Cancer biology and machine learning represent two seemingly disparate yet intrinsically linked fields of study. Cancer biology, with its complexities at the cellular and molecular levels, brings up a myriad of challenges. Of particular concern are the deviations in cell behaviour and rearrangements of genetic material that fuel transformation, growth, and spread of cancerous cells. Contemporary studies of cancer biology often utilise wide arrays of genomic data to pinpoint and exploit these abnormalities with an end-goal of translating them into functional therapies. Machine learning allows machines to make predictions based on the learnt data without explicit programming. It leverages patterns and inferences from large datasets, making it an invaluable tool in the modern era of large scale genomics. To this end, this doctoral thesis is underpinned by three themes: the application of machine learning, multi-omics, and cancer biology. It focuses on employment of machine learning algorithms to the tasks of cell annotation in single-cell RNA-seq datasets and drug response prediction in pre-clinical cancer models. In the first study, the author and colleagues developed a pipeline named Ikarus to differentiate between neoplastic and healthy cells within single-cell datasets, a task crucial for understanding the cellular landscape of tumours. Ikarus is designed to construct cancer cell-specific gene signatures from expert-annotated scRNA-seq datasets, score these genes, and distribute the scores to neighbouring cells via network propagation. This method successfully circumvents two common challenges in single-cell annotation: batch effects and unstable clustering. Furthermore, Ikarus utilises a multi-omic approach by incorporating CNVs inferred from scRNA-seq to enhance classification accuracy. The second study investigated how multi-omic analysis could enhance drug response prediction in pre-clinical cancer models. The research suggests that the typical practice of panel sequencing — a deep profiling of select, validated genomic features — is limited in its predictive power. However, incorporating transcriptomic features into the model significantly improves predictive ability across a variety of cancer models and is especially effective for drugs with collateral effects. This implies that the combined use of genomic and transcriptomic data has potential advantages in the pharmacogenomic arena. This dissertation recapitulates the findings of two aforementioned studies, which were published in Genome Biology and Cancers journals respectively. The two studies illustrate the application of machine learning techniques and multi-omic approaches to address conceptually distinct problems within the realm of cancer biology.
View lessDormancy represents a vital biological mechanism facilitating the continuity of various life forms across generations and in response to challenging environmental conditions. In the early stages of mammalian development, embryos can enter a state of dormancy known as diapause. In diapause they can remain viable within the uterus for extended periods, lasting from weeks to months. This dormancy state can be mimicked in vitro by inhibiting the central cellular growth pathway, mTOR. However, the cellular mechanisms that maintain the original cell identity amidst the transcriptionally silent landscape of dormancy remain elusive. This thesis demonstrates the significance of safeguarding cis-regulatory elements from transcriptional silencing to preserve pluripotency during dormancy. Further, this thesis elucidates a TET-transcription factor (TF) axis, wherein TET-mediated DNA demethylation and the recruitment of methylation-sensitive TFs orchestrate chromatin modifications essential for transitioning into dormancy. Disruption of TET activity compromises both pluripotency and the viability of dormant embryos, whereas its augmentation enhances survival rates. These findings uncover a critical mechanism governing the preservation of cellular identity during dormancy, with implications for regenerative medicine and understanding disease processes.
View lessThis thesis describes the effects of bedrock properties, climate, and biota on erosion, weathering, and landscape morphology along the Coastal Cordillera of Chile. Field sites sit along a climate and vegetation gradient, and include a semi-arid, mediterranean, and humid site, all underlain by granitoid lithology. In situ 10Be cosmogenic radionuclide analysis was used to measure erosion and weathering rates of bedrock, boulders, soils, and stream sediment in each field site, and topographic analysis tools (Topotoolbox in MATLAB) were used to quantify topographic metrics such as slope and drainage density. Field surveys were additionally conducted, including sediment and boulder grain size distributions, and bedrock geochemistry and mineralogy. The first study focuses on the effects of bedrock fractures and immobile boulders on differential denudation rates within in each field site. Results from cosmogenic radionuclide analysis and field measurements indicate that unfractured bedrock and large hillslope boulders erode more slowly than the surrounding soil, and form topographic highs. The second study focuses on boulders in streams, and results from cosmogenic radionuclide analysis indicate that boulders in more humid climates are more easily transported and therefore have shorter residence times in streams. The third study focuses on lithological controls on landscape morphology, and results imply that subtle differences in granitoid lithology can set drainage density through differences in infiltration and erodibility.
