Methylation of lysine residues in histone tails is an intensively studied epigenetic signal that regulates transcription throughout development. Methylation of histone 3 lysine 4 (H3K4) is usually associated with promoters of actively transcribed genes whereas H3K27 or H3K9 methylation silences genes. Yeast possess only one H3K4 methyltransferase, Set1. In contrast, there are six enzymes capable of catalyzing this modification in mammals implying a certain specialization or division of labor. The present study examined the functions of the mouse H3K4 methyltransferase paralogs, Mixed Lineage Leukemia 1 (Mll1) and Mll2, during neural differentiation and reprogramming of neural stem (NS) cells to induced pluripotency. We could show that Mll2 is required for differentiation of embryonic stem (ES) cells to neural progenitors and identified Nuclear transport factor 2-like export factor 2 (Nxt2) as essential target gene. Mll2 trimethylated the Nxt2 promoter in ES cells in order to allow for transcriptional upregulation during subsequent neural differentiation. Additionally, Mll2 prevented apoptosis of differentiating cells by regulating B cell leukemia/lymphoma 2 (Bcl2) levels. Mll1 could replace Mll2 after the first steps of cell commitment towards epiblast stem (EpiS) cells. While Mll2 activity was only required briefly when ES cells started to differentiate, the influence of Mll1 seemed to increase with developmental progression. It stabilized the NS cell state by regulating expression of the neural transcription factor Orthodenticle homolog 2 (Otx2). Thereby, Mll1 impeded early steps of reprogramming to induced pluripotency and its inactivation increased the efficiency. Besides their specificity for certain target genes, both enzymes also differed in their activity. The major function of Mll1 was to prevent silencing by H3K27 methylation and possibly recruitment of transcription factors. In contrast, Mll2 conducted H3K4 trimethylation of its target genes. Importantly, once established in NS cells, the expression of Nxt2 became independent of promoter H3K4 methylation. Thus, Mll2 and its target gene Nxt2 represent an example for H3K4 methylation functioning as priming mechanism rather than for fine-tuning or maintenance of transcription levels.

Bei den konventionellen Krebstherapien kommt es häufig zu einer Wiederkehr des Tumors, da meist einzelne Tumorzellen und abgesiedelte Metastasen im Körper verbleiben. Vor diesem Hintergrund hat die Entwicklung neuer Behandlungsmethoden, die spezifisch die Tumorzellen erkennen und eliminieren und zudem gesunde Körperzellen schonen, eine große Bedeutung in der heutigen Krebsforschung. Eine erfolgsversprechende Strategie ist die Generierung von tumorspezifischen, zytotoxischen Immuneffektorzellen, zum Beispiel T-Lymphozyten und Natürlichen Killerzellen, durch die genetische Modifikation mit einem chimären Antigenrezeptor (CAR). Dabei gibt es bereits weitreichende Studien mit T-Lymphozyten, so dass sich nun das Forschungsinteresse immer mehr auf die NK-Zellen richtet. Im Gegensatz zu CAR-armierten T-Lymphozyten sind sie in der Lage ihr antitumorales Potenzial nicht nur gegen Antigen-positive sondern auch MHC-Klasse I-negative Tumorzellen zu richten. Mögliche Zielstrukturen der CAR sind tumorassoziierte Antigene, wie das Prostata-spezifische Stammzellantigen (PSCA). Es wird auf über 94 % der humanen primären Prostatakarzinome und deren Knochenmetastasen verstärkt exprimiert, jedoch kaum auf Normalgewebe. PSCA ist somit ideal für eine Immuntherapie geeignet. Die bisher in Studien verwendeten CAR-armierten NK-Zellen wiesen eine feststehende Spezifität gegenüber einem bestimmten Tumorantigen auf. Allerdings ist die Expression von Tumorantigenen innerhalb des Tumors sehr heterogen oder wird durch Tumorevasionsmechanismen herunterreguliert. Dies begrenzt die Reaktivität CAR-armierter NK-Zellen. Durch die Generierung eines CAR, dessen Spezifität gegenüber einem Tumorantigen ausgetauscht werden kann, wäre der universelle Einsatz CAR-armierter NK-Zellen in der adjuvanten Immuntherapie von Tumorerkrankungen möglich. Im Hauptteil dieser Arbeit wurden die permanente NK-Zelllinie YTS und primäre humane NK-Zellen mittels lentiviralen Gentransfers mit einem PSCA-spezifischen CAR, bestehend aus dem gegen PSCA gerichteten Einzelkettenantikörper αPSCA und dem aktivierenden NK-Zellrezeptor NKp46, armiert. Die generierten NK-Zellen wiesen eine über längere Zeiträume stabile Oberflächenexpression des CAR αPSCA-NKp46 auf. Die Kreuzvernetzung des CAR mit seinem Antigen führte zunächst zu keiner selektiven Immunantwort der CAR-armierten YTS und primären NK-Zellen gegenüber histogenetisch verschiedenen, PSCA-exprimierenden Tumorzelllinien. Erst nach gleichzeitiger Überexpression des mit NKp46 assoziierten Signaladaptermoleküls CD3-ζ wurde eine Aktivierung der Effektorfunktionen der YTS NK-Zellen induziert. Dies zeigte sich zum einen in der Expression von CD107a als Degranulationsmarker sowie der Freisetzung des inflammatorischen Zytokins IFN-γ. Zum anderen wiesen die CAR-armierten und CD3-ζ-exprimierenden YTS NK-Zellen eine spezifische Zytotoxizität gegenüber MHC-Klasse I- und PSCA-exprimierenden Tumorzellen auf. Im anschließenden Teil der Arbeit wurde ein modular aufgebauter CAR generiert, bei dem der Einzelkettenantikörper und folglich die Spezifität gegenüber Tumorantigenen austauschbar ist. Dazu wurden YTS NK-Zellen durch lentiviralen Gentransfer mit dem biotinylierbaren NKp46-NK-Zellrezeptor NKp46-KiBAP modifiziert, der über mehrere Monate stabil auf der Oberfläche exprimiert wurde. Die exogene als auch endogene Biotinylierung des Rezeptors wurde mittels einer Biotinproteinligase demonstriert. Unter Ausnutzung der sehr starken Biotin-Avidin-Bindung wurde die Assoziation mit einem Einzelkettenantikörper nachgewiesen. Dafür wurde exemplarisch der gegen PSCA gerichtete, biotinylierbare Einzelkettenantikörper αPSCA-BAP verwendet. Diese Arbeit zeigt, dass eine spezifische Erkennung und effiziente Lyse von PSCA-exprimierenden Tumorzellen durch die generierten CAR-armierten NK-Zellen erfolgte, wobei zum ersten Mal NKp46 als Bestandteil eines CAR verwendet wurde. Zudem wurde ein modular aufgebauter CAR generiert, dessen Spezifität gegenüber Tumorantigenen austauschbar ist. Diese neuartige Strategie ermöglicht erstmalig eine flexible Armierung von NK-Zellen und stellt damit einen wesentlichen Vorteil bei der Behandlung verschiedener Krebserkrankungen dar.

