Many polypeptide growth factors act by binding to cell surface receptors that have intrinsic tyrosine kinase activity. Binding of these growth factors to their cognate receptors results in the initiation of mitogenic signals which then get transduced to the interior of the cell. A critical target for extracellular signals is the nucleus. A plethora of recent evidence indicates that extracellular signals can affect nuclear gene expression by modulating transcription factor activity. In this study, I have determined that the transactivation domain of c-Myc (protein product of the c-myc proto-oncogene) is a direct target of mitogen-activated signaling pathways involving protein kinases. Further, my study demonstrates that transactivation of gene expression by c-Myc is regulated as a function of the cell cycle. c-Myc is a sequence-specific DNA binding protein that forms leucine zipper complexes and can act as a transcription factor. Although, significant progress has been made in understanding the cellular properties of c-Myc, the precise molecular mechanism of c-Myc function in oncogenesis and in normal cell growth is not known. I have focused my attention on the property of c-Myc to function as a sequence-specific transcription factor. In my studies, I have employed a fusion protein strategy, where the transactivation domain of the transcription factor c-Myc is fused to the DNA binding domain and nuclear localization signal of the yeast transcription factor GAL4. This fusion protein was expressed together with a plasmid consisting of specific GAL4 binding sites cloned upstream of a minimal E1b promoter and a reporter gene. The activity of the c-Myc transactivation domain was measured as reporter gene activity in cell extracts. This experimental approach enabled me to directly monitor the activity of the c-Myc transactivation domain. Results listed in Chapter II demonstrate that the transactivation domain of c-Myc at Ser-62 is a target of regulation by mitogen-stimulated signaling pathways. Furthermore, I have determined that a mitogen activated protein kinase, p41mapk, can phosphorylate the c-Myc transactivation domain at Ser-62. Phosphorylation at this site results in a marked increase in transactivation of gene expression. A point mutation at the MAP kinase phosphorylation site (Ser-62) causes a decrease in transactivation. c-Myc expression is altered in many types of cancer cells, strongly implicating c-myc as a critical gene in cell growth control. The molecular mechanisms by which c-Myc regulates cellular proliferation are not understood. For instance, it is not clear where in the cell cycle c-Myc functions and what regulates its activity. In exponentially growing cells, the expression levels of c-Myc remain unchanged as the cells progress through the cell cycle. The function of c-Myc may therefore be regulated by a mechanism involving a post-translational modification, such as phosphorylation. Results described in chapter IV demonstrate that the level of c-Myc mediated transactivation oscillates as cells progress through the cell cycle and was greatly increased during the S to G2/M transition. Furthermore, mutation of the phosphorylation site Ser-62 in the c-Myc transactivation domain diminishes this effect, suggesting a functional role for this phosphorylation site in the cell cycle-specific regulation of c-Myc activity. Taken together, my dissertation study reveals a molecular mechanism for the regulation of nuclear gene expression in response to mitogenic stimuli.

No description available.

Duchenne Muscular Dystrophy (DMD) is a disorder caused by loss-of-function mutations in dystrophin, a critical protein that maintains muscle fiber integrity. Our lab discovered that dystrophin-deficient skeletal muscle stem cells, also known as satellite cells, cannot generate enough myogenic progenitors for proper muscle regeneration. Previously, we demonstrated that WNT7A, a protein expressed during muscle regeneration, stimulates symmetric division of satellite cells, and gives rise to two daughter satellite cells. Conversely, epidermal growth factor (EGF) induces asymmetric division, which generates one daughter satellite cell and one committed precursor cell. We aimed to investigate these satellite cell division mechanisms following WNT7A or EGF treatment in a human model using healthy and DMD-patient derived hiPSCs differentiated into the myogenic lineage. The presence of satellite-like cells was confirmed in both lines by their characteristic expression of PAX7 and other myogenic markers. Intriguingly, DMD-patient hiPSCs precociously differentiated compared to healthy control human induced pluripotent stem cells (hiPSCs). More notably, WNT7A treatment had a potent effect on the DMD differentiated cells. High content analysis revealed an expansion of the satellite-like cell pool as observed by a higher number of PAX7+ cells within the total population and gene expression analysis demonstrated a significant increase in global PAX7 expression. In contrast, EGF treatment reduced the number of PAX7+ cells and increased the proportion of MYOG+ cells within the myogenic population, indicating an increase in myogenic progenitors. Taken together, WNT7A and EGF can alter the myogenic differentiation program of healthy and DMD-patient derived hiPSCs by modulating the satellite-like cell division dynamics.

