proteins. Because RUNX factors contain a conserved intranuclear targeting signal, we examined whether RUNX1 and RUNX2 are targeted to common subnuclear domains. The results show that RUNX1 and RUNX2 colocalized in common subnuclear foci. Furthermore, RUNX subnuclear foci contain the co-regulatory protein CBFβ, which heterodimerizes with RUNX factors, and nascent transcripts as shown by BrUTP incorporation. These results suggest that RUNX subnuclear foci may represent sites of transcription containing multi-subunit transcription factor complexes. RUNX2 transcription factors induce expression of the osteocalcin promoter during osteoblast differentiation and to study both RUNX2 and osteocalcin function, it would be helpful to have transgenic mice in which OC expression could be easily evaluated. Therefore, to assess the in vivo regulation of osteocalcin by RUNX protein, we generated transgenic mice expressing EGFP controlled by the osteocalcin promoter. Our results show that EGFP is expressed from the OC promoter in a cultured osteosarcoma cell line, but not in a kidney cell line, and is induced by vitamin D3. Furthermore, the OC-EGFP transgenic mice specifically express EGFP in osteoblasts and osteocytes in bone tissues. Moreover, EGFP is expressed in mineralized bone nodules of differentiated bone marrow derived from transgenic mice. Thus, these mice produce a good model for studying the in vivo effects of RUNX-mediated osteocalcin regulation and for developing potential drug therapies for bone diseases. Taken together, our results in living cells support the conclusion that RUNX transcription factors dynamically associate with stationary subnuclear foci in a C-terminal dependent mechanism to regulate gene expression. Moreover, RUNX subnuclear foci represent transcription sites containing nascent transcripts and co-regulatory interacting proteins. These conclusions provide a mechanism for how RUNX transcription factors may associate with subnuclear foci to regulate gene expression. Furthermore, the OC-EGFP transgenic mice now provide a useful tool for studying the in vivo function and regulation of osteocalcin by RUNX proteins during osteoblast differentiation and possibly for developing therapeutic drugs for treatment of bone diseases in the future.

Introdução: A terapia com laser de baixa potência (LBP) vem sendo utilizada em Odontologia com diversos objetivos, em especial o de diminuir o tempo de cicatrização de feridas cirúrgicas. Objetivo: O objetivo do presente estudo in vivo foi avaliar qualitativamente e quantitativamente o efeito da irradiação com LBP no processo de remodelação óssea após a extração dentária em ratos jovens. Material e Método: Foram utilizados 60 ratos Wistar, distribuídos aleatoriamente nos seguintes grupos: Grupo Controle (n=30) animais com extração dentária sem aplicação do LBP, e Grupo Experimental (n=30) animais que tiveram extração dentária (Ext) e aplicação do LBP (Ext+LBP) nos três primeiros dias (54 J/cm2 por dia). Os animais foram sacrificados nos períodos de 1, 2, 3, 5, 7 e 10 dias após o procedimento de extração dentária. Neste estudo foram analisados os efeitos da aplicação do laser sobre o reparo alveolar através de microscopia de luz, luz polarizada e imunomarcação. Para isso foram avaliados os seguintes parâmetros: 1) porcentagem de formação óssea no interior do alvéolo; 2) grau de processo inflamatório; 3) grau de amadurecimento do colágeno; 4) imunomarcação para TRAP e RUNX-2. Todos os resultados obtidos foram submetidos à análise estatística através do teste ANOVA e teste de Mann-Whitney U (p<0.05). Resultados: Observou-se que os alvéolos do Grupo Experimental apresentaram processo de reparo mais evoluído quando comparados ao Grupo Controle, caracterizado pela organização mais rápida do coágulo sanguíneo, proliferação de fibroblastos nos restos do ligamento periodontal mais pronunciada, organização do colágeno e formação óssea mais precoce e mais intensa. Conclusão: A utilização do laser de baixa potência acelerou o processo de formação óssea durante as fases iniciais do experimento, embora nos períodos finais não houve diferença no processo de ossificação.
Introduction: Low Power Laser (LPL) therapy has been used in Dentistry to achieve many objectives, particularly to decrease the healing period on wound healing. Objectives: The purpose of this in vivo study was to evaluate qualitatively and quantitatively the irradiation effect with LPL in the bone remodeling process after tooth extraction in young rats. Material and Method: 60 Wistar rats were used, randomly distributed in the following groups: Control Group (n=30) animals with tooth extraction without LPL application, and Experimental Group (n=30) animals with tooth extraction (Ext) and LPL application (Ext+LPL) on the three fist days (54 J/cm2 per day). The animals were euthanized after the end periods of 1, 2, 3, 5, 7 and 10 days after the tooth extraction. This study looked into the effects of laser application on the alveolar repair through light microscopy, polarized light and immunostaining. After that, the following parameters were evaluated: 1) percentage of bone formation inside the dental alveolus; 2) degree of inflammatory process; 3) degree of collagen maturation; 4) immunostaining for TRAP and RUNX-2. All the results obtained were submitted to statistical analysis over the ANOVA and Mann- Whitney (p<0.05) test. Results: It was observed that the alveolus from the Experimental Group presented an improved repair process when compared to the Control Group, characterized by faster blood clot organization, more apparent fibroblasts proliferation on the remnants of the periodontal ligament, earlier and more intense collagen organization and bone generation. Conclusion: The use of Low Power Laser accelerated the bone generation process during the experimental initial period, although there was no difference in the ossification process in the final periods.

Characterization of new pathways in Acute Myeloid Leukemia and T-cell Acute Lymphoblastic Leukemia which contribute to oncogenesis is necessary to relieve dependence on conventional chemotherapy for treatment of these diseases. In this dissertation, I characterized the role of signaling molecules (IGF1R) and transcription factors (RUNX1, RUNX3, NOTCH1) in regulating mechanisms of leukemia initiation and maintenance. I discovered that committed myeloid progenitor cells with genetically reduced levels of IGF1R were less susceptible to myelogenous leukemogenic transformation due, at least in part, to a cell-autonomous defect in clonogenic activity. Genetic deletion of IGF1R by inducible Cre recombinase however had no effect on growth/survival of established leukemia cells. I raise the possibility that IGF1R inhibitors in clinical development may be acting through alternate/related pathways. Second, in a retroviral insertional mutagenesis study, I cloned retroviral integration sites from hNOTCH1ΔE mouse leukemias to find genes which collaborate with Notch signaling in T-ALL initiation. Common integration sites include the previously identified Ikzf1, and a novel potentially Notch-collaborating gene, Runx3. Using a multicistronic lentiviral system, I show that RUNX1A, RUNX1B and RUNX3 were able to collaborate with the ΔEΔL allele of NOTCH1 to initiate leukemia. Finally, I sought to understand how RUNX1 and RUNX3 contribute to the biology of established T-cell leukemias. I found that both RUNX1 and RUNX3 contribute to T-ALL cell proliferation and survival. Although RUNX3 can induce cell proliferation, RUNX1 expression is finely tuned with overexpression and knockdown resulting in negative growth phenotypes. This may be in part to regulation of MYC, IL7R, IGF1R, and CDKN1B as well as affecting genome-wide H3K27Ac. I found that RUNX1 expression was targeted by the CDK7 inhibitor, THZ1. RUNX1 and RUNX3 are mediators of Notch-directed regulation of PKCθ, and as such are indirect regulators of LIC-activity. Finally, I showed that RUNX1 and Notch signaling provide complimentary, additive signals for growth of T-ALL cells. These experiments provide insight into the role of RUNX1 mutations in T-cell leukemia and point to a complementary role in supporting the Notch pathway.
Medicine, Faculty of
Graduate

