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The current thesis is devoted to a systematic study of fluctuations and correlations in heavy-ion collisions, which might be considered as probes for the phase transition and the critical point in the phase diagram, within the Hadron-String- Dynamics (HSD) microscopic transport approach. This is a powerful tool to study nucleus-nucleus collisions and allows to completely simulate experimental collisions on an event-by-event basis. Thus, the transport model has been used to study fluctuations and correlations including the influence of experimental acceptance as well as centrality, system size and collision energy. The comparison to experimental data can separate the effects induced by a phase transition since there is no phase transition in the HSD version used here. Firstly the centrality dependence of multiplicity fluctuations has been studied. Different centrality selections have been performed in the analysis in correspondence to the experimental situation. For the fixed target experiment NA49 events with fixed numbers of the projectile participants have been studied while in the collider experiment PHENIX centrality classes of events have been defined by the multiplicity in certain phase space region. A decrease of participant number fluctuations (and thus volume fluctuations) in more central collisions for both experiments has been obtained. Another area of this work addresses to transport model calculations of multiplicity fluctuations in nucleus-nucleus collisions as a function of colliding energy and system size. This study is in full correspondence to the experimental program of the NA61 Collaboration at the SPS. Central C+C, S+S, In+In, and Pb+Pb nuclear collisions at Elab = 10, 20, 30, 40, 80, 158 AGeV have been investigated. The expected enhanced fluctuations - attributed to the critical point and phase transition - can be observed experimentally on top of a monotonic and smooth ‘hadronic background’. These findings should be helpful for the optimal choice of collision systems and collision energies for the experimental search of the QCD critical point. Other observables are fluctuations of ratios of hadrons (e.g. pions, kaons, protons, etc.) which are not so much affected by volume fluctuations. In particular HSD results for the kaon-to-pion ratio fluctuations, which has been regarded as promising observable for a long time, are presented from low SPS energies up to high energies at RHIC. In addition to the HSD calculations statistical model is also used in terms of microcanonical, canonical and grand canonical ensembles. Further a study of the system size event-by-event fluctuations causing rapidity forward-backward correlations in relativistic heavy-ion collisions is presented. The HSD simulations reveal strong forward-backward correlations and reproduce the main qualitative features of the STAR data in A+A collisions at RHIC energies. It has been shown that strong forward-backward correlations arise due to an averaging over many different events that belong to one centrality bin. An optimization of the experimental selection of centrality classes is presented, which is relevant for the program of the NA61 collaboration at CERN, the low-energy program at RHIC, as well as future experiments at FAIR.
Ein wesentliches Ziel der Physik mit schweren Ionen ist die Untersuchung der Zustände von Kernmaterie bei hohen Dichten bzw. Temperaturen. Solche Zustände lassen sich durch Kollisionen von hochenergetischen schweren Ionen in Teilchenbeschleunigern wie dem Super Proton Synchrotron SPS am Europäischen Kernforschungszentrum CERN in Genf erzeugen und untersuchen. Die vorliegende Arbeit beschäftigt sich mit der Analyse des Einflusses des in einer solchen Kollision erzeugten Mediums auf hochenergetische Teilchen, welche dieses Medium durchqueren. Hierzu werden Korrelationen zwischen Teilchen mit hohem Transversalimpuls pt als Funktion der Zentralität der Kollisionen und der Ladung der beteiligten Teilchen untersucht. Ziel ist es, hierdurch eine experimentelle Grundlage für die theoretische Beschreibung der Eigenschaften des Mediums in solchen Kollisionen bereitzustellen. ...
Kaon and pion production in centrality selected minimum bias Pb+Pb collisions at 40 and 158A GeV
(2009)
Results on charged kaon and negatively charged pion production and spectra for centrality selected Pb+Pb mininimum bias events at 40 and 158A GeV have been presented in this thesis. All analysis are based on data taken by the NA49 experiment at the accelerator Super Proton Synchrotron (SPS) at the European Organization for Nuclear Research (CERN) in Geneva, Switzerland. The kaon results are based on an analysis of the mean energy loss <dE/dx> of the charged particles traversing the detector gas of the time projection chambers (TPCs). The pion results are from an analysis of all negatively charged particles h- corrected for contributions from particle decays and secondary interactions. For the dE/dx analysis of charged kaons, main TPC tracks with a total momentum between 4 and 50 GeV have been analyzed in logarithmic momentum log(p) and transverse momentum pt bins. The resulting dE/dx spectra have been fitted by the sum of 5 Gaussians, one for each main particle type (electrons, pions, kaons, protons, deuterons). The amplitude of the Gaussian used for the kaon part of the spectra has been corrected for efficiency and acceptance and the binning has been transformed to rapidity y and transverse momentum pt bins. The multiplicity dN/dy of the single rapidity bins has been derived by summing the measured range of the transverse momentum spectra and an extrapolation to full coverage with a single exponential function fitted to the measured range. The results have been combined with the mid-rapidity measurements from the time-of-flight detectors and a double Gaussian fit to the dN/dy spectra has been used for extrapolation to rapidity outside of the acceptance of the dE/dx analysis. For the h- analysis of negatively charged pions, all negatively charged tracks have been analyzed. The background from secondary reactions, particle decays, and gamma-conversions has been corrected with the VENUS event generator. The results were also corrected for efficiency and acceptance and the pt spectra were analyzed and extrapolated where necessary to derive the mean yield per rapidity bin dN/dy. The mean multiplicity <pi-> has been derived by summing up the measured dN/dy and extrapolating the rapidity spectrum with a double Gaussian fit to 4pi coverage. The results have been discussed in detail and compared to various model calculations. Microscopical models like URQMD and HSD do not describe the full complexity of Pb+Pb collisions. Especially the production of the positively charged kaons, which carry the major part of strange quarks, cannot be consistently reproduced by the model calculations. Centrality selected minimum bias Pb+Pb collisions can be described as a mixture of a high-density region of multiply colliding nucleons (core) and practically independent nucleon-nucleon collisions (corona). This leads to a smooth evolution from peripheral to central collisions. A more detailed approach derives the ensemble volume from a percolation of elementary clusters. In the percolation model all clusters are formed from coalescing strings that are assumed to decay statistically with the volume dependence of canonical strangeness suppression. The percolation model describes the measured data for top SPS and RHIC energies. At 40A GeV, the system size dependence of the relative strangeness production starts to evolve from the saturation seen at higher energies from peripheral events onwards towards a linear dependence at SIS and AGS. This change of the dependence on system size occurs in the energy region of the observed maximum of the K+ to pi ratio for central Pb+Pb collisions. Future measurements with heavy ion beam energies around this maximum at RHIC and FAIR as well as the upgraded NA49 successor experiment NA61 will further improve our understanding of quark matter and its reflection in modern heavy ion physics and theories.
This thesis contributes to the field of soft matter research and studies the importance of hydrodynamic interactions during free-solution electrophoresis of linear polyelectrolytes by means of coarse-grained molecular dynamics simulations including full electro-hydrodynamic interactions. The center of attention is the specific role of hydrodynamic interactions on the electrophoretic behaviour of charged macromolecules. Points of interest are the dependence of hydrodynamic interactions on the chain length, the chain flexibility and the surrounding counterions, and their combined influence on important observables such as the static chain conformations and the dynamic transport coefficients, i.e., the diffusion and the electrophoretic mobility. These problems are addressed by extensive computer simulations that are quantitatively matched with experimental results. Existing theoretical predictions are carefully examined and are augmented by the observations in this thesis.
Central America is one of the world’s most herpetological diverse areas in relation to its size. Nicaragua is the largest country in this region and separates Nuclear from Lower Central America. It is one of the least herpetological explored countries in Central America and few studies dealing with the herpetofauna of a potion or the entire country have been published. I here update the checklist of the Nicaraguan herpetofauna, present taxonomic revisions of some difficult species complexes, compare the similarities of the composition of the herpetofaunal communities in the major forest formations present in the country within a zoogeographical context, and identify those species with a greater vulnerability risk in Nicaragua. Taxonomy The herpetofauna of Nicaragua currently consists of 244 species representing 134 genera and 42 families with 78 amphibian species representing 35 genera and 15 families, and 166 reptile species representing 99 genera and 27 families, which includes six marine species. Sixteen species (12 amphibians and four reptiles) are endemic to the country. Of the 12 endemic amphibian species, three are here described. In addition, five genera (Anotheca, Cerrophidion, Duellmanohyla, Isthmohyla, and Rhinobothryum) and two species (Rhadinea godmani and Urotheca decipiens) are known to occur both north and south of Nicaragua although there are no voucher specimens of these taxa to confirm their presence in country. I complete a bibliographic research updating the nomenclature changes and provide a brief herpetological history of Nicaragua, a recompilation of all species described upon Nicaraguan material and their current synonymy, the first time each species was recorded from the country, and a list of all recognized subspecies occurring in Nicaragua. I discuss the taxonomic uncertainties among the Nicaraguan populations of amphibians and reptiles and take further detailed taxonomic revisions on selected Nicaraguan species groups from the genera Anolis, Bolitoglossa, and Craugastor along their known distributional range. I describe five new species of herpetofauna (three of which are based on Nicaraguan material), redescribe five species of Anolis (three of which occur in Nicaragua), and provide voucher specimens of five other species for the first time in Nicaragua. In detail: • I studied the pholidosis, morphometrics as well as hemipenis and dewlap morphology in Anolis wermuthi, an anole endemic to the highlands of northern Nicaragua. I examine patterns of geographic variation using discriminant function analysis and discuss the characters that vary both individually and among populations. The results indicate that A. wermuthi is a single species with several disjunct, slightly divergent populations. I provide a standardized description, illustrations of the everted hemipenis of an adult topotype, the male and female dewlap, and a distribution map. I also provide brief descriptions of the localities where this species occurs and some ecological notes. • I studied the pholidosis, morphometrics as well as hemipenis morphology in the Central American anole species Anolis humilis, A. quaggulus, and A. uniformis. The three taxa are distinct in hemipenis morphology. However, very little differentiation in pholidotic and morphometric characters is documented. I document interspecific variation in several characters but with overlap of the documented ranges. A discriminant function analysis based on five pholidotic characters yielded a scatter diagram that showed large overlap between the clusters of the three taxa. I provide head scalation illustrations, an identification key, a distribution map, and standardized descriptions of the commonly distributed in Nicaragua A. quaggulus as well as of the other two species. • I describe two new species of anoles (genus Anolis) from Panama formerly referred to as Anolis limifrons. The two new species, Anolis apletophallus and Anolis cryptolimifrons, differ from A. limifrons by having a large bilobed hemipenis (small and unilobed in A. limifrons). The new species differ from each other in male dewlap size and coloration. I provide illustrations of the head scalation, everted hemipenis, and dewlap, an identification key, a distribution map, and standardized descriptions of the commonly distributed in Nicaragua A. limifrons and the two new species described herein. • I describe two new species of salamanders of Bolitoglossa from southern Nicaragua. Bolitoglossa indio is known from Río Indio in the lowlands of the Río San Juan area and Bolitoglossa insularis from the premontane slopes of Volcán Maderas on Ometepe Island. The two new species are of unknown affinities but both differ from their congeners in coloration. Bolitoglossa indio is most similar to B. mexicana and B. odonnelli from which differ by having both broad dorsolateral pale brown stripes not clearly delimited in outline. Bolitoglossa insularis is most similar to B. mombachoensis and B. striatula from which differ by the absence of dark or light defined stripes on dorsum and venter. • I describe a new species of frog of the genus Craugastor from Río San Juan, Nicaragua. The new species, Craugastor chingopetaca, is assigned to the fitzingeri group and differs from most Central American species of that group by the absence of a midgular pale stripe. Within the fitzingeri group it is most similar to C. crassidigitus and C. talamancae from which it differs in several morphological characteristics such as more extensive webbing, retuse disk covers on some digits, and relative toe length. • I provide voucher specimens of Cochranella spinosa, Kinosternon angustipons, Mesaspis moreletii, Cnemidophorus lemniscatus and Adelphicos quadrivirgatum for the first time in Nicaragua. I include descriptions, illustrations, and brief ecological notes for the five new country records. Zoogeography Based on the concept of ecological formations proposed by HOLDRIDGE (1967), nine forest formations are found in Nicaragua. Of the total number of terrestrial species of herpetofauna found in Nicaragua, 131 species (55.0%) occur in Lowland Wet Forest, 21 of which (8.8%) are restricted to this forest formation, 168 species (70.6%) occur in Lowland Moist Forest, 15 of which (6.3%) are restricted to this forest formation, 84 species (35.3%) occur in Lowland Dry Forest, four of which (1.7%) are restricted to this forest formation, 47 species (19.7%) occur in Lowland Arid Forest, with no species restricted to this forest formation, 59 species (24.8%) occur in Premontane Wet Forest, three of which (1.3%) are restricted to this forest formation, 116 species (48.7%) occur in Premontane Moist Forest, 10 of which (4.2%) are restricted to this forest formation, 51 (21.4%) species occur in Premontane Dry Forest, with no species restricted to this forest formation, 13 species (5.5%) occur in Lower Montane Wet Forest, two of which (0.8%) are restricted to this forest formation, and 50 species (21.0%) occur Lower Montane Moist Forest, seven of which (2.9%) are restricted to this forest formation. The Coefficient of Biogeographic Resemblance algorithm show a distinct composition of the herpetofauna from the isolated highlands of northeastern Nicaragua, which is characterized by a high proportion of endemic species. Two other clusters are evident when analyzing the herpetofaunal similarities among Nicaragua, the Pacific versant and the central mountains and the Atlantic lowlands. In addition, the Pacific lowlands are characterized by a relatively homogeneous composition of the herpetofauna. In contrast, many species have their northern limit of distribution in the Atlantic lowlands with the ranges of most of these species ending in southern Nicaragua. The central mountains constitute the southern limit of distribution of several highland species. In general, there is a greater contribution of reptile than amphibian species to the total herpetofauna present in each forest formation. This unbalance is slightly higher in the dry than in the moist parts of the country. The similarities in the composition of the reptiles between the different forests formations seem to be relatively distinct on an elevation factor, whereas in amphibians similarities might be better explained in correlation with humidity. The total amount of amphibian and reptile species in Nicaragua has a Middle American Element dominance and varies between amphibians and reptiles, with and a greater South American Element influence in anurans and a greater Old Northern Element influence in reptiles. In general, there is a greater percentage of species with a South American Element in extreme southeastern Nicaragua with a decreasing tendency towards northern Nicaragua. Taking in account the geography and geologic history of Nicaragua as well as the known Central American dispersal routes, I identify species of probable occurrence in Nicaragua as well as those places with a greater potential to hold undescribed endemic species. Conservation In Nicaragua, no amphibian or reptile populations are entirely free from anthropogenic impact. I determine the endangerment level of all Nicaraguan amphibian and reptile species using the IUCN categorizations and the Environmental Vulnerability Scores. Seventy-six species (31.9%) of Nicaraguan amphibians and terrestrial reptiles have high vulnerability, 118 (49.6%) medium vulnerability, and 44 (18.5%) low vulnerability. Eighteen species (7.4% of the total herpetofauna) are unknown from protected areas, including 13 high vulnerability species (three are endemic), four medium vulnerability species, and one low vulnerability species. To preserve the future of Nicaragua’s amphibians and reptiles, every species should reside in at least one protected area, the protected areas must be guarded, and monitoring programs are needed to detect changes in amphibian and reptile populations, prioritizing highly vulnerable species.
