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Next Generation Sequencing (NGS)-technologies developed very fast in recent years and is used widely in current research areas. The aim of this study was to use NGS (i) for the identification of pathogens in outbreaks and (ii) for the identification of virulence-relevant sequencepolymorphisms when comparing whole genome sequences. Therefore, a previous developed workflow was used to identify a new virus of the family Bornaviridae. The generation of whole genome sequences elucidated the molecular epidemiological connection of infection of variegated squirrels (Sciurus variegatoides) and three human cases of fatal encephalitis. By generating the whole genome sequence of a Porcine Epidemic Diarrhea Virus (PEDV) in Germany it was possible to find difference compared to circulating high virulent strains in the USA. This led to potential virulence marker to distinguish strain in the USA and Germany. Connections between sequence variation and virulence were further investigated for the bovine viral diarrhea virus 2c (BVDV-2c), cowpox viruses (CPXV) and classical swine fever virus (CSFV). Here, for a highly virulent BVDV-2c strain a mixture of different genome structure variants could be found. The majority of these genomes harbors a duplication within the p7/NS2 coding region and might cause a high virulence. For CPXV virus isolated of different hosts were analyzed and a correlation between genome sequence and the A-type inclusion body phenotype could be found. Furthermore, several deletion/insertion events were detected which might influence the virulence of these strains. Finally, the virus population of CSFV strains in pigs was characterized. However, the population of the inoculum as well as of acute-lethal and chronically infected animals gave no indication that the virus itself causes the different types of disease outcome. In conclusion, this thesis shows the great potential of NGS for virus identification and characterization. Furthermore, it makes the identification of potential virulence marker possible which subsequently can be analyzed by reverse genetics.
A method employing labeling of cell-surface proteins with Sulfo-NHS-SS-biotin and subsequent affinity enrichment with NeutrAvidin has been optimized in order to make cell-surface proteins from Gram-positive bacteria reliably accessible to quantitative mass spectrometric analyses. The optimized biotinylation approach was applied for analysis of the lipoproteome from S. aureus and S. pneumoniae on a global scale and the influence of mutations in the lipoprotein maturation pathway on the cell-surface and exoproteomes of both species was investigated. The biotinylation approach was integrated into a proteomic workflow that employs metabolic labeling with heavy nitrogen for relative protein quantification to investigate proteomic differences between S. aureus in a biofilm model and its free-floating, planktonic counterparts.
Microbial infections can be either caused by a single species or complex multi-species consortia. One of the most prominent opportunistic human pathogens leading to mono- or mixed-species infections is the Gram-negative bacterium Pseudomonas aeruginosa. Understanding the molecular basis of its adaptation to infection-related stresses is an essential prerequisite for the prevention and treatment of P. aeruginosa infections. We therefore employed state-of-the-art proteomics approaches to elucidate the molecular adaptation mechanisms of P. aeruginosa to infection-related conditions. Moreover, structure, function and interaction of complex microbial consortia containing P. aeruginosa and causing catheter-associated urinary tract infections were investigated by metaproteomics analyses. Our investigations revealed that the adaptation of P. aeruginosa during infection is either based on gene expression changes caused by environmental signal integration or by gene mutations leading to a selective advantage in a particular host environment. In study I, investigating the proteome response of P. aeruginosa biofilms to the clinical relevant antibiotic ciprofloxacin, global changes in the protein profile were observed. Ciprofloxacin induced the expression of proteins involved in the Lex-induced SOS-response, drug efflux pumps and gene products of the ciprofloxacin-responsive prophage cluster and repressed the expression of porins and DNA-binding proteins. In study II the transcriptome and proteome of two clonal P. aeruginosa lineages during long-term colonization of cystic fibrosis (CF) patient’s lungs were analyzed. Point mutations in global regulator genes, i.e. retS, gacS, and gacA, were identified by genomic sequencing. Inactivation of RetS, found two years after the initial colonization, induced the expression of genes involved in chronic infections and coding for the type 6-secretion system (T6SS). Additional mutations in the GacS/GacA two-component regulatory system (TCS) were found to repress the expression of T6SS proteins and to induce the expression of proteins belonging to the type 3-secretion system (T3SS). In study III we elucidated the niche-specific adaptation of P. aeruginosa isolates from different infection sites by investigating their protein expression patterns and glucose metabolic fluxes. We could show that isolates from the urinary tract express a higher amount of proteins involved in the acquisition of micronutrients (i.e. iron) and carbohydrates compared to isolates from the CF lung. In study IV 16S rDNA sequencing and metaproteomics were employed to demonstrate that the investigated CAUTI-related biofilms consisted of two to five different species with one or two species dominating the mixed community. Following this line of research, we investigated in study V structure and function of a biofilm of a long-term catheterized