One of the primary goals of active research in molecular biology is to better understand the process of transcription regulation. An important objective in understanding transcription is identifying transcription factors that directly regulate target genes. Identifying these transcription factors is a key step toward eliminating genetic diseases or disease susceptibilities that are encoded inside deoxyribonucleic acid (DNA). There is much uncertainty and variation associated with transcription factor binding sites, requiring these sites to be represented stochastically. Although typically each transcription factor prefers to bind to a specific DNA word, it can bind to different variations of that DNA word. In order to model these uncertainties, we use a Bayesian approach that allows the binding probabilities associated with the motif to vary. This project presents a new method for motif searching that uses expert prior information to scan DNA sequences for multiple known motif binding sites as well as new motifs. The method uses a mixture model to model the motifs of interest where each motif is represented by a Multinomial distribution, and Dirichlet prior distributions are placed on each motif of interest. Expert prior information is given to search for known motifs and diffuse priors are used to search for new motifs. The posterior distribution of each motif is then sampled using Markov Chain Monte Carlo (MCMC) techniques and Gibbs sampling.

L'hématopoïèse est un processus physiologique permettant la production des cellules sanguines. Ce processus est notamment contrôlé par les facteurs de transcription des familles RUNX et GATA qui jouent des rôles essentiels, depuis l'émergence des cellules souches hématopoïétiques jusqu'à leur différenciation en plusieurs lignages. Chez l'Homme, de nombreuses altérations génétiques affectant RUNX1 sont associées au développement d'hémopathies. Ainsi, la translocation t(8;21), qui entraîne l'expression de la protéine de fusion RUNX1-ETO (RE), est à l'origine de ±12% des Leucémies Myéloïdes Aiguës (LAM). Au cours de ma thèse, je me suis attachée à mieux comprendre comment les facteurs RUNX régulent d'une part le développement normal des cellules sanguines, et d'autre part le développement des leucémies. Pour cela, j'ai tiré profit de la conservation des réseaux géniques régulant la formation des cellules sanguines des vertébrés à la Drosophile. En particulier, les facteurs Lozenge (LZ) et Serpent (SRP), homologues des facteurs RUNX1 et GATA1 respectivement, participent aussi à l'hématopoïèse chez cet insecte. Afin de comprendre comment les facteurs RUNX et GATA contrôlent l'hématopoïèse, nous avons réalisé un crible in cellulo par RNAi pour identifier des régulateurs de l'activité du complexe SRP/LZ. Parmi les candidats issus de ce crible, je me suis concentrée sur l'étude de MLF (Myeloid Leukemia Factor), dont l'homologue chez l'Homme (hMLF1) a été identifié comme cible de la translocation t(3;5) dans des LAM. Les résultats que nous avons obtenus montrent que mlf contrôle l'homéostasie du système hématopoïétique de la Drosophile. Ainsi, MLF participe à une boucle de rétrocontrôle positif de l'activité du facteur LZ au cours de l'hématopoïèse. D'autre part, j'ai réalisé un crible génétique chez la Drosophile afin d'identifier de nouveaux régulateurs de RE, dont l'expression induit des phénotypes de type " pré-leucémique " chez la Drosophile. Ainsi, en induisant par RNAi la perte de fonction de gènes spécifiquement dans les cellules LZ+, j'ai pu identifier 26 gènes candidats requis pour l'activité de RE chez la Drosophile. De fait, j'ai pu montrer que l'inhibition de l'un de ces gènes, Pontin52, réduit la clonogénicité des cellules leucémiques humaines exprimant RE. Enfin, mes données montrent que MLF est requis pour l'induction des phénotypes préleucémiques par RE chez la Drosophile. Ces résultats suggèrent que le contrôle de la stabilité des facteurs RUNX par MLF pourrait jouer un rôle important dans l'hématopoïèse et la leucémogenèse
Hematopoiesis is the physiological process allowing the production of blood cells. This process is finely tuned by many transcription factors and in particular by members of the GATA and RUNX families that play essential roles, from the emergence of hematopoietic stem cells up to their differentiation into multiple lineages. In humans, many genetic alterations affecting RUNX1 are associated with blood cell diseases. In particular, the translocation t(8; 21), which causes the expression of the fusion protein RUNX1-ETO (RE), is associated with ± 12% of cases of acute myeloid leukemia (AML). During my PhD, I studied how RUNX factors regulate both normal and leukemic blood cell development. For this, I took advantage of the conservation of the gene networks regulating hematopoiesis from vertebrates to Drosophila. In particular, Lozenge (LZ) and Serpent (SRP), the respective homologues of RUNX1 and GATA1 also control blood cell development in this insect. To decipher how the activity of RUNX and GATA factors is regulated, we performed an in cellulo RNAi screen to identify regulators of SRP/LZ. Among the candidates from this screen, I focused on MLF (Myeloid Leukemia Factor), whose counterpart in humans (hMLF1) was identified as the target of the t(3; 5) associated with LAM. The results we obtained show that MLF control homeostasis of drosophila hematopoietic system. Thus, MLF is involved in a positive feedback loop controlling LZ activity during hematopoiesis. Moreover, I made a genetic screen in vivo in Drosophila to identify new regulators of the human oncogenic protein RE, which induce leukemic like phénotypes in Drosophila. By screening for genes whose loss of function, induced by RNAi specifically in LZ+ cells, I recovered 26 candidate genes required for RE activity in Drosophila. In fact, I could show that inhibition of one of these genes, Pontin52, reduced the clonogenicity of human leukemic cells expressing RE. Finally, my results show that MLF is required for RE-induced preleukemic phenotypes in Drosophila. These results suggest that the control of RUNX factors stability by MLF may play an important role in hematopoiesis and leukemogenesis