Zusammenfassung Die Alzheimersche Krankheit (AD) ist mit 60% die am häufigsten auftretende Art der Demenz. Weltweit sind ca. 24 Mio. Menschen von der neurodegenerativen Krankheit betroffen, welche sich durch den Verlust der kognitiven Fähigkeiten auszeichnet. Es gibt zwei Ausprägungen der Demenz, zum einen die sporadische Verlaufsform, die bei Menschen in einem Alter ab 65 Jahren auftritt und zum anderen die familiäre Alzheimersche Krankheit (FAD), die schon weitaus jüngere Menschen betrifft und auf genetische Mutationen zurück zu führen ist. Beide Formen der Demenz zeigen den gleichen neuropathologische Phänotyp, der zur Ausbildung von extrazellulären Plaques und intrazellulären Neurofibrillen führt. Durch die Entstehung der Plaques und der Neurofibrillen werden die Verbindungen zwischen den einzelnen Neuronen verringert und die Neuronen sterben ab. Für das Auftreten der FAD sind Mutationen in den Genen des Amyloid Vorläufer Proteins (APP, Substrat) sowie der Aspartatprotease Einheit des γ-Sekretase Komplexes, Presenilin 1 (PS1) oder Presenilin 2 (PS2), verantwortlich. Die γ-Sekretase ist ein membranständiger Komplex bestehend aus den vier Untereinheiten PS1 oder PS2, Nicastrin (Nct), Aph-1 und Pen-2. Um ausreichende Informationen über den γ-Sekretase Komplex bezüglich seiner Interaktionsflächen, seines Katalysemechanismus und seiner Substraterkennung zu erhalten, wäre es hilfreich seine 3 Dimensionale Struktur aufzuklären, wozu große Mengen der sauberen und homogenen Proteine benötigt werden. Die Herstellung von ausreichenden Proteinmengen stellt derzeit aber einen Engpass für die strukturelle und funktionelle Charakterisierung des γ-Sekretase Komplexes in-vitro dar. Alzheimer’s disease (AD) is the most common cause of dementia, which affects 24 million people worldwide. It is a neurodegenerative disorder, which occurs either in its most common form in people over 65 years or in the rare early-onset familial AD (FAD). Responsible for the autosomal dominant FAD are mutations in the genes encoding for the β-amyloid precursor protein (APP) and the two homologues integral membrane proteins Presenilin 1 (PS1) and Presenilin 2 (PS2). The two PSs are major but alternative components of the intramembrane aspartyl protease γ-secretase. Further components are the membrane proteins Nicastrin (Nct), Aph-1 and Pen-2. Production of sufficient amounts of protein samples is still the major bottleneck for the detailed functional and structural in-vitro characterization of the γ-secretase complex. Due to toxicity, stability and targeting problems, the overproduction of MPs in conventional in-vivo systems often has only limited success. Therefore, efficient expression protocols using the cell-free (CF) system were established in this work. After optimization, I was able to produce up to milligram amounts of the single proteins PS1 and PS2, the cleavage products PS1-NTF and PS1-CTF, and Pen-2. The in-vitro produced γ-secretase subunits were further characterized, concerning their purity, secondary fold, thermal stability and homogeneity. Highest purities with over 90% after affinity chromatography could be achieved for PS1-CTF and Pen-2. Reconstitution of PS1, PS1-NTF, PS1-CTF and Pen-2 into E. coli liposomes results in a homogeneously distribution, which gives evidence for a structural folding. This was confirmed by CD spectroscopy of PS1-CTF and Pen-2. The thermal stability of Pen-2 shows a transition at 68°C, whereas PS1-CTF is stable up to 95°C. Both proteins show in addition homogeneous elution profiles investigated by analytical SEC and exhibit a monomeric (Pen-2) or dimeric (PS1-CTF) character analyzed by blue native PAGE. Different methods were performed to get evidence about the assembly of the complex, like pull-down experiments, immunoprecipitation, co-expression of radioactive labeled subunits and titration assays by liquid-state NMR. First hints for an interaction of the CF synthesized proteins could be observed by co-expression. Supplemental, Pen-2 and CTF could be purified in sufficient amounts and to apparent homogeneity that allow structural approaches by X-ray crystallography and liquid-state NMR spectroscopy. First conditions for protein crystals were achieved for Pen-2 and structural investigations of PS1-CTF by liquid-state NMR could be performed after optimization of the expression-, purification- and detergent conditions.
Despite the well-known importance of ribonucleic acids (RNA) in cell biology, it is astounding to realize the pace at which new fundamental functions of RNAs have been discovered. One of the fundamental reasons for the multitude of functions of RNA is the property of RNA to adopt different conformations or folds. The primary sequence of RNA, a linear polymer built from four different repetition units, can fold into alternate secondary structure motifs which in turn form alternate long-range interactions in complex tertiary structures. Ligands such as metal ions or small molecular weight metabolites and also proteins or peptides can bind to RNA and induce the changes in tertiary conformation. For example, in the cell, RNA participates in gene regulation in the form of riboswitches. Riboswitches are found in untranslated regions of messenger RNA (mRNA) and adopt alternate conformations depending on the presence or absence of specific metabolites. If a metabolite is present above a specific concentration, it induces a conformational change in the respective riboswitch by binding and thereby alters gene expression. Another example is the RNA thermometer which participates in the cell translational mechanism by a similar strategy. Translation initiation requires the binding of RNA thermometers to the ribosome. The ribosome binding region is located in the 5’ untranslated region of mRNA. At low temperatures this region is prevented from binding to the ribosome by forming basepairs. At higher temperatures, these basepairs dissociate allowing ribosome binding and subsequent translation. Therefore, the characterization and delineation of the kinetics and pathway of RNA folding is important to understand the function of RNA and is an important contribution to fundamentally understand RNA’s role in the cell. RNA conformational transitions occur over a wide range of timescales. Depending on the timescale, various biophysical techniques are used to study RNA conformational transitions. In these biophysical studies, achieving good structural and temporal resolution constitute frequently encountered challenges or limitations. For example, single molecule FRET spectroscopy provides high temporal resolution in the milliseconds at high sensitivity but lacks atomic resolution. Recent advances in the field of Nuclear Magnetic Resonance (NMR) spectroscopy have enabled the elucidation of tertiary folding events to be characterized with atomic resolution. This thesis involves the use of NMR spectroscopy to characterize the folding of RNA molecules. Kinetics experiments require rapid initiation of the kinetics followed by monitoring of the reaction. In this thesis, two different folding initiation techniques have been applied and coupled to the subsequent detection of RNA folding using NMR spectroscopy, namely, photocaging and rapid mixing. The method of photocaging is well established (Kuhn and Schwalbe, 2000) and builds on the following principle: A photolabile moiety is attached to a molecule that prevents a specific interaction. Upon irradiation of the molecule with the photolabile group using laser light at a specific wave length, at which the molecule of interest is not absorbing, the protecting group is released. In our group, together with the group of S. Pitsch, ETH Lausanne, we could "cage" RNA at its equilibrium state by a photolabile molecule (similar work has been carried out in the group of A. Heckel). Rapid and traceless release of the photolabile precursor compound by a laser pulse releases the RNA to fold into its native state; the build-up of the native state of the RNA is monitored by NMR signals that are uniquely characteristic for the native state of the RNA. By optically coupling a laser source to an NMR magnet, the above procedure can take place in situ and the kinetics recorded by NMR. Several different molecules can be caged: The photocage can be attached to RNA. Then, a modified photolabile nucleotide can be placed at strategic positions of a target RNA whose folding properties is to be studied. The photocage can also be attached to a ligand: if folding is dependent on ligand binding then the ligand can be modified to carry a photosensitive unit whose degradation allows binding to RNA. In this thesis, an alternative method for photocaging is introduced. Here, metal ions essential for folding of the RNA are photocaged using the photolabile chelating agent Dimethyl-nitrophen (DMN). Photolysis of DMNr releases the metal ion, thereby RNA folding is initiated. In the rapid-mixing technique, one of (several) components required for proper folding of the RNA is rapidly injected into an NMR sample in situ by the use of a pneumatic injection device. ...
The study of the electromagnetic structure of hadrons plays an important role in understanding the nature of matter. In particular the emission of lepton pairs out of the hot and dense collision zone in heavy-ion reactions is a promising probe to investigate in-medium properties of hadrons and in general the properties of matter under such extreme conditions. The first experimental observation of an enhanced di-electron yield in the invariant-mass region 0:3 - 0:7 GeV/c2 in p+Be collisions at 4:9 GeV/u beam energy [2] was announced by the DLS collaboration [1]. Recent results of the HADES collaboration show a moderate enhancement above n Dalitz decay contributions for 12C+12C at 1 and 2 GeV/u [3, 4] confirming the DLS results. There are several theoretical explanations of this observation, most of them focusing on possible in-medium modifications of the properties of vector mesons. At low beam energies the question whether the observed excess is related to any in-medium effects remains open because of uncertainties in the description of elementary di-electron sources. In this work the di-electron production in p+p and d+p reactions at a kinetic beam energy of 1:25 GeV/u measured by the HADES spectrometer is discussed. At Ekin = 1:25 GeV/u, i.e. below the n meson production threshold in proton-proton reactions, the delta Dalitz decay is expected to be the most abundant source above the pi 0 Dalitz decay region. The observed large difference in di-electron production in p+p and d+p collisions suggests that di-electron production in the d+p system is dominated by the n+p interaction. In order to separate delta Dalitz decays and np bremsstrahlung the di-electron yield observed in p+p and n+p reactions, both measured at the same beam energy, has been compared. The main interest here is the investigation of iso-spin effects in baryonic resonance excitations and the off-shell production of vector mesons [5]. We indeed observe a large difference in di-electron production in p+p and n+p reactions. Results of these studies will be compared to recent calculations. We will also present our experimentally defined cocktail for heavy-ion data. At much higher beam energies experimental results of the CERES [6] and NA60 [7] collaborations also show an enhancement in the invariant mass region 0:3 - 0:7 GeV/c2, in principle similar to the situation in DLS. A strong excess of lepton pairs observed by recent high energy heavy-ion dilepton experiments hint to a strong influence of baryons, however no data exist at highly compressed baryonic matter, achievable in heavy-ion collisions from 8 - 45 GeV/u beam energy. These conditions would allow to study the expected restoration of chiral symmetry by measuring in-medium modifications of hadronic properties, an experimental program which is foreseen by the future CBM experiment at FAIR. The experimental challenge is to suppress the large physical background on the one hand and to provide a clean identification of electrons on the other hand. In this work, strategies to reduce the combinatorial background in electron pair measurements with the CBM detector are discussed. The main goal is to study the feasibility of effectively reducing combinatorial background with the currently foreseen experimental setup, which does not provide electron identification in front of the magnetic field.
