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Pentathiepine sind siebengliedrige, heterocyclische Polysulfane. Sie gehören damit zur Gruppe organischer Polysulfide und somit zu einer Stoffklasse, die in den letzten Jahren wachsendes Interesse hinsichtlich pharmazeutisch/medizinisch nutzbarer Eigenschaften geweckt hat. Sie besitzen unterschiedliche biologische Wirkungen, die möglicherweise auf die Aktivierung durch Thiole, wie zum Beispiel Glutathion (GSH), zurückzuführen sind. Dazu gehören die Erzeugung von reaktiven Sauerstoffspezies und die oxidative Fragmentierung von DNA.
Pentathiepine zeigen sich als gelbe, schwer lösliche Feststoffe und sind in sauren Lösungen sehr stabil. In Lösungen, die Basen oder Nukleophile enthielten, nahm der Gehalt an Pentathiepinen jedoch sehr schnell ab. In dieser Arbeit sollte hauptsächlich untersucht werden, inwieweit sich die Stabilität der Pentathiepine auf die biologischen Eigenschaften auswirkt. Neben der Ermittlung der Verteilungskoeffizienten 23 verschiedener Pentathiepine, wurden auch enzymbasierte Assays durchgeführt.
Dazu gehörte die Bestimmung der Reversibilität der Hemmung an boviner Glutathionperoxidase-1 (GPx-1) sowie der Einfluss unterschiedlicher Inkubationsbedingungen auf die inhibitorische Wirkung. Dabei wurde für das untersuchte Pentathiepin mittels jump dilution keine irreversible Hemmung an boviner GPx-1 gefunden. Eine irreversible Inhibierung konnte jedoch für Mercaptobernsteinsäure gezeigt werden. Die Ergebnisse der unterschiedlichen Inkubationsbedingungen erlauben die Schlussfolgerung, dass der intakte Pentathiepinring wahrscheinlich nicht an der Hemmung der GPx-1 beteiligt ist, sondern die aus der Reaktion mit GSH gebildeten Abbauprodukte. Es konnte jedoch auch gezeigt werden, dass der Pentathiepinring mindestens als „Schwefeltransporter“ benötigt wird. Ein Übertrag des GPx-Assays auf die HPLC konnte als prinzipiell möglich, für die Pentathiepine jedoch als nicht geeignet gezeigt werden.
Im zweiten Teil der Arbeit wurden sechs Pentathiepine mit vier unterschiedlichen Grundgerüsten hinsichtlich ihrer Stabilität in Gegenwart von GSH untersucht. Dabei gab es hinsichtlich der Reaktivität der Pentathiepine sehr starke Unterschiede. Trotz dieser großen Unterschiede konnten keine Unterschiede hinsichtlich der GPx-Hemmung und der antiproliferativen Eigenschaften beobachtet werden. Auch eine Absenkung der intrazellulären GSH-Konzentration durch Inkubation mit DL-Buthioninsulfoximin in drei humanen Krebszelllinien mit unterschiedlichem Glutathiongehalt ergab keine Unterschiede zwischen den getesteten Substanzen. Sie waren nach Vorinkubation der Zellen durchgehend aktiver.
Aufgrund der vergleichsweise hohen Reaktivität in Gegenwart von GSH sollte ein Pentathiepin in einem proof of concept in Liposomen formuliert werden. Diese Formulierung sollte einerseits das Pentathiepin vor Reaktionen mit Thiolen wie GSH schützen, andererseits die Wasserlöslichkeit erhöhen. Dabei ergab sich, dass die Wasserlöslichkeit der Pentathiepine durch Formulierung in DOPC-Liposomen von unter 3 μM auf über 400 μM erhöht werden konnte. In Hinsicht auf die Stabilität ergab sich eine erhöhte Stabilität des untersuchten Pentathiepins in Anwesenheit von 10 mM GSH um den Faktor 4 in der Zeit bis zum vollständigen Abbau. Hinsichtlich der antiproliferativen Eigenschaften ergab sich keine Abnahme der Wirkung des Pentathiepins durch Formulierung in Liposomen.
In den Weltmeeren findet rund die Hälfte der jährlichen globalen Kohlenstofffixierung statt, davon ein großer Anteil in küstennahen Regionen. Hier kommt es zu wiederkehrenden saisonalen Algenblüten, die durch eine zeitlich begrenzte explosionsartige Vermehrung von Mikroalgen (hauptsächlich Diatomeen und Coccolithophoren) charakterisiert sind. Vor allem Frühjahrsblüten (März-Mai) haben aufgrund ihrer zeitlichen und räumlichen Vorhersagbarkeit einen hohen Stellenwert als Modellsysteme, anhand deren sich der Kohlenstoffkreislauf der Meere untersuchen lässt.
Mikroalgen produzieren eine große Vielfalt an Makromolekülen, die für die mit ihnen vergesellschafteten Bakterien als Nahrungsgrundlage dienen. Besonders im Fokus stehen hier die für den Kohlenstoffkreislauf relevanten Polysaccharide. Im Gegensatz zu anderen natürlichen Makromolekülen wie DNA oder Proteinen können Polysaccharide aus vielen verschiedenen Monomeren mit unterschiedlichsten Bindungen bestehen. Zusätzlich finden sich an diesen Zuckermonomeren viele Modifikationen wie Acetylierungen, Methylierungen oder Sulfatierungen, die die Komplexität weiter erhöhen. Diese Variabilität bedingt eine hohe strukturelle und funktionale Diversität. So können Polysaccharide Speicherstoffe, Zellwandbestandteile oder Teile der extrazellulären Matrix darstellen.
Komplementär hierzu besitzen Polysaccharid-verwertende Bakterien entsprechend komplexe, enzymatische Abbaumechanismen. Besonders hervorzuheben sind hier die Bakterien des Phylums Bacteroidota, die sich in verschiedensten Nischen auf den Abbau von Polysacchariden spezialisiert haben. Sie finden sich in Bodenproben, als Teil der menschlichen Darmflora, oder eben auch als bedeutende Begleiter von Algenblüten.
Bacteroidota (und in marinen Systemen hauptsächlich die zu ihnen gehörenden Flavobakterien) besitzen zum Abbau diverser Polysaccharide sogenannte Polysaccharide utilization loci (PULs), genomische Inseln, die alle notwendigen Proteine zur Aufnahme und Abbau eines bestimmten Polysaccharids codieren. Hierzu gehören hochspezifische Enzyme (Carbohydrate-active enzymes, CAZymes), transkriptionelle Regulatoren sowie Transportersysteme, die initial gespaltene Oligosaccharide über die Membran in das Bakterium transportieren, wo sie von weiteren Enzymen vollständig abgebaut werden. Diese Co-Lokalisation der benötigten Gene und deren gemeinsame Regulation stellt einen enormen Selektionsvorteil der Bacteroidota dar und ist der Grund, warum sie, ähnlich wie Algen, einer jährlich wiederkehrenden Sukzession folgen, die sich gut untersuchen lässt.Die Forschungsartikel, die Teil dieser Doktorarbeit sind, untersuchen das Zusammenspiel von Polysaccharid-produzierenden Algen mit den Bakterien, die sie abbauen, aber auch darauf basierende Beziehungen der Bakterien untereinander. Die erste Publikation beschäftigt sich mit dem weit verbreiteten Speicherpolysaccharid α-Glucan, für das der Großteil der blütenbegleitenden Bakterien einen spezifischen aktiven PUL besitzt. Eine Untersuchung der in der Blüte vorhandenen Algenarten bestätigte, dass die Blüte von β-Glucan-produzierenden Algen dominiert wird. Da Bakterien aber selbst α-Glucane als Speicherpolysaccharide verwenden, konnte gezeigt werden, dass nicht die Algen selbst, sondern die Bakterien Hauptproduzent dieser Polysaccharide während einer Phytoplanktonblüte sind. Bakterielle Proteine, die dem Abbau von Algen-β-Glucan und dem daraus folgenden Aufbau von bakteriellem α-Glucan dienen, waren in Umweltproben und in Laborkulturen unter ähnlichen Bedingungen abundant. Die Untersuchung von extrahiertem bakteriellem Polysaccharid bewies, dass dieses nicht nur α-Glucan enthält, sondern dass dieses Polysaccharid auch in der Lage war, α-Glucan PULs mariner Bakterien zu induzieren. Hier zeigte sich ein innerhalb des marinen Kohlenstoffkreislaufs bisher wenig berücksichtigter Kreislauf, indem Bakterien Polysaccharide anderer Bakterien nutzen, die z.B. durch Viren lysiert wurden.
Die anderen zwei Artikel dieser Arbeit befassen sich mit dem Abbau von Zellwandpolysacchariden durch blütenassoziierte Modellbakterien. In einer der Studien wird detailliert der Abbau eines β-Mannans (ein Polysaccharid das hauptsächlich aus dem Monosaccharid Mannose besteht) durch ein Bakterium des Genus Muricauda beschrieben. Die PUL-Struktur dieses Bakteriums kam in mehreren anderen Phytoplanktonblüten-assoziierten Bakterien vor. Diese Beobachtung wies darauf hin, dass es sich hier um ein Mannan mit zusätzlichen Galactose- und Glucose-Substitutionen handelte. Proteom-Untersuchungen bestätigten, dass das Bakterium derartige Substrate unter Induktion des β-Mannan-PULs nutzen können. β-Mannan konnte durch Antikörpermarkierung in Blütenproben sowie spezifischen Mikroalgenarten (Chaetoceros, Coscinodiscus) nachgewiesen werden. Die in dieser Publikation charakterisieren β-Mannan-PUL-codierten Enzyme waren in der Lage, dieses Signal zu löschen, was bewies, dass Muricauda sp. Mannan-basierte Zellwandpolysaccharide bestimmter Arten von Mikroalgen abbauen kann.
Die dritte Studie geht näher auf den Abbau von Xylanen (bestehend aus Xylose) durch ein blütenassoziiertes Bakterium des Genus Flavimarina ein. In diesem Bakterium wurden anhand der enthaltenen Xylanasen zwei putative Xylan-PULs annotiert. Wachstumsexperimente und Proteom-Untersuchungen zeigten, dass einer dieser PULs hauptsächlich bei Wachstum auf Glucoronoxylan induziert wird, während der andere PUL aufArabinoxylane stärker reagierte. Untersuchung der PUL-CAZymes bestätigte diese Ergebnisse durch Charakterisierung mehrerer Xylanasen sowie Glucoronidasen und Arabinofuranosidasen. Zusätzlich codierten beide PULs für Esterasen, die eine Modifikation der natürlichen Substrate durch Acetylierungen oder Methylierungen nahelegen. Da all diese Merkmale von terrestrischen Xylanen geteilt werden und in Blütenproben aus Küstennahen Regionen Xylane nachgewiesen wurden, ist es möglich, dass Bakterien aus solchen Regionen sowohl Xylane terrestrischen Ursprungs (z.B. durch Flusseinspeisung) sowie marinen Ursprungs abbauen können.
During infections, innate immune cells are crucial for initiating a pro-inflammatory immune response and clearing the invading pathogen. Delay in pathogen clearance or initiation of an immune response due to impaired functionality of immune cells can result in devastating consequences. The cellular compartment of the innate immune system comprises an array of specialized cell types: Macrophages are tissue-resident professional phagocytes that clear cellular debris, pathogens, and foreign objects. Dendritic cells (DCs) are immune sentinels specialized in antigen uptake and subsequent T cell priming. They are primary sources of cytokines in response to infection. Neutrophils are efficient effector cells that respond rapidly to infection and clear bacteria by different mechanisms. If effector mechanisms of these cells are affected by either bacterial or other factors, infections might not be resolved and can spread throughout the host. Cobalt-chromium-molybdenum biomaterial is widely used in arthroplasty. Implant-derived wear particles and ions lead to macrophage-driven adverse local tissue reactions: Such reactions have been linked to an increased risk of periprosthetic joint infection after revision arthroplasty. While metal-induced cytotoxicity is well characterized in human macrophages, direct effects on their functionality remain elusive. In Paper I, we show that local peri-implant tissue is exposed to Co and Cr in situ. Influx of macrophages is also evident. Exposure of isolated human monocytes/macrophages to Cr3+ in vitro had only minor effects. However, exposure of monocytes/macrophages to pathologic concentrations of Co2+ significantly impaired both phenotype and functionality. High concentrations of Co2+ induced loss of surface markers, including CD14 and CD16. Both Co2+ and Cr3+ impaired macrophage responses to Staphylococcus aureus infection. Co2+ -exposed macrophages, in particular, showed decreased phagocytic activity. These findings demonstrate the immunosuppressive effects of locally elevated metal ions on the innate immune response. Streptococcus pyogenes (group A streptococcus, GAS) causes a variety of diseases ranging from mild to severe necrotizing soft tissue infections (NSTIs). In the host environment hypervirulent GAS variants carrying mutations within the genes encoding for control of virulence (Cov)R/S two component system are enriched. This adaptation is associated with loss of SpeB secretion. In Paper II, we show that in vitro infections with hyper-virulent GAS variants harboring dysfunctional CovR/S suppress secretion of IL-8 and IL-18 by human monocytic cells. This phenotype was mediated by a caspase-8 dependent mechanism. Knockout of streptococcal SLO in a GAS strain carrying functional CovR/S even increased secretion of IL1β and IL-18 by moDCs. Of 67 fully sequenced GAS NSTI isolates, 28 contained covS or covR mutations that rendered the TCS dysfunctional. However, no differences in systemic IL-8 and IL-18 were detected in these patients. GAS isolates recovered from patients often display a mixed phenotype, consisting of SpeB positive (SpeB+ ) and SpeB negative (SpeB- ) clones. Irreversible loss of SpeB expression is often caused by loss of function mutations in regulatory components (CovR/S, RopB). Loss of SpeB is often associated with hyper-virulence. In Paper III, we show that the host environment induces transiently abrogated secretion of SpeB by GAS. Tissue inflammation, neutrophil influx, and degranulation correlated with increased frequencies of SpeB- GAS clones. Isolates recovered from tissue expressed but did not secrete SpeB, which was reversible. Neutrophilderived ROS were identified as the main factor responsible for abrogated SpeB secretion. Hyper-virulent SpeB- clones also exhibit better survival within and induce excessive degranulation of neutrophils.
Hepatitis E virus (HEV) is emerging worldwide as a zoonotic pathogen that has remained largely undetected for decades, if not centuries. Its enormous success can be attributed to the wide range of host species, which can transmit the virus to humans, depending on the viral genotype. As a result, HEV is likely to remain a challenge even when the remaining hepatitis viruses (HAV, HBV, HCV), which are transmitted exclusively between humans, are under control. Although millions of HEV infections occur each year, little is known about this puzzling pathogen. One major issue in HEV research is the lack of reliable model systems. Established animal models are inefficient, expensive, or simply not representative of human HEV. On the other hand, cell culture systems are limited by the slow growth of the virus and inefficient replication and infection. The aim of this work is to with deepen the understanding of zoonotic HEV in animal hosts in Germany. For this purpose, a molecular and phylogenetic characterization of HEV sequences from rabbits and swine was conducted. A novel subtype of the zoonotic genotype HEV-3 was identified in a rabbit sample, further emphasizing the role of rabbits as HEV host species and possible reservoir of zoonotic HEV infections in Germany. On the other hand, a molecular biological screening of pigs and wild boars in Mecklenburg-Western Pomerania indicates a wide range of HEV-3 subtypes circulating in swine in north-east Germany. Furthermore, an optimized replicon system was established in order to enable characterization of various HEV sequences by reverse genetics. As a proof of concept, two rabbit HEV derived replicons were compared with two established, cell culture adapted HEV strains. The influence of different regions of the nonstructural protein on HEV replication was determined and quantified. In particular, a system was established, to reproducibly compare different strains and genotypes. This refined replicon system will enable the characterization of further HEV sequences and thus expand the knowledge on the determinants of the viral life cycle.
Die orale Einnahme stellt für Patienten die einfachste und unkomplizierteste Möglichkeit dar, ein Arzneimittel zu applizieren und ist das angestrebte Ziel der Arzneimittelentwicklung. Dem entgegen stehen jedoch die evolutionär entstandenen Möglichkeiten des Körpers, aufgenommene Fremdstoffe zu inaktivieren und zu eliminieren. Ein Zusammenspiel aus anatomischen Gegebenheiten und den Enzymen des Fremdstoffmetabolismus sorgt dafür, dass ein Teil der oral applizierten Dosis bereits verstoffwechselt wird, bevor er über das arterielle System an den Wirkort gelangen kann (first-pass-Effekt). Als Ort dieses Metabolismus wurde, neben der Leber, auch der Darm identifiziert. Um das Ausmaß des first- pass-Effektes abschätzen zu können, werden Daten über den Gehalt der arzneistoffmetabolisierenden Enzyme in diesen Organen benötigt. Als Methode der Wahl bietet sich dazu die LC-MS/MS an, da mit ihr verschiedene Enzyme in einem analytischen Lauf bestimmt werden können und sie sich durch eine hohe Empfindlichkeit, Reproduzierbarkeit und Spezifität auszeichnet.
Mit der vorliegenden Arbeit wurde das analytische Spektrum der bisher publizierten Methoden zur Bestimmung von CYP- und UGT-Enzymen erweitert. Mit der neuen Methode können nun zwei Carboxylesterasen, 17 CYP-Enzyme und fünf UGT-Enzyme quantifiziert werden. Weiterhin wurde die Methode anhand von Richtlinien für bioanalytische Methoden umfassend validiert. Durch die Verwendung von rekombinant hergestellten arzneistoffmetabolisierenden Enzymen konnte der gesamte analytische Prozess, von der Probe bis zum Endergebnis, erstmalig umfassend charakterisiert werden. Dabei zeigte sich eine, für einen derart komplexen Prozess bemerkenswerte Präzision von maximal 15,5% Variation nach sechsmaliger Durchführung.
Die entwickelte Methode wurde dann auf gepaarte Proben aus Leber und Jejunum von elf gesunden Organspendern angewendet. Im Jejunum wurden CES1, CES2, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2J2, CYPA4, CYP3A5, CYP4F2, CYP4F12, UGT1A1, UGT1A3, UGT2B7 und UGT2B17 gefunden. In der Leber konnten alle untersuchten Enzyme (CES1, CES2, CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP2J2, CYP3A4, CYP3A5, CYP3A7, CYP4F2, CYPF12, UGT1A1, UGT1A3, UGT2B7, UGT2B15 und UGT2B17), bis auf CYP4A11 nachgewiesen werden. Für einige Enzyme (CES2, CYP2C18, CYP2C19, CYP2J2, CYP3A4, CYP4F2, CYP4F12) wurden im Jejunum Enzymgehalte gemessen, die mit denen in der Leber vergleichbar sind, was noch einmal unterstreicht, dass der Darm auch als klinisch relevanter Ort des Arzneistoffmetabolismus betrachtet werden muss. Auffällig war hier zudem die deutlich höhere Variabilität in den Darmproben, verglichen mit den Leberproben, die ihre Ursache in Umwelteinflüssen oder dem Mikrobiom des Darms haben könnten. Außerdem wurde die Expression der zugehörigen Gene mittels quantitativer real-time PCR untersucht. Hier bestand nur in einigen Fällen eine signifikante Korrelation zwischen Genexpression und Proteingehalt, was für zwischengeschaltete regulatorische Mechanismen spricht.
Weiterhin wurden mit dieser Methode Leberproben einer Kohorte von Patienten mit Krankheitsbildern, die mit einer Einschränkung der Leberfunktion einhergehen, untersucht. Dazu wurden die Patienten nach der verbleibenden Leberfunktion (Child-Pugh-Score) und nach der zugrundeliegenden Erkrankung eingeteilt. Es zeigt sich eine generelle Abnahme des Gehaltes an arzneistoffmetabolisierenden Enzymen mit fortschreitender Verschlechterung der Leberfunktion, wobei sich CYP2E1 als besonders anfällig erwiesen hat und bereits in Child- Pugh-Klasse A signifikant erniedrigt war. Bei den verschiedenen Erkrankungen zeigt sich ein uneinheitliches Bild, die prozentuale Verteilung der Enzyme ist jedoch bei allen Erkrankungen gegenüber den gesunden Kontrollproben verändert.
Über die Regulation der Expression von arzneistoffmetabolisierenden Enzymen ist bisher noch wenig bekannt. Es gibt aber Hinweise aus der Literatur, dass bestimmte nukleäre Rezeptoren an der Regulation der Enzyme beteiligt sein können. Deshalb wurde eine LC-MS/MS-basierte targeted-proteomics-Methode zur Quantifizierung von nukleären Rezeptoren in Darm- und Lebergewebe entwickelt und validiert. Im Gewebe konnten nur AhR und HNF4α nachgewiesen werden, da die Empfindlichkeit des verwendeten experimentellen Ansatzes vermutlich nicht ausreichend ist. Dabei war HNF4α in Darmgewebe deutlich höher exprimiert als AhR. Außerdem wurde die Expression der nukleären Rezeptoren auf Genebene durch quantitative real-time PCR untersucht. Dabei wurde eine höhere Expression von CAR in der Leber gefunden, während PXR in Darm stärker exprimiert wird. Dies entspricht den Erkenntnissen aus der Literatur, nach denen CAR einen regulatorischen Effekt auf arzneistoffmetabolisierende Enzyme in der Leber hat, während dies für PXR in Darm zutrifft. Diese Arbeit kann einen Beitrag zum weitergehenden Verständnis der Regulation von arzneistoffmetabolisierenden Enzymen durch nukleäre Rezeptoren beitragen.
Bei allen diesen Arbeiten gilt es zu beachten, dass das Vorhandensein eines Proteins nicht zwangsläufig mit seiner Aktivität gleichzusetzen ist. Jedoch zeigen zahlreiche Beispiele aus der Literatur, dass sich mit den Daten aus Proteomics-Studien PBPK-Modelle aufstellen lassen, die die in klinischen Studien erhobenen Daten mit beeindruckender Genauigkeit reproduzieren können.
Antimicrobial resistance (AMR) is of paramount importance in the context of One Health, an integrated and unifying approach that aims to achieve a sustainable balance in the well-being of people, domestic and wild animals, plants, and their shared environments. Whenever bacteria become resistant to the therapeutic effects of antibiotics, they can cause infections that are difficult to treat effectively, increasing the risk of severe disease progression and death. Although AMR can develop naturally over time and is per se “ancient”, the excessive use of antibiotics in human and veterinary medicine over the past century has significantly accelerated its emergence and spread. Opportunistic Gram-negative enterobacteria, particularly Escherichia coli (E. coli ) and Klebsiella pneumoniae (K. pneumoniae) strains, increasingly exhibit resistance to multiple classes of clinically used antibiotics, thus presenting multidrug-resistant (MDR) phenotypes. To make matters worse, some of these strains combine multidrug resistance with high-level virulence, posing a threat to both immunocompromised and healthy individuals. Consequently, MDR E. coli and K. pneumoniae have been designated as high-risk pathogens by the World Health Organization, underscoring the urgent need for new antibiotic development.
This thesis is motivated by the fact that only a limited number of international high-risk clonal E. coli and K. pneumoniae lineages stand out across all One Health dimensions and dominate the broad pool of MDR enterobacteria. While we only know little about the underlying drivers and contributing factors impacting their occurrence, emergence, and adaptation across different ecologies, this thesis employs a diverse range of bioinformatics and phenotypic approaches to identify the key factors important for the success of these lineages, also in rather under-explored settings. It includes three main components: (i) the analysis of genomic survey data of MDR E. coli isolates from ecologies in sub-Saharan Africa, (ii) the application of functional genomics and phenotyping techniques to characterize bacterial virulence and assess its clinical relevance in a food-borne E. coli strain, and (iii) the investigation of evolutionary pathways that promote the development of resistance to a novel drug combination and exploring compensatory mechanisms in a K. pneumoniae strain. To achieve these objectives, this research integrates genomics and transcriptomics with molecular biology and functional studies encompassing a comprehensive set of in vitro and in vivo virulence and resilience assays to explore MDR bacteria in-depth.
We provide compelling evidence for the broad occurrence of successful high-risk clonal lineages in the One Health context and their circulation among clinics, wildlife, and food in international locations. In the first study, we isolated extended-spectrum β-lactamase (ESBL)-producing E. coli strains from houseflies collected from various wards at the University Teaching Hospital of Butare (Rwanda). In a follow-up study, we then examined in-depth the genomes of additional ESBL-producing E. coli from the same clinic and obtained from hospitalized patients, their caregivers, associated community members, and pets. The analyses revealed that the sample sets from this sub-Saharan African context consisted predominantly of globally recognized E. coli lineages, including sequence types (ST)131, ST167, ST410, and ST617. They play a pivotal role in the further dissemination and stabilization of AMR across diverse habitats within the One Health context. Moreover, our genomic results emphasize that these One Health-related high-risk clonal lineages exhibit the ability to successfully combine multidrug resistance with high-level bacterial virulence.
To gain a more detailed understanding of the sophisticated interplay of virulence and AMR, we developed and refined a set of in vitro and in vivo methods for virulence phenotyping. These methodologies enabled us to characterize pathogens based on crucial clinical aspects such as biofilm formation, siderophore secretion, resistance to complement-mediated killing, and their capacity to cause mortality in Galleria mellonella larvae. By using a food-borne E. coli strain from an internationally recognized high-risk clonal lineage, we verified the remarkable combination of a MDR phenotype with clinically significant virulence properties, including synthesis of curli fibers and cellulose as part of biofilm formation, extensive secretion of siderophores, resilience against complement-containing human serum and pronounced mortality in the infection model.
Nevertheless, the success of One Health-related high-risk clonal lineages does not rely solely on an “ideal” synergistic interplay between bacterial virulence and AMR. It also depends on their ability to rapidly mitigate the fitness costs associated with AMR acquisition, as these costs manifest in the form of reduced competitiveness and virulence in the absence of antibiotics. However, this is at odds with the observation of the global distribution of One Health-related high-risk clonal lineages across various One Health dimensions, even in environments with expectedly low selection pressures. To comprehensively address this, we conducted experimental evolution studies selecting for ceftazidime-avibactam-resistant mutants, which illuminated the rapid adaptations to changing environments. The adaptations and compensatory mechanisms were seemingly driven by major bacterial regulators, including the envelope stress response regulator RpoE on genomic and transcriptomic levels.
In conclusion, the results of this thesis shed light on the fundamental principles that govern the character and interplay between AMR and bacterial virulence and advance our understanding of the contributors and drivers of successful MDR international high-risk clonal lineages in the One Health context. This is also important for effective and alternative intervention strategies to prospectively further address the global threat of AMR.
Mass spectrometry-based Proteome analysis of porcine cells infected with African swine fever virus
(2023)
ASFV, a highly contagious, pathogenic and lethal pathogen of swine, poses a major threat to domestic and wild suids worldwide as neither vaccines nor treatments are available. Compared to other well-characterized similarly complex viruses like herpesviruses or adenoviruses, the understanding of ASFV biology is poor.
To improve the understanding of ASFV biology, following the establishment of a robust protocol for the isolation of primary monocyte-derived porcine macrophages (moMΦ) and their infection with ASFV for mass spectrometry (MS)-based proteome analysis was performed.
Under both conditions, naïve and infected, the isolated cells showed cell type-specific characteristics like phagocytosis and antigen presentation and protein expression patterns, including the expression of swine leucocyte antigens and CD markers. Furthermore, moMΦ could be reproducibly infected with ASFV isolates of different genotypes and pathogenicity.
The ASFV protein expression patterns in moMΦ correlate well with those observed in established cell lines at transcript and protein level. The expression of 27 ASFV proteins was confirmed at the protein level. Among them, 9 members of multi-gene families (MGF) and 12 novel open reading frames (nORFs) were recently predicted based on transcription start site mapping.
The direct comparison of closely related ASFV genotype II isolates revealed no virulence-associated protein expression patterns beyond those expected based on the genome sequences of the isolates.
Using different MS quantification strategies, it was shown that ASFV affects both static protein expression levels and protein synthesis. These changes in protein expression impact proteins and pathways known to be targeted by ASFV, including CD-markers, ER-stress and cell death pathways, and cellular antiviral responses. Beyond these observations that further validated the moMΦ infection model, novel effects of the ASFV infection on the cellular proteome were noticed.
These effects include the decreased expression levels of cathepsins, especially cathepsins D (CTSD), H (CTSH) and L (CTSL) as well as the transient activation of MAPK14/p38 prior to its strong downregulation. In addition to MAPK14/p38 further members of the MAPK14/p38 signaling pathway, like MAPKAPK2, were affected by ASFV infection.
As these modulations of the cellular proteome would in general result in decreased pro-inflammatory responses, it did stand out that the synthesis of interferon-response related genes including MX1 and ISG15 evaded the ASFV-induced global reduction of protein synthesis. In contrast, the synthesis of genes involved in RNA processing and splicing was significantly impaired. In total, the regulations of individual host proteins assessed in the context of the whole cellular proteome integrate well with each other and other cellular responses to ASFV infection and may help to improve the understanding of host-virus interactions.
Overall, this thesis provides novel insights into the expression of ASFV-encoded ORFs of different isolates and the host response to ASFV infection. It points out that the current knowledge of the ASFV coding capacity, temporal protein expression patterns, protein functionality, post-translational modifications and host interactions is still sketchy as many aspects of ASFV replication have yet to be understood. The established moMΦ-model to study ASFV infections in vitro provides a powerful tool for future applications to increase the understanding of ASFV biology.
Age is the single biggest risk factor for most major human diseases. As such, understanding the intricate molecular changes that drive biological aging holds great promise in attempting to slow
the onset of systemic diseases and thereby increase the effective health-span in modern societies.
This thesis explores several computational approaches to capture and analyze the molecular biological alterations triggered by intrinsic and extrinsic aging using skin as a model tissue to deliver genes and pathways as potential targets for intervention strategies.
Publication 1 demonstrates the utility of multi-omics data integration strategies for aging research, leading to the identification of four latent aging phases in skin tissue through an integrated cluster analysis of gene expression and DNA methylation data. The four phases improved the detection of molecular aging signals and were shown to be associated with sunbathing habits of the test subjects. Deeper analysis revealed extensive non-linear alterations in various biological pathways particularly at the transition into the fourth aging phase, coinciding with menopause, with potentially wide-reaching functional implications. Publication 2 describes the development of a novel type of age clock, that provides a new level of interpretability by embedding biological pathway information in the architecture of an artificial neural network. The clock not only generates meaningful biological age estimates from gene expression data, but further allows simultaneous monitoring of the aging states of various biological processes through the activations of intermediate neurons. Analyses of the inner workings of the clock revealed a wide-spread impact of aging on the global pathway landscape. Simulation experiments using the transcriptomic clock recapitulated known functional aging gene associations and allowed deciphering of the pathways by which accelerated aging conditions such as chronic sun exposure and Hutchinson-Gilford progeria syndrome exert their effects. Publication 3 further explores the molecular alterations caused by the pro-aging effector UV irradiation in the skin. The multi-omics data analysis of repetitively irradiated skin revealed signs of the immediate acquisition of aging- and cancer-related epigenetic signatures and concurrent wide-spread transcriptional changes across various biological processes. Investigations into the varying resilience to irradiation between subjects revealed prognostic biomarker signatures capable of predicting individual UV tolerances, with accuracies far surpassing the traditional Fitzpatrick classification scheme. Further analysis of the transcripts and pathways associated with UV tolerance identified a form of melanin-independent DNA damage protection in individuals with higher innate UV resilience.
Together, the approaches and findings described in this thesis explore several new angles to advance our understanding of aging processes and external drivers of aging such as UV irradiation in the human skin and deliver new insight on target genes and pathways involved.
The respiratory epithelium acts as both, a barrier of the respiratory tract to Nipah virus (NiV) entry and at the same time as a significant determinant of virus shedding. Both, for humans and pigs, replication in the respiratory tract epithelia is considered a major factor in transmission to other hosts. To understand why the virus constitutes a high-risk pathogen for livestock and humans, knowledge about
viral replication and host responses in relevant cells and tissues is crucial. Most in vitro studies, however, have been performed in conventional cell lines or non-differentiated lung cells. Only a few examples exist where Henipavirus infections have been investigated in fully-differentiated lung
epithelial cell models.
Thus, one aim of this thesis was to investigate infection, replication, spread and host protein dynamics of NiV in primary bronchial epithelial cells (BEC) cultivated at the air-liquid-interphase (ALI). By
immunofluorescence imaging, the NiV infection dynamics in BEC-ALI cultures were monitored over a 12 day time course, in order to provide detailed information about the infection process in the
respiratory epithelium of pigs and ferrets. Compared to undifferentiated primary BEC, the specific infectivity of NiV in BEC-ALI cultures was low. Infections remained focal and complete infection of the
cultures was not observed, even at 12 dpi. Analysis of viral titers and viral mRNA indicated a limited
virion release from the infected ALI-cultures while most of the newly synthesized NiV-RNA remained
cell associated. Immunofluorescence analysis of cross sections from infected ALI-cultures revealed
large infected areas that exhibited a strong cytopathic effect (CPE). Disruption of the epithelium
resulted in apical release of virus antigen-positive cell detritus while ciliated areas and basal cells were
less affected. From these data it was concluded, that NiV transmission could be supported by
exhalation of cell debris associated NiV and thus may contribute to rapid spread of infection in swine
populations.
A second aim was to explore the dynamics of host responses to NiV infection in differentiated BEC-ALI
culture and to assess whether this differs to conventional cell line data available from literature. Even
though strong CPE appeared in later phases of NiV infection, at least the porcine PBEC-ALI cultures
remained robust enough to allow protein sampling over 12 days infection course. Subsequent MS-based proteomics enabled unprecedent insight in complex cell culture response upon NiV infection.
Previous reports indicated a lack of efficient interferon type I induction in non-differentiated pig or
human BEC which were considered a prerequisite for efficient replication in the respiratory epithelium
and virusspread. In contrast to non-differentiated pig BEC (PBEC), in PBEC-ALI cultures multiple factors
involved in interferon responses were upregulated upon NiV infection. Thereby it was demonstrated
that NiV infection induced a robust innate immune response upon infection with elevated components of antigen processing and presentation resulting in the conversion from the constitutive proteasome to the immunoproteasome. In contrast to previous reports about NiV-infected non-differentiated
PBEC or endothelial cells, incomplete immunoproteasome formation and limitations in interferon
response could be excluded. Thus, a model is proposed in which NiV infection and spread in differentiated PBECs is slowed by potent innate immune responses to the virus infection. Overall, the
findings highlight the important role of the respiratory epithelium not only as a physical barrier to virus
infections but also indicate itsrole as a primary site of adaptive immune induction through NiV induced
antigen processing and MHC I presentation.
Finally, to allow functional studies of Henipaviruses at the BSL-2 biosafety level a recombinant CedPV
was generated and rescued. An imaging based screening and quantitative analysis pipeline was established to investigate the role of cellular factors and to screen for potential virus and host gene
directed inhibitory factors. Accordingly, different host and viral genes were targeted with a siRNA-pool
either targeting virus or selected cellular mRNAs followed by the infection with the CedPV and the
quantification of infected cells. With proof of concept of the siRNA screening pipeline, the recombinant
CedPV clone was used as a backbone to insert variousfluorescence reporter genesin order to optimize
the analysis workflow by allowing direct virus quantification in live, unstained samples. Consequently,
this thesis provides a valuable proof for future approaches related to the function of virus proteins,
influence of host-factors and virusreplication and Henipavirus-inhibitorscreens at low biosafety levels.
The role of cell-penetrating peptides in the induction of T cell responses by virus-like particles
(2023)
Many viral structural proteins can self-assemble into virus-like particles (VLPs). VLPs can serve as an effective vaccine or be used as a vaccine platform. One of these structural proteins is the hepatitis B virus core antigen (HBcAg), which appears to be suitable as an antigen carrier due to its high immunogenicity. HBcAg has a major immunodominant region (MIR) that is presented on the surface of the VLPs after self-assembly. Foreign antigens can be inserted into this region. Since HBcAg VLPs, unlike the Hepatitis B virus (HBV), do not have an envelope, they are not able to penetrate cell membranes efficiently. As an extracellular antigen, HBcAg VLPs primarily induce a strong humoral immune response.
In the present study, we investigated the extent to which HBcAg can be modified to also elicit an enhanced cellular, particularly a cytotoxic, immune response. A cytotoxic CD8+ T cell response is predominantly induced by intracellular antigens. Therefore, our goal was to increase the cell penetration capacity of VLPs. We aimed to achieve this by fusing cell-penetrating peptides (CPPs) to HBcAg. CPPs can spontaneously penetrate cell membranes to enter the cytoplasm of cells. To guarantee that the CCPs were localized to the surface of the VLPs, we fused CPPs to the N-terminus of HBcAg. The CCPs were followed by a tag to allow the purification of VLPs. The T cell epitopes, against which the induced CTL should be directed, were derived from the Large T antigen and inserted into the MIR of HBcAg. Finally, we fused fluorescent proteins to the C-terminus of HBcAg to track the entry of VLPs into cells.
Modifications of HBcAg may lead to reduced stability or altered structure of VLPs. To analyze the stability of VLPs, we used nanoscale differential scanning fluorimetry (nanoDSF) analysis. This revealed that the N-terminal fusion of CPPs or the tag to HBcAg does not reduce VLP stability. However, some peptides incorporated into the MIR had a significant effect on the structure and stability of the VLPs. While the incorporation of a Flag-tag or a peptide from ovalbumin had no negative effect on VLP stability, the incorporation of peptides representing T cell epitopes of Large T antigen interfered with VLP formation. Denaturation and reassembly of the aggregates significantly improved the homogeneity of the VLPs, and the C-terminal addition of arginine-rich domains enhanced stability.
Using live cell imaging and flow cytometry, we demonstrated that HBcAg VLPs functionalized with CPP exhibited up to 40% more efficient penetration into professional antigen-presenting cells (JAWS II) than HBcAg VLPs without CPP. This resulted in the increased presentation of integrated T cell epitopes by dendritic cells. In vivo, we detected significantly increased induction of SV40 Large T antigen-specific CTL in mice immunized with CPP-conjugated VLPs compared to unconjugated VLPs.
In this study, we demonstrated that a stronger cellular immune response can be induced by CPP-functionalized HBcAg VLPs than with the unmodified HBcAg VLPs in vitro as well as in vivo. This discovery may have positive implications for future vaccine development where an enhanced cellular component of the immune response is desirable.
As the animal-to-human interface becomes increasingly narrow, transmission events of zoonotic pathogens between animals and humans become more and more probable. While SARS-CoV-2 already accomplished a spillover infection to humans and is responsible for the current pandemic, the bat H9N2 IAV with so far unknown zoonotic potential was only recently discovered. In order to identify I) the role and potential of a newly discovered, potentially pre-pandemic virus, such as the bat H9N2, or II) possible future prevailing virus mutant variants of an already known pandemic virus, such as SARS-CoV-2, it is important to characterize these emerging viruses in vivo as soon and as good as possible.
The first objective in this dissertation (Publications I and II) therefore deals with the characterization of bat H9N2 and the estimation of its zoonotic or even pandemic potential.
In Publication I, a general susceptibility of directly inoculated Egyptian fruit bats to bat H9N2 was confirmed by successful seroconversion, although exhibiting only moderate viral shedding. All three contact animals remained seronegative, though one contact bat showed slight lesions in the histopathological analysis.
Publication II further addressed the question of the zoonotic potential of this virus. Inoculation of day-old turkey hatchlings demonstrated moderate susceptibility to bat H9N2 infection with a measurable seroconversion, while day-old chicken hatchlings were not susceptible to bat H9N2. Ferrets proved to be highly susceptible to bat H9N2 with high viral shedding, a transmission efficiency rate of 100% to direct contact animals at 2 days post contact, but with only minimal clinical signs. Importantly, the virus demonstrated the ability to evade the MxA-restriction factor and to replicate efficiently in human lung tissue explants. Furthermore, seasonal IAV- and standard IAV-vaccines showed no cross reactivity against the bat-N2 protein in humans. Therefore, further research on such viruses is urgently needed in order to prevent a renewed pandemic situation in the future as caused by SARS-CoV-2.
The second objective in this dissertation dealt with the identification and characterization of emerging SARS-CoV-2 Variants of Concern (VOCs).
Therefore, in Publication III, competitive infection experiments were performed using the Syrian golden hamster, the ferret, and transgenic mouse models (K18-hACE2 and hACE2-KI). These studies revealed replicative and transmissive predominance of Alpha VOC over Beta VOC, but not over SARS-CoV-2 WT in the hamster model, although Beta VOC substantially replicated in the lungs of donor animals. In contrast, the Alpha VOC had an unambiguous replication and transmission advantage over WT SARS-CoV-2 in the ferret and both mouse models. A recombinant SARS-CoV-2 WT-SAlpha virus helped to assign the fitness advantage of this variant particularly to the spike protein-associated mutations.
In Publication IV, in vitro results inferred an early replicative fitness advantage of Omicron BA.1 over Delta VOC, although the opposite was observed in competitively inoculated hamsters, ferrets and naive hACE2-KI mice. In addition, Publication IV demonstrated a disadvantage in transmission for the VOC Omicron BA.1 over the Delta VOC and a lack of susceptibility of ferrets after a single infection with the VOC Omicron BA.1. An mRNA vaccination of K18-hACE2 mice caused a drastic reduction of infectious virus particles in organ material following an infection with a recombinant SARS-CoV-2 WT-SDelta, but not when challenged with the SARS-CoV-2 SOmicron BA.1 clone.
This dissertation includes numerous, comprehensive experimental studies that are generally important for the characterization of emerging, potentially pre-pandemic viruses and may provide crucial information about the future dominance of certain virus variants in an ongoing pandemic. Here, the need for the use of a variety of animal models becomes apparent. By characterizing and classifying potentially zoonotic strains, these methods will help to better prepare for potentially upcoming pandemics and, in the case of a zoonotic or even pandemic event, to better detect and understand the circulating strains and their evolution.
Emerging infectious diseases are among the greatest threats to human, animal and plant health as well as to global biodiversity. They often arise following the human-mediated transport of a pathogen beyond its natural geographic range, where host species are typically not well adapted due to a lack of co-evolutionary host-pathogen dynamics. One such pathogen is the fungus Pseudogymnoascus destructans (Pd), which causes White-Nose disease in hibernating bats. While Pd was first observed in North America where it has led to mass-mortalities in some bat species, the pathogen originates from Eurasia where infection is not associated with mortality. Most of the Pd research has focused on the invasive North American range, which likely underestimated the genetic structure of the pathogen and the role it might play in the disease dynamics.
In my work, I therefore evaluated the genetic structure of Pd in its native range with the aim of uncovering cryptic diversity and further use population genetic data to address some key ecological aspects of the disease dynamics. With an extensive reference collection of more than 5,000 isolates from 27 countries I first demonstrated strong differentiation between two monophyletic clades across several genetic measures (multi-locus genotypes, full genome long-read sequencing and Illumina NovaSeq on isolate pools). These findings are consistent with the presence of two cryptic species which are both causative agents of bat White-Nose disease (‘Pd-1’, which corresponds to P. destructans sensu stricto, and ‘Pd-2’). Both species exist in the same geographic range and co-occur in the same hibernacula (i.e., in sympatry), though with specialised host preferences. I further described the fine-scale population structure in Eurasia which revealed that most genotypes are unique to single hibernacula (more than 95% of genotypes). The associated differences in microsatellite allele frequencies among hibernacula allowed the use of assignment methods to assign the North American isolates (exclusively Pd-1) to regions in Eurasia. Hence, a region in Ukraine (Podilia) is the most likely origin of the North American introduction.
To gain further insights into the spatial and temporal dynamics of White-Nose disease on a localised scale, several hibernacula were sampled with high intensity (artificial hibernaculum in Germany and natural karst caves in Bulgaria). Low rates of Pd gene flow were observed even among closely situated hibernacula. This indicates that Pd does not remain viable on bats over summer or it would be frequently exchanged among bats (and hence hibernacula) resulting in a homogenous distribution of genotypes. Instead, bats need to become re-infected each hibernation season to explain the yearly re-occurrence of White-Nose disease. Given the distribution and richness of Pd genotypes on hibrnacula walls and infected bats of the same hibernacula, bats become infected from the hibernacula walls when they return after summer. This means that environmental reservoirs exist within hibernacula (i.e., the walls) on which Pd spores persist during bat absence and which drive the yearly re-occurrence of White-Nose disease. In an experimental setup, I confirmed the long-term viability of Pd spores on abiotic substrate for at least two years and furthermore discovered temporal variations in Pd spores’ ability to germinate. In fact, these variations followed a seasonal pattern consistent with the timing of bats absence (reduced germination) and presence (increased germination) and could indicate adaptations of Pd to the bats’ life-cycle. The infection of bats from environmental reservoirs hence seems to be a central aspect of White-Nose disease dynamics and Pd biology.
Pds ability to remain viable for extended periods outside the host increases its risk of being anthropogenically transported and might have played a role in the emergence of White-Nose disease in North America. The existence of a second species (Pd-2) poses a great additional danger to North American bats considering that its introduction there could lead to deaths and associated population declines in so-far unaffected species given what is known about differing host species preferences in Eurasian bats. Even within the native range of Pd, the movement of Pd between differentiated fungal populations could facilitate genetic exchanges (e.g., through sexual reproduction) between genetically distant genotypes. Such genetic exchanges could lead to phenotypic jumps in pathogenicity or host-species preferences and should hence be prevented.
The native range of a pathogen holds great potential to better understand the genetic and ecological basis of a (wildlife) disease. My work informs about the dangers associated with the accidental transport of Pd (and other pathogens) and highlights the need for ‘prezootic’ biosecurity-oriented strategies to prevent disease outbreaks globally. Once a pathogen has arrived in a new geographic range, and particularly if it has environmentally durable spores (as demonstrated for Pd), it will be difficult/impossible to eradicate. Furthermore, a pathogen’s ability to remain viable outside the host and infect them from environmental reservoirs has been associated with an increased risk of species extinctions and needs to be considered when designing management strategies to mitigate disease impact.
In den letzten Jahren gewannen ω-Transaminasen zunehmend an Bedeutung. Ihr breites Substratspektrum, das sowohl Aminosäuren als auch Amine umfasst, macht sie interessant für biotechnologische Anwendungen. Im Gegensatz zu α-Aminotransferasen sind ω-Aminotransferasen nicht auf α-Aminosäuren als Aminodonor bzw. α-Ketosäuren als Aminoakzeptoren beschränkt. Auch sind einige ω-Transaminasen in der Lage, Aldehyde oder Ketone zu aminieren. Dadurch sind sie vielseitig einsetzbar. Seit ihrer Entdeckung wurden ω-Transaminasen in einer Vielzahl von Organismen nachgewiesen. Viele dieser Enzyme stammen aus Pilzen und Bakterien. Da es ständig Bedarf an neuen Transaminasen gibt, wurden verschiedene Organismen auf das Vorhandensein solcher Enzyme untersucht. Die Hefe Blastobotrys raffinosifermentans LS3 ist einer dieser Organismen. Für diese Hefe existiert bereits eine Vielzahl biotechnologischer Anwendungen, was unter anderem an ihren vielseitigen physiologischen Möglichkeiten liegt. Um das Spektrum dieses Stammes noch zu erweitern, wurde sein Genom auf ORFs gescannt. Die ermittelten ORFs wurden translatiert und die so erhaltenen, theoretischen Proteine in einer Proteindatenbank gespeichert. Die Einträge dieser Datenbank wurden einem „hmmerscan“ (hmm ist kurz für „hidden Markov model“) unterzogen. Dabei werden die Proteine in sogenannte Pfams, kurz für Proteinfamilien, eingeteilt. Drei Proteine wurden der Familie PF00202.21 zugeordnet. Das ist die sogenannte Aminotran_3 Familie. In dieser Familie befinden sich eukaryotische ω-Transaminasen. Die Gene brota1, brota2 und brota3 codieren für diese Enzyme. Jeweils eins der Gene wurde in den Vektor XPLOR®3 kloniert, damit die potentiellen ω-Transaminasen in B. raffinosifermentans G1212 [aleu2 atrp1:ALEU2] [1] überexprimiert werden können. Eine Besonderheit von BroTA1 ist, dass es neben der Aminotran_3 Domäne noch eine AAA Domäne aufweist. Deshalb ist es mit etwa 85 kDa auch deutlich größer als die meisten ω-Transaminasen, die meist zwischen 45 und 50 kDa liegen. BroTA2 und BroTA3 beinhalten nur die Aminotran_3 Domäne. Alle drei Enzyme zeigen niedrige Aktivität bei der kinetischen Auflösung racemischer β-Aminosäuren.
Neben den eukaryotischen ω-Transaminasen wurden auch einige bakterielle Enzyme untersucht. Literatursuche und das Screenen der Stammsammlung der Arbeitsgruppe Hefegenetik des Leibniz-Instituts für Pflanzengenetik und Kulturpflanzenforschung führten zu mehreren potentiellen bakteriellen ω-Transaminasen. Das zu Beginn dieser Arbeit noch als hypothetisches Protein bezeichnete Enzym von Variovorax boronicumulans hat sich als ω-Transaminase herausgestellt. Das Enzym wurde detailliert hinsichtlich des Substratspektrums und seiner biochemischen Eigenschaften charakterisiert. Es handelt sich hierbei um eine ω-Transaminase mit β-Aktivität. Diese Transaminase akzeptiert sowohl aromatische als auch aliphatische β-Aminosäuren als Substrat. Sequenzvergleiche dieses Enzyms mit anderen ω-Transaminasen, die nur aliphatische Aminosäuren akzeptieren, führten zu tieferen Einblicken in konservierte Bereiche dieser beiden Gruppen von ω-Transaminasen.
Der dritte Ansatz war das Anpassen einer bekannten ω-Transaminase des thermophilen Bakteriums Sphaerobacter thermophilus an ein potentielles Motiv für aromatische ω-Transaminasen. Dadurch sollte die Aktivität des Enzyms erhöht werden. Dieser Ansatz führte zu 7 Varianten des Enzyms mit höherer Aktivität als der Wildtyp. Durch diese Versuche wurden einige für die Transferaseaktivität wichtige Aminosäurereste offenbart. So hat sich zum Beispiel herausgestellt, dass N70 offenbar wichtig für den Umsatz von γ-Aminosäuren ist, da ein Austausch gegen Glutamat zu einer verminderten Aktivität mit γ-Aminopentansäure führte.
Zerebrale kavernöse Malformationen (CCMs) sind Gefäßfehlbildungen im Gehirn oder Rückenmark und können sich klinisch aufgrund einer erhöhten Blutungsbereitschaft mit Kopfschmerzen, Gefühls- und Sprachstörungen bis hin zu Krampfanfällen äußern. Sie treten sporadisch oder im Rahmen einer autosomal-dominant erblichen Form auf. Kausale Sequenzveränderungen sind dabei in den drei Genen CCM1, CCM2 und CCM3 bekannt. Die Detektionsrate für pathogene Varianten ist mit bis zu 60 % für sporadische Fälle und mit weit über 90 % für familiäre Fälle sehr hoch. Während Genpanel-Analysen sehr verlässlich Einzelnukleotidveränderungen, kleine Insertions- und Deletionsvarianten sowie Kopienzahlveränderungen detektieren können, werden komplexe Strukturvarianten oder Veränderungen in nicht-kodierenden Regionen kaum erfasst. Diese rücken jedoch für die bisher genetisch unaufgeklärten Fälle immer mehr in den Fokus des Interesses. Diese Arbeit adressiert daher zum einen die Identifizierung neuer Strukturvarianten und deren funktionale Interpretation im Kontext der CCM-Erkrankung.
Im Rahmen der vorliegenden Arbeit ist der erstmalige Nachweis einer interchromosomalen Insertion bei einem CCM-Patienten gelungen. Die unbalancierte Insertion genomischen Materials von Chromosom 1 in die kodierende Region des CCM2-Gens konnte durch die Verbindung von bioinformatischen Auswertestrategien der Next Generation Sequencing-Genpanel-Daten, molekularzytogenetischen Analysen und einer molekularen Bruchpunktkartierung genau charakterisiert werden. Die Identifikation einer weiteren Strukturvariante, einer Deletion des Transkriptionsstarts von CCM1, verdeutlichte die Herausforderungen bei der Bewertung von Veränderungen in nicht-kodierenden Genbereichen. Für eine eindeutige Klassifikation der Variante wurden daher funktionale Analysen durchgeführt, die auf einer CRISPR/Cas9-vermittelten Nachbildung der Deletion in iPSCs und der anschließenden Differenzierung in Endothelzellen beruhte. Damit konnte gezeigt werden, dass die Deletion zu einem Verlust der CCM1 mRNA- und Proteinexpression führt. Zudem wurde in den differenzierten Endothelzellen eine für die CCM-Pathogenese charakteristische Deregulation von KLF2, THBS1, NOS3 und HEY2 beobachtet. Schließlich war es auf Basis dieser in vitro-Analysen möglich, die Variante entsprechend den ACMG-Richtlinien als wahrscheinlich pathogen zu bewerten und somit die molekulare CCM-Diagnose zu sichern.
Die Verbindung des CRISPR/Cas9-Systems mit iPSCs ist nicht nur für die Variantenbewertung von großem Nutzen, sondern bietet auch das Potential zum besseren Verständnis von Krankheitsmechanismen. Ein weiterer Fokus der vorliegenden Arbeit lag daher auf der Etablierung und Verwendung iPSC-basierter Zellkulturmodelle für die CCM-Modellierung. Zunächst ist es gelungen, mehrere iPSC-Linien mit einer kompletten CRISPR/Cas9-vermittelten CCM1-, CCM2- oder CCM3-Inaktivierung zu generieren. Diese wurden anschließend für die Differenzierung in hBMEC-ähnliche Zellen und innovative dreidimensionale vaskuläre Organoide verwendet. In diesen Systemen konnte beispielsweise eindrücklich eine tumorähnliche Proliferation CCM3-defizienter Endothelzellen nachvollzogen werden, die nur in Kontakt mit Wildtyp-Zellen auftrat. RNA-Sequenzierungen in einem CCM1-basierten Knockout-Modell konnten darüber hinaus die Rolle von CCM1 als Endothel-spezifisches Suppressorgen stärken. Die im Rahmen der Arbeit etablierten Systeme werden zukünftig für weitere Fragestellungen der CCM-Pathogenese wie der endothelialen Barrierestörung eingesetzt und stellen darüber hinaus sehr gut geeignete Plattformen für die effektive Entwicklung dringend benötigter therapeutischer Ansätze dar.
Posttranslational modifications are involved in the regulation of virtually all cellular processes, including immune response, nevertheless, they are also targets manipulated by invading pathogens. The first investigated example is protein citrullination which is an important posttranslational modification that acts on a multitude of processes like supervision of cell pluripotency and rheumatoid arthritis. Citrullination of targeted arginine residues is performed by the Peptidylarginine deiminase. Within the first published manuscript, being part of this thesis, it was possible to show the use of this posttranslational modification by the human pathogen Porphyromonas gingivalis to facilitate innate immune evasion at three distinct level. P. gingivalis was demonstrated to citrullinate proteins by Porphyromonas peptidylarginine deiminase resulting in diminished phagocytosis and subsequent killing by neutrophils. Furthermore, it was shown that citrullination of histone H3 enables P. gingivalis to survive in neutrophil extracellular traps and incapacitate the lysozyme-derived peptide LP9.
The second investigated posttranslational modification is ubiquitination and its role in respiratory tract infections. Ubiquitination is the covalent attachment of a small protein that consisting of only 76 amino acids to the ε-amino group of lysine residues to posttranslational modify proteins. Acute infections of the lower respiratory tract such as viral and bacterial co-infections are among the most prevalent reasons of fatal casualties worldwide. Therefore, the interactions between host and pathogens resulting in the impairment of the hosts immune response and immune evasion of the pathogens, need to be elucidated. To get new insights in the infection driven changes in protein polyubiquitination and alterations in the abundance of ubiquitin E3 ligases involved in ubiquitination, cellular proteomes were monitored in detail by high resolution mass spectrometry. Therefore, the epithelial cell lines 16HBE14o- (Manuscript II) and A549 (Manuscript III) were co-infected with influenza A virus H1N1 and Streptococcus pyogenes or Staphylococcus aureus or with influenza A virus H1N1 and Streptococcus pneumoniae, respectively. Here, it could be shown in 16HBE14o- cells that co-infection of epithelial cells is not characterized by decreased cell survival and that observable effects on the proteome and ubiquitinome are mostly additive rather than synergistic. S. pyogenes infection affected the mitochondrial function, cell-cell adhesion, endocytosis and actin organization. Viral infection affected mRNA processing and Rho signaling. Viral and bacterial co-infection was detected to affect processes that were already affected by both of the corresponding single infections. No further pathways were strongly affected by the co-infection. A similar result has been observed in A549 cells co-infected IAV and S. pneumoniae. Overrepresented gene ontology terms depict the sum of those observed in the viral and bacterial single infection. Moreover, no significant change in cell survival upon co-infection compared to single bacterial infection was noticed for A549 cells either. This led to the suggestion that co-infection of investigated epithelial cells under examined conditions possesses additive rather than synergistic effect and thus, may not worsen the outcome of the infection within the studied conditions. Infections in other systems, may provide varying results and thus should be examined in future studies.
Amid the current global biodiversity crisis, being able to accurately monitor the changing state of biodiversity is essential for successful conservation actions and policy. Despite the pressing need for reliable and cost-effective monitoring methods, collecting such data remains extremely difficult for elusive species, such as temperate zone bats. Although bats are important indicators of environmental changes, monitoring bat populations is challenging because they are nocturnal, volant, small, and highly sensitive to human activities and disturbance. Thus far, population trends of temperate zone bats have been mainly based on visual surveys, including winter hibernation counts at underground sites. However, as bats may not always be roosting in visible locations within the hibernacula, it is currently unknown how these estimates relate to actual population sizes.
Infrared light barriers combined with camera traps are a novel method to monitor bats at underground sites. When installed at the entrance of hibernacula, infrared light barriers have the potential to estimate site-level population sizes more accurately than visual surveys, by counting all bats flying in and out of the site. Moreover, camera traps, consisting of a digital camera and white flash, can be used for species-level identification. However, for this new method to be applicable as a large-scale bat monitoring technique, it is important to characterize it with regard to three main criteria: is the method minimally invasive, is it accurate, and is it scalable in terms of spatial and temporal resolution? Therefore, the purpose of this thesis was to investigate the invasiveness and accuracy of this novel bat monitoring method, and to develop standardized and automated data analysis pipelines, both for the light barrier and camera trap data, to support the deployment of this method at scale.
In Publication I, we used light barrier data, infrared video recordings and acoustic data from an experimental field study to investigate whether the white flash of the camera trap has any measurable short- or long-term effect on bat activity and behavior. The flash of the camera trap was turned on and off every week at each site, which allowed us to compare the activity and behavior of bats between flash-on and flash-off nights. We found that despite the high sensitivity of bats to disturbance, they did not change their nightly activity patterns, flight direction, echolocation behavior, or long-term site use in response to the white flash of the camera trap. Based on these results, we concluded that camera traps using a white flash are a minimally invasive method for monitoring bat populations at hibernacula, providing high quality images that allows species-level identification.
In Publication II, we used infrared video surveillance to quantify the accuracy of infrared light barriers, and we described a standardized methodology to estimate population sizes and trends of hibernating bat assemblages using light barrier data. We showed that light barrier accuracy varies based on the model and location of the installation relative to the entrance, with the best combination achieving nearly perfect accuracy over the spring emergence phase. When compared to light barrier-based estimates, we found that visual counts markedly underestimated population sizes, recovering less than 10% of the bats at the most complex hibernacula. Moreover, light barrier-based population trends showed regional patterns of growth and decline that were not detectable using the visual count data. Overall, we established that the light barrier data can be used to estimate the population size and trends of hibernating bat assemblages with unprecedented accuracy and in a standardized way.
In Publication III, we described a deep learning-based tool, BatNet, that can accurately and efficiently identify bat species from camera trap images. The baseline model was trained to identify 13 European bat species or species complexes using camera trap images collected at 32 hibernation sites (i.e., trained sites). We showed that the baseline model performance was very high across all 13 bat species on trained sites, as well as on untrained sites when the camera angle and distance from the entrance were comparable to the training images. At untrained sites with more atypical camera placements, we demonstrated the ability to retrain the baseline model and achieve an accuracy comparable to the trained sites. Additionally, we showed that the model can learn to identify a new species, while maintaining high classification accuracy for all original species. Finally, we established that BatNet can be used to accurately describe ecological metrics from camera trap images (i.e., species diversity, relative abundance, and species-specific phenology) that are relevant for bat conservation.
We conclude that infrared light barriers and camera traps offer a minimally invasive and accurate method to monitor site-level bat population trends and species-specific phenological estimates at underground sites. Such remote data collection approaches are particularly relevant for monitoring large, complex hibernation sites, where traditional visual surveys are not feasible or account only for a small fraction of the actual population. Combining this automated monitoring method with a deep learning-based species identification tool, BatNet, allows us quickly and accurately analyze millions of camera trap images resulting from large-scale, long-term camera trap studies. As a result, we can gain unprecedented insights into the behavior and population dynamics of these enigmatic species, drastically improving our ability to support data-driven bat conservation.
Until today, more than 100 years after its first description in Italy, the highly pathogenic avian influenza virus (HPAIV) has not lost its fearsome character for wild birds, poultry and humans. On the contrary, the number of outbreaks with high casualty rates in wild birds and poultry has multiplied in recent years and cases of zoonotic infections are also increasingly reported from HPAI endemic areas. The epidemiology of these infections is complex and also involves surface water and possibly sediments of shallow standing waters, which could play a role as a vector medium and/or virus reservoir. The goal of this project was to expand current knowledge of the influence of water on the spread of AIV. As part of this project, we were able to ...
1. ...improve AIV detection methods using real time RT-PCR in terms of sensitivity and breadth of viruses detected. In addition, we succeeded in economizing the procedure so that fewer resources are required and results are obtained faster (publication I: [173]).
2. ...develop an ultrafiltration-based enrichment method for AIV from surface water and evaluate it with field samples from HPAI outbreak areas in wild bird habitats (Wadden Sea coast of Schleswig-Holstein) and previously unaffected regions (Antarctic Weddell Sea) (publication II: [174]). Furthermore, protocols for testing different environmental sample matrices for AIV screening were tested and compared to results of passive monitoring by dabbing diseased or dead wild birds. AIV was detected in more than half (61%) of 44 water samples. We received additional sediment samples from 36 of the 44 water samples. In 18 of 36 of the sediments tested, as well as in 4.16% of 1705 fecal samples tested AIV was detected. However, the studies of the environmental samples mostly yielded only generic AIV detections, with viral loads in the range of the detection limit. This massively hampered further investigations for sub- and pathotyping. In contrast, 79.41% of 68 samples from passive monitoring showed high to very high HPAIV viral loads which also allowed sub- and pathotyping.
3. ...demonstrate in animal experiments that even very low titers (0.1 TCID50 ml-1) of HPAI viral infectivity in water can induce productive infection in susceptible but clinically largely resistant mallard ducks (publication III: [175]). Furthermore, we were able to develop evidence that there is a difference in virus spread that depends on the type of (contaminated) water source. This means that infections on poultry farms with inverted or nipple drinkers may follow a different course than infections in the wild, which are mediated via larger surface waters.
Overall, the results of this project highlight the important role of surface and drinking water, as well as aquatic sediments, in the spread of AIV. The methods developed here for AIV detection extend the possibilities for surveillance of AIV infections; however, passive remains superior to active surveillance of HPAIV infections in several aspects. Examination of various environmental samples did not yield a significant advantage in terms of an early warning system that would indicate the presence or spread of HPAIV in wild bird habitats prior to the occurrence of lethal infections in wild birds.
Das Afrikanische Schweinepestvirus (ASPV) ist ein wirtschaftlich wichtiger und in Haus- und Wildschweinen Hämorrhagie mit hoher Sterblichkeitsrate verursachender viraler Erreger.
1921 erstmals in Kenia beschrieben, breitete sich die ASP seit 2007 auch über den
Kaukasus, ins Baltikum (2014), weiter in europäische und asiatische Länder und seit 2020 in Deutschland aus. Trotz der hohen genetischen Stabilität des Afrikanischen
Schweinepestvirus (ASPV) wurden Genomvarianten identifiziert, bei denen Unterschiede
in der Genexpression von Multigenfamilien (MGF) dominieren. Letztlich divergieren ASPV-Stämme in ihrer Virulenz und verursachen akut-letale bis chronische Verläufe im Schwein. Aufgrund der enormen Komplexität des Virus und seiner vielfältigen
Immunevasionsstrategien sind viele Mechanismen der Virus-Wirts-Interaktion, die zur
Immunpathogenese beitragen, nicht ausreichend verstanden und erschweren somit die
Impfstoffentwicklung. Dabei können virale Subversionsmechanismen der Wirtszelle die
antivirale Immunantwort modulieren und stehen deshalb im Fokus dieser Arbeit. Zur
Charakterisierung und mechanistischen Aufklärung dieser ASPV-spezifischen
Immunsubversionsmechanismen wurden primäre porzine Monozyten von Hausschweinen
mit hochvirulentem (Armenia) und natürlich-attenuiertem (Estonia) ASPV infiziert. Die
Resultate ergaben sowohl stammunabhängige als auch -abhängige Unterschiede in der
Regulation myeloider Oberflächenmarker infizierter Monozyten. Insbesondere
beobachteten wir eine stammunabhängige Suppression des Phagozytose-regulierenden
CD172a und eine stammabhängige Regulation von porzinem MHC I (SLA I). Weitere
Experimente zur Untersuchung der zugrundeliegenden Mechanismen ergaben, dass zwar
beide Stämme die Oberflächenexpression von CD172 unterdrücken, jedoch nur Armenia-,
im Gegensatz zu Estonia-infizierten Monozyten, eine reduzierte Recyclingrate sowie eine Abspaltung (Shedding) von CD172a von der Zelloberfläche zeigten. Dies lässt vermuten, dass die Virus-vermittelte Suppression von CD172a der beiden ASPV-Stämme auf unterschiedlichen Subversionsmechanismen beruht. Reinfektionsexperimente und
molekularbiologische Untersuchungen belegten zudem, dass das abgespaltene
Oberflächen-CD172a der Armenia-infizierten Monozyten mit einer gesteigerten
Infektionsrate einhergeht, dies ist wahrscheinlich das Ergebnis (entweder direkt oder indirekt) einer Komplexbildung zwischen dem virulenten Armenia-Virus und löslichem
CD172a. Im Gegensatz dazu resultierte die Infektion von Monozyten mit Armenia, jedoch nicht mit Estonia, in einem deutlichen Oberflächenverlust von porzinem SLA I, welches für die Antigenpräsentation gegenüber CD8+ T-Zellen essentiell ist. Weitere Versuche zeigten einen Reifungsdefekt von SLA I, der mit dem Abbau funktioneller ER-Strukturen und der Induktion von ER-Stress in Armenia-infizierten Monozyten in Zusammenhang stand. Gleichzeitig wurde eine deutlich reduzierte Überlebensfähigkeit Armenia-infizierter Monozyten beobachtet, die mit einem Verlust mitochondrialer Funktionen und der Bildung von Aggresomen aus fehlgefalteten Proteinen im Zytoplasma einherging. Vertiefende Analysen dazu zeigten einen Caspase-3 aktivierten Zelltodmechanismus und ein infektionsbedingtes, progressives Abschalten der Proteintranslation in Armenia-infizierten Zellen. Um einen möglichen Zusammenhang zwischen den beobachteten
Subversionsmechanismen und der Expression bestimmter viraler MGF-Gene zu finden,
wurden weitere ASPV-Stämme in die Untersuchungen zur CD172a- und SLA I-Oberflächenexpression einbezogen. Ähnlich wie Armenia zeigte sich auch für die Stämme
NHV und OURT88/3 eine deutliche Reduktion der SLA I-Oberflächenlevel, auch wenn diese
in vivo gering-virulent sind. Andererseits zeigte das hochvirulente Benin97/1-Isolat im Gegensatz zu Armenia keine SLA I-Subversion, sondern ähnlich wie nach Estonia-Infektion kaum veränderte SLA I-Level, was vermuten lässt, dass der SLA I Subversionsmechanismus nicht alleinig den Virulenzgrad der ASPV-Stämme bestimmt. Ein direkter Genomvergleich identifizierte verschiedene Mitglieder der MGF110- und MGF505-Gene als möglicherweise beteiligte virale Genkandidaten. Im Gegensatz hierzu ergaben sich keine detektierbaren Unterschiede bei den Analysen zur Oberflächensuppression von CD172a innerhalb der verwendeten Isolate, wie bereits bei Armenia und Estonia Infektion beobachtet. Interessanterweise beobachteten wir dabei das Vorhandensein von MGF110-14 als eine genomische Gemeinsamkeit, die für die generelle Oberflächenreduktion von CD172a, zusätzlich zu anderen Genen, die ein Shedding und die Armenia-spezifische Interaktion bestimmen könnten, verantwortlich sein könnte.
Insgesamt zeigen die Resultate dieser Arbeit erstmals, dass das virulente ASPV Armenia, anders als das attenuierte ASPV Estonia, einen ausgeprägten Funktions- und Vitalitätsverlust in seinen primären Zielzellen (z. B. Monozyten) bewirkt. Die gesteigerte Infektiosität, Induktion von zellulärem Stress und Beeinträchtigung der SLA I-vermittelten Antigenpräsentation werden in infizierten Schweinen eine entscheidende Rolle in der Virus-Verbreitung und der Immunevasion spielen. Zusammenfassend lässt sich sagen, dass die Befunde dieser Arbeit neue und vertiefte Einblicke in die zellulären Mechanismen der SLA I- und CD172a-Subversion im Zusammenhang mit der Immunevasion durch hoch-virulentes ASPV Armenia und attenuiertes ASPV Estonia gibt und zudem wichtig für das bessere Verständnis der ASP-Immunpathogenese sind.
The present study deals with the spread and population genetics of the invasive Asian bush
mosquito Ae. japonicus in Europe and Germany. Since the first detection of Ae. japonicus
in Europe in 2000, the species spread rapidly through Europe, either actively by flying or
passively by human activities. In 2017, four confirmed populations of Ae. japonicus existed
in Europe. The largest population covered western Germany, parts of France, Switzerland,
Liechtenstein, Austria and Italy. The most northern population around Hanover, Germany,
did not spread since 2013. A very small population existed in Belgium and the second largest
population covered parts of Austria, Italy, Slovenia, Croatia and Hungary. By 2019, Ae.
japonicus had established in 15 European countries.
Most of the monitoring programmes in Europe dealing with the distribution and spread of
Ae. japoncus investigate cemeteries for juvenile stages. However, activities are not
harmonised, e.g. regarding numbers of investigated collection sites and declaration of
negative sites, making data comparison between different studies difficult. Therefore,
suggestions for a standardised Ae. japonicus monitoring method have been developed and
provided.
In the present study, 445 individuals of Ae. japonicus originating from five different
European countries were investigated for population genetic analyses by sequencing parts
of the nad4 gene and genotyping seven polymorphic microsatellite loci. In total, 16 different
nad4 haplotypes were identified with haplotype H1 being the most common and widespread
one through all populations.
Within Germany, Ae. japonicus has been spreading immensely over the last decade. Even
though the present results (2017) demonstrate incipient genetic admixture of populations as
compared to previous studies (2012-2015), no complete genetic mixture has taken place yet.
The populations of Ae. japonicus still fall into two genetic clusters, but the genetic diversity
on individual level had increased considerably (from three nad4 haplotypes in 2012 to 12
according to the present thesis). Both additional introductions and mutation are possible
reasons, but determining the origin of the German populations is not possible anymore.
In the years following the invasion of Germany, Ae. japonicus spread to southeastern
Europe. In 2013, it established in Croatia, in 2017 in Bosnia and Herzegovina and in 2018
in Serbia. In the current study, immature stages of Ae. japonicus were found at 19 sites in
Croatia, two sites in Bosnia and Herzegovina and one site in Serbia. The population genetic
analyses indicate at least two independent introductions in that area. Aedes japonicus collected west of Orahovica (Croatia) seemed to be genetically similar to samples previously
investigated from Southeast Germany/Austria and Austria/Slovenia. By contrast, samples
from east of Orahovica, together with those from Serbia and Bosnia and Herzegovina, were
characterised by another genetic make-up, but their origin could not be determined.
In 2021, individuals of Ae. japonicus were detected at two collection sites in the Czech
Republic for the first time: Prachatice close to the Czech-German border and Mikulov on
the Czech-Austrian border. Population genetics and comparison of genetic data showed a
close relationship of the Prachatice samples to a German population, while for Ae. japonicus
from Mikulov close relatives could not be identified.
In the future, the global spread and establishment of invasive mosquitoes through
international trade and travel will increase. Potential vectors, like the Asian bush mosquito
Ae. japonicus, can become a problem in Europe and Germany, especially in the course of
global warming which supports pathogen transmission. Monitoring the known populations
and identifying introduction and migration routes are therefore essential for vector
managing.
Pancreatic ductal adenocarcinoma (PDAC), due to its genomic heterogeneity and lack of development of effective therapies, will become the second leading cause of cancer-related death within 10 years. Therefore, identifying novel targets that can predict response to specific treatments is a key goal to personalize pancreatic cancer therapy and improve survival. Given that the occurrence of oncogenic KRAS mutations is a characteristic event in PDAC leading to genome instability, a better understanding of the role of DNA repair mechanisms in this process is desirable. The aim of our study was to investigate the role of the error-prone DNA double strand breaks (DSBs) repair pathway, alt-EJ in the presence of KRAS G12D mutation in pancreatic cancer formation. Our findings showed that oncogenic KRAS contributes to the activation of the alt-EJ mechanism by increasing the expression of Polθ, Lig3 and Mre11, key components of alt-EJ in both mouse and human PDAC models. In addition, we demonstrated that alt-EJ has increased activity in DNA DSBs repair pathway in a mouse and human model of PDAC bearing KRAS G12D mutation. We further focused on estimating the impact of alt-EJ inactivation by polymerase theta (Polθ) deletion on pancreatic cancer development and survival in genetically engineered mouse models (GEMMs). Here, we described that although deficiency of Polθ resulted in delayed cancer progression and prolonged survival of experimental mice, it can lead to full-blown PDAC. Our study showed that disabling one component of the alt-EJ may be insufficient to fully suppress pancreatic cancer progression and a complete understanding of all alt-EJ factors and their involvement in DSB repair and oncogenesis is required.
Methane (CH4) is a potent greenhouse gas with rising atmospheric concentrations.
Microorganisms are essential players in the global methane cycle. In fact, the largest part of methane emissions derives from microbial production by methanogenic Archaea (methanogens). Microorganisms do not only produce methane: methanotrophs can also oxidize the methane produced by methanogens. In addition, soil methanotrophs are the only biological methane sink, oxidizing up to 30-40 Tg of this potent greenhouse gas per year worldwide.
However, intensified management of grasslands and forests may reduce the methane sink capacity of soils.
In general, the interaction of methanogens and methanotrophs determines whether a soil is a source or a sink for methane. It is, therefore, crucial to understand the microbial part of the methane cycle and which factors influence the abundance and activity of methane-cycling microbes. However, capturing the soil microbiome's abundances, activity, and identity is
challenging. There are numerous target molecules and myriad methods, each with certain
limitations. Linking microbial markers to methane fluxes is therefore challenging. This thesis aimed to understand how methane-cycling microbes in the soil are related to soil methane fluxes and how soil characteristics and human activity influence them.
The first publication investigated the biotic and abiotic drivers of the atmospheric methane sink of soils. It assessed the influence of grassland land-use intensity (150 sites) and forest management type (149 sites) on potential atmospheric methane oxidation rates (PMORs) and the abundance and diversity of CH4-oxidizing bacteria (MOB) with qPCR in topsoils of three temperate regions in Germany. PMORs measured in microcosms under defined conditions were approximately twice as high in forest than in grassland soils. High land-use intensity of grasslands negatively affected PMORs (−40%) in almost all regions. Among the different aspects of land-use intensity, fertilization had the most adverse effect reducing PMORs by 20%.
In contrast, forest management did not affect PMORs in forest soils. Upland soil cluster (USC)α was the dominant group of MOBs in the forests. In contrast, USCγ was absent in more than half of the forest soils but present in almost all grassland soils. USCα abundance had a direct positive effect on PMOR in forests, while in grasslands, USCα and USCγ abundance affected PMOR positively with a more pronounced contribution of USCγ than USCα.
In the second publication, we used quantitative metatranscriptomics to link methane-cycling microbiomes to net surface methane fluxes throughout a year in two grassland soils. Methane fluxes were highly dynamic: both soils were net methane sources in autumn and winter and net methane sinks in spring and summer. Correspondingly, methanogen mRNA abundances per
gram soil correlated well with methane fluxes. Methanotroph to methanogen mRNA ratios were higher in spring and summer when the soils acted as net methane sinks. Furthermore, methane uptake was associated with an increased proportion of USCα and γ pmoA and pmoA2 transcripts. High methanotroph to methanogen ratios would indicate methane sink properties.
Our study links the seasonal transcriptional dynamics of methane-cycling soil microbiomes for the first time to gas fluxes in situ. It suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes.
We conclude that reduction in grassland land-use intensity and afforestation can potentially increase the methane sink function of soils and that different parameters determine the microbial methane sink in forest and grassland soils. Furthermore, this thesis suggests mRNA transcript abundances as promising indicators of dynamic ecosystem-level processes. Methanogen transcript abundance may be used as a proxy for changes in net surface methane emissions from grassland soils.
Responses of bovine and human neutrophils to members of the Mycobacterium tuberculosis complex
(2023)
PMN are one of the most important cells of the innate immune system and are responsible for fast clearance of invading pathogens in most circumstances. The role of human PMN during mycobacterial infection have been widely studied. Nevertheless, there are contradicting results regarding their role in protection or pathology during TB. Similar studies focusing on bovine PMN and their role in M. bovis infection remain understudied. Also, not much is known about attenuation of M. tb in cattle and responses of PMN to this MTBC member.
The major aims of this study were to i) gain insights into bovine PMN biology and the cellular processes triggered by challenge with virulent mycobacteria and to ii) find out whether interspecies differences result in different outcomes upon in vitro challenge. In the first part of the work, a new isolation method for bovine PMN from whole blood was developed. Human and bovine PMN have different buoyant properties and hence need to be isolated using different procedures. The magnetic isolation method developed within this thesis is robust and results in very good yields of highly pure, viable bovine PMN populations. This is extremely advantageous and indispensable for downstream functional assays that are required to be performed on a single day.
The second goal of this study was to compare and contrast the functional differences between bovine and human PMN upon BCG infection. The findings reveal for the first time that human PMN phagocytose more BCG in comparison to bovine counterparts. Non-opsonized bacteria were internalized via the lectin-like C-domain, require cholesterol and an active cytoskeleton in human PMN, whereas opsonized bacteria entered cells via the CR3 and, in particular, CD11b. It remains unresolved why bovine PMN reacted differently, notably phagocytosis remained unaltered, to various treatments, including blocking monoclonal antibodies to CD11b and chemical inhibitors altering the cell membrane. Nonetheless, the increased uptake of BCG by human PMN correlates to more potent response of these cells in functional assays in comparison to bovine PMN. No PMN intrinsic differences were found in the basal cholesterol content. Comparative assays with the virulent strains would be essential in order to generalize these observations.
The third aim was to investigate the responses of bovine PMN to BCG, M. tb and M. bovis. While there was no difference in uptake between BCG and M. tb, serum opsonized BCG was taken up at a higher amount. This finding suggests differential binding of bacterial epitopes to host cell receptors which modulates mycobacteria uptake. However, between the virulent strains M. tb and M. bovis, the human-adapted bacillus was phagocytosed at a higher rate which hints towards the possibility of rapid recognition and clearance of M. tb in bovine host thereby possibly preventing pathology. The release of selective cytokines by PMN post infection with the virulent strains offers baseline information relevant for processes that probably occur in vivo. This work for the first time provides insights into responses of bovine PMN to mycobacteria in a two-tier approach: by cross-species analysis of PMN responses to selected mycobacterium and by head-to-head analysis of bovine PMN to animal-adapted and human-adapted mycobacteria.
As a prospect for future research in bovine PMN biology in the context of mycobacterial infection, it would be highly advantageous to compare the subcellular localization of M. tb and M. bovis in bovine PMN using confocal and/or electron microscopy. This analysis would confer proof on attachment or internalization of mycobacteria by PMN and identify the features of the mycobacteria-containing compartments. Also, in-depth investigations of additional entry pathways for the pathogen in bovine cells would be informative for unlocking downstream cell signaling events. In addition, PMN viability studies will be meaningful particularly in bovine PMN challenged with M. bovis and M. tb, given the impact of death patterns on tissue pathology. Current results and follow up studies will contribute to the understanding of the roles of PMN in controlling elimination or growth of M. bovis and M. tb in cattle.
Coding constraints imposed by the very small genome sizes of negative-strand RNA viruses (NSVs) have led to the development of numerous strategies that increase viral protein diversity, enabling the virus to both establish a productive viral replication cycle and effectively control the host antiviral response. Arenaviruses are no exception to this, and previous findings have demonstrated that the nucleoprotein (NP) of the highly pathogenic Junín virus (JUNV) exists as three additional N-terminally truncated isoforms of 53 kD (NP53kD), 47 kD (NP47kD), and 40 kD (NP40kD). The two smaller isoforms (i.e. NP47kD and NP40kD) have been characterized as products of caspase cleavage, which appears to serve a decoy function to inhibit apoptosis induction. However, whether they have additional functions in the viral replication cycle remains unknown. Further, the origin and function of NP53kD has not yet been described.
In order to first identify the mechanism responsible for production of the NP53kD variant, a possible role of additional caspase cleavage sites was first excluded using a site mutagenesis approach. Subsequently, alanine mutagenesis was then used to identify a region responsible for NP53kD production. As a result, three methionine residues were identified within the characterized sequence segment of NP, linking the production of NP53kD to an alternative in-frame translation initiation. Further site-directed mutagenesis of the previously identified putative in-frame methionine codons (i.e. M78, M80 and M100) finally led to the identification of translation initiation at M80 as being predominantly responsible for the production of NP53kD. Once the identity of all three NP isoforms was known, it was then of further interest to more deeply characterize their functional roles. Consistent with the N-terminal domain containing RNA binding and homotrimerization motifs that are relevant for the viral RNA synthesis process, it could be demonstrated that all three truncated NP isoforms lost the ability to support viral RNA synthesis in a minigenome assay. However, they also did not interfere with viral RNA synthesis by full-length NP, nor did they affect the ability of the matrix protein Z to inhibit viral RNA synthesis. Moreover, it was observed that loss of the oligomerization motifs in the N-terminus also affected the subcellular localization of all three NP isoforms, which were no longer localized in discrete perinuclear inclusion bodies, but rather showed a diffuse distribution throughout the cytoplasm, with the smallest isoform NP40kD also being able to enter the nucleus. Surprisingly, the 3'-5' exonuclease function of NP, which is associated with the C-terminal domain and plays a role in inhibiting interferon induction by digestion of double-stranded RNAs, was found to be retained only by the NP40kD isoform, despite that all three isoforms retained the associated domain. Finally, previous studies using transfected NP and chemical induction of apoptosis have suggested that cleavage of NP at the caspase motifs responsible for generating NP47kD and NP40kD plays a role in controlling activation of the apoptosis pathway. Therefore, to further characterize the connection between the generation of NP isoforms and the regulation of apoptosis in a viral context, recombinant JUNVs deficient in the respective isoforms were generated. Unlike infections with wild-type JUNV, mutations of the caspase cleavage sites resulted in the induction of caspases activation. Surprisingly, however, this was also the case for mutation of the alternate start codon responsible for NP53kD generation.
Taken together, the data from this study suggest a model whereby JUNV generates a pool of smaller NP isoforms with a predominantly cytoplasmic distribution. As a result of this altered localization, NP53kD appears to be able to serve as the substrate for further generation of NP47kD and NP40kD by caspase cleavage. Not only does this cleavage inhibit apoptosis induction during JUNV infection, it also results in a cytoplasmic isoform of NP that retains strong 3'-5' exonuclease activity (i.e. NP40kD) and thus may play an important role in preventing viral double-stranded RNA accumulation in the cytoplasm, where it can lead to activation of IFN signaling. Overall, such results emphasize the relevance of alternative protein isoforms in virus biology, and particularly in regulation of the host response to infection.
Relative importance of plastic and genetic responses to weather conditions in long-lived bats
(2022)
In the light of the accelerating pace of environmental change, it is imperative to understand how populations and species can adapt to altered environmental conditions. This is a crucial step in predicting current and future population persistence and limits thereof. Genetic adaption and phenotypic plasticity are two main mechanisms that can mediate the process of adaptation and are of particular importance for non-dispersing species. While phenotypic plasticity may enable individuals to cope with short term environmental changes, genetic adaptation will often be required for populations to survive in situ over longer time spans. However, a rapid genetic response is expected particularly in species with fast life histories or large population sizes, leaving species with slow life histories potentially at higher extinction risk. The Bechstein’s bat (Myotis bechsteinii) is a mammal of 10 g weight that - despite its small size - is characterized by a slow life history, with low reproductive output and long lifespan, and is already considered to be of high conservation concern. Past work demonstrated body size to be a highly fitness-relevant trait in Bechstein’s bats. Body size is further known to be a pivotal trait shaping the pace of life histories in numerous species. Simultaneously, many studies reported noteworthy changes in body size as a response to shifting environments across different taxa. This suggested a potential for high plasticity in this trait in Bechstein’s bats as well; however, changes in body size could have vital impacts on demographic rates.
Therefore, this dissertation investigated the following questions: firstly, what shapes the fundamental development of body size in M. bechsteinii, and, specifically, is there an impact of weather conditions on body size? If so, in what form and magnitude? Secondly, how does body size subsequently influence the pace of life in females? What is the cost of a faster or slower pace of life, and how does fitness compare across individuals with slow and fast life histories? And finally, to what extent can changes in body size be attributed to either phenotypic plasticity or genetic adaptation? What is the evolutionary potential of body size in the populations? And, consequently, what implications can we draw regarding population persistence of these colonies?
To answer these questions, we analyzed a long-term dataset of over two decades collected from four wild Bechstein’s bat colonies. We used individual-based data on survival, reproduction and body size, built multi-generational pedigrees, and combined everything with meteorological data. In Manuscript 1 we found that, in contrast to the declining body size observed in many species, body size in Bechstein’s bats increased significantly over the last decades. We demonstrated that ambient temperature was linked to the development of body size and identified a sensitive time period in the prenatal growth phase, in which body size was most susceptible to the impact of temperature. We established that warmer summers resulted in larger bats, but that these large bats had higher mortality risks throughout their lives. Manuscript 2 then revealed the influence of body size on the pace of life in Bechstein’s bats and demonstrated high plasticity in intraspecific life history strategies. Large females were characterized by a faster pace of life and shorter lifespans, but surprisingly, lifetime reproductive success remained remarkably stable across individuals with different body sizes. The acceleration of their pace of life means that larger females compensated for their reduced longevity by an earlier reproduction and higher fecundity to reach similar overall fitness. Ultimately, differences in body size resulted in changes in population growth rate via the impact of size on generation times. Results of Manuscript 3 were then able to clarify the extent to which changes in body size were founded on either phenotypic plasticity or genetic adaptation. We demonstrated a particularly low heritability in hot summers, indicating that variance in body size was mostly driven by phenotypic plasticity, with few genetic constraints. During cold summers, behavioural adaptations by reproducing bats seem to be able to mitigate negative effects of cold temperatures. These behaviours, such as social aggregation or preference for warm roosts, are, however, essentially irrelevant in hot environments. In addition, a low evolvability of forearm length points to a low capacity to respond to selection pressures associated with the trait.
We can conclude that body size in M. bechsteinii has increased over the last two decades as a response to global warming and is only slightly constrained by its genetic underpinnings. We can further demonstrate a direct link between body size and the pace of life histories in the Bechstein’s bat populations and how changes in body size impact demographic rates via this linkage. In the context of climate change and hotter summers, our findings consequently suggest that body size will likely increase further if warm summers continue to become more frequent. Whether this plastic response of body size proves to be adaptive in the long term, however, remains to be seen. While, up to this point, switching to a faster life history has been successful in compensating fitness losses, this strategy requires sufficient habitat quality and is likely risky in times when extreme weather events are becoming more frequent, as predicted by most climate change scenarios.
The success of pregnancy depends on precisely adjusted, local immune mechanisms. In early pregnancy, fetal trophoblast cells implant into the endometrium to build and anchor the placenta. Simultaneously, they mediate fetal tolerance and defense against infections. To cover these versatile requirements, local immune factors must be in balance. A too tolerogenic milieu can lead to an inadequate placentation; while a too inflammatory milieu can cause rejection of the semi-allogenic fetus. Bacterial infections can provoke these inflammatory pregnancy complications as well. Therefore, the pregnant uterus was long thought to be sterile. Descriptions of a placental microbiome opened a scientific discourse, which is unsolved due to contrary studies. The colonization of the non-pregnant endometrium is, however, confirmed. It is supposed to affect both, uterine pathologies and fertility. Precise data are lacking. Aim of this work was to assess if and under which circumstances a bacterial colonization would be tolerable.
One of the described species in placental and endometrial samples is Fusobacterium nucleatum. It is an opportunistic bacterium, which is known from the human oral cavity and associated with the development of colon carcinomas. F. nucleatum supports tumorigenesis by the induction of epithelial proliferation, survival, migration and invasion as well as angiogenesis and tumor tolerance. Since similar processes are required for implantation and placentation, F. nucleatum might support these as well. In this work, the effects of F. nucleatum on leukocyte-trophoblast-interactions, especially of macrophages and innate lymphoid cells type 3 (ILC3), were assessed.
The monocytic cells (THP-1) were differentiated into inflammatory M1 (IFN-γ) or tissue-repairing and tolerogenic M2a (IL-4) and M2c (TGF-β) macrophages. Inactivated F. nucleatum, LPS or E. coli was added. Only small concentrations of inactivated bacteria were used (bacteria:leukocyte ratio of 0.1 or 1), since it was not the aim to analyze infections. Conditioned medium of treated leukocytes was added to trophoblastic cells (HTR-8/SVneo). Migratory, invasive and tube formation behavior of trophoblastic cells was quantified.
Treated M1 macrophages impaired trophoblast function, whereas M2a macrophages induced trophoblast invasion. M2c macrophages supported trophoblast migration and tube formation if treated with the smaller, but not with the higher concentration of F. nucleatum. This treatment induced the accumulation of HIF-1α and the secretion of VEGF-A in M2c macrophages as well. Moreover, the higher concentration of F. nucleatum caused rather inflammatory responses (NF-κB activation and cytokine expression). The activation of the HIF-1α-VEGF-A axis under the influence of TGF-β might serve as a mild immune stimulation by low abundant commensal bacteria supporting placentation.
In contrast to macrophages, the function of ILC3s during pregnancy is still unknown. In general, ILC3s are located in mucosal tissue, such as the gut. They participate in tolerance mechanisms and form the local micromilieu by the secretion of cytokines and the presentation of antigens. In order to characterize local, uterine ILC3s, murine ILC3s were compared to peripheral, splenic ILC3s. Uterine ILC3s were more activated and produced higher levels of IL-17 compared to splenic ILC3s. However, uterine ILC3s barely expressed MHCII on their surface. A reduced antigen presentation potential was confirmed in human ILC3s differentiated from cord blood stem cells by the addition of TGF-β or hCG. The treatment with bacteria increased MHCII expression, but not to the initial level. The higher bacterial concentration induced IL-8 secretion and led to an increased trophoblast invasion. ILC3s were less sensitive to bacterial stimulation than macrophages.
Recent studies on the uterine or placental presence of bacteria during pregnancy are discrepant. The results of this project indicate that bacteria or bacterial residues might serve as a mild stimulus under certain circumstances to support implantation without negative effects. The current discussion must therefore not only be expanded by additional studies, but especially include differentiated local conditions. In this context, the sheer presence of bacteria or bacterial components must not be equated with an infection representing a known hazard.
Podocytes are highly specialized kidney cells that are attached to the outer aspect of the glomerular capillaries and are damaged in more than 75% of patients with an impaired renal function. This specific cell type is characterized by a complex 3D morphology which is essential for proper filtration of the blood. Any changes of this unique morphology are directly associated with a deterioration of the size-selectivity of the filtration barrier. Since podocytes are postmitotic, there is no regenerative potential and the loss of these cells is permanent. Therefore, identification of small molecules that are able to protect podocytes is highly important. The aim of this work was to establish an in vivo high-content drug screening in zebrafish larvae. At first, we looked for a reliable podocyte injury model which is fast, reproducible and easy to induce. Since adriamycin is commonly used in rodents to damage podocytes, we administered it to the larvae and analyzed the phenotype by in vivo microscopy, (immuno-) histology and RT-(q)PCR. However, adriamycin did not result in a podocyte-specific injury in zebrafish larvae. Subsequently, we decided to use a genetic ablation model which specifically damages podocytes in zebrafish larvae. Treatment of transgenic zebrafish larvae with 80 µM metronidazole for 48 hours generated an injury resembling focal and segmental glomerulosclerosis which is characterized by podocyte foot process effacement, cell depletion and proteinuria. Following this, we established an in vivo high-content screening system by the use of a specific screening zebrafish strain. This screening strain expresses a circulating 78 kDa eGFP-labeled Vitamin D-binding fusion protein, which passes the filtration barrier only after glomerular injury. Therefore, we had an excellent readout to follow podocyte injury in vivo. We generated a custom image analysis software that measures the fluorescence intensity of podocytes and the vasculature automatically on a large scale. Furthermore, we screened a specific drug library consisting of 138 compounds for protective effects on larval podocytes using this in vivo high-content system. The analysis identified several initial hits and the subsequent validation experiments identified belinostat as a reliable and significant protective agent for podocytes. These results led to a patent request and belinostat is a promising candidate for a clinical use and will be tested in mammalian podocyte injury models.
This thesis deals with the characterisation and engineering of new thermophilic PET hydrolases as potential candidates for an eco-friendly biocatalytic recycling approach for the upcycling or downcycling of polyethylene terephthalate (PET) on industrial scale. Furthermore, high-throughput screening methods are described that detect the products of PET hydrolysis. The high demand of PET in the packaging and textile industries with a global production of 82 million metric tons per year has significantly contributed to the global solid waste stream and environmental plastic pollution after its end-of-life. Although PET hydrolases have been identified in various microorganisms, only a handful of benchmark enzymes have been engineered for industrial applications. Therefore, the identification of new PET hydrolases from metagenomes or via protein engineering approaches, especially thermophilic PET hydrolases with optimal operating temperatures (i.e., increased thermostability and activity) near the glass transition temperature of the polymer PET, is a crucial step towards a bio-based circular plastic economy. Article I demonstrates that metagenome-derived thermophilic PET hydrolases can be significantly improved using different engineering approaches to achieve a similar activity level as the well-established leaf-branch-compost cutinase (LCC) F243I/D238C/S283C/Y127G variant (LCC ICCG). In Article II, thermostable variants of a mesophilic enzyme (PETase from Ideonella sakaiensis) were identified from a mutant library and characterised against PET substrates in various forms. Articles III and IV describe the application of high-throughput methods for the identification of novel PET hydrolases by directly assaying terephthalic acid (TPA), one of the monomeric building blocks of PET. Furthermore, Article IV describes the possibility of a one-pot conversion of the TPA-based aldehydes produced to their diamines as example for an open-loop upcycling method.
Hintergrundinformationen: Bakterien gehören zu den ältesten Lebensformen und sind ein elementarer Bestandteil aller ökologischen Lebensräume auf der Erde. Der Mensch als Holobiont ist ein eigenständiges Ökosystem mit einer Vielzahl von ökologischen Nischen und einer großen bakteriellen Vielfalt. Durch innere oder äußere Einflüsse kann es zu Veränderungen der Umweltbedingungen kommen, die eine veränderte Zusammensetzung des Mikrobioms zur Folge haben. Eine solche Dysbiose wirkt sich auf den Gesundheitszustand des Menschen aus und kann zu schweren Krankheiten führen. Das orale Mikrobiom gehört mit zu den komplexesten Mikrobiomen des Menschen. Es bildet eine natürliche Barriere gegen Krankheitserreger und beugt somit u.a. lokalen Krankheiten wie Karies oder Parodontitis vor. Die Metaproteomik ermöglicht es, die exprimierten Proteine des Mikrobioms und deren Interaktion mit dem Wirt zu untersuchen. Diese Technologie überwindet somit die Beschränkung auf Laborkulturen und ermöglicht die Untersuchung des Mikrobioms direkt in seinem natürlichen Lebensraum. Die Metaproteomik bietet eine Reihe von Instrumenten zur Vertiefung des Verständnisses des oralen Mikrobioms hinsichtlich des Gesundheitszustandes des Menschen.
Ziele: Ein Ziel dieser Dissertation war es einen Arbeitsablauf für die Durchführung von Metaproteomstudien des oralen Mikrobioms zu erarbeiten, beginnend bei der Probensammlung über die Präparation der Proben für die Massenspektrometrie bis hin zur bioinformatischen Auswertung. Diesen Arbeitsablauf galt es für das Mikrobiom des Speichels sowie für die Biofilme auf der Zunge und des supragingivalen Plaques zu etablieren bzw. zu adaptieren. Darauf aufbauend wurden Metaproteomstudien durchgeführt, um die drei Mikrobiome bei gesunden Probanden hinsichtlich ihrer exprimierten Proteine, deren metabolischer Bedeutung und Interaktionen mit dem Wirt sowie deren taxonomische Zuordnung zu studieren.
Studiendesign: Die Dissertation umfasst drei Studien mit drei unterschiedlichen Kohorten. Allen Studien ist gemein, dass die Kohorten sich aus oral gesunden Probanden im Alter von 20-30 Jahren zusammensetzten.
In der ersten Studie verglichen wir die Salivette® sowie den Paraffinkaugummi anhand von fünf Probanden, um die effektivste Methode zur Sammlung von Speichel für Metaproteomstudien zu identifizieren.
In der zweiten Studie wurden die Mikrobiome von Speichel und Zunge anhand von 24 Probanden miteinander verglichen und dafür eine Auswertestrategie entwickelt, um der Komplexität dieser Metaproteomstudie gerecht zu werden.
Im Rahmen unserer dritten randomisierten Einzelblindstudie, die auf einem Cross-over-Design basierte, erhielten 16 Probanden vier unterschiedliche lokale Behandlungsschemata, um deren Auswirkung auf das Plaque-Mikrobiom zu untersuchen. Die Behandlungen bestanden aus zwei Lutschtabletten, die Bestandteile des Lactoperoxidase-Systems in unterschiedlichen Konzentrationen enthielten, einer Lutschtablette mit einem Placebo-Wirkstoff sowie Listerine® Total Care™ Mundspülung als Positivkontrolle.
Alle Proben wurden, basierend auf einem Bottom-Up-Ansatz, unter Verwendung von nano LC-MS/MS Massenspektrometern in einer datenabhängigen Messstrategie (DDA, data- dependant acquisition mode) vermessen. Die bioinformatische Auswertung erfolgte für die erste Studie mit Hilfe der Proteome Discoverer Software. Für die Studien zwei und drei wurde die Trans-Proteomic Pipeline eingesetzt. Die taxonomische sowie funktionelle Zuordnung der identifizierten Proteine erfolgte für alle Studien anhand der Prophane Software.
Ergebnisse:
Für den Paraffinkaugummi konnten wir mit 1.005 bakteriellen Metaproteinen dreimal so viele Metaproteine identifizieren im Vergleich zur Salivette® mit 313 Metaproteinen. 76,5 % der Metaproteine der Salivette® wurden ebenfalls mit dem Paraffinkaugummi gefunden. Insgesamt wurden 38 Genera und 90 Spezies identifiziert, wovon 13 Genera und 44 Spezies nur mit dem Paraffinkaugummi identifiziert werden konnten. Die größte funktionelle Diversität wurde ebenfalls mit dem Paraffinkaugummi detektiert.
Das Metaproteom des Speichel- und Zungen-Mikrobioms basiert auf 3.969 bakteriellen Metaproteinen sowie 1.857 humanen Proteinen. Die Anzahl der nur für das Zungen-Mikrobiom identifizierten Metaproteine, war doppelt so hoch, im Vergleich zum Speichel.
Die Metaproteine konnten 107 Genera sowie 7 Phyla zugeordnet werden. Funktionell wurden für das Speichel-Mikrobiom signifikant höhere Metaproteinabundanzen für die Zellmotilität gefunden. Beim Zungen-Mikrobiom hingegen wiesen die Metaproteine der Biosynthese von sekundären Metaboliten, Signaltransduktion oder der Replikation höhere Abundanzen auf.
Im Rahmen der Plaque-Studie identifizierten wir durchschnittlich 1.916 (± 465) bakterielle Metaproteine je Probe, die wir taxonomisch und funktionell 116 Genera sowie 1.316 Proteinfunktionen zuordnen konnten. Die Plaque inhibierende Wirkung von Listerine® zeigte sich durch eine Reduktion der Metaproteinidentifikation von durchschnittlich 23,5 % nach der Behandlung. Darüber hinaus zeigte die Mehrheit der bakteriellen Metaproteine reduzierte relative Abundanzen während für die Metaproteine humanen Ursprungs eine Erhöhung der Proteinabundanzen gegenüber der Kontrolle vor Behandlung zu verzeichnen war. Aus funktioneller Sicht waren insbesondere metabolische Prozesse, welche für das Zellwachstum und die Zellteilung wichtig sind, betroffen. Im Gegensatz dazu erhöhten sich durch die LPO Lutschtabletten sowohl die Identifikation der Metaproteine als auch die relative Abundanz für die Mehrheit der Proteine. Nach den durch die Metaproteomdaten erhaltenen funktionellen Informationen liegen Hinweise für einen wachsenden Biofilm vor. Die Metaproteine, die eine erhöhte Abundanz nach Behandlung mit den LPO-Dragees zeigten, wurden taxonomisch hauptsächlich Erst- (S. gordonii) und Zweitbesiedlern (F. nucleatum) sowie Bakterien zugeordnet, die einem gesunden Biofilm zuträglich sind.
Fazit: Im Rahmen dieser Dissertation wurde ein vollständiger Metaproteom Arbeitsablauf von der Probensammlung, über die Probenpräparation bis hin zu Datenanalyse für das Speichel-, Zungen- und Plaque-Mikrobiom erarbeitet. In drei Studien konnten wir dessen Anwendbarkeit demonstrieren und erreichten vergleichbare Ergebnisse zu anderen Metaproteomstudien, beispielsweise bezüglich der Proteinidentifikation. Für die Sammlung von Speichelproben stellte sich der Paraffinkaugummi für Metaproteomstudien als die Methode der Wahl heraus. Für das Zungen-Mikrobiom veröffentlichten wir die ersten Metaproteomdaten. Darüber hinaus publizierten wir die erste Metaproteomstudie, welche die beiden Mikrobiome von Speichel und Zunge miteinander vergleicht. Hinsichtlich des Plaque-Mikrobioms handelte es sich ebenfalls um die erste Metaproteomstudie, die ein
anerkanntes und etabliertes zahnklinisches Modell mit den Vorzügen der Metaproteomiks verbindet. Die Ergebnisse liefern erste Daten, um (auf längere Sicht gesehen) ein Produkt zur täglichen Mundhygiene entwickeln zu können, welches die bakterielle Zusammensetzung des Plaque-Biofilms positiv beeinflusst.
The aquaculture industry has been consistently and successfully growing over the
years, supplying over 50% of the fish humans consume. A large part of this success is due
to the implementation of vaccination, which is by far the most reliable prophylactic method
in large-scale fish farming. Nonetheless, although recent fish vaccines have greatly
contributed to the development and sustainability of the aquaculture industry, they not
always offer sufficient protection to provide acceptable survival rates when infectious
diseases outbreaks occur. Therefore, infectious diseases and effective vaccines still
constitute major problems for aquaculture.
Different practical aspects and biological factors of fish have also contributed to the
unsuccessful outcome of fish vaccines. To date, many of the most effective vaccines for fish
are injectable, and their formulation includes aluminum or oil emulsion adjuvants. Both facts
constitute a major issue for animal welfare due to the stress and side effects they trigger.
Great strides have been made in innovative technologies for fish vaccines. However, as of
today, they are not available on the market. Thus, improvements in vaccine formulations and
delivery routes remain an open topic and leads the to-do list of science with the aquaculture
of the future.
Vaccination provides immunity against a determined pathogen, and this is inherent
to the immune system. Therefore, thorough knowledge about the fish immune system and
how it is influenced by internal and external factors will certainly support rational vaccine
design. Thereby, the immune responses triggered by a vaccine can be exhaustively
characterized, and the formulations improved in case it is needed.
Hence, the goal of this PhD thesis, is to provide knowledge to improve fish
vaccination, both in its formulation and in its efficacy, aiming to promote the rational design
of fish vaccines. Additionally, this work proposes a holistic view of fish, where the
physiology and culture conditions of the fish are the starting points for the development and
application of vaccines. Thus, concepts and considerations for rational vaccine design
specific for fish are presented here.
Article I of this thesis offers a comprehensive review on the current situation in
Chile, but also worldwide aquaculture and the challenges it must face in the future. Namely,
recurrent pathogenic outbreaks and sub-optimal levels of protection due to inefficient
vaccination. This article established an open and flexible ground upon which to reflect on
how and what to improve in fish vaccines, leading the efforts towards rational vaccine
design.
In Article II, we investigated whether the current most used vaccination route,
intraperitoneal, can be improved by reducing the side effects of adjuvants, replacing them
with in the vaccine formulations with Poly-(D,L-lactic-co-glycolic) acid (PLGA)
microparticles, that serve simultaneously as vaccine vehicle and adjuvants.
Article III summarizes the scientific literature about what is known about the teleost
thymus. From this, it became clear how external factors such as photoperiod and seasonality
can modulate this primary lymphatic organ, and probably, immune responses. These are
essential factors to consider if effective and protective vaccines are needed in species highly
influenced by the environment such as fish.
As discussed in Article III, fish are poikilotherm animals, highly sensitive to
environmental factors like light. In Article IV, we reported for the first time, light generates
daily rhythms in cells’ circulation and gene expression, entraining the trout immune
response. Therefore, “when” (time of the day) we stimulate fish matters in order to get
optimal immune responses. Article V provides valuable knowledge about what happens
with fish immune responses, against a bacterial agent, under constant cues like light/dark
cycles and temperature. Once again, “when” we stimulate fish (season), influences the fish
immune status and therefore, their immune responses.
Finally, Article VI reports, for the first time, leukocytes extracted from fins of trout
directly respond to a parasitic infection. This article supports the idea that further research
must be done on fish mucosal surfaces, since they are key to stimulating/vaccinating fish, as
they are a natural entry route for pathogens and modulate the immune responses mounted.
Overall, the information provided by these articles is highly relevant for the
aquaculture industry. Firstly, because the vaccine platform based on PLGA microparticles
is promising for the future of fish vaccination, harmful adjuvants can be avoided, while still
providing enhanced stimulation thanks to the timed-released capacity of the particles.
Additionally, they offer the possibility to adapt them to in-feed vaccine pellets, which is the
ideal delivery route for fish. Secondly, accurate vaccination protocols can be established;
vaccination should be done during daytime, and preferably during the morning, where the
physiological status of fish provide optimal conditions for induction of an ultimately
protective immune response after vaccination. Furthermore, vaccination should be done
during warm months, spring, or summertime, as apparently fish have free-run internal clocks
that negatively modulate adaptive immune responses during wintertime.
In summary, the present thesis provides a novel concept for vaccination of
aquacultured species based on new data for rational vaccine design, with optimal application
procedures based on the optimal timing (season and daytime), reduced stress by oral
application and considerations about improving “first-line defenses” by vaccination via
mucosal surfaces of gut or skin.
Staphylococcus aureus (S. aureus) endocarditis is still one of the most fatal heart diseases, with a mortality rate of 20-45%. In recent years, the importance of endothelial cells (ECs) in the context of endocarditis has become more evident. The vascular endothelium forms a selective barrier between blood and the adjacent tissue by maintaining an anti-inflammatory and anti-thrombogenic phenotype. However, in case of insertion of cardiac implants, an injury of the endothelium can occur which promotes platelet aggregation followed by S. aureus adherence to the platelets, especially in areas with low hemodynamic shear stress. This process is considered as a key event in the development of infective endocarditis (IE) and allows bacteria to colonize the heart valves. Despite extensive research, the pathogenesis of IE is still not completely understood. Therefore, further investigations are needed to enable an effective prevention of this life-threatening disease.
In order to study the infection process of S. aureus, internalization experiments with two different S. aureus strains, one control strain (HG001) and one strain isolated from an endocarditis patient (T-72949) were performed in human coronary artery endothelial cells (HCAEC). Subsequently, an extensive proteome analysis of the host cells was carried out. More specific analyses were performed using peptidoglycan (PGN), a cell wall component of Gram-positive bacteria, which causes a pro-inflammatory response in ECs. In this context, the focus remained on the analysis of cellular changes in terms of cell stiffness, wound healing, and additionally platelet aggregation.
The analysis of the HCAEC host proteome revealed a time-related difference depending on the infecting bacterial strain. Several proteins involved in host cell signaling pathways exhibited a higher abundance at earlier time points in host cells infected with endocarditis strain T-72949 compared to those infected with HG001. Further proteome analysis uncovered several adaptations on the cellular side that enable internalization and replication of both S. aureus strains as well as the activation of pathways that promote cellular recovery. Furthermore, it could be shown that PGN reduced cellular stiffness which could lead to an increased bacterial uptake and would thereby promote the development of a chronic S. aureus infection. Additionally, PGN prevented effective wound healing which promotes a pro-thrombotic and pro-inflammatory condition. This status could facilitate the bacterial infection of further cells. Apart from that, PGN induced platelet aggregation which could ease bacterial adhesion to thrombotic surfaces (e.g., dysfunctional endothelium). The following formation of a mature vegetation might protect the bacteria from the immune system and antibiotics.
The results of the present work emphasize the central role of ECs in the context of IE. It could be demonstrated that a healthy monolayer of ECs enables a beneficial cell response and may prevent the development of vascular diseases. Moreover, the comprehensive proteome dataset which was generated in this project provides a valuable source of information for future studies to unravel further molecular mechanisms of endocarditis and possible therapeutic approaches.
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea referring to infections of the gastrointestinal tract in the course of (broad-spectrum)antibiotic therapy. While antibiotic therapy, preferentially with fidaxomicin or vancomycin, often stops the acute infection, recurrence events due to remaining spores and biofilm-associated cells are observed in up to 20% of cases. Therefore, new antibiotics, which spare the intestinal microbiota and eventually clear infections with C. difficile are urgently required. In this light, the presented work aimed at the evaluation and characterization of three natural product classes, namely chlorotonils, myxopyronins and chelocardins, with respect to their antimicrobial activity spectrum under anaerobic conditions and their potential for the therapy of C. difficile infections. Briefly, compounds of all three classes were screened for their activity against a panel of anaerobic bacteria. Subsequently, the systemic effects of selected derivatives of each compound class were analyzed in C. difficile using a proteomics approach. Finally, appropriate downstream experiments were performed to follow up on hypotheses drawn from the proteomics datasets. Thereby, all three compound classes demonstrated significant activity against C. difficile. However, chelocardins similarly inhibited the growth of other anaerobes excluding chelocardins as antibiotic candidates for C. difficile infection therapy. In contrast, chlorotonils demonstrated significantly higher in vitro activity against C. difficile and close relatives compared to a small panel of other anaerobes. In addition, it could be shown that chlorotonils affect intracellular metal homeostasis as demonstrated in a multi-omics approach. The data led to speculate that chlorotonils eventually affect cobalt and selenate availability in particular. Moreover, a metaproteomics approach verified that oral chlorotonil treatment only marginally affected the intestinal microbiota of piglets on taxonomic and functional level. Furthermore, the proteome stress response of C. difficile 630 to myxopyronin B, which similarly showed elevated activity against C. difficile compared to a few other anaerobes, indicated that the antibiotic inhibited early toxin synthesis comparatively to fidaxomicin. Finally, evidence is provided that C. difficile 630 responds to dissipation of its membrane potential by production and accumulation of aromatic metabolites.
Untersuchungen zur Immunantwort gegen potenzielle Vakzinkandidaten von Streptococcus pneumoniae
(2022)
Das Gram-positive Bakterium Streptococcus pneumoniae (Pneumokokken) stellt vor allem bei der sehr jungen und älteren sowie immungeschwächten Bevölkerung einen immer mehr an Bedeutung gewinnenden Krankheitserreger dar. Krankheitsbilder wie die Pneumokokken-Meningitis, -Pneumonie und -Sepsis, um nur einige zu nennen, können z.T. schwere Verläufe nehmen. Neue Serotyp-unabhängige Impfstoffe sollen flächendeckenden Schutz vor Infektionen mit S. pneumoniae bieten. Das Hauptaugenmerk der Impfstoffforschung liegt unter anderem auf der Untersuchung von Pneumokokken Protein-basierten Impfstoffen als Bestandteil eines Konjugat- bzw. Multikomponenten Impfstoffes. In diesem Zusammenhang wurde in dieser Arbeit die Immunantwort humaner Immunzellen gegenüber den vier Pneumokokken Oberflächen-Lipoproteinen MetQ, DacB, PnrA und PsaA untersucht. Diese Lipoproteine wurden sowohl in lipidierter als auch in nicht-lipidierter Form als heterologe Proteine generiert, um den Einfluss der Lipidierung auf die Immunreaktion beurteilen zu können. Zur Untersuchung der Reaktion des menschlichen Immunsystems wurden humane Blut-Monozyten (hPBMCs) isoliert und zu pro-inflammatorischen Makrophagen (M1) einerseits und anti-inflammatorischen Makrophagen (M2a) andererseits differenziert. Die Zellen wurden mit den lipidierten bzw. nicht-lipidierten Proteinen stimuliert. In den Überständen wurden zur Beurteilung der abgelaufenen Immunreaktion die Konzentrationen von IL-1β, IL-2, IL-6, IL-8 und TNF bestimmt. Eine Produktion von IL-1β und IL-2 durch die Makrophagen konnte hierbei nicht nachgewiesen werden. M1 Makrophagen zeichneten sich durch eine kaum messbare Cytokin-Produktion auf beide Proteinstimuli aus. Anti-inflammatorische Makrophagen zeigten eine signifikant verstärkte IL-6, IL-8 und TNF Produktion (p< 0,05) nach Stimulation mit allen vier lipidierten Proteinen im Gegensatz zur Stimulation mit nicht-lipidierten Proteinen. Das stärkere Stimulationspotenzial der lipidierten Proteine konnte auf deren Agonismus am TLR2 zurückgeführt werden. Weiterhin konnte die starke Reaktion der M2a Makrophagen mit deren Plastizität sowie mit dem Potenzial von Lipoproteinen zur Umpolarisation von Makrophagen aufgrund des TLR2 Agonismus erklärt werden. Die Ergebnisse zeigen, dass die eingesetzten lipidierten Proteine einen suffizienten und signifikant potenteren Immunstimulus im menschlichen Organismus darstellen, als die gleichen Proteine in nicht-lipidierter Form. Somit könnten diese lipidierten Proteine geeignete Vakzinkandidaten gegen S. pneumoniae darstellen.
Streptococcus pneumoniae (S. pneumoniae, pneumococci) and Staphylococcus aureus (S. aureus) belong to the Gram-positive, facultative pathogenic bacteria. They are typical commensals of the human upper respiratory tract and most people get colonized at least once during their life. Nevertheless, these potentially pathogenic bacteria are able to spread from the site of colonization to invade into deeper tissues and the blood circulation. Thereby, severe local and invasive infections like bacteremia and life-threatening sepsis can be caused. Once reaching the bloodstream, bacteria get in contact with platelets. Platelets are small, anucleated cells and the second most abundant cell type in the circulation. The role of platelets in hemostasis is well known. Circulating resting platelets sense vessel injury independent of its cause. Platelets bind to injured endothelium and exposed molecules of the underlying extracellular matrix, get activated and release intracellular adhesion proteins and different modulatory molecules. This in turn initiates activation and binding of nearby platelets resulting in closure of vascular injury by formation of small thrombi. Despite being pivotal in maintenance of the endothelial barrier they got increasingly recognized as cells with important immune functions. Platelets excert functions of the immune response by either, i) interacting with immune cells of different pathways of the immune response, ii) releasing immunomodulatory molecules stored in their granules or iii) interacting with invading pathogens via direct or indirect binding.
The basis for this study were results demonstrating direct binding of different S. aureus proteins to platelets resulting in platelet activation. The identified proteins in the mentioned study are the S. aureus proteins Eap, AtlA-1, CHIPS and FlipR. Severe invasive infections with S. pneumoniae are quite often associated with development of thrombocytopenia or disseminated vascular dissemination. This frequent observation hints towards either a direct or indirect interplay of platelets with pneumococci. Hence, this study aims to analyze potential interactions and aims to decipher involved factors on both the platelet- and bacterial site.
A screening of recombinant pneumococcal surface proteins identified proteins belonging to the group of lipoproteins, sortase-anchored proteins and choline-binding proteins to directly activate human platelets. Besides these surface proteins also the intracellular pneumococcal pneumolysin (Ply) induced highly increased values for the platelet activation marker P-selectin. Since Ply is a major virulence factor of
S. pneumoniae the primary focus was set on involvement of this pore forming toxin on platelet activation. Surprisingly, our data revealed Ply induced platelet activation to be a false positive result based on formation of large Ply pores in the platelet membrane. In fact, it was clearly demonstrated that Ply lyses platelets even at low concentrations and thereby rendering them non-functional. Lysis of platelets could be inhibited by the addition of pharmaceutical immunoglobulin preparations as well as antibodies specifically targeting Ply. Inhibition of Ply also resulted in fully rescued platelet function either in washed platelets or in whole blood as shown by thrombus formation. Next to pneumococci also S. aureus expresses pore forming toxins, namely α-hemolysin (Hla) and different pairs of bicomponent pore forming leukocidins. Whereas the different tested leukocidins did not affect platelets, Hla acted in a two-step mechanism on human platelets. The results confirm previous data on Hla induced platelet activation via Hla resulting in e.g., reversible platelet aggregation or surface expression of activation markers. Nevertheless, platelet activation by Hla is followed by dose- and time-dependent lysis of platelets resulting in loss of platelet function and abrogated thrombus formation. Platelet lysis by Hla could neither be rescued with specific monoclonal anti-Hla antibodies nor with pharmaceutical IgG preparations containing anti-Hla IgGs. Taken together, the presented data reveal new pathomechanisms involving disturbance of platelets by bacterial pore forming toxins. Platelet lysis as well as impaired platelet function play an important role in development of severe complications during invasive infections. In life threatening infections caused by S. pneumoniae the usage of antibody formulations containing antibodies targeting Ply might be a promising approach for the prevention or even intervention and improvement of clinical outcome.
With the aim to discover and create suitable biocatalysts for the synthesis of chiral amines in a faster and more efficient way, this thesis includes protein engineering studies (Article I), explores transaminase substrate specificities (Articles II and IV), and an ultrahigh-throughput growth system-based for the directed evolution of amine-forming enzymes (Article III).
The protein engineering studies described in Article I deal with the creation of a (R)-amine transaminase activity in the α-amino acid transaminase scaffold to expand our knowledge of the evolutionary relationship between amine transaminase and α-amino acid transaminase. Article II describes the broadening of the limited substrate scope of transaminases to enable the conversion of bulky substrates. In Article III, a growth selection system is described for an ultra-high throughput screening strategy to accelerate the identification of desired mutants, which can be widely applied to the directed evolution of amine-forming enzymes.
The order of bats (Chiroptera) account for ~20% of all mammalian species and attracted immense global attention due to their identification as important viral reservoir. Bats can harbour a plethora of high-impact zoonotic viruses, such as filoviruses, lyssaviruses, and coronaviruses without displaying clinical signs of disease themselves. Given this striking diversity of the bat virome, their ability of self-powered flight, and global distribution, understanding chiropteran immunity is essential to facilitate assessment of future spillover events and risks.
However, scarcity of bat-specific or cross-reactive tools and standardized model systems impede progress until today. Furthermore, the richness of species led to generation of isolated datasets, hampering data interpretation and identification of general immune mechanisms, applicable for various chiropteran suborders/families. The key to unlocking bat immunity are coordinated research approaches that comprehensively define immunity in several species. In this work, an in-depth study of innate and adaptive immune mechanisms in the fructivorous Egyptian Rousette bat (Rousettus aegyptiacus, ERB) is presented.
Detailed stability analyses identified EEF1A1 as superior reference gene to ACTB, and GAPDH, which rendered unstable upon temperature increase or presence of type-I-IFN. Since the body core temperatures of pteropid bats reach from 35°C to 41°C and it has been postulated that bats display constitutive expression of IFNs, a suitable reference gene has to be stable under these physiologically relevant conditions. To study cellular innate immunity in detail, cell lines from the nasal epithelium, the olfactory compartment and the cerebrum were generated. To include immune responses of epithelia cells, essential for immunity at sites of primary viral infection, primary epithelia cells from the nasal epithelium, trachea, lung and small intestine were generated. Cellular identities were determined by comprehensive analyses of transcripts and proteins expressed by each cell line. The capacity of each cell line to produce type-I- and III-IFNs was assessed at 37°C and 40°C upon stimulation with viral mimetics. This revealed cell type-dependent differences is the capability to express IFNs upon stimulation. Furthermore, the constitutive expression of type-I- and III-IFNs was significantly elevated in higher temperatures and quantified at mRNA copy levels. To characterize ERB innate immunity upon infection with high-impact zoonotic viruses, cells from the nasal epithelium, the olfactory system, and the brain were infected with several lyssaviruses. This revealed striking differences in susceptibility: cells from the nasal epithelium rendered least whereas cells from the olfactory epithelium rendered most susceptible to viral infection and replication. Additionally, due to a lack of IFN expression in infected cells, it could be shown that LBV possibly possesses advanced strategies to ensure successful replication in ERB cells. Since the current SARS-CoV-2 pandemic put bats even further in the focus of zoonotic research, primary epithelial cells and animals were infected with this virus to monitor ERB-specific immune transcripts in cells and tissues. These studies revealed a notably early IFNG expression in the respiratory tract of infected individuals.
To understand immunomaturation in bats, the immune cell landscape in periphery and various tissue in adult and juvenile ERB was analyzed by flow cytometry and scRNA-seq, revealing intriguing, age-dependent variations in the abundance of granulocytes and lymphocytes. Flow cytometry revealed a significantly higher number of granulocytes in adults, as well as higher numbers of B cells in juveniles. scRNA-seq allowed detailed identification of different leukocyte subsets, uncovering the presence of highly-abundant NKT-like cells and a unique PLAC8 expressing B cell population. A functional characterization of phagocytic cells and lymphocytes derived from adult and juvenile ERB revealed no significant differences in cellular functionality.
In conclusion, the presented work demonstrated suitability of all established ERB cell lines to study bat immunity in vitro, which led to striking findings regarding IFN expression at steady state, or upon stimulation or viral infection. In addition, established qRT-PCR protocols allowed definition of constitutive and temperature-dependent elevation of IFN expression magnitudes, as well as insights into expression of immune-related transcripts in SARS-CoV-2 infected ERB. Finally, based on optimized scRNA-seq technologies and flow cytometry, frequencies and absolute cell counts could be determined in ERB of different ages, revealing e.g. age-dependent variations in leukocyte profile compositions.
Zur Untersuchung molekularer Prozesse sind die Wechselwirkungen der beteiligten Faktoren von zentraler Bedeutung, was besonders für die präzise Steuerung der eukaryotischen Genregulation zutrifft, die im Mittelpunkt dieser Arbeit steht. Die Transkription wird durch den Zusammenbau des Präinitiationskomplexes (PIC) am Promotor der Zielgene initiiert. Neben der RNA-Polymerase II, dem Mediatorkomplex und mehreren generellen Transkriptionsfaktoren sind daran Aktivatorproteine beteiligt, welche an UAS-Elemente (upstream activation site) im Promotor binden. Daneben können aber auch Repressoren an URS-Elemente (upstream repression site) binden oder mit Promotor- gebundenen Aktivatoren interagieren und durch Rekrutierung sog. Corepressoren (z. B. Sin3, Cyc8 und Tup1) die Transkription hemmen. Diese Corepressoren können dann über assoziierte Histon- deacetylasen (z. B. Rpd3) die Chromatinstruktur im Promotorbereich spezifischer Gene verdichten und damit eine Bindung der Transkriptionsmaschinerie verhindern. In der Regel führt dies zu einer reduzierten Expression des jeweiligen Gens.
Untersuchungen zu den Wechselwirkungen zwischen genspezifischen Repressoren und pleiotropen Corepressoren haben in der Vergangenheit bereits zur Identifizierung einzelner Sequenzmotive und individueller Strukturen geführt. Um dieses Netzwerk zu ergänzen, wurden in dieser Arbeit zahlreiche Repressor-Corepressor-Interaktionen in der Hefe Saccharomyces cerevisiae in vitro und in vivo charakterisiert und durch Verkürzung der interagierenden Proteine (Dal80, Mot3, Sko1, Ure2, Xbp1 und Yox1) hierfür relevante Aminosäuresequenzen ermittelt. Durch systematische Vergleiche solcher Repressorsequenzen konnten Varianten eines hydrophob-amphipathischen Konsensusmotivs identifiziert und z. T. durch gerichtete Mutagenese als funktionell wichtig nachgewiesen werden. Sekundärstrukturvorhersagen zeigten oft die Beteiligung α-helikaler, aber auch β-Faltblatt- oder ungeordneter Strukturen. Diese strukturelle Varianz lässt die Vermutung zu, dass es sich bei solchen Corepressor-Interaktionsdomänen (CID) um IDRs (intrinsically disorderd regions) handeln könnte, die erst durch Kontaktherstellung zum Corepressor eine definierte Konformation annehmen.
Ein in dieser Arbeit intensiv untersuchter Repressor war Gal80, der bekanntermaßen das GAL-System der Hefe solange abschaltet, bis Galactose als induzierender Zucker verfügbar ist. Man unterscheidet hierbei drei Zustände: Die Glucoserepression beschreibt das Abschalten der GAL-Gene durch den Repressor Mig1 bei Glucoseverfügbarkeit. Bei Glucosemangel und Verfügbarkeit einer alternativen Kohlenstoffquelle (z. B. Lactat oder Ethanol) wird der Aktivator Gal4 synthetisiert und bindet an UASGAL- Motive in Promotoren der GAL-Gene. Unter diesen Derepressionsbedingungen wird die Transkriptionsaktivierungsdomäne von Gal4 noch durch den Gal80-Repressor maskiert. In dieser Arbeit wurde gezeigt, dass Gal80 zusätzlich in der Lage ist, den Corepressorkomplex Cyc8/Tup1 zu rekrutieren und die Transkription der Strukturgene dadurch zu reprimieren. Chromatinimmunopräzi- pitationsstudien belegten die Gal80-abhängige Präsenz der Corepressoren Cyc8 und Tup1 am GAL1 Promotor. Außerdem stellte sich bei der Charakterisierung von cyc8 und tup1 Mutantenstämmen heraus, dass Corepressoren durchaus auch aktivierende Wirkungen entfalten können. So fiel die Expression eines GAL1-lacZ Reportergens in einer cyc8 Nullmutante unter allen getesteten Bedin- gungen geringer aus als im Wildtyp. Die duale Wirkung solcher Transkriptionsfaktoren wurde in der Vergangenheit immer wieder beobachtet und steht auch im Einklang mit den Befunden dieser Arbeit.
Drainage has commonly been a pre-requisite for the productive use of peatlands. The biased focus on agriculture, forestry and peat extraction has long ignored the destructive effects of drainage and the successive degradation of ecosystem functions of wet peatlands. Accelerated by the climate crisis, the finite nature of drainage-based peatland use is increasingly recognised. Consequently, productive land use options for wet or rewetted peatlands (paludiculture) are required as sustainable alternatives. A wide range of paludiculture plants and options of biomass utilisation are identified as suitable and promising. Despite the growing interest, experiences with and research on the economic viability of paludiculture are still rare.
This thesis addresses the lack of knowledge on paludiculture in terms of practical feasibility, costs and benefits at the farm level, market prospects and framework conditions. I selected the two currently most advanced paludicultural practices in Europe: a) Harvesting natural reed beds as a traditional ‘low-input’ paludiculture, i. e. the utilisation of existing ‘wild’ vegetation stands; b) ‘Sphagnum farming’ as a novel ‘high-input’ paludiculture including stand establishment and water management required for the active transformation from drainage-based peatland use to paludiculture. In both cases, I investigate three different biomass utilisation avenues. This thesis adds to the fields of problem-driven sustainability and land-use science. Procedures and costs of paludiculture were studied in transdisciplinary research projects in close cooperation with practitioners. Due to the novelty of the topic, I put special emphasis on the triangulation of methods and data sources: pilot trials, field measurements, semi-structured expert interviews, structured questionnaires, secondary data from trade statistics and literature. To account for uncertainty related to costs and revenues, I conduct stochastic scenario analysis (Monte Carlo simulation) for the extended contribution margin accounting of harvesting reeds and sensitivity analysis for the investment appraisal of Sphagnum farming.
Paludiculture on fens: harvesting reeds
Paper I investigates harvesting procedures for reed-dominated (Phragmites australis) vegetation stands. In many European countries special-purpose tracked machinery is applied for large-scale conservation management and the commercial harvest of thatching reed. Stochastic scenario analysis reveals a wide range of possible economic outcomes (ca. € -1000 to € 1500 ha-1 a-1) and identifies material use of reed superior to its use as a source of energy. Winter harvest of high-quality thatching reed in bundles is the most profitable option. Winter harvest of bales for direct combustion is suitable for low-quality stands and has a limited risk of loss. In the case of summer harvest, revenues for green chaff for biogas production cannot cover harvesting costs but non-market income via subsidies and agri-environmental payments may ensure profitability. While biomass for energy generation is limited to a local market, thatching reed is traded as an international commodity. The market situation for thatching reed is investigated for Europe (Paper II) and Germany (Paper III). The major reed consuming countries in Western Europe (Netherlands, Germany, UK, Denmark) rely on imports of up to 85 % of the national consumption, with reed being imported from Eastern and Southern Europe and since 2005 also from China. The total market volume for reed for thatching in Northern Germany is estimated with 3 ± 0.8 million bundles of reed with a monetary value at sales prices of € 11.6 ± 2.8 million. Most of the thatchers (70 %) did not promote reed of regional origin to their customers due to insufficient availability in the first place and a lack in quality as second reason. The cultivation of reed in paludiculture may improve quantity and quality of domestic thatching reed. An area of 6000 ± 1600 ha with an average yield of 500 bundles per hectare would allow covering the current total demand of 3 million bundles of the German thatching reed market (Paper III).
Paludiculture on bogs: Sphagnum farming
Sphagnum farming provides an alternative to peatland degradation in two ways: Firstly, Sphagnum mosses can be cultivated as new agricultural crops on rewetted peatlands. Secondly, the produced Sphagnum biomass is a high-quality raw material suitable to replace peat in horticultural growing media (Paper V). Pilot trials have demonstrated the practical feasibility of establishing Sphagnum cultures on former bog grassland, cut-over bogs and mats floating on acidic waters bodies; Paper IV compares for the three types of production sites the specific procedures, costs and area potential in Germany. Water-based Sphagnum farming is not recommended for large-scale implementation due to highest establishment costs, major cultivation risks and limited area potential. For soil-based Sphagnum farming, the most important cost positions were Sphagnum shoots to set up pilots, investment for water management and regular weed management. Bog grassland has the highest area potential, i. e. 90,000 ha in NW Germany. Paper V assesses the profitability of Sphagnum farming on former bog grassland based on extrapolating five years of field experience data (establishment ņ management ņ harvest) to a total cultivation time of twenty years. Cultivating Sphagnum biomass as founder material for Sphagnum farming or restoration was profitable even in pessimistic scenarios with high costs, high bulk density and low yields. Selling Sphagnum for orchid production was economically viable in the case of medium to high yields with a low bulk density. Cost-covering prices for Sphagnum biomass substituting peat seem achievable if end consumers pay a surcharge of 10 % on the peat-free cultivated horticultural end-product. An area of 35,000 ha of Sphagnum farming suffices to meet the annual demand of the German growing media industry for slightly decomposed Sphagnum peat.
Framework conditions affecting feasibility of paludiculture
The relation of revenues from selling biomass to its production costs is an important piece of the paludiculture feasibility puzzle. Further aspects effecting the economic viability and competitiveness of paludiculture encompass the market demand, the availability of mature technology, legal restrictions, the eligibility for agricultural subsidies, a remuneration of external benefits and the opportunity costs of present farming activities (Paper I, V). Legal and policy regulations are of major importance for land use decisions on peatlands – both for keeping up drainage and for shifting to paludiculture.
Conclusion and Outlook
This thesis provides a first assessment of the costs and profitability of large-scale harvesting of reeds and Sphagnum farming based on real-life data. The paludicultural practices investigated may be a solution for a minor share of the more than 1 million ha of peatlands drained for agriculture in Germany. Future research should also address other biomass utilisation options and other crops. Large-scale pilots are required to improve technical maturity of procedures and machinery, gather reliable data to replace assumptions on costs and revenues and study long-term effects on economics and ecosystem services. The micro-economic perspective needs to be complemented by the societal perspective quantifying and monetising external effects of peatland restoration, paludiculture and drainage-based peatland use. There is a high need for intensified research, large-scale implementation and accelerated adaption of the policy and legal framework to develop paludiculture as an economically viable option for degraded peatlands.
Group A streptococcus (GAS) and Streptococcus pneumoniae are both Gram-positive bacteria that asymptomatically colonise various human body parts. Both microbes cause diseases ranging from mild to severe invasive infections. The later are associated with high mortality. GAS is the major microbial aetiology of type II necrotising skin and soft tissue infections (NSTIs). Type II NSTIs typically affect the lower and upper limbs of healthy young adults and often require debridement as a surgical intervention to prevent the spread of infection. S. pneumoniae is the major cause of respiratory tract infections including community-acquired pneumonia in young children and the elderly. Although most respiratory tract infections are successfully treated with antibiotics, emerging antibiotic resistance is a major cause of concern. Secreted virulence factors of Gram-positive bacteria play a major role in the successful invasion of host tissues causing different diseases. Additionally, they facilitate the spread of infection, contribute to tissue pathology, and potentially act as immune evasion mechanisms. This thesis summarises the consequences of streptococcal pyrogenic exotoxin B (SpeB), a potent cysteine protease secreted by GAS and pneumococci-derived hydrogen peroxide (H2O2) on host responses.
GAS have developed genetic or phenotypic ways of adapting to the immune response to escape immune clearance. Analysis of GAS clones recovered from NSTI patient biopsies exhibit a mixed SpeB phenotype, with most clones being SpeB negative. SpeB negative clones have been associated with hyper-virulence. In Paper II, we showed that SpeB negative GAS clones recovered from tissue exhibit reversible impaired SpeB secretion due to environmental factors. In addition, mutations in covS and ropB, the major transcriptional regulators of SpeB expression, were responsible for the irreversible loss of SpeB expression. Immunohistochemistry analysis demonstrated that neutrophil degranulation, necrosis and excessive inflammation observed in NSTIs patient biopsies correlated with bacterial load and SpeB negativity of clones. Proteomic data analysis showed that SpeB negative GAS recovered from neutrophil infection harboured the protease intracellularly suggesting that the bacteria expressed but did not secrete SpeB. We have also shown that neutrophil-derived reactive oxygen species, H2O2 and hypochlorous acid, drive the SpeB negative phenotype. The SpeB negative clones survived neutrophil-mediated antimicrobial killing and induced excessive degranulation when compared with SpeB positive clones. These results provide new insights into GAS fitness induced by host factors in tissue and may be useful for the development of new treatment strategies in NSTIs.
Pneumococci produce H2O2 as a by-product of carbohydrate metabolism in a reaction catalysed by pyruvate oxidase SpxB. However, very little is known about the effects of pneumococcal H2O2 as a virulence factor. Our study aimed to investigate the role of H2O2 in initiating epithelial cell death, focusing on apoptosis and pyroptosis. In Paper III, we showed that pneumococci-derived H2O2 caused epithelial cell cytotoxicity by priming and activating the NLRP3 inflammasome resulting in subsequent IL-1β production and release. Additionally, H2O2 caused apoptotic and pyroptotic cell death as evidenced by activation of caspase-3/7 and caspase-1, respectively. However, the release of IL-1β was dependent on apoptosis and not pyroptosis since inactive gasdermin D was detected post-infection. These observations were not detected in the absence of H2O2. Overall, we showed the damaging effects of pneumococci-derived H2O2 on human bronchial epithelial cells.
Avian influenza viruses (AIVs) have their natural reservoir in wild aquatic birds but occasionally
spread to terrestrial poultry. While AIVs of subtypes H5 and H7 are well known to evolve highly
pathogenic avian influenza viruses (HPAIVs) during circulation in domestic birds, non-H5/H7
subtypes exhibit only a low to moderate pathogenicity. Furthermore, spillover events to a broad
range of mammalian hosts, including humans, with self-limiting to severe illness or even fatal
outcomes, were reported for non-H5/H7 AIVs and pose a pandemic risk. The evolution of high
virulent phenotypes in poultry and the adaptation of AIVs to mammalian hosts are predominantly
linked to genetic determinants in the hemagglutinin (HA). The acquisition of a polybasic cleavage
site (pCS) is a prerequisite for the evolution of HPAIVs in poultry, while changes in the receptor
binding preference and virus stability are essential for adaptation of AIVs to mammals.
In August 2012, an H4N2 virus with the pCS motif 322PEKRRTR/G329 but preserved trypsin
dependend replication and low pathogenicity in chickens was isolated on a quail farm in California.
In the first two publications, we followed different approaches to investigate virulence factors and
the potential risk for the transition of H4N2 to high virulence in chickens. The loss of N-terminal
glycosylations in the vicinity of the pCS resulted in decreased binding to avian-like receptors and
dramatically decreased virus stability. On the other hand, one deglycosylation increased virus
replication and tissue tropism in chicken embryos but did not alter virulence or excretion in
chickens. Furthermore, additional basic amino acids in the natural pCS motif improved the trypsin-independent
cleavage of HA and caused slightly increased tissue tropism in chickens. However,
the engineered motifs alone did not affect virulence in chickens. Intriguingly, they even had a
detrimental effect on virus fitness, which was restored after reassortment with segments of HPAIV
H5N1. Together, the results show the importance of HA glycosylations on the stability of H4N2 and
reveal the important role of non-HA segments in the transition of this virus to high virulence in
poultry.
The transmission of another non-H5/H7 AIV of subtype H10N7 from birds to seals resulted in mass
deaths in harbor seals in 2014 in northern Europe. The third publication describes nine mutations
in the HA1 subunit of seal isolates compared to avian H10Nx viruses. We found that some of these
mutations conferred a dual specificity for avian and mammalian receptors and altered
thermostability. Nevertheless, the H10N7seal remained more adapted to avian host cells, despite
of the alteration in the receptor binding specificity.
Altogether, this thesis demonstrates that naturally evolved AIVs beside H5 and H7 subtypes
support a highly pathogenic phenotype in the appropriate viral background and alter virulence and
host receptor specificity by few amino acid substitutions in the HA. These findings improve our
knowledge of the potential of non-H5/H7 AIVs to shift to high virulence in birds and the adaptation
in mammals.
Kardiovaskuläre Erkrankungen gehören trotz zahlreicher medikamentöser und apparativer Therapiemaßnahmen noch immer zu den häufigsten Todesursachen in den Industrienationen. Die Herzinsuffizienz (HI) stellt dabei das Endstadium vieler Herzerkrankungen dar und beschreibt das Unvermögen des Herzens, die Blutzirkulation im Organismus bei normalem Ventrikeldruck konstant zu halten. Unabhängig von ihrer Ätiologie, wie Koronarerkrankungen, langjähriger Hypertonie oder auch Kardiomyopathien ist die HI neben der Funktionsreduktion des linken und/oder rechten Ventrikels gleichzeitig durch strukturelle Veränderungen (Remodeling) mit Gefäßverengung (Vasokonstriktion), endotheliale Dysfunktion mit Vasokonstriktion, sowie eine generalisierte neurohumorale Aktivierung gekennzeichnet. Die Suche nach neuen und alternativen Therapieverfahren zur Verbesserung der Symptomatik und Prognose der betroffenen Patienten ist daher notwendig. Einer der wichtigsten Mediatoren für die Regulation des Gefäßwiderstandes ist Stickstoffmonoxid (NO, nitric oxide), welches durch NO-Synthasen synthetisiert wird. NO aktiviert die lösliche Guanylatzyklase (sGC, soluble guanylate cyclase), wodurch es zu einer erhöhten Produktion des second messengers cGMP (cyclic guanosine monophosphate) kommt. Eine Beeinträchtigung des NO-sGC-cGMP-Signalweges und der dadurch bedingte Mangel an cGMP trägt zu den Prozessen der myokardialen und endothelialen Dysfunktion bei der Entwicklung und Progression einer HI bei. Die Entwicklung pharmakologisch aktiver Moleküle, die die sGC direkt stimulieren können, ist dabei von besonderem Interesse, da z.B. keine Toleranzentwicklung bei längerer Medikation oder andere negative Nebenwirkungen wie bei der Gabe von NO-Donatoren als Vasodilatatoren entstehen.
Im Rahmen dieser Arbeit sollte der Einfluss einer sGC-Stimulation mittels Riociguat (RIO), einem bereits für die Behandlung der pulmonal arteriellen Hypertonie (PAH) und der chronisch thromboembolischen pulmonalen Hypertonie (CTEPH) zugelassenen Medikament, auf die experimentelle HI untersucht werden. Neben Echokardiographie und histologischen Analysen zur Charakterisierung des Krankheitsphänotyps und der Auswirkung einer Behandlung darauf wurde ebenfalls auf Multi-Omics-Ansätze wie Proteomics und Transcriptomics zurückgegriffen, um detaillierte Einblicke in die molekularen Veränderungen auf Genexpressionsebene, Proteinebene und microRNA-Expressionsebene zu erlangen. Als Modell wurde die transverse Aortenkonstriktion (TAC) an C57BL/6N Mäusen verwendet, welche einen permanenten hämodynamischen Stressreiz auf das Herz ausübt, der schließlich zum Herzversagen führt. Im Hinblick auf die Pathogenese der HI simuliert TAC dabei auf elegante Weise eine arterielle Hypertonie, die unter anderem zu einer progressiven linksventrikulären Hypertrophie und einer reduzierten Herzfunktion unter chronischen Bedingungen führt. Für die medikamentöse Behandlung mit RIO wurde eine experimentelle Strategie gewählt, die der klinischen Situation entspricht. Dementsprechend wurde mit der Medikation zu einem Zeitpunkt begonnen, als die Herzfunktion bereits verschlechtert war und eine pathologische Hypertrophie und interstitielle Fibrose ausgebildet bzw. nachweisbar war.
TAC führte zu einer kontinuierlichen Abnahme der linksventrikulären Ejektionsfraktionsfraktion (LVEF) und einer kontinuierlichen Zunahme der linksventrikulären Masse (LVM). Eine fünfwöchige Behandlung mit RIO (3 mg/kg/d) ab der vierten postoperativen Woche führte zu einer Verbesserung der LVEF und zu einer Verringerung des Verhältnisses von LVM zu Gesamtkörpergewicht (LVM/BW), myokardialer Fibrose und Myozytenquerschnittsflächen. RNA-Sequenzierungsanalysen der linken Ventrikel ergaben, dass RIO die Expression von myokardialen Stress- und Remodeling-Genen, wie z.B. Nppa, Nppb, Myh7 und Kollagen, verringerte und die Aktivierung biologischer Signalwege abschwächte, die mit kardialer Hypertrophie und HI in Verbindung stehen. Diese protektiven Effekte einer RIO-Behandlung konnten auch auf Proteinebene beobachtet werden und spiegelten sich in einer deutlichen Reduktion der TAC-induzierten Veränderungen des linksventrikulären Proteoms wider. Durch die Aortenkonstriktion betroffene Signalwege, die mit kardiovaskulären Erkrankungen assoziiert sind, wie gewebe- und zellstrukturspezifische Signalwege, besonders aber Signalwege des Energiemetabolismus, zeigten eine Verbesserung nach einer RIO-Behandlung. Zudem schwächte RIO auch die TAC-induzierten Veränderungen auf microRNA-Ebene in den linken Ventrikeln ab.
Mit dieser Arbeit konnte gezeigt werden, dass eine Behandlung mit RIO positive Auswirkungen auf die kardiale Struktur bzw. das pathologische kardiale Remodeling und die Funktion in einem murinen Modell der chronischen Nachlasterhöhung/Drucküberlastung hat, was mit einer Umkehrung bzw. Abschwächung der TAC-induzierten Veränderungen des kardialen linksventrikulären Genexpressions-, Proteom- und microRNA-Profils einhergeht. Die vorliegenden Ergebnisse unterstützen die bisherigen Vermutungen und Erkenntnisse zum Potential von RIO als neuartigem HI-Therapeutikum. Des Weiteren wurden große Omics-Datensätze generiert, die als Informationsquelle zukünftigen Untersuchungen helfen können, die molekularen Mechanismen der chronischen HI und möglicher therapeutischer, medikamentöser Interventionen besser zu verstehen und weiter zu entschlüsseln.
Das Gram-positive Bakterium S. aureus besiedelt rund 20 % der Menschen persistent und asymptomatisch, während sich bei den anderen Phasen der Kolonisation und Nicht-Kolonisation abwechseln. Als opportunistisches Pathogen kann S. aureus seinen Wirt auch infizieren und eine Vielzahl von Krankheitsbildern hervorrufen. Diese reichen von oberflächlichen Haut- und Weichteilinfektionen bis hin zu komplexen Infektionsgeschehen wie der Sepsis und können den Tod der betroffenen Person zur Folge haben. Antibiotika-resistente Varianten wie Methicillin-resistente S. aureus (MRSA) verkomplizieren die Therapie und sind als „Krankenhauskeime“ gefürchtet. Die Kolonisierung und Infektion mit MRSA beschränkt sich allerdings nicht nur auf Gesundheitseinrichtungen, sondern etablierte sich auch in der Allgemeinbevölkerung sowie in Landwirtschaftsbetrieben. Da S. aureus neben dem Menschen ebenfalls eine Vielzahl von Wild- und Nutztieren kolonisieren und infizieren kann, welche als Reservoir, Überträger sowie als Brutstätten neuer Varianten fungieren, ist ein holistischer Ansatz wie das „One Health“-Konzept gefordert, um Ausbreitung und Infektionen unter Kontrolle zu halten.
Dies erfordert geeignete Tiermodelle, um die komplexen Interaktionen von S. aureus mit seinem Wirt zu analysieren und therapeutisch zu beeinflussen. Am häufigsten werden dafür etablierte Labormaus-Stämme (z.B. C57BL/6, BALB/c) eingesetzt und mit S. aureus-Stämmen des Menschen kolonisiert oder infiziert. Weil S. aureus jedoch einen Wirtstropismus ausbildet, ist die Aussagekraft solcher Mausmodelle durch die Inkompatibilität zwischen Erreger und Wirt limitiert. Manche Aspekte der Wirt-Pathogen-Interaktion lassen sich in diesen Modellen gar nicht untersuchen. Hier könnten murin-adaptierte S. aureus-Stämme eine bessere Option sein, zumal Vorarbeiten unserer Arbeitsgruppe zeigten, dass Mäuse natürliche Wirte von S. aureus sind.
In dieser Arbeit sollte daher untersucht werden, ob Befunde aus dem Menschen in der Maus repliziert werden können, wo die Limitationen von Mausmodellen liegen und wie mögliche Optimierungsansätze aussehen könnten. Weitere Schwerpunkte lagen auf Analysen der Populationsstruktur von S. aureus in murinen Spezies unterschiedlicher Habitate und der Adaptation muriner S. aureus-Isolate an ihren Wirt. Außerdem wurden Maus-adaptierte Stämme in Infektions- und Kolonisationsmodellen eingesetzt, um ihre Eignung im Mausmodell zu testen.
In einer Originalarbeit (Mrochen et al.; Front. Immunol.; 2021) haben wir anhand der Immunantwort auf die beiden S. aureus-Virulenzfaktoren SplB und GlpQ beschrieben, dass Daten aus klinischen Studien in der Maus rekapituliert werden können. S. aureus-naive Mäuse zeigten nach Vakzinierung mit SplB eine sehr ähnliche Polarität der Immunantwort wie Menschen nach natürlicher Besiedlung/Infektion mit S. aureus. Mäuse reagierten mit einer Th2-Antwort auf das nicht-adjuvantierte Protein SplB, zudem war die Anzahl an Eosinophilen in der Milz signifikant erhöht. Im Serum der Mäuse ließ sich SplB-spezifisches IgE messen. Damit spiegelte das Mausmodell den beim Menschen bekannten Typ2-Bias der Immunreaktion auf Spls von S. aureus wider. GlpQ löste hingegen ohne Adjuvans keine messbare Immunreaktion aus, hatte also eine geringe Immunogenität. Dies zeigt, dass S. aureus-naive Mäuse sich dazu eignen könnten, die intrinsische Immunogenität und das Immunpolarisationspotential von S. aureus-Proteinen zu untersuchen, was für die Entwicklung von S. aureus-Vakzinen von Bedeutung ist.
In einem Übersichtsartikel (Mrochen et al.; Int. J. Mol. Sci.; 2020) haben wir die Limitationen von konventionellen S. aureus-Infektionsmodellen, bei denen Mäuse mit human-adaptierten S. aureus-Isolaten infiziert werden, veranschaulicht und Alternativen aufgezeigt. Zunächst stellten wir den Wirtstropismus von S. aureus und Mechanismen der Wirtsanpassung dar. Darauf aufbauend diskutierten wir einige Limitationen konventioneller Mausmodelle. Wir betrachteten Aspekte der genetischen Variation der verwendeten Maus- und S. aureus-Stämme, wirtsspezifische Virulenzfaktoren, Unterschiede des humanen und murinen Immunsystems, den Einfluss des murinen Mikrobioms und der verwendeten Infektionsdosen. Zusammenfassend kann dazu gesagt werden, dass durch die Inkompatibilitäten zwischen humanen S. aureus-Isolaten und der Maus die bakterielle Fitness und Virulenz eingeschränkt ist. Dies kann die Aussagekraft von Experimenten massiv einschränken. Beispielsweise können in ihrer Affinität verminderte Rezeptor-Ligand-Interaktionen die Akquisition von Nährstoffen erschweren und die Wirkungslosigkeit bestimmter Virulenzfaktoren (wie z.B. Superantigenen) die Immunevasion behindern. Wir haben daraufhin alternative Modell-Ansätze vorgestellt und diskutiert, welche unterschiedliche Aspekte der Wirt-S. aureus-Interaktion verbessern sollen (humanisierte Mäuse, dirty mice, Wildlinge). Die ebenfalls mögliche Verwendung murin-adaptierter S. aureus-Stämme beseitigt Inkompatibilitäten zwischen Maus und S. aureus komplett, kann aber manche humanspezifischen Vorgänge nicht modellieren.
In zwei weiteren Originalarbeiten (Mrochen et al.; Int. J. Med. Microbiol.; 2018 und Raafat et al.; Toxins; 2020) haben wir die Populationsstruktur von S. aureus in Labormäusen bzw. Ratten unterschiedlicher Habitate (Labor, Wildnis) beschrieben und die Adaptation der Bakterien an diese Wirte dargestellt. Rund um den Globus sind Labormäuse mit S. aureus besiedelt. Einige murine Isolate gehörten zu klonalen Komplexen wie CC1, CC5, CC8 und CC15, die sich auch beim Menschen finden, sodass hier eine Übertragung vom Menschen auf die Maus wahrscheinlich ist. Dennoch zeigten viele der Isolate eindeutige Zeichen einer Wirtsadaptation. So waren humanspezifische Virulenzfaktoren seltener als bei humanen Referenzisolaten gleicher Linien vorhanden. 47 % der Isolate gehörten jedoch zum klonalen Komplex CC88, der selten beim Menschen ist. Diese Linie war in Vorarbeiten unserer Arbeitsgruppe bereits als murin-adaptiert identifiziert worden, was sich hier bestätigte.
Bei Laborratten zeigte sich ein ähnliches Bild. Auch hier wurden viele Stämme isoliert, die zu typisch humanen Linien (z.B. CC1, CC8, CC15) gehören, außerdem CC88-Isolate. Sie zeigten Zeichen einer Adaptation an Ratten. S. aureus-Isolate aus Wildratten und aus von Wildratten abstammenden Ratten in Gefangenschaft besaßen eine vollkommen andere Populationsstruktur. Hier fanden sich u.a. Linien (CC49, CC130, ST890), die wir in einer anderen Studie aus Wildmäusen isoliert haben. Auch sie wiesen die Zeichen einer Wirtsadaptation auf.
Diese Studien zeigen, dass die Besiedlung von Labormäusen und -ratten durch S. aureus weit verbreitet ist und vermutlich meist vom Menschen ausgeht. Dennoch weisen die Laborstämme Anzeichen einer Adaptation an die Nager auf, was eine längere Kontaktzeit voraussetzt, die diese evolutionären Vorgänge ermöglicht. Die Besiedlung der Labortiere hat zudem Folgen für die Konstitution des Immunsystems, da es auf dieses Bakterium geprimt wird. Weiterhin kann eine Besiedlung zu opportunistischen Infektionen führen. Folglich sollte bei Experimenten stets der S. aureus-Besiedlungsstatus erfasst werden, um einen etwaigen Einfluss auf die erzielten Ergebnisse ausschließen bzw. nachweisen zu können. Bei Wildnagern und ihren Verwandten weist S. aureus eine andere Populationsstruktur auf, welche über einen gewissen Zeitraum auch in Gefangenschaft stabil zu sein scheint. Wildtiere sind damit ein bedeutendes Reservoir und potentielle Überträger von S. aureus, aber ebenfalls eine Quelle neuer Stämme, die zu Forschungszwecken eingesetzt werden könnten.
In zwei weiteren Originalarbeiten (Trübe et al.; Int. J. Med. Microbiol.; 2019 und Fernandes et al.; Microorganisms; 2021) haben wir die Eignung verschiedener murin-adaptierter Stämme in Infektions- und Kolonisationsmodellen diskutiert. S. aureus-Isolate aus Wild- und Labormäusen wurden in BALB/c-Mäusen mit dem humanen Stamm Newman verglichen. Ein CC49-Isolat (S. aureus DIP), das aus Rötel- und Gelbhalsmäusen stammte, erwies sich als besonders virulent und provozierte selbst in einer im Vergleich mit dem Stamm Newman zehnfach geringeren Infektionsdosis vergleichbare Symptome und Immunreaktionen. Die geringere Infektionsdosis ist wahrscheinlich klinisch relevanter, da pathophysiologische Eigenschaften von S. aureus auch dichteabhängig reguliert werden (quorum sensing).
In einem Kolonisationsmodell mit dem murin-adaptierten Laborstamm JSNZ wurde die dekolonisierende Wirkung von Aurintricarbonsäure (ATA) evaluiert. ATA war zuvor in breit angelegten in vitro-Screenings als potenter Adhäsionsinhibitor identifiziert worden. C57BL/6-Mäuse wurden mit JSNZ kolonisiert und anschließend mit ATA behandelt. Leider war ATA im Mausmodell wirkungslos, während mit der in der Klinik eingesetzten Kontrollsubstanz Mupirocin eine vollständige Dekolonisation erreicht werden konnte. JSNZ bestätigte sich jedoch als persistierender Besiedler der Maus. Dieses Besiedlungsmodell ist daher sehr gut geeignet, um neue Agenzien für eine S. aureus-Dekolonisierung zu testen oder die Wirt-Pathogen-Interaktion bei der Kolonisation im Detail zu analysieren.
Die Ergebnisse dieser Arbeit zeigen, dass sich Mausmodelle besser für die Forschung an S. aureus eignen als bisher angenommen. Trotzdem muss die Übertragbarkeit der Ergebnisse auf den Menschen stets kritisch überprüft werden. Die Maus-adaptierten S. aureus-Stämme sind ein neues und potentes Werkzeug, die S. aureus-Forschung zu optimieren. Von besonderem Interesse ist die Möglichkeit, Mäuse persistent zu kolonisieren, wie dies typisch für die Interaktion von S. aureus mit seinem menschlichen Wirt ist. Diese wichtige Facette im Zusammenspiel zwischen dem Erreger und seinem Wirt wird nun erstmals der experimentellen Forschung zugänglich.
Pentathiepins are cyclic polysulfides that exert antiproliferative and cytotoxic activity in cancer cells, induce oxidative stress and apoptosis, and potently inhibit GPx1. These properties render this class of compounds promising candidates for the development of anticancer drugs. However, the biological effects and how they intertwine to promote high cytotoxicity have not been systematically assessed throughout a panel of cancer cell lines from distinct tissues of origin. In this thesis, six novel pentathiepins were analyzed and constitute the second generation of compounds with additional properties such as fluorescence or improved water solubility to facilitate cellular testing. All compounds underwent extensive biological evaluation in 14 human cancer cell lines. These studies included investigations of the inhibitory potential with regards to GPx1 and cell proliferation, examined the cytotoxicity in human cancer cell lines, as well as the induction of oxidative stress and DNA strand breaks. Furthermore, selected hallmarks of apoptosis, ferroptosis, and autophagy were studied. Experimental approaches regarding these cellular mechanisms included observing morphological changes, detecting phosphatidyl serine exposure and caspase activity, and quantifying cleaved PARP1 and levels of LC3B II. In addition, the analysis of the cell cycle aimed to identify aberrations or arrests in cell division.
Five of the six tested pentathiepins proved to be potent inhibitors of the GPx1, while all six exerted high cytotoxic and antiproliferative activity, although to different extents. There was a clear connection observed between the potential to provoke oxidative stress and damage to DNA in the form of single- and double-strand breaks both extra- and intracellularly. Furthermore, various experiments supported apoptosis but not ferroptosis as the mechanism of cell death in four different cell lines. In particular, the externalization of PS, the detection of activated caspases, and the cleavage of PARP1 corroborated this conclusion. Additionally, indications for autophagy were found, but more investigations are required to verify the current data. The findings of this dissertation are mainly in line with the postulated mechanism of action proposed for pentathiepins and a previous publication from our group that described their biological activity. However, the influence of modulators such as oxygen and GSH on the biological effects was ambiguous and dependent on the compound. The expression profile of the cell lines concerning GPx1 and CAT did not influence the cellular response toward the treatment, whereas the cell doubling time correlated with the cytotoxicity.
As the various pentathiepins give rise to different biological responses, modulation of the biological effects depends on the distinct chemical structures fused to the sulfur ring. This may allow for future optimization of the anticancer activity of pentathiepins. An analysis of the structure-activity relationships revealed that the piperazine scaffold was associated with superior biological activity compared to the pyrrolo-pyrazine backbone. Furthermore, substituents with electron-withdrawing properties or those providing a free electron pair, such as fluorine or morpholine, were advantageous. These findings should help design and synthesize the next generation of pentathiepins, thereby expanding the library of compounds, allowing for the further deduction of structure-activity relationships and an improved understanding of their mechanism of action.
VER155008 konkurriert als ATP-Analogon um die Bindung an HSP70 und agiert hierbei als
spezifischer Inhibitor dieses Hitzeschockproteins. Bisherige Studien konnten einen
zytotoxischen Effekt von VER155008 auf verschiedene Tumorentitäten zeigen, die
vielfältigen Wirkmechanismen bleiben bisher allerdings noch weitgehend ungeklärt.
Hitzeschockproteine (HSPs) sind molekulare Chaperone, sie vermitteln korrekte Faltung,
Stabilisierung, Transport und Abbau von Proteinen, regulieren Transkriptionsfaktoren und
können auf Zellsignalkaskaden Einfluss nehmen. Diverse Tumorentitäten, wie auch das
Prostatakarzinom (PCa) zeigen eine gesteigerte HSP-Expression. HSPs tragen durch
antiapoptotische Effekte zur Proliferation, Invasion und Metastasierung des Tumors bei und
können Resistenzmechanismen gegenüber Therapeutika im PCa vermitteln.
Diese Arbeit konnte zunächst einen wachstumshemmenden, konzentrationsabhängigen
Effekt des HSP70-Inhibitors VER155008 auf die PCa-Zelllinien PC-3 und LNCaP nachweisen.
Geeignete Wirkstoffkonzentrationen, um einen halbmaximalen inhibitorischen Effekt (IC50)
zu erzielen wurden in PC-3-Zellen bei 3μM und LNCaP-Zellen bei 10μM VER155008 ermittelt.
Anschließende Proteinanalysen zeigten eine Modulation der Expression verschiedener HSPs,
sowie des Androgenrezeptors (AR), einem zentralen Proliferationsfaktor des PCa, als
Reaktion auf die HSP70-Inhibition. Untersucht wurde die Expression von HSP27, HSP70,
HSP90α/ß, sowie der Co-Chaperone HSP40, HSP60 und HOP und des AR. Die Expression von
HSP90ß, dem Bindungspartner des AR im AR-Multi-Chaperonkomplex, sowie HOP, seinem
Co-Chaperon, wurde in beiden PCa-Zelllinien um bis zu 50% signifikant supprimiert.
Zusätzlich zeigt sich eine um bis zu 70% supprimierte Expression von HSP27 nach
VER155008-Behandlung beider PCa-Zelllinien im Vergleich zur Kontrolle. HSP27 ist ein
wichtiges zytoprotektives Chaperon, dessen vermehrte Expression mit Therapieresistenzen
gegenüber Docetaxel, sowie einer schlechten Prognose des PCa assoziiert wird. Es vermittelt
die Translokation des AR in den Zellkern und reguliert dadurch die proliferative Wirkung der
AR-Aktivierung. Die HSP70-Inhibierung zeigte zusätzlich eine signifikante Reduktion des AR
um 40% in LNCaP-Zellen.
VER155008 zeigt sich als effektiver Wachstumsinhibitor des Prostatakarzinoms, der sowohl
in der hormonsensitiven LNCaP-, als auch in der kastrationsresistenten PC-3-Zelllinie
antiproliferative Wirkung zeigt, die unter anderem durch eine Modulation der Expression
von Hitzeschockproteinen und des Androgenrezeptors vermittelt wird.
Die Pankreatitis ist gekennzeichnet durch den Selbstverdau des Organs. Dabei werden pankreatische Proteasen aktiviert und es entstehen lokale Entzündungsherde. Diese aktivieren die Immunantwort durch Ausschüttung pro- inflammatorischer Mediatoren und der Rekrutierung von Immunzellen in das geschädigte Gewebe. Als erste Schutzinstanz reagiert das angeborene Immunsystem inklusive der Neutrophilen, Granulozyten und Makrophagen. Es ist bekannt, dass diese Immunzellen Mustererkennungsrezeptoren nutzen, um die Infektion zu erkennen. Zu diesen gehören die Toll-like Rezeptoren, welche u.a. über den MyD88/IRAK Signalweg den Transkriptionsfaktor NF-κB aktivieren können. In dieser Signalkaskade existiert ein negativer Feedback Regulator IRAK-M, auch bekannt als IRAK-3. Dieser ist in der Lage die Signalweiterleitung zu inhibieren. In dieser Arbeit wurde untersucht ob und inwieweit IRAK-M Einfluss auf den Verlauf einer experimentell induzierten Pankreatitis in Mäusen hat. Bisherige Studien zeigten die Expression von IRAK-M in verschiedenen Zelltypen und Geweben, jedoch nicht im Pankreas sowie den Azinuszellen. In dieser Arbeit konnte nachgewiesen werden, dass IRAK-M in Pankreasgewebe sowie isolierten Azini von C57BL/6 Mäusen exprimiert wird. Die Stimulation von isolierten C57BL/6-Azinuszellen mit CCK hatte eine Expressionserhöhung von IRAK-M zur Folge. Es konnte zudem gezeigt werden, dass Toll-like Rezeptoren (TLR), insbesondere 2, 3, 4 und 9, in bzw. auf Azini exprimiert werden. Die TLR1, 2, 3, 7 und 9 zeigten ein höheres Expressionslevel in den Azinuszellen der defizienten Tiere. Die Caerulein induzierte akute Pankreatitis zeigte einen milderen Verlauf in Bezug auf die Schweregradmarker Amylase und Lipase im Serum der IRAK-M -/- Tiere sowie einen geringen lokalen pankreatischen Schaden. Die Entzündungsreaktion erhöhte die MPO-Aktivität in der Lunge der defizienten Tiere. Zudem zeigten die Tiere eine erhöhte T-Zellaktivierung und Sekretion pro-inflammatorischer Zytokine wie TNFα und IL12 sowie des anti-inflammatorischen Zytokins IL10. Tendenziell wanderten mehr Neutrophile, M1- sowie M2- Makrophagen in das Pankreasgewebe während der Entzündung. Der Transkriptionsfaktor NF-κB konnte nach 8h akuter Pankreatitis, transloziert im Zellerkern, vermehrt in den IRAK-M defizienten Tieren nachgewiesen werden. Die Untersuchung von IRAK-M -/- BMDM zeigte, dass das Zytokin Milieu zur Differenzierung des M1 -Phänotyps dominierend war. Zudem lag eine verstärkte Phagozytose vor und die Makrophagen wiesen eine verstärkte Sekretion und Expression von TNFα, IL6, IL10 und IL12 auf. Nach 3d schwerer akuter Pankreatitis (SAP) wurde eine höhere Konzentration an Serumlipase sowie ein stärkerer pankreatischer Schaden beobachtet. Die MPO-Aktivität in der Lunge der defizienten Tiere war vermindert. Dennoch konnten vermehrt pro-inflammatorische Zytokine wie TNFα, IL6, IL12 und MCP1 im Serum gemessen werden. Die T-Zellen der defizienten Tiere zeigten zudem eine erhöhte Aktivierung. Die Visualisierung von infiltrierten Zellen im Pankreas zeigte keine Unterschiede. Der Vergleich der beiden experimentellen Pankreatitis-Modelle zeigte, dass die Caerulein induzierte Pankreatitis bei den IRAK-M -/- Tieren zu einer lokal begrenzten Entzündung im Pankreas führte. Wohingegen die Pankreatitis nach Gangligatur einen deutlich stärkeren Schaden aufwies und in einer signifikant erhöhten Zytokinsekretion resultierte. Der Vergleich von IL6 zeigte, dass die defizienten Tieren das 14-fache ins Serum sekretieren nach SAP, während die Kontrolltiere nur einen Anstieg um das 4,5- fache zeigten. Somit lässt sich zusammenfassen, dass eine kontrollierte und in Maßen ablaufende Immunantwort protektiv bzw. förderlich für den Krankheitsverlauf ist. Andererseits kann eine überschießende Immunantwort zu systemischen Komplikationen sowie Multiorganversagen führen. IRAK-M nimmt dabei eine regulierende Rolle ein und verhindert u.a., dass die Immunreaktion überschießt.
In Germany, around 5.7 million people suffer from osteoporosis. Osteoporosis is characterised by a reduced bone mineral density that leads to an increased risk of fractures. The 11β-hydroxysteroid dehydrogenase 1 (11β-HSD1) is an important regulator of local cortisol metabolism. It converts biologically inactive cortisone to biologically active cortisol, but can also catalyse the reverse reaction. 11β-HSD1 is strongly expressed in liver, but 11β-HSD1 expression and activity were also reported in bone. Moreover, polymorphisms in intron 5 of HSD11B1 (the gene encoding for 11β-HSD1) are associated with bone mineral density (BMD) and risk of fractures.
This work aimed to confirm and refine the associations between polymorphisms in intron 5 of HSD11B1 and BMD, and to identify the underlying molecular and cellular mechanisms. To this end, analyses were performed on three different levels:
i) studies in humans, to confirm and refine the association of polymorphisms in intron 5 of HSD11B1 with BMD, suppressed cortisol levels (PDC) and stiffness index,
ii) cellular analyses, to identify the role of 11β-HSD1 in differentiation of the immortalised human mesenchymal stem cell line SCP-1,
iii) molecular genetic analyses, to reveal the effect of intron 5 polymorphisms on transcriptional regulation.
Fine-mapping analyses of already existing clinical data from 452 osteoporosis patients (HSD study) did not point to another intron 5 SNP as being causative for the observed clinical association. A second prospective clinical study (OsteoGene) was performed to confirm the association of rs11811440 and rs932335 with PDC levels and BMD. A trend to decreased PDC levels and increased BMD was observed in homozygous carriers of the minor A-allele of rs11811440 in patients above the age of 65 years. Pooled analyses of the HSD and the OsteoGene studies revealed a significant association of the minor A-allele with increased Z-scores of the left femoral neck. No associations of rs11811440 and rs932335 with stiffness index, BMI and fat depots were detected the general population using data from the SHIP study.
To analyse the effect of 11β-HSD1 on differentiation of mesenchymal stem cells, HSD11B1 overexpressing and HSD11B1 knockout SCP-1 cells were generated. HSD11B1 was stably overexpressed in SCP-1 cells using targeted chromosomal integration. The successful overexpression was shown by 243-fold increased HSD11B1 mRNA expression levels and a 9 fold increased 11β-HSD1 activity, compared to the wildtype cells. Knockout cells were generated by CRISPR-Cas9 mediated gene editing targeting exon 2 and exon 5 of HSD11B1. Using next generation sequencing, the clones 1C4 and 2D10 were confirmed to carry two inactive HSD11B1 alleles and were chosen for further analyses. mRNA expression was unchanged in both knockout clones. However, a clear enzyme activity was detected in the 2D10 clone, whereas no cortisol production was detected in the 1C4 clone. SNaPshot analyses revealed the presence of wildtype cells in the 2D10 clone that became predominant with increased passages. Therefore, further analyses were focused on the 1C4 clone only. The protein expression in the 1C4 clone decreased to 30% of the expression of the wildtype cells.
HSD11B1 expression and cortisol production were compared between wildtype, knockout and overexpressing SCP-1 cells under three differentiation conditions: adipogenic, osteogenic with 1α,25-dihydroxyvitamin D3 and osteogenic with dexamethasone. HSD11B1 expression increased upon adipogenic differentiation and in the presence of cortisone in the wildtype and the overexpressing, but not in the knockout cells. Also, the cortisol production from cortisone increased over time in the overexpressing and the wildtype cells, but not in the knockout cells. The increase was dependent on the differentiation used between 3-fold and 9-fold higher in the overexpressing than in the wildtype cells.
The generated and validated overexpressing and knockout cell lines were used to analyse the influence of 11β-HSD1 on adipogenic and osteogenic differentiation. Upon adipogenic differentiation, the overexpressing cells accumulated significantly more lipid droplets than the wildtype cells. The accumulation of lipid droplets was not abolished in the knockout. However, when dexamethasone was substituted by cortisone, the knockout cells accumulated less lipid droplets than in the presence of dexamethasone, supporting the involvement of 11β-HSD1 in adipogenic differentiation. Expression of the adipogenic markers FABP4 and LPL increased upon adipogenic differentiation, but a distinct influence of the presence or absence of HSD11B1 on the FABP4 and LPL expression was not detected. Upon osteogenic differentiation with 1α,25-dihydroxyvitamin D3, ALP activity increased only in the knockout cells (more than 5-fold). Accordingly, the strongest increase in ALPL expression was detected also in the knockout cells. Both, ALP activity and gene expression were independent of cortisone. Addtionally, BGLAP expression was increased upon osteogenic differentiation. Unexpectedly, in the presence of cortisone, BGLAP expression increased in the overexpressing cells. Expression of the Wnt inhibitor DKK1 also increased in the overexpressing cells in the presence of cortisone indicating a decreased osteogenic differentiation. Moreover, expression of the adipogenic markers FABP4 and LPL increased in the overexpressing cells in the presence of cortisone indicating a switch from osteogenic to adipogenic differentiation. Upon osteogenic differentiation with dexamethasone, ALP activity and matrix mineralisation was lowest in the overexpressing cells.
Finally, the effects of the SNPs rs11811440, rs11119328, rs1000283 and rs932335 in intron 5 of HSD11B1 on transcriptional regulation were analysed by reporter gene assays and electrophoretic mobility shift assays. All four SNPs are genetically linked and are localized within evolutionary conserved regions. The minor C-allele of rs932335 significantly increased luciferase activity. In contrast, the major G-allele of rs932335 showed strong protein binding. However, no transcription factor binding sites were identified at the SNP sites. Additionally, bioinformatics analyses of publicly available RNA-Seq data of adipose tissue and liver confirmed the absence of alternative splicing. Alignment of HSD11B1 intron 5 to the Rfam database predicted the presence of non-coding RNAs (ncRNAs) in intron 5. However, none of the ncRNAs overlapped with the SNP sites.
In conclusion, 11β-HSD1 was shown to be involved in adipogenic differentiation and peripheral cortisol production by 11β-HSD1 promotes a switch from osteogenic to adipogenic differentiation. Moreover, among osteoporosis patients, homozygous carriers of the minor A-allele of rs11811440 have increased Z-scores of the femoral neck. Furthermore, HSD11B1 knockout and overexpressing cell lines were successfully generated and validated. These cell lines could be a useful tool in future analyses of the role of peripheral cortisol activation by 11β-HSD1 in differentiation of mesenchymal stem cells.
Under the influence of human activities, increased climate variability induces changes in
multiple marine environments. Especially vulnerable are the coastal ecosystems where organisms
must cope with constant extreme changes of environmental drivers, such as temperature, salinity, pH,
and oxygen content. In coastal areas, brachyuran crabs are important animals that have a high impact
on ecosystem functioning and serve as a link in food webs and pelagic-benthic coupling. Larval stages
of crabs are crucial for population persistence and dispersal. They are generally more vulnerable to
changes of environmental drivers and failure to adapt to new conditions may result in population
collapse. To analyse the effects of multiple environmental drivers on larval performance and to
elucidate interspecific and intraspecific difference, this project examined larval performance in the
European shore crab Carcinus maenas. In this study, larvae of C. maenas from three native
populations (Cádiz: Cádiz Bay, Helgoland: North Sea, Kerteminde: Baltic Sea) were reared in a
factorial design consisting of different temperature (15-24 °C) and salinity treatments (20, 25, 32.5
PSU). Results demonstrated how descriptors of larval performance (growth, physiological, and
developmental rates, and survival) were affected by combined environmental drivers. Larval
responses to temperature and salinity showed contrasting patterns and differed among native
populations originating from distant or contrasting habitats, as well as within the populations. The
highest overall performance was recorded in the Cádiz population, while the Kerteminde population
had the lowest performance in most of tested traits. The interactive effects of multiple drivers differed
among the populations. In the Cádiz and Helgoland populations, higher temperatures mitigated the
effect of lower salinity while the Kerteminde population showed a maladaptive response when
exposed to lower salinity. Differences in performance showed better locally adapted populations (e.g.
Cádiz) that could acclimate faster, have better adaptive mechanisms or stronger dispersive abilities.
Because of their wider tolerance to increased temperature and decreased salinity, interactive effects
in particular populations may favour some populations in a changing climate, especially in coastal
habitats. Variation in larval performance showed complex interactions in larval performance and
highlighted the necessity to quantify inter-population responses to climate-driven environmental
change where responses of species should not be generalised. This study emphasizes the need for
inclusion of multiple traits, drivers, and populations in experimental studies to properly characterize
performance of marine coastal animals.
In vitro and in vivo analyses of mono- and mixed-species biofilms formed by microbial pathogens
(2022)
Microbial biofilms can be defined as multicellular clusters of microorganisms embedded in a self-produced extracellular matrix (ECM), which is primarily composed of polymeric biomolecules. Biofilms represent one of the most severe burdens in both industry and healthcare worldwide, causing billions of dollars of treatment costs annually because biofilms are inherently difficult to prevent, treat, and eradicate. In health care settings, patients suffering from cystic fibrosis, or patients with medical implants are highly susceptible to biofilm infections. Once a biofilm is formed, it is almost impossible to quantitatively eradicate it by mechanical, enzymatical, chemical, or antimicrobial treatment. Often the only remaining option to fully eradicate the biofilm is removing of the infected implant or body part. The primary reasons for the inherent resistance of biofilms against all forms of antimicrobial treatment are (I) a reduced metabolic activity of biofilm-embedded cells climaxing in the presence of metabolic inactive persister cells, as well as (II) the protective nature of the biofilm matrix acting as a (diffusion) barrier against antimicrobials and the host immune system. Consequently, there is an urgent need to better understand microbial biofilms from a structural and (patho-) physiological point of view in order to be able to develop new treatment strategies.
Therefore, the aims of this study were to investigate fundamental physiological properties of different clinically relevant single and multi-species biofilms, both in vitro and in vivo. Furthermore, the effectiveness of a novel treatment strategy using cold atmospheric pressure plasma was evaluated in vitro to treat biofilms of the pathogenic fungus C. albicans.
In article I, the intracellular and ECM protein inventory of Staphylococcus aureus during in vitro biofilm growth in a flow reactor was analyzed by liquid-chromatography coupled to tandem mass-spectrometry (LC-MS/MS) analysis combined with metabolic footprint analysis. This analysis showed that anaerobiosis within biofilms releases organic acids lowering the ECM pH. This, in turn, leads to protonation of alkaline proteins – mostly ribosomal proteins originating from cell lysis as well as actively secreted virulence factors – resulting in a positive net charge of these proteins. As a consequence, these proteins accumulate within the ECM and form an electrostatic network with negatively charged cell surfaces, eDNA, and metabolites contributing to the overall biofilm stability.
In article II, the in vivo metaproteome of the multi-species biofilm community in cystic fibrosis sputum was investigated. To this end, an innovative protocol was developed allowing the enrichment of microbial cells, the extraction of proteins from a small amount of cystic fibrosis sputum, and subsequent metaproteome analysis. This protocol also allows 16S sequencing, metabolic footprint analysis, and microscopy of the same sample to complement the metaproteome data. Applying this protocol, we were able to significantly enhance microbial protein coverage providing first insights into important physiological pathways during CF lung infection. A key finding was that the arginine deaminase pathway as well as microbial proteases play a so far underappreciated role in CF pathophysiology.
In articles III and IV, a novel treatment strategy for biofilms formed by the important fungal pathogen Candida albicans was evaluated in vitro. Biofilms were treated with two different sources of nonthermal plasma (with the Nonthermal Plasma Jet “kINPen09” as well as with the Microwave-induced plasma torch “MiniMIP”) and the effect on growth, survival, and viability was assessed by counting colony-forming units (CFU), by cell proliferation assays, as well as by live/dead staining combined with fluorescence microscopy, confocal laser scanning microscopy, (CLSM) and atomic force microscopy (AFM). These tests revealed that biofilms were effectively inactivated mostly on the bottom side of biofilms, indicating a great potential of these two plasma sources to fight biofilms.
American and European foulbrood (AFB and EFB) are devastating bacterial brood diseases of honey bees (Apis mellifera), which cause colony and economic losses worldwide. The causative agent of AFB, Paenibacillus larvae, are grouped into different ERIC-genotypes (Enterobacterial repetitive intergenic consensus) the two most common of which are ERIC I and ERIC II. In the field, the differentiation between the symptoms of AFB and EFB (caused by Melissococcus plutonius) can be difficult. The differentiation between the ERIC-genotypes in the field based on the symptoms is not possible at all. The differentiation between the ERIC-genotypes of P. larvae during diagnosis can help to understand the spread of the AFB disease. Hence, a tool capable of detection and distinction between the bacterial brood diseases and the P. larvae-genotypes is needed. For the optimal prevention of disease spread, the diagnosis needs to be fast, cheap and reliable.
This study focuses on the development of a diagnostic sandwich ELISA and a lateral flow device (LFD) for the detection and distinction of EFB and AFB, including the differentiation of the two main occurring P. larvae genotypes. The therefore necessary specific monoclonal antibodies (mAbs) were obtained by immunizing mice with M. plutonius or P. larvae strains belonging to either ERC I or ERIC II. The generated mAbs were characterized for their specificity towards the target bacteria and for their cross reactivity towards other bee-associated bacteria. The screening for suitable mAbs resulted in two specific mAbs against M. plutonius, two against P. larvae in general and two against ERIC II. In combination with the anti-P. larvae mAbs, the anti-ERIC II mAbs were used for genotyping.
In order to evaluate the suitability of the mAbs, their antigens were identified. The target antigens of the produced mAbs turned out to be proteins that could be of further interest as they seem to be involved in the pathogenesis and host-pathogen-interaction. The mAbs with the same antigens were used in the sandwich ELISA for testing the cross reactivity and strain detection. Suitable mAb combinations were used for LFD production. The LFDs were then successfully tested against several field isolates of AFB and EFB causing agents and no cross reactivity with bee-associated bacteria was detected. The P. larvae strains used for mAb testing were genotyped to obtain information about the respective genetic variance. In the process atypical P. larvae strains were identified and further characterized using the generated mAbs. The ability of the mAbs to also recognise the atypical strains as well indicates that the mAbs bind to an antigen that is common among different P. larvae strains.
All in all, a fast tool for detection and differentiation of EFB, AFB and the two ERIC-genotypes was developed that has to be further tested for its reliability in the field.
Gram-negative bacteria are known to naturally produce outer membrane vesicles (OMVs), which are closed nanoparticles (10 to 450 nm) containing virulence factors and pathogen associated molecular patterns (PAMPs). For over 20 years, OMVs of Neisseria meningitidis (N. meningitidis), in combination with three purified outer membrane proteins, have been successfully used as parts of human vaccines which illustrates the safety and potential of OMV based vaccines. So far only little is known about the OMVs of fish pathogenic bacteria. The production of OMVs has been described for the fish pathogenic gram-negative bacterium Aeromonas salmonicida (A. salmonicida) which is the causative agent of furunculosis resulting in high morbidity and mortality of salmonid fish. The immunostimulatory potential of OMVs derived from A. salmonicida as well as the possibility of establishing an oral vaccine model in Oncorhynchus mykiss (O.mykiss) (Rainbow trout) has been investigated in this study by conducting in vitro and in vivo experiments. Innate immune cells such as macrophages are one of the first cells to respond to pathogens once they breach the skin barrier, therefore the monocyte/macrophage cell line RTS-11 as well as leukocytes from the head kidney, consisting of a high percentage of phagocytic cells have been investigated. Additionally, leukocytes isolated from the peritoneal cavity as the main target for injectable vaccines have been studied in the in vitro experiments. These experiments indicate that OMVs derived from A. salmonicida are recognized by the monocyte/macrophage cell line RTS-11 as well as by leukocytes from the head kidney resulting in significant changes of the mRNA expression pattern of early inflammatory markers (IL-1β, IL-6, IL-8, IL-10, TGFβ). Having used the established peritoneal inflammation model of rainbow trout it could be shown that intraperitoneal (i.p.) vaccination of rainbow trout with OMVs results in a similar local immune response, especially in the recruitment of myeloid cells, compared to the injection of inactivated bacteria. The systemic cellular immune response differed between the two vaccine groups, even though a similar humoral immune response could be observed. Interestingly, i.p.vaccination with 10 µg of OMVs resulted in similar antibody titers as observed for fish, that were i.p. vaccinated with 108 CFU of inactivated A. salmonicida. The similar antibody titers after vaccination with OMVs might be explained by a stronger activation of CD8- T cells (likely CD4+ T cells) in the head kidney as well as in the blood in the OMV vaccinated group alone, which might result in an increased stimulation of B cells to produce antibodies.
Oral vaccination has been described as the ideal vaccination method for fish, but only few vaccines for oral application are licensed. Therefore, the established oral model for vaccination of rainbow trout with attenuated viral hemorrhagic septicemia virus (VHSV) was adapted to be used for inactivated A. salmonicida, even though initial trials indicated great similarities in the cellular response after i.p. and oral vaccination with inactivated strains of A. salmonicida, particularly in the response of the myeloid cells and lymphocytes in the target organs as well as the thrombocytes in the spleen. This could not be confirmed in a second oral vaccination trial. These results show how challenging the development of oral vaccines for fish is. The main challenge is the reproducibility of reliable results, since this is influenced by the difference in uptake of vaccine pellets or antigen degradation in the gut. Future oral vaccine trials should investigate different vaccination regimes, e.g., consecutive feeding, or a different composition of vaccine pellets, in order to further investigate the possibility of establishing an oral vaccine model for trout and so that future vaccine candidates, like OMVs, can be reliably tested in fish.
Infectious diseases remain a significant threat to the wellbeing of humans and animals
worldwide. Thus, infectious disease outbreaks should be investigated to understand the
emergence of these pathogens, leading to prevention and mitigation strategies for future
outbreaks. High-throughput sequencing (HTS) and bioinformatic analysis tools are reshaping
the surveillance of viral infectious diseases through genome-based outbreak investigations. In
particular, analyzing generic HTS datasets using a metagenomic analysis pipeline enable
simultaneous identification, characterization, and discovery of pathogens.
In this thesis, generic HTS datasets derived from the 2018-19 WNV epidemic and USUV
epizooty in Germany were evaluated using a unified pipeline for outbreak investigation and an
early warning system (EWS). This pipeline obtained 34 West Nile virus (WNV) whole-genome
sequences and detected several sequences of Usutu virus (USUV) and other potential
pathogens. A few WNV and USUV genome sequences were completed using targeted HTS
approaches. Phylogenetic and phylogeographic inferences, reconstructed using WNV wholegenome sequences, revealed that Germany experienced at least six WNV introduction events.
The majority of WNV German variants clustered into the so-called “Eastern German clade
(EGC),” consisting of variants derived from birds, mosquitoes, a horse, and human cases. The
progenitors of the EGC subclade probably circulated within Eastern Europe around 2011. These
flavivirus genome sequences also provided substantial evidence for the first reported cases of
WNV and USUV co-infection in birds. Phylogenetic inferences of USUV genome sequences
showed the further spread of the USUV lineage Africa 3 and might indicate the overwintering
of the USUV lineage Europe 2 in Germany. Among viral sequences reported in the EWS, Hedwig
virus (HEDV; a novel peribunyavirus) and Umatilla virus (UMAV; detected in Europe for the
first time) were investigated using genome characterization, molecular-based screening, and
virus cultivation since these viruses were suspected of causing co-infections in WNV-infected
birds. The EWS detected overall 8 HEDV-positive and 15 UMAV-positive birds in small sets of
samples, and UMAV could be propagated in a mosquito cell culture Future studies are necessary
to investigate the pathogenicity of these viruses and their role in the health of wild and captive
birds.
In conclusion, this study provided a proof-of-concept that the developed unified and
generic pipeline is an effective tool for outbreak investigation and pathogen discovery using the
same generic HTS datasets derived from outbreak and surveillance samples. Therefore, this
thesis recommends incorporating the unified pipeline in the key response to viral outbreaks to
enhance outbreak preparedness and response.