L'hématopoïèse est un processus complexe et dynamique qui conduit à la formation ainsi qu'au remplacement continu et régulé des cellules sanguines. Au cours de ce processus, une série de facteurs de transcription contrôle l'apparition, l'engagement et la différentiation des cellules souches dans un lignage déterminé. En particulier, chez les vertébrés, le facteur RUNX1/AML1 (pour Acute Myeloid Leukemia 1) est requis pour l'émergence des cellules souches hématopoïétiques ainsi que pour la différentiation des lignées myéloïdes et lymphoïdes. Chez l'homme, différentes altérations génétiques affectant AML1 sont liées au développement de pathologies du système hématopoïétique. Notamment, la translocation chromosomique t(8;21), codant la protéine de fusion AML1-ETO, est associée à 10-15 % des cas de leucémies myéloïde aiguës. Il a été décrit que AML1-ETO agit essentiellement en interférant avec la fonction de AML1 au cours de la différentiation hématopoïétique. Cependant, le mode d'action de cet oncogène reste mal compris et peu de facteurs modulant son activité sont connus. Récemment, de nombreux travaux ont mis en évidence que divers aspects du développement des cellules hématopoïétiques sont conservés de la Drosophile aux vertébrés. Notamment, les facteurs de transcription des familles RUNX et GATA, acteurs clefs de l'hématopoïèse chez les vertébrés, contrôlent aussi le développement des cellules sanguines chez la Drosophile. Tirant profit d'une part de la conservation phylogénétique des circuits géniques régulant l'hématopoïèse chez l'homme et la Drosophile et d'autre part des puissants outils d'analyses génétiques disponibles chez la Drosophile, nous avons cherché à utiliser la Drosophile comme système modèle pour étudier le mécanisme d'action de l'oncogène humain AML1-ETO et identifier des modulateurs de son activité. Nos résultats montrent que AML1-ETO exerce dans des cellules sanguines de la Drosophile dont la différentiation dépend de l'expression d'un facteur RUNX (Lozenge, LZ), des effets similaires à ceux observés dans des cellules leucémiques humaines portant la translocation t(8;21), à savoir : un blocage de la différenciation des cellules hématopoïétiques exprimant LZ et une augmentation de leur nombre. Grâce à la réalisation d'un crible génétique in vivo par interférence à l'ARN, nous avons identifié calpainB comme requis pour que AML1-ETO induise ces effets. De plus, nous avons pu montrer que l'inhibition des calpaines provoque la dégradation de AML1-ETO et diminue le potentiel clonogénique de cellules leucémiques humaines exprimant cette chimère. Ces travaux montrent que la Drosophile peut être utilisée comme modèle alternatif pour mieux comprendre la fonction de AML1-ETO et identifier de nouveaux facteurs régulant son activité
Hematopoiesis is a complex and dynamic process that leads to the formation and continuous blood cells replenishment. During this process, a series of transcription factors controls the appearance, commitment and differentiation of stem cells into specific lineages. In particular, in vertebrates, the factor RUNX1/AML1 (for Acute Myeloid Leukemia 1) is required for the emergence of hematopoietic stem cells and for the differentiation of both myeloid and lymphoid lineages. In humans, several genetic alterations affecting AML1 are linked to the development of different hemopathies. Notably, the chromosomal translocation t (8; 21), encoding the fusion protein AML1-ETO, is associated with 10-15% of cases of acute myeloid leukemia. It has been described that AML1-ETO acts essentially by interfering with AML1 function during hematopoietic differentiation. However, the mode of action of this oncogene remains poorly understood and few factors modulating its activity are known. Recently, numerous studies have shown that several aspects of hematopoietic development are conserved from Drosophila to vertebrates. Notably, transcription factors of RUNX and GATA families, which are key players in vertebrate's hematopoiesis, also control the development of blood cells in Drosophila. Taking advantage of the phylogenetic conservation of genetic circuitry regulating hematopoiesis between humans and Drosophila and of the powerful genetic tools available in Drosophila, we assessed whether Drosophila can provide a suitable model system to study the mechanism of action of the human oncogene AML1-ETO and to identify modulators of its activity. Our results show that AML1-ETO exerts in Drosophila blood cells expressing a RUNX factor (Lozenge, LZ) similar effects to those observed in human leukemic cells carrying the t(8;21), namely a differentiation blockage and an increased proliferation. In addition, by performing a large scale in vivo screen based on RNA interference, we identified calpainB as required for AML1-ETO-induced blood cell disorders in Drosophila. In addition, we showed that calpains inhibition resulted in AML1-ETO degradation and reduced the clonogenic potential of human leukemic cells expressing intrinsically this chimera. Our results establish that Drosophila can be used as an alternative model to better understand AML1-ETO function and to identify new factors regulating its activity

L'hématopoïèse regroupe les phénomènes menant à la formation des différents types de cellules sanguines. Chez l'embryon de Drosophile, les prohémocytes génèrent deux types cellulaires, les plasmatocytes et les cellules à cristaux. Nous avons entrepris de caractériser les mécanismes de régulation de l'hématopoïèse chez la Drosophile. Nous avons montré que le gène serpent code pour deux isoformes du facteur de transcription GATA, Serpent, dont l'activité est modulée par recrutement de cofacteurs de type FOG (U-Shaped) et RUNX (Lozenge). D'autre part, nous avons montré in vivo que la ségrégation des deux lignages sanguins à partir d'une population de prohémocytes bipotents est un processus très dynamique, contrôlé par un mécanisme en deux étapes. Cette régulation fait intervenir Lozenge et Glial-Cell-Missing (Gcm) et Gcm2. Cette régulation contrôle précocement la détermination des précurseurs et tardivement le maintient de l'identité de ces cellules dans les phases de différenciation
Haematopoietic development give rise to different specialised blood cell types. In Drosophila embryo, the blood cell progenitors (prohemocytes) give rise to two differentiated cell types : plasmatocytes and crystal cells. We have investigated the mechanism of regulation of this process in the fruit fly. We have shown that serpent encodes different isoforms and that the activity of the GATA transcription factor Serpent is modulated by different cofactors, U-Shaped (FOG) or Lozenge (RUNX), during haematopoiesis. Secondly, we have undertaken an in vivo analysis of the mechanism of segregation of the two embryonic blood cell lineages. We find that prohemocytes are bipotent progenitors, which the fate is determined by a dynamic interplay between the lineage-specific transcription factors, Gcm/Gcm2 and Lz. The resolution of the choice of blood cell fate correspond to an original two-steps process in which Gcm/Gcm2 control the initiation and next the maintenance of the crystal cell fate

