500 Naturwissenschaften
Refine
Year of publication
Document Type
- Doctoral Thesis (79)
Has Fulltext
- yes (79)
Is part of the Bibliography
- no (79)
Keywords
- Biokatalyse (4)
- Biopharmazie (4)
- Streptococcus pneumoniae (4)
- Pharmazeutische Technologie (3)
- Wirkstofffreisetzung (3)
- 3D-Druck (2)
- Amine (2)
- Antikörper (2)
- Antimicrobial (2)
- Biocatalysis (2)
Institute
- Institut für Chemie und Biochemie (19)
- Institut für Pharmazie (18)
- Abteilung für Mikrobiologie und Molekularbiologie (9)
- Institut für Immunologie u. Transfusionsmedizin - Abteilung Immunologie (6)
- Interfakultäres Institut für Genetik und Funktionelle Genomforschung (5)
- Institut für Mathematik und Informatik (4)
- Institut für Anatomie und Zellbiologie (3)
- Institut für Botanik und Landschaftsökologie & Botanischer Garten (3)
- Institut für Pharmakologie (2)
- Zoologisches Institut und Museum (2)
Tafazzin is an acyltransferase with key functions in remodeling of the mitochondrial phospholipid cardiolipin (CL) by exchanging single fatty acids species in CL. Tafazzin-mediated CL remodeling determines the actual CL compositions and has been implicated in mitochondrial morphology and function. Thus, any deficiency of tafazzin leads to altered fatty acid composition of CL which is directly associated with impaired mitochondrial respiration and ATP production. Mutations in the tafazzin encoding gene TAZ, are the cause of the severe X-linked genetic disease, BARTH syndrome (BTHS).
Previous work provided first hints on a linkage of CL composition and subsequent limitations in the cellular ATP levels which may contribute to the restriction of growth. However, in C6 cells ATP levels remained unaltered due to compensatory activation of glycolysis. Moreover, it has been demonstrated that the substantial changes in CL composition are similarly resulting from knocking down either cardiolipin synthase (CRLS) or TAZ. This has also been shown in C6 glioma cells. Most notably only the knock down of TAZ, but not that of CRLS, compromised proliferation of C6 glioma cells. Therefore, a CL- independent role of TAZ in regulating cell proliferation is postulated.
In this study, any linkage of the lack of tafazzin to cellular proliferation should be investigated in more detail to allow first insight into underlying mechanisms.
The results of the current study demonstrate that the tafazzin knockout in C6 glioma cells show changes in global gene expression by applying transcriptome analysis using the- microarray Clarion S rat Affymetrix array. Out of 22,076 total number of genes detected, 1,099 genes were differentially expressed in C6 knockout cells which were either ≥2 and ≥4 fold up or down regulated genes. Furthermore, expression of selected target genes was validated using RT-qPCR. We have hypothesised that the changes in TAZ dependent gene expression is via PPAR transcription factor. According to eukaryotic promoter database (EPD) for selected target genes, exhibited at least one putative binding site for PPARG and PPARA transcription factors. However, pioglitazone and LG100268, synthetic ligands of PPARG and RXR, could not show any effect on changes in gene expression in C6 TAZ cells. Another class of cellular lipids, oxylipins were found to occur in significantly higher amounts in C6 TAZ cells compared to C6 cells which makes them candidates for mediating cellular effects and regulating gene expression via PPARs. A computational tool CiiiDER was used to for the prediction of transcription factor binding site. The transcription factors enriched in TAZ- regulated genes were found to be HOXA5 and PAX2, binding sites of which could be detected in 100 % of TAZ- regulated genes (>2-fold). By applying IPA to the differentially expressed genes we could identify lipid metabolism, and cholesterol superpathway in particular as the most affected pathway in C6 TAZ cells. This pathway consists of 20 genes, of which all (20/20) appeared to be differentially regulated in C6 TAZ cells. Of all the 20 genes, 4 of the differentially expressed genes were selected for further validation by RT-qPCR. By IPA it was possible to identify the upstream regulators that might be responsible for the differential expression of genes in C6 deficient cells. Some of the genes ACACA, HMGCR, FASN, ACSL1, 3 and, 5 identified was decreased by predicted activation and inhibition of the regulators. Further we have analysed the levels of cellular cholesterol content in C6 and C6 TAZ (w/o Δ5 and FL) cells. In C6 cells cholesterol is present more in its free form. C6 TAZ cells have increased amount of cholesterol compared to C6 cells. However, Δ5 and FL expressed C6 TAZ cells showed less amount of cholesterol.
Previous work established that knockout of tafazzin in C6 cells showed decreased cell proliferation in the absence of any changes in ATP content. To understand this phenomenon cellular senescence associated β-galactosidase in C6 and C6 TAZ cells was performed. C6 TAZ cells showed increased percentage of β-gal positive cells compared to C6 cells. Moreover, senescent associated secretory phenotype (SASP) represented by e.g. CXCL1, IL6, and IL1α was determined using RT-qPCR. Gene expression of these SASP factors was significantly upregulated in C6 TAZ cells.
Several human tafazzin isoforms exists due to alternate splicing. However, whether these isoforms differ in function and in CL remodelling activity or specificity, in particular, is unknown. The purpose of this work was to determine if specific isoforms, such as human isoform lacking exon 5 (Δ5), rat full length tafazzin (FL) and enzymatically dead full length tafazzin (H69L), can restore the wild type phenotype in terms of CL composition, cellular proliferation, and gene expression profile. Therefore, in the second part, it was demonstrated that expression of Δ5 to some extent and rat full length tafazzin can completely restore CL composition, in C6 TAZ cells which is naturally linked to the restoration of mitochondrial respiration. As expected, a comparable restoration of CL composition could not be seen after re-expressing an enzymatically dead full-length rat TAZ, (H69L; TAZ Mut). Furthermore, re-expression of the TAZ Mut largely failed to reverse the alterations in gene expression, in contrast re-expression of the TAZ FL and the Δ5 isoforms reversed gene expression to a larger extent. Moreover, only rat full length TAZ was able to reverse proliferation rate. Surprisingly, the expression of Δ5 in C6 TAZ cells did not promote proliferation of the wild type. Different effects of Δ5 and FL on CL composition and cell proliferation points to the specific and in part non-enzymatic functions of tafazzin isoforms, but this certainly requires further analysis.
Die Kenntnis über die im Gastrointestinaltrakt ablaufenden Prozesse spielt in der Entwicklung neuer Arzneiformen eine entscheidende Rolle. Besonders im Dickdarm ist dabei neben den physiologischen Bedingungen die bakterielle Besiedlung zu beachten, welche sowohl inter- als auch intraindividuell hoch variabel ist. Bislang gibt es keine einheitliche Methode zur Untersuchung des Einflusses der intestinalen Mikrobiota auf die Metabolisierung von Arzneistoffen. Diese Methoden sind jedoch entscheidend für das Verständnis des Einflusses der bakteriellen Metabolisierung auf die Pharmakokinetik und -dynamik der Arzneistoffe.
Übergeordnetes Ziel dieser Arbeit war es, ein In vitro-Modell zu entwickeln und anzuwenden, welches die dynamischen Bedingungen im Colon ascendens, insbesondere im Hinblick auf die pH-Werte, Durchmischung und bakterielle Besiedlung, darstellt.
Um dieses Ziel zu erreichen, wurde im Rahmen erster Versuche untersucht, wie es sowohl mit monographierten als auch biorelevanten Modellen möglich ist, die mechanische Belastung, die auf eine Arzneiform im GIT ausgeübt wird, darzustellen. Die Verwendung der SmartPill™ eröffnete die Möglichkeit, in den Apparaturen auftretende Drücke aufzuzeichnen. Außerdem konnten die gemessenen Drücke anschließend mit Daten aus In vivo-Studien verglichen werden. Die Untersuchungen ergaben, dass in den monographierten Apparaturen keine Drücke auftreten, die den während der Magen-Darm-Passage auftretenden Drücken entsprechen. Im Gegensatz dazu können im DOFTA gezielt Drücke und so auch vollständige Druckprofile simuliert werden.
Im weiteren Verlauf der Arbeit waren die zuvor gewonnenen Erkenntnisse hilfreich für die Entwicklung des neuen Modells zur Darstellung des Colon ascendens. In das MimiCol wurden pH-Wert-Daten aus einer SmartPill™-Studie implementiert. Die Vorteile des neuartigen Bioreaktors MimiCol sind das kleinere Medienvolumen, das den In vivo-Bedingungen näherkommt, die Möglichkeit, Medienwechsel durchzuführen und dadurch Metabolite abzuführen und neue Nährstoffe hinzuzufügen sowie die genauere Simulation von In vivo-Durchmischungsmustern.
Ziel der durchgeführten Untersuchung war der Vergleich der Metabolisierung des Modellarzneistoffs Sulfasalazin in dem neuartigen dynamischen Bioreaktor MimiCol und einem statischen Standard-Batch-Fermenter. Beide wurden mit der gleichen, kryokonservierten fäkalen Standardmikrobiota beimpft. Die Experimente zeigten, dass das MimiCol in der Lage ist, die dynamischen Bedingungen im aufsteigenden Dickdarm zu simulieren. Die dynamischen Bedingungen im MimiCol führten zu einer Verdopplung der Metabolisierungskonstanten im Vergleich zum statischen Batch-Fermenter. Das MimiCol ahmt, besonders in Bezug auf pH-Fluktuationen und Bakterienwachstum, die dynamischen Bedingungen im aufsteigenden Dickdarm nach und könnte sich in allen Phasen der Arzneimittel- und Formulierungsentwicklung als nützlich erweisen.
Zur Erleichterung und Beschleunigung der Datengenerierung wurde im nächsten Schritt eine Erweiterung des Modells angestrebt. Hierbei war es die größte Herausforderung, die ursprünglichen Parameter auf ein erweitertes Modell mit einer anderen Steuerung und anderen Komponenten zu übertragen. Außerdem wurde in diesem Zuge die Charakterisierung komplexer Bakterienkulturen mittels 16S rRNA-Sequenzierung eingeführt. Bei der Erweiterung des Modells wurde besonderes Augenmerk auf die Einfachheit des Designs und die leichte Skalierbarkeit gelegt.
Um zu beweisen, dass die Übertragung der Parameter erfolgreich war, wurde erneut der Abbau von Sulfasalazin untersucht und die bakterielle Zusammensetzung während des Experiments durch 16S rRNA-Sequenzierung analysiert. Die Übertragung der Versuchsbedingungen auf das neue Modell war erfolgreich. Kommerziell erhältliche Komponenten wurden in den Aufbau implementiert. Das Modell MimiCol³ repräsentierte das Colon ascendens in seinen Eigenschaften bezüglich des Volumens, pH-Werts und Redoxpotentials zufriedenstellend. Die 16S rRNA-Sequenzierung führte zu weiteren Erkenntnissen über die bakterielle Zusammensetzung in den drei Gefäßen. Der Abbau von Sulfasalazin stand in guter Übereinstimmung mit den In vivo-Daten und den im MimiCol gewonnenen Daten. Das neue Modell des Colon ascendens MimiCol³ ermöglichte es, zuverlässigere Daten zu sammeln, da drei Experimente gleichzeitig unter denselben Bedingungen durchgeführt wurden.
Die durchgeführten Untersuchungen zeigen, dass ein wichtiges Instrument zur Untersuchung des Einflusses unseres Mikrobioms im Darm auf den Abbau von Arzneistoffen und Arzneiformen entwickelt wurde.
The aim of this work was to characterize the distribution of TULV in European common vole populations, to clarify the host association of TULV and to investigate correlations between host population dynamics and changes in TULV prevalence. Furthermore, the potential of common voles as reservoir for other rodent-borne pathogens was examined in comparison to other rodent species.
Molecular and serological analysis of rodents captured at 87 locations in Germany, France, Luxembourg, and Austria revealed TULV infections at 53.6 % of all trapping locations. The seroprevalence in common voles was low with a mean of 8.5 % (range: 0 – 19 %). TULV RNA was more often detected (mean: 15.3 %, range 0 - 37.5 %). Field voles (Microtus agrestis) and water voles (Arvicola amphibius) were less often tested positive for TULV: mean seroprevalence was 7 % for field voles and 6.7 % for water voles. RNA could be detected in 5.4 % of all tested field voles and 3.2 % of water voles and with exception of a single field vole only when TULV-RNA-positive common voles were trapped at the same location. Those results indicate that TULV infections of field and water voles are spillover infections from sympatric TULV-infected common voles. Phylogenetic analysis revealed distinct genetic differences between TULV sequences of regions of greater geographical distance which were associated with different evolutionary common vole lineages. Furthermore, we could detect genetic differences between TULV strains from trapping sites close to each other (ca. 10 km).
In a capture-mark-recapture study 1042 common voles captured in live traps in Germany were sampled as well as 225 captured in snap traps. When analyzing the seroprevalence of fluctuating common vole populations over several years and seasons we found a negative correlation between prevalence and population density in the current season but a delayed density-dependent positive correlation between the current population density and seroprevalence in the next season. However, this trend varied geographically between the four trapping locations. Usually, population density as well as seroprevalence peaked at the end of the reproductive period in autumn with the exception of Weissach (2010-2012), Jeeser (2010) and Gotha (2012) where population peaks in summer were observed.
In a pilot study in Austria common voles were captured as well as three other rodent species. They were investigated not only for presence of different viruses (TULV, Dobrava- Belgrade orthohantavirus (DOBV), Puumala orthohantavirus (PUUV), Lymphocytic choriomeningitis mammarenavirus (LCMV), Cowpox virus (CPXV)) but also pathogenic bacteria and endoparasites (Leptospira spp., Toxoplasma gondii, Borrelia afzelii, Coxiella burnetii, Rickettsia spp. und Bartonella spp.). Of all four captured species, common voles were most often infected with at least one pathogen (66.7 %), followed by wood mice (Apodemus sylvaticus) (57.7 %), bank voles (Myodes glareolus) (35 %) and yellow-necked field mice (Apodemus flavicollis) (34.5 %). Common voles were also exceptionally susceptible to multiple infections: 66.7 % of them were infected with two or three different pathogens, compared to 6.9 % of yellow-necked field mice and 2.5 % of bank voles. No multiple infections could be detected in wood mice.
The broad geographic distribution of TULV in its reservoir host is in contrast to the rare reports of human infection but might be explained with a low pathogenicity for humans or with the low prevalence in host populations. In addition, the rare detection of human TULV infections could be a result of the used diagnostic methods. Since the reservoir population is known for its dramatic changes in population density and recurring superabundances which facilitates frequent contact to humans, TULV should more often be considered as cause for human disease in future analysis. In
addition, several other zoonotic pathogens could be detected in common voles which could influence TULV infections in the reservoir host but also TULV transmission to humans and therefore deserve more attention in future research.
Die Kv7-Kaliumkanalöffner Flupirtin und Retigabin waren wertvolle Alternativen bei der Pharmakotherapie von Schmerzen und Epilepsie. Beide Wirkstoffe werden aufgrund von unerwünschten Arzneimittelwirkungen derzeit jedoch nicht mehr eingesetzt. Die Flupirtin-induzierte Hepatotoxizität und die durch Retigabin hervorgerufenen Gewebeverfärbungen scheinen dabei auf den ersten Blick nicht zusammenzuhängen. Gleichwohl lassen sich wahrscheinlich beide Nebenwirkungen auf das gemeinsame oxidationsempfindliche Triaminoaryl-Grundgerüst zurückführen, welches zur Bildung von reaktiven Chinondiimin-Metaboliten neigt. Da hingegen der Wirkungsmechanismus, d. h. die Öffnung der Kv7-Kanäle, nicht an der Toxizität beteiligt zu sein scheint, hatte diese Arbeit zum Ziel, sicherere Alternativen für Flupirtin und Retigabin zu entwickeln. In einem Liganden-basierten Ansatz wurde eine Umgestaltung des Triaminoaryl-Kerns, den beide Wirkstoffe gemeinsam haben, vorgenommen, was zu Carba-Analoga führte, die durch eine erhöhte Oxidationsbeständigkeit sowie ein vernachlässigbares Risiko für die Bildung von chinoiden Metaboliten charakterisiert sind. Zusätzlich zu diesen verbesserten Sicherheitsmerkmalen offenbarten einige der neuartigen Derivate eine überlegene Kv7.2/3-Kanalöffnungsaktivität. Im Vergleich zu Flupirtin konnte die Potenz der Verbindungen um den Faktor 150 gesteigert werden, während die intrinsische Aktivität auf bis zu 176 % verbessert werden konnte, was die betreffenden Carba-Analoga zu vielversprechenden Kandidaten für eine weitergehende Entwicklung macht. Andererseits ermöglichten einige inaktive Verbindungen sowie die insgesamt deutlich abgestuften Kv7.2/3-Aktivitätsdaten die Etablierung von validen Struktur-Wirkungs-Beziehungen und Hypothesen zum Bindungsmodus, die mit Dockingergebnissen und Molekulardynamik-Simulationen korrelierten.
In dieser Doktorarbeit konnte in zwei verschiedenen experimentellen Modellen der chronischen Pankreatitis in C57BL/6 Mäusen gezeigt werden, dass die chronische Pankreatitis mit einem Gewichtsverlust und einer Verminderung der muskuloskelettalen Kraft assoziiert sind. Untersuchungen im Kleintier-MRT belegten eine signifikante Verminderung des Durchmessers des Quadrizepsmuskels in beiden Modellen. Auf Proteinebene fanden sich im Skelettmuskel von Mäusen mit chronischer Pankreatitis Expressionssteigerungen von growth differentiation factor 8 (GDF8) und Muscle RING-finger protein-1 (MuRF1). Auf mRNA Ebene konnten wir zeigen, dass Activin A und das transforming growth factor β (TGFβ) in beiden Modellen erhöht waren, wohingegen Follistatin und teilweise auch Inhibin A vermindert waren. Die Anzahl apoptotischer Zellen stieg im Quadrizepsmuskel in beiden Modellen signifikant an, was darauf schließen lässt, dass die Apoptose beim Muskelabbau eine Rolle spielt. Des Weiteren fanden sich in Mäusen mit chronischer Pankreatitis und Sarkopenie Veränderungen des Serummetaboloms und des Stuhlmikrobioms, die jedoch in Abhängigkeit des verwendeten Modells stark variierten. Modellübergreifend war eine Vermehrung von Akkermansia spp. in der chronischen Pankreatitis nachweisbar.
Pancreatitis is an inflammatory disorder of the pancreas with a mortality rate of 5% and severe negative effects on the quality of life. Of all non-malignant gastrointestinal diseases, it is the most common reason for hospitalization. Pancreatitis is a disease of multiple etiologies with different underlying pathomechanisms. Due to the diversity of mechanisms by which homeostasis within the exocrine pancreas can be disrupted, finding appropriate therapeutic approaches is challenging. Current treatment options are inadequate and are mostly limited to supportive treatment like fluid administration, bowel rest, antibiotics and pain control. Although significant advancements have been achieved in recent decades, the mortality rate for pancreatitis has not decreased. Furthermore, progress is slow due to limited patient sample availability and lack of an appropriate cell model. Taking samples from a human pancreas is typically avoided, because damaging the pancreatic tissue can itself induce pancreatitis. Additionally, while it is possible to keep individual acini in culture, it is not possible to grow pancreatic acinar cells. Thus, less appropriate cell models, often derived from pancreatic cancer samples, have to be used. The most common animal model for pancreatitis is mice, with caerulein administration being the most common method of inducing pancreatitis. However, the use of animal models has significant drawbacks, as they are time-consuming, costly, and pose ethical questions. Furthermore, exposing the pancreas to appropriate stimuli in animal models is difficult. For example, alcohol is the leading cause of pancreatitis in humans, but is typically avoided by animals. Thus, alcohol feeding methods had to be developed to overcome the natural aversion of rodents to alcohol. Results obtained from animal models are also often not transferable into clinical trials and outcomes in humans remain largely unpredictable. Due to the lack of experimental models, our understanding of this highly complex disease is still limited and significant progress is required for the development of effective therapy options.
In this dissertation recombinantly expressed trypsin isoforms and variants of the serine protease inhibitor Kazal-type 1 (SPINK1) inhibitor are used to investigate mechanisms, by which tryptic activity is regulated in pancreatic acinar cells. With premature tryptic activity in the exocrine pancreas being the common focal point of most etiologies connected to pancreatitis, trypsin represents by far the most promising target for treating pancreatitis. Understanding the mechanisms by which the pancreas protects itself and rationalizing mutations that can undermine these protective mechanisms, are important steps towards developing effective therapies.
The discovery of antibiotics around one century ago was a milestone for medicine. However, despite the warning of Alexander Fleming in 1945, antibiotics were used poorly, resulting in many antibiotic-resistant pathogens. Patients infected with resistant pathogens need to get treated with additional antibiotics or, as a last resort, trust completely on their immune system. This causes 700,000 deaths per year. Most clinically used antibiotics have been derived from soil microorganisms, while other niches stayed unexplored. Exploring new niches inhabiting antibiotic-producing microorganisms may result in novel antibiotics. Furthermore, expanding the search from frequently investigated soluble metabolites to volatiles may open up numerous compounds as potential future antibiotics. This thesis is about the search for antimicrobial volatiles produced (among others) by microorganisms from social spider ecosystems, a niche that was little explored until now.
Volatiles are characterized by their high vapor pressure at ambient temperatures, allowing them to distribute fast in both the gas and water phase. They can spread quickly even in complex ecosystems using the air and potentially fulfill functions like communication and antimicrobial defense. Especially, volatiles with antimicrobial activities caught the attention of many scientists because of their potential role in pathogen defense, as we have reviewed (Article I). Volatiles are usually produced in the primary metabolism and belong to diverse chemical classes, like hydrocarbons, aromates, alcohols, aldehydes, acids, esters, amides, and thiols. Their antimicrobial spectrum ranges from antifungal, to antibacterial, anti-oomycete, and even broad-spectrum activity. Volatiles are ubiquitously produced. Especially Bacillus and Streptomyces species are often reported to produce antimicrobial volatiles. Knowledge about antimicrobial volatiles – for example, details about their modes of action – is lacking yet, but these compounds may help to overcome the antimicrobial resistance crisis in the future. Volatiles could be used in medicine and agriculture, either alone or in combination with traditional antibiotics, opening new strategies against antimicrobial resistance.
A promising source of (volatile) antimicrobials is the ecosystem of social arthropods. Due to their lifestyle in dense colonies, they likely spread pathogens between individuals, making antimicrobial defense crucial. Since the presence of antimicrobial volatiles was reported in social insect ecosystems, we investigated the unexplored volatilome of the Namibian social spider Stegodyphus dumicola (Articles II and III). In the first study, we analyzed the in situ volatilomes of the spiders’ nest, web, and bodies using GC/Q-TOF and revealed that more than 40 % of the tentatively identified volatiles were already known for their antimicrobial activities (Article II). We proved the antimicrobial activity of five pure compounds found in the samples, among others against the suggested spider pathogen Bacillus thuringiensis. These results indicate the potential role of antimicrobial volatiles for pathogen defense and could ultimately help explain the spiders’ ecological success.
Volatiles from the spider volatilome can originate from various sources, including microorganisms, surrounding plants, the spiders themselves, the spiders’ prey, so we analyzed the volatilomes of microbial nest members in a second study. The microbial nest members we selected for this were the bacteria Massilia sp. IC2-278, Massilia sp. IC2-477, Sphingomonas sp. IC-11, and Streptomyces sp. IC-207, and the fungus Aureobasidium sp. CE_32 (Article III). Several volatilomes showed antibacterial and/or antifungal activities against two suggested spider pathogens. The subsequent volatilome analyses using GC/Q-TOF revealed the presence of many volatiles that have already been described as antimicrobials. Five pure volatiles were tested against two suggested spider pathogens, revealing all volatiles as antibacterial, antifungal, or both. These results support the potential role of antimicrobial volatiles in social spider pathogen defense and indicate microbial nest members as the origin of (novel) antimicrobial volatiles.
Together, the articles that constitute this thesis highlight the antimicrobial power of volatiles (Article I), indicates the volatilome of the ecosystem of S. dumicola as a potential pathogen defense (Article II), and finally reveal the spider nest microbiome as a source for antimicrobial volatiles (Article III). This knowledge not only adds to the understanding of social spider ecosystems (and likely other social arthropod ecosystems) but also has the potential to open a novel source for antimicrobial compounds that may help to counter the antimicrobial resistance crisis.
Universal products provide an axiomatic framework to study noncommutative independences general enough to include, besides the well known "single-faced" case (i.e., tensor, free, Boolean, monotone and antimonotone independence), also more recent "multi-faced" examples like bifree independence. Questions concerning classification have been fully answered in the single-faced case, but are in general still open in the multi-faced case. In this thesis we discuss how one can use insights in the relation between universal products and their associated moment-cumulant formula as a starting point towards a combinatorial approach to (multi-faced) universal products. We define certain classes of partitions and discuss why the defining axioms are sufficient to associate to each of them a multi-faced universal product. For the two-faced case we present our result that every positive and symmetric universal product can be produced in this fashion and we outline how these results might contribute to a classification of positive and symmetric universal products.
This thesis summarizes the published works by Robert Hieronymus which were done in the group of bioorganic chemistry of Prof. Dr. Sabine Müller. The different works had the goals to design, develop, and test catalytically active RNA systemes that might have been plausible for an early RNA world scenario.
The different RNA systems presented in this thesis were developed via rational design, for which each time the hairpin ribozyme (HPR) was utilized as a design template. The HPR belongs to the group of self-cleaving ribozymes and comes with features that make it a very attractive candidate for the contemplated tasks: It’s small, it’s variable in sequence, and it can cleave or ligate bound RNA substrates depending on the substrate binding strength. Substrates with weak binding to the ribozyme tend to be cleaved while substrates with stronger binding become ligated. This feature was utilized to develop RNA systems with catalytic cascades.
The first of the catalytic RNA systems that is presented in this thesis establishes a HPR mediated recombination system. In a one-pot reaction two RNA strands without function but with pro-functional regions are getting bound and cleaved by the HPR in separate ways. The generated fragments with the pro-functional parts are designed to bind stronger to the HPR than their non-functional counterparts and are ligated in a subsequential reaction by the HPR. The recombination product is a hammerhead ribozyme (HHR), and thus, a self-cleaving ribozyme on its own, whose synthesis can be monitored by the addition and cleavage of a separate RNA substrate.
The second RNA system is also a recombination system mediated by a HPR, but this time it starts with the functional HHR product from the previous system as an educt. Via a similar mechanism as before the recombination is done with another functional RNA: an RNA aptamer (sensoric RNA). The recombination of HHR and aptamer leads to the generation of a hammerhead aptazyme, an HHR whose cleavage functions are now regulated via ligand binding on the aptamer part. This novel system was successfully demonstrated with RNA sequences of theophylline and FMN aptamers as different educts for the recombination reaction.
The HPR in the final work presented here was designed as a self-splicing ribozyme. Here the HPR sequence is located within the intron and is flanked by two exon sequences on both its ends. The developed HPR is able to fold itself in two alternative conformations, both with either one of the intron-exon interfaces located within the formed catalytic site. Subsequently to the first cleavage and dissoziation of one of the exons, the HPR folds into the alternative conformation, which triggers the cleavage reaction of the remaining exon. Once both exons are cleaved off, the fragments are ligated by the HPR, which concludes the catalytic cascade with the healing of the RNA source strand.
The various works presented in this thesis demonstrate nicely the flexibility of the HPR and how well suited it is to be utilized as a template in rational design of RNA systems. Furthermore, it is plausible to assume that the HPR, due to its many features, must have had a place in the early RNA world.
Infective endocarditis (IE) is a potentially life-threatening infection of the endocardial surfaces of the heart, most frequently the valves. It is typically caused by bacteria, less commonly by fungi. Over the past years, the morbidity and mortality of IE have gradually increased, and it is now the fourth most common life-threatening infection after sepsis, pneumonia, and intra-abdominal abscess. Despite advances in cardiac imaging and diagnostic techniques, the diagnosis of IE remains challenging. The lack of fast and reliable diagnosis of IE can lead to serious complications. Therefore, new diagnostic and therapeutic tools are urgently needed.
This study had two main aims: (i) to investigate whether a pathogen-specific antibody response in IE patients is mounted against different IE pathogens and whether analysis of such a response might be useful for complementing the classical blood culture diagnosis, and (ii) generate and characterize neutralizing monoclonal antibodies (mAbs) against three virulence factors of Staphylococcus aureus (S. aureus), which is the most common etiological agent in IE.
Our research group has recently established an xMAP® (Luminex®) technology-based serological assay that simultaneously quantifies the antibody response against 30 different pathogens. Within the research consortium Card-ii-Omics, we conducted a prospective, observational clinical discovery study involving 17 IE patients and 20 controls (i.e., patients with non-infectious heart-related conditions). Plasma samples were obtained on the day of IE diagnosis from all patients, while samples at later dates over the course of infection were available for only some patients. Invasive pathogens were identified by blood culture.
The infection array revealed antibodies against a broad range of pathogens in both controls and IE patients, suggesting a broad immune memory. Overall, antibody levels did not significantly differ between both groups, but we observed high antibody titers against those pathogens that were detected by blood culture. Whenever available (in the case of 13/17 IE patients), back-up and follow-up plasma samples (obtained before or after diagnosis, respectively) were included in the analyses that provided valuable information about the kinetics of antibody response during the course of infection. Notably, infection array data confirmed (and extended) the blood culture data in only 2/13 cases. In three cases, serology contradicted the microbiological diagnosis, and in three cases, the infection array was able to identify pathogens, while the microbiological diagnosis failed. In three cases, serology was negative while microbiological diagnosis was positive, and in two cases, both serology and microbiological diagnosis were negative. In 6 out of 8 cases with increases in antibody levels, this response was directed against gut microbes. This supports the leaky gut hypothesis, which assumes that breaching of the gut barrier causes translocation of gut microbes into the bloodstream, which then infect the heart valves. Moreover, we observed an increase in antibody titers in 4 patients against the yeast C. albicans, suggesting a secondary fungal infection. Finally, this study emphasized that the timing of plasma collection is crucial for studying antibody kinetics in IE.
After demonstrating that pathogen-specific antibodies are generated during IE, we aimed to generate mAbs against the prime IE pathogen S. aureus and study their functions on a molecular level. Using the hybridoma technology, our research group has recently generated mAbs against two S. aureus surface proteins/adhesion factors (clumping factor A (ClfA) and fibronectin-binding protein A (FnBPA)), both involved in biofilm formation, as well as an extracellular enzyme, the staphylococcal serine protease–like protein B (SplB), a virulence factor. In this work, the sequences of the mAbs were determined from hybridoma RNA. Then those mAbs were produced at a larger scale in order to determine their binding and neutralizing capacities using in vitro assays such as ELISA, Western blot, Dot blot, microscale thermophoresis, and in a mouse model.
The anti-SplB mAb specifically targeted SplB, with no cross-reactivity to other Spls or extracellular proteins (ECP) of S. aureus. Though anti-SplB mAb showed moderate binding to SplB with a Kd value of 2.54 μM and high sequence homology to the germline sequence, it neutralized the enzymatic activity of SplB up to 99% in 5-fold molar excess as showed in an in vitro substrate cleavage assay. Previous work showed that SplB facilitates the release of proinflammatory cytokines in endothelial cells and induces endothelial damage in mice. Here, we demonstrated that the anti-SplB mAb efficiently blocked the function of SplB in vivo, thus markedly reducing the damage to the endothelial barrier. In conclusion, we identified the strong neutralizing potential of a mAb against SplB, which merits further investigation as a candidate for the immunotherapy of SplB-induced S. aureus pathologies, including IE.
High antibody titers against S. aureus adhesins, including ClfA and FnBPA, have been reported in IE patients. Besides, ClfA is involved in serious S. aureus bloodstream and biofilm-related infections. Similarly, FnBPA facilitates biofilm formation and inhibits macrophage invasion. These important properties make the two bacterial adhesins ideal candidates for a passive vaccination strategy. We generated two murine ClfA-mAbs, ClfA-002 and ClfA-004, which showed strong specificity to ClfA. However, ClfA-004 showed reduced binding strength compared to ClfA-002 due to a single non-synonymous nucleotide change (Phe Tyr) at the CDR3 region. While the ClfA-002 mAb reduced the binding of ClfA to fibrinogen by around 60%, the ClfA-004 had no inhibitory capacity. We also generated two murine and twelve humanized anti-FnBPA mAbs, which showed similar and moderate binding to FnBPA. One murine mAb (anti-FnBPA D4) partially inhibited the binding of FnBPA to fibronectin. FnBPA contains 11 tandem repeats that can all bind to fibronectin. This redundancy could be the reason for the lack of complete inhibition. Hence, in this work, we characterized the properties of neutralizing mAbs against two adhesins of S. aureus. These mAbs should be tested in the future, alone and in combination with other mAbs and antibiotics, for their ability to reduce staphylococcal biofilm formation.
In conclusion, we showed that antibody profiling of IE patients can provide valuable insights into the causative agent(s), and can help in guiding the antibiotic therapy. However, sampling is crucial in IE, which often dwells for many weeks before being clinically diagnosed. Because of the severity of IE, which can be life-threatening, I suggest to establish biobanks to store patient samples upon hospital admission that will provide a baseline in case of a later microbial infection. Moreover, our results suggest that C. albicans plays an important and so far underestimated role in IE. In the second part of the thesis, we characterized several mAbs against an S. aureus protease and two adhesins. Of high interest is a neutralizing mAb against SplB, which shows promising results in vitro and in vivo. Further in vitro and in vivo tests need to be conducted to study the anti-biofilm activity of the anti-FnBPA- and anti-ClfA-mAbs and explore their utility as therapeutic agents.