Pluripotente Stammzellen haben das Potential, in unterschiedliche Zelltypen zu differenzieren und können genutzt werden, um organähnliche Mikrostrukturen zu generieren. Somit können molekulare Unterschiede verschiedenster künstlich differenzierter Gewebe, etwa zwischen Mensch und Schimpanse, anhand von pluripotenten Ausgangszellen untersucht werden. Da die Genome unserer nächsten ausgestorbenen Verwandten Neandertaler und Denisovaner aus konservierter DNA in alten Knochen sequenziert wurden, könnten ebenso Unterschiede zwischen Mensch und diesen Spezies oder dem letzten gemeinsamen Vorfahren untersucht werden. Dies erfordert jedoch die Generierung neandertalisierter Stammzellen durch künstliche Integration von Neandertalerallelen in humane Stammzellen, etwa durch die CRISPR Genomeditierungstechnik. Durch CRISPR kann ein DNA-Doppelstrangbruch an einer gewünschten Stelle im Genom eingefügt werden. Die zelluläre Reparatur des Doppelstrangbruchs ermöglicht dann die Editierung des Genoms. Basierend auf einer DNA-Matrize, die die gewünschte Modifikation trägt, kann das Genom an dieser Stelle präzise editiert werden. Die Effizienz präziser Editierung ist jedoch sehr niedrig im Vergleich zu unpräziser Reparatur. Um möglichst effizient neandertalisierte Stammzellen generieren zu können, wurden im Zuge dieser Doktorarbeit Methoden entwickelt, welche die präzise Genomeditierungseffizienz drastisch steigern. Zum einen wurde aus mehreren niedermolekularen Substanzen, welche mit Proteinen der DNA-Reparaturen interagieren, ein optimierter Mix entwickelt. Weiterhin konnte durch eine Mutation in einem zentralen Reparaturprotein die Effizienz für die Editierung eines einzelnen Gens auf 87% erhöht werden. Diese hohe Effizienz ermöglicht erstmals die präzise homozygote Editierung von vier Genen auf einmal in ein und derselben Zelle

G-Protein-gekoppelte Rezeptoren (GPCR) nehmen eine Schlüsselfunktion bei zahlreichen (patho)-physiologischen Prozessen ein und sind daher von herausragender Bedeutung für die Forschung und Entwicklung pharmakologischer Wirkstoffe. Jedoch sind sowohl die physiologische Funktion als auch endogene Liganden von etwa 100 dieser Rezeptoren bis heute nicht bekannt. Das Verständnis der Funktion jedes einzelnen dieser sogenannten orphanen Rezeptoren könnte potentiell ganze Forschungsfelder mit neuen therapeutischen Optionen für den Menschen eröffnen. Beim GPR133/ADGRD1 handelt es sich um einen dieser orphanen Rezeptoren. Über genomweite Assoziationsstudien konnten Varianten des GPR133-Gens im Menschen bereits unter anderem mit einer veränderten Herzfrequenz, Körpergröße und Knochendichte in Verbindung gebracht werden. Welche exakte Rolle der Rezeptor dabei im Menschen oder anderen Organismen spielt, konnte bis heute nicht geklärt werden. Das Ziel der hier vorliegenden Arbeit war es deshalb, die physiologische Bedeutung des GPR133 mit Hilfe eines Knockout-Mausmodells zu charakterisieren. Die Verpaarung von heterozygot transgenen Weibchen und Männchen resultierte in gesunden Nachkommen ohne makroskopische Auffälligkeiten. Expressionsdaten sowie publizierte Assoziationsstudien legten eine Funktion des GPR133 im Herz, in glatter Muskulatur und in der Wirbelsäule nahe. Deshalb wurden zunächst diese Organe und Gewebe im Mausmodell untersucht. In den Herzen von GPR133-defizienten Mäusen (KO) konnten im Vergleich zu Wildtyp-Mäusen Veränderungen gefunden werden, welche der im Menschen vorkommenden dilatativen Kardiomyopathie (DCM) entsprachen. Auch zeigten die KO-Mäuse eine deutlich reduzierte kardiovaskuläre Belastungsfähigkeit. Weiterhin konnte in KO-Mäusen eine zumindest in der Harnblase verminderte Muskelkontraktilität, in den Wirbelkörpern eine niedrigere Knochendichte und im zur Bandscheibe gehörenden Nucleus pulposus veränderte Zelleigenschaften identifiziert werden. Welche (patho)-physiologischen Auswirkungen diese gefundenen Veränderungen für die GPR133-KO-Mäuse haben und inwieweit dies auf den Menschen übertragbar ist, konnte nicht abschließend geklärt werden. Mit der DCM konnte jedoch eine Verbindung zu einer schwerwiegenden Erkrankung beim Menschen hergestellt werden.