Cox11 (cytochrome c oxidase 11) is an ancient and conserved protein family present in most respiring organisms. Studies of several family members, mainly in yeast and bacteria, have revealed that these proteins are in charge of Cu+ delivery to the respiratory complex IV (COX). Absence of Cox11 leads to a non-functional COX complex and a complete respiratory deficiency. Although it is assumed that homologues in other species perform the same function, experimental data supporting this notion are lacking. The aim of this work was to characterize the putative Arabidopsis homologue AtCox11 (encoded by locus At1g02410) and to determine its functions. Comparison of AtCox11 with the well-studied ScCox11 in yeast revealed that the two proteins share high similarity in their sequences (32% amino acid identity) and in the predicted secondary structures. Surprisingly, despite this high similarity AtCox11 proved not to be able to functionally replace the yeast protein in ΔSccox11 yeast deletion strains. As presumed, AtCox11 is localized to mitochondria, probably tethered to the inner mitochondrial membrane with its C-terminus facing the intermembrane space. The subsequent experimental work addressed the functions of AtCox11. To this end AtCOX11 knock-down (KD) and overexpression lines (OE) were generated and their impact on plant phenotype was investigated. KD lines that were obtained by artificial micro RNA technology, possess approximately 30% of the WT AtCOX11 mRNA levels. Overexpression resulting in 4-6 fold higher AtCOX11 mRNA levels, was achieved by placing AtCOX11 under the control of the 35S promoter. Remarkably, both KD and OE plants had reduced levels of COX complex activity (~45% and ~80%, respectively) indicating that AtCox11 is, as expected, involved in COX complex assembly. The KD and OE plants exhibited reduced root lengths and pollen germination rates (compared to WT). As both processes are dependent on respiratory energy, these phenotypic changes seemingly result from the reduced COX activity. Interestingly, the short-root phenotype in OE plants was rescued by a surplus of copper in the media, whereas copper deficiency intensified the phenotype. By contrast, KD plants did not respond to changes of the copper concentration. This difference in the copper response between KD and OE plants hints at a different cause for the reduced COX activity. It is proposed that the concentration of AtCox11 in KD plants limits the efficient insertion of Cu+ into COX, independent of the available copper concentration. In OE plants, binding of the limited copper by the high AtCox11 level may lead to a copper deficiency for the copper chaperone AtHcc1 that is required to load copper to subunit AtCoxII. Indeed, addition of copper to the media was able to rescue the phenotype. In line with these data, the analysis of the expression pattern of AtCOX11 revealed that it is expressed in tissues which require substantial mitochondrial and COX biogenesis to sustain their high metabolic and/or cell division rates. Furthermore AtCOX11 was shown to be up-regulated as part of the plant’s response to increased oxidative stress induced by the addition to the plant media of peroxides or inhibitors of respiratory complexes. The up-regulation of AtCOX11 in response to oxidative stress was corroborated with publicly available RNA microarray data and analysis of the AtCOX11 promoter, which revealed the presence of a number of potential oxidative stress responsive elements. Taken together, the experimental results presented in this thesis support the conclusion that AtCox11 is a member of the conserved Cox11 protein family. Most probably, this mitochondrial protein participates in the assembly of the COX complex by inserting Cu+ into the CuB center of the AtCoxI subunit. In addition to this expected role, the data indicate that AtCox11 might participate in cellular oxidative stress response and defense via a yet unknown mechanism.