The documentation of life on Earth, that is, the inventorization of nature and the naming and classification of organisms found therein, is a major task for biologists today and a fundamental precondition for nature conservation efforts. This study aimed at contributing to the inventory of amphibians and reptiles in selected, previously understudied ecoregions of Bolivia. I strove to document diversity patterns and seek possible ecological and historical reasons for these patterns. Special attention was paid to the Chiquitano Region situated in the eastern lowlands of Bolivia in a climatic transition zone between the humid evergreen Amazon Forests and the deciduous thorn-scrub vegetation of the Gran Chaco. In congruence with its location in the transition zone, the Chiquitano Region displays a mosaic of habitats: The vegetation is dominated by the endemic Chiquitano Dry Forest, which is probably the largest extant patch of Seasonal Dry Tropical Forest, with enclaves of savanna, the western outliers of the Cerrado biome of central Brazil. Taxonomic revisions: The taxonomic data in this study are used as a tool to measure biodiversity, to assess biogeographic relationships, and to evaluate conservation needs. Since all is predicated on the taxonomic decisions made, an adequate taxonomy is essential, and taxonomy can be regarded as the foundation of this study. The methodology encompassed a variety of herpetological field techniques, such as different survey methods, preparation and documentation of voucher specimens, recording of frog calls, and herpetological laboratory techniques, such as morphology, molecular procedures with mtDNA, phylogenetic analyses, and bioacoustic analysis and descriptions of frog calls. A total of 1251 specimens belonging to 200 species were obtained during this study, including 87 amphibian and 123 reptile species. This constitutes about 36% of the herpetofauna currently known for Bolivia, about 34% of the amphibians currently known for Bolivia and about 40% of the reptiles, respectively. In the course of this study, a new species of frog was described from the study site Caparu in the eastern lowlands of Bolivia; this species, Hydrolaetare caparu Jansen, Gonzales & G. Köhler 2007, differs from the other two congeners in external morphology (e.g., lateral fringes and relative length of fingers, size of palmar tubercle, webbing of toes, and colouration) and advertisement call. Two new colubrid snake species were also described from the study site San Sebastián. Thus far, both are known only from the Chiquitano Region, Provincia Ñuflo de Chávez. Phalotris sansebastiani Jansen & G. Köhler 2008 differs from all the other species in the genus in having a triangular projection of the red snout colouration reaching onto the parietals. Xenopholis werdingorum Jansen, Gonzales & G. Köhler 2009 can be identified as a member of the genus Xenopholis by its vertebral morphology. It differs from the other two species of Xenopholis in having a unique uniform dorsal colour pattern, and from X. scalaris in having two prefrontals and a narrow septum within the neural spine and perpendicular to its long axis as evident in the x-ray images. A review of a small collection of pitvipers from different lowland localities and from the Inter-Andean dry valleys of the region of Pampagrande revealed one new species of Bothrops and one of Bothrocophias (both to be formally described elsewhere). The two pitviper species differ morphologically and genetically from their congeners. The results of a brief review of a small collection of frogs of the genus Scinax (Anura: Hylidae) from different localities in the lowlands, together with analyses of their bioacoustics, suggest an unknown cryptic diversity in Bolivian species of Scinax cf. fuscomarginatus and allies. However, further studies are necessary to clarify the taxonomic status of these populations. In addition, this study provides new data on the morphology (e.g., pholidosis) of snakes, many of them previously known only from few museum specimens. Keys to the Bolivian lizard species of Cercosaura and the Bolivian snake species of Chironius, Clelia, Liophis, Lystrophis, Phalotris, and Xenodon are presented here for the first time. New information on distribution includes many range extensions of amphibian and reptile species, such as five new country records (one frog species, four snake species) and six new departmental records (two frog species, four snake species). Observations on ecology and natural history: Several observations on ecology and natural history were made during field work. Visual signaling, an aspect of territorial behavior that was already known for several species of the genus Phyllomedusa, could be described for the first time for Phyllomedusa boliviana (Jansen & J. Köhler 2007). Furthermore, during audio surveys of an anuran community at the study site San Sebastián from 2005 to 2007, a decline of certain amphibian populations was observed in the rainy season 2006/2007 (Jansen et al., in press). This is possibly related to an extreme drought in the dry season of 2006 where 158 consecutive days without rainfall were recorded. In addition, a new method for measuring intensity of anuran choruses by means of a continuous sound pressure metre was developed (Jansen 2009). The method was suitable to detect calling phenology (during one night), as well as differences in calling activity (between two nights). Biodiversity and biogeographical relationships: Species lists were compiled at the six study sites Pampagrande, Los Volcanes, San Sebastián, Caparú, El Espinal und El Corbalan. The total amphibian and reptile species numbers observed ranged from 37 to 101 with the highest species numbers in San Sebastián (101) and Caparú (89) and the lowest in Los Volcanes (37) and El Espinal (41). A preliminary species list of the herpetofauna of the Chiquitano Region was presented, including 60 amphibian and 84 reptile species. The majority of the amphibians of the Chiquitano Region are classified predominantly as inhabitants of open formations (41 species, 68.3%). Interestingly, even the majority of species recorded from the Chiquitano Dry Forest (32 species) are usually associated with open formations (22 species, 66.7%), followed by the number of species associated with open and forest formations (8 species, 24.4%). Only two of the observed species (6.0%) are predominant forest dwellers. The amphibian assemblage of the Chiquitano Region is most similar in composition to that of the Cerrado biome: 46 species (76.7%) occur in the Cerrado as well, and three species are regarded as Cerrado endemics (5.0%). The Chiquitano Region shares considerably fewer amphibian species with the other biomes (Amazon: 22 species, 36.7%; Gran Chaco: 13 species, 21.7%; Caatinga: 16 species, 26.7%). The reptile assemblage also has significant affinities to the Cerrado, which can be seen in the high proportion of reptile species distributed in that biome (68 species; 81.0%). Affinities to the other biomes are as follows: Amazon (48 species, 57.1%), Chaco (37 species, 40.1%), and Caatinga (30 species, 35.7%). When arranged in mutually exclusive biome categories, reptiles and amphibians showed similar patterns so that the majority of both amphibians and reptiles of the Chiquitano Region can be regarded as widespread. The high proportion of reptile species probably endemic to this region (5 species, 6.0%) is remarkable (i.e. Tropidurus xanthochilus, Apostolepis phillipsi, Phalotris sansebastiani, Xenopholis werdingorum, and Micrurus diana). In an analysis of the biodiversity patterns and biogeographical relationships of the herpetofauna of the study sites, these sites were compared with literature data from 37 localities and included in a presence/absence matrix with a total of 657 amphibian and reptile species in the surrounding South American biomes Amazon, Cerrado and Gran Chaco. The biogeographic relationships between these sites were evaluated using the Coefficient of Biogeographic Resemblance (CBR), cluster analysis, and multidimensional scaling (MDS) of sites. The analyses were first conducted on amphibians and reptiles combined, and than group-specific each for amphibians, reptiles, lizards, and snakes, separately. A “bias-reduced analysis” was developed for a better understanding of the affinities of the amphibians. In this analysis, e.g., the distinct habitat types of the Chiquitano Region, the Chiquitano Dry Forest and the Cerrado were taken into account. Analyses of the biodiversity patterns revealed that the sites in the Amazon comprise highest species numbers, as expected, followed successively by the sites in the Cerrado biome and sites in-between the two biomes. Within the eastern lowlands of Bolivia, the Chiquitano Region is the most rich in species. Comparing it with the other South American sites, the Chiquitano Region has a surprisingly high alpha diversity, especially in amphibians. The microgeographic variation in species composition (beta diversity) in the Chiquitano Region is also remarkably high and obviously related to the mosaic character of the vegetation and habitats. However, the bias-reduced analysis revealed that the amphibian fauna of the open areas and savannas at Hacienda San Sebastián (with 36 species in the Cerrado and pastureland) was one of the most species-rich savanna sites known for amphibians in South America. Considering that the Hacienda San Sebastián site is only ca. 3300 ha (= 1.29 amphibian species per km2), this outcome is particularly suprising. The results of the analyses of the biogeographical relationships suggest that the herpetofauna of Bolivia’s lowlands, including the Beni, the Pantanal and the Chiquitano Region, is as distinct from the herpetofauna of the Gran Chaco, Amazon, and Cerrado as these biomes are from each other. The Chiquitano herpetofauna in particular represents a unique and well-defined herpetofaunal assemblage when compared to all surrounding localities and biomes. This is supported by high CBR-values, findings from the cluster analysis, as well as a clear separation of the Chiquitano sites in the MDS. Biogeographic relations exist in all the surrounding biomes, but are strongest to Cerrado, followed by the Amazon. This study strongly suggests that the Chiquitano herpetofauna is composite and has multiple affinities. This is congruent with a well-defined Chiquitano flora, avifauna and mammalian fauna, suggesting a similar history. The bias-reduced analysis revealed a more detailed picture of the biogeographic relations of the Chiquitano Region, especially the Chiquitano Dry Forest. I argue here that the Chiquitano Dry Forest herpetofauna is a “young”, and “former savanna herpetofauna”. Whereas the Chiquitano Dry Forest is rather poor in amphibian and reptile species, and endemics are lacking from this forest type, the isolated Cerrado enclaves are especially diverse in species and probably contain locally endemic species, such as Phalotris sansebastiani and Xenopholis werdingorum. The colonization of the young Chiquitano Dry Forest may have taken place from savannas by mainly open area species, and only briefly through the Amazon. The results emphasise the importance of bias-reduction in studies of biogeography, e.g., by using group-specific analyses or by taking into account criterias as area size and heterogeneity of compared sites. The different biogeographic patterns of reptiles and amphibians of the Andean valleys indicate a different history of these two groups. In regard to reptiles, dispersals and withdrawals into the valleys in warm humid and dry cool periods in the Pleistocene seem likely, supported by a relation between the valleys and the dry lowland (e.g., Chaco). However, it is more plausible that, during these climatic fluctuations, amphibians migrated to adjacent, more humid regions, such as Yungas. The study verified the known patterns of sister-species pairs in the Inter-Andean Dry Forest and the lowlands. Additionally, pairs of populations with slight differences in morphology were found in the valleys and in the lowlands (Cercosaura parkeri and Xenodon rhapdocephalus). Further studies must test the taxonomic status of these populations. The discovery of new species of Bothrops and Bothrocophias from the Andean valleys has several implications, and possible reasons for the high endemism in the dry valleys are discussed. Conservation and outlook: The high local alpha and beta diversity of the Chiquitano herpetofauna shows that this is a region of complex faunal interaction, which reflects the present heterogeneity of the region, but which is possibly also related to a complex geological and environmental history. The Chiquitano Region can be assessed as a region of distinct regional herpetofaunal diversity charaterised by small scale diversity patterns. It therefore merits recognition as a unique ecoregion, and conservation effort should be increased. Further research is necessary to solve the taxonomic problems addressed in this study. Moreover, future work should be directed towards the development and institution of longterm monitoring programs to evaluate the effects of climate change and changes in land-use on biodiversity, especially that of the Chiquitano Region.