Indiana University-Purdue University Indianapolis (IUPUI) / A crucial task in computer vision and biomedical image applications is to represent images in a numerically compact form for understanding, evaluating and/or mining their content. The fundamental step of this task is the segmentation of images into regions, given some homogeneity criteria, prior appearance and/or shape information criteria. Specifically, segmentation of cells in microscopic images is the first step in analyzing many biomedical applications. This thesis is a part of the project entitled "Construction and profiling of biodegradable cardiac patches for the co-delivery of bFGF and G-CSF growth factors" funded by National Institutes of Health (NIH). We present a method that simultaneously segments the population of cells while partitioning the cell regions into cytoplasm and nucleus in order to evaluate the spatial coordination on the image plane, density and orientation of cells. Having static microscopic images, with no edge information of a cytoplasm boundary and no time sequence constraints, traditional cell segmentation methods would not perform well. The proposed method combines deformable models with a probabilistic framework in a simple graphical model such that it would capture the shape, structure and appearance of a cell. The process aims at the simultaneous cell partitioning into nucleus and cytoplasm. We considered the relative topology of the two distinct cell compartments to derive a better segmentation and compensate for the lack of edge information. The framework is applied to static fluorescent microscopy, where the cultured cells are stained with calcein AM.

No description available.

La plupart des espèces bactériennes possèdent un chromosome circulaire qui est répliqué de façon bidirectionnelle au cours du cycle cellulaire. Bien que la réplication et la ségrégation du chromosome bactérien se développent simultanément, la ségrégation du chromosome s’accomplit après la fin de la réplication et avant la fermeture du septum. La circularité du chromosome bactérien et le grand nombre d’événements de recombinaison homologue donnent lieu à la création des dimères de chromosome dans une fraction de la population cellulaire. Chez Escherichia coli et Bacillus subtilis, la dimérisation des chromosomes se produit respectivement dans 15% et 25% des cas. Un chromosome dimérique doit être résolu avant la fermeture du septum. Chez les espèces bactériennes les plus étudiées, les chromosomes dimériques sont résolus par un système de recombinaison site spécifique hautement réservé incluant deux recombinases à tyrosine, XerC et XerD, et un site génomique dans la région terminus du génome bactérien, appelé le site dif (deletion induced filamentation). L’organisation spatio-temporelle du système de recombinaison site spécifique Xer/dif et l’activation de ce dernier sont réglementées par la protéine transmembranaire impliquée dans la division cellulaire, FtsK. D’autre part, des études récentes ont mis en évidence l’existence de plusieurs éléments mobiles appelés IMEXs (Integrative Mobile Elements Exploiting Xer), capables d’exploiter le système Xer/dif pour leur intégration dans le génome bactérien. Chez E. coli, des déficiences dans la résolution des dimères de chromosome se terminent par le guillotinage du chromosome dimérique au cours de la division cellulaire, ce qui entraîne l’induction de la réponse SOS chez les cellules filles et la mort de ces dernières. Dans cette thèse, le site dif a été identifié et caractérisé chez Caulobacter par une combinaison d’approches in vivo et in vitro. Fait intéressant, il a été démontré que chez Caulobacter, contrairement à E. coli, la perturbation du système Xer/dif ne mène pas au guillotinage du chromosome, et les cellules portant un système Xer/dif défectueux contourne cette déficience en adoptant un nouveau mode de cycle cellulaire. De plus, notre analyse comparative entre les terminus des souches sauvages de C. crescentus a également permis de révéler la présence d’un IMEX putatif de 71 kb dans le terminus de C. crescentus NA1000. / Most bacteria possess a single circular chromosome which is replicated bidirectionally during the cell cycle. Although replication and segregation of the chromosome in bacteria develops simultaneously, the segregation of the chromosome occurs after the completion of replication and before the closure of the septum. The circularity of the bacterial chromosome and the high number of homologous recombination events that occur during replication result in the creation of chromosome dimers in a fraction of the cell population. In Escherichia coli and Bacillus subtilis, chromosome dimer formation occurs, respectively, in 15% and 25% of the cell population during replication, which needs to be resolved before the closure of division septum. In most of the well-studied bacterial species, chromosome dimers are resolved by a highly conserved site-specific recombination system which employs two tyrosine recombinases, XerC and XerD, and a recombination genomic site located in the terminus region of the bacterial chromosome called dif (deletion induced filamentation). The temporo-spatial organization of the Xer/dif site-specific recombination system, along with its activation, is regulated by a cell division transmembrane protein, FtsK. In E. coli, deficiencies in the resolution of chromosome dimers result in the guillotining of the dimeric chromosome during the cell division leading to the continuous induction of SOS response in the daughter cells and the death of the latter ones. In my thesis, the dif site in Caulobacter is identified and characterized by a combination of in vitro and in vivo approaches. Interestingly, it was observed that, unlike E. coli, in Caulobacter perturbations in the chromosome dimer resolution system do not result in the guillotining of the chromosome dimers. Instead, Caulobacter cells bearing deficiencies in the resolution of dimeric chromosomes adopt a new mode of cell cycle to bypass this deficiency.

