O câncer cervical é um dos tipos de câncer mais comuns entre as mulheres, e a infecção persistente pelos HPV-16 e HPV-18 é responsável por 70% dos casos. As vacinas profiláticas disponíveis possuem alta eficácia na prevenção da infecção pelos tipos mais prevalentes de HPV. No entanto, este tipo de abordagem não beneficia mulheres que já apresentam lesões precursoras ou tumores cervicais avançados, e a busca por abordagens terapêuticas para esse tipo de câncer é considerada uma necessidade. A qualidade do antígeno representa um aspecto fundamental para o sucesso de vacinas terapêuticas baseadas em proteínas recombinantes. Neste sentido, os sistemas de expressão em células eucarióticas, como leveduras e células de mamíferos são considerados adequados para a produção de proteínas com aplicação biotecnológica. O objetivo principal deste trabalho contemplou a expressão das proteínas de fusão gDE7E6 do HPV-16 e do HPV-18 e a oncoproteína E7 do HPV-16 em células da levedura Pichia pastoris e expressão da gDE7E6 do HPV-16 e do HPV-18 em células de mamífero HEK293T e CHODG-44 para obtenção de antígenos purificados com futura aplicação em vacinas terapêuticas contra tumores associados ao HPV-16 e HPV-18. Os genes que codificam as proteínas gDE7E6 dos HPV-16 e HPV-18 e da E7 do HPV-16 foram clonados no vetor pPIC9K, os quais foram linearizados por digestão enzimática e utilizados na transformação da P. pastoris. A expressão das proteínas foi analisada nos tempos de 24, 48, 72 e 96 horas, no entanto, não foi observada a produção das proteínas no sobrenadante e nem no lisado celular. Diante desta constatação, iniciamos a expressão das proteínas gDE7E6 do HPV-16 e gDE7E6 do HPV-18 em células de mamíferos HEK293T e CHODG-44. As sequências genéticas das proteínas gDE7E6 do HPV-16 e do HPV-18 foram clonadas no vetor de expressão pNU1 e analisadas por digestão enzimática. Análises de SDS-PAGE e western blot demonstraram a expressão das proteínas gDE7E6 do HPV-16 e do HPV-18 em até 96 horas em células HEK293T. Em paralelo, realizamos a transfecção estável dos plasmídeos contendo as sequencias da gDE7E6 do HPV-16 e gDE7E6 do HPV-18 em células CHO-DG44. Com o intuito de aumentar a expressão das proteínas de interesse na população mista de CHODG-44, realizamos amplificação genômica com metotrexato (MTX), sendo possível observar aumento da expressão das proteínas, conforme aumento gradativo nas concentrações de MTX. Posteriormente, foram feitas tentativas para isolar um clone produtor das proteínas gDE7E6 HPV-16 e HPV-18, através de clonagem por diluição limitante e sistema automatizado, sendo possível isolar um clone para cada construção através de matriz semisólida, confirmado por western blot e citometria de fluxo. Apesar de demonstrar a expressão das proteínas de interesse em sistema de expressão baseado em células de mamífero, o rendimento obtido após a purificação por afinidade ao níquel foi extremamente baixo, o que dificulta a obtenção dos antígenos para fins vacinais. / Cervical cancer is one of the most common cancers among women, and persistent infection with HPV-16 and HPV-18 accounts for 70% of the cases. Available prophylactic vaccines are highly effective in preventing infection by the most prevalent types of HPV. However, this type of approach does not benefit women who already have precursor lesions or advanced cervical tumors, and the search for therapeutic approaches to this type of cancer is considered a necessity. Antigen quality represents a key aspect for the success of therapeutic vaccines based on recombinant proteins. In this sense, expression systems based in eukaryotic cells such as yeast and mammalian cells are considered suitable for the production of proteins with biotechnological applications. The main objective of this work was to express the gDE7E6 fusion proteins HPV-16 and HPV-18 and the E7 oncoprotein HPV-16 in Pichia pastoris and expression of gDE7E6 HPV-16 and HPV-18 in mammalian cells HEK293T and CHODG-44 to obtain purified antigens with future applications in therapeutic vaccines against HPV-16 and HPV-18 associated tumors. The genes encoding the gDE7E6 proteins HPV-16 and HPV-18 and E7 HPV-16 were cloned into the pPIC9K vector, which were linearized by enzymatic digestion and used in the transformation of P. pastoris. Expression of the proteins was analyzed at 24, 48, 72 and 96 hours, however, the production of the proteins in the supernatant and in the cell lysate was not observed. In light of this finding, we initiated the expression of gDE7E6 proteins HPV-16 and HPV-18 in mammalian cells HEK293T and CHODG-44. The genetic sequences of gDE7E6 proteins HPV-16 and HPV-18 were cloned into the pNU1 expression vector and analyzed by enzymatic digestion. SDSPAGE and western blot analyzes demonstrated expression of gDE7E6 proteins HPV-16 and HPV-18 within 96 hours in HEK293T cells. In parallel, we performed stable transfection of plasmids containing gDE7E6 HPV-16 and HPV-18 sequences into CHODG44 cells. In order to increase the expression of the proteins in the mixed population of CHODG-44, we performed genomic amplification with methotrexate (MTX), and it was possible to observe an increase in protein expression, as a gradual increase in MTX concentrations. Therefore, attempts were made to isolate a clone producing gDE7E6 proteins HPV-16 and HPV-18 by limiting dilution and automated system, being possible to isolate one clone for each construct through a semisolid matrix, confirmed by western blot and flow cytometry. Despite observing protein expression in mammalian cell-based expression system, the yield obtained after nickel affinity purification was extremely low, which makes it difficult to obtain the antigens for vaccine purposes.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants that can be modified to oxygenated PAH (oxyPAHs) derivatives. It is well known that oxyPAHs tend to be much more reactive than their parent compounds. Toxicity can be attributed to direct interaction with target molecules or generation of reactive oxygen species (ROS). Metals are another class of contaminant found ubiquitously throughout the environment. Some metals are toxic at levels below the 1:1 ratio predicted by the biotic ligand model and are thought to manifest toxicity through ROS generation. Often metals and PAHs occur as co-contaminants in industrialized environments, yet little is known about their potential co-toxicity or mechanisms of action in mammalian reproductive function. Previously, we described that a PAH, 9, 10-phenanthrenequinone (PHEQ), inhibited LH-stimulated progesterone secretion in dispersed rat corpus luteal (CL) cells (Nykamp et al., 2001). Viability was decreased in CL cells exposed to PHEQ and 1,2-dihydroxy-anthraquinone (1,2-dhATQ), but not their parent compounds phenanthrene (PHE) or anthracene (ANT). Similarly, LH-stimulated progesterone production in CL cells was inhibited by PHEQ and 1,2-dhATQ, but not PHE. Further investigation revealed that PHEQ, but not PHE, ANT nor 1,2-dhATQ generated ROS in CL cells. Viability experiments were repeated using the choriocarcinoma cell line JEG-3 with similar results. Various metals were assessed for their toxicity to both CL and JEG-3 cells. The endpoints used to measure viability were metabolic activity and membrane integrity. In general, metabolic activity was a more sensitive indicator of toxicity than membrane integrity. The order of toxicity for metals in CL cells was Hg2+ > Cd2+ > Zn2+ > Ni2+ > Cu2+ for metabolic activity and Hg2+ ≈ Zn2+ > Cd2+ > Cu2+ > Ni2+ for membrane integrity. Only Hg2+ and Cu2+ were tested in JEG-3 cells. While Cu2+ was non-toxic, EC50s for Hg2+ metabolic activity and membrane integrity were 20 mM and 23 mM, respectively. Experiments were designed to study the mixtures of metals and PAHs on viability, ROS production, and LH-stimulated progesterone production in CL cells. Mixtures of each metal with either PHEQ or 1,2-dhATQ were incubated with CL cells and their effect on metabolic activity and membrane integrity assessed. Generally, most metal/oxyPAH mixtures displayed only additive toxicity. However, mixtures of Cu2+ and PHEQ showed synergistic toxicity to both metabolic activity and membrane integrity. Mixture studies in JEG-3 cells used only combinations of Cu2+ or Hg2+ with PHEQ or 1,2-dhATQ. Similar results to metabolic activity and membrane integrity in CL cells were observed. Mixtures of Cu2+ and PHEQ or 1,2-dhATQ were tested in CL cells for their effect on LH-stimulated progesterone secretion and ROS production. Additive effects were observed in both LH-stimulated progesterone secretion and ROS production for Cu2+/1,2-dhATQ mixtures while synergistic effects for both parameters were seen with Cu2+/PHEQ. Efforts to determine the site of action for mixtures of Cu2+/PHEQ involved adding the cholesterol analogue, 22-OH cholesterol (22-OHC) to CL cells in the absence of LH. Cytochrome P450 side-chain cleavage (CYP450scc) enzyme operates constitutively and the addition of 22-OHC to CL cells resulting in a 5-fold increase in progesterone production without added LH. Kinetic assays with 22-OHC show that while progesterone secretion was inhibited with PHEQ addition alone, a further significant reduction with both Cu2+ and PHEQ was not observed. The use of forskolin, an activator of adenylate cyclase, did not show any significant enhancement of progesterone secretion with the addition of Cu2+/PHEQ compared to PHEQ alone. The potential targets of Cu2+/PHEQ mixture include any step in the steroidogenic cascade from activation of protein kinase A onward with the proteins of the mitochondria, cytochrome P450 side chain cleavage enzyme and steroidogenic acute regulatory protein, being the most likely. Differential display polymerase chain reaction (ddPCR) was a molecular approach taken to determine the effect of PHEQ on JEG-3 gene expression. The genes whose expression appeared to be up-regulated with PHEQ exposure were serine protease inhibitor, Alu repeat sequence, heterogeneous ribonuclear ribonucleoprotein C (hnRNP C), eukaryotic translation initiation factor 3 (eIF3), nucleoporin-like protein, eukaryotic translation elongation factor 1a1 (eEF1 a 1), autophagy-linked FYVE domain (Alfy), spectrin, and proteasome. Apparent down-regulated genes in JEG-3 cells after PHEQ exposure included poly(ADP-ribose) polymerase 10 (PARP10), polyglutamine binding protein-1 (PQBP-1), heterogeneous ribonuclear ribonucleoprotein C (hnRNP C), eukaryotic translation initiation factor 5A (eIF5A), and keratin. In both cell types, oxyPAHs were more toxic than their parent compounds. Metals showed greater toxicity to metabolic activity than to membrane integrity. Of the combinations tested, only PHEQ and Cu2+ exhibited synergistic toxicity. ROS generation was the likely mechanism behind PHEQ/Cu2+ toxicity. Both cell types used represent critical roles in human reproductive health. The proper production of progesterone, a critical hormone for the maintenance of pregnancy in mammals, represents a unique endpoint for the assessment of toxicity. These results illustrate the need to study modified oxyPAHs, metals and metal/oxyPAH mixtures for their potential impact on human reproductive health.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental contaminants that can be modified to oxygenated PAH (oxyPAHs) derivatives. It is well known that oxyPAHs tend to be much more reactive than their parent compounds. Toxicity can be attributed to direct interaction with target molecules or generation of reactive oxygen species (ROS). Metals are another class of contaminant found ubiquitously throughout the environment. Some metals are toxic at levels below the 1:1 ratio predicted by the biotic ligand model and are thought to manifest toxicity through ROS generation. Often metals and PAHs occur as co-contaminants in industrialized environments, yet little is known about their potential co-toxicity or mechanisms of action in mammalian reproductive function. Previously, we described that a PAH, 9, 10-phenanthrenequinone (PHEQ), inhibited LH-stimulated progesterone secretion in dispersed rat corpus luteal (CL) cells (Nykamp et al., 2001). Viability was decreased in CL cells exposed to PHEQ and 1,2-dihydroxy-anthraquinone (1,2-dhATQ), but not their parent compounds phenanthrene (PHE) or anthracene (ANT). Similarly, LH-stimulated progesterone production in CL cells was inhibited by PHEQ and 1,2-dhATQ, but not PHE. Further investigation revealed that PHEQ, but not PHE, ANT nor 1,2-dhATQ generated ROS in CL cells. Viability experiments were repeated using the choriocarcinoma cell line JEG-3 with similar results. Various metals were assessed for their toxicity to both CL and JEG-3 cells. The endpoints used to measure viability were metabolic activity and membrane integrity. In general, metabolic activity was a more sensitive indicator of toxicity than membrane integrity. The order of toxicity for metals in CL cells was Hg2+ > Cd2+ > Zn2+ > Ni2+ > Cu2+ for metabolic activity and Hg2+ ≈ Zn2+ > Cd2+ > Cu2+ > Ni2+ for membrane integrity. Only Hg2+ and Cu2+ were tested in JEG-3 cells. While Cu2+ was non-toxic, EC50s for Hg2+ metabolic activity and membrane integrity were 20 mM and 23 mM, respectively. Experiments were designed to study the mixtures of metals and PAHs on viability, ROS production, and LH-stimulated progesterone production in CL cells. Mixtures of each metal with either PHEQ or 1,2-dhATQ were incubated with CL cells and their effect on metabolic activity and membrane integrity assessed. Generally, most metal/oxyPAH mixtures displayed only additive toxicity. However, mixtures of Cu2+ and PHEQ showed synergistic toxicity to both metabolic activity and membrane integrity. Mixture studies in JEG-3 cells used only combinations of Cu2+ or Hg2+ with PHEQ or 1,2-dhATQ. Similar results to metabolic activity and membrane integrity in CL cells were observed. Mixtures of Cu2+ and PHEQ or 1,2-dhATQ were tested in CL cells for their effect on LH-stimulated progesterone secretion and ROS production. Additive effects were observed in both LH-stimulated progesterone secretion and ROS production for Cu2+/1,2-dhATQ mixtures while synergistic effects for both parameters were seen with Cu2+/PHEQ. Efforts to determine the site of action for mixtures of Cu2+/PHEQ involved adding the cholesterol analogue, 22-OH cholesterol (22-OHC) to CL cells in the absence of LH. Cytochrome P450 side-chain cleavage (CYP450scc) enzyme operates constitutively and the addition of 22-OHC to CL cells resulting in a 5-fold increase in progesterone production without added LH. Kinetic assays with 22-OHC show that while progesterone secretion was inhibited with PHEQ addition alone, a further significant reduction with both Cu2+ and PHEQ was not observed. The use of forskolin, an activator of adenylate cyclase, did not show any significant enhancement of progesterone secretion with the addition of Cu2+/PHEQ compared to PHEQ alone. The potential targets of Cu2+/PHEQ mixture include any step in the steroidogenic cascade from activation of protein kinase A onward with the proteins of the mitochondria, cytochrome P450 side chain cleavage enzyme and steroidogenic acute regulatory protein, being the most likely. Differential display polymerase chain reaction (ddPCR) was a molecular approach taken to determine the effect of PHEQ on JEG-3 gene expression. The genes whose expression appeared to be up-regulated with PHEQ exposure were serine protease inhibitor, Alu repeat sequence, heterogeneous ribonuclear ribonucleoprotein C (hnRNP C), eukaryotic translation initiation factor 3 (eIF3), nucleoporin-like protein, eukaryotic translation elongation factor 1a1 (eEF1 a 1), autophagy-linked FYVE domain (Alfy), spectrin, and proteasome. Apparent down-regulated genes in JEG-3 cells after PHEQ exposure included poly(ADP-ribose) polymerase 10 (PARP10), polyglutamine binding protein-1 (PQBP-1), heterogeneous ribonuclear ribonucleoprotein C (hnRNP C), eukaryotic translation initiation factor 5A (eIF5A), and keratin. In both cell types, oxyPAHs were more toxic than their parent compounds. Metals showed greater toxicity to metabolic activity than to membrane integrity. Of the combinations tested, only PHEQ and Cu2+ exhibited synergistic toxicity. ROS generation was the likely mechanism behind PHEQ/Cu2+ toxicity. Both cell types used represent critical roles in human reproductive health. The proper production of progesterone, a critical hormone for the maintenance of pregnancy in mammals, represents a unique endpoint for the assessment of toxicity. These results illustrate the need to study modified oxyPAHs, metals and metal/oxyPAH mixtures for their potential impact on human reproductive health.

Hydroxyurea was used as a model teratogen to investigate the role of oxidative stress and stress-response pathways in mediating developmental toxicity. When administered to pregnant mice during early organogenesis, hydroxyurea induced fetal death and growth retardation, as well as external and skeletal malformations. The malformed fetuses displayed hindlimb, vertebral column, and tail defects. Hydroxyurea treatment enhanced the production of 4-hydroxynonenal, a lipid peroxidation end product, in malformation sensitive regions of the embryo. Depletion of glutathione, a major cellular antioxidant, specifically enhanced hydroxyurea-induced malformations and elevated the region-specific production of 4--hydroxynonenal protein adducts in the embryo, without affecting the incidence or extent of hydroxyurea-induced fetal death or growth retardation. The major proteins modified by 4-hydroxynonenal were involved in energy metabolism. Thus, oxidative stress is important in the induction of malformations by hydroxyurea. / Exposure to hydroxyurea stimulated the DNA binding activity of activator protein 1 (AP-1), an early response redox-sensitive transcription factor. Activated AP-1 was composed mainly of c-Fos heterodimers. Glutathione depletion did not change the effects of hydroxyurea on AP-1/c-Fos DNA binding activities despite an augmentation of the incidence of embryo malformations. Mitogen-activated protein kinases (MAPKs) activate AP-1 in response to stress by post-transcriptional phosphorylation of AP-1 proteins. Hydroxyurea treatment dramatically enhanced the activation of stress-responsive p38 MAPKs and JNKs (c-Jun N-terminal protein kinases). Selectively blocking p38 MAPKs enhanced the incidence of fetal death, whereas selective inhibition of JNKs specifically elevated the limb defects induced by hydroxyurea. Thus, activation of stress-response pathways impacts on the response of the embryo to a teratogenic insult.

DNA methylation entails the addition of a methyl group to the 5-carbon of the cytosine base of the DNA. This modification is important during many biological processes such as imprinting, X-chromosome inactivation, cell differentiation as well as silencing of transposable elements (TEs). DNA methylation is dynamic during early mammalian development, despite being a more static mark in somatic cells. Global hypomethylation is a hallmark of epigenetic reprogramming in mammalian primordial germ cells (PGCs), the early embryo and in naïve embryonic stem cells (ESCs). Genome integrity is crucial during early development, as the germline DNA needs to be protected for future generations. Therefore, epigenetic reprogramming presents a critical phase for TE defence since presumably alternative silencing pathways need to be employed to limit their activity. In this thesis, I investigate the role of small RNAs to control TEs during global waves of DNA demethylation in cellular reprogramming, naïve pluripotency as well as early mammalian development. Following an introduction to the research questions, in chapter 3 I investigate the mechanism of TE regulation in an in vitro model of Dnmt1 deletion in mouse ES cells to recapitulate in vivo epigenetic reprogramming. I find that certain classes of TEs become transcriptionally upregulated and subsequently resilenced by a mechanism independent of DNA methylation. I identify ARGONAUTE 2 (AGO2) bound siRNAs as the prominent mechanism to control certain classes of TEs, while others appear to be regulated by redistribution of repressive histone modifications. In chapter 4, I construct Dicer constitutive and conditional KO ESCs in the background of the Dnmt1f l/f l ESCs using CRISPR-Cas9. I dissect the role of DNA methylation and of DICER dependent small RNAs on transcriptional changes of ESCs. Additionally, I find that DICER dependent small interfering RNAs (siRNAs) re-silence transcriptionally active TE classes. Finally, in chapter 5, I examine the role of small RNAs in TE silencing in different models of global hypomethylation in vivo and in vitro PGCs, during iPSC reprogramming and in a transition from serum to 2i culturing of mouse ESCs.

Essential genes are those whose presence is imperative for an organism's survival, whereas the functions of non-essential genes may be useful but not critical. Abnormal functionality of essential genes may lead to defects or death at an early stage of life. Knowledge of essential genes is therefore key to understanding development, maintenance of major cellular processes and tissue-specific functions that are crucial for life. Existing experimental techniques for identifying essential genes are accurate, but most of them are time consuming and expensive. Predicting essential genes using computational methods, therefore, would be of great value as they circumvent experimental constraints. Our research is based on the hypothesis that mammalian essential (lethal) and non-essential (viable) genes are distinguishable by various properties. We examined a wide range of features of Mus musculus genes, including sequence, protein-protein interactions, gene expression and function, and found 75 features that were statistically discriminative between lethal and viable genes. These features were used as inputs to create a novel machine learning classifier, allowing the prediction of a mouse gene as lethal or viable with the cross-validation and blind test accuracies of ∼91% and ∼93%, respectively. The prediction results are promising, indicating that our classifier is an effective mammalian essential gene prediction method. We further developed the mouse gene essentiality study by analysing the association between essentiality and gene duplication. Mouse genes were labelled as singletons or duplicates, and their expression patterns over 13 developmental stages were examined. We found that lethal genes originating from duplicates are considerably lower in proportion than singletons. At all developmental stages a significantly higher proportion of singletons and lethal genes are expressed than duplicates and viable genes. Lethal genes were also found to be more ancient than viable genes. In addition, we observed that duplicate pairs with similar patterns of developmental co-expression are more likely to be viable; lethal gene duplicate pairs do not have such a trend. Overall, these results suggest that duplicate genes in mouse are less likely to be essential than singletons. Finally, we investigated the evolutionary age of mouse genes across development to see if the morphological hourglass pattern exists in the mouse. We found that in mouse embryos, genes expressed in early and late stages are evolutionarily younger than those expressed in mid-embryogenesis, thus yielding an hourglass pattern. However, the oldest genes are not expressed at the phylotypic stage stated in prior studies, but instead at an earlier time point - the egg cylinder stage. These results question the application of the hourglass model to mouse development.

Tato diplomová práce se zabývá popisem principů kultivace embryonálních fibroblastových buněk myší (3T3), lidských endoteliálních buněk odebraných z pupečníkové žily (HUVEC) a epiteliálních buněk vaječníku čínského křečka (CHO) v mikrofluidních systémech simulujících kapiláry. Byly provedeny literární rešerše v oblasti realizací experimentu “Scratch Wound Healing Assay” v mikrofluidních systémech s použitím fibroblastů a endotheliálních buněk. V práci jsou dále popsány principy konfokální a fluorescenční mikroskopie a metody zpracování obrazů pro sledování buněčné migrace. Experimentální nastavení pro mikrofluidní realizaci “Scratch Wound Healing Assay” s použitím trypsinu – EDTA pro vytvoření rýhy, a konfokálního mikroskopu Leica TCS SP8 X pro následující snímání pořízených dat bylo navrženo a otestováno s dostatečným počtem opakování. Vhodný algoritmus pro analýzu buněčné migrace byl napsán v programovacím prostředí Matlab. Závěrem této práce je diskuze získaných výsledků.

Meiosis is a specialized cell division that produces haploid cells (gametes) from diploid progenitors. During meiosis parental chromosomes (homologs) need to pair, synapse and eventually segregate. Faithful chromosome segregation depends on chromosome recombination. In the beginning of prophase I programmed double strand breaks (DSBs) are introduced in meiotic cells by SPO11 enzyme. DSBs are positioned at hotspot sites that are specified by that action of DNA-binding histone methyltransferase PRDM9. Specific enzymes act at the site of breaks to create 5’ single stranded DNA ends. With the assistance of the strand exchange proteins DMC1 and RAD51 these ends invade homologous DNA sequence and DSB repair is initiated. DSB repair can be completed either as a crossover (reciprocal exchange of DNA) or as a non-crossover. Crossover events lead to the formation of chiasmata between homologs and ensure proper segregation during the first meiotic division. An interesting feature in male meiosis is the XY chromosomes. The shared region between sex chromosomes is short and is called pseudoautosomal region (PAR). Due to their large non synapsed region, XY chromosomes need to be transcriptionally silenced. Thus they are covered with the phosphorylated histone variant H2AX (γH2AX) forming the so called sex body. PAR region has higher density of DSBs than autosomes and it had been shown that sex chromosomes undergo delayed homologous pairing. Nevertheless little is known how meiotic recombination is regulated in PAR region of sex chromosomes. In close proximity with sex body it has been found a structure named dense body (DB). There are few reports suggesting that DB contains RNAs/proteins but no DNA. Its role in meiosis was unclear because no structural component had been described. In the present thesis the role of two meiotic expressed genes is described. In our group after performing RNA screens we identified several genes that are highly expressed during meiotic prophase I. Based on the expression profile we selected polycomb-related sex comb on midleg like 1 (Scml1) gene and the ankyrin repeat domain 31 (Ankrd31) to study their role in mammalian meiosis.:List of figures i List of abbreviations ii 1. Introduction 1 1.1 Gametogenesis 1 1.2 Meiotic prophase I 2 1.2.1 Meiotic recombination 4 1.2.2 Regulation of meiotic recombination 7 1.2.2.1 Meiotic recombination hotspots and PRDM9 activity 7 1.2.2.2 Meiotic surveillance mechanisms 8 1.3 Unique properties of XY recombination 9 1.4 Sex chromatin associated structure: The dense body 10 1.5 Aim of the thesis 11 2. Publications 12 3. Discussion 92 4. Summary 98 5. References 102 Acknowledgements 108 Declarations 109

The goal of this thesis was to develop a high-throughput shotgun-MS lipidomics method to qualitatively and quantitively analyze the major mammalian brain ganglioside classes: GM1, GD1, GT1 and GQ1. As a starting point for the method to be developed, a modified ganglioside extraction method from Svennerholm and Ladisch was used (Svennerholm and Fredman, 1980; Ladisch and Gillard, 1985). The efficiencies and the impact of different extraction procedures to the overall performance were evaluated with a software called OptiVal™. The evaluation showed that the most important steps of the protocol are the salt concentration of the water phase during the 2-phase extraction, and 10 mM NaCl yielded the best sensitivity. Also, the number of washing steps with water during reverse solid phase extraction using C18 resin has a significant effect. The next step was to find suitable standards for quantification of the individual ganglioside classes. Since deuterated and alike ganglioside standards were commercially not available, we initially used a deuterated PE standard with limited success. A collaboration with the Ludger Johannes lab provided us with modified C17-ganglioside standards. The term “modified” describes the enzymatic exchange of the fatty acid in the hydrophobic tail by a 17-carbon atom long fatty acid. Since odd numbered fatty acids occur very rarely in nature, it is possible to use the measured intensity of the modified ceramide headgroup of 35:1 (Sphingosine C18:1 + Fatty Acid C17:0) to quantify natural gangliosides. Ideally, we would need to have a fitting modified C17-ganglioside standard for each class to be quantified. Since first only GM1 as a modified standard was available, it was necessary to determine response factors (RFs) for the ganglioside classes GD1, GT1 and GQ1. RFs were assessed empirically by titrating a variety of equimolar concentrations of the modified C17-GM1 standard versus wildtype standards of the other ganglioside classes. After establishment of the RFs it was possible to determine the limits of detection (LOD) and quantification (LOQ) for the ganglioside classes GD1, GT1 and GQ1 - with regard to the modified C17-GM1 standard. When the modified C17-standards for GD1 and GT1 became available, I was able to find out whether the correct internal standards are superior to the proxy method via response factors. The results clearly showed that the use of a correct class standards is preferable. For GQ1 no modified C17-standard was obtainable, therefore this class still has to be quantified via RFs. Experiments showed that the modified C17-GT1 standard is best suited for that. Another major goal was to integrate the ganglioside method into the general lipid analysis workflow of the high-throughput shotgun mass spectrometry platform that we were using. To achieve these goals adjustments on the evaluated (=old) protocol had to be done. These adjustments included changes in the extraction steps from the Svennerholm & Ladisch more into the direction of a Bligh & Dyer based extraction method. This meant abandoning the 2-phase extraction step as well as the chloroform/methanol/water (C/M/W) 4:8:3 extraction, in favor of a C/M 10:1 followed by a C/M 2:1 extraction of 150 mM ammonium-bicarbonate water solution. The goal behind this was to enable a combination of the global lipidome extraction (Surma et al., 2015) with the ganglioside extraction. Another important improvement was scaling up the extraction process. The use of standard single solid phase extraction (SPE) cartridges was limiting the extraction throughput to only 24 samples at a time, therefore the single SPE cartridges were replaced with the 96-well SPE SOLA™ plates. To process the SOLA™ plates it was necessary to establish the usage of a vacuum manifold. Combined, these changes lowered the overall process time of the protocol from nearly two working days to one working day, without significant loss of sensitivity regarding the measured sample concentrations. This was assessed by performing the mouse brain tissue titration experiment, with all three modified C17-ganglioside class standards GM1, GD1 and GT1. Finally, the established method was applied to investigate the difference in ganglioside levels in the cerebellum compared to the brain hemispheres in mice of different age. First the C/M 10:1 and 2:1 extraction was done for the analysis of all non-ganglioside lipids in the sample. The leftover water phase was then loaded onto the SOLA™ plates and processed with the new protocol. The results matched the given goals - to establish a protocol to measure and quantify the four major brain ganglioside classes in combination with the global lipidomics in a high-throughput manner - and thus were a success. To the best of our knowledge, this was the first time such a broad lipidomic measurement has been performed, hence no other studies exist to which the outcome could be compared.

This review provides a short historical background to the field of axonal regeneration and discusses the advances made in over 100 studies between 2007 and 2012 in understanding the molecular mechanisms underlying the conditioning lesion and regeneration of primary sensory axons in the dorsal columns of the spinal cord. Treatment strategies to stimulate axon growth and reinnervation of the spinal cord through the dorsal root entry zone and of the dorsal column nuclei in the medulla are highlighted. Major breakthroughs have been made, e.g., reinnervating the nucleus gracilis in the medulla using neurotrophic factor gradients and grafts as relays and identifying chondroitin sulfate proteoglycan receptors. The experimental accessibility of the dorsal column axons has also resulted in new technological advances, including live imaging. Last, future directions are discussed, including some challenges of translation to humans.