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Balancing selection maintains advantageous genetic diversity in populations through a variety of mechanisms including overdominance, negative frequency-dependent selection, temporal or spatial variation in selective pressures, and pleiotropy. If environmental pressures are constant through time, balancing selection can affect the evolution of selected loci for millions of years, and its targets might be shared by different species. This thesis is comprised of two different approaches aimed at detecting shared signatures of balancing selection in the genomes of humans and other great apes. In the first part of the thesis, we focus on extreme loci where the action of balancing selection has maintained several coding trans-species polymorphisms in humans, chimpanzees and bonobos. These trSNPs segregate since the common ancestor of the Homo-Pan clade and have survived for ~14 million years of independent evolution. These loci show the characteristic signatures of long-term balancing selection, as they define haplotypes with high genetic diversity that show cluster of sequences by allele rather than by species, and segregate at intermediate allele frequencies. Apart from several trSNPs in the MHC region, we were able to uncover a non-synonymous trSNP in the autoimmune gene LAD1. In the second part of the thesis we explore shared signatures of balancing selection outside trSNPs. We first implement a genome scan designed to detect signatures of balancing selection using NCD2 in the genomes of nine great ape species, including chimpanzee, bonobo, gorilla and orangutan. We show that targets of balancing selection are shared between species that have diverged millions of years ago, and that this observation cannot be explained by shared ancestry. We further demonstrate that targets of balancing selection primarily affect the evolution of genic regions of the genome, although we see evidence for their involvement in the regulation of gene expression. Overall, we provide comprehensive evidence that similar environmental pressures maintain advantageous diversity through the action of balancing selection in humans and other great apes, notwithstanding the deep divergence times between many of these species.

Since 1980 worldwide obesity has doubled in incidence to 52 % of people being overweight or obese. Obesity causes various comorbidities such as cardiovascular diseases, type II diabetes, dyslipidemia and several cancer types, making it one of the biggest challenges in worldwide health care systems. It is well known that obesity is highly heritable by either monogenetic causes or multifactorial interactions of different genes that superimpose on environmental factors and behavior. To answer questions in understanding mechanisms of obesity and/or associated metabolic pathways, mouse models have been a powerful tool. Several approaches in characterizing genes involved in obesity development through mouse engineering have been implemented, with the Cre/loxP system emerging as one of the most informative and widespread techniques. Using this approach, promoter-dependent temporal and tissue-specific regulated recombination can be achieved by Tamoxifen administration. To investigate effects of Tamoxifen on adipocyte biology in vivo, we characterized 12 weeks old male C57BL/6NTac mice after Tamoxifen treatment. We found that Tamoxifen treatment caused transient body composition changes, increased HbA1c, triglyceride and free fatty acid serum concentrations as well as smaller adipocytes in combination with browning of subcutaneous adipose tissue. Therefore, we suggest considering these effects when using Tamoxifen as a tool to induce conditional transgenic mouse models and to treat control mice in parallel. Another methodology used to identify genes involved in obesity related traits is QTL mapping in combination with congenic and subcongenic strains of mice or rats. One candidate gene that was previously identified on rat chromosome 4 is replication initiator 1 (Repin1 ). This gene was first described as a 60 kDa zinc finger protein involved in replication activation of the Chinese hamster dihydrofolate reductase (dhfr ) gene. Moreover, a triplet repeat (TTT) in the 3’UTR is associated with facets of the metabolic syndrome, including body weight, serum insulin, cholesterol and triglyceride levels. In vitro studies in 3T3-L1 cells revealed that Repin1 regulates adipocyte size, glucose transport and lipid metabolism. In this thesis functional analyses of Repin1 were performed using different Repin1 deficient mouse models. In the first study we generated a whole body Repin1 deficient db/db double knockout mouse (Rep1−/−x db/db) and systematically characterized the consequences