The physiology of our most complex organ, the brain, is still not comprehensively understood. The brain basically serves the processing, storing and binding of external and internal information, and thereby generates amazing phenomena like the understanding of oneself as an individual entitiy. How exactly information is encoded and represented, how individual neurons or networks of neurons actually interact, is a gigantic puzzle, whose pieces were collected since many decades. Subject of scientific discussions are the basic spatiotemporal structures of neuronal representations. Suggestions and observations reach hereby from simple rate coding of individual neurons to synchronous activity of larger ensembles. To approach answers to these questions, our working group has used a combination of different recording techniques that allowed for the comparison of neuronal interactions on different spatial scales. We focused on prefrontal neuronal interactions during visual short-term memory. Herefore two rhesus monkeys had been trained to perform a visual short-term memory task. We measured and recorded their neuronal activity by means of a microelectrode matrix that could be inserted into the cortex via a closable chamber, which had been previously implanted above prefrontal cortex. The acquired signal was separated into two components: a high-frequency component, that represents the spiking output activity of few neurons in the vicinity of each electrode tip (multi-unit activity), and a low-frequency component, that results from dendritic input activity of larger neuronal assemblies (local field potential). From one of the experimental animals we also recorded mass signals of even larger neuronal populations by means of small silverball electrodes, that had been implated into the skull above prefrontal cortex (skull EEG) in the context of a pilot project. In the first subproject, we analyzed the selectivity of output signals with respect to the memorized stimulus and task performance. We compared selectivities of local recording sites (multi-unit activity) with the selectivities of patterns created by the combined activity of all recording sites, thus representing the activity of large and distributed ensembles. Local neuronal activity correlated with the course of the visual short-term memory task, but was not highly discriminative with respect to different visual stimuli. We could show that the population activity was significantly more specific. Concerning task performance, we obtained the same result, albeit less pronounced. Further analyses revealed that the patterns of distributed ensemble activity were only partly based on realtime coordination of neuronal activity, and in addition, did not remain stable across the time course of the short-term memory task. In the second subproject, we focused on the oscillatory behavior of the local field potential. After a time-frequency analysis, we studied different frequency bands concerning stimulus selectivity and task performance of the monkey. We hereby found significant modulations of oscillations in the beta- and gamma-frequency range, that correlated with different periods of the task. Especially for oscillations in beta- and low-gamma-range, we observed phase-locking of oscillations between different recording sites, which could play an important role as internal clock to coordinate spatially separate activity. Local high-gamma oscillations themselves seemed to be important for the maintenance of information. These results could be partly confirmed by mass signals of EEG. In sum, our results support the hypothesis that information is represented in the brain by means of concerted activity of spatially distributed neuronal ensembles. This activity again appears to be coordinated by oscillatory activity in beta- and low-gamma-frequency ranges. A deeper understanding of central nervous information processing could contribute to better treatment of diseases like Parkinson’s, Alzheimer’s as well as epilepsy, and neuropsychiatric disorders like schizophrenia.
Epidermal growth factor (EGF) receptor belongs to the broad family of enzymatic receptors called receptor tyrosine kinases (RTKs). Generally, the binding of a ligand to these receptors leads to activation of their intracellular kinase activity that sets in motion a cascade of signaling events. In order to ensure appropriate responses to physiological stimuli, the cell is endowed with the ability to regulate signal transduction via numerous mechanisms such as dephosphorylation of the RTK and its substrates as well as downregulation of the RTK. Activation of EGFR is a potent mitogenic (proliferative) and motogenic (cell motility) signal that plays crucial roles during embryonic development and maintenance of adult tissue. EGFR signaling is primarily regulated by ligand-induced receptor internalization with subsequent degradation in lysosomes. While the complex of proteins that are recruited to EGFR after its activation is well understood, proteins that interact with the receptor in the absence of ligand binding are still not systematically studied. With the goal of identifying novel binding partners of non-activated EGFR, a membrane based yeast-two hybrid screen (MYTH) was conducted. MYTH is based on the principle of in vivo reconstitution of the N-terminus (Nub) and C-terminus (Cub) halves of ubiquitin once brought into close proximity. A chimeric protein consisting of EGFR fused to Cub and a transcription factor was used as a bait to screen Nub-tagged cDNA library. Analysis of resultant yeast transformants revealed a total of 87 proteins to interact with EGFR. Of these only 11 were previously shown to bind to EGFR. A majority of the other proteins were shown to interact with the receptor by yeast retransformation. Fifteen were confirmed to bind to EGFR by coimmunoprecipitation assays in mammalian cells. One of the novel EGFR interactors identified in the screen was histone deacetylase 6 (HDAC6). This deacetylase is localized in the cytoplasm and known to deacetylate alpha-tubulin, HSP90 and cortactin. The juxtamembrane region of EGFR binds to the Cterminus of HDAC6. Functionally, overexpression of wild type HDAC6 stabilized ligand-induced degradation of the receptor. On the other hand, deacetylase deficient or EGFR binding compromised mutants of HDAC6 were able to stabilize EGFR only partially. Downmodulation of HDAC6 expression by RNAi markedly accelerated degradation of the receptor. Taken together, HDAC6 is a negative regulator of EGFR downregulation that is dependent on its deacetylase activity and ability to bind to the receptor. Imaging studies revealed that HDAC6 does not affect internalization of EGFR from the plasma membrane but rather influences the post-endocytic trafficking of the receptor-ligand complex to lysosomes. Pulse-chase experiments using fluorophoretagged EGF showed that EGFR is transported faster towards the peri-nuclear region and delivered to late endosomes rapidly in HDAC6 depleted cells. HDAC6 is demonstrated to act, at least partly, by regulating the acetylation of alpha-tubulin. Upon EGFR activation, acetylation of alpha-tubulin on lysine 40 is progressively increased as shown by mass spectrometry and immunoblotting. Forced expression of a dominant negative mutant of alpha-tubulin, but not wild type alpha-tubulin, led to reduced speed and processive movement of early endosomes in GFP-Rab5 expressing cells. In a surprising twist, EGFR is able to phosphorylate HDAC6 on Tyr570. Phosphorylation of Tyr570 and Ser568 leads to inactivation of the deacetylase function of HDAC6 as shown by in vivo and in vitro assays. In summary, HDAC6 diminishes EGFR downregulation by slowing the transport of intracellular vesicles. The inhibitory effect is removed once HDAC6 is phosphorylated on key residues. In line with these findings, two recent reports have shown that hyper-acetylation of alpha-tubulin induced by inhibition of HDAC6 increases the transport of brain derived neurotrophic factor and JNK interacting protein-1 in different cell systems. Acetylated microtubules are more efficient in recruiting motor proteins like kinesin-1 and dynein. These findings indicate that HDAC6 plays an important regulatory role in intracellular trafficking pathways. However, several outstanding issues still remain unresolved. How does acetylation of microtubules influence vesicular trafficking? In this regard, the temporal and spatial dynamics of alpha-tubulin acetylation following EGFR activation should be studied. Furthermore, whether HDAC6 affects the trafficking of other endocytic cargos and additional organelles is an interesting question to address.
In this thesis we have studied the physics of different ultracold Bose-Fermi mixtures in optical lattices, as well as spin 1=2 fermions in a harmonic trap. To study these systems we generalized dynamical mean-field theory for a mixture of fermions and bosons, as well as for an inhomogeneous environment. Generalized dynamical mean-field theory (GDMFT) is a method that describes a mixture of fermions and bosons. This method consists of Gutzwiller mean-field for the bosons, and dynamical mean-field theory for the fermions, which are coupled on-site by the Bose-Fermi density-density interaction and possibly a Feshbach term which converts a pair of up and down fermions into a molecule, i.e. a boson. We derived the self-consistency equations and showed that this method is well-controlled in the limit of high lattice coordination number z. We develop real-space dynamical mean-field theory for studying systems in an inhomogeneous environment, e.g. in a harmonic trap. The crucial difference compared to standard DMFT is that we are taking into account that different sites are not equivalent to each other and thus take into account the inhomogeneity of the system. Different sites are coupled by the real-space Dyson equation. ...
Breaking tolerance to the natural human liver autoantigen cytochrome P450 2D6 by virus infection
(2009)
Autoimmune hepatitis (AIH) is a chronic liver disease of unknown etiology, characterized by a loss of tolerance against hepatocytes leading to the progressive destruction of hepatic parenchyma and cirrhosis. Clinical signs for AIH are interface hepatitis and portal plasma cell infiltration, hypergammaglobulinemia, and autoantibodies. Based on serological markers AIH is defined in subtypes. The hallmark of AIH type 2 are type 1 liver/kidney microsomal autoantibodies (LKM-1), whereas AIH type 1 is characterized by the presence of anti-nuclear (ANA) and/or anti-smooth muscular (SMA) autoantibodies. The major autoantigen recognized specifically by LKM-1 autoantibodies was identified as the 2D6 isoform of the cytochrome P450 enzyme family (CYP2D6). Not much is known about the etiology and pathogenic mechanisms of AIH so far and most animal models available result in only transient hepatic liver damage after a rather complex initiation method. It was the aim of my project to generate a novel animal model for AIH that reflects the chronic and progressive destruction of the liver characteristic for the human disease while using a defined and feasible initiating event to further analyze the pathogenic mechanisms leading to the autoimmune-mediated destruction of the liver. Therefore, mice transgenically expressing the human CYP2D6 in the liver and wild-type mice were infected with a liver-tropic adenovirus expressing the human CYP2D6 (Ad-2D6). Selftolerance to CYP2D6 was broken in Ad-2D6-infected mice, resulting in persistent autoimmune liver damage, apparent by cellular infiltration, hepatic fibrosis and necrosis. Similar to type 2 AIH patients, Ad-2D6-infected mice generated LKM-1-like antibodies recognizing the same immunodominant epitope of CYP2D6. Taken together, we could introduce a new animal model that reflects the persistent autoimmune-mediated liver damage as well as the serological marker characteristic for AIH type 2 and we could demonstrate that chronic autoimmune diseases targeting the liver can be triggered by molecular mimicry occurring in the context of a hepatotropic viral infection.
In this work, we extend the Hegselmann and Krause (HK) model, presented in [16] to an arbitrary metric space. We also present some theoretical analysis and some numerical results of the condensing of particles in finite and continuous metric spaces. For simulations in a finite metric space, we introduce the notion "random metric" using the split metrics studies by Dress and al. [2, 11, 12].
SIVsmmPBj-derived lentiviral vectors are capable of efficient primary human monocyte transduction, a capacity which is linked to the viral accessory protein Vpx. To enable novel gene therapy approaches targeting monocytes, in this thesis it was aimed to generate enhanced lentiviral vectors that meet the required standards for clinical applications with respect to gene transfer efficiency and safety. The vectors were tested for their suitability in a relevant therapeutic gene transfer approach. At first, it was investigated whether vectors derived from another Vpx-carrying lentivirus reveal the same capacity for monocyte transduction as SIVsmmPBj-derived vectors. A transduction experiment using HIV-2-derived vectors in comparison to PBj-derived vectors revealed a comparable transduction capacity, thus disproving the assumed uniqueness of the PBj vectors. The further generation and analysis of expression constructs for the vpx genes of HIV-2 and SIVmac demonstrated a similar functionality in monocyte transduction as the Vpx of PBj. As VpxPBj, both Vpx proteins facilitated monocyte transduction of a vpx-deficient PBj-derived vector system. For the generation of enhanced SIVsmmPBj and HIV-2 vector systems, only the transfer vectors were optimized, since the packaging vectors available already meet current standards. At first, several modifications were introduced into an available preliminary PBj-derived transfer vector by conventional cloning. The modifications included insertions of cPPT/CTS and WPRE as well as the deletions of the remaining pol sequence, the second exons of tat end rev, and the U3-region within the 3’LTR to generate a SIN vector. Thus, beside safety enhancement, the vector titers were also increased from 9.1x105 TU/ml achieved after concentration with the initial transfer vector up to 1.1x107 TU/ml with the final transfer vector. The PBj vector retained its capability of monocyte transduction when supplemented with Vpx. This conventional method of vector enhancement is time-consuming and may result in only sub-optimal vectors, since it depends on the presence of restriction sites which may not allow deletion of all needless sequences. Moreover, mutations may accumulate during the high number of cloning and amplification steps. Therefore, a new and easier method for lentiviral transfer vector generation was conceived. Three essential segments of the viral genome (5‘ LTR, RRE, ΔU3-3’ LTR) are amplified on the template of the lentiviral wild-type genome and fused by Fusion-PCR. Further necessary elements namely the cPPT/CTS-element, MCS, and PPT are included into the resulting vector by extension of the nucleotide primers used for the PCRs. The amplified and fused vector-scaffold can easily be integrated into a plasmid backbone, followed by insertion of the expression cassette of choice. By applying this approach, two novel lentiviral transfer vectors, based on the non-human SIVsmmPBj and the human HIV-2, were derived. Vector titers achieved for PBj and HIV-2 vectors supplemented with Vpx reached up to 4.0x108 TU/ml and 5.4x108 TU/ml, respectively. The capacity for monocyte transduction was maintained. Thus, safe and efficient, state of the art HIV-2- and PBj-derived vector systems are now available for future gene therapy strategies. Finally, the new vectors were used to set up an approach for gene correction of gp91phox-deficient monocytes for the treatment of X-linked chronic granulomatous disease (xCGD). The administration of autologous, gene-corrected monocytes to counteract systemic and acute infections could lead to a decreased infection load, dissolve granulomas and therefore improve the survival rate of hematopoietic stem cell transplantation (HSCT) which is the current treatment of choice for this disease. First, methods for analysis of gp91phox function were established. Next, they were employed to demonstrate the capacity of monocytes, obtained from healthy humans or mice, for phagocytosis, oxidative burst, and Staphylococcus aureus killing. The in vivo half-life of murine monocytes in the bloodstream and their distribution to specific tissues was determined. Lastly, HIV-1 vectors were used to transfer the gp91phox gene into monocytes from gp91phox-deficient mice. This resulted in the successful restoration of the oxidative burst ability in the cells. In summary, the general suitability of the new vectors for treatment of CGD by monocyte transduction was demonstrated. The results of the mouse experiments provide the foundation for future challenge experiments to evaluate the capability of gene-corrected monocytes to kill off microbes in vivo.