View lessLiver disease causes two million deaths annually and represents a significant and growing public health burden, with cirrhosis and primary liver cancer accounting for the majority of these deaths. Liver cirrhosis, resulting from chronic inflammation and fibrosis of the liver, is a significant risk factor for the most prevalent type of primary liver cancer, hepatocellular carcinoma. The pleiotropic chemokine (C-X-C motif) ligand 12 (CXCL12) has been implicated in both liver fibrosis and primary liver cancer. By signaling through its two cognate receptors, C-X-C motif receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3), CXCL12 may promote both liver fibrosis and tumor growth, progression, and metastasis. In addition, CXCL12 can also control immune cell egress from the bone marrow and their recruitment to the tumor, which may shape a pro-tumorigenic tumor microenvironment. In this study, the role of CXCL12 on liver fibrosis and primary liver cancer was further investigated, using experimental settings intended to explore CXCL12 inhibition as a potential target for novel interventions in these disease conditions. To address this in liver fibrosis, NOX-A12, a CXCL12-neutralizing RNA oligomer, was applied in two experimental mouse models, induced either by chronic carbon tetrachloride (CCl4) injections or by feeding a high fat methionine-choline deficient (MCD) diet. To explore the impact of CXCL12 on primary liver cancer, NOX-A12 was used in a model of diethylnitrosamine (DEN) induced liver cancer combined with either CCl4 to create a fibrotic environment or with a high-fat, high-sugar, and high-cholesterol Western diet (WD) to induce non-alcoholic fatty liver disease (NAFLD). CXCL12 inhibition with NOX-A12 had no impact on liver fibrosis but led to a prolonged inflammation after injury cessation. Furthermore, NOX-A12 increased chemokine levels in blood plasma, which was accompanied by an increase of peripheral blood myeloid cells. In the liver, CXCL12 inhibition provoked changes in hepatic monocyte-derived macrophage (MoMF) populations characterized by a decrease of CD11c+MHC-II+ MoMF and a relative increase of immature Ly6C+ MoMF. In addition, CXCL12 inhibition drastically reduced eosinophils in the liver of CCl4-treated, but not in NAFLD livers. Intriguingly, NOX-A12 promoted tumor growth both in the fibrosis- and in the NAFLD-associated model of DEN-induced liver cancer, despite reducing tumor-infiltrating MoMF and increasing cytotoxic CD8+ T cells in tumor lesions. Moreover, CXCL12 inhibition activated vascular remodeling in tumor microvessels, evident by an upregulation of CXCR4 on endothelial cells and increased expression of angiogenic and anti-angiogenic genes, particularly pronounced in NASH-HCC after therapeutic treatment with NOX-A12. Taken together, these data suggest a role for CXCL12 in chronic inflammation resolution, and in limiting primary liver cancer, mediated by a multi-faceted re-shaping of the tumor microenvironment.
View lessAn increasing number of people engage in endurance exercise, however, current literature lacks information regarding changes during ultramarathons of very long distances at very low intensity, i.e., walking instead of running. In addition, adverse conditions, like very cold climate, have not been investigated in such settings. Furthermore, the physiological processes linking functions like energy expenditure, metabolism, stress, and resilience, are still not well understood or lack investigation all together. The Yukon Arctic Ultra (YAU) has been coined to be the longest and the coldest ultramarathon in the world, as it challenges athletes to complete the very long distance of 690 km under the extremely cold climate conditions of North-Canadian subarctic winter. YAU athletes face the challenges of long-term endurance exercise in a very cold climate and under diminished resting conditions. Thusly, the YAU served as a model to investigate physiological changes among healthy athletes during an ultra-long endurance exercise in extremely cold climate. The presented investigation revealed considerable increases in energy expenditure among the athletes, of up to more than four times resting metabolic rate, along with a marked energy deficit, changes in body composition with reductions in fat mass while fat free mass could mostly be retained, possibly to the exercise- and cold-induced release of myokines like irisin and follistatin. Furthermore, analysis of vegetative control expressed through heart rate variability, as well as of mood through psychometric measurements, revealed that the more successful athletes, who would eventually be able to finish the race, showed better adaptation to the race demands, with less depression, anxiety and anger, but greater vigor and higher alertness. They also exhibited a faster restoration of vagal predominance during the race with a better ability to relax and restore, leading to less sleepiness and greater vigilance compared to the non-finishing athletes. Resilience, as the ability to cope with stressful events, appears to be a key element during such a race and neuropeptide Y has been discussed as a mediator in resilience reactions. The analyses revealed that during this race, neuropeptide Y was associated with less confusion and better quality of recovery among the finisher group and that overall neuropeptide Y was increasingly released among the athletes compared to the less challenged control group. Another influence was the factor sex, indicating that the female athletes were not only as successful as the male participants to complete the whole race, but that women completed an overall greater distance, when accounting for all covered distances. Women, with a moving speed of 3.7 km/h, were considerably slower than men at 4.6 km/h, which may have saved energy stores and allowed them to predominantly use fat as a long-term energy source. In addition, it was shown that ultra-long endurance exercise may lead to shedding of endothelial glycocalyx elements and that these elements appear to be differently susceptible to that shedding. Sex, age, and covered distance all appeared to have an influence on the observed changes. The analyses of physiological changes during the Yukon Arctic Ultra have revealed a multitude of endurance- and cold-exposure-related alterations. This ultramarathon has thusly proven to be an outstanding model to study human adaptation capabilities to extreme environments under real-life field conditions that could otherwise not be replicated in a laboratory setting.