patient, which was predominantly composed of P. aeruginosa and Morganella morganii, but also contained a minor proportion of the obligate anaerobe Bacteroides sp.. The comparison of in vivo and in vitro protein expression profiles of P. aeruginosa and M. morganii indicated that iron and carbohydrates are the major growth-limiting factors in the bladder. These results indicate different nutritional strategies of the two pathogens in the bladder environment. A comparison of urinary protein profiles of healthy persons and catheterized patients suggested that the human innate immune system is induced by CAUTIs. Moreover, numerous proteins involved in nutritional immunity, e.g. iron-, calcium- and magnesium-binding proteins, were found to be more abundant in the urine of catheterized patients. A follow-up (meta)proteomics study (study VI) aiming at the elucidation of interspecies interactions during multi-species infections indicated that the urease-positive uropathogen Proteus mirabilis induces the precipitation of metal ions by urine alkalization and thereby limits the availability of these important micronutrients for other co-infecting bacteria. This limitation seems to be sensed by the P. aeruginosa PhoP-PhoQ two-component system (TCS) leading to an increased resistance to antimicrobial peptides and biofilm-forming capacity of the pathogen. Also during co-cultivation of P. aeruginosa with Staphylococcus aureus a slight increase in the expression of the PhoP-PhoQ TCS and the alkaline protease could be observed (study VII). In study VIII a combined metagenomics and metaproteomics approach was employed to investigate structure and function of the lichen Lobaria pulmonaria, a complex consortium consisting of a fungus, an algal partner, cyanobacteria, and a highly diverse bacterial microbiome. The results presented in this work contribute to a better understanding of the manifold and complex bacterial adaptation mechanisms to infection-related and environmental stress and thereby foster the development of novel treatment and prevention strategies.
This work focuses the glycoprotein H of PrV which was analysed by structure-based functional analyses by targeted site-directed mutagenesis. Disulfid bridges were introduced at specific sites and the effects on the fusion mechanism investigated. A revertant was obtained and characterised during the studies, as well as chimeric glycoprotein H proteins were constructed, combining the different domains of the glycoproteins Hs of PrV and HSV1.
The immune system of all vertebrates primarily is responsible to maintain the organisms homeostasis by either eliminating neoplastic or altered body cells and to protect against foreign invaders (viruses, bacteria, fungi, parasites) (Murphy 2012). It is a highly regulated network of innate and adaptive mechanisms between humoral factors and leukocytes. The successful elimination or protection is crucially based on differentiation of self from non-self. Pathogens and altered body cells are recognized by different receptor complexes on immune cells. Expressed pathogen- or danger-associated molecular patterns (PAMPs or DAMPs, respectively) are bound by pattern recognition receptors (PRR) (Takeuchi and Akira 2010). Missing major histocompatibility (MHC) class I molecules or non-self (e.g. allogeneic or xenogeneic cells) MHC are recognized by natural killer cell receptors (Fischer, Koppang and Nakanishi 2013, Raulet 2006). Foreign non-self peptides are presented through MHC class I (intracellular) or through MHC class II (extracellular) to B- cell or T cell receptor complexes. This initial activation is regulated by humoral factors or cellular interactions (receptor-ligand interactions) resulting in the activation, proliferation and effector function within an immune response. Some of the cellular receptors are permanently expressed on all leukocytes on a high level (MHC class I), whereas others only are expressed during certain developmental or activation stages or on certain leukocyte populations (monocytes, granulocytes, NK cells, lymphocytes) (Murphy 2012, Biosciences 2010). For different mammals (man, mouse, rat, but also swine, cattle, dog), a system of characterized leukocyte surface molecules primarily based on the recognition of these molecules by specific monoclonal antibodies (mabs) was summarized at international workshops as clusters of differentiation (CD) (Cobbold and Metcalfe 1994, Hopkins, Ross and Dutia 1993, Haverson et al. 2001, Mason et al. 2001). Using these mabs, it is not only possible to characterize the developmental and functional stage of different leukocyte subpopulations but also to define the interactions between these populations. For bony fish, such a system does not exist. Only a limited number of mabs against leukocyte surface molecules is available and most of them are strongly specific for species (Köllner et al. 2004, Köllner et al. 2001, Zhang et al. 2010, Ramirez-Gomez et al. 2012, Wen et al. 2011, DeLuca, Wilson and Warr 1983, Toda et al. 2011, Toda et al. 2009, Takizawa et al. 2011a, Hetland et al. 2010, Araki et al. 2008). The goal of this PhD work, therefore, was to develop monoclonal antibodies against surface markers of rainbow trout (Oncorhynchus mykiss) T cell population (chapter 2). The lymphocytes are characterized by the expression of a T cell receptor complex composed of TCR chains (α and β) and CD3 chains (α, β, γ, δ, ε and ζ). Cytotoxic T lymphocytes (CTLs) binds to MHC class I bound peptide on the infected host cell using their T cell receptor (TCR) and its co-receptor CD8 resulting in specific killing. Th cells recognize peptides through their T cell receptor (TCR) and their co-receptor CD4 after extracellular antigens uptake, processing and presentation via MHC class II by professional antigen presenting cells (macrophages, dendritic cells and B