In the United States, metastatic breast cancer kills approximately 40,000 women and 400 men annually, and approximately 200,000 new cases of breast cancer are diagnosed each year. Worldwide, breast cancer is the leading cause of cancer deaths among women. Despite advances in the detection and treatment of metastatic breast cancer, mortality rates from this disease remain high because the fact is that once metastatic, it is virtually incurable. It is widely accepted that a major reason breast cancer continues to exhibit recurrence after remission is that current therapies are insufficient for targeting and eliminating therapy-resistant cancer cells. Emerging research has demonstrated that these therapy-resistant cells possess stem cell-like properties and are therefore commonly referred to as breast cancer stem cells (BCSCs). A major hallmark of BCSCs is the cell surface expression of CD44 and lack of expression of CD24, the so-called CD24-/CD44+ phenotype. Research indicates that this dangerous and rare subpopulation of BCSCs may be responsible for cancer onset, recurrence, and ultimately metastasis that leads to death. Two different model systems were utilized in this research. The first was the MCF7 cell line, a luminal A tumor subtype representative of a mildly invasive breast ductal carcinoma with an ER+/PR+/-/HER2- immunoprofile. The second was the MCF10A breast cancer progression model, which consists of three cell lines: MCF10A, MCF10AT1, and MCF10CA1a. In this system, spontaneously immortalized, non-malignant MCF10A cells were transfected with constitutively active H-Ras to form pre-malignant MCF10AT1 cells, which were then subcutaneously injected into mice and allowed to metastasize in order to form the oncogenic MCF10ACA1a cell line. This thesis presents evidence of a CD24low/-/CD44+ BCSC subpopulation within the MCF10A breast cancer progression model system. Findings indicate that RUNX1 and RUNX2 expression levels are involved in maintaining the BCSC phenotype. Across two different model systems, qRT-PCR analysis revealed that decreased levels of RUNX1 expression and increased levels of RUNX2 expression are essential for the maintenance of the BCSC subpopulation. It was also shown that low expression levels of RUNX1 and high expression levels of RUNX2 are present in CD24low/-/CD44+ BCSCs as compared to CD24+/CD44+ non-BCSCs. Furthermore, shRNA knockdown of RUNX1 was shown to enhance tumorigenicity, while shRNA knockdown of RUNX2 repressed tumorigenicity in BCSCs, as measured by the tumorsphere-formation assay. This research lays the groundwork for future investigations into the roles of RUNX1 and RUNX2 in regulating stemness in breast cancer.

The “Kalevala” is one of the most beautiful and archaic epos in world literature. It is composed from ancient Finnish poems by Elias Lönnrot, son of a poor village tailor, who started his career as a medical doctor, but who became a Professor of the Finnish language. The “Kalevala” is supposed to be a central source of identity for a nation that has been awaking to a consciousness of itself and also Finland’s most important contribution to world literature. Archaeological and linguistic data point out that in the prehistory period the Finno-Ugric tribes had near relations with the Balts. Their contacts, even coexistence, continued for a long time. In the process of cultural assimilation the more advanced culture of the Balts dominated, and the evidence of this can be seen in the Balt loanwords for social, administrative and agricultural innovations. A lot of names of incipient village, agrarian life in Finish appear to derive from ancient Balt loan. From the Balts the Finns borrowed even the most important terms of relationship, such like family, sister, daughter, cousin, daughter-in-law. That is why in the folklore of the Balts and the Finns we can find some parallels and affinities. In comparison Finnish national epos with Lithuanian folk songs there is seen that obvious affinities have the rune of the great oak, the rune of Aina, the episode about the birth of beer. Some parallels with Lithuanian folk songs and ballads also can be seen in the rune of Kulervo. Genetic... [to full text]

Thyroid Tumorigenesis is typically a well understood process, with well delineated oncogenic factors. Follicular and papillary thyroid cancers are typically survivable, with 5-year survival rates being >95% for Stage I-III of both cancer types. Anaplastic thyroid cancer, in contrast, lacks this prognosis, and is the most lethal of all endocrine-related cancers. The median survival time after a diagnosis is generally between 6-8 months, with a 5-year survival rate of <10%. Current treatment for anaplastic thyroid cancers routinely meet roadblocks, as resistance is quickly developed. Even non-discriminatory kinase inactivators, such as sorafenib, which are generally considered a drug of last resort, are unable to effect survival rates. As such, there is a clear need for further investigation of the causes of anaplastic thyroid cancer mechanisms. Previous work in the Carr lab revealed a novel regulatory pathway of an oncogene that is associated with several other endocrine-related cancers, as well as other non-endocrine-related cancers. Specifically, the Runt-related transcription factor 2 (Runx2) was found to be suppressed via direct binding of the thyroid hormone receptor beta 1 isoform (TRß1) to its proximal promotor. Runx2 was previously shown to be associated with increasing malignancy, with Runx2 occurring at low-levels in indolent cell lines, whilst occurring at high-levels in more malignant cell lines. TRß1, conversely, exhibited the opposite relationship. Endogenous levels of TRß1 were found to be high in indolent cell lines and were depleted in malignant cell lines. These findings were further confirmed via tissue microarrays. Restoration of TRß1 in malignant cell lines diminished Runx2 mRNA and protein levels, which was corroborated by evidence from electrophoretic mobility-shift assays, and chromatin immunoprecipitations that TRß1 was able to directly bind Runx2 promotor 1. Current studies have investigated the nuclear protein profile that associates with TRß1 to alter Runx2 transcription. Through EMSA-to-Mass Spectrometry methodologies, as well as novel DNA pulldown techniques, binding partners have been elucidated. Findings have also been confirmed via classical immunoprecipitations. Specifically, our findings show that TRß1 complexes with the brahma-related gene 1 (BRG1) protein, the nuclear co-repressor (NCOR), and BRG1-associated protein 60 (BAF60). BRG1 functions by preferentially recruiting histone deacetylases (HDAC), with BRG1 and the HDAC’s acting to alter chromatin, and thus transcription. Future studies aim at examining whether other proteins complex with TRß1 to alter Runx2 transcription, and whether these complexes are altered in aggressive cell lines.

