Gotowa bibliografia na temat „Metazoan development”

In this review, we consider transformations of axial symmetry in metazoan evolution and development, the genetic basis, and phenotypic expressions of different axial body plans. In addition to the main symmetry types in metazoan body plans, such as rotation (radial symmetry), reflection (mirror and glide reflection symmetry), and translation (metamerism), many biological objects show scale (fractal) symmetry as well as some symmetry-type combinations. Some genetic mechanisms of axial pattern establishment, creating a coordinate system of a metazoan body plan, bilaterian segmentation, and left–right symmetry/asymmetry, are analysed. Data on the crucial contribution of coupled functions of the Wnt, BMP, Notch, and Hedgehog signaling pathways (all pathways are designated according to the abbreviated or full names of genes or their protein products; for details, see below) and the axial Hox-code in the formation and maintenance of metazoan body plans are necessary for an understanding of the evolutionary diversification and phenotypic expression of various types of axial symmetry. The lost body plans of some extinct Ediacaran and early Cambrian metazoans are also considered in comparison with axial body plans and posterior growth in living animals.

Communication among cells was paramount to the evolutionary increase in cell type diversity and, ultimately, the origin of large body size. Across the diversity of Metazoa, there are only few conserved cell signalling pathways known to orchestrate the complex cell and tissue interactions regulating development; thus, modification to these few pathways has been responsible for generating diversity during the evolution of animals. Here, we summarize evidence for the origin and putative function of the intracellular, membrane-bound and secreted components of seven metazoan cell signalling pathways with a special focus on early branching metazoans (ctenophores, poriferans, placozoans and cnidarians) and basal unikonts (amoebozoans, fungi, filastereans and choanoflagellates). We highlight the modular incorporation of intra- and extracellular components in each signalling pathway and suggest that increases in the complexity of the extracellular matrix may have further promoted the modulation of cell signalling during metazoan evolution. Most importantly, this updated view of metazoan signalling pathways highlights the need for explicit study of canonical signalling pathway components in taxa that do not operate a complete signalling pathway. Studies like these are critical for developing a deeper understanding of the evolution of cell signalling. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.

The chromatin environment plays a central role in regulating developmental gene expression in metazoans. Yet, the ancestral regulatory landscape of metazoan embryogenesis is unknown. Here, we generate chromatin accessibility profiles for six embryonic, plus larval and adult stages in the sponge Amphimedon queenslandica. These profiles are reproducible within stages, reflect histone modifications, and identify transcription factor (TF) binding sequence motifs predictive of cis-regulatory elements operating during embryogenesis in other metazoans, but not the unicellular relative Capsaspora. Motif analysis of chromatin accessibility profiles across Amphimedon embryogenesis identifies three major developmental periods. As in bilaterian embryogenesis, early development in Amphimedon involves activating and repressive chromatin in regions both proximal and distal to transcription start sites. Transcriptionally repressive elements (“silencers”) are prominent during late embryogenesis. They coincide with an increase in cis-regulatory regions harboring metazoan TF binding motifs, as well as an increase in the expression of metazoan-specific genes. Changes in chromatin state and gene expression in Amphimedon suggest the conservation of distal enhancers, dynamically silenced chromatin, and TF-DNA binding specificity in animal embryogenesis.

Morphologically complex metazoans appear abruptly during the Cambrian explosion. Suggested measures of metazoan complexity include number of cell morphotypes and aspects of the genome such as the amount of DNA, the number of genes, and the information content of the genome or egg. Estimates of gene numbers are now available for metazoan species belonging to five different phyla or subphyla. There is little correlation between gene number and morphological complexity in the invertebrates: relatively complex forms can have fewer genes than relatively simple forms. Presumably, the more complex forms use more gene-expression events during development, implying that, on average, cis-regulatory elements of more complex invertebrates are richer in binding sites than are those of simpler forms. Vertebrates have many more genes than invertebrates and therefore have more total gene-expression events during development, although they may have, on average, fewer expression events per gene than the invertebrates. There are thus two genomic pathways in the evolution of metazoan complexity: one involves increasing the number of genes, the other involves increasing the number of cis-regulatory binding sites. Both modes were associated with the origin of bodyplans that first appear as fossils during the Cambrian explosion.