of Repin1 deficiency. Our study provided evidence that loss of Repin1 in db/db mice improves insulin sensitivity and reduces chronic hyperglycemia most likely by reducing fat mass and adipose tissue inflammation. We next generated a liver-specific Repin1 knockout mouse (LRep1−/−) and could show that loss of Repin1 in liver leads to reduced body weight gain in combination with lower fat mass. Liver specific Repin1 deficient mice also show lower triglyceride content in the liver, improved insulin sensitivity and altered gene expression of genes involved in lipid and glucose metabolism. Finally, we inactivated the Repin1 gene in adipose tissue (iARep−/−) at an age of four weeks using Tamoxifen-inducible gene targeting strategies on a background of C57BL/6NTac mice. Mice lacking Repin1 in adipose tissue showed reduced body weight gain, decreased fat mass with smaller adipocytes, improved insulin sensitivity, lower LDL-, HDL- and total cholesterol serum concentrations and reduced expression of genes involved in lipid metabolism (Cd36 and Lcn2 ). In conclusion, the thesis presented here provides novel insights into Repin1 function. Moreover, the data clearly indicate that Repin1 plays a role in insulin sensitivity and lipid metabolism by regulating key genes involved in those pathways.

The human brain, as much as it is “unaccountable” in the eyes of Virginia Woolf, is a marvel. It is the evolutionary increase in brain size, especially in the cerebral cortex, that both allowed Mrs Woolf to create and us to perceive the beautiful imagery that exists in her fictional world. The evolutionary increase in brain size in part reflects the increase in the number of neurons generated during neocortical development. This in turn reflects two principal features of cortical expansion, namely, an increase in the number of neural stem and progenitor cells (from here on referred to as progenitor cells) and their neurogenic potential. Strikingly, in order to cater for this increase in progenitor cells and neurogenic potential, there is a significant expansion and diversification of basal progenitors in the subventricular zone (SVZ). Basal progenitors can be divided into three types: basal intermediate progenitors (bIPs), basal radial glias (bRGs) and transit-amplifying progenitors (TAPs). bIPs are the most abundant progenitors in the mouse SVZ. These cells are non-polar and are Pax6 and Sox2 negative, but Tbr2 positive. They have limited proliferative capacity as they can divide only once to produce two neurons. bRGs and TAPs, on the other hand, are able to undergo multiple rounds of division and exist in higher abundance in gyrencephalic brains (for bRG, in humans up to 50% versus mouse 5% at mid-neurogenesis). The morphology of bRGs are reported to be dynamic (fluctuating between states of having process(es) to none), whereas TAPs are generally described to be non-polar during mitosis. bRGs are known to express Pax6 and Sox2 but not Tbr2 while TAPs are known to express both Pax6 and Tbr2. The increase in the proportion of these self-renewing basal progenitors (more specifically bRGs) might allow for cortical expansion. Hence, the main objective of this doctoral work was to generate more bRGs in the mouse dorsal telencephalon, the region that ultimately develops to become the cerebral cortex. To achieve this objective, two approaches were used– (i) a general approach by microinjecting a pool of ferret poly-A+ RNA and (ii) a candidate approach by conditionally expressing the transcription factor Pax6. In the general approach, the microinjection technique was first established and validated in an organotypic slice culture of the mouse dorsal telencephalon. A pool of ferret poly-A¬+ RNA extracted at P1, the developmental stage corresponding to the peak of bRG production, was then microinjected into the dorsal telencephalon. We hypothesized that at the peak of bRG production, the “instructive” messages on how to generate bRG would be at their peak. Hence, by introducing these “instructive” messages into a apical radial glia (aRG), these cells would thus “know” how to generate bRGs. At 24 h after microinjection, only aRGs, the predominant progenitor residing in the ventricular zone during mid-neurogenesis were recovered. At 48 h after microinjection, however, 75% of cells that translated the ferret poly-A¬+ RNA had a morphology reminiscent of bRG. These cells were located away from the ventricular surface and had a basal but not apical process. We conclude from these experiments that we did indeed generate bRG-like cells in the mouse dorsal telencephalon via microinjection of the ferret poly-A¬+ RNA. In the candidate approach, this work aimed to conditionally express Pax6, a transcription factor that has been linked to proliferation