Anhydrobiotic organisms have the remarkable ability to lose extensive amounts of body water and survive in an ametabolic, suspended animation state. Distributed to various taxa of life, these organisms have evolved strategies to efficiently protect their cell membranes and proteins against extreme water loss. At the molecular level, a variety of mutually non-exclusive mechanisms have been proposed to account particularly for preserving the integrity of the cell membranes in the desiccated state. Recently, it has been shown that the dauer larva of the nematode Caenorhabditis elegans is anhydrobiotic and accumulates high amounts of trehalose during preparation for harsh desiccation (preconditioning), thereby allowing for a reversible desiccation / rehydration cycle. Here, we have used this genetic model to study the biophysical manifestations of anhydrobiosis and show that, in addition to trehalose accumulation, the dauer larvae exhibit a systemic chemical response upon preconditioning by dramatically reducing their phosphatidylcholine (PC) content. The C. elegans strain daf-2 was chosen for these studies, because it forms a constitutive dauer state under appropriate growth conditions. Using complementary approaches such as chemical analysis, time-resolved FTIR-spectroscopy, Langmuir-Blodgett monolayers, and fluorescence spectroscopy, it is shown that this chemical adaptation of the phospholipid (PL) composition has key consequences for their interaction with trehalose. Infrared-spectroscopic experiments were designed and automated to particularly address structural changes during fast hydration transients. Importantly, the coupling of headgroup hydration to acyl chain order at low humidity was found to be altered on the environmentally relevant time scale of seconds. PLs from preconditioned larvae with reduced PC content exhibit a higher trehalose affinity, a stronger hydration-induced gain in acyl chain free volume, and a wider spread of structural relaxation rates during lyotropic transitions and sub- headgroup H-bond interactions as compared to PLs from non-preconditioned larvae. The effects are related to the intrinsically different hydration properties of PC and phosphatidylethanolamine (PE) headgroups, and lead to a larger hydration-dependent rearrangement of trehalose-mediated H-bond network in PLs from preconditioned larvae. This results in a lipid compressibility modulus of ∼0.5 mN/m and 1.2 mN/m for PLs derived from preconditioned and non-preconditioned larvae, respectively. The ensemble of these changes evidences a genetically controlled chemical tuning of the native lipid composition of a true anhydrobiote to functionally interact with a ubiquitous protective disaccharide. The biological relevance of this adaptation is the preservation of plasma membrane integrity by relieving mechanical strain from desiccated trehalose- containing cells during fast rehydration. Finally, the thermo-tropic lipid phase behavior was studied by temperature-dependent ATR-FTIR and fluorescence spectroscopy of LAURDAN-labeled PLs. The results show that the adaptation to drought, which is accomplished to a significant part by the reduction of the PC content, relies on reducing thermo-tropic and enhancing lyotropic phase transitions. The data are interpreted on a molecular level emphasizing the influence of trehalose on the lipid phase transition under biologically relevant conditions by a detailed analysis of the lipid C=O H-bond environment. The salient feature of the deduced model is a dynamic interaction of trehalose at the PL headgroup region. It is proposed here that the location of trehalose is changed from a more peripheral to a more sub-headgroup-associated position. This appears to be particularly pronounced in PLs from preconditioned worms. The sugar slides deeper into the inter-headgroup space during hydration and thereby supports a quick lateral expansion such that membranes can more readily adapt to the volume changes in the swelling biological material at reduced humidity. The data show that the nature of the headgroup is crucial for its interaction with trehalose and there is no general mechanism by which the sugar affects lipidic phase transitions. The intercalation into a phosphatidylethanolamine-rich membrane appears to be unique. In this case, neither the phase transition temperature nor its width is affected by the protective sugar, whereas strong effects on these parameters were observed with other model lipids. With respect to membrane preservation, desiccation tolerance may be largely dependent on reducing phosphatidylcholine and increasing the phsophatidylethanolamine content in order to optimize trehalose headgroup interactions. As a consequence, fast mechanical adaptation of cell membranes to hydration-induced strain can be realized.

Die Bildung neuen Nervenzellen im erwachsenen Gehirn—adulte Neurogenese—ist bei Säugetieren auf spezifische Regionen beschränkt. Eine der beiden bekannten ist der Hippokampus, eine Gehirnstruktur, die eine wichtige Rolle beim Lernen sowie der Gedächtnisbildung spielt. Ein Reservoir von neuralen Stammzellen befindet sich in der subgranulären Zone des hippokampalen Gyrus dentatus. Diese Zellen teilen sich fortwährend und bilden neue Nervenzellen. Die Regulation adulter hippokampaler Neurogenese wird sowohl von der Umgebung beeinflusst als auch von mehreren Genen gesteuert. In der vorliegenden Arbeit wurden mittels Hochdurchsatz- Genexpressionsverfahren die an der Neurogenese beteiligten Gene identifiziert und ihr Zusammenspiel untersucht. Anhand von genetischen, umgebungsbedingten und zeitlichen Angaben und Variationen wurde ein vielseitiger Datensatz erstellt, der einen multidimensionalen Blick auf den proliferativen Phänotyp verschafft. Netzwerke aus Gen-Gen und Gen-Phänotyp Interaktionen wurden beschrieben und in einer mehrschichtigen Ressource zusammengefasst. Ein Kern-Netzwerk bestehend aus immerwiederkehrenden Modulen aus verschiedenen Ebenen wurde anhand von Proliferation als Keim-Phänotyp identifiziert. Aus diesem Kern-Netzwerk sind neue Gene und ihre Interaktionen hervorgegangen, die potentiell bei der Regulierung adulter Neurogenesis beteiligt sind.:Zusammenfassung i Abstract iii Acknowledgements vii Contents ix Preface xiii General Introduction 1 Adult Neurogenesis 1 Historical setting 1 Neurogenesis exists in two regions of the adult mammalian brain 1 Implications of neurogenesis in the hippocampus 1 The Hippocampal Formation 2 Function of the hippocampus in learning and memory 2 The