Despite large changes in salt intake, the mammalian kidney is able to maintain the extracellular sodium concentration and osmolarity within very narrow margins, thereby controlling blood volume and blood pressure. In the aldosterone-sensitive distal nephron (ASDN), aldosterone tightly controls the activities of epithelial sodium channel (ENaC) and Na,K-ATPase, the two limiting factors in establishing transepithelial sodium transport. It has been proposed that the ENaC/degenerin gene family is restricted to Metazoans, whereas the α- and β-subunits of Na,K-ATPase have homologous genes in prokaryotes. This raises the question of the emergence of osmolarity control. By exploring recent genomic data of diverse organisms, we found that: 1) ENaC/degenerin exists in all of the Metazoans screened, including nonbilaterians and, by extension, was already present in ancestors of Metazoa; 2) ENaC/degenerin is also present in Naegleria gruberi , an eukaryotic microbe, consistent with either a vertical inheritance from the last common ancestor of Eukaryotes or a lateral transfer between Naegleria and Metazoan ancestors; and 3) The Na,K-ATPase β-subunit is restricted to Holozoa, the taxon that includes animals and their closest single-cell relatives. Since the β-subunit of Na,K-ATPase plays a key role in targeting the α-subunit to the plasma membrane and has an additional function in the formation of cell junctions, we propose that the emergence of Na,K-ATPase, together with ENaC/degenerin, is linked to the development of multicellularity in the Metazoan kingdom. The establishment of multicellularity and the associated extracellular compartment (“internal milieu”) precedes the emergence of other key elements of the aldosterone signaling pathway.

Cell cycle investigations have focused on relentless exponential proliferation of cells, an unsustainable situation in nature. Proliferation of cells, whether microbial or metazoan, is interrupted by periods of quiescence. The vast majority of cells in an adult metazoan lie quiescent. As disruptions in this quiescence are at the foundation of cancer, it will be important for the field to turn its attention to the mechanisms regulating quiescence. While often presented as a single topic, there are multiple forms of quiescence each with complex inputs, some of which are tied to conceptually challenging aspects of metazoan regulation such as size control. In an effort to expose the enormity of the challenge, I describe the differing biological purposes of quiescence, and the coupling of quiescence in metazoans to growth and to the structuring of tissues during development. I emphasize studies in the organism rather than in tissue culture, because these expose the diversity of regulation. While quiescence is likely to be a primitive biological process, it appears that in adapting quiescence to its many distinct biological settings, evolution has diversified it. Consideration of quiescence in different models gives us an overview of this diversity.

Patterns of variability in growth, development and mortality in early life histories were examined at two levels--general and specific. At the general level, I examined the functional significance of larvae in metazoan life cycles. This was achieved by surveying the metazoa at the class level and categorizing mode of development by habitat. Three long-standing hypotheses for the paucity of larval development in fresh water were rejected. I argue that viewing metazoan larvae as a means for feeding and growth provides a unifying framework for evaluating the features of habitats which correlate with the range of variation expressed in development modes. I offer a modelling framework to investigate variation in developmental modes within and between habitats. The suggested model requires input on larval growth rates, larval period duration (development time), and size-specific mortality rates. These variables, and the interactions between them, are also central to the specific analysis which addresses the ecological processes and mechanisms which affect survival and hence recruitment during the early life histories periods of marine fishes. Winter flounder (Pleuronectes americanus) was used as a model species to investigate phenotypic variability in patterns of growth and development and their survival consequences. Using laboratory-reared fish, I demonstrate that size-at-age does not diverge continuously during the larval and juvenile periods. The results show that fish which grow slowly as larvae, compensate for their slow growth by growing rapidly as juveniles. This compensation in growth rate causes juvenile size-at-age to converge, or at least, prevents divergence in juvenile size-at-age. In addition, I provide some of the first estimates of individual variability in larval growth trajectories for a marine fish. I conducted the first experiment which separates the effects of both size and age on the vulnerability to predation in recently metamorphosed fishes. Th