and neurogenesis in aRG. More specifically, as there is a significant increase in the number of Pax6 positive cells (bRGs) in the SVZ of gyrencephalic animals during mid-neurogenesis, we wanted to recapitulate this phenomenon in the mouse dorsal telencephalon, where Pax6 is normally downregulated. To achieve this, the Tis21–CreERT2 mouse was used. Tis21 is a pan-neurogenic marker that is switched on once aRG switches from a proliferative division (i.e. 1 aRG⇒2aRG) to a neurogenic division (i.e. 1aRG⇒1aRG+1bIP). Consequently, the neurogenic aRGs and its progeny, bIPs would thus be Tis21 positive. By conditionally expressing Pax6 in Tis21 positive aRGs, the ectopic expression of Pax6 was successfully induced in the SVZ of the mouse dorsal telencephalon. Interestingly, conditional expression of Pax6 increased the percentage of proliferating cells in the SVZ. However, instead of producing more bIPs as predicted by the neurogenic division of Tis21 positive aRGs, these cells had the cell morphology, transcription factor expression profile, and division-type of bRGs and/or TAPs. Thus, using the conditional expression of Pax6 we were able to generate more bRG-like progenitors in the mouse dorsal telencephalon. The fate of these conditionally expressing Pax6 progenitors at a later stage was then investigated. A phenotypic change in the behaviour of neurons generated was observed. Instead of migrating into the cortical plate, cells that were highly expressing Pax6 formed a heterotopia at the SVZ or intermediate zone, suggestive of Pax6 interfering with neuronal migration. Interestingly, of those lowly expressing Pax6 cells that successfully migrated to the CP, a disproportionate majority became upper layer neurons. As the fate of neurons are dependent on their date of birth (i.e early born neurons are normally found in the deep layer while late born neurons are normally found in the upper layer), the increase in the upper layer neurons is consistent with the fact that conditionally expressing Pax6 delayed the birth of these neurons by delaying neurogenesis in order to increase the number of proliferative divisions. Interestingly, this increase in upper layer neurons is consistent with the difference between small- and large-brained species. In conclusion, through this work more bRGs was successfully generated in the mouse dorsal telencephalon through two distinct but complementary approaches.

The precise positioning of the mitotic spindle to the cell center during mitosis is a fundamental process for chromosome segregation and the division plane definition. Despite its importance, the mechanism for spindle centering remains elusive. To study this mechanism, the dynamic of the microtubules was characterized at the bulk and at the cortex in the C. elegans embryo. Then, this dynamic was correlated to the centering forces of the spindle that were studied by applying calibrated magnetic forces via super-paramagnetic beads inserted into the cytoplasm of one- and two-cell C. elegans embryos. Finally, these results were confronted with the different centering models: cortical pushing model, cortical pulling model and the cytoplasmic pulling model. This thesis shows that: (i) The microtubules dynamic of the spindle aster is controlled spatially in the C. elegans embryo, with not rescues and catastrophes in the cytoplasm but in the centrosome and the cortex, respectively. (ii) The centering mechanism of the spindle behaved roughly as a damped spring with a spring constant of 18 12 pN/ m and a drag coefficient of 127 65 pN s/ m (mean SD). This viscoelastic behavior is evidence of a centering force that recovers and/or maintains the position of the spindle in the cell center. (iii) It seems to be two mechanisms that recover/maintain the spindle position. A fast one that may work for transient displacements of the spindle and a slow one that work over large and long perturbations. (iv) The centering forces scale with the cell size. The centering forces are higher in the two-cell embryo. This result argues against a centering mechanism mediated by cytoplasmic factors. It seems to be a limit for the relation of centering force to size, as the forces found in the four-cell embryo are comparable to the single-cell ones. (v) The centering forces scale with the amount of microtubules in the cell. This strengthens the belief that the microtubules are the force transmission entities of the centering mechanism. (vi) The boundary conditions are important to maintain the centering forces. A transient residency time of microtubules at the cortex, which is controlled by cortical catastrophe factors, is indispensable for a proper force transmission by the microtubules. (vii) The elimination of cortical catastrophe factors provides evidence