functional role of adult neurogenesis 2 Anatomy of the hippocampal formation 2 Neural Precursor Biology 3 The subgranular zone as a neurogenic niche 3 Neuronal maturation is a multi-step pathway 3 Regulation of Adult Neurogenesis 3 Neurogenesis is modulated by age 3 Neurogenesis is modulated by environmental factors 4 Neurogenesis is modulated by genetic background 4 Genetics of the BXD RI Cross 5 C57BL/6 and DBA/2 5 Recombinant Inbred Lines 5 The BXD panel 6 Quantitative genetics 6 Microarray Analysis 7 The concept of ‘whole genome’ expression analysis 7 Technical considerations 8 Theoretical considerations 9 Current Analytical Methods 9 Network Analysis 10 Network Description and Terminology 10 Graph Theory 10 Multiple-Network Comparison 11 Biological networks 11 Types of Biological Network 11 Sources of Network Data 12 Biological Significance of Networks 12 Aim of the current work 13 Methods and Materials 15 Animals 15 BXD panel 15 Progenitor strains 15 Animal behaviour 15 Running wheel activity 15 Enriched environment 16 Morris water maze 16 Open field test 16 Corticosterone assay 16 Histology 17 Tissue collection 17 BrdU staining 17 Statistics 17 Cell culture 18 Maintenance and differentiation 18 Immunostaining 18 RNA isolation 18 Microarray processing 18 Affymetrix arrays 18 M430v2 probe reannotation 19 Illumina arrays 19 Illumina probe reannotation 19 Bioinformatics 19 Translating the STRING network 19 QTL mapping 20 Network graph layout 20 Triplot 20 Enrichment analysis 20 Mammalian Adult Neurogenesis Gene Ontology 21 Introduction 21 Results 25 The cell stage ontology 25 The process ontology 25 Genes known to regulate hippocampal adult neurogenesis 26 Enrichment analysis 27 The MANGO gene network 27 Discussion 28 Hippocampal Coexpression Networks from the BXD Panel 31 Introduction 31 Results 32 Variation and covariation of gene expression across a panel of inbred lines 32 A hippocampal expression correlation network 32 Diverse neurogenesis phenotypes associate with discrete transcript networks 34 Discussion 34 Interactions Between Gene Expression Phenotypes and Genotype 37 Introduction 37 Results 39 QTL analysis and interval definitions 39 Pleiotropic loci and ‘trans-bands’ 39 Transcript expression proxy-QTLs can help in dissection of complex phenotypes 41 Interaction network 43 Discussion 43 Strain-Dependent Effects of Environment 47 Introduction 47 Results 48 Effects of strain and environment on precursor cell proliferation 48 Effects of strain and environment on learning behaviour 52 Transcript expression associated with different housing environments 53 Strain differences in transcript regulation 55 Distance-weighted coexpression networks 57 Discussion 58 Expression Time Course from Differentiating Cell Culture 61 Introduction 61 Results 63 Differentiation of proliferating precursors into neurons in vitro 63 Transcripts associated with stages of differentiation 63 Early events in NPC differentiation 64 A network of transcript coexpression during in vitro differentiation 66 Discussion 67 Integrated Gene Interaction Networks 71 Introduction 71 Results 72 Description of network layers 72 Merging of network layers to a multigraph 74 A network of genes controls neural precursor proliferation in the adult hippocampus 75 Novel candidate regulators of adult hippocampal neurogenesis 77 Novel pathways regulating adult hippocampal neurogenesis 77 Discussion 79 General Discussion 81 References 89 Selbständigkeitserklärung 107 / Neurogenesis, the production of new neurons, is restricted in the adult brain of mammals to only a few regions. One of these sites of adult neurogenesis is the hippocampus, a structure essential for many types of learning. A pool of stem cells is maintained in the subgranular zone of the hippocampal dentate gyrus which proliferate and can differentiate into new neurons, astrocytes and oligodendroctytes. Regulation of adult hippocampal neurogenesis occurs in response to en- vironmental stimuli and is under the control of many genes. This work employs high-throughput gene expression technologies to identify these genes and their interactions with each other and the neurogenesis phenotype. Harnessing variation from genetic, environmental and temporal sources, a multi-faceted dataset has been generated which offers a multidimensional view of the neural precursor proliferation phenotype. Networks of gene-gene and gene-phenotype interac- tions have been described and merged into a multilayer resource. A core subnetwork derived from modules recurring in the different layers has been identified using the proliferation phenotype as a seed. This subnetwork has suggested novel genes and interactions potentially involved in the regulation of adult hippocampal neurogenesis.:Zusammenfassung i Abstract iii Acknowledgements vii Contents ix Preface xiii General Introduction 1 Adult Neurogenesis 1 Historical setting 1 Neurogenesis exists in two regions of the adult mammalian brain 1 Implications of neurogenesis in the hippocampus 1 The Hippocampal Formation 2 Function of the hippocampus in learning and memory 2 The functional role of adult neurogenesis 2 Anatomy of the hippocampal formation 2 Neural Precursor Biology 3 The subgranular zone as a neurogenic niche 3 Neuronal maturation is a multi-step pathway 3 Regulation of Adult Neurogenesis 3 Neurogenesis is modulated by age 3 Neurogenesis is modulated by environmental factors 4 Neurogenesis is modulated by genetic background 4 Genetics of the BXD RI Cross 5 C57BL/6 and DBA/2 5 Recombinant Inbred Lines 5 The BXD panel 6 Quantitative genetics 6 Microarray Analysis 7 The concept of ‘whole genome’ expression analysis 7 Technical considerations 8 Theoretical considerations 9 Current Analytical Methods 9 Network Analysis 10 Network Description and Terminology 10 Graph Theory 10 Multiple-Network Comparison 11 Biological networks 11 Types of Biological Network 11 Sources of Network Data 12 Biological Significance of Networks 12 Aim of the current work 13 Methods and Materials 15 Animals 15 BXD panel 15 Progenitor strains 15 Animal behaviour 15 Running wheel activity 15 Enriched environment 16 Morris water maze 16 Open field test 16 Corticosterone assay 16 Histology 17 Tissue collection 17 BrdU staining 17 Statistics 17 Cell culture 18 Maintenance and differentiation 18 Immunostaining 18 RNA isolation 18 Microarray processing 18 Affymetrix arrays 18 M430v2 probe reannotation 19 Illumina arrays 19 Illumina probe reannotation 19 Bioinformatics 19 Translating the STRING network 19 QTL mapping 20 