Bone mineral density (BMD) is a reflection of the action of osteoblasts compared to osteoclasts. An imbalance in the activity of osteoblasts or osteoclasts, results in bone disease such as osteoporosis caused by overactive osteoclasts. BMD is influenced by genetic and environmental factors as demonstrated through twin studies, association studies and linkage analysis (Ralston, 1999). Several polymorphisms involved in the determination of BMD have been identified, with Vitamin D receptor and Collagen Type 1 showing reproducible associations. To identify genes influencing BMD two distinct strategies have been employed: 1) To determine if DNA polymorphism within the runt related transcription factor (RUNX2) gene is a determinant of BMD and fracture in women. 2) The identification of RANKL target genes in osteoclastogenesis. RUNX2 is a runt domain transcription factor (Werner et al., 1999) essential for osteoblast differentiation (Lee et al., 1997). RUNX2 gene knock-out mice have no osteoblasts due to a failure in osteoblast differentiation and consequently unmineralised skeletons, (Komori et al., 1997; Otto et al., 1997). In humans, mutations in RUNX2 cause cleidocranial dysplasia (CCD), a disorder characterised by hypoplasia or aplasia of the clavicles, short stature, supernumerary teeth, patent fontanelles and other changes in skeletal patterning and growth (Mundlos et al., 1997). RUNX2 contains a poly-glutamine poly-alanine (polyQ/polyA) repeat where mutations causing cleidocranial dysplasia have been observed. BMD has not been routinely examined in CCD, two studies have identified CCD patients with lower BMD with one fracture case identified (Quack et al., 1999; Bergwitz et al., 2001). The central role of RUNX2 in determining osteoblast differentiation makes RUNX2 a prime candidate gene for regulating adult bone density. To determine if polymorphism was present in the polyQ/polyA tract the repeat was amplified within the upper and lower deciles of femoral neck (FN) BMD in the Geelong Osteoporosis study (GOS). The upper and lower deciles of FN BMD acted as a surrogate for genotyping the entire cohort. This study identified two common variants within the polyA repeat: an 18 base pair deletion (11Ala) and a synonymous alanine codon polymorphism with alleles, GCA and GCG (noted as A and G alleles, respectively). The 11Ala and SNP polymorphism are found on codon 64 and 66 respectively (RUNX2 MRIPV variant). A allele frequencies were significantly different in a comparison of the upper and lower deciles of FN BMD (p=0.019). In 495 randomly selected women of the Geelong Osteoporosis Study (GOS), the A allele was associated with higher BMD at all sites tested. The association was maximal at the ultra-distal radius (p=0.001). In a separate fracture study, the A allele was significantly protective against Colles' fracture in elderly women but not spine and hip fracture. The 11Ala polymorphism was not related to BMD in GOS. To further decipher the role of the RUNX2 A allele we genotyped 992 women from a Scottish cohort. The alleles of RUNX2 within the glutamine/alanine repeat were determined by MspA1I restriction digest. To examine the possible influence on estrogen related therapies or estrogen status on the potential genetic effect conferred by RUNX2, we divided the cohort by menopausal and hormone replacement therapy status. Within postmenopausal Scottish women the RUNX2 A allele was associated with significantly higher FN BMD (p=0.028, n=312) but not lumbar spine (LS) BMD. The A allele was associated with higher FN BMD (p=0.035) within a postmenopausal subgroup of the population (n=312). To investigate the effect of weight on the RUNX2 alleles the Scottish cohort was segregated into thin/normal (BMI ≥ 25 kg/m2) and overweight /obese (BMI > 25 kg/m2). RUNX2 A allele showed a stronger effect on FN BMD in postmenopausal women above the median BMI. The 11Ala RUNX2 deletion allele was significantly associated with decreased LS BMD (p=0.018) within overweight/obese women (n=546). The 11Ala allele was significantly associated with increased levels of pyridinoline (p=0.014) and deoxypyridinoline (p=0.038) in the HRT treated subgroup of the population (n=492). Glutamine variants and an alanine insertion were identified within the group. These data suggest that the RUNX2 11Ala and A alleles exert differing affects on BMD showing preference for different skeletal sites in a weight dependent manner. We genotyped 78 individuals from an osteoarthritic population to elucidate the role of the RUNX2 alleles on markers of bone turnover and inflammation. The RUNX2 11Ala allele was significantly associated with decreased osteocalcin (OC) serum levels (p = 0.01). The RUNX2 A allele was significantly related to reduced tumor necrosis factor alpha (TNF-alpha) serum levels (p = 0.004). RUNX2 is known to bind to the OC promoter. An OC promoter polymorphism is found 7bp upstream from a putative RUNX2 binding site. We hypothesized that OC polymorphism may effect the RUNX2 transactivation of the OC gene and thus affect OC serum levels. OC promoter polymorphism was not related to OC serum levels (n=78). These data present a novel link between RUNX2 alleles and OC and TNF serum levels, providing putative mechanisms of action for the RUNX2 alleles. Further studies in larger populations are required to confirm these findings. Ten individuals within the GOS and the Scottish cohort were found to carry rare mutations of the polyQ/polyA repeat. All polyQ variants had a normal polyA repeat (17 amino acids) and were heterozygous for a normal 23Q/17A allele. Variants observed were 15, 16, 24 and 30Q. One individual was observed with an extended polyA repeat (24A). Patient records indicated otherwise unremarkable clinical history except for fracture in 4/10 individuals from GOS (hip and spine). BMD data from the LS and the FN were expressed as T-scores, a measure that relates BMD in terms of standard deviations below the young normal value. In addition, BMD data were also expressed as Z-scores around the age-mean. Under the null hypothesis, where RUNX2 Q repeat variation has no effect on BMD, Z scores would be expected to be distributed around a mean of zero. However, when all variants were pooled the BMD was significantly lower than expected. This effect persisted when deletion variants were considered alone. The effect was stronger on FN BMD (p=0.001) rather than LS BMD (p=0.096), reflecting either difference in precision of BMD measurements at these sites or perhaps a differential genetic effect on different skeletal sites. These data suggest that polyQ and polyA variants are associated with significantly lower BMD, and may be an important determinant for fracture. Glutamine variants exist at high frequency (~0.7%): this rate of mutation could be important when considering large populations at risk of age related osteoporosis. Considering that these subjects are heterozygous for a normal allele, it suggests that a more severe phenotype might be expected in rare subjects homozygous for glutamine repeat variants. In summary, this study investigated the role of novel polymorphisms and rare variants of the RUNX2 gene in influencing BMD, fracture and markers of bone turnover. Two common polymorphisms were identified within the polyA repeat: an 18 base pair deletion and a synonymous alanine codon polymorphism with alleles, A and G. The A allele was associated with increased BMD and was protective against a common form of osteoporotic fracture within a Geelong population. To verify these findings the RUNX2 alleles were genotyped in 992 women from a Scottish cohort. The magnitude and the direction of the effect of the A allele was maintained in the Scottish cohort. Interestingly, the A allele was shown to exert a menopause specific effect, with postmenopausal women showing the strongest effect. On re-analysis of the GOS data the post-menopausal women were found to drive the significance identified in the cohort. The magnitude of the effect of the A allele on BMD was greater in overweight/obese postmenopausal women indicating a gene-weight interaction for RUNX2. The RUNX2 11Ala allele showed a significant relationship with decreased LS BMD in overweight/obese Scottish women. The 11Ala allele was also associated with higher levels of urinary PYD and DPD in women treated with HRT, indicating higher levels of bone turnover in carriers of the 11Ala allele. In contrast to the Scottish cohort, no significant association with heterozygous carriers of 11Ala was observed in GOS, although a significant association was detected for homozygous carriers and LS BMAD. The 11 Ala RUNX2 allele was significantly associated with decreased serum osteocalcin levels and the A allele was significantly associated with TNF in OA patients. Glutamine variants and an alanine insertion were identified within Geelong and Scottish cohorts, which showed low Z and T scores suggesting that RUNX2 variants may be related to genetic effects on BMD and osteoporosis. Polymorphism of the polyQ/polyA region of RUNX2 were identified within this study were shown to associate with significant differences in BMD. The A allele showed a significant association with increased BMD in postmenopausal women from a Geelong and Scottish cohort, with a decreased frequency of the A allele observed in Colles' fracture patients from Geelong. The 11Ala deletion allele was significantly associated with decreased LS BMD and increases in markers of bone turnover in the Scottish cohort. A significant decrease in OC serum levels was observed in OA patients suggesting a direct effect of the allele on the transactivation of the RUNX2 gene. Rare variants of RUNX2 were identified which showed low BMD. These studies have provided insight into the role of RUNX2 in influencing BMD, further studies are required to verify the role of the A allele on BMD and fracture, the role of the rare variants and to identify the precise mechanisms behind the observed changes in BMD. - 2) The identification of RANKL target genes in osteoclastogenesis. Osteoclastogenesis is regulated in vivo by the action of osteoblast/stromal cells that express membrane bound, receptor activator of NF-kB ligand (RANKL). Monocytes treated in vitro with a soluble form of RANKL and macrophage colony stimulating factor (M-CSF) differentiate to osteoclasts, whereas monocytes treated with M-CSF alone differentiate to macrophage-like cells. The gene expression profile of human osteoclasts has not been extensively explored. Genes highly expressed by rabbit osteoclasts were identified through random sequencing of an osteoclast cDNA library (Sakai et al., 1995). Differential gene expression of mouse osteoclastogenesis was elucidated by array analysis (Cappellen et al., 2002). To identify genes important for human osteoclastogenesis, total RNA was isolated from monocytes treated for three weeks with either M-CSF alone or with RANKL and M-CSF. RANKL treatment for 3 weeks and 12 hours was investigated in this study, to complement previous data. Differential display was performed on RNA (12 hour treatment with RANKL) and differential gene expression profiles examined. The differential display products were pooled to generate a probe for screening a gene array system derived from a human osteoclast cDNA library. cDNA (3 week treatment with RANKL) hybridisation experiments against the array revealed additional regulated genes. Gene clones that showed significant regulation in M-CSF and RANKL treated cells compared M-CSF treated cells represent genes that are targets for RANKL-specific regulation. Osteopontin, creatine kinase and various mitochondrial genes were up regulated by the treatment of RANKL. Changes in gene expression observed in the array data were confirmed with real-time PCR using mRNA derived from in vitro induced osteoclasts. Cathepsin K gene expression was more than 300 fold greater in osteoclasts compared to macrophage-like cells after one week treatment with RANKL and M-CSF. Cystatin C expression showed a six-fold induction at two weeks of RANKL and M-CSF treatment and cystatin B showed a steady increase in expression. Some of these regulated genes may provide useful targets for influencing BMD.

