Ca2+/Calmodulin-dependent protein kinase type II (CaMK-II) is a Serine/Threonine protein kinase that is activated by Ca2+ and Calmodulin to phosphorylate substrates involved in myriad developmental processes. This project implicates CaMK-II in specification of HSCs, and zebrafish provide an ideal embryonic model to study hematopoiesis. Zebrafish genetic manipulation was achieved through: incubation in chemical inhibitors; injection of notochord-targed WT and DN CaMK-II constructs with Transposase; and injection of camk2g1 translation-blocking morpholino antisense oligonucleotide (MO). Whole-mount in situ hybridization (WISH) and immunolocalization on zebrafish embryos allowed visualization of key HSC markers and pathway components that implicated CaMK-II in the specification of HSCs. CaMK-II is a negative regulator of shh expression during HSC specification, but CaMK-II does not influence Shh during its well-documented role in vasculogenesis. CaMK-II appears to affect the spatial distribution of Shh protein, which accumulates near the notochord source and differentially affects expression of Shh target genes based on their distance from the notochord. This project also identifies the specific timing requirement for CaMK-II during HSC specification, as inhibition of CaMK-II consistently reduces HSC specification, but only if administered before 18hpf. CaMK-II also downregulates ezh2 in the DA during the time of HSC specification, and the Ezh2 inhibition rescues the loss of HSCs, suggesting that CaMK-II regulates the secretion of Shh from the notochord to epigenetically regulate expression of key HSC specification genes in the DA through EZH2 methyltransferase.

The desmosome is one of the major cell adhesion junctions found in the epithelia, heart, and hair follicle. Described as a “rivet” that hold cells together, it provides these tissues with the integrity to withstand the tremendous forces they face in everyday life. Defects in this junction can lead to devastating diseases where patients are susceptible to skin infections and cardiovascular defects. Limited treatments exist for diseases of the desmosome, and strategies do not target all symptoms. Therefore, delineating the function and regulation of desmosomes is of paramount importance for the development of prevention and treatment strategies. The Xenopus laevis has been utilized for the study of embryonic development and tissue movements. This study takes advantage of the frog model to study a key desmosomal protein, desmoplakin (Dsp), in the epidermal development of the embryo. First, Xenopus embryonic epidermis has junctional desmosomes as early as the blastula stages. Desmosomes numbers per junction increase as the embryo develops. Dsp is present in many epidermally-derived structures in the embryo at varying levels. Xenopus embryos deficient in desmoplakin have phenotypic defects in epidermal structures and the heart, mimicking mammalian models. Embryos with reduced Dsp exhibit an increased susceptibility to epidermal damage under applied mechanical forces. Assays also reveal a potential role for desmosomes in radial intercalation, a process through which cells move from the inner to the outer epidermal layers. Embryos with reduced Dsp exhibit a slight reduction in intercalation and defects in intercalating cell types, including multiciliated cells and small secretory cells. Finally, c-Jun N-terminal kinase (JNK) may have a potential role in the regulation of desmosome assembly and adhesion. Embryos with deficient Dsp display a partial recovery of mechanical integrity when treated with a JNK inhibitor.

Thermogenic fat is a promising target for new therapies in diabetes and obesity. Understanding how thermogenic fat develops is important to develop rational strategies to treat obesity. Previously, we have shown that Tyk2 and STAT3, part of the JAK-STAT pathway, are necessary for proper development of classical brown fat. Using primary preadipocytes isolated from newborn mice we demonstrate that STAT3 is required for differentiation and robust expression of Uncoupling Protein 1. We also confirm that STAT3 is necessary during the early induction stage of differentiation and is dispensable during the later terminal differentiation stage. Without STAT3, the brown preadipocytes have increased apoptosis early in the terminal differentiation phase. We also show that the block in differentiation is caused by an inability of STAT3 knockouts to down regulate β-catenin by the end of the induction phase. Application of Wnt/β-catenin inhibitors or knockdown of β-catenin during the induction phase is sufficient to fully rescue differentiation of brown adipocytes from the Myf5+ lineage, including reduction in apoptosis, restoration of histone acetylation in the UCP1 promoter and enhancer regions, and full restoration of the expression of brown fat genes. Finally, we show that in the beige lineage, STAT3 is also necessary during the induction phase and can be rescued by Wnt/β-catenin inhibitors, although the rescue is not as robust as it is in the Myf5+ lineage.

In this thesis, several techniques were combined to optimize, evaluate and characterize craniofacial development in Xenopus, with additional focus on understanding the alterations made during maturation in the craniofacial region and the cartilage. Three important techniques used were: confocal microscopy in conjunction with Acridine Orange (AO) labeling, Alcian Blue (AB) labeling, and geometric morphometric analysis. I found that facial width increased across all techniques used to evaluate it. Included within this focus was the study of the development of the ceratohyal (CH) cartilage, which supported the mouth and snout. This was also found to increase width wise, in unison with facial and orofacial growth. This data may suggest a link between the face, mouth and CH growth, in which the developing cartilage elongates and widens causing the increase seen in the width and distension of the mouth.

Lung cancer is the leading cause of cancer-related death and the second most diagnosed cancer in the United States. Unfortunately, many patients either do not have any common mutations for which there are already targetable agents, or they eventually become resistant to these compounds. As such, there is a high demand for new, effective methods of treating this disease as well as predicting patient prognosis and potential benefit from chemotherapy. In this work, numerous strategies for treating lung cancer are explored. The first method described here is through the use of a pan-early 2 factor (E2F) inhibitor, HLM006474, which is shown to synergize with paclitaxel in non-small cell lung cancer (NSCLC). Next, we explored the creation and utilization of an E2F signature that is prognostic and predictive of early-stage NSCLC patient benefit from adjuvant chemotherapy (ACT). The third project examined possible targets to enhance sensitivity to cisplatin in NSCLC lacking Kirsten rat sarcoma viral oncogene homolog (KRAS) and epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma receptor tyrosine kinase (ALK) fusions (triple-negative), for which cisplatin is one of the few treatment options. These studies led to the identification of a kinase that is overexpressed in NSCLC and whose knockdown sensitizes cells to platinum agents.

Elastic fibres, a major component of many connective tissues, are composed of an amorphous elastin core surrounded by fibrillin - containing microfibrils. The function of these microfibrils appears to require the co - ordinated interactions of fibrillins with a range of extracellular matrix ( ECM ) macromolecules including, latent transforming growth factor - β ( TGF - β ) binding proteins ( LTBPs ). LTBPs share a high degree of structural similarity to fibrillins, since they both contain unique 8 - cysteine motifs. Of the four members of the LTBP family, LTBPs - 1, - 3 and - 4 covalently bind to latent forms of TGF - β. LTBP - 1 has been shown to interact with the N - terminal domains of fibrillin - 1 and - 2 and LTBP - 4 interacts with the N - terminal domains of fibrillin - 1, suggesting that fibrillin - containing microfibrils may act as TGF - β stores and localise latent TGF - β complexes to the ECM. LTBP - 2 differs from other members of the LTBP family since it does not covalently bind latent TGF - β. However, LTBP - 2 strongly co - localises with fibrillin - containing microfibrils in a number of tissues suggesting that LTBP - 2 could have a structural role associated with these elements presumably independent of TGF - β storage, or could act to mediate specific microfibril - ECM interactions. To understand more about the function of LTBP - 2, this study involved screening for potentially important molecular interactions of LTBP - 2 with fibrillins and a variety of ECM proteins. Human recombinant LTBP - 2 ( r - LTBP - 2 ) was cloned, expressed and purified using a mammalian cell culture system. Solid phase binding assays were used to screen for interactions between r - LTBP - 2 and continguous fragments of fibrillin - 1 and - 2 as well as MAGPs, tropoelastin, collagens and proteoglycans. A cation dependant interaction was found between the C - terminal domains of LTBP - 2 and the N - terminal domains of fibrillin - 1, but not with the analogous region of fibrillin - 2. Thus, LTBP - 2 seems to have an exclusive role associated with fibrillin - 1 - containing microfibrils. Further studies found that the C - terminal region of LTBP - 2 competes with LTBP - 1 for binding to fibrillin - 1, suggesting that the binding site for LTBP - 2 on fibrillin - 1 is the same or in close proximity to that for LTBP - 1. Immunohistochemical analysis of LTBP - 1 and - 2 within developing human aorta indicated that both LTBPs co - localised with fibrillin - 1. However, the two LTBPs did have distinct distribution patterns in relation to each other, in that LTBP - 2 was found throughout the medial layer whereas LTBP - 1 was mainly located in patches of the outer medial layer. No regions of strong co - localisation of the two LTBPs were found. Thus, these findings suggest that LTBP - 2 could indirectly modulate the presence of TGF - β upon the fibrillin - containing microfibrils by competing for binding with the LTBP- 1 / TGF - β complex to these structures. Other binding studies showed a cation independent interaction between r - LTBP - 2 and an as yet unidentified component of a crude bovine collagen - IV extract. Since collagen - IV is a major component of basement membranes, an interaction between r - LTBP - 2 and a protein within this bovine collagen - IV preparation suggests LTBP - 2 may have a further function involving a basement membrane component. It will be interesting to determine if LTBP - 2 acts as a bridging molecule between basement membrane structures and fibrillin - containing microfibrils or if it has another function independent of these microfibrils. / Thesis (Ph.D.)--School of Medical Sciences, 2006.

<p>The development of a multicellular organism is programmed by complex patterns of gene expression. In eukaryotic cells, genes are packaged by histone proteins into chromatin. Chromatin regulators often function as transcription co-factors. </p><p>In this study, we have investigated the function of four co-factors, dAda2b, Reptin, Ebi and Brakeless during development of the fruit fly<i> Drosophila</i> <i>melanogaster</i>. dAda2b and Reptin belong to histone acetyl transferase (HAT) complexes, a SAGA-like complex and the Tip60 complex, respectively. We generated <i>dAda2b </i>mutants and found that lack of dAda2b strongly affects global histone acetylation and viability. We further propose that Ada2 may be involved in DNA repair. Our studies revealed new roles of Reptin and other Tip60 complex components in Polycomb Group mediated repression and heterochromatin formation, thereby promoting generation of silent chromatin.</p><p>During embryogenesis, transcriptional repressors establish localized and tissue-specific patterns of gene expression. In this thesis, we identified two novel co-repressors in the early embryo, Ebi and Brakeless. Ebi genetically and physically interacts with the Snail repressor. The Ebi-interaction motif in the Snail protein is essential for Snail function<i> in</i> <i>vivo</i> and is evolutionarily conserved in insects. We further demonstrated that Ebi associates with histone deacetylase 3 (HDAC3) and that histone deacetylation is part of the mechanism by which Snail mediates transcriptional repression. </p><p>We isolated Brakeless in a genetic screen for novel regulators of gene expression during embryogenesis. We found that mutation of <i>brakeless</i> impairs function of the Tailless repressor. Brakeless associates with Atrophin, another Tailless corepressor, and they function together in Tailless-mediated repression. </p><p>In summary, transcription co-factors, including chromatin regulators, are selectively required in distinct processes during development.</p>

<p>In this project I have tried to obtain stable transformants of <em>Drosophila</em> melanogaster flies using electroporation. I have completed approximately 200 tests using different DNA concentrations, voltages and cuvettes, including a novel Petri dish cuvette which I developed and manufactured myself. I also developed new and more efficient procedures of egg collection and egg dechorionation. Although I was not  successful in obtaining true stable transformants, control experiments indicate that electroporation of DNA into embryos could be accomplished under the conditions used. The lack of stable transformants was probably due to failure of the electroporated DNA to integrate into the host genome. The reasons for why the DNA did not integrate was not further investigated in this study.</p>

In this thesis I present a language for instructing a sheet of identically-programmed, flexible, autonomous agents (``cells'') to assemble themselves into a predetermined global shape, using local interactions. The global shape is described as a folding construction on a continuous sheet, using a set of axioms from paper-folding (origami). I provide a means of automatically deriving the cell program, executed by all cells, from the global shape description. With this language, a wide variety of global shapes and patterns can be synthesized, using only local interactions between identically-programmed cells. Examples include flat layered shapes, all plane Euclidean constructions, and a variety of tessellation patterns. In contrast to approaches based on cellular automata or evolution, the cell program is directly derived from the global shape description and is composed from a small number of biologically-inspired primitives: gradients, neighborhood query, polarity inversion, cell-to-cell contact and flexible folding. The cell programs are robust, without relying on regular cell placement, global coordinates, or synchronous operation and can tolerate a small amount of random cell death. I show that an average cell neighborhood of 15 is sufficient to reliably self-assemble complex shapes and geometric patterns on randomly distributed cells. The language provides many insights into the relationship between local and global descriptions of behavior, such as the advantage of constructive languages, mechanisms for achieving global robustness, and mechanisms for achieving scale-independent shapes from a single cell program. The language suggests a mechanism by which many related shapes can be created by the same cell program, in the manner of D'Arcy Thompson's famous coordinate transformations. The thesis illuminates how complex morphology and pattern can emerge from local interactions, and how one can engineer robust self-assembly.

Drosophila male is an example of achiasmatic meiosis which lacks crossingover and chiasmata during meiosis. Previous studies showed that homologous pairing of both euchromatin and centromeres is lost during middle prophase I, however, homologs are still connected as they form bivalents. The X-Y pair utilizes a specific repeated sequence within the heterochromatic ribosomal DNA blocks as a pairing site. No pairing sites have yet been identified for the autosomes. To search for such sites, we utilized probes specifically targeting heterochromatin regions to assay pairing sequences and behavior in meiosis by fluorescence in situ hybridization (FISH). We found that the fourth homologs pair at the heterochromatic region 61 and associate with the X chromosome throughout prophase I. The pairing of the fourth homologs is disrupted in the homolog conjunction complex mutants. Conversely, six tested heterochromatic regions of the major autosomes (second and third chromosomes) have proved to be largely unpaired after early prophase I. This suggests that pairing mechanism of the major autosomes may differ from the sex and fourth chromosomes; stable connections between major autosomal homologs might occur at different sites along chromosomes in different cells by analogy to chiasmata. Moreover, FISH analysis also revealed two distinct patterns of sister chromatid cohesion in heterochromatin: regions with stable cohesion and regions lacking cohesion, suggesting that sister chromatid cohesion is incomplete within heterochromatin but with preferential sites in male meiosis.Modifier of Mdg4 in Meiosis (MNM) and Stromalin in Meiosis (SNM) are components of homolog conjunction complex and essential for homolog pairing and segregation in male meiosis. Using yeast two-hybrid assay and co-immunoprecipitation, we showed that the MNM and SNM interact with each other. Specifically, the BTB domain of MNM is responsible for the interaction with SNM, whereas FLYWCH domain of MNM is crucial for this interaction but does not directly interact with SNM. Additionally, point mutation analysis revealed that L9K replacement of the BTB domain weakened the MNM-SNM interaction and caused high frequencies of chromosome nondisjunction. In conclusion, these results provide a biochemical basis for the mechanism of homolog pairing and support the role of homolog conjunction complex in male meiosis.