Network graph layout 20 Triplot 20 Enrichment analysis 20 Mammalian Adult Neurogenesis Gene Ontology 21 Introduction 21 Results 25 The cell stage ontology 25 The process ontology 25 Genes known to regulate hippocampal adult neurogenesis 26 Enrichment analysis 27 The MANGO gene network 27 Discussion 28 Hippocampal Coexpression Networks from the BXD Panel 31 Introduction 31 Results 32 Variation and covariation of gene expression across a panel of inbred lines 32 A hippocampal expression correlation network 32 Diverse neurogenesis phenotypes associate with discrete transcript networks 34 Discussion 34 Interactions Between Gene Expression Phenotypes and Genotype 37 Introduction 37 Results 39 QTL analysis and interval definitions 39 Pleiotropic loci and ‘trans-bands’ 39 Transcript expression proxy-QTLs can help in dissection of complex phenotypes 41 Interaction network 43 Discussion 43 Strain-Dependent Effects of Environment 47 Introduction 47 Results 48 Effects of strain and environment on precursor cell proliferation 48 Effects of strain and environment on learning behaviour 52 Transcript expression associated with different housing environments 53 Strain differences in transcript regulation 55 Distance-weighted coexpression networks 57 Discussion 58 Expression Time Course from Differentiating Cell Culture 61 Introduction 61 Results 63 Differentiation of proliferating precursors into neurons in vitro 63 Transcripts associated with stages of differentiation 63 Early events in NPC differentiation 64 A network of transcript coexpression during in vitro differentiation 66 Discussion 67 Integrated Gene Interaction Networks 71 Introduction 71 Results 72 Description of network layers 72 Merging of network layers to a multigraph 74 A network of genes controls neural precursor proliferation in the adult hippocampus 75 Novel candidate regulators of adult hippocampal neurogenesis 77 Novel pathways regulating adult hippocampal neurogenesis 77 Discussion 79 General Discussion 81 References 89 Selbständigkeitserklärung 107

The cardiac conduction system is vital for the initiation and maintenance of the heartbeat. Over the recent years, the zebrafish (Danio rerio) has emerged as a promising model organism to study this specialized system. The embryonic zebrafish heart’s unique accessibility for light microscopy has put it in the focus of many cardiac researchers. However, imaging cardiac conduction in vivo remained a challenge. Typically, hearts had to be removed from the animal to make them accessible for fluorescent dyes and electrophysiology. Furthermore, no technique provided enough spatial and temporal resolution to study the importance of individual cells in the myocardial network. With the advent of light sheet microscopy, better camera technology, new fluorescent reporters and advanced image analysis tools, all-optical in vivo mapping of cardiac conduction is now within reach. In the course of this thesis, I developed new methods to image and manipulate cardiac conduction in 4D with cellular resolution in the unperturbed zebrafish heart. Using my newly developed methods, I could detect the first calcium sparks and reveal the onset of cardiac automaticity in the early heart tube. Furthermore, I could visualize the 4D cardiac conduction pattern in the embryonic heart and use it to study component-specific calcium transients. In addition, I could test the robustness of embryonic cardiac conduction under aggravated conditions, and found new evidence for the presence of an early ventricular pacemaker system. My results lay the foundation for novel, non-invasive in vivo studies of cardiac function and performance.

In the cell, the genetic information encoded in the DNA is transcribed to RNA. All RNAs that are transcribed in the cell are initially produced as precursor RNAs, which have to undergo various steps of processing to obtain their mature form. The maturation and processing for all RNA classes requires the activity of multiple RNA binding proteins (RBPs). An important family of RBPs that is involved in RNA maturation and processing is the SR-protein family. SR proteins are important for the regulation of a multitude of processes that include: splicing, transcription, export, RNA stabilization, translation and ncRNA processing. As of yet, there have been no comprehensive studies that describe how SR proteins dynamically regulate the maturation of RNAs. The results presented in this thesis provide new insights into the function and activity of SR proteins during RNA maturation. My experiments greatly expand the knowledge surrounding the action of RNA-binding proteins in vivo and in different cell compartments. To study the action of two different SR proteins in different cell compartments, I developed a new technique that combines cell fractionation and iCLIP, which I named FRACKING. For the first time, this method allowed me to collect information regarding the subcellular location where the RNA-protein interactions are taking place, giving a dynamic picture of the in vivo binding of SR proteins and of RNA binding proteins (RBP) in general. By using FRACKING on two heavily shuttling SR proteins, SRSF3 and SRSF7, I showed that both SR proteins are very dynamic in their binding behavior with RNAs. My research showed that both SRSF3 and SRSF7 strongly associate with RNAs during transcription (co-transcriptionally) and that they often remain bound to these transcripts until they are exported to the cytoplasm. The functions of SRSF3 and SRSF7 are closely related to their binding location on the target RNAs. I identified a subset of highly conserved introns that associated with SR proteins and are retained in their transcripts. These intron-retaining isoforms, contrary to textbook knowledge, are exported to the cytoplasm. I showed, for the first time, that SRSF3 and SRSF7 strongly interact with snoRNAs in the chromatin, and that this snoRNA-SR-protein binding behavior is distinct between SRSF3 and SRSF7. SRSF3 binds to the mature snoRNA sequence, and also to the surrounding intronic sequences, pointing towards a possible activity in guiding snoRNA maturation. Whereas SRSF7 associates to mature snoRNA sequences. Taken together, my study identified a dynamic pool of interactions for two SR proteins, in different cell compartments and discovered new activities for the two SR proteins. Importantly, this study challenges textbook knowledge on splicing and export of mRNAs by identifying a subset of transcripts that can be exported even when they retain introns.