No description available.

Hematopoietic stem cells (HSCs) are critical to the development of the hematopoietic system during ontogeny and maintaining hematopoiesis under steady-state. Several genes implicated in asymmetric cell division (ACD) have been found to influence HSC self-renewal in normal hematopoiesis and various leukemias. From a separate survey of genes associated with ACD, I now present the results from dedicated functional studies on two genes – Arhgef2 and Staufen1 – in HSCs and identify their potential contributions to benign hematopoietic disorders. Specifically, I present evidence that demonstrates a conserved role of Arhgef2 in orienting HSC division, the loss of which leads to HSC exhaustion that may underlie and contribute to the pathogenesis of Shwachman-Diamond syndrome. I also identify Staufen1 as a critical RNA-binding protein (RBP) in HSC function, downregulation of which elicits expression signatures consistent with clinical anemias reminiscent of aplastic anemia and/or paroxysmal nocturnal hemoglobinuria. I end by reviewing how RBPs function in HSCs and discuss future research directions that could further elucidate how bone marrow failure syndromes arise at the stem cell level. / Thesis / Doctor of Philosophy (PhD)

During embryogenesis, a single cell gives rise to a multi-cellular embryo through successive rounds of cell division. As cells become smaller, cellular organelles adapt their sizes accordingly. The size of the mitotic spindle—the microtubule-based structure controlling these divisions—is particularly important as it determines the distance over which chromosomes are segregated. To perform its function properly, spindle size scales with cell size. However, we still lack a mechanistic understanding of the underlying microtubule-based processes that regulate spindle scaling. In this thesis, I combined quantitative microscopy and laser ablation in zebrafish embryos and Xenopus laevis egg extract encapsulated in oil droplets. My measurements revealed the influence of microtubule length dynamics, transport, and nucleation on cell size-dependent spindle scaling. Strikingly, I discovered a hierarchical regulation of spindle size. In large cells, microtubule nucleation exclusively scales spindle size relative to cell size by changing the number of microtubules within the spindle. In small cells, microtubule dynamics fine-tune spindle size by modulating microtubule length. To understand the mechanism of spindle scaling, I proposed a theoretical model based on a limiting number of microtubule nucleators and microtubule-associated proteins that regulate microtubule length. The transition from nucleation- to dynamics-based scaling requires that microtubule number and the number of microtubule-associated proteins that promote microtubule growth scale differently with cell size. This can be achieved by sequestering an inhibitor of microtubule nucleation to the cell membrane, which is consistent with my measurements of microtubule nucleation. The differential regimes of spindle scaling modulated by microtubule nucleation and dynamics imply a gradual change in spindle architecture, which may ensure faithful chromosome segregation by spindles of all sizes.