for microtubules buckling, which is taken as a proof of polymerization forces. (viii) The cortical pulling forces mediated by the gpr-1/2 pathway do not seem to be involved in centering and it is proposed they are present in the cell for off-center positioning purposes. (ix) The forces generated by vesicle transport are enough to displace the spindle and they are suggested to be auxiliary forces to centering. (x) The forces associated with the spindle change dramatically during cell division. From metaphase to anaphase the forces associated with the spindle scale up to five times. This behavior was consistent during the development of the embryo as the same pattern was observed in the one-, two- and four-cell embryo. (xi) The higher forces found during anaphase are not cortical pulling (via pgr-1/2 pathway) depended, and it is proposed the spindle is `immobilised' by tethering or by an unknown cortical pulling pathway. To this date, this thesis presents the most complete in-vivo measurements of the centering forces in association with the microtubules dynamics. Taken together the results constrain molecular models of centering. This thesis concludes that most probably the predominant forces of the spindle centering mechanism during mitosis are generated by astral microtubules pushing against the cortex. Additionally, this thesis presents the most complete map of forces during cell division during development, which will prove to be indispensable to understand the changes the spindle undergoes when it changes its function.

Biomolecular motor based transport reconstituted in synthetic environment has been recently established as a promising component for the development of nanoscale devices. A minimal system consisting of microtubules propelled over a surface of immobilized kinesin motor proteins has been used to transport and manipulate cargo for molecular sorting, analyte detection, and other novel nanotechnological applications. Despite these achievements, further progress of the field and translation of the reported applications to a real-world setting require overcoming several key challenges, such as, development of effective cargo conjugation strategies and precise control of the transport directionality with the reconstituted biomolecular motor systems. The challenge of cargo conjugation is addressed in this thesis through the development of a robust bioorthogonal strategy to functionalize microtubules. The versatility of the developed method is demonstrated by covalently conjugating various types of cargos to microtubules. Further, the effect of the linker length on cargo attachment to microtubules is investigated by attaching cargo to microtubules via linkers of different lengths. By using kinesin-driven transport of microtubules that are covalently conjugated to antibodies, detection of various clinically relevant analytes is demonstrated as proof-of-principle applications for biosensing. Finally, the challenge of gaining control over transport directionality is addressed through topographical guiding of microtubules in nanostructures, and optimization of assay parameters to achieve successful guiding of microtubules. Spatio-temporal analyte concentration, using transport in these nanostructues, is also explored to make the biomolecular-motor based applications more suitable for use real-world point-of-care setting. Taken together, the experimental work in this thesis contributes to the field of nanotechnological applications of biomolecular motors. The developed microtubule functionalization method and understanding of the effect of cargo attachment via linkers provide useful design principles for efficient cargo loading to microtubules. Moreover, establishment of assay components for successful guiding of microtubules in nanostructures is a vital step forward for practical translation of future nanoscale devices.

In dieser Arbeit wurden über 100 Pseudomonas-ähnliche Bakterienstämme, einige Bradyrhizobium-ähnliche und ein Ralstonia-ähnlicher Bakterienstamm mit der Fähigkeit zum aeroben Abbau chlorierter Aromaten isoliert. Die Bradyrhizobium-ähnlichen Isolate können vermutlich einer neuen Art zugeordnet werden. Die Pseudomonas- und Ralstonia-ähnlichen Isolate stammen aus einer Umweltprobe und zeigen die sehr geringe Diversität an Schadstoff-Verwertern in einem stark belasteten Standort. Spezifische PCR-Primer für die Gensequenzen der Chlorbrenzcatechin-1,2-Dioxygenase und Chlormuconat-Cycloisomerasen wurden anhand dieser Isolate überpüft. Diese Ergebnisse bestätigten die Aussagekraft der Primer in Bezug auf die Abbaugene des modifizierten ortho-Brenzcatechin-Weges für diesen Taxa. Diese kultivierungsunabhängige Methode ermöglicht die Überwachung des mikrobiellen Schadstoffabbaus in der Umwelt.