There are major gaps in our understanding of the evolution of microRNA (miRNA) genes and how this relates to evolutionary changes in metazoan development. miRNAs function as trans-acting post-transcriptional modulators of gene expression. They are implicated in the canalization of development and the consequent provision of evolvability. Here I present data and analyses on miRNA evolution in insects and mammals, both on a phylogenetic scale as well as at the level of individual miRNA genes. I also perform case studies cross-comparing the expression and functions of intronic miRNAs to those of their host genes, and compare tissue-specific enrichment of miRNAs in a specific tissue (butterfly ovary) relative to the whole body. A broad overview of miRNA evolution across a clade is presented for the Lepidoptera using a combination of small RNA sequencing in two lepidopteran species coupled with bioinformatic analysis of available genomic and miRNA data across the clade. This analysis reveals a burst of rapid miRNA gain on the stem lineage of the Lepidoptera prior to the radiation of the diverse butterfly and moth lineages. I also propose that the uneven distribution of miRNA gain across the lepidopteran phylogeny, coupled with observations of high numbers of newly-emergent miRNAs on terminal branches, is evidence for a model of miRNA evolution comprising high rates of turnover for newly-acquired miRNAs with variable rates of stable miRNA retention. In depth examination is carried out on two miRNA genes, both of which occur within homeobox gene introns - eutherian-specific mir-615 and lepidopteran-specific mir-2768. Phylogenetic distribution and theories for the acquisition of mir-615 in Eutheria are considered. A combination of publicly available expression data and epigenetic modification data is used to demonstrate the existence of transcriptional regulation for mir-615 independent from that of its host gene. The study of mir-2768 reveals the first experimental evidence for an intronic miRNA performing a complementary function to that of its host gene. I also present the first miRNA transcriptome from a butterfly ovary and compare this to whole-body miRNA expression in the same species. This provides insights into the roles performed by miRNAs in the butterfly ovary, including conserved functions, and enables comparison of ovarian miRNA tissue specificity relative to time of origin. Overall, this work provides a multi-faceted analysis of miRNA evolution in animals and presents an integrated approach to our understanding of the roles of miRNAs in evo-devo.

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

El origen de la multicelularidad animal tiene sus raíces en el proceso de división celular. Conocer las bases moleculares del control de la divisón celular en animales y en sus parientes unicelulares tiene el potencial de permitirnos comprender qué cambios ocurrieron para permitir el origen de la multicelularidad. Sin embargo, nuestra capacidad experimental en los parientes unicelulares de los animales está bastante limitada. En esta tesis se ha contribuido al desarrollo de la especie Capsaspora owczarzaki como un organismo modelo, al desarrollar herramientas genéticas de transfección y herramientas de sincronización de ciclo celular. La caracterización del ciclo celular de Capsaspora ha permitido saber que muchos genes importantes en el ciclo celular de animales también poseen actividad transcripcional en Capsaspora, incluyendo los ortólogos principales de las ciclinas y CDKs de animales. Asimismo, el desarrollo de herramientas de transfección abre la puerta a nuevos estudios funcionales a nivel molecular en esta especie, lo cual podrá permitir conocer las funciones de muchos genes relacionados con la multicelularidad animal en el contexto de una especie unicelular.
The origin of animal multicellularity has its roots in the process of cell division. Understanding the molecular basis of cell division in animals and their unicellular relatives has the potential to elucidate what changes in the control of cell division played a role, if any, in the transition to multicellularity. However, the experimental amenability of the closest relatives of animals is yet very limited. This thesis contributes to the development of Capsaspora owczarzaki, a close unicellular relative of animals, as a model organism, by developing genetic tools for DNA transfection and culture synchronization tools to study the cell cycle. Our characterization of the Capsaspora cell cycle revealed that many genes important in the cell cycle of animal cells are also transcriptionally regulated in Capsaspora, including the main orthologs of animal cyclins and CDKs present in Capsaspora. Likewise, the development of genetic tools opens the door to new functional studies in this species, which will allow to understand the role of many genes related to multicellularity under the context of a unicellular species.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2004.
Includes bibliographical references.
The process of gene amplification in Drosophila ovaries provides a means of increasing the amount of template for transcription, thus increasing the amount of protein that can be made over a short developmental period. At a specific developmental point (egg chamber stage l0B-13), several clusters of genes encoding the eggshell (chorion) proteins in the follicle cells of each egg chamber are overreplicated 20 or 60 fold (for the X chromosome and third chromosome amplicons, respectively). Gene amplification is accomplished using the normal eukaryotic DNA replication machinery and a bidirectional DNA replication mechanism, and as such, is a powerful system for the study of metazoan DNA replication. Furthermore, the nature of the ovaries, with egg chambers of various ages arrayed in the order they were created, coupled with the use of cell biology, allows for the visualization of gene amplification at multiple timepoints in a single sample. We employed confocal and deconvolution microscopy to visualize the replication proteins ORC2, DUP/Cdtl, PCNA, and MCM2-7, as well as the nucleotide analog BrdU, at sites of gene amplification. These studies revealed that the BrdU staining pattern resolves from a focus of incorporation at the third chromosome locus in egg chamber stage lOB, to a coffee-bean structure in stage 11 egg chambers, to a double-bar structure in egg chamber stages 12 and 13. When coupled with quantitative real-time PCR calculations of copy number at the third chorion cluster during egg chamber stages lOB-13, these studies demonstrated that amplicon origin firing ends by stage 11 and that only the existing replication forks move out during stages 12 and 13 to produce the double bar BrdU pattern.
(cont.) The localization patterns of replication initiation and elongation factors also support this model. The initiation protein, ORC2 is only found in foci during stages 1OA to 11, while the elongation factors PCNA and MCM2-7 resolved from foci at origins in stage lOB into the double bar staining structure representing replication forks in stages 12 and 13, similar to BrdU. We also observed that the replication initiation factor DUP/Cdtl colocalized with BrdU throughout amplification, and resolved into double bars, suggesting that DUP/Cdtl travels with replication forks during elongation. We hypothesize that DUP/Cdtl may be necessary for the nuclear trafficking and/or the adherence of the MCM2-7 to replicating DNA. In sum, this work has increased our understanding of the process of gene amplification and has provided a powerful tool for the study of replication fork progression and the proteins involved, an aspect of replication that has proven difficult to examine in vivo in other systems. Related BrdU studies revealed that there were two uncharacterized amplified regions in the follicle cells, thus we devised a comparative genomic hybridization microarray approach to systematically identify amplified portions of the genome. This approach identified the two uncharacterized amplicons, at cytological positions 62D5 and 30B 10. Using FISH/BrdU co-labeling and real-time PCR, we verified that these regions were amplified over a 75-100kb region. The new amplicon DAFC-62D was shown to have a final origin firing in stage 13, a time when the other amplicons are only elongating ...
by Julie Michelle Claycomb.
Ph.D.