In summary, this study investigated the role of novel polymorphisms and rare variants of the RUNX2 gene in influencing BMD, fracture and markers of bone turnover. Two common polymorphisms were identified within the polyA repeat: an 18 base pair deletion and a synonymous alanine codon polymorphism with alleles, A and G. The A allele was associated with increased BMD and was protective against a common form of osteoporotic fracture within a Geelong population. To verify these findings the RUNX2 alleles were genotyped in 992 women from a Scottish cohort. The magnitude and the direction of the effect of the A allele was maintained in the Scottish cohort. Interestingly, the A allele was shown to exert a menopause specific effect, with postmenopausal women showing the strongest effect. On re-analysis of the GOS data the post-menopausal women were found to drive the significance identified in the cohort. The magnitude of the effect of the A allele on BMD was greater in overweight/obese postmenopausal women indicating a gene-weight interaction for RUNX2. The RUNX2 11Ala allele showed a significant relationship with decreased LS BMD in overweight/obese Scottish women. The 11Ala allele was also associated with higher levels of urinary PYD and DPD in women treated with HRT, indicating higher levels of bone turnover in carriers of the 11Ala allele. In contrast to the Scottish cohort, no significant association with heterozygous carriers of 11Ala was observed in GOS, although a significant association was detected for homozygous carriers and LS BMAD. The 11 Ala RUNX2 allele was significantly associated with decreased serum osteocalcin levels and the A allele was significantly associated with TNF in OA patients. Glutamine variants and an alanine insertion were identified within Geelong and Scottish cohorts, which showed low Z and T scores suggesting that RUNX2 variants may be related to genetic effects on BMD and osteoporosis. Polymorphism of the polyQ/polyA region of RUNX2 were identified within this study were shown to associate with significant differences in BMD. The A allele showed a significant association with increased BMD in postmenopausal women from a Geelong and Scottish cohort, with a decreased frequency of the A allele observed in Colles’ fracture patients from Geelong. The 11Ala deletion allele was significantly associated with decreased LS BMD and increases in markers of bone turnover in the Scottish cohort. A significant decrease in OC serum levels was observed in OA patients suggesting a direct effect of the allele on the transactivation of the RUNX2 gene. Rare variants of RUNX2 were identified which showed low BMD. These studies have provided insight into the role of RUNX2 in influencing BMD, further studies are required to verify the role of the A allele on BMD and fracture, the role of the rare variants and to identify the precise mechanisms behind the observed changes in BMD.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Health Sciences
Full Text

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1991.
Includes bibliographical references (leaves 115-118).
by Ármann Ingólfsson.
M.S.

This essay is based on a survey of student’s attitudes and knowledge about global warming. A survey was used to obtain answers. The questionnaire is divided into three different stages. Some whit knowledge- based questions, one whit self-assessing questions and some with selffulfilling questions. Several studies have been created to survey students’ attitudes and knowledge, to see if there are knowledge gaps among university student, and to see if the universities lack certain teaching components. In the results, it was noted that Karlstad’s students had relatively low level of knowledge and assessed their own knowledge relatively high to the actual knowledge they hold. The students felt that society cares about global warming to some extent, and they want to counteract global warming but at the same time adapt society to the climate of the future. As an Australian study, (Pfautsch . and Gray 2017), the Karlstad students had an equal view as the Australian students of how to evaluate various sources of global warming, for example, politicians, classic media and social media were ranked among all as very unreliable sources.

These eleven chapters comprise Part One of a novel of thirty-seven chapters, entitled As Runs the Deer. It is a dialectic play on the processes of Time, as well as a play with evolving dialects. Nominally set in the 19th c., in an Appalachian-like terrain, it shows the difficulties James Ian Pierson meets when emerging out of his wilderness to re-enter his former life. Opening his own story by means of his sycamore cane, the 19- yr.-old amnesiac must soon reconcile his past with the invading "Now!" He evades the intrusion of a drunken hunter, is overcome by the wintry elements, brought from his icebed by Welsh woodsman Eustace, befriended by Mercury, ancient herbalist, keeper of the Myths. Frivolous Emily Marie Marchault must also reconcile herself with Ian's uneasy re-entry. Shackled by gilded chains of manners, she sees herself as overprotected by her guardian, Breton, and chips away at his ivory tower.

