Bacterial research has been flourishing ever since 17th century. Bacteria play an important role in clinical microbiology, food microbiology and environmental microbiology. Therefore, the rising need to detect bacteria in clinical, food and environmental samples is emerging onto a craving research frenzy. There are some established methods to study bacteria, such as genetic techniques like PCR, culturing and RNA based analysis, but these require time, resources and labor. This thesis concentrates on highlighting the importance of MALDI-MS in rapid, direct, and simple detection of bacteria from food and clinical samples. The method is to enable detection of bacteria in real samples. First attempts were made to detect bacteria from yogurt sample, because as already known commercial yogurt samples contain bacteria. And yogurts were used in this study to demonstrate the capability of MALDI-MS technique to detect the bacteria directly by culture-free methods. Since the bacterial signals were quenched because of the strong milk peaks, we had to employ nanoparticles and ionic solution for affinity capture of the bacteria for bacterial detection. The results showed that addition of ionic solution and Ag nanoparticles lead to enhanced bacterial detection. The deterioration of the yogurt bacteria on improper storage ( at room temperature) and after extended storage in refrigerator beyond expiry date was studied using MALDI-MS. The day by day deterioration in the microbiological quality of the yogurt was also detected. A special selective media for growth of the yogurt bacteria, DifcoTM Lactobacilli MRS Broth (Agar) was used to quantify the bacteria in various experiments. MALDI-MS results were useful in understanding the shelf life and quality control on extended storage. The second part of this thesis concentrates on the use of MALDI-MS in clinical analysis. The major goal in this work was to use MALDI-MS to detect bacteria in mousy blood and urine. Phase I of this study involved detection of the bacteria by direct MALDI-MS in blood and urine samples spiked with bacteria. We call these experiments as in vitro experiments. Analysis using MALDI was a challenge since the blood peaks interfered with the bacterial peaks and subdued them. Ionic liquid is a pretty excellent extraction solvent when combined with SDME (Single-drop Microextraction). Just one drop of 1-butyl-3methylimidazolium hexafluorophosphate can extract bacteria from spiked samples. What¡¦s more, the LOD can be lower to ~105 cfu / mL using SDME with ionic liquid. It¡¦s definitely showing that 1-butyl-3methylimidazolium hexafluorophosphate, that is to say, the ionic liquid has good ability to trap pathogenic bacteria. This bacterium is injected into mouse and the growth kinetics of bacteria in vivo was studied as a function of time. Samples taken at specific time points were simultaneously analyzed using standard plate count method as well as MALDI-MS. Analysis using MALDI was a challenge since the blood peaks interfered with the bacterial peaks and subdued them. Therefore, we employ the use of silver and zinc oxide nanoparticles and ionic liquid.

Zugl.: Clausthal, Techn. Univ., Diss., 2007

Kohlenhydrat-Protein-Wechselwirkungen sind häufig entscheidend beteiligt an verschiedenen einer Infektion oder malignen Erkrankung zugrunde liegenden molekularen Erkennungs-prozessen, die zu Adhäsion, Zell-Zell-Interaktion sowie Immunreaktion und -toleranz führen. Trotz der hohen Relevanz für Diagnostik und Therapie dieser Erkrankungen sind die betreffenden Strukturen und Mechanismen bisher nur ungenügend untersucht und verstanden. Ziel dieser stark interdisziplinär angelegten Arbeit war es daher, Methoden der Fachbereiche Chemie und Pharmazie, Biologie und Medizin, aber auch Physik zu kombinieren, um Kohlenhydraterkennungsprozesse im Detail zu untersuchen und auf dieser Basis strukturell neuartige diagnostische und therapeutische Anwendungen zu entwerfen. Die hochkomplexe Zusammensetzung einer Zelloberfläche wurde zunächst auf ihren Glycan-anteil reduziert und stark vereinfacht auf der Oberfläche sogenannter Glycochips imitiert. Die verwendeten Systeme auf Basis einer Gold- bzw. Glasoberfläche ergänzen sich optimal in ihrer Eignung für komplementäre analytische Methoden wie Massenspektrometrie sowie quantifizierbare Fluoreszenzspektroskopie. Der Übergang auf die lebende Zelloberfläche gelang mit Hilfe des Metabolic Glyco-engineering, das die kovalente Präsentation definierter Motive durch eine Cycloaddition zwischen zwei bioorthogonalen Reaktionspartnern (z.B. Azid und Alkin) ermöglicht. Auf diese Weise wurden in Zusammenarbeit mit der Arbeitsgruppe Sauer (Universität Würzburg) zunächst die Dichte und Verteilung verschiedener Oberflächenglycane auf humanen Zellen mittels hochauflösender Fluoreszenzmikroskopie (dSTORM) bestimmt. Diese Parameter zeigten im Modell des Glycochips einen entscheidenden Einfluss auf Bindungsereignisse und multivalente Erkennung und zählen auch auf natürlichen Zelloberflächen – in engem Zusammenhang mit der lateralen und temporalen Dynamik der Motive – zu den wichtigen Faktoren molekularer Erkennungsprozesse. Die gezielte Modifikation zellulärer Oberflächenglycane eignet sich aber auch selbst als Methode zur Beeinflussung molekularer Wechselwirkungsprozesse. Dies wurde anhand des humanpathogenen Bakteriums S. aureus gezeigt, dessen Adhäsion auf Epithelzellen der Blasenwand durch Metabolic Glycoengineering partiell unterdrückt werden konnte. In einem ergänzenden Projekt wurden zwei potentielle Metabolite eines konventionellen Antibiotikums – des Nitroxolins – mit bakteriostatischer sowie antiadhäsiver Wirksamkeit dargestellt. Diese dienten als Referenzsubstanzen zur Verifizierung der postulierten Struktur der Derivate, werden aber auch selbst auf ihr Wirkprofil hin untersucht. Gleichzeitig stehen sie zusammen mit der Grundverbindung zudem als Referenz für die Wirkstärke potentieller neu entwickelter Antiadhäsiva zur Verfügung. / Interactions between carbohydrates and proteins often are crucial factors in the molecular recognition processes of infectious diseases or cancer, leading to adhesion and cell cell interaction, as well as immune response and immune tolerance. Despite of their high pertinence for diagnostics and successful therapeutic treatment of those diseases, the structures and mechanisms involved are still insufficiently studied and poorly understood. So it was the aim of this strongly interdisciplinary oriented dissertation, to study carbohydrate recognition processes on molecular basis and in detail by combining methods from different scientific schools like chemistry and pharmacy, biology and medicine, as well as physics. Based on the achieved results innovative diagnostic and therapeutic applications should be proposed. Initially the highly complex structural composition of a living cells’ surface was reduced to its’ glycan fraction and mimicked on the surface of so-called glycochips in a very simplified manner. Two systems, based on gold and glass surfaces respectively, were used due to their complementary applicability for different analytical methods like mass spectrometry and quantitative fluorescence spectroscopy. The step forward towards living cell surfaces was achieved by metabolic glycoengineering, a method that enables the covalent installation of defined binding motifs by performing a cycloaddition between two bioorthogonal reaction partners (e.g. azide and alkyne). In cooperation with the group of Prof. Dr. Markus Sauer (Universität Würzburg) this technique was used to determine the density and spatial distribution of different cell surface glycans on human cell lines with high resolution fluorescence microscopy (dSTORM). In the glycochip model these parameters exhibited a key value for binding processes and multivalent recognition. Even on native cell surfaces they are crucial factors of molecular recognition processes – closely related to the lateral and temporal dynamics of the structural motifs. In addition the specific modification of cell surface glycans itself can be used to manipulate molecular interaction processes. This could be shown for the human pathogenic bacterium Staphylococcus aureus by significant reduction of its adhesion potential towards epithelial cells derived from the human bladder after metabolic glycoengineering. Finally a supplementary project aimed to synthesize two prior postulated metabolites of the conventional antibiotic agent nitroxoline that shows bacteriostatic as well as antiadhesive effects. They were used as reference compounds to verify the postulated structure of the two derivatives and currently undergo further studies concerning their intrinsic mode of action. In addition to the parent molecule they also serve as reference compounds to estimate the potential of novel antiadhesives.

This report demonstrates a UV-embossed polymeric chip for protein separation and identification by Capillary Isoelectric Focusing (CIEF) and Matrix Assisted Laser Desportion/Ionization Mass Spectrometry (MALDI-MS). The polymeric chip has been fabricated by UV-embossing technique with high throughput; the issues in the fabrication have been addressed. In order to achieve high sensitivity of mass detection, five different types of UV curable polymer have been used as sample support to perform protein ionization in Mass Spectrometry (MS); the best results is compared to PMMA, which was the commonly used plastic chip for biomolecular separation. Experimental results show that signal from polyester is 12 times better than that of PMMA in terms of detection sensitivity. Finally, polyester chip is utilized to carry out CIEF to separate proteins, followed by MS identification. / Singapore-MIT Alliance (SMA)

Ulm, Univ., Diss., 2008.

Stuttgart, Univ., Diss., 2007.

Universiẗat, Diss., 2004--Kiel.

Matrix assisted laser desorption/ionisation mass spectrometry (MALDI-MS) for small molecule analysis has been plagued with inherent problems associated with matrix interference. The matrix plays an important role in MALDI-MS where it has the ability to absorb UV energy from the laser employed and transfer it to the analyte, acts as a proton donor and protecting the analytes from being obliterated. For decades, research has been performed to eradicate matrix interference by matrix avoidance, finding alternative matrices, suppression through sample preparation methods and via chemical modification.In this investigation a number of the above mentioned approaches have been undertaken. First, a mesoporous silica powder, SBA-16, functionalised with a phenyl group to absorb UV from the MALDI-MS laser gave unfruitful results due to inhomogeneous dispersion of the SBA-16 powder. Therefore the same material was prepared but as a thin film and a homogeneously coated surface was generated with the phenyl group incorporated into the silica and this was compared with a conventional matrix, 2,5-dihydroxybenzoic acid (DHB). This was by far the most sensitive method which was accurate, with little background noise and importantly for small molecule analysis clear of matrix interference. Other surface systems were also tested such as graphene on copper and silver on copper, but the functionalised SBA-16 thin film remained the best. Graphite and 2B pencil were also investigated for MALDI-MS but were compared with conventional matrices (DHB and α-cyano-4-hydroxycinnamic acid (CHCA)) in a functional genomics study. The ability of all methods to find subtle phenotypic differences in various yeast strains was assessed with the help of multivariate data analysis (MVDA). Although DHB came out best, 2B pencil produce notably good separations that correlated nicely with the different genotypes. Therefore in addition to conventional matrices, 2B pencil should be considered for functional genomic studies when MALDI-MS is used as it is such a rapid and inexpensive method. Finally, chemical modifications were performed on amino acids where picolinic acid was used to attach a chromophore to the compounds, therefore, allowing UV absorption from the laser. Upon attaching the picolinate UV absorbing group, the amino acid compounds were detected LC-MS at an increased intensity of 10 to 100-fold. Moreover, enhanced separation in LC-MS was also observed.This project has successfully investigated alternative approaches to matrix-free MALDI-MS analysis. Functionalised SBA-16 thin films were by far the best method and this novel surface for MALDI-MS has the potential to transform small molecule analysis.

Detection trace compound from human serum by matrix-assited laser desorption ionization mass spectrometry and second dimensional gel ectrophoresis

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