View lessNeuronal branching is a developmental program, by which neurons acquire their complex morphologies. This highly dynamic process relies on various signaling molecules, cues and proteins such as the phospholipid-phosphatase related protein (PLPPR) family. PLPPR3, a family member of PLPPRs, is a transmembrane protein with a long intracellular domain (ICD) that primarily localizes to the axonal plasma membrane. Previous work demonstrated that PLPPR3 is highly expressed during neuronal development and can induce axonal filopodia. Prior to my project, no work had described a conclusive model of PLPPR3 ICD-facilitated filopodia formation. The work presented here, establishes the purification of intracellular domain of PLPPR3 (Chapter 1). I gathered evidence that PLPPR3 ICD is a highly disordered protein domain utilizing circular dichroism spectroscopy and limited proteolysis (Chapter 2). Using in vitro assays, I showed that PLPPR3 ICD undergoes liquid-liquid phase separation (LLPS) (Chapter 3). LLPS is an interaction-driven process that orchestrates intrinsically disordered regions to form condensates, which serve as membrane less reaction compartments. PLPPR3 ICD condensates, follow liquid-like properties of phase separating proteins such as coalescence, fusion and circularity. With help of a blue-light inducible optogenetic PLPPR3 ICD CRY2 fusion construct, I was able to validated these properties in cells. To identify driving regions of PLPPR3 ICD LLPS, I utilized various deletion constructs and narrowed down the region to the membrane distal part of the protein. I further conceptualize a model of PLPPR3 ICD-facilitated filopodia formation in vitro (Chapter 4). I provide evidence that PLPPR3 ICD condensates can reshape giant unilamellar vesicle (GUV) membranes, by attracting PLPPR3 ICD condensates to the GUV interface. Using fluorescence microscopy, I demonstrate that PLPPR3 ICD condensates co-partion actin monomers and serve as actin nucleating compartments. Hence, I exhibit ring-shaped F-actin structures that polymerize out of PLPPR3 ICD condensates. I revealed that the formation of ring-shaped F-actin structures depends on the formation of PLPPR3 ICD condensate, while the polymerization from the condensates depend on the local actin concentration. In summary, the presented work showed that PLPPR3 ICD forms liquid-like condensates, which nucleate actin. Considering PLPPR3s proven function to induce filopodia, this thesis provides a compelling model mechanism of PLPPR3 ICD condensates facilitating filopodia formation.
View lessDas Buch von Julia Weber zeigt, auf welche Weise das von Aristoteles herrührende Verständnis von virtuellen Kräften als real nicht nachweisbaren, aber dennoch wirksamen Kräften den philosophischen Diskurs bis in die Moderne geprägt hat. Es verfolgt die Entwicklungen von den philosophischen Diskussionen um die Existenz von virtuellen Kräften in der Antike und im Mittelalter über das Aufkommen von virtuellen Räumen in der Frühen Neuzeit bis hin zur Entstehung von virtuellen Welten in der Literatur des 18. Jahrhunderts und macht auf diese Weise die bisher kaum nachvollzogenen Kontinuitäten und Verschiebungen zwischen antiken philosophischen Kraftdiskussionen und zeitgenössischen virtual realities sichtbar.
View lessThis work is focused on systematic studies of the correlation between the morphology of semiconductor nanoparticles (NPs), their luminescence properties and the application relevant features of polymer microparticles (PMPs) stained with these NPs. The synthesis of luminescent, quantum dot (QD)-stained polystyrene microparticles (PSMPs) was first developed and optimized for CdSe/CdS-QDs, which was later expanded to quantum rods (QRs) and nanoplatelets (NPLs) of the same composition. Apart from nanoscale luminophores, the organic dye Nile red has been employed. While the incorporation of dyes is comparatively easy and well studied, the use of luminescent NPs such as QDs often goes along with challenges such as NP aggregation or excessive loss of fluorescence intensity, which were addressed in this work. Additionally, a systematic investigation of nanoscale, core/shell-type luminophores of different shell thicknesses, materials/composition and shapes before, during and after the PSMP synthesis was performed to deduce a connection of NP architecture with their applicability for the synthesis. The work also includes the introduction of surface functional groups (carboxy) to the PSMP surface, and evaluates the influence of the exact synthesis route on the properties of the formed particle, comparing NP addition before the polymerization and incorporation by a postsynthetic swelling procedure.
View lessGene delivery is a powerful and promising therapeutic tool for treating a wide range of diseases. To ensure the safe and efficient delivery of the genetic material and to prevent degradation, the use of cationic dendritic vectors is particularly popular because of their ability to complex negatively charged genetic material and to form polyplexes. Branched cationic polymers, also called dendrimers, like poly(amidoamine) (PAMAM) have already demonstrated promising results in gene delivery. However, PAMAM has also been associated with cytotoxic effects and heterogeneity. To overcome these limitations, in this thesis, four well- defined polylysine-based dendrons with different functional groups have been synthesised in a reproducible manner using solid-phase peptide synthesis. Targeted gene therapy is a valuable tool for the more specific treatment of cancer or other diseases without the destruction or damage of healthy cells. In this work, as a proof of concept, cancer and liver cells were investigated as targets. For liver targeting, the large surface protein (LSP) derived from hepatitis virus B and its preS1 binding domain, as well as apolipoprotein A1 (ApoA1), which is part of the high-density lipoprotein, were chosen as liver specific targeting moieties. The epidermal growth factor (EGF) was used as a cancer targeting ligand. To avoid cross-linking and to obtain a homogeneous platform, ligand plasmids were designed to have only a single conjugation site. Two ligand variants were successfully recombinantly expressed in Escherichia coli Rosetta (K-EGFRR) and NiCo21 (C-ApoA1) with a yield of 4–6 mg/L expression approach. The ligand-cell interaction was evaluated by flow cytometry and fluorescence microscopy while the ligand-receptor interaction was evaluated by enzyme-linked immunosorbent assay and surface plasmon resonance. The affinity of the EGF variant was even higher than that of wild-type EGF (KD: 5.9 vs 7.3 nM). In addition, heterobifunctional polyethylene glycol linkers were attached to the ligands to allow orthogonal click conjugation to a cargo of choice, in this case the synthesised dendrons. The dendrons were polyplexed with plasmid DNA encoding for enhanced green fluorescence protein (eGFP) or luciferase at different N (dendron amines)/P (DNA phosphates) ratios (0.5–16). In addition, K-EGFRR was either electrostatically incorporated into the polyplex or covalently bound by strain promoted azide-alkyne cycloaddition using different EGF/DNA weight/weight ratios (0.1, 1, 10). The polyplexes were analysed by dynamic light scattering (size: 270–1412 nm and polydispersity index: 0.13–0.99). Transfection efficiency was assessed by measuring the expression levels of eGFP or luciferase. As most of the DNA cargos are trapped and degraded inside endolysosomes, the saponin SO1861 (0.4 μM and 4 μM) was added as an endosomal escape enhancer to the cells either alone (SO1861) or in targeted form conjugated to K-EGFRR (SO1861-EGF). While the polyplexes containing the newly synthesizing polylysine dendrons did not show successful transfection of genetic material, it was demonstrated that PAMAM was able to do so and that the efficiency of PAMAM polyplexes was increased 6-fold by using SO1861-EGF.