Vor zirka 45 Jahren wurde das La Protein (SS-B) erstmals als Autoantigen von Patienten mit Systemischen Lupus Erythematodes (SLE) oder Primären Sjögren’s Syndrom beschrieben. Jahrzehntelange Forschungen befassten sich mit seiner Struktur- und Funktionsaufklärung, sowie der Untersuchung von monoklonalen anti-La Antikörpern (anti-La mAK). Doch noch immer werfen nukleäre Antigene wie das La Protein und die gegen sie gerichteten Autoantikörper verschiedene Fragen auf. Diese betreffen besonders deren Entstehung und die pathophysiologische Bedeutung. So war es die Zielsetzung dieser Arbeit, die pathophysiologische Bedeutung des La Proteins in der Autoimmunkrankheit und der Krankheitsentstehung bei SLE-Patienten weiter aufzuklären. Im Zentrum der Untersuchungen stand dabei die Redoxsensitivität des La Proteins und deren Einfluss auf die räumliche Proteinstruktur, die zelluläre Lokalisation, die Funktion der Nukleinsäurebindung, sowie die Antigenität. Dabei konnte erstmals mit Hilfe von CD-Spektroskopieanalysen deutlich gezeigt werden, dass die drei Cysteine (C18, C232 und C245) des La Proteins für die Struktur eine zentrale Rolle spielen. Es konnte demonstriert werden, dass die Fähigkeit zur redoxabhängigen Strukturumfaltung zum Verlust der protektiven Wirkung des La Proteins auf gebundene Nukleinsäure führt, wodurch diese für Nukleasen zugänglich gemacht wird und abgebaut werden kann. Dies ließ sich in der vorliegenden Arbeit mit Hilfe verschiedener Experimente verifizieren, beispielsweise durch die Anwesenheit von Kupferionen (Cu2+), oder auch durch die Änderung des pH-Wertes von 7,0 auf 4,5. Parallel hierzu wurden neben Wildtyp La Protein auch verschiedene Cysteinmutanten getestet, um die Redoxabhängigkeit auch durch den Austausch der Cysteine C18, C232 und C245 zu zeigen. Die Änderungen des Redoxzustands beeinflussten jedoch nicht nur Sekundär- und Tertiär-struktur des La Proteins, sondern auch sein Di- und Oligomerisationsverhalten, sowie die Antigenerkennung durch bestimmte anti-La mAK (mAK der 312B Gruppe). Erstmals konnte in dieser Arbeit auch gezeigt werden, dass Patientenautoantikörper nicht nur gegen die nor-malerweise nukleär vorliegende, reduzierte Form des La Proteins existieren. Es waren eben-so Patientenautoantikörper gegen die zytoplasmatische, oxidierte Form nachweisbar. Auch auf zellulärer Ebene wurde die Wirkung einer redoxabhängigen Umfaltung des La Proteins deutlich. Durch den Einfluss von reaktiven Sauerstoffspezies (ROS) konnte eine zytoplasmatische Anreicherung beobachtet werden. Die dazu bereits bekannten Daten aus der Literatur konnten mit dieser Arbeit nochmals belegt und darüber hinaus ergänzt werden. Die zytoplasmatische Anreicherung wurde in der vorliegenden Arbeit für verschiedene ROS Stimuli gezeigt, darunter H2O2, Cu(II)SO4, Fe(II)Cl2 und darüber hinaus auch für NO-Glutathion (Stimulus reaktiver Stickstoffspezies NO). Des Weiteren konnte erstmals eine zytoplasmatische La Anreicherung durch eine Veränderung des intrazellulären ROS Levels nach Rezeptorstimulation gezeigt werden. Spannender Weise gelang dies für dendritische Zellen, wie moDCs und slanDCs, als auch für Endothelzellen (HUVECs). Die Induktion erfolgte dabei über Toll-like Rezeptoren (TLR), wie TLR4 (LPS-abhängiger Toll-like Rezeptor) und auch über TLR7/8, zwei Toll-like Rezeptoren, die für die Bindung von ssRNA, beispielsweise nach Virusinfektion zuständig sind. Unter dem Einfluss dieser Stimuli, kommt es zur Umfaltung des La Proteins, zum Loslösen von seinem potentiellen, indirekt über den anti-La mAK 7B6 nachgewiesenen Bindepartner und zum Verlust der nukleären Lokalisation. Im Zytoplasma kann die oxidierte Proteinvariante ihre protektive Aufgabe bezüglich der gebundenen Nukleinsäure nicht weiter ausführen. Es kommt unter normalen Umständen zu Dissoziation der gebundenen Nukleinsäuren und einem potentiellen Abbau dieser. Da bei Autoimmunpatienten jedoch sehr häufig eine Reduktion der Nukleaseaktivität nachweisbar ist, könnte der Nukleinsäureabbau in diesen Patienten gestört sein, was zu einem oxidierten La Protein mit noch gebundener Nukleinsäure führen würde. Neben der zytoplasmatischen Lokalisation wurde für das La Protein auch eine Lokalisation an der Zelloberfläche diskutiert. Die hier durchgeführten Studien mit den verschiedenen Sauerstoff- oder Stickstoffstressstimuli zeigten jedoch unter den gewählten Bedingungen keine Exposition des La Proteins auf die Zelloberfläche. Daher wurden apoptotische und nekrotische Zellen als mögliche La Proteinquelle für die Dekoration lebender Nachbarzellen untersucht. War in der Literatur noch über „apototic bodies“ als Quelle des La Proteins als Autoantigen spekuliert wurden, so konnte hier gezeigt werden, dass das La Protein aus humanen, apoptotischem Zellmaterial zu keiner nachweislichen Oberflächendekoration lebender Zellen führte. Anders verhielt es sich bei nekrotischem Zellmaterial. Hier konnte zum Beispiel humanes oxidiertes La Protein auf den murinen Zellen nachgewiesen werden. Im Rahmen dieser Analysen zeigte sich darüber hinaus, dass sowohl oxidiertes als auch reduziertes La Protein auf die Oberfläche verschiedener Zelltypen binden kann. Insgesamt konnte jedoch mehr oxidiertes La Protein auf den verschiedensten Zellentypen nachge-wiesen