Resource management have been, and still are essential for humans, partly because of the constantly changing environment. The landscape provides basic material for survival and therefore it becomes important to understand the different stages of environmental influences and developments in parallel to the increasing complexity of Bronze- and Iron Age societies. Investigating the causes for human interactions with the environment and the following consequences for the biodiversity provides crucial information about organized systems for a sustainable resource management in our modern society. Finding archaeological traces of “hävd” (claimed land) and other types of manifestations in the landscape stress the fact that land becomes a more valuable resource from both a social and practical view. Over a longer perspective the process of going from a mobile hunter-gatherer lifestyle to a sedentary agricultural one also becomes a process of going from a collective to a private managing of resources. This project aims to investigate that development.

Il Modello Standard descrive la fenomenologia delle interazioni fondamentali con estrema precisione; tuttavia è incompleto e deve esistere nuova fisica oltre tale modello. Al momento non si è in grado di prevedere come e a che scala di energia tale fisica si manifesti. Un’eventuale risonanza nello stato finale μ + μ − a masse elevate costituirebbe un segnale di nuova fisica. Un fenomeno di questo tipo viene catalogato come produzione della particella Z' , la quale non rappresenterebbe necessariamente un nuovo bosone vettore sequenziale alla Z_0 . Questa tesi si colloca nell’ambito della ricerca della Z' nei processi di interazione protone-protone a LHC in termini di una generica risonanza che decade in coppie di muoni di carica opposta. I limiti attualmente fissati stabiliscono che non vi siano segnali di nuove risonanze per il Modello Sequenziale (SSM) al di sotto dei 2960 GeV. In questo lavoro di tesi si effettua un’analisi per un’eventuale Z ', fino a 5 TeV di massa. A Maggio 2015, LHC ha raggiunto un’energia nel centro di massa di 13 TeV aumentando di un fattore 10 o più il potere di scoperta per oggetti con massa superiore a 1 TeV. In questo scenario, favorevole all’osservazione di fenomeni rari, si inserisce la mia ricerca.

China Run is a 92 1/2 minute documentary film which portrays an ultramarathon runner's record-setting 2,125 mile run across China in 53 days, starting at the Great Wall north of Beijing and concluding in Guangjhou (Canton). It is a story of the difficulties, both physical and emotional, suffered by the runner, as well as the story of his encounters with the people of China.

The thesis begins with an introductory chapter that helps to define and locate the point of view from which the novella is told. The introduction also cites modern authors who influenced the tone, structure, and content of the novella. Thirteen chapters and an epilogue follow the introduction. Every third or fourth chapter is written as a vignette. The vignettes function as interchapters with the intention of giving contrast and balance to the main plot chapters.

Les leucémies aiguës lymphoblastiques de la lignée B (LAL-B) sont les cancers pédiatriques les plus fréquents. Dans ce type de leucémie, l'une des anomalies génétiques les plus fréquentes est la translocation t(12 ;21) aboutissant à la protéine de fusion ETV6-RUNX1. Cette pathologie est décrite comme un modèle à deux « hits ». Le premier, se produit in utero et génère la protéine de fusion. Le second, correspond à l’acquisition d’anomalies génétiques après la naissance. Ces réarrangements génomiques aberrants ont été décrits comme provenant d’une activité anormale de la recombinasse RAG. Notre travail a consisté dans un premier temps à compléter le modèle de leucémogénèse à plusieurs « hits ». En continuant notre étude des LAL B à translocation ETV6-RUNX1, nous nous sommes concentrés sur le rôle de RUNX1, gène dérégulé dans ce type de leucémie.L’ensemble de nos résultats confirme le rôle prépondérant de RUNX1 dans l’hématopoïèse et la leucémogenèse grâce à sa capacité à s’associer à des protéines aux fonctions différentes et grâce à son implication dans la transcription de gènes clé en hématologie. Nos résultats ouvrent donc de nouvelles perspectives dans la compréhension du contrôle de l’activité transcriptionnelle de RUNX1 et dans son rôle dans les hémopathies malignes
B-cell precursor acute lymphoblastic leukemia (B-ALL) is the most common pediatric cancer. In this type of leukemia, one of the most common genetic abnormalities is the ETV6-RUNX1 rearrangement. This malignancy is described as a two "hits" model. The first event occurs mainly in utero and generates the fusion gene ETV6-RUNX1. The second event consists in the acquisition of additional genetic abnormalities after birth. These aberrant genomic modifications have been described as resulting from abnormal activity of the RAG recombinase. Our work consisted initially in completing the leukemogenesis model. In continuing our study of ETV6-RUNX1 B-ALL, we focused on the role of RUNX1, an upregulated gene in this type of leukemia. All results confirm the predominant role of RUNX1 in hematopoiesis and leukemogenesis thanks to its ability to associate with proteins with different functions and its involvement in the transcription of key genes in hematology. Our results therefore open new perspectives in understanding the control of transcriptional activity of RUNX1 and its role in malignant hematology

The University of ManchesterCarlos Alberto Duran VillalobosDoctor of Philosophy in the Faculty of Engineering and Physical SciencesDecember 2015This thesis presents an innovative batch-to-batch optimisation technique that was able to improve the productivity of two benchmark fed-batch fermentation simulators: Saccharomyces cerevisiae and Penicillin production. In developing the proposed technique, several important challenges needed to be addressed:For example, the technique relied on the use of a linear Multiway Partial Least Squares (MPLS) model to adapt from one operating region to another as productivity increased to estimate the end-point quality of each batch accurately. The proposed optimisation technique utilises a Quadratic Programming (QP) formulation to calculate the Manipulated Variable Trajectory (MVT) from one batch to the next. The main advantage of the proposed optimisation technique compared with other approaches that have been published was the increase of yield and the reduction of convergence speed to obtain an optimal MVT. Validity Constraints were also included into the batch-to-batch optimisation to restrict the QP calculations to the space only described by useful predictions of the MPLS model. The results from experiments over the two simulators showed that the validity constraints slowed the rate of convergence of the optimisation technique and in some cases resulted in a slight reduction in final yield. However, the introduction of the validity constraints did improve the consistency of the batch optimisation. Another important contribution of this thesis were a series of experiments that were implemented utilising a variety of smoothing techniques used in MPLS modelling combined with the proposed batch-to-batch optimisation technique. From the results of these experiments, it was clear that the MPLS model prediction accuracy did not significantly improve using these smoothing techniques. However, the batch-to-batch optimisation technique did show improvements when filtering was implemented.

Uppsatsen handlar om pedagogiska spel i skolundervisningen. Författarna har konstruerat och provspelat ett pedagogiskt spel kallat ”Norden runt” i två skolor i Stockholmsområdet. I uppsatsen redovisas resultaten av undersökningen samt förs en diskussion kring pedagogiska spel och hur de kan användas i skolan.

