Abteilung für Mikrobiologie und Molekularbiologie
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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.
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.
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.
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.