Das libor Markt Modell (LMM) ist seit seiner Entwicklung in den Veröffentlichungen von Brace, Gatarek, Musiela (1997), einerseits, und unabhängig von diesen von Miltersen, Sandmann, Sondermann (1997), andererseits, zu dem anerkanntesten Instrument zur Modellierung der Zinsstruktur und der damit verbundenen Preisfindung für relevante Finanzderivate geworden. libor steht dabei für London Inter-Bank Offered Rate, ein täglich in London fixierter Referenz-Zins für kurzfristige Anlagen. Drei- oder sechsmonatige Laufzeiten sind in Verbindung mit dem LMM üblich. Die Forschung zur Verbesserung dieses Modells hat in den letzten Jahren an Zuwachs gewonnen. Beim Versuch den Fehler der Anpassung an die täglich beobachteten Preise von Zinsoptionen wie Caps und Swaptions zu verringern, erhält man in der Folge auch genauere Bewertungen für andere, exotischere, Derivate. Die zugrunde liegende und zentrale Idee des LMM besteht darin, die Forward (Termin) Zinsen direkt als primären (Vektor) Prozess mehrerer libor Sätze zu betrachten und diese simultan zu modellieren, anstatt sie nur herzuleiten aus einem übergeordneten, unendlich dimensionalen Forward Zinsprozess, wie im zeitlich früher entwickelten Heath-Jarrow-Morton Modell. Das überzeugendste Argument für diese Diskretisierung ist, dass die libor Sätze direkt im Markt beobachtbar sind und ihre Volatilitäten auf eine natürliche Weise in Beziehung gebracht werden können zu bereits liquide gehandelten Produkten, eben jenen Caps und Swaptions. Dennoch beinhaltet das Modell eine gravierende Insuffizienz, indem es keine Krümmung der Volatilitätsoberfläche, im Hinblick auf Optionen mit verschiedenen Basiszinsen, abbildet. Wie im einfachen eindimensionalen Black-Scholes Modell prägen sich auch hier die Ungenauigkeiten der Verteilung in fehlenden heavy tails deutlich aus. Smile und Skew Effekte sind erkennbar. Im klassischen liborMarkt Modell wird in Richtung der Basiszinsdimension nur eine affine Struktur erzeugt, welche bestenfalls als Approximation für die erwünschte Oberfläche dienen kann. Die beobachteten Verzerrungen führen naturgemäss zu einer ungenauen Abbildung der Realität und fehlerhaften Reproduktion der Preise in Regionen, die ein wenig entfernt vom Bereich am Geld liegen. Derartig ungewollte Dissonanzen in Gewinn und Verlustzahlen führten z.B. in 1998 zu gravierenden Verlusten im Zinsderivateportfolio der heutigen Royal Bank of Scotland. ...
The bulk viscosity of several quark matter phases is calculated. It is found that the effect of color superconductivity is not trivial, it may suppress, or enhance the bulk viscosity depending on the critical temperature and the temperature at which the bulk viscosity is calculated. Also, is it found that the effect of neutrino-emitting Urca processes cannot be neglected in the consideration of the bulk viscosity of strange quark matter. The results for the bulk viscosity of strange quark matter are used to calculate the r-mode instability window of quark stars with several possible phases. It is shown that each possible phase has a different structure for the r-mode instability window.
In this thesis the first fully integrated Boltzmann+hydrodynamics approach to relativistic heavy ion reactions has been developed. After a short introduction that motivates the study of heavy ion reactions as the tool to get insights about the QCD phase diagram, the most important theoretical approaches to describe the system are reviewed. To model the dynamical evolution of the collective system assuming local thermal equilibrium ideal hydrodynamics seems to be a good tool. Nowadays, the development of either viscous hydrodynamic codes or hybrid approaches is favoured. For the microscopic description of the hadronic as well as the partonic stage of the evolution transport approaches have beeen successfully applied, since they generate the full phse-space dynamics of all the particles. The hadron-string transport approach that this work is based on is the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) approach. It constitutes an effective solution of the relativistic Boltzmann equation and is restricted to binary collisions of the propagated hadrons. Therefore, the Boltzmann equation and the basic assumptions of this model are introduced. Furthermore, predictions for the charged particle multiplicities at LHC energies are made. The next step is the development of a new framework to calculate the baryon number density in a transport approach. Time evolutions of the net baryon number and the quark density have been calculated at AGS, SPS and RHIC energies and the new approach leads to reasonable results over the whole energy range. Studies of phase diagram trajectories using hydrodynamics are performed as a first move into the direction of the development of the hybrid approach. The hybrid approach that has been developed as the main part of this thesis is based on the UrQMD transport approach with an intermediate hydrodynamical evolution for the hot and dense stage of the collision. The initial energy and baryon number density distributions are not smooth and not symmetric in any direction and the initial velocity profiles are non-trivial since they are generated by the non-equilibrium transport approach. The fulll (3+1) dimensional ideal relativistic one fluid dynamics evolution is solved using the SHASTA algorithm. For the present work, three different equations of state have been used, namely a hadron gas equation of state without a QGP phase transition, a chiral EoS and a bag model EoS including a strong first order phase transition. For the freeze-out transition from hydrodynamics to the cascade calculation two different set-ups are employed. Either an in the computational frame isochronous freeze-out or an gradual freeze-out that mimics an iso-eigentime criterion. The particle vectors are generated by Monte Carlo methods according to the Cooper-Frye formula and UrQMD takes care of the final decoupling procedure of the particles. The parameter dependences of the model are investigated and the time evolution of different quantities is explored. The final pion and proton multiplicities are lower in the hybrid model calculation due to the isentropic hydrodynamic expansion while the yields for strange particles are enhanced due to the local equilibrium in the hydrodynamic evolution. The elliptic flow values at SPS energies are shown to be in line with an ideal hydrodynamic evolution if a proper initial state is used and the final freeze-out proceeds gradually. The hybrid model calculation is able to reproduce the experimentally measured integrated as well as transverse momentum dependent $v_2$ values for charged particles. The multiplicity and mean transverse mass excitation function is calculated for pions, protons and kaons in the energy range from $E_{\rm lab}=2-160A~$GeV. It is observed that the different freeze-out procedures have almost as much influence on the mean transverse mass excitation function as the equation of state. The experimentally observed step-like behaviour of the mean transverse mass excitation function is only reproduced, if a first order phase transition with a large latent heat is applied or the EoS is effectively softened due to non-equilibrium effects in the hadronic transport calculation. The HBT correlation of the negatively charged pion source created in central Pb+Pb collisions at SPS energies are investigated with the hybrid model. It has been found that the latent heat influences the emission of particles visibly and hence the HBT radii of the pion source. The final hadronic interactions after the hydrodynamic freeze-out are very important for the HBT correlation since a large amount of collisions and decays still takes place during this period.
Induced charge computation
(2009)
One of the main aspects of statistical mechanics is that the properties of a thermodynamics state point do not depend on the choice of the statistical ensemble. It breaks down for small systems e.g. single molecules. Hence, the choice of the statistical ensemble is crucial for the interpretation of single molecule experiments, where the outcome of measurements depends on which variables or control parameters, are held fixed and which ones are allowed to fluctuate. Following this principle, this thesis investigates the thermodynamics of a single polymer pulling experiments within two different statistical ensembles. The scaling of the conjugate chain ensembles, the fixed end-to-end vector (Helmholtz) and the fixed applied force (Gibbs), are studied in depth. This thesis further investigates the ensemble equivalence for different force regimes and polymer-chain contour lengths. Using coarse-grained molecular dynamic simulations, i.e. Langevin dynamics, the simulations were found to complement the theoretical predictions for the scaling of ensemble difference of Gaussian chains in different force-regimes, giving special attention to the zero force regime. After constructing Helmholtz and Gibbs conjugate ensembles for a Gaussian chain, two different data sets of thermodynamic states on the force-extension plane, i.e. force-extension curves, were generated. The ensemble difference is computed for different polymer-chain lengths by using force-extension curves. The scaling of the ensemble difference versus relative polymer-chain length under different force regimes has been derived from the simulation data and compared to theoretical predictions. The results demonstrate that the Gaussian chain in the zero force limit generates nonequivalent ensembles, regardless of its equilibrium bond length and polymer-chain contour length. Moreover, if polymers are charged in confinement, coarse-graining is problematic, owing to dielectric interfaces. Hence, the effect of dielectric interfaces must be taken into account when describing physical systems such as ionic channels or biopolymers inside nanopores. It is shown that the effect of dielectrics is crucial for the dynamics of a biopolymer or an ion inside a nanopore. In the simulations, the feasibility of an efficient and accurate computation of electrostatic interactions in the presence of an arbitrarily shaped dielectric domain is challenging. Several solutions for this problem have been previously proposed in the literature such as a density functional approach, or transforming problem at hand into an algebraic problem ( Induced Charge Computation (ICC) ) and boundary element methods. Even though the essential concept is the same, which is to replace the dielectric interface with a polarization charge density, these approaches have been analyzed and the ICC algorithm has been implemented. A new superior boundary element method has been devised utilizing the force computation via the Particle-Particle Particle-Mesh (P3M) method for periodic geometries (ICCP3M). This method has been compared to the ICC algorithm, the algebraic solutions, and to density functional approaches. Extensive numerical tests against analytically tractable geometries have confirmed the correctness and applicability of developed and implemented algorithms, demonstrating that the ICCP3M is the fastest and the most versatile algorithm. Further optimization issues are also discussed in obtaining accurate induced charge densities. The potential of mean force (PMF) of DNA modelled on a coarsed-grain level inside a nanopore is investigated with and without the inclusion of dielectric effects. Despite the simplicity of the model, the dramatic effect of dielectric inclusions is clearly seen in the observed force profile.
In this work the preparation of organic donor-acceptor thin films was studied. A chamber for organic molecular beam deposition was designed and integrated into an existing deposition system for metallic thin films. Furthermore, the deposition system was extended by a load-lock with integrated bake-out function, a chamber for the deposition of metallic contacts via stencil mask technique and a sputtering chamber. For the sublimation of the organic compounds several effusion cells were designed. The evaporation characteristic and the temperature profile within the cells was studied. Additionally, a simulation program was developed, which calculates the evaporation characteristics of different cell types. The following processes were integrated: evaporation of particles, migration on the cell walls and collisions in the gas phase. It is also possible to consider a temperature gradient within the cell. All processes can be studied separately and their relative strength can be varied. To verify the simulation results several evaporation experiments with different cell types were employed. The thickness profile of the prepared thin films was measured position-dependently. The results are in good agreement with the simulation. Furthermore, the simulation program was extended to the field of electron beam induced deposition (EBID). The second part of this work deals with the preparation and characterization of organic thin films. The focus hereby lies on the charge transfer salt (BEDT-TTF)(TCNQ), which has three known structure variants. Thin films were prepared by different methods of co-evaporation and were studied with optical microscopy, X-ray diffraction and energy dispersive X-ray spectroscopy (EDX).The formation of the monoclinic phase of (BEDT-TTF)(TCNQ) could be shown. As a last part tunnel structures were prepared as first thin film devices and measured in a He4 cryostat.