The subject of this thesis is the pedagogic game in education. The researchers have created and developed a pedagogic game called “Nordic tour”, and tested the game in two schools in

Haninge and Sollentuna. The result of the test, the game and a discussion of the pedagogic game and how they can be used in education is presented in this thesis.

The study on the longest stretch of consecutive successes in \random" trials dates back to 1916 when the German philosopher Karl Marbe wrote a paper concerning the longest stretch of consecutive births of children of the same sex as appearing in the birth register of a Bavarian town. The result was actually used by parents to \predict" the sex of their children. The longest stretch of same-sex births during that time in 200 thousand birth registrations was actually 17 t log2(200 103): During the past century, the research of longest stretch of consecutive successes (longest runs) has found applications in various areas, especially in the theory of reliability. The aim of this thesis is to study large deviations on longest runs in the setting of Markov chains. More precisely, we establish a general large deviation principle for the longest success run in a two-state (success or failure) Markov chain. Our tool is based on a recent result regarding a general large deviation for the longest success run in Bernoulli trails. It turns out that the main ingredient in the proof is to implement several global and local estimates of the cumulative distribution function of the longest success run.

Genom en fallstudie av planeringsverktyget grönytefaktorn undersöks i denna masteruppsats offentliga och privata aktörers samverkan och strategier i arbetet för mer miljövänliga städer. Det insamlade materialet bygger på intervjuer med olika aktörer som arbetat med grönytefaktorn samt analys av styrdokument. De teorier som används för att förstå samverkan runt planeringsverktyget är Bulkeley och Kerns teori om styrning, Hrelja et al samt Youngs perspektiv på samverkan och de Certeaus begreppspar strategi och taktik. Resultatet visar att planeringsverktyget kräver en genomgående samverkan i hela planprocessen och att offentliga aktörer behöver hitta nya sätt att kombinera styrande genom auktoritet med dialog och förhandlade överenskommelser. Genom att studera planeringsverktygets implementeringsprocess uppstår nya kunskaper om dess operationella svårigheter och insikter om att det i ett planeringslandskap med en mängd olika privata och offentliga aktörer krävs kontinuerliga kombinationer av styrning och samverkan, exempelvis möjliggörande, tillhandahållande och stegvist förtroendebyggande. Det krävs även en delad förståelse hos de inblandade aktörerna om hur och varför planeringsverktyget ska användas.

The lichen population in the vicinity of Domsjö factory, Örnsköldsvik, was studied since many common species seemed to be negatively affected. The first lichen inventory in Örnsköldsvik was done in 1960 and the last one was made in 1988. A connection between the effected lichen and the sulphur dioxide emission as well as the distance from Domsjö factory was then made. The purpose of this study was to investigate if any change could be found in the population of pendoulus lichen in the vicinity of Domsjö factory, Örnsköldsvik, since the last study dating back to 1988. This study investigated the following facts; which are presence, length, and at what height on the trees the lichen Alectoria sarmentosa, Bryoria capillaris and Usnea spp. Only lichen on spruce, with trunks bigger than 150mm at breast hight were also included in the inventory. The results are based on data from 42 sites. No connection between the Domsjö factory, and the presence of Bryoria capillaris could be made, while Usnea spp. still seem to be affected. The length and the height of the investigated lichen did not seem to be affected; by the distance from Domsjö factory nor by the inventoried tree structures. No samples of Alectoria sarmentosa were found in the inventory.

The malfunction of the transcriptional regulator RUNX1 is the major cause of several variants of acute human leukemias and its normal function is to regulate the development of the blood system in concert with other transcriptional co-regulators. RUNX1 belongs to a conserved family of heterodimeric transcription factors that share a conserved DNA binding domain, the Runt domain (RD), named after the first member of this group – Runt - found in Drosophila melanogaster. The binding partner CBFβ serves as a regulator of RUNX by enhancing its DNA binding affinity through an allosteric mechanism.

The main focus ofo my thesis work has been the crystallization and structural analysis of the RUNX1 RD and involved also more technical methodological aspects that can be applied to X-ray crystallography in general.

The high resolution crystal structure of the free RD shows that this immunoglobulin-like molecule undergoes significant structural changes upon binding to both CBFβ and DNA. This involves a large flip of the L11 loop from a closed conformation in the free protein to an open conformation when CBFβ and/or DNA are bound. We refer to this transition as the “S-switch”. Smaller but significant conformational changes in other parts of the RD accompany the “S-switch”. We suggest that CBFβ triggers and stabilizes the “S-switch” which leads to the conversion of the RD into a conformation enhanced for DNA binding.

During the structural analysis of the RD we identified two chloride ions that are coordinated by residues otherwise involved in DNA binding. In electrophoretic mobility-shift analyses (EMSA) we demonstrated a chloride ion concentration dependent stimulation of the DNA binding affinity of RUNX1. We further showed by NMR line width broadening experiments that the chloride binding occurred within the physiological range. A comparable DNA binding stimulation of RUNX1 was seen in the presence of negative amino acids. This suggests a regulation of the DNA binding activity of RUNX1 proteins through acidic amino acid residues possibly provided by activation domains of transcriptional co-regulators that interact with RUNX1.

The use of the anomalous signal from halide ions has become a powerful technique for obtaining phase information. By replacing the sodium chloride with potassium bromide in the crystallisation conditions of the RD, we could demonstrate in a single wavelength anomalous diffraction (SAD) experiment that the anomalous signal from 2 bromide ions were sufficient to phase a 16 kDa protein. Due to lack of completeness in the low-resolution shells caused by overloaded intensities, density modification schemes failed and the resulting electron density maps were not interpretable. By combining the highresolution

synchrotron data with low-resolution data from a native data set collected on a home X-ray source, the density modified bromide phases gave easily traceable maps.

Let It Run is the story of Oakley Isom, a neurotic, disturbed young woman stuck in a small town of two thousand people where she lives with her father, Waldemyre, a fly-fishing guide. Oakley works at the local newspaper as the editor of the "What's Biting?" section, something the fishermen live by. Oakley also works nights at a therapeutic boarding school for troubled youth. Entrenched in a world of self-loathing and obsessive thoughts, Oakley spends her time dreaming of a way out of Victor, Idaho. When a murder in the small town pulls Oakley into its eddy, she attempts to escape into her own compulsive thoughts, and the friendship of a striking young therapist at the boarding school. Unusual events continue to unfold, reeling Oakley in, and she must face a reality far more disturbing than a killer on the loose. Cosmic bottom line, the dissertation novel is about the issues of human identity, and if memory is fixed or dynamic, unified or multiple—and how readers deal with loss, guilt, and regret.

This is a full-length novel with a critical afterward. Run Me Dusk is a falling-out of love narrative about twenty-seven-year-old Milo who, after being broken up with by his boyfriend Red, flees from Illinois back to his hometown in southwestern Colorado to meditate on his place and purpose in life. The themes covered in this book are gay relationships, family relationships, mortality, and the natural world.