The aim of this work was to gain new knowledge about mechanisms of autoimmune uveitis and to test new therapeutic possibilities that have not yet been studied in uveitis or whose effect is questionable. The main emphasis was placed on the role of microorganisms in the process of uveitis. A mouse model of experimental autoimmune uveitis including a germ-free model was used to achieve the aims and samples of patients' intraocular fluids were analyzed. In the experimental model, the intensity of inflammation was evaluated in vivo clinically and post mortem histologically. The effect of immunomodulatory treatment was evaluated. The intensity of inflammation was compared between groups of germ-free and conventional mice. The therapeutic effect of antibiotics administered to affect microbiome was investigated in conventional mice. In intraocular fluid samples of patients with autoimmune uveitis signs of infection were monitored and levels of cytokines and other factors were evaluated. Evaluation of the effect of immunomodulatory therapy has demonstrated the efficacy of mycophenolate mofetil, which supports its wider use in the treatment of autoimmune posterior uveitis in human medicine. The decrease in bacterial load has led to a decrease in the intensity of inflammation, thereby confirming the importance of...

Introduction:Uveitis in an ocular inflammation affecting mostly people of working age. Uveitis is responsible for severe visual impairment despite of expanding new therapeutics. The animal models of uveitis were established, because the wide clinical variability of uveitis limits the studies in human medicine. The goal our project was to establish a reproducible model of experimental autoimmune uveitis in Czech Republic, and further on this model to observe the frequency of CD3+ and F4/80+ cells in retina, to assess the influence of microbial environment on intensity of intraocular inflammation and to test the therapeutical possibilities. Material and methods: The C57BL/6J mice were immunized by retinal antigen (IRBP 1-20, interphotoreceptor retinoid binding protein), enhanced by complete Freund's adjuvant and pertussis toxin and mild posterior autoimmune uveitis was induced. The mice were bred in conventional and germ-free (gnotobiotic) conditions. The uveitis intensity was evaluated in vivo biomicroscopically and post mortem histologically on hematoxylin eosin stained sections according to the standard protocol. The histological eye specimen were analyzed also by imunohistochemisty and by flow cytometry. Each experiment was performed for 35 days. The conventional mice with uveitis were treated...

This project studies the signal detection and identification problem in high-dimensional noisy data and the possibility of using it on microbiome data. An extensive simulation study was performed on generated data using as well as a microbiome dataset collected on patients with Parkinson's disease, using Donoho and Jin's Higher criticism, Jager and Wellner's phi-divergence-based goodness-of-fit-test and Stepanova and Pavlenko's CsCsHM statistic . We present some novel approaches based on established theory that perform better than existing methods and show that it is possible to use the signal identification framework to detect differentially abundant features in microbiome data. Although the novel approaches produce good results, they lack substantial mathematical foundations and should be avoided if theoretical rigour is needed. We also conclude that while we have found that it is possible to use signal identification methods to find abundant features in microbiome data, further refinement is necessary before it can be properly used in research. / Detta projekt studerar signaldetekterings- och identifieringsproblemet i högdimensionell brusig data och möjligheten att använda det på mikrobiomdata från människor. En omfattande simuleringsstudie utfördes på genererad data samt ett mikrobiomdataset som samlats in på patienter med Parkinsons sjukdom, med hjälp av ett antal goodness-of-fit-metoder: Donoho och Jins Higher criticis , Jager och Wellners phi-divergenser och Stepanova och Pavelenkos CsCsHM. Vi presenterar några nya tillvägagångssätt baserade på vedertagen teori som visar sig fungera bättre än befintliga metoder och visar att det är möjligt att använda signalidentifiering för att upptäcka olika funktioner i mikrobiomdata. Även om de nya metoderna ger goda resultat saknar de betydande matematiska grunder och bör undvikas om teoretisk formalism är nödvändigt. Vi drar också slutsatsen att medan vi har funnit att det är möjligt att använda signalidentifieringsmetoder för att hitta information i mikrobiomdata, är ytterligare experiment nödvändiga innan de kan användas på ett korrekt sätt i forskning.