This dissertation consists of three chapters. The first two chapters investigate the real effects of inflation and the third chapter the role of child care for fertility and female female labor supply. Chapter 1 introduces a generalized panel threshold model to analyze the relation between inflation and economic growth for a sample of developing countries. It is demonstrated that allowing for regime intercepts can be crucial for obtaining unbiased estimates of both, inflation thresholds and its marginal effects on growth in the various regimes. The empirical results confirm that the omitted variable bias of standard panel threshold models can be statistically and economically significant. Chapter 2, which is joined work with Dieter Nautz, investigates the impact of inflation on relative price variability (RPV) as a further important channel of the real effects of inflation. With a view to the recent debate on the Fed's implicit lower and upper bounds of its inflation objective, the econometric model introduced in Chapter 1 is used to explore the inflation-RPV linkage in U.S. cities. Chapter 3 investigates the relationship between fertility, female labor supply and child care in the context of a life cycle model for Germany. A particular emphasis is placed on the differences between West and East Germany. Counterfactual policy experiments mimicking recent policy reforms on maternal leave and the provision of subsidized child care are conducted with a structurally estimated version of the model.
Global warming is expected to be associated with diverse changes in freshwater habitats in north-western Europe. Increasing evaporation, lower oxygen concentration due to increased water temperature and changes in precipitation pattern are likely to affect the survival ratio and reproduction rate of freshwater gastropods (Pulmonata, Basommatophora). This work is a comprehensive analyse of the climatic factors influencing their ranges both in the past and in the near future. A macroecological approach showed that for a great proportion of genera the ranges were projected to contract by 2080, even if unlimited dispersal was assumed. The forecasted warming in the cooler northern ranges predicted the emergence of new suitable areas, but also reduced drastically the available habitat in the southern part of the studied region. In order to better understand the ranges dynamics in the past and the post glacial colonisation patterns, an approach combining ecological niche modelling and phylogeography was used for two model species, Radix balthica and Ancylus fluviatilis. Phylogeographic model selection on a COI mtDNA dataset confirmed that R. balthica most likely spread from two central European disjunct refuges after the last glacial maximum. The phylogeographic analysis of A. fluviatilis, using 16S and COI mtDNA datasets, also inferred central European refugia. The absence of niche conservatism (adaptive potential) inferred for A. fluviatilis puts a cautionary note on the use of climate envelope models to predict the future ranges of this species. However, the other model species exhibited strong niche conservatism, which allow putting confidence into such predictions. A profound faunal shift will take place in Central Europe within the next century, either permitting the establishment of species currently living south of the studied region or the proliferation of organisms relying on the same food resources. This study points out the need for further investigations on the dispersal modes of freshwaters snails, since the future range size of the species depend on their ability to establish in newly available habitats. Likewise, the mixed mating system of these organisms gives them the possibility to fund a new population from a single individual. It will probably affect the colonisation success and needs further investigation.
A solid-supported membrane (SSM) is an alkanethiol/lipid hybrid membrane with comparable lipid mobility, conductivity, and capacitance than a black lipid membrane (BLM). However, mechanical perturbations, which usually destroy a BLM, do not influence the life-time of a SSM, which is mechanically so stable that solutions may be rapidly exchanged at its surface. This key property has been utilized in this thesis to characterize electrophysiologically two bacterial secondary active transporters (MelB and LacY) as well as to investigate the specific interactions between ions and lipid membranes. These three different projects are summarized below: (1) The properties of lipid membranes, which represent the most important biological interface between intracellular and extracellular compartments, are essentially modulated by the ionic composition of the surrounding aqueous medium. To investigate specific interactions between ions and lipid membranes, solutions of different ionic composition were exchanged at the surface of a SSM through a flow system. This solution exchange resulted in charge translocations that were interpreted in terms of binding of the ions to the lipid headgroups at the SSM surface. We found that chaotropic anions and kosmotropic cations are attracted to the membrane independent of the membrane composition. In particular, the same behaviour was found for lipid headgroups bearing no charge like monoolein. This general trend is modulated by the electrostatic interaction of the ions with the lipid headgroup charge. Our experimental results are in agreement with recent molecular dynamic simulations of PC membranes. (2) Rapid solution exchange on a solid-supported membrane (SSM) is investigated using fluidic structures and a solid-supported membrane in a wall jet geometry. The flow was analyzed with a new technique based on specific ion interactions with the surface combined with an electrical measurement. The critical parameters affecting the time course of the solution exchange and the transfer function describing the time resolution of the SSM system were determined. The experimental data indicate that the solution transport follows a plug flow geometry while the rise of the surface concentration can be approximated by Hagen Poiseuille flow with ideal mixing at the surface of the SSM. Using an improved cuvette design a solution exchange as fast as 2 ms was achieved at the surface of a solid supported membrane. As an application of the technique the rate constant of a fast electrogenic reaction in the melibiose permease MelB, a bacterial (Escherichia coli) sugar transporter, is determined. For comparison, the kinetics of a conformational transition of the same transporter was measured using stopped-flow tryptophan fluorescence spectroscopy. The relaxation time constant obtained for the charge displacement agrees with that determined in the stopped-flow experiments. This supports the previous proposition that upon sugar binding MelB undergoes an electrogenic conformational transition with a rate constant of k ~ 250 s-1. (3) Electrogenic events due to activity of wild-type lactose permease from Escherichia coli (LacY) were investigated with proteoliposomes containing purified LacY adsorbed on a solid-supported membrane electrode. Downhill sugar/H+ symport into the proteoliposomes generates transient currents. Studies at different lipid to protein ratios and at different pH values, as well as inactivation by N-ethylmaleimide, show that the currents are due specifically to the activity of LacY. From analysis of the currents under different conditions and comparison with biochemical data, it is apparent that the predominant electrogenic event in downhill sugar/H+ symport is H+ release. In contrast, LacY mutants E325A and C154G, which bind ligand normally but are severely defective with respect to lactose/H+ symport, exhibit a minor electrogenic event upon addition of LacY-specific substrates, representing only 6% of the total charge displacement of the wild-type. This activity is due either to substrate binding per se or to a conformational transition following substrate binding. We propose that turnover of LacY involves at least two electrogenic reactions: (i) a minor reaction that occurs upon sugar binding and is due to a conformational transition in LacY; and (ii) a major reaction due to cytoplasmic release of H+ during downhill sugar/H+ symport, which is the limiting step for this mode of transport.
Information sent to and received by cells is essential for a homeostatic development of tissues and organs. These same signals are responsible for the good functioning of lymphatic organs and therefore govern the immune response. Dysfunctioning of the signaling networks is related to pathological situations, among which one can find cancer and auto-immune diseases. Intercellular communication involves the synthesis and the adjustment of signals by the secreting/emitting cell in order to reach the needed threshold. Diffusion of the signal to the target cell in addition to its interpretation lead to functional changes like cell migration and aggregation. Individual cells such as bacteria find food or increase their virulence through taxis (directional stimulus) and/or kinesis (speed stimulus). Immune cells appear to use the same processes to find bacteria and cellular debris, as well as to perform the cellular dance observed in germinal centers. This behavior is a result of an up or down regulation of specific signals that suggest to B and T-cells the paths to follow. Furthermore, cell segregation in the white pulp of the spleen, was also shown to be a result of a tight adjustment of T-cell kinesis. Restriction to cellular tracks and other experimentally provided measurements does not ensure a full comprehension of the observed cellular behavior. Thus, the study of patterns opens new gates to our understanding of the immune system. With the help of the agent-based modeling technique, cellular migration and aggregation are investigated in response to various cell-cell interactions. This work aims to explore different mechanisms that lead to cellular migration and aggregation, by defining the emergent properties of interest and that will help distinguish between interactions, starting by a simple look at the emergent patterns, followed by an analysis of their size, their degree of aggregation and the effective communication distances. Finally, the results obtained from the in silico experiments provided a guideline to differentiate between many cell-cell interactions under specific circumstances. Chemotaxis and phototaxis with and without diffusive cellular motion were shown to be distinguishable through an analysis of the emerging aggregation profiles.
The present PhD-thesis was prepared within subproject B8 of the DFG-Sonderforschungsbereich (SFB) 641 “The Tropospheric Ice Phase”. The subproject B8 was entitled “Interactions of volatile organic compounds with airborne ice crystals”. Results of previous studies have shown that various volatile organic compounds (VOC) and semivolatile organic compounds (SVOC) are incorporated into the atmospheric ice phase and several uptake mechanisms are discussed in the literature. The aim of this study was to identify the dominating VOC and SVOC in airborne snow collected at Jungfraujoch in the Swiss Alps (3580 m asl) and to study in laboratory experiments the uptake mechanism of organic compounds into snow and ice. For this purpose an analytical method to analyse freshly fallen snow samples was developed and evaluated in a first step. The method consists of headspace (HS) solid phase dynamic extraction (SPDE) followed by gas chromatography combined with mass spectrometry (GC/MS). During the extraction process a new cooling device was successfully integrated into the HS-SPDE-GC/MS method to enhance the extraction yield. Extraction and desorption parameters such as the number of extraction cycles, extraction temperature, desorption volume and desorption flow rate have been optimized. Detection limits for benzene, toluene, ethylbenzene, m-, p-, o- xylene (BTEX) ranged from 19 ng L-1 (benzene) to 30 ng L-1 (m/p-xylene), while those for C6-C10 n-aldehydes ranged from 21 ng L-1 (n-heptanal) to 63 ng L-1 (n-hexanal). Furthermore, freshly fallen snow samples were collected at the High Altitude Research Station Jungfraujoch (3580 m asl, Switzerland) during the field campaigns “Cloud and aerosol characterization experiment” (CLACE) 4 and 5 in February and March 2005 and 2006, respectively. Freshly fallen snow samples collected directly in-cloud on a high altitude remote location were used as approximation of airborne ice crystals since sampling of airborne ice crystals in quantities sufficient for analysis of individual organic compounds is not yet possible. In the collected snow samples a wide range of organic compounds were identified, namely BTEX, n-aldehydes (C6-C10), terpenes, chlorinated hydrocarbons and alkylated monoaromatics. The most abundant organic compounds in snow samples from Jungfaujoch during CLACE 4 and 5 were n-hexanal with a median concentration of 1.324 μg L-1 (CLACE 5) followed by n-nonanal (CLACE 5) with a median concentration of 1.239 μg L-1. High concentration variations of the analytes in snow samples collected at the same time at the same place argue for a heterogeneous composition of snow and ice. Several indicators were found that the origin of the n-aldehydes in the snow can be attributed to direct biogenic emissions from vegetation and indirect biogenic emissions through photochemical oxidation of fatty acids and alkenes. In a second step laboratory experiments were carried out to clarify the uptake mechanism of volatile and semivolatile organic compounds into snow/ice. Organic compounds can be incorporated into the atmospheric ice phase either by the process of gas scavenging, liquid scavenging (riming) or particle scavenging. Gas scavenging (incorporation of the organic compounds from the gas phase during growing of ice crystals) revealed to be ineffective based on previous laboratory experiments in which ice crystals were growing in the presence of aromatic hydrocarbons (BTEX) in the gas phase. In the present study the process of liquid scavenging (riming) was investigated in the laboratory using aqueous standard solutions containing BTEX, naldehydes (C6-C10), methyl tert-butyl ether (MTBE) and ethyl tert-butyl ether (ETBE). The headspace above the standard solution was sampled after adjusting the aqueous solutions to definite temperatures by use of a thermostat. Measurement were carried out at 25°C, 15°C and 5°C (water), -5°C and -15°C (supercooled water) and -25°C (ice). Results have shown that the known trend of lower gas phase concentrations over water concomitant with lower temperatures (Henry’s Law) is only valid for temperatures above 0°C. At temperature below 0°C, increasing concentrations of the analytes (BTEX, MTBE, ETBE and n-aldehydes) were determined in the gas phase together with decreasing temperatures. Dimensionless Henry’s law coefficients (KAW) were calculated from the concentrations of the organic compounds in the headspace above the standard solutions at temperatures between 25°C and -25°C. The observed inversion of Henry’s law coefficients of volatile and semivolatile organic compounds at a water temperature of approximately 0°C is explained by the formation of ordered zones of H2O molecules in supercooled water called “ice-like-clusters”. Together with decreasing temperatures the degree of formation of ordered zones increases which results in the removal of the organic molecules from the liquid phase and transfer into the gas phase. At a temperature of -25°C the supercooled water is converted into ice and a further significant increase of the gas phase concentrations of hydrophobic compounds such as BTEX is observed. In comparison, less hydrophobic compounds such as MTBE, ETBE and n-aldehydes are detected in lower amounts in the gas phase above the water/ice phase due to the higher water solubility and lower Henry coefficients compared to BTEX. The results show that in the absence of particles the uptake of BTEX MTBE, ETBE and C6-C10-naldehydes into ice not enhanced during freezing of a supercooled liquid, since at -25°C for these analytes the concentrations in the gas phase are higher at -25°C (ice) compared with -15°C (supercooled liquid). The heterogeneous distribution of BTEX and n-aldehydes concentrations in snow samples collected during the CLACE field campaigns suggests that adsorption of the organic compounds to particles followed by incorporation of the particles into the snow and ice might play a major role in the uptake process of organic compounds into snow and ice. To increase the knowledge about uptake processes of organic compounds into snow and ice further experiments are required with should include aerosol particles in the experimental setup to evaluate the influence of particle scavenging in the uptake processes.
Misregulated receptor tyrosine kinases (RTKs), i.e. the epidermal growth factor receptor EGFR or the insulin-like growth factor receptor 1 (IGF-1R), can be involved in the development of cancer. Monoclonal antibodies specifically inhibit the RTKs in cancer therapy. The scope of this thesis is to investigate the molecular basis of the inhibition through the therapeutic antibodies matuzumab (EMD72000) against EGFR and EMD1159476 against IGF-1R. The 3D crystal structure of matuzumab in complex with the EGFR domain III shows an eptiope connected with a novel inhibition mechanism: a non-competitive, sterical inhibition of receptor acitivation. The anti-IGF-1R targeted monoclonal antibody EMD1159476 shows a reduced binding capacity to the receptor in the presence of ligand indicating a competitive inhibition mechanism. The epitope of EMD1159476 is within domain II of the receptor. The results of these molecular interaction studies are important for the clinical therapies with these monoclonal antibodies. The matuzumab-EGFR complex crystal structure shows that a simultaneous binding of matuzumab and cetuximab (Erbitux) is possible. The latter antibody is already in clinical use. A combination of several therapeutic antibodies in cancer treatment might show synergistic effects and benefits for the patients.
New industries are recognized as new impetus to national wealth. At the same time, they are increasingly becoming geographically concentrated in some well defined areas. But current studies on the emergence of industrial clusters tend to analyze favorable driving factors. This dissertation takes the example of a Chinese endogenous industrial cluster, the traditional Chinese medicine (TCM) cluster at Tonghua, a small peripheral city in Northeastern China, to contribute to the theoretical understanding of the emergence of industrial cluster as a co-evolutionary process of organizations, institutions and firms, or, to put it more broadly, as economic evolution embedded in complex socio-economic contexts. The recent advance in evolutionary and co-evolutionary economics which considers the economy and economic landscape as dynamic process instead of equilibrium can be regarded as a part of broader and more intellectual turn of quest for history in social sciences. Although the principle of "history matters" is widely acknowledged, it tends to be reduced to a quite simple concept of "path dependence". However, path dependence cannot offer space for new path creation, except from an external shock. Accordingly, the role of human conscious action or Schumpeterian innovation should be added to path analysis through the concept of path creation. Furthermore, and more importantly, history should be understood as context, and historical context can be explored through the understanding of multi-paths and interaction among them over time. So path inter-dependence (co-evolution between paths) would be useful to better understand the complexity of real history. Since the industrial cluster is composed of interconnected firms and is also subject to changes in institution and technology, I will focus on the multi-way causal relationship between firm, institution and technology. The theorizing is not entirely new, but most of the theoretical and empirical discussions are at the national or industrial level, not regional or local one. A competitive cluster can be regarded as a co-evolutionary hotspot in which multiple populations actively interact and are interconnected. Co-evolution itself is a dynamic and evolutionary process. So I will adopt a dynamic and evolutionary view to examine co-evolutionary degree or co-evolutionary effects in the Tonghua pharmaceutical cluster through time. After a brief introduction which deals with the national institutional changes that are highly associated with new venture creation, entrepreneurship, and innovation, with registrations on drug and healthcare system, and with changes in market demand of China’s pharmaceutical industry and geographical distribution, I will collect evidences from three aspects based upon field survey and second hand data, i.e., the history of the enterprises, the origin of entrepreneurship, and the knowledge of evolution, linking their respective generative relationships through the genealogical method. In this volume, the evolution of the Tonghua pharmaceutical firm organization, the formation of local entrepreneurship, historical accumulation of knowledge, and particular knowledge of transfer among generations of firms will be discussed, then I will probe into co-adaption and co-evolution between local formal and informal institutions and organizations in Tonghua’s TCM industry. In addition, I will try to understand the co-evolutionary process at different geographical levels (namely, national and local). In summary, my main findings include the following several points. Firstly, in the course of the emergence of Tonghua’s pharmaceutical industry, local social networks and the traditional alliance between enterprises and government have played important roles. Secondly, the most important factor that influences the evolution of endogenous industrial clusters such as the Tonghua pharmaceutical industry in transitional countries is not the change in technology, but the change in fundamental national institutions. Thirdly, the success of the Tonghua pharmaceutical industry can be ascribed to the creation of multiple paths largely based on initial conditions, which implies that economic policy should have historical consciousness, namely, new economic innovation should make full use of both historical legacies and existing assets. Finally, it is co-adaption and co-selection of firm organization, institution, and technology that have jointly made Tonghua’s pharmaceutical industry become highly competitive, which means that whether one region can grasp new opportunities partially depends on its capabilities to coordinate a varity of development agents.
Trace elemental concentrations of bivalve shells content a wealthy of environmental and climatic information of the past, and therefore the studies of trace elemental distributions in bivalve shells gained increasing interest lately. However, after more than half century of research, most of the trace elemental variations are still not well understood and trace elemental proxies are far from being routinely applicable. This dissertation focuses on a better understanding of the trace elemental chemistry of Arctica islandica shells from Iceland, and paving the way for the application of the trace elemental proxies to reconstruct the environmental and climatic changes. Traits of trace elemental concentrations on A. islandica shells were explored and evaluated. Then based the geochemical traits of the shells, four non-environmental/climatic controlling is indentified. (1) Trace elemental concentrations of bivalve shells are effected by early diagenesis by the leach or exchange of elemental ions, especially in shell tip part, even with the protection of periostrucum; (2) The analytical methods also affect the results of trace elemental concentrations, especially for the element, such as Mg, which is highly enriched in organic matrices; (3) Shell organic matrices are found play a dominating role on the concentration of trace elements on A. islandica shells. Most trace elements only occurred in insoluble organic matrices (IOM), although others are only found in the carbonate fraction. IOM of A. islandica shells is significantly enriched in Mg, while Li and Na are more deplete in IOM, but enriched in shell carbonate. Ba is more or less even contented in IOM and shell carbonate. The concentrations of certain elements vary between primary layer and secondary layer; (4) The vital /physiological controlling on trace elemental distributions of bivalve shells is also confirmed. Six elemental (B, Na, Mg, Mn, Sr, and Ba) concentrations show significant correlation (exponential functions) with ontogenetic age and shell grow rates (logarithmic equations). It is worthy to remark that B, Mg, Sr and Ba concentrations are negatively correlated with shell growth rate, positive with ontogenetic age, while the concentrations of Na and Mn show the opposite trends. At last, all the controlling described above can be taken into account and corrected to extract the environmental and climatic signal by a kind of standardization. The derived six exponential functions of the high correlations between six trace elemental concentrations and ontogenetic year are applied to make the standardization of these element-Ca ratios. The gotten standardized indices are compared with the variations of environmental and climatic parameters in this region, and many correlations are found. Standardized indices of Sr/Ca ratios are strongly related to the sun spot number, autumn NAO, autumn Europe surface air temperature (SAT) and Arctic sea surface temperature anomaly (TA), and those of Mg/Ca ratios are strongly associated with Arctic TA, Europe SAT and Solar variation (irradiance). The variations of autumn Europe SAT demonstrated more similarity with standardized indices of B/Ca than other parameters. Except for the SAT index of Arctic, the standardized indices of Na/Ca showed no distinct relation to temperature. European precipitation and the Arctic sea level pressure index compared well the Na/Ca ratios of the shells, and so did the autumn NAO. Standardized indices of Mn/Ca were correlated with the number of hurricanes in the North Atlantic, Northern Europe SAT and sun spot number.
Mitochondria are dynamic organelles indispensible for viability of eukaryotic cells. Diffusion of proteins in mitochondrial membranes is a prerequisite for the correct functionality of the organelles. However, its study is made complicated due to the nontrivial geometry, small size and positional instability of the organelle, restricting the usability of regular experimental methods and theoretical understanding of acquired data. Therefore, here the molecular transport along the main mitochondrial axis was investigated using highly accurate computational methods combining them with traditional experimental approaches. Using recently reported electron microscopic tomography data concerning the constitution of mitochondria [Fre02], a lattice model of the inner mitochondrial membrane (IM) reproducing its structure in great details was built up. With Monte Carlo (MC) simulations of particle dynamics on this model, it was found that the membrane geometry induces nonlinear effects in the motion of molecules along the mitochondrial axis, which in turn lead to a transient violation of the 2nd Fick?s equation. We show that mere curvature of the IM resulting from the presence of cristae is sufficient for the emergence of transient anomalous diffusion (TAD) in the membrane. The MC calculations have enabled an accurate estimation of regularities in the extent of deviations from the normal regime, therefore allowing us to propose non-homogenous power law as a suitable generalization of the current approach to the analysis of experimental data for the transient dynamics. The general cause of TAD resulting from the membrane curvature alone, without any involvement of specific inter-particle interactions prompted us to predict the similar dynamical effect also for other curved cellular membranes, be it diffusion in endoplasmic reticulum or in plasma membrane of cells possessing dense microvilli. The data indicate that the geometry-induced anomalous diffusion should be easily detectable with current experimental methods, but only in the restricted range of time scales corresponding to high temporal resolution. Until now, experimental measurements of molecular diffusion in biological membranes indiscriminately assumed either pure normal or pure anomalous diffusion schemes for the analysis of data acquired in very wide range of temporal resolutions, which often lead to ambiguities in the interpretation of diffusion parameters. The MC calculations have clearly illustrated the necessity for a more subtle treatment of experimental conditions: the assumption of pure Gaussian diffusion model is justified only if the applied temporal resolution is sufficiently low (as is often the case when using scanning techniques exemplified further); otherwise, the transient regime should be tested for by means of the non-homogenous power function. In the second part of the study the Fluorescence Recovery after Photobleaching (FRAP) with the laser scanning microscope is introduced as a method of choice for studying protein mobility within mitochondrial membranes. The conventional FRAP methodology [Axe76] was extended to enable its application for the determination of confined diffusion with conventional laser scanning microscopes which allowed us to communicate for the first time the direct measurement of protein diffusion in mitochondrial membranes of living cells. This is achieved through adaptation of FRAP data analysis to account for the spatial dimensions of the organelle and the spatiotemporal pattern of light pulses induced by the microscope. The experimental circumstances existing during the particular measurement session are computationally recreated and this way the best suited values of diffusion parameters are found. The method is validated experimentally for four FP-tagged mitochondrial membrane proteins: the IM OxPhos complexes F1F0 ATPase and cytochrome c oxidase and for Tom7 and hFis1 - components of the mitochondrial protein import and fission machineries respectively localized in the outer membrane. We find that for all proteins simple normal diffusion is not a sufficient description. In the inner membrane, diffusion coefficient of F1F0 ATPase expressed in HeLa cell line is found to be 0.2 ?m2/s, with more than 1/3 of the protein molecules being immobilized, while cytochrome c oxidase (in CEF primary cells) demonstrated a similar diffusivity pattern (0.4 ?m2/s, 30% immobile). In the outer membrane, the D (0.7 ?m2/s) and immobile fraction (7-8%) of GFP-Tom7 and GFP-hFis1 (both in HeLa cells) are identical, which designates a substantial difference in comparison to the IM protein mobility. Diffusion coefficients of mitochondrial membrane proteins studied here lay in the intermediate region between those measured in artificial bilayers and in plasma membranes. Protein crowding and intermolecular interactions will be among the major causes responsible for the detected slowdown of diffusion.
Amphibians of Malawi : an analysis of their richness and community diversity in a changing landscape
(2009)
This study summarizes the state of the knowledge of the amphibian diversity in Malawi highlighting the possible threats impending on this fauna correlated with human encroachment and land use change. New data about diversity, distribution and ecology have been gathered, whereas the old ones have been summarised, reviewed and commented. In order to put in context the responses of the amphibian communities to land use change, the main environmental characteristics of the country at a broad space and time scale have been explored. Furthermore, the original habitats and vegetation have been described, and their status in the present day Malawi discussed. In the same way, an overview of the actual state of the knowledge about the Malawian amphibians has been provided, and their ability to act as surrogate of environmental integrity in Sub-Saharan Africa commented on the basis of the available studies. Afterwards, the results of the study of the selected areas and samples have been analysed within this newly generated context. Different field and laboratory methods were applied for the quantitative analysis of the richness and diversity of the communities. Opportunistic search was used to detect species richness, whereas the visual encounter survey was applied to detect the relative abundance of species. Several indices of diversity and similarity, and extrapolations by means of true richness estimators were used for the analysis of the alpha and beta diversities. Additional information were gathered by means of pitfall traps with drift fence, and by the recording of the advertisement calls. Supplementary methods were applied for the analysis of the taxonomic composition of the collected material. In Malawi 84 amphibian species are recorded, two of which still undescribed (Leptopelis sp. and Phrynobatrachus sp.). Three further species need to be confirmed and might be possibly present too: Amietia viridireticulata, Hemisus guineensis, and Hyperolius minutissimus. Additionally, other unrecognised cryptic species — at least one — are present within the Hyperolius nasutus complex. Most of the species belong to the order Anura (82 species; 97.6%), whereas only two species belong to the Gymnophiona (2.4%). Anurans are divided into 12 families and 23 genera, whereas the two caecilians species into one family (Caecilidae) and two genera. The more diverse family is the Hyperoliidae (21 species, 25%) followed by the families Ptychadenidae (13 species, 15%), Arthroleptidae (11 species, 13%), Phrynobatrachidae (10 species, 12%), and Bufonidae and Pyxicephalidae (9 species, 11% respectively). The remaining high family diversity (seven families, Caecilidae included) is contrasted by a low number of species (11 species in total, 14%). Based on the available distribution data, the value of species richness of the anuran communities in Malawi is comprised between 5‒45 species. In average 16.8 ± 9.0 species (N=80) are to be found, 75% of the sites have less than 21 species, and only two sites have more than 25 species. Four hot spots of amphibian diversity were identified: the Nyika Plateau (24 species), Mangochi-Malombe (25 species), Zomba Plateau (32 species) and the Mulanje Massif (45 species). In the studied areas a mean of 14.7 ± 1.6 species was observed and extrapolations by means of the true richness estimators were in good agreement with this result. Among the studied areas the richest was Palm Forest Reserve (17 species), followed by Kaningina Forest Reserve (16 species) and Vinthukutu F. R., and Vwaza W. R (15 species). The poorest area was the Misuku Mountains with 12 species only and a slightly different ranking was generated by the true richness estimators. The mean of the species present in the samples was 4.8 ± 2.1 species, considerably less than the true species richness detected in the respective areas. Basing on the ranking generated by the K-dominance plot the most diverse samples were Palm F. R. and Misuku, whereas the less diverse were Kaningina F. R. and Fort Lister, confirmed by the values of the diversity indices. The main finding of this study was the observation of the lack of a clear match between environmental degradation and amphibian diversity, and the crucial importance of temporary water bodies for the preservation of the amphibian diversity. In fact, despite most of the original habitat formerly present in Malawi have been destroyed and replaced by cultivations, the amphibian communities of different areas showed a comparable diversity at both family and species richness level, and no evident match between environmental degradation and amphibian diversity was recognisable. Differences in species richness could mostly be explained by natural factors such the elevation gradient and the presence of temporary water bodies. However, it was not possible to exclude that the communities have changed during historical time and the shift in species composition already occurred together with the modification of their relative frequencies. Most of the species showed a remarkable ecological plasticity and several species were found in a variety of both natural and altered habitats. The classification of the Malawian amphibians on the basis of ecological guilds based on the available natural history data showed the preponderance (76%) of generalist pond breeders. As a consequence, most of these amphibians possessed a scarce capacity to act as surrogates of habitat integrity. Based on the result of this study the farm bush landscape with traditional agriculture practices bears a great potential to support amphibian diversity in terms of species richness, representing a compromise between local economic development and conservation. Furthermore, the results of this study indicate the outstanding importance of the southern-east region of Malawi for the conservation of the country’s amphibians.
5-lipoxygenase (5-LO) is the key enzyme in the formation of inflammatory leukotrienes, which are mediators of inflammation and allergy. The 5-LO catalyses the oxidation of arachidonic acid to 5-HPETE and subsequently to LTA4. The leukotrienes are involved in the development and maintenance of inflammatory diseases, like asthma and allergic rhinitis. Additionally, 5-LO is overexpressed in some cancer types, although its relevance is still not fully understood. 5-LO expressing cells are B- lymphocytes and cells of myeloid origin like monocytes, macrophages and granulocytes. The 5-LO promoter lacks a TATA or CCAT box and covers two CpG islands. These are characteristics of a housekeeping gene, but as the 5-LO is not expressed ubiquitiously, the expression of the 5-LO is tightly regulated. Epigenetic mechanisms were known to be involved in the control of the 5-LO expression. The HDAC inhibitor TsA significantly induced the transcriptional activity of the 5-LO promoter in reporter gene assays as well as on 5-LO mRNA transcript level in MM6 cells. The GC-boxes GC4 and GC5 in the proximal 5-LO promoter were identified to be essential for the TsA effect, as deletion of these element led to an attenuated TsA effect in reporter gene assay. Recruitment of the transcription factors Sp1 and Sp3 and the RNA polymerase II to the 5-LO promoter was detectable after TsA treatment in MM6 cells by chromatin immunoprecipitation assays (ChIP), while the acetylation status of histone H4 remained unchanged. Likewise it is known that DNA methylation leads to silencing of 5-LO expression in-vitro and in-vivo. The 5-LO promoter is densely methylated in the cell line U937, but unmethylated in HL-60 cells and - elucidated in this study - also in MM6 cells. Reporter gene assays with in-vitro methylated 5-LO promoter containing plasmids revealed that the frequency of methylated CpGs is directly proportional to reduction of 5-LO promoter activity. Incubation of U937 cells with 5-AdC, an inhibitor of DNA methyltransferases, was able to reactivate 5-LO transcription and to demethylate CpG dinucleotides. In the first part of this study the mechanism of TsA induced promoter activation was further investigated. I elucidated the mechanism of Sp1 and Sp3 recruitment to the 5-LO promoter after TsA treatment. Immnoprecipitation assay was used to detect a transcription factor complex containing Sp1 or Sp3 interacting with HDAC proteins, which might change its composition after TsA treatment. Besides the posttranslational modifications of the transcription factors Sp1 and Sp3 after TsA treatment were investigated, potentially causing an increased interaction of the proteins with the 5-LO promoter. Both aspects and their response in HDAC inhibition have been described. TsA did not affect the composition of the Sp1/HDAC1/HDAC2 complex. Sp3 was not located in a complex with the HDAC enzymes. Acetylation of Sp1 and Sp3 was detectable, but no change occurred after TsA treatment. Since neither release of the transcription factors off a complex, nor alterations in posttranslational modifications of Sp1 and Sp3 are the reason for the increased Sp1 and Sp3 binding to the 5-LO promoter, I elucidated alterations in the chromatin structure. The acetylation status of the histone proteins H3 and H4, as well as the chromatin marks H3K4me3, representing active chromatin, and H3K9me, representative for repressive state, were investigated. Additionally, the time course of the TsA effect was determined on 5-LO mRNA level using real-time PCR. The acetylation status of the histone proteins on the 5-LO core promoter correlated with the basal 5-LO mRNA transcript expression in MM6, HL-60 and U937 cells. The highest 5-LO mRNA level was detectable in MM6 cells, followed by HL-60 cells. The lowest 5-LO mRNA level was detected in 5-LO promoter methylated U937 cells. The order of the basal 5-LO mRNA expression of the three cell lines correlates with the basal acetylation status of histone proteins H3 and H4. In MM6 cells the highest basal levels in acH3 and acH4 were detected, followed by HL-60 and U937 cells. Moreover, the data obtained in U937 cells revealed that the correlation between DNA methylation and histone hypoacetylation is alike on the 5-LO promoter. TsA treatment induced the 5-LO mRNA level in the three cell lines with different intensity: 5-LO mRNA level in MM6 cells was induced 11-fold, in HL-60 cells 6- fold and in U937 cells 4- fold. The histone acetylation and methylation levels on the 5-LO promoter after TsA incubation were investigated. No increase in acH3 and acH4, but in H3K4me3 was detectable in MM6 cells by ChIP assay. HL-60 cells showed an increase in acH3 and acH4 as well as in H3K4me3. H3K9me was only detectable in untreated U937 cells, but disappeared after TsA treatment, while acH3, acH4 and H3K4me3 increased constantly after TsA treatme nt. A strong correlation between the histone modifications and the time course of the mRNA expression was detectable in all three cell lines. The combination of the posttranslational modifications acH3, acH4 and H3K4me3 led to a fast effect in transcriptional activation and the maxima of acH3 and acH4 were usually associated with the maximum in 5-LO mRNA transcript level. An increase in H3K4me3 alone, as detected in MM6 cells, led to continuous increase in the 5-LO mRNA expression with a late maximum. Additionally, we detected a slight overall decrease in 5-LO promoter methylation in U937 cells after TsA treatment. This fact taken together with the observed histone modifications could explain the 4- fold response in 5-LO mRNA level to TsA treatment of the methylated cell line U937. Another aim of the present study was to identify the specific HDAC enzymes involved in the 5-LO promoter regulation. Reporter gene assays and real-time PCR with selective HDAC inhibitors revealed that HDACs of class I are involved in 5-LO promoter regulation, namely HDAC 1, 2 and 3. The influence of each of the enzymes seemed to depend on the cell type, as inhibition of HDACs 2, 3 strongly induced 5-LO promoter activity in reporter gene assay in HeLa cells, whereas in MM6 cells HDACs 1 and 2, 3 seemed to be responsible for the 5-LO promoter regulation, measured as 5-LO mRNA level. The HDACs of class IIa and class III are not involved in the regulation of 5-LO mRNA expression. The second part of this study investigated the influence of MBD proteins on the methylated 5-LO promoter and the 5-LO mRNA expression. ChIP assays revealed MBD1, 2 and MeCP2 protein binding to the proximal 5-LO promoter in U937 cells. MBD1 was detectable on the 5-LO promoter in unmethylated HL-60 cells, while no MBD protein was located on the 5-LO promoter in MM6 cells. To elucidate the functional role of the MBD proteins, stable knocked down of MBD proteins was established in U937 cells. 5-LO mRNA transcript level was determined in the knock down clones by real-time PCR. The 5-LO transcript level was increased in all knock down samples. MBD2 knock down clones showed the highest effect in activating 5-LO with a 3- and 4.4-fold increase in the 5-LO mRNA level, followed by MBD1 (3.5- fold) and MeCP2 (2.5-fold) knock down clones. A combined participation of these three enzymes in the corepression of the methylated 5-LO promoter is indicated. Taken together, the data reveal that epigenetic mechanisms are strongly involved in the regulation of 5-LO transcription and might function as a crucial control mechanism of 5-LO expression.
Acute myeloid leukemia (AML) is a hematopoietic cell disorder characterized by a block in differentiation and increased proliferation and survival of malignant blasts. Expansion of the malignant cell clone effects the normal production of blood cells and – if left untreated – leads to death. Receptor tyrosine kinases (RTKs) play an important role in the pathogenesis of AML, as they are either often mutated or overexpressed. In normal hematopoiesis, RTK signal termination is tightly controlled, and involves ubiquitination, internalization, endocytosis and degradation. Cbl proteins are E3 ligases and have been shown to ubiquitinate several activated RTKs, including Flt3 and Kit, targeting them for degradation. Recently, several Cbl mutations have been identified: Cbl-R420Q was identified in an AML patient and Cbl-70Z was identified in a mouse lymphoma model. In this thesis work, the role of these Cbl mutants in Kit signaling and in a mouse transplantation model was studied. Cbl mutants (Cbl-R420Q, Cbl-70Z) have the ability to transform the myeloid 32D cell line in cooperation with Kit WT. Cbl mutants along with Kit promoted interleukin-3 (IL3)-independent proliferation and enhanced the cell survival of 32D cells. In contrast, expression of the Cbl mutants alone did not confer IL3-independent growth. Stem cell factor (SCF, the Kit ligand) dependent growth was enhanced in the presence of Cbl mutants and Cbl mutants promoted colonogenic growth in the presence of Kit. Furthermore, Cbl mutants inhibited the ubiquitination of the activated Kit receptor. In addition, Cbl mutants inhibited the endocytosis of the activated Kit receptor. Retroviral expression of Cbl mutants in transplanted bone marrow induced a generalized mastocytosis, a myeloproliferative disease and, in rare care cases, myeloid leukemