Multicellular organisms need to control their size throughout development and adult life in the face of challenges such as rapid growth. Unraveling the mechanisms that regulate tissue growth in epithelial tissues, in order to generate organs of correct size and proportion, remains a crucial goal of developmental biology. A suitable epithelial tissue for studying tissue growth in Drosophila, is the proliferative monolayer epithelial sheet of imaginal wing discs, which gives rise to the adult wing. The Hippo signaling pathway regulates tissue growth in wing development. There are several observations that link tissue growth/Hippo signaling with cell polarity and the actin cytoskeletal organization. The aim of this thesis was the study of the interplay between cell polarity, cytoskeletal organization and tissue growth. To gain further insight into how apical polarity proteins regulate tissue growth, an enhancer/suppressor screen that was previously conducted in our lab by Linda Nemetschke, was used. The screen was based on the modification of a dominant smaller wing phenotype induced upon overexpression of CrbextraTM-GFP. One of the enhancers identified in this screen is a gene called big bang (bbg). The absence of bbg results in smaller wings with a slower cell cycle and increased apoptosis in wing discs. bbg encodes a protein expressed in the apical cortex in wing disc cells and is required for the proper localization of apical proteins, like Crb, in wing disc epithelia. Bbg is also in the same complex with Spaghetti Squash (Sqh) in the apical cortex of the wing disc epithelia. sqh encodes an actin-binding protein that has actin cross-linking and contractile properties. Bbg stabilizes Sqh in the apical compartment of the cell. It is reported that both Crb and Sqh regulate tissue growth through the Hippo signaling pathway. In conclusion, Bbg regulates wing tissue growth, acting as a scaffolding molecule, through the proper localization of apical components of the cells like Crb and the cytoskeletal component Sqh.

During vertebrate embryo development, the body axis is subdivided into repeated structures, called somites. Somites bud off from an un-segmented tissue called the pre-somitic mesoderm (PSM) in a sequential and periodic manner, tightly controlled by an in built molecular clock, called the "segmentation clock". According to current understanding, the clock is comprised of: (i) an autonomous cellular oscillator consisting of an intracellular negative feedback loop of Her genes within the PSM cells, (ii) Delta-ligand and Notch-receptor coupling that facilitates synchronization of oscillators among the PSM cells, (iii) Tissue level waves of gene expression that emerge in the posterior PSM and move coherently towards anterior, leading to global arrest of oscillations in the form of somites. However, the movement of cellular oscillators within the PSM before the formation of somitic furrows, a prominent feature of the tissue as observed through this work has not been experimentally considered as a constituent of the segmentation clock so far. Our work aims to incorporate movement of cellular oscillators in the framework of the segmentation clock. It is well known from theoretical studies that the characteristics of relative motion of oscillators affect their synchronization properties and the patterns of oscillations they form. Particularly, theoretical studies by Uriu et al., PNAS (2010) suggest that cell movements promotes synchronization of genetic oscillations. Here, we established experimental techniques and image analysis tools to attain quantitative insight on (i) diffusion co-efficient of cellular oscillators, (ii) dynamics of a population of oscillators, within the PSM aiming towards concomitant understanding of the relationship between movement and synchronization of cellular oscillators. In order to quantitatively relate cellular oscillators and their motion within the PSM, I established imaging techniques that enabled visualization of fluorescenctly labeled nuclei as readouts of cell positions in live embryo, and developed dedicated segmentation algorithm and implemented tracking protocol to obtain nuclei positions over time in 3D space. Furthermore, I provide benchmarking techniques in the form of artificial data that validate segmentation algorithm efficacy and, for the first time proposed the use of transgenic embryo chimeras to validate segmentation algorithm performance within the context of in vivo live imaging of embryonic tissues. Preliminary analysis of our data suggests that there is relatively high cell mixing in the posterior PSM, within the same spatial zone where synchronous oscillations emerge at maximum speed. Also, there are indications of gradient of cell mixing along the anterior-posterior axis of the embryo. By sampling single cell tracks with the help of nuclei markers, we have also been able to follow in vivo protein oscillations at single cell resolution that would allow quantitative characterization of coherence among a population of cellular oscillators over time. Our image analysis work flow allows testing of mutant embryos and perturbation of synchrony dynamics to understand the cause-effect relationship between movement and synchronization properties at cellular resolution. Essentially, through this work, we hope to bridge the time scales of events and cellular level dynamics that leads to highly coordinated tissue level patterns and thereby further our understanding of the segmentation clock mechanism.

Histone methyltransferases are key players in eukaryotic gene regulation. The goal of this thesis was to study the role of the histone methyltransferase Mll2 in developing embryos and adult mice. Targeting of mouse ES cells with a multipurpose allele and blastocyst injection had previously generated a mouse line allowing analysis of Mll2 function by knock-out and conditional mutagenesis using Cre/loxP. The first part of the thesis comprised the analysis of the Mll2-/- phenotype, and included the cloning of a targeting construct to generate an ubiquitous, ligand-regulated Cre line. In the second part, we did conditional mutagenesis using the Rosa26-CreER(T2) line obtained from collaborators, and achieved complete knock-out of Mll2 in most tissues of embryos, neonates and adult mice. Mll2 is essential during embryonic development, as mutant embryos were severely growth retarded, had significant increases in apoptosis, and failed in gestation between E 9.5 and E11. Conditional removal of Mll2 protein at gastrulation (E 6.5) produced a similar phenotype at E 11. In contrast, the absence of Mll2 function after E 11 did not result in obvious defects at E16 and indicates an essential role for Mll2 between E6 and E11. Indeed, we identified a loss of expression of 3 important developmental regulators in mutants of this developmental stage: Hoxb1, Mox1 and Six3 are candidate targets for Mll2 regulation that encode homeobox type transcription factors involved in specifying cellular identity. We observed correct establishment of their developmental expression patterns, which than decay in Mll2-/- mutants at E9.5. These data concord with and extend current thoughts about the fly orthologue of Mll2, Trithorax, which suggest that it acts as an epigenetic lock in chromatin to maintain expression of certain transcription factors key to respective cellular identities, after their expression patterns have been established. After birth, Mll2 is dispensable in most tissues, as conditional knock out in neonates and adult mice did not produce any pathological findings except infertility of mutant males and females. Histological analysis of testis revealed progressive loss of spermatogonia, associated with increases in apoptosis but without overt proliferation, meiotic or differentiation defects or loss of the supporting Sertoli cells. Consequently, in addition to its regulation of homeotic genes during development, Mll2 is required for the maintenance of various mitotic cell populations including ES cells, embryonal cells and germ cells.

Eine der häufigsten kardiovaskulären Erkrankungen ist die Atherosklerose. Bei der Entstehung einer Atherosklerose spielt eine Hyperlipoproteinämie eine entscheidende Rolle. Ein weiterer Faktor für die Entstehung kardiovaskulärer Erkrankungen ist ein hoher Blutdruck. In dieser Arbeit wurde eine mögliche Interaktion zwischen Lipoproteinen und den blutdruckregulierenden Endothelin- und Renin-Angiotensin-Systemen untersucht. Weiterführende Analysen erfolgten an Rezeptoren für die Aufnahme von nLDL und oxLDL. Abschließend wurden Signalwege untersucht, die durch nLDL und oxLDL aktiviert werden. Tierexperimentielle Untersuchungen in Aorten und Herzen fettreich gefütterter Wildtyp- Mäuse unterstützen die Zellkultur-Ergebnisse einer Induzierung des Endothelin-Systems durch erhöhte Lipoproteine. Zusammenfassend zeigt diese Arbeit neue Mechanismen der Interaktion von Lipoproteinen und blutdruckregulierenden Systemen in Endothelzellen. Die Rezeptoren scheinen dabei eine Schlüsselrolle zu spielen. Dies spricht für eine Potenzierung von Hyperlipoproteinämie und Hypertonie bei der Entstehung von Herz-Kreislauf-Erkrankungen.

Bei der Replikation monotoner Sequenzen tritt theoretisch ein Vorgang auf, den wir als „Basenkonkurrenz“ bezeichnen: Da sich an jeder Replikations-Stelle mehrere Basenbausteine bewerben, aber immer nur einer benötigt wird, bewerben sich die übrig gebliebenen Bausteine an den jeweils nächsten Replikations - Positionen und erlangen wegen der fortwährenden Beschleunigung durch elektrostatische Anziehung immer größere kinetische Energien. Das führt dazu, dass an einer bestimmten Stelle der replizierenden monotonen Sequenz der eine Partner der Wasserstoffbrückenbindung ein hohes Energieniveau erreicht. Es wird berechnet, dass sich dadurch kurzzeitig eine sehr hohe Bindungsenergie zwischen den beiden Partnern der Wasserstoffbrückenbindung einstellt, wodurch der in dieser kurzen Zeitspanne wirkende DNA-Reparaturmechanismus unterdrückt wird. Die Auswirkungen der hohen Basenkonkurrenz – Energien werden berechnet (hohe Bindungsenergien der Wasserstoffbrückenbindungen, Tunnelvorgänge, irreparable Mutationen). Die Folgen dieser Erscheinung sind Tumorbildung, Alterung, Veränderung der DNA – Struktur, Beeinflussung der Evolution, worauf im Einzelnen eingegangen wird. Es zeigt sich, dass die negativen Auswirkungen der Basenkonkurrenz vorwiegend bei zu niedriger Viskosität des Zellplasmas auftreten.