The work was comprehensively focused on the development of adhesive forms of probiotics in the form of a biofilm on combined carriers with a prebiotic component. The second part dealed with the influence of food on the multiplication and survival of selected types of probiotic bacteria. Subsequently, the effect of individualized probiotic supplements on changes in the human intestinal microbiome was monitored. Suitable adherent probiotic strains for biofilm formation were selected and tested. Methods have been introduced and different variants of carriers for culturing and binding bacteria have been tested. In vitro experiments verified the stability of biofilm stucture and its resistance to low pH, bile and antibiotics in comparison with the planktonic cell form. The antimicrobial effect of probiotic strains in the form of a biofilm was studied. The cultivation of the multispecies biofilm on the combined carrier was optimized and the stability of the biofilm and the final viability of probiotic bacteria were confirmed. Furthermore, the influence of various foods and beverages on the viability of probiotic bacteria was evaluated with emphasis on the simulation of passage through the gastrointestinal tract. Both models, solutions with standardised concentrations of alcohol, sugar, salts, proteins or different pH and different types of real foods and beverages were tested. The effect of food and beverages was tested on monocultures of Lactobacillus acidophilus, Bifidobacterium breve and on probiotic capsules containing a mixed culture of probiotic microorganisms. The survival of probiotics in various food matrices in the simulated gastrointestinal tract was quantitatively different. We managed to define foods suitable for supporting the multiplication of probiotic bacteria. A separate part of the work was focused on the targeted modulation of the intestinal microbiome by individualized probiotics that were prepared on the basis of molecular biological analyzes of the intestinal microbiome aimed at detecting the percentage of lactobacilli, bifidobacteria and phylum Firmicutes and Bacteroidetes. Personalized probiotic supplementation confirmed the positive effect of this approach on microbiome changes, especially on the increase of the content of lactobacilli, bifidobacteria and the overall diversity of the microbiome.

Inositolpolyphosphate (InsPs) bilden eine ubiquitäre Gruppe an hochphosphorylierten, intrazellulären Signalmolekülen in eukaryotischen Zellen. Trotz deren Beteiligung an unzähligen biologischen Prozessen bleibt die Detektion von InsPs (insb. einzelner Enantiomere) eine Herausforderung, da die momentan verfügbaren Analysemethoden immer noch limitiert sind. In der vorliegenden Arbeit wird die stabile Isotopenmarkierung von myo-Inositol (Ins) und InsPs in Kombination mit Kernspinresonanzspektroskopie (engl. Nuclear Magnetic Resonance spectroscopy, NMR) erkundet, um diese Lücke zu schließen. Die Abhängigkeit von NMR-Daten und chemischer Struktur erlaubte die Analyse komplexer Mixturen aus InsPs aus in vitro-Experimenten und biologischen Proben. Durch stereospezifische 13C-Markierung konnten sogar Enantiomere voneinander unterschieden werden. Mit Hilfe dieser Methode wurden mehrere InsP-Stoffwechselwege untersucht. Als Erstes wurde das menschliche, Phytase-artige Enzym MINPP1 (engl. Multiple Inositol Polyphosphate Phosphatase 1) detailliert in vitro und in lebenden Zellen charakterisiert. Dabei wurde ein bisher unbeschriebener InsP-Stoffwechselweg in menschlichen Zellen erstmals beschrieben. Als Zweites wurden InsP verdauende Bakterien aus der menschlichen Darmflora untersucht, sodass der Abbauweg von Inositolhexakisphosphat beleuchtet werden konnte. Als Drittes wurden DUSP-Enzyme (engl. Dual-Specificity Phosphatases) identifiziert und in vitro charakterisiert, die in der Lage sind, die Phosphoanhydrid-Bindung von Inositolpyrophosphaten (PP-InsPs) zu spalten. Die vorliegende Arbeit demonstriert, dass 13C-Markierung in Verbindung mit NMR ein mächtiges Werkzeug darstellt, um InsP-Stoffwechselvorgänge zu untersuchen. / Inositol polyphosphates (InsPs) comprise a ubiquitous group of densely phosphorylated intracellular messengers in eukaryotic cells. Despite their contributions to a myriad of biological processes the detection of InsPs remains challenging to this day, especially with regards to differentiating enantiomers, as the available analytical toolset is still limited. In this thesis the use of stable isotope labelling of myo-inositol (Ins) and InsPs is explored to address this shortcoming. Combining 13C-labelling and nuclear magnetic resonance spectroscopy (NMR) provides both enhanced sensitivity and makes use of NMR’s strong structure-data dependency. This enabled the deconvolution of complex mixtures of InsPs from in vitro experiments or biological samples. With stereo-specific 13C-labels InsP mixtures could be resolved to individual enantiomers. Using this technique several InsP metabolic pathways were examined. Firstly, the human phytase-like enzyme Multiple Inositol Polyphosphate Phosphatase (MINPP1) was characterized in depth in vitro and in living cells, establishing a hitherto undescribed inositol polyphosphate metabolic path in humans. Secondly, inositol phosphate digesting bacteria isolated from the human gut microbiome were investigated, shedding light on the metabolic fate of inositol hexakisphosphate in the digestive track. Thirdly, a set of Dual-Specificity Phosphatases (DUSPs) were identified to be able to hydrolyze the phosphoanhydride bond of inositol pyrophosphates (PP-InsPs) and characterized in vitro. The 13C-labelling approach of InsPs in junction with NMR represents a powerful tool for the study of inositol polyphosphate metabolism. In the thesis at hand, this method has facilitated our understanding of inositol polyphosphate pathways and it will be continuing doing so in the future in several biological contexts.