cells). During recent years, genes encoding MHC class I and II, TCR and their co-receptors CD8 and CD4 have been cloned in several fish species and antibodies have been developed to study protein expression in morphological and functional contexts. However, mabs specific for TCR or CD3 have not been established yet. Therefore, using pan-T cell marker specific mabs, the activation and kinetics of T cell subpopulation should be investigated (chapter 2). Moreover, a flow cytometry method was established using different lineage marker specific mabs to measure different leukocyte populations and their involvement in immune mechanisms of trout using a single tube assay (chapter 3). The first line of defense against altered body cells or pathogens is provided by evolutionarily ancient macrophages and natural killer (NK) cells. These innate mechanisms are well developed in bony fish. Two types of NK cell homologues have been described in fish: non-specific cytotoxic cells and NK-like cells (Shen et al. 2002, Shen et al. 2003, Shen et al. 2004, Fischer et al. 2013). Functional assays for innate and adaptive lymphocyte responses have been developed in only a few fish species. However, there are no tools available until now in trout to follow these cells directly in the immune response. The molecular characteristics and the expression on leukocyte subpopulations of CD56 were therefore analyzed. Furthermore, a mab that is specific for a molecule expressed only in NK cells but with uncommon expression kinetics was established (chapter 4). Overall, the established tools and methods allow a more detailed characterization of cellular immune mechanisms against intracellular pathogens in rainbow trout.
The following work is describing the development of two innovative biosensors for the detection of biologically relevant molecules in the field of ecology and medical diagnostics. Biosensors have the particularity to possess a biological partner which recognizes the target molecule and a physical detection method responsible for the transformation of this biological interaction into measurable information. In the present case, both biosensors are designed following the same strategy and use a recombinant produced human receptor as biological partner and the surface plasmon resonance (SPR) technique to transform the biological interaction in quantitative information. The progesterone biosensor is aimed to detect and quantify substances with affinity to the human progesterone receptor. The recent discoveries that some chemicals present in low quantities in the ecosystem called endocrine disrupting chemicals (EDCs) have a negative impact on the aquatic life fitness raised concerns about the effects of these same molecules to the human health. In order to assess the effects of these EDCs, the use of classical analytical detection methods like high performance liquid chromatography (HPLC) or gas chromatography (GC) is not sufficient as these techniques only quantify a defined molecule without giving information about its biological activity. By integrating a recombinant human progesterone receptor, the progesterone biosensor can determine the biological activity of an unknown molecule or of a mixture of molecules in a real sample. In this work, two different yeasts – one methylotrophic (Hansenula polymorpha) and one non-methylotrophic (Arxula adeninivorans) - were selected as host for the recombinant protein production and their performances were compared. Different purification strategies were assayed and the binding activity of the purified progesterone receptor was then confirmed by enzyme like receptor assay (ELRA) and SPR. This led to the design of a first version of the biosensor with the immobilization of a progesterone-BSA ligand to the surface of a SPR chip and the use of a progesterone receptor mixed with the target molecule as sample. This competitive assay format was successfully utilized with a commercial progesterone-BSA ligand as target molecule and the next step will be the adaptation of this biosensor for real samples measurements. The HER-2 biosensor was developed as an answer for one of the most critical issue in the field of breast cancer diagnostics. In approximately 30 % of cancer cases, the transmembrane protein HER-2 can be found in large amount at the surface of the carcinoma cells and these cases are known to be particularly aggressive. Based on the amount of HER-2 protein at the surface of the cells, the pathologists established a scale with four levels to adapt the treatment to each patient. Although effective therapies have been developed to treat the HER-2 positive breast cancer, one of the major challenges remains the classification of breast sample in this scale as the only accepted determination methods are immunohistochemistry (IHC) and fluorescent in situ hybridization (FISH) which are only qualitative. In this work, a biosensor has been designed to quantify the amount of the HER-2 protein in a crude cell extract from a breast cancer tissue sample. To achieve this, the strategy is to utilize an antibody specifically targeted against the HER-2 protein and bound to a SPR chip. As the development of this biosensor necessitated the use of large amount of purified HER-2 protein, it was decided to produce recombinant full-length HER-2 in two different yeasts and to purify it by chromatography. This recombinant protein production required particular attention due to the membrane localization of HER-2. The structural integrity of the recombinant protein was confirmed by Western Blot and ELISA and different antibodies were bound to SPR chips in order to detect the HER-2 protein. After finding the conditions giving an optimal SPR signal, a protocol was developed to extract native HER-2 from breast tissue sample and the biosensor was assayed with this crude cell extract.