The present thesis is a contribution to unravel the molecular mechanisms that underlie urodele regeneration. Urodele amphibians (newts and salamanders) are among the few vertebrates with the remarkable ability to regenerate lost body appendages, like the limbs and the tail. Urodele tail and limb regeneration occurs via blastemal epimorphic regeneration. A blastema is a mound of progenitor cells that accumulates at the amputation plane and eventually gives rise to the missing structures. It is known today that dedifferentiating muscle fibers at the amputation plane contribute to the blastema cell pool, but how this process occurs on the cellular and molecular level is hardly understood, which is in part due to the lack of molecular methods to test gene function in urodeles. Furthermore, little is known about how coordinated growth and patterning occurs during urodele regeneration, and if the patterning mechanisms in regeneration are related to the ones in development. The goal of this study was to better understand these processes on the molecular level. To address these questions, I first established several methods in our model systems, which are the mexican salamander Ambystoma mexicanum (axolotl) and a cell line derived from the newt Notophthalmus viridescens. In order to monitor gene expression on a cellular level during regeneration, I worked out a good in situ hybridization protocol on axolotl tissue cryosections. To be able to test gene function, I established electroporation conditions to both overexpress genes in the cultured newt cells and to deliver morpholinos into axolotl cells in vivo and newt cells in culture. I demonstrate here that morpholinos are an effective tool to downregulate protein expression in urodele cells in vivo and in culture. Testing the role of two candidate genes in muscle fiber dedifferentiation, the homeobox containing transcription factor Msx1 and Rad, a GTP-binding protein of a new Ras-related protein family, revealed that neither seems to play a major role in muscle dedifferentiation, both in culture and in vivo. In addition to testing gene function I have examined the muscle dedifferentiation process in more detail. I show here that dedifferentiating muscle fiber nuclei undergo morphological changes that are likely due to chromatin remodeling events. I also demonstrate that the axolotl spinal cord expresses embryonic dorsoventral (d/v) patterning markers of the neural tube. The transcription factors Msx1, Pax7 and Pax6 are expressed in their respective d/v domains in both the differentiated and the regenerating axolotl spinal cord. Furthermore, the secreted signaling molecule sonic hedgehog (Shh) is expressed in the floor plate in both the differentiated and the regenerating cord. Using a chemical inhibitor (cyclopamine) and an activator of the hedgehog pathway, I discovered that hedgehog signaling is required for overall tail regeneration. Blocking hedgehog signaling does not only result in d/v patterning defects of the regenerating spinal cord, but it also strongly reduces blastema cell proliferation. In addition, I identified cartilage and putative muscle progenitor cells in the blastema, marked by the expression of the transcription factors Sox9 and Pax7, respectively. Both progenitor populations are reduced in the blastema in the absence of hedgehog signaling. The continuous expression of marker genes for embryonic progenitor cell domains in the mature axolotl may be related to their ability to regenerate.

Two fundamental problems of developmental biology are the understanding of cell fate specification, and the integration of broader environmental contexts into developmental programs. While cell fate specification is largely achieved by differential gene expression programs, environmental integration relies on cellular receptors. A predominant mechanism to mediate both processes utilizes nuclear hormone receptors (NHRs). However, it remains unclear how diverse the NHR’s modes of action are in regulating gene expression. This thesis utilizes the development of the C. elegans germ line as a model system to study a novel link that integrates cell fate specification and the nutritional environment. In C. elegans, germ cell fate specification is chiefly controlled by posttranscriptional mechanisms. Furthermore, overall germline development is influenced by the animal’s nutritional status. However, it remains unknown whether germline posttranscriptional control mechanisms and germ cell fate decisions are linked to nutrition, and if so, how this link may operate in molecular terms. This thesis reports the characterization of the nuclear hormone receptor nhr-114 and its crucial functions for germline development and fertility. Depending on the tissue of expression, nhr-114 regulates overall germline organization, germ cell proliferation and oogenesis. Importantly, all aspects of nhr-114 function are linked to diet. Feeding nhr-114 mutants with a specific E. coli strain, or a tryptophan-supplemented diet significantly reduces germline development defects and sterility. Based on mutant analysis, nhr-114 was found to have overlapping functions with gld-4 cytoplasmic poly(A) polymerase (cytoPAP). This thesis provides evidence that nhr-114 may function in germ cells in a posttranscriptional manner linked to gld-4 cytoPAP. Further evidence shows that NHR-114 interacts with GLD-4 cytoPAP. Together these findings suggest that NHR-114 may control gene expression by transcriptional and posttranscriptional mechanisms in a tissue-specific manner. This thesis proposes that NHR-114 ensures the input of tryptophan to allow germline development; and that this function integrates nutritional information into the germline gene expression programs according to the environment of the worm. Therefore, NHR-114 potentially provides a direct molecular link to how a developmental program is coordinated with the nutritional status of an animal.

S-layer proteins of S. ureae ATCC 13881 form on the cell surface an S-layer lattice with p4 square type symmetry and a period of about 13.5 nm. These lattices were shown to be the excellent nanotemplates for deposition of regular metal clusters. The synthesis of the S. ureae S-layer protein is highly efficient, the protein accounts for approximately 10-15 % of the total cell protein content, judged by the SDS-PAGE results. Besides, the S-layer protein production is tightly regulated, since only negligible amounts of S-layer proteins are observed in the medium at different cell growth phases. At the same time, mechanisms of the regulation of S-layer protein synthesis are poorly understood. As several hundreds of S-layer proteins are produced per second during the cell growth, the S-layer gene promoters are among the strongest prokaryotic promoters at all. However, little is known about factors regulating the expression of S-layer genes, furthermore, no experimental identification of other upstream regulatory sequences except for -35/-10 and RBS sequences was presented to our knowledge to date. A sequence of the S-layer gene of S. ureae ATCC 13881, encoding the previously described S-layer protein, was identified in this work by combination of different approaches. The largest part of the gene, excluding its upstream regulatory and ORF 5’ regions, was isolated from a genomic library by hybridization. The sequence of the isolated fragment proved to contain additionally an 1.9 kb non-coding region and an incomplete 0.8 kb ORF region in its 3’-part. No RBS sequence and apparent promoter regions could be identified in front of the latter sequence, suggesting that it might represent a pseudogene sequence. The sequences of the 5’ and upstream regions of the S. ureae ATCC 13881 S-layer gene were identified by combination of PCR-sequencing and chromosome walking. Totally, a sequence of the 6.4 kb long region of S. ureae genomic DNA was established. The sequence of the S. ureae S-layer protein was deduced from the respective gene sequence and agreed with the peptide sequences, obtained after N-terminal sequencing of tryptic peptides of the S. ureae ATCC 13881 S-layer protein. For the protein the name SslA was proposed, which is an abbreviation for “Sporosarcina ureae S-layer protein A”. Several specific features were observed in gene organisation of sslA, which are also characteristic for other S-layer genes. The distance between the -35/-10 region and the ATG initiation codon is unusually long and a 41 bp palindromic sequence is present in the immediate vicinity of the -35/-10 region. Besides, a distant location of the rho-independent transcription terminator, which is 647 bp remote from the stop codon, will result in the mRNA transcripts with unusually long trailer region. Both the long 5’ UTR and the long 3’ trailer may have a regulatory function, either by conferring increased mRNA stability and/or by affecting translation efficiency. Potentially these sequences may define the binding sites of regulatory proteins. For example, palindromic sequences constitute the regulatory sites in several bacterial operons and may act as the binding sites of regulatory dimeric proteins. In respect to the conservation of the sslA sequence high similarity to the sequences of other functional S-layer genes, especially the slfA and slfB genes of B. sphaericus, was observed, whereas the results of phylogenetic analysis support the hypothesis that S-layer genes may have evolved via the lateral gene transfer. Based on the sslA sequence, several recombinant proteins with truncations of the terminal protein parts or C-terminal fusion of either EGFP or histidine tags were constructed. For all the truncated or EGFP-fusion SslA derivatives high level overexpression in E. coli was possible. For native SslA a moderate level of expression was observed suggesting that its high intracellular concentration may downregulate the protein synthesis. Interestingly, fluorescence microscopy indicates the same intracellular localization for heterologously produced recombinant proteins with fusions of EGFP either to the precursor or to the native SslA protein, suggesting that SslA secretion signal is not functional in E. coli. Heterologously produced SslA derivatives with truncations of N-, C- or both N- and C-terminal parts were shown to self- assemble in vitro, although the size of self-assembly structures was different from that observed upon the self-assembly of the native SslA. In the latter case extended self-assembly layers with the size up to 5x10 µm were observed, with a surface area of up to two orders of magnitude higher than that of S-layer patches, routinely isolated from S. ureae surface. Dependent on the applied recrystallization conditions preferential formation of single- or multilayer self-assembly structures was observed.

The correct patterning of embryos requires the exchange of information between cells. This is in part achieved by the proper distribution of signaling molecules, many of which exert their function by establishing gradients of concentration. Because of this property they were named "morphogens", or "form giving" substances. Among these, proteins belonging to the Hedgehog (Hh) family have received much attention, owing to their unusual double lipid modification and their involvement in human disease, causing congenital birth defects and cancer. Great efforts have been made in order to elucidate the mechanisms by which Hh molecules are propagated in the embryo. However, no conclusive evidence exists to date to which structures these molecules localize and how they, despite their membrane association, establish a gradient of concentration. Therefore, I decided to study the distribution of the vertebrate Hh homolog, Sonic Hedgehog (Shh) in developing zebrafish embryos. By fluorescently tagging Shh proteins, I found that these localize to discrete punctate structures at the membranes of expressing cells. These were often regions from which filopodial protrusions emanated from the cells. Puctate deposits of Shh were also located outside of expressing cells. In dividing cells, Shh accumulated at the cleavage plane. Furthermore, by making use of confocal microscopy and time lapse analysis, I visualized Shh proteins moving in filopodial extensions present between cells. This suggests a novel mechanism of Shh distribution, which relies on the direct contact of cells by filopodia for the exchange of signaling proteins. In a second part of my thesis, I characterized genes implicated in regulating Shh protein distribution and signaling function. I cloned three zebrafish genes belonging to the Ext1 (exostosin) family of glycosyltransferases required for the synthesis of Heparan Sulfate Proteoglycans and established a tentative link of these genes to somitic Hh signaling. In addition, I characterized the developmental expression and function of zebrafish Rab23, a small GTPase, which acts as a negative regulator of the Shh signaling pathway. Performing knock-down experiments of zebrafish Rab23, I found that Rab23 functions in left-right axis specification, a process previously shown to depend on proper Shh signaling.

Mammals have two orthologs, Mll and Trx2, for the Drososphila protein Trithorax (TRX), which is the founding member of the trithorax group (TrxG) of epigenetic regulators. TrxG proteins are characterized by an evolutionary conserved SET domain. A major function of all SET domain- containing proteins is to modulate gene activity, but the underlying mechanisms are poorly understood. Apparently TRX, Mll and Trx2 are histone H3 lysine 4 specific methyltransferases. So far all evidence points to roles in expression of specific target genes. However, target genes and function of the epigenetic regulator Trx2 were still unknown. Homozygous trx2 mutant embryos arrest in development because of severe and widespread defects {Glaser, 2005 #296}. Thus mouse embryonic stem (ES) cells carrying a null mutation of trx2 were used as an alternative model system to address the implication of Trx2 in differentiation. This study showed that Trx2 is redundant for ES cell self-renewal. Homozygous trx2 knockout ES cells did not exhibit cell cycle defects. However, loss of Trx2 resulted in reduced proliferation and increased apoptosis rates in trx2-/- ES cells. Due to the fact that differentiation requires an appropriate rate of population growth, trx2-/- cells were affected adversely upon in vitro differentiation. Neurogeneic differentiation of trx2 mutant cells generated fewer mature neurons than wild type cells. Moreover a temporal delay in the developmental progression to differentiation became apparent. Cardiac differentiation of trx2-/- cells confirmed the developmental defect and temporal delay. Notably differentiation of trx2-/- cells was merely delayed or impaired but it was not absent, implying that Trx2 is not required for gene expression programs specific for neurons or cardiac myocytes. We propose that differentiation of trx2-/- ES cells is impaired because apoptosis is disturbing differentiation. Apart from analyzing the phenotype of trx2 mutant cells, this work was focused on the identification of Trx2 target genes. Oligonucleotide expression arrays were used to identify genes whose expression levels were affected by the absence of Trx2. In general, loss of Trx2 function resulted in more genes with decreased than increased expression levels. This is consistent with the hypothesis that Trx2 functions as a transcriptional activator. Comparison of gene expression profiles for constitutive and conditional trx2 mutant cells enabled a distinction between direct and indirect target genes for Trx2. As a result Magoh2 was identified as the key candidate target gene for Trx2. Interaction between Trx2 and Magoh2 suggested a potential regulatory role for Trx2 in alternative splicing. Furthermore this work provided evidence that Trx2 could be involved in the maintenance of CpG island promoter gene expression, thus providing a potent regulatory mechanism for ubiquitously expressed genes.