werden, als reduziertes La Protein unter gleichen Bedingungen. Auch ergaben sich Unterschiede bezüglich der Proteinbindung zwischen einzelnen Zelltypen. Vertreter von Anti-gen präsentierenden Zellen, wie Monozyten oder B-Zellen (Radji), sowie Endothelzellen (HUVECs), aber auch murine A9 Fibroblasten konnten im Vergleich zu T-Zellen und NK-Zellen, mehr La Protein auf ihrer Oberfläche binden. Diese Resultate lassen eine pathophysiologische Bedeutung des La Proteins bei SLE Patienten erkennen. Im Zuge von Zellschä-digungen, wie beispielsweise nach UV-Stress, kommt es zu einem nekrotischen Zellzerfall. Dieser führt zur Freisetzung von oxidiertem La Protein, welches auf benachbarte Zellen bindet. Dadurch können sie zum Ziel einer komplementsystemvermittelten Immunreaktion, sowie einer antikörpervermittelten, NK-Zellen gestützten Zelllyse (ADCC) werden. Für die Initiation einer Immunantwort, und im Besonderen für die Reifung autoreaktiver B-Zellen zu autoantikörpernproduzierenden Plasmazellen, bedarf es jedoch zunächst einer Aktivierung von dendritischen Zellen. Im Rahmen dieser Arbeit konnte gezeigt werden, dass lösliches La Protein dendritische Zellen aktivieren kann, belegt über die dokumentierte, finale TNFα Sekretion. Dabei war jedoch nicht entscheidend, ob La in einem reduzierten oder oxidierten Zustand vorlag, sondern das es assoziierte Nukleinsäuren aufwies. Experimentell führten an La Protein gebundene Nukleinsäuren zur Aktivierung von dendritischen Zellen (slanDCs). Wurde die Nukleinsäuren jedoch zuvor durch RNaseA Behandlung oder die Inkubation in Serum eines gesunden Spenders abgebaut, so lag keine oder eine nur sehr geringe Aktivierung von slanDCs vor. Eine Inkubation von La Protein in SLE Patientenserum hatte keine solche verminderte Aktivierung dendritischer Zellen zur Folge. Unter Berücksich-tigung der oben geschilderten Versuchsergebnisse ließ sich dieses Resultat mit der geringeren Nukleaseaktivität bei SLE Patienten begründen, was bereits aus der Literatur bekannt ist. Diese reduzierte Nukleaseaktivität stellt somit offensichtlich einen entscheidenden Faktor bei der Aktivierung einer Autoimmunantwort in Zusammenhang mit dem La Protein und anti-La Autoantikörpern dar. Mit dieser Arbeit konnte also eindeutig gezeigt werden, dass das La Protein unter sich wechselnden Redoxbedingungen seine Struktur ändert. Dabei spielen die drei enthaltenden Cysteine eine bedeutende Rolle. Derartige Strukturveränderungen beeinflussen die Nukleinsäureschutzfunktion und die Erkennung durch Antikörper. Darüber hinaus bestätigte sich eine ROS induzierte Anreicherung von La im Zytoplasma. Auch die Fähigkeit des La Proteins, aus nekrotischem Zellmaterial auf die Oberflächen von lebenden Zellen zu binden, wurde gezeigt. Dadurch wäre es für Autoantikörper bei SLE Patienten zugänglich und somit pathophysiologisch relevant. Außerdem konnte auch die Eigenschaft von nukleinsäurege-koppelten La Proteins zur Aktivierung dendritischer Zellen belegt werden, was zur krankheitsauslösenden Aktivierung von autoreaktiven T- und im weiteren Verlauf von B-Zellen führen kann. Dadurch konnten die in dieser Arbeit erhaltenen Resultate deutliche Hinweise auf die pathophysiologische Bedeutung des La Proteins, nicht nur während der Autoimmunerkrankung, sondern auch für die Frühphase der Krankheitsentstehung, geben.

The neocortex is the most recently evolved part of the mammalian brain which is involved in a repertoire of higher order brain functions, including those that separate humans from other animals. Humans have evolved an expanded neocortex over the course of evolution through a massive increase in neuron number (compared to our close relatives-­‐‑ the chimpanzees) in spite of sharing similar gestation time frames. So what do humans do differently compared to chimpanzees within the same time frame during their development? This dissertation addresses this question by comparing the developmental progression of neurogenesis between humans and chimpanzees using cerebral organoids as the model system. The usage of cerebral organoids, has enabled us to compare the development of both the human neocortex, and the chimpanzee neocortex from the very initiation of the neural phase of embryogenesis until very long periods of time. The results obtained so far suggest that the genetic programs underlying the development of the chimpanzee neocortex and the human neocortex are not very different, but rather the difference lies in the timing of the developmental progression. These results show that the chimpanzee neocortex spends lesser time in its proliferation phase, and allots lesser time to the generation of its neurons than the human neocortex. In more scientific terms, the neurogenic phase of the neocortex is shorter in chimpanzees than it is in humans. This conclusion is supported by (1) an earlier onset of gliogenesis in chimpanzees compared to humans which is indicative of a declining neurogenic phase, (2) an earlier increase in the chimpanzee neurogenic progenitors during development, compared to humans, (3) a higher number of stem cell– like progenitors in human cortices compared to chimpanzees, (4) a decline in neurogenic areas within the chimpanzee cerebral organoids over time compared to human cerebral organoids.