View lessDiese Studie nimmt den Straftatbestand des Feminizids im lateinamerikanischen Kontext in Romanen von Diego Zúñiga (Chile, 2015), Laura Restrepo (Kolumbien, 2018) und Fernanda Melchor (Mexiko, 2017) in den Blick. Es wird gezeigt, wie die literarischen Texte die systemische und intersektionale Dimension des Feminizids beleuchten. Dabei wird deutlich, dass Feminizid interdisziplinär untersucht werden muss, um die Begrenzungen völker- und strafrechtlicher Normen aufzuzeigen. Feminizid ist nur im Strafrecht lateinamerikanischer Staaten verankert. Dieses Alleinstellungsmerkmal wird von den literarischen Texten aufgegriffen, die in der Studie in ihren Verbindungen zu einschlägigen Rechtstexten analysiert werden. Die Studie versteht Literatur als eigene Erkenntnisform, die eine Korrekturforderung für den gesellschaftlichen und juristischen Umgang mit Feminiziden über Lateinamerika hinaus beinhaltet und dabei insbesondere deren Straflosigkeit markiert. Sie leistet dabei einen Beitrag zur interdisziplinären Feminizidforschung, die gerade im deutschsprachigen Raum noch ganz am Anfang steht.
View lessThe Amaranthaceae are a nearly cosmopolitan flowering plant family that encompasses species of high economic value as food, forage, and ornamentals. Other species are of cultural value for traditional medicine or in traditional rituals of African tribes. Amaranthaceae are notable in terms of their diverse ecology, physiology and morphology, and represent a perfect study group for diverse scientific questions. In recent molecular studies there was evidence for the existence of the so-called achyranthoid clade, within Amaranthaceae, which includes most of the genera with African distribution plus a few genera outside the African continent. Many African genera of the Amaranthaceae exhibit unique inflorescences that include sterile flowers modified to form hooks or spines. Considering that the abundance of large terrestrial herbivores increased on the African continent with the expansion of grassland and savannah ecosystems, modified sterile flowers facilitating dispersal by large animals through epizoochory could have been an innovation that boosted the diversification of an African achyranthoid clade within the Amaranthaceae. To test this hypothesis, for Chapter 2 an extensively sampled phylogeny comprising 26 of the 31 achyranthoid genera as well as representatives of all other lineages of Amaranthaceae was generated, which also served as a base for downstream analyses presented in the other chapters. Phylogenetic tree inference employed the nuclear genomic region ITS as well as the plastid genomic regions trnK/matK, rpl16, and trnL-F, using parsimony, likelihood and Bayesian inference methods. Moreover, in the second chapter divergence times were estimated for this clade, trait-dependant changes of species diversification rates were evaluated using state-dependent speciation and extinction models, and ancestral character states for modified sterile flowers were reconstructed. The Achyranthoids were found to be a major clade of the Amaranthaceae, comprising mostly African members. Phylogenetic relationships within this clade were well resolved and supported two main subclades. Several genera were found to be polyphyletic. According to the results, the Achyranthoids started to diversify ~28 million years ago, and modified sterile flowers evolved multiple times within this clade. An asymmetry in transition rates towards the gain of sterile flowers was observed, whereas no trait-dependent increase in species diversification rates was detected. Bayesian rate heterogeneity analyses indicated that the Achyranthoids diversified without significant rate shifts. The accumulation of modified sterile flowers within Achyranthoids appears to result from the higher transition rates in favour of modified sterile flowers. Multiple gains suggest an adaptive value for this trait. However, epizoochory does not appear to have fuelled species diversification in Achyranthoids, possibly due to extensive gene flow through regularly migrating mammals, which limits the possibility of speciation by isolation. In Chapter 3 the pollen of the achyranthoid taxa was investigated, based on the phylogeny obtained in the previous chapter. The aim was to detect synapomorphies for monophyletic groups derived from analyses of molecular data. Morphological characters should thereby substantiate molecular results and facilitate the description of taxonomic entities. The complete character syndrome, to which was referred to as stellate pore ornamentation in earlier studies was shown to be limited to genera of subclade I within Achyranthoids. Several pollen characters were observed as highly discriminant between subclade I and II of Achyranthoids as well as between genera and species within these clades, such as the number of apertures in species of Psilotrichum Blume, the strongly vaulted mesoporia in Kyphocarpa (Fenzl) Schinz, and the dodecahedral pollen shape in Sericocoma heterochiton Lopr. and Kyphocarpa, as well as the unique pollen shape observed in Centemopsis Schinz, where pollen grains resemble the geometry of a football. The shape depicts a truncated icosahedral, constituted of 12 pentagons, corresponding to the placement of apertures, and 20 hexagons, corresponding to the areas of mesoporia. Also, the mesoporia was observed to be uniquely vaulted inwards while apertures appear uplifted and microspines are specially arranged throughout all species of Centemopsis. Chapter 4 focused on the achyranthoid subclade II, in which a high degree of non-monophyly was observed at genus- and species level in the molecular phylogeny derived in the second chapter. In order to facilitate the description of taxonomic entities, generate a new genus concept which renders genera and species monophyletic, and complement the pollen morphological data, a set of 24 characters covering habit and vegetative morphology as well as inflorescence and floral morphology, was established to be used in ancestral character state reconstructions. In order to further improve tree resolution and node support compared to the second chapter, the sequence data were complemented with sequences of the plastid intergenic spacer between rpl32-trnLUAG and the two spacers in the rps4-trnT-trnLUAA region. Phylogenetic trees of the nuclear and the combined plastid regions were largely congruent and almost fully resolved with maximum support for most lineages and showed a further subdivision of Achyranthoids II into subclade II A (Achyranthes L. plus allies) and subclade II B (Cyathula Blume plus allies). Based on molecular and morphological results, a new genus concept for the genera and species of subclade II was established, which renders the genera of subclade II monophyletic, and a commented checklist was provided, including complete homotypic and heterotypic synonymy of the genera and species, two newly established genera, resurrection of one species name, and several new combinations.
View lessAging processes and biological sex influence physiological and pathophysiological mechanisms in the heart and may, therefore, affect the treatment effects in patients with CVD. The research projects included in this habilitation thesis contribute to better understanding of age and sex differences in inflammatory processes and mitochondrial homeostasis in cardiomyopathies (i.e., dilated cardiomyopathy and inflammatory dilated cardiomyopathy). We demonstrated age and sex-specific mechanisms in the healthy aging heart, leading to a female-specific impaired metabolic sensing and a pro-inflammatory shift due to downregulation of two key NAD+-dependent deacetylases (Sirt1 and Sirt3) in older women. In addition, we identified an impaired mitochondrial homeostasis and reduced anti-oxidative defense in older hearts of patients with end-stage DCM, which was accompanied by an enhanced pro-inflammatory response in both sex-dependent and -independent manners. To further demonstrate the role of age and biological sex in cardiomyopathies, we examined their effects on inflammation, mitochondrial homeostasis, autophagy, and cellular senescence in patients with end-stage inflammatory dilated cardiomyopathy. Our study demonstrated a compromised expression of mitochondrial proteins, which was accompanied by disturbed autophagy, pro-inflammatory shift and cellular senescence in older women with DCMI. In contrast, older male DCMI hearts showed a preserved mitochondrial homeostasis and pro-inflammatory/anti-inflammatory balance, but accelerated autophagy. The study of sex differences in autoimmune myocarditis, using the animal model of experimental autoimmune myocarditis, revealed a pro-inflammatory and pro-fibrotic phenotype in male EAM rats, which was accompanied by a severe cardiac dysfunction in males with autoimmune myocarditis. In this animal model, female rats showed less inflammation and cardiac remodeling, leading to a preserved cardiac function. Part of this thesis deals with the study of sex differences in the polarization of murine macrophages, which might influence the development and progression of myocarditis and dilated cardiomyopathy. The study suggests a stronger pro-inflammatory response to a pro-inflammatory environment in male murine bone marrow macrophages, which was accompanied by a sex-dependent pro-inflammatory and pro-fibrotic responses in male activated cardiac fibroblasts. The sex-dependent macrophage and fibroblast activation might have important effects on cardiac inflammatory diseases, e.g., myocarditis.
View lessClinical experience has shown that patients who undergo total knee arthroplasty (TKA) may develop ankle symptoms. This habilitation aimed to analyze if this phenomenon could be replicated in a clinical trial. Another goal was to understand the biomechanical mechanisms which are responsible for ankle pain after TKA. In retrospective as well as prospective clinical trials it could be proven that about 20-25 % of the patients after TKA developed ankle pain after TKA. Preoperatively, the presented studies here could show that the hind foot is unable to sufficiently compensate for high-grade frontal deformities of the knee which can ultimately lead to osteoarthritis at the ankle joint. In another publication on the preoperative status it could be demonstrated that high-grade frontal deformities at the knee joint do not induce ligamentous ankle instabilities. Risk factors for developing ankle pain after TKA were identified. Patients with varus knee osteoarthritis and increased ankle pain after TKA had an increased talar tilt on radiographs already before the operation which could not be corrected by TKA. Patients with valgus knee osteoarthritis and increased ankle pain after TKA had a pathologically lateralized gait line before the operation. These studies underscore the importance to clinically evaluate the ankle joint before TKA in order not to miss patients who could potentially develop ankle pain. Patients with varus knee osteoarthritis and a pathologically increased talar tilt could benefit from insoles with a lateral wedge if they develop ankle pain after TKA. Patients with valgus knee osteoarthritis and a pathologically lateralized gait pattern could be treated using physiotherapy.
View lessA fundamental defense mechanism against pathogens is the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). These PRRs are integral components of the innate immune system. This recognition process initiates the interferon (IFN) response mechanism, triggering expression of interferon-stimulated genes (ISGs). Many of these ISGs possess antiviral properties that inhibit viruses, including HIV-1. The PPRs and their following signal pathways vary based on cell type. Publications have shown that an unknown pathway mediated over MAVS is activated by intron-containing RNA from HIV-1 in monocyte-derived macrophages (MDMs). However, the mechanism behind the sensing of the viral genomic RNA is yet unknown.
This work identified two distinct stages of immune recognition in MDMs triggered by HIV-1 infection. The first stage occurred prior to reverse transcription and was influenced by the stability of the viral capsid. In the second stage, characterized by a more robust immune response, a short peptide sequence encoded by the N-terminus of gag was crucial to inducing inflammatory responses. While partially spliced or full-length viral RNA in the cytoplasm was required for Gag protein translation, the myristoylation site of Gag was essential to induce innate sensing in MDMs. Furthermore, we examined whether THP-1 or U937 cells in differentiated state showed a similar phenotype to MDMs during HIV-1 infection to identify the molecular mechanisms involved in sensing the virus. We found that U937 cells exhibited robust innate response at a late-stage of virus replication, whereas pre-integration determinants, observed in MDMs, differ. Surprisingly, THP-1 cells exhibited minimal innate immune responses against HIV-1 and showed significant differences from the responses observed in MDMs and U937 cells. Our findings reveal that HIV-1 sensing in differentiated THP-1 and U937 cells does not parallel the responses seen in primary cells. These results enable new research targets in regard to find the cellular sensor, which induces HIV-1 chronic inflammation in MDMs and highlight the importance of research in primary cell systems.
View lessAntimicrobial peptides are an interesting class on ribosomally and non-ribosomally synthesised peptides found in all kingdoms of life. Among these is the underexplored class of bacteriocins: Short ribosomally synthesized and post-translationally modified peptides that often show high potency, and low toxicity. One subclass requires a glycosylation to show antimicrobial activity and thus have been termed glycoactive bacteriocins, Glycocins. The glycosylation of glycocins is installed by a specific subfamily of glycosyltransferases, part of the CaZy transferase family 2. Despite being in the same family, these glycosyltransferases show a remarkable diversity in terms of donor specificity, peptide specificity, acceptor selectivity and number of glycosylations that are carried out. I identified several putative Glycocins and their cognate transferases using bioinformatics. The recombinant production and purification of several glycosyltransferases was established. These were characterised in regard of the metal ion dependency and the carbonucleotide specificity. Using SPPS several glycocin-peptides were synthesized and their selective glycosylation by the cognate transferase could be proven. A facile and scalable method to obtain the mature, glycosylated, and folded glycocin by heterologous expression of the peptide and its transferase in E. coli was established. To investigate the molecular determinants for the observed differences in specificity in terms of preferred sugars and their acceptor selectivity, X-ray crystallography was used as method of choice. For four glycosyltransferases with noticeably different specificities, crystals could be obtained, and the structure could be solved. For the transferase of Enterocin 96 it was possible to obtain snapshots of the enzyme-substrate complex during its reaction.
View lessIn the 1990s, the economic downturn and hyperinflation in Brazil motivated many descendants of Japanese migrants (Nikkeijin) living in Brazil to ‘return’ to Japan, where an aging population and a booming economy had led to a labor shortage. Another incentive was the revision of the Japanese Immigration Law in 1990 that allowed Nikkeijin up to the third generation to obtain special permanent residency visa. Approximately 220.000 Latin American returnees arrived in the 1990s, and more than 200.000 Brazilians live in Japan today, constituting the fifth largest group of foreigners. As many have decided to stay in Japan for the time being, integration and multiculturalism have become important societal challenges, especially at the local level.
This dissertation examines the role of mediating institutions for the integration of Brazilian return migrants in Japan. Based on ethnographic field research in Hamamatsu, the Japanese city with the highest number of Brazilian residents, three research areas have been determined: everyday life and community, religion, and education. The relevant mediating institutions, such as cultural centers, libraries, churches, schools, and civil society institutions, were identified and their activities analyzed with regard to the research question of what role these institutions play for the process of integration into the host society and the relation to Japanese residents.
The analysis revealed that as spaces of interaction and encounter and as providers of knowledge, education, and information, mediating institutions serve as promoters of multiculturalism, mutual understanding, and integration. At the same time, they offer a space of belonging and creation of an ethnic support network, which facilitates the formation of a parallel society and exacerbates existing divisions. In other words, mediating institutions simultaneously foster and hinder integration processes.
View lessThe purpose of my project is to identify novel functions of circRNAs with a particular focus on the effects of RNA--RNA interactions (RRI) on RNA processing. Computational prediction of RRI has revealed the biological function and mechanism of action of multiple genes. However, computational RRI prediction is limited by 2 major challenges: knowing the full sequence of the transcript and a high false-positive rate. Discovering the full sequence identity of circRNA has been a challenging task for bioinformatics in the last decade. In addition, the lack of knowledge of the full sequence of the transcripts in a sample leads to skewed quantification based on RNA-seq data, as well as incorrect results from analyses of NGS-derived techniques (e.g., CLIP-seq, SPLASH etc.). The problem of false discovery of new RRIs can be mitigated by dedicated experimental datasets. To overcome the first hurdle of my project, I developed CYCLeR , a computational tool that compares ribo-depleted and circRNA enriched RNA-seq libraries and outputs a high-confidence set of circRNA transcripts. The true strength of CYCLeR is the quantification module that can robustly estimate the abundances of both circular and linear transcripts. I have shown the advantage of CYCLeR over alternative tools in terms of transcript assembly and quantification. I have also shown that CYCLeR has is the only tool suitable to search for the functional association of circRNA transcripts. The second part of my work focuses on predicting functional RRIs that influence pluripotency. A co-expression network based on the output of CYCLeR can show the association of circRNA with known biological pathways and significantly facilitate the discovery of the function of circRNA. In vivo RNA proximity ligation experiments provide information on the dynamics of RNA-RNA interaction inside the cell. The combination of RNA-seq and RNA interactome data allows me to significantly enhance the strength of computational predictions. I build a co-expression network based on time series experiment of H1ESC treated with retinoic acid. I combine the co-expression information with results from analysis of RNA-RNA proximity ligation data (SPLASH). The analysis is supplemented with localisation information based on RNA-seq libraries specific for nuclear localisation. The results two circRNAs that participate in functional RRIs. circFIRRE is significantly enriched in SPLASH data, indicating a high probability of interaction with other RNAs. Interestingly, circFIRRE is one of the few circRNAs specifically enriched in the nucleus. The enrichment can be explained by the binding site for the hnRNPU protein, which keeps the circRNA in the nucleus. Knockout of the circFIRRE locus in human leads to a viral response. Multiple interaction sites of circFIRRE with ALU-specific sequences indicate that the viral response is triggered by disruption of A-to-I editing in cells. circLARP7 is another nuclear-specific circRNA. circLARP7 is co-expressed with all major markers for pluripotency. It is also expressed in high proximity to MIR302CHG -- a microRNA host gene related to maintaining the pluripotent state. High complementarity and conservation of a duplex between the circLARP7 and the nascent MIR302CHG indicate that circLARP7 might be related to the processing of the microRNAs from the miR-302/367 cluster.
View lessThis habilitation thesis addresses the relevance and necessity of preventive sports medicine diagnostics, with a particular focus on the importance of preventive diagnostics in sports medicine, especially for young top athletes. While the existing literature on preventive diagnostics for adults and athletes in general tends to focus on the general population, this thesis aims to provide insights into the specific needs of elite athletes in their respective sports or on adolescent elite athletes. In particular, this group of elite athletes has received less scientific attention with regard to preventive sports medicine diagnostics in the past. In order to ensure effective preventive care of these athletes, however, it is important to be able to recognize the physical condition of the entire organism in connection with high physical demands. This study focuses on less recognized sports, such as ski mountaineering, and aims to expand knowledge and understanding of the broad complex of preventive sports medicine examinations. It also addresses previously marginalized areas, such as oral health, gingival inflammatory reactions, and their effects on athletic performance. A comparative study of performance diagnostic and echocardiographic data in 31 world-class winter athletes (biathletes, cross-country skiers, and ski mountaineers) revealed significant echocardiographic differences between the participating disciplines. With excellent performance data for all athletes, there were significant differences between the cross-country skiers and biathletes on the one hand and the ski mountaineers on the other. In order to conduct validated stress tests on the ergometer with children and young athletes, there was not yet sufficient knowledge available on the stress-induced blood pressure behavior of these trained children and adolescents. In a study of the maximum exercise blood pressure, age-adjusted percentiles were created in order to establish a standard basis for assessing physicians. Similarly, it has only been speculated whether an increased parasympathetic influence, as is assumed in children participating in elite sports, leads to similar ECG changes as in obese children, in whom an increased parasympathetic tone is also assumed to be a possible cause. Although no relevant pathological findings were identified in children of normal weight, obese children, or children involved in competitive sports, children involved in sports exhibited a significantly shorter QTc time than obese children. Additionally, two further studies investigated dental health and individual oral health behavior, as well as the interaction of oral health and systemic inflammation in relation to athletic performance in competitive athletes. These studies demonstrated that this aspect is crucial for the prevention and optimization of performance development. The results indicated that an increased inflammation in the oral cavity had no significant influence on individual performance. Furthermore, systemic inflammatory processes were not associated with low oral inflammation in the athletes studied.
View lessThe Kupferschiefer district in the Southern Permian basin of central Europe hosts several sediment-hosted stratiform copper (SCC) deposits. The Cu and Zn-Pb sulfide mineralized rocks in the uppermost part of the terrestrial Rotliegend sandstones (S1), organic matter-rich marine Kupferschiefer mudstones (T1), and Zechstein Limestone (Ca1) units in the Kupferschiefer district are located at a major stratigraphic redox boundary. Various genetic models, including syngenetic, early diagenetic, and late diagenetic to epigenetic, have been proposed to explain the formation of stratabound-stratiform, fine-grained sulfide mineralization in the Kupferschiefer district. Most of these models were constructed based on bulk geochemical and isotopic data interpretations without complimentary detailed petrographic investigations.
In this thesis, work has been focused on samples from three drill holes (Sangerhausen, Allstedt, and Wallendorf) in the Saale subbasin, eastern Germany. All drill holes intersect the S1, T1, and Ca1 in different base metal zones which provides an opportunity to investigate their diagenetic and hydrothermal assemblages. The focus of this thesis is to determine the mineralogy and paragenesis of diagenetic assemblages that controlled fluid flow during ore-stage sulfide mineralization, constrain the processes responsible for the formation and distribution of the calcite cement and assess if hotter mineralizing fluids overprinted its isotopic signature, and constrain the timing between the ore-stage sulfides and pore-filling illite. This has been done using detailed petrography, quantitative mineralogy, bulk rock geochemistry, major element chemistry of carbonates, microanalyses of δ13C and δ18O values of calcite cement using secondary ion mass spectrometry (SIMS), and nanoscale investigations of pore-filling illite adjacent to ore-stage sulfides using ultrahigh-resolution transmission electron microscopy (TEM).
The results of this study showed Cu and Zn-Pb sulfide (bornite, sphalerite, and galena) mineralized rocks in the S1 and T1 formed primarily via the replacement of early diagenetic carbonate cement, mostly predating alteration of detrital clasts. The highest base metal grades were found in the carbonate-rich samples of the T1, deposited under reducing conditions. A minor part of the ore-stage sulfides in the S1 and T1 involved the replacement of detrital feldspar clasts. In the Ca1, the sulfides are dominantly formed in vuggy pores. Vein sulfides in the T1 and Ca1 are also formed as a replacement of calcite veins. The calcite cement in the three units has a similar cathodoluminescence response and major element chemistry, suggesting a common origin. Overlapping δ13C and δ18O values of calcite cement in samples from the S1 and T1 in the Sangerhausen and Wallendorf drill cores suggest that the calcite cement was derived from fluids of similar composition. The δ13C values indicate carbonate alkalinity sourced from seawater-derived fluids and organic matter degradation products. However, the high variability in the δ13C values in the calcite veins in the T1 without significant change in their δ18O values suggests that the alkalinity of the porewater during calcite precipitation in veins was derived from organic matter degradation. The δ18O values suggest the influence of alteration of detrital clasts, with a minor contribution from meteoric water and evaporitic fluids. Furthermore, in pores surrounding the ore-stage bornite, Cu chloride nanoparticles (CuCl NPs) are intergrown with pore-filling illite, which indicates illite precipitation during sulfide mineralization, and limited availability of aqueous reduced sulfur in certain microenvironments and steep chemical gradients between these pores.
Overall, this thesis demonstrates that the reduced nature of the T1 provided the necessary redox gradient for sulfide precipitation and the dissolution of carbonate cement was the main control on the lateral migration of mineralizing fluids in the Saale subbasin. This thesis also provides new constraints that the mineralizing fluid flux or temperature was not sufficient to overprint the isotopic composition of the calcite cement. Furthermore, the results in this study demonstrate that Cu was soluble as chloride complexes, in low-temperature brines that infiltrated the host units during burial diagenesis when both illite formation and organic maturation were active processes.
View lessCompliance ist in Deutschland der Ausdruck der Regeltreue im Unternehmen: Kapitalgesellschaften, die keine Handlungsfähigkeit besitzen, deren Haftung auf die Ziffer des Stamm- bzw. Grundkapitals beschränkt ist und deren Geschäftsleiter in aller Regel nicht den Dritten gegenüber haften, müssen rechtssystematisch für die Regeltreue ihrer Organe und Beschäftigten sorgen, anderenfalls würde ein Missbrauch des Privilegs der beschränkten Haftung vorliegen. So begründet im Innenverhältnis bereits der Sorgfaltsmaßstab eines deutschen Geschäftsleiters seine Compliance-Pflicht der Gesellschaft gegenüber. Im Außenverhältnis wird diese Pflicht durch delikts- und bußgeldrechtliche Vorschriften sowie durch allgemeine Verkehrspflichten flankiert. Darüber hinaus zwingen die wirtschaftliche Abhängigkeit und die Internationalisierung einige Kapitalgesellschaften zur freiwilligen Übernahme einer (zusätzlichen) Compliance-Pflicht als Selbstverpflichtung. In Russland ist die Rechtslage vergleichbar gestaltet. Auch dort lässt sich die Compliance-Pflicht aus dem Sorgfaltsmaßstab des Unternehmensleiters (des Einzelexekutivorgans) ableiten. Öffentlich-rechtliche, deliktsrechtliche und arbeitsrechtliche Normen erweitern die rechtliche Grundlage der Compliance-Pflicht und verdeutlichen die Notwendigkeit einer auf die Einhaltung rechtlicher Vorschriften gerichteten Unternehmensorganisation. Ebenso wie die deutschen werden auch russische Unternehmen von ihren internationalen Geschäftspartnern angehalten, sich selbst zur Errichtung einer Compliance-Organisation zu verpflichten.
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