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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.