Intracellular transport of membrane-bound vesicles and organelles is a process fundamental for many cellular functions including cell morphogenesis and signaling. The transport is mediated by ensembles of motor proteins, such as kinesins, walking on microtubule tracks. When transporting membrane-bound cargo inside a cell, the motors are linked to diffusive lipid bilayers either directly or via adaptor molecules. The fluidity of the lipid bilayers induces loose inter-motor coupling which is likely to impact the collective motor dynamics and may induce cooperativity. Here, we investigate the influence of loose coupling of kinesin motors on its transport characteristics. In the first part of this thesis, we used truncated kinesin-1 motors with a streptavidin-binding-peptide (SBP) tag and performed gliding motility assays on streptavidin-loaded biotinylated supported lipid bilayers (SLBs), so called ‘membrane-anchored’ gliding motility assays. We show that the membrane-anchored motors act cooperatively; the microtubule gliding velocity increases with increasing motor density. This is in contrast to the transport behavior of multiple motors rigidly bound to a substrate. There, the motility is either insensitive to the motor density or shows negative interference at higher motor density, depending on the structure of the motors. The cooperativity in transport driven by membrane-anchored motors can be explained as following: while stepping on a microtubule, membrane-anchored motors slip backwards in the viscous membrane, thus propelling the microtubule in the solution at a velocity, given by the difference of the motor stepping velocity and the slipping velocity. The motor stepping on the microtubule occurs at maximal stepping velocity because the load on the membrane-anchored motors is minute. Thus, the slipping velocity of membrane-anchored motors determines the microtubule gliding velocity. At steady state, the drag force on the microtubule in the solution is equal to the collective drag force on the membrane-anchored motors slipping in the viscous membrane. As a consequence, at low motor density, membrane-anchored motors slip back faster to balance the drag force of the microtubule in the solution. This results in a microtubule gliding velocity significantly lower than the maximal stepping velocity of the individual motors. In contrast, at high motor density, the microtubules are propelled faster with velocities equal to the maximal stepping velocity of individual motors. Because, in this case, the collective drag force on the motors even at very low slipping velocity, is large enough to balance the microtubule drag in the solution. The theoretical model developed based on this explanation is in good agreement with the experimental data of gliding velocities at different motor densities. The model gives information about the distance that the diffusing motors can isotropically reach to bind to a microtubule, which for membrane-anchored kinesin-1 is ~0.3 µm, an order of magnitude higher as compared to rigidly bound motors, owing to the lateral mobility of motors on the membrane. In addition, the model can be used to predict the number of motors involved in transport of a microtubule based on its gliding velocity. In the second part of the thesis, we investigated the effect of loose inter-motor coupling on the transport behavior of KIF16B, a recently discovered kinesin motor with an inherent lipid-binding domain. Recent studies based on cell biological and cell extract experiments, have postulated that cargo binding of KIF16B is required to activate and dimerize the motor, making it a superprocessive motor. Here, we demonstrate that recombinant full-length KIF16B is a dimer even in the absence of cargo or additional proteins. The KIF16B dimers are active and processive, which demonstrates that the motors are not auto-inhibited in our experiments. Thus, in cells and cell extracts Kif16B may be inhibited by additional factors, which are removed upon cargo binding. Single molecule analysis of KIF16B-GFP reveals that the motors are not superprocessive but exhibit a processivity similar to kinesin-1 indicating that additional factors are most likely necessary to achieve superprocessivity. Transport on membrane-anchored KIF16B motors exhibited a similar cooperative behavior as membrane-anchored kinesin-1 where the microtubule gliding velocity increased with increasing motor density. Taken together, our results demonstrate that the loose coupling of motors via lipid bilayers provides flexibility to cytoskeletal transport systems and induces cooperativity in multi-motor transport. Moreover, our ‘membrane-anchored’ gliding motility assays can be used to study the effects of lipid diffusivity (e.g. the presence of lipid micro-domains and rafts), lipid composition, and adaptor proteins on the collective dynamics of different motors.:Abstract vii 1 Introduction 1 1.1 Intracellular transport driven by motor proteins 2 1.2 Attachment of motor proteins to cargo 13 1.3 In vitro approaches to study transport by motor proteins 16 1.4 Aim of this study 23 2 Transport by kinesin-1 anchored to supported lipid bilayers 24 2.1 Formation and characterization of biotinylated SLBs 26 2.2 Anchoring kinesin-1 to biotinylated SLBs 28 2.3 Gliding motility of microtubules by kinesin-1 linked to SLBs 34 2.4 Theoretical description of gliding motility on diffusing motor proteins 40 2.5 Comparison of the gliding velocity between experiment and theory 46 2.6 Gliding motility on phase-separated SLBs 53 2.7 Discussion 55 3 Transport by KIF16B with an inherent lipid-binding domain 62 3.2 Biophysical characterization of KIF16B 70 3.3 Gliding motility of microtubules by KIF16B linked to SLBs 78 3.4 Transport of SUVs and lipid-coated beads attached to KIF16B 87 3.5 Discussion 90 4 Conclusion and outlook 96 5 Materials and methods 99 5.1 Reagents and solutions 99 5.2 Molecular biology 100 5.3 Protein expression and purification 104 5.4 In vitro motility assays 110 5.5 Image acquisition and data analysis 118 References 126 List of figures 141 List of tables 143 Abbreviations and symbols 144 Acknowledgements 147