The PhD thesis is on the studsy of the influence of the ftsZ antisense RNA and FtsH protease on the synthesis and function of the Escherichia coli cytokinetic protein, FtsZ, which mediates septation during cell division. Thus, it involves three molecules, FtsZ, ftsZ antisense RNA, and FtsH protease. While the E. coli ftsZ antisense RNA is being identified and structurally and functionally characterised for the first time, there has been some earlier studies in the laboratory in which the FtsH protease was found to have influence on the presence of the FtsZ rings at the mid-cell site. The Chapter 1 is the Introduction to the thesis presented in 3 parts –Part 1A, 1B, and 1C, introducing FtsZ and bacterial cell division, bacterial antisense RNAs, and FtsH protease, respectively. The Chapter 2 gives the description of the Materials and Methods used in the study. The Chapter 3 presents the identification, structural and functional characterisation of the ftsZ cis-antisense RNA, and its role in the regulation of FtsZ protein levels. Initially, the expression of cis-encoded antisense RNA from E. coli ftsZ loci was demonstrated during the different growth phases of the bacterium (RT-PCR/qPCR data). Antisense RNA is expressed from three promoters (primer extension and promoter probe data) on the complementary strand of the ftsZ coding region and terminates at the singletrand te complementary toftsAthegenethat 3’islocatedregionupstreamof theofftsZ the gene. Induced overexpression of a portion (423 bp) of the antisense RNA, spanning the ftsZ AUG codon and the ribosome binding site of ftsZ mRNA, from pBS(KS) could downregulate the synthesis of FtsZ protein to approximately 30%, leading to cell division arrest and filamentation of the cells at 42°C. This effect was less dramatic at 30ºC, probably due to less melting of the antisense RNA. Immunostaining performed on the induced culture did not show FtsZ ring formation after overnight induction whereas reduction in the proportion of the cells carrying FtsZ rings could be clearly observed after 2 hrs of induction. Real time PCR analysis performed for relative quantitation of ftsZ mRNA and ftsZas RNA from different growth phases (0.2 to 2.5 OD600 nm) showed growth phase dependent expression of the antisense RNA. While the levels of ftsZas RNA were found to be high at lower OD cultures or early growth phase cultures, the levels were found to be low at the late log phase and stationary phase cultures. Thus, when the cells are actively dividing and therefore need more FtsZ, the levels of the ftsZas RNA are high, while the cells are not actively dividing and therefore the FtsZ levels are low, the levels of the ftsZas RNA are low. At any phase of the growth, the ratio of the ftsZ mRNA to the ftsZas RNA was always found to be 6:1. Thus, the physiological role the ftsZas RNA is to maintain the availability of the ftsZ mRNA at a level that is commensurate with the requirement for the FtsZ protein during the different stages of the cell growth and division. The Chapter 4 is on the study of the possible mechanism behind the influence of FtsH protease on the presence of FtsZ rings at the mid-cell site during septation in cell division. Immunostaining for FtsZ in the mid-log phase E. coli cells showed that 82% of the AR3289 (ftsH wild type) cells possessed FtsZ rings, while only 18% of the AR3291 (ftsH-null maintained viable by a suppressor mutation) cells showed Z-rings. While the AR3289 cells showed a cell doubling time of 20 min, the AR3291 cells had a cell doubling time of 45 min. The mass doubling time of AR3289 and AR3291 were 24 min and 54 min, respectively. These distinct differences were found in spite of the suppressor mutation suppressing all the deleterious effects of the lack of the essential protease, FtsH. Complementation of the ftsH-null cells (AR3291) with the wild type FtsH but not with the ATP-binding or ATPase, or protease-defective mutants of FtsH, restored the FtsZ ring status to about 80% of the cells. The growth rate of AR3291 was also partly restored to comparable to that of the wild type cells upon complementation. Western blotting for FtsZ, and the FtsZ-stabilising proteins, FtsA and ZipA, showed that the ftsH-null cells have low levels of FtsA, as compared to those in the isogenic wild type cells (AR3289). The levels of FtsZ and ZipA were comparable in both the cells. Quantitative PCR performed for different cell division genes within the dcw cluster showed no sign of change in the ftsA transcript levels in the ftsH-null cells, suggesting that the low levels of FtsA in the ftsH-null cells were not due to transcriptional downregulation. Further experiments showed that the half-life of FtsA protein in the AR3289 cells was 45 min, while that in the AR3291 cells was 24 min. This experiment showed that the low levels of FtsA in the ftsH-null cells was due to the low half-life of FtsA in the cells. Growth synchronisation of the AR3289 and AR3291 cells showed that the levels of FtsA prior to cell division stage do not increase in the ftsH-null cells as much as in the isogenic wild type cells. Thus, the ftsH-null cells must be somehow managing the division through the partial stabilisation of FtsZ rings by ZipA. Interestingly, immunostaining for FtsH in AR3289 cells showed the presence of FtsH at the mid-cell site, as co-localised with FtsZ, for a brief period prior to cell constriction. These observations suggest the involvement of FtsH in cell division process. The faster degradation of FtsA in the absence of FtsH protease implies that another protein, which may be a protease that directly degrades FtsA or a chaperone that helps the unfolding of FtsA for degradation, might be the substrate of FtsH protease. The absence of FtsH protease brings up the levels of this unknown protein, which in turn facilitates (if it is a chaperone) degradation of or directly degrades (if it is a protease) FtsA. This model for the link among FtsH, FtsA levels, and the presence of FtsZ has been proposed based on the observations. Thus, the present study reveals for the first time an FtsA-linked role for FtsH protease in the presence of FtsZ ring at the mid-cell site and hence in bacterial septal biogenesis. The thesis is concluded with the list of salient findings, publications, and references.