Les éponges (Porifera) sont l'une des premières lignées d'animaux à avoir émergé. De ce fait, elles sont considérées comme des espèces clés pour retracer l’origine et l'évolution des gènes et des voies de signalisation qui ont sous-tendu l'apparition de la pluricellularité chez les métazoaires. Entre autres, les voies Wnt ont été décrites comme des cascades génétiques essentielles du control de nombreux mécanismes cellulaires (prolifération, communication, adhésion, motilité, etc.) au cours du développement précoce des bilatériens et des cnidaires. C’est pourquoi, l'étude de ces voies, chez les lignées d’émergences plus anciennes sont essentielles afin de comprendre l'origine des plans d’organisation des animaux.J’ai alors entrepris de nombreuses analyses bioinformatiques sur différentes bases de données d’éponges. Il apparait alors que l’ancêtre commun des éponges possédait déjà certainement tous les composants des voies Wnt. Néanmoins, à ce jour, puisque l’intégralité de ces composants n’a été identifiée que dans le genre Oscarella (lignée des Homoscleromorpha), différentes pertes secondaires sembleraient s’être produites chez les démosponges, les éponges calcaires et les hexactinellides. Afin de tester si ces gènes orthologues sont impliqués dans la mise en place du plan d’organisation des éponges, des études fonctionnelles ont été mises en œuvre. Ces approches fonctionnelles réalisées sur deux lignées d’éponges différentes tendent alors à confirmer la conservation des voies de signalisation Wnt dans les processus de mise en place des plans d’organisation des animaux, à la fois au cours de l'embryogenèse mais aussi lors du renouvellement cellulaire chez l'adulte
Sponges (Porifera) are one of the earliest emerged animal lineages. They are thus considered as key species to retrace early evolution of genes and pathways underlying the emergence of multicellularity in metazoans. Among others, the Wnt pathways have been described as crucial modules controlling cell proliferation, cell communication, cell adhesion and cell motility during the early development of Bilaterians and Cnidarians. Therefore the study of these signaling pathways in more basally branching lineages is essential for unraveling the origin of animal body plans. I performed numerous bioinformatic analyses on different poriferan databases. One of my main results is that the last common ancestor of Porifera probably already possessed all the components of the Wnt pathways. Nevertheless, because, to date, all these components were only retrieved in the Oscarella genus (Homoscleromorpha lineage), several secondary gene losses would have occurred in other sponge lineages, namely Demospongia, Calcarea and Hexactinellida.In order to test whether or not these retrieved orthologous genes, are involved in patterning sponge body plan (as they do in Bilateria and Cnidaria), functional studies were implemented. These functional studies performed on two different lineages tend to confirm that Wnt signaling pathways were conserved from sponges to vertebrates to pattern animal body plan during both embryogenesis and cell renewal in adult