Surface plasmon fluorescence spectroscopy and microscopy studies for biomolecular interaction studies

ABSTARCT Biotechnology has enabled the modification of agricultural materials in a very precise way. Crops have been modified through the insertion of new traits or the inhibition of existing gene functions, named Genetically Modified Organism (GMO), and resulted in improved tolerance of herbicide and/or increased resistance against pests, viruses and fungi. Commercial cultivation of GMO started in 1996 and increased rapidly in 2003 according to a recently released report by the International Service for the Acquisition of Agri-Biotech Applications (ISAAA), depicted continuing consumer resistance in Europe and other part of the world. Upon these developments, the European Union regulations mandated labeling of GMOs containing food and as a consequence, the labeling of GMO containing product in the case of exceeding the1% threshold of alien DNA is required. The aim of the study is to be able to detect and quantify the GMO from the mixture of natural food components. The surface plasmon resonance (SPR) technique combined with fluorescence was used for this purpose. During the presented studies, two key issues are addressed and tried to solve; what is the best strategy to design and built an interfacial architecture of a probe oligonucletide layer either on a two dimensional surface or on an array platform; and what is the best detection method allowing for a sensitive monitoring of the hybridisation events. The study includes two parts: first part includes characterization of different PNAs on a 2D planar surface by defining affinity constants using the very well established optical method “Surface Plasmon Fluorescence Spectroscopy”(SPFS) and on the array platform by “Surface Plasmon Fluorescence Microscopy” (SPFM), and at the end comparison of the sensitivity of these two techniques. The second part is composed of detection of alien DNA in food components by using DNA and PNA catcher probes on the array platform in real-time by SPFM.

Magnetic spectroscopy and microscopy of functional materials

Heusler intermetallics Mn$_{2}Y$Ga and $X_{2}$MnGa ($X,Y$=Fe, Co, Ni) undergo tetragonal magnetostructural transitions that can result in half metallicity, magnetic shape memory, or the magnetocaloric effect. Understanding the magnetism and magnetic behavior in functional materials is often the most direct route to being able to optimize current materials and design future ones.rnrnSynchrotron soft x-ray magnetic spectromicroscopy techniques are well suited to explore the the competing effects from the magnetization and the lattice parameters in these materials as they provide detailed element-, valence-, and site-specific information on the coupling of crystallographic ordering and electronic structure as well as external parameters like temperature and pressure on the bonding and exchange.rnrnFundamental work preparing the model systems of spintronic, multiferroic, and energy-related compositions is presented for context. The methodology of synchrotron spectroscopy is presented and applied to not only magnetic characterization but also of developing a systematic screening method for future examples of materials exhibiting any of the above effects. rnrnChapters include an introduction to the concepts and materials under consideration (Chapter 1); an overview of sample preparation techniques and results, and the kinds of characterization methods employed (Chapter 2); spectro- and microscopic explorations of $X_2$MnGa/Ge (Chapter 3); spectroscopic investigations of the composition series Mn$_{2}Y$Ga to the logical Mn$_3$Ga endpoint (Chapter 4); and a summary and overview of upcoming work (Chapter 5). Appendices include the results of a “Think Tank” for the Graduate School of Excellence MAINZ (Appendix A) and details of an imaging project now in progress on magnetic reversal and domain wall observation in the classical Heusler material Co$_2$FeSi (Appendix B).

Surface-plasmon optical and electrochemical characterization of biofunctional surface architectures

The development and characterization of biomolecule sensor formats based on the optical technique Surface Plasmon Resonance (SPR) Spectroscopy and electrochemical methods were investigated. The study can be divided into two parts of different scope. In the first part new novel detection schemes for labeled targets were developed on the basis of the investigations in Surface-plamon Field Enhanced Spectroscopy (SPFS). The first one is SPR fluorescence imaging formats, Surface-plamon Field Enhanced Fluorescence Microscopy (SPFM). Patterned self assembled monolayers (SAMs) were prepared and used to direct the spatial distribution of biomolecules immobilized on surfaces. Here the patterned monolayers would serve as molecular templates to secure different biomolecules to known locations on a surface. The binding processed of labeled target biomolecules from solution to sensor surface were visually and kinetically recorded by the fluorescence microscope, in which fluorescence was excited by the evanescent field of propagating plasmon surface polaritons. The second format which also originates from SPFS technique, Surface-plamon Field Enhanced Fluorescence Spectrometry (SPFSm), concerns the coupling of a fluorometry to normal SPR setup. A spectrograph mounted in place of photomultiplier or microscope can provide the information of fluorescence spectrum as well as fluorescence intensity. This study also firstly demonstrated the analytical combination of surface plasmon enhanced fluorescence detection with analyte tagged by semiconducting nano- crystals (QDs). Electrochemically addressable fabrication of DNA biosensor arrays in aqueous environment was also developed. An electrochemical method was introduced for the directed in-situ assembly of various specific oligonucleotide catcher probes onto different sensing elements of a multi-electrode array in the aqueous environment of a flow cell. Surface plasmon microscopy (SPM) is utilized for the on-line recording of the various functionalization steps. Hybridization reactions between targets from solution to the different surface-bound complementary probes are monitored by surface-plasmon field-enhanced fluorescence microscopy (SPFM) using targets that are either labeled with organic dyes or with semiconducting quantum dots for color-multiplexing. This study provides a new approach for the fabrication of (small) DNA arrays and the recording and quantitative evaluation of parallel hybridization reactions. In the second part of this work, the ideas of combining the SP optical and electrochemical characterization were extended to tethered bilayer lipid membrane (tBLM) format. Tethered bilayer lipid membranes provide a versatile model platform for the study of many membrane related processes. The thiolipids were firstly self-assembled on ultraflat gold substrates. Fusion of the monolayers with small unilamellar vesicles (SUVs) formed the distal layer and the membranes thus obtained have the sealing properties comparable to those of natural membranes. The fusion could be monitored optically by SPR as an increase in reflectivity (thickness) upon formation of the outer leaflet of the bilayer. With EIS, a drop in capacitance and a steady increase in resistance could be observed leading to a tightly sealing membrane with low leakage currents. The assembly of tBLMs and the subsequent incorporation of membrane proteins were investigated with respect to their potential use as a biosensing system. In the case of valinomycin the potassium transport mediated by the ion carrier could be shown by a decrease in resistance upon increasing potassium concentration. Potential mediation of membrane pores could be shown for the ion channel forming peptide alamethicin (Alm). It was shown that at high positive dc bias (cis negative) Alm channels stay at relatively low conductance levels and show higher permeability to potassium than to tetramethylammonium. The addition of inhibitor amiloride can partially block the Alm channels and results in increase of membrane resistance. tBLMs are robust and versatile model membrane architectures that can mimic certain properties of biological membranes. tBLMs with incorporated lipopolysaccharide (LPS) and lipid A mimicking bacteria membranes were used to probe the interactions of antibodies against LPS and to investigate the binding and incorporation of the small antimicrobial peptide V4. The influence of membrane composition and charge on the behavior of V4 was also probed. This study displays the possibility of using tBLM platform to record and valuate the efficiency or potency of numerous synthesized antimicrobial peptides as potential drug candidates.

Microscopic and spectroscopic analysis of biogenic aerosols

Aerosol particles are important actors in the Earth’s atmosphere and climate system. They scatter and absorb sunlight, serve as nuclei for water droplets and ice crystals in clouds and precipitation, and are a subject of concern for public health. Atmospheric aerosols originate from both natural and anthropogenic sources, and emissions resulting from human activities have the potential to influence the hydrological cycle and climate. An assessment of the extent and impacts of this human force requires a sound understanding of the natural aerosol background. This dissertation addresses the composition, properties, and atmospheric cycling of biogenic aerosol particles, which represent a major fraction of the natural aerosol burden. The main focal points are: (i) Studies of the autofluo-rescence of primary biological aerosol particles (PBAP) and its application in ambient measure-ments, and (ii) X-ray microscopic and spectroscopic investigations of biogenic secondary organic aerosols (SOA) from the Amazonian rainforest.rnAutofluorescence of biological material has received increasing attention in atmospheric science because it allows real-time monitoring of PBAP in ambient air, however it is associated with high uncertainty. This work aims at reducing the uncertainty through a comprehensive characterization of the autofluorescence properties of relevant biological materials. Fluorescence spectroscopy and microscopy were applied to analyze the fluorescence signatures of pure biological fluorophores, potential non-biological interferences, and various types of reference PBAP. Characteristic features and fingerprint patterns were found and provide support for the operation, interpretation, and further development of PBAP autofluorescence measurements. Online fluorescence detection and offline fluorescence microscopy were jointly applied in a comprehensive bioaerosol field measurement campaign that provided unprecedented insights into PBAP-linked biosphere-atmosphere interactions in a North-American semi-arid forest environment. Rain showers were found to trigger massive bursts of PBAP, including high concentrations of biological ice nucleators that may promote further precipitation and can be regarded as part of a bioprecipitation feedback cycle in the climate system. rnIn the pristine tropical rainforest air of the Amazon, most cloud and fog droplets form on bio-genic SOA particles, but the composition, morphology, mixing state and origin of these particles is hardly known. X-ray microscopy and spectroscopy (STXM-NEXAFS) revealed distinctly different types of secondary organic matter (carboxyl- vs. hydroxy-rich) with internal structures that indicate a strong influence of phase segregation, cloud and fog processing on SOA formation, and aging. In addition, nanometer-sized potassium-rich particles emitted by microorganisms and vegetation were found to act as seeds for the condensation of SOA. Thus, the influence of forest biota on the atmospheric abundance of cloud condensation nuclei appears to be more direct than previously assumed. Overall, the results of this dissertation suggest that biogenic aerosols, clouds and precipitation are indeed tightly coupled through a bioprecipitation cycle, and that advanced microscopic and spectroscopic techniques can provide detailed insights into these mechanisms.rn

NMR spectroscopy and imaging of hyperpolarized gases

Since the discovery of the nuclear magnetic resonance (NMR) phenomenon, countless NMR techniques have been developed that are today indispensable tools in physics, chemistry, biology, and medicine. As one of the main obstacles in NMR is its notorious lack of sensitivity, different hyperpolarization (HP) methods have been established to increase signals up to several orders of magnitude. In this work, different aspects of magnetic resonance, using HP noble gases, are studied, hereby combining different disciplines of research. The first part examines new fundamental effects in NMR of HP gases, in theory and experiment. The spin echo phenomenon, which provides the basis of numerous modern experiments, is studied in detail in the gas phase. The changes of the echo signal in terms of amplitude, shape, and position, due to the fast translational motion, are described by an extension of the existing theory and computer simulations. With this knowledge as a prerequisite, the detection of intermolecular double-quantum coherences was accomplished for the first time in the gas phase. The second part of this thesis focuses on the development of a practical method to enhance the dissolution process of HP 129Xe, without loss of polarization or shortening of T1. Two different setups for application in NMR spectroscopy and magnetic resonance imaging (MRI) are presented. The continuous operation allows biological and multidimensional spectroscopy in solutions. Also, first in vitro MRI images with dissolved HP 129Xe as contrast agent were obtained at a clinical scanner.

Transcriptional regulation and functional characterization of the tumor suppressor genes Hugl-1 and Hugl-2

Cancer is a multi-step process in which both the activation of oncogenes and the inactivation of tumor suppressor genes alter the normal cellular programs to a state of proliferation and growth. The regulation of a number of tumor suppressor genes and the mechanism underlying the tumor suppression have been intensively studied. Hugl-1 and Hugl-2, the human homologues of Drosophila lgl are shown to be down-regulated in a variety of cancers including breast, colon, lung and melanoma, but the mechanism responsible for loss of expression is not yet known. The regulation of gene expression is influenced by factors inducing or repressing transcription. The present study was focused on the identification and characterization of the active promoters of Hugl-1 and Hugl-2. Further, the regulation of the promoter and functional consequences of this regulation by specific transcription factors was analyzed. Experiments to delineate the function of the mouse homologue of Hugl-2, mgl2 using transgenic mice model were performed. This study shows that the active promoter for both Hugl-1 and Hugl-2 is located 1000bp upstream of transcription start sites. The study also provides first insight into the regulation of Hugl-2 by an important EMT transcriptional regulator, Snail. Direct binding of Snail to four E-boxes present in Hugl-2 promoter region results in repression of Hugl-2 expression. Hugl-1 and Hugl-2 plays pivotal role in establishment and maintenance of cell polarity in a diversity of cell types and organisms. Loss of epithelial cell polarity is a prerequisite for cancer progression and metastasis and is an important step in inducing EMT in cells. Regulation of Hugl-2 by Snail suggests one of the initial events towards loss of epithelial cell polarity during Snail-mediated EMT. Another important finding of this study is the induction of Hugl-2 expression can reverse the Snail-driven EMT. Inducing Hugl-2 in Snail expressing cells results in the re-expression of epithelial markers E-cadherin and Cytokeratin-18. Further, Hugl-2 also reduces the rate of tumor growth, cell migration and induces the epithelial phenotype in 3D culture model in cells expressing Snail. Studies to gain insight into the signaling pathways involved in reversing Snail-mediated EMT revealed that induction of Hugl-2 expression interferes with the activation of extracellular receptor kinase, Erk. Functional aspects of mammalian lgl in vivo was investigated by establishing mgl2 conditional knockout mice. Though disruption of mgl2 gene in hepatic tissues did not alter the growth and development, ubiquitous disruption of mgl2 gene causes embryonic lethality which is evident by the fact that no mgl2-/- mice were born.

A soft-tetramer model for diblock copolymer melts: structure formation and geometric characterization

The ability of block copolymers to spontaneously self-assemble into a variety of ordered nano-structures not only makes them a scientifically interesting system for the investigation of order-disorder phase transitions, but also offers a wide range of nano-technological applications. The architecture of a diblock is the most simple among the block copolymer systems, hence it is often used as a model system in both experiment and theory. We introduce a new soft-tetramer model for efficient computer simulations of diblock copolymer melts. The instantaneous non-spherical shape of polymer chains in molten state is incorporated by modeling each of the two blocks as two soft spheres. The interactions between the spheres are modeled in a way that the diblock melt tends to microphase separate with decreasing temperature. Using Monte Carlo simulations, we determine the equilibrium structures at variable values of the two relevant control parameters, the diblock composition and the incompatibility of unlike components. The simplicity of the model allows us to scan the control parameter space in a completeness that has not been reached in previous molecular simulations.The resulting phase diagram shows clear similarities with the phase diagram found in experiments. Moreover, we show that structural details of block copolymer chains can be reproduced by our simple model.We develop a novel method for the identification of the observed diblock copolymer mesophases that formalizes the usual approach of direct visual observation,using the characteristic geometry of the structures. A cluster analysis algorithm is used to determine clusters of each component of the diblock, and the number and shape of the clusters can be used to determine the mesophase.We also employ methods from integral geometry for the identification of mesophases and compare their usefulness to the cluster analysis approach.To probe the properties of our model in confinement, we perform molecular dynamics simulations of atomistic polyethylene melts confined between graphite surfaces. The results from these simulations are used as an input for an iterative coarse-graining procedure that yields a surface interaction potential for the soft-tetramer model. Using the interaction potential derived in that way, we perform an initial study on the behavior of the soft-tetramer model in confinement. Comparing with experimental studies, we find that our model can reflect basic features of confined diblock copolymer melts.

Laser systems for collinear spectroscopy and the charge radius of 12 Be

Die kollineare Laserspektroskopie hat sich in den vergangenen drei Jahrzehnten zur Bestimmung der Kernladungsradien mittelschwerer und schwerer kurzlebiger Atomkerne in ausgezeichneter Weise bewährt. Auf die Isotope sehr leichter Elemente konnte sie allerdings erst kürzlich erweitert werden. Dieser Bereich der Nuklidkarte ist von besonderem Interesse, denn die ersten ab-initio Modelle der Kernphysik, die den Aufbau eines Atomkerns basierend auf individuellen Nukleonen und realistischenWechselwirkungspotentialen beschreiben, sind gegenwärtig nur für die leichtesten Elemente anwendbar. Außerdem existiertrnin dieser Region eine besonders exotische Form von Atomkernen, die sogenanntenrnHalokerne. Die Isotopenkette der Berylliumisotope zeichnet sich durch das Auftreten des Ein-Neutronen Halokerns 11Be und des Zwei- oder Vier-Neutronen-Halos 14Be aus. Dem Isotop 12Be kommt durch seine Position zwischen diesen beiden Exoten und den im Schalenmodell erwarteten magischen Schalenabschluss N = 8 eine besondere Bedeutung zu.rnIm Rahmen dieser Arbeit wurden mehrere frequenzstabilisierte Lasersysteme für die kollineare Laserspektroskopie aufgebaut. An TRIGA-SPEC stehen nun unter anderem ein frequenzverdoppeltes Diodenlasersystem mit Trapezverstärker und frequenzkammstabilisierter Titan-Saphirlaser mit Frequenzverdopplungsstufe für die Spektroskopie an refraktären Elementen oberhalb von Molybdän zur Verfügung, die für erste Testexperimente eingesetzt wurden. Außerdem wurde die effiziente Frequenzvervierfachung eines Titan-Saphirlasers demonstriert. An ISOLDE/CERN wurde ein frequenzkammstabilisierter und ein jodstabilisierter Farbstofflaser installiert und für die Laserspektroskopie an 9,10,11,12Be eingesetzt. Durch das verbesserte Lasersystem und den Einsatz eines verzögerten Koinzidenznachweises für Photonen und Ionen gelang es die Empfindlichkeitrnder Berylliumspektroskopie um mehr als zwei Größenordnungen zu steigern und damit die früheren Messungen an 7−11Be erstmals auf das Isotop 12Be auszuweiten. Außerdem wurde die Genauigkeit der absoluten Übergangsfrequenzen und der Isotopieverschiebungen der Isotope 9,10,11Be signifikant verbessert.rnDurch den Vergleich mit Ergebnissen des Fermionic Molecular Dynamics Modells kann der Trend der Ladungsradien der leichteren Isotope durch die ausgeprägte Clusterstruktur der Berylliumkerne erklärt werden. Für 12Be wird ersichtlich, dass der Grundzustand durch eine (sd)2 Konfiguration statt der vom Schalenmodell erwarteten p2 Konfiguration dominiert wird. Dies ist ein klares Indiz für das bereits zuvor beobachtete Verschwinden des N = 8 Schalenabschlusses bei 12Be.

Stationary in-situ measurements of aerosols, gaseous pollutants and meteorology : chemical and physical characterization of natural and anthropogenic sources

Natural and anthropogenic emissions of gaseous and particulate matter affect the chemical composition of the atmosphere, impact visibility, air quality, clouds and climate. Concerning climate, a comprehensive characterization of the emergence, composition and transformation of aerosol particles is relevant as their influence on the radiation budget is still rarely understood. Regarding air quality and therefore human health, the formation of atmospheric aerosol particles is of particular importance as freshly formed, small particles penetrate into the human alveolar region and can deposit. Additionally, due to the long residence times of aerosol particles in the atmosphere it is crucial to examine their chemical and physical characteristics.This cumulative dissertation deals with stationary measurements of particles, trace gases and meteorological parameters during the DOMINO (Diel Oxidant Mechanism In relation to Nitrogen Oxide) campaign at the southwest coast of Spain in November/December 2008 and the ship emission campaign on the banks of the Elbe in Freiburg/Elbe in April 2011. Measurements were performed using the Mobile research Laboratory “MoLa” which is equipped with state-of-the-art aerosol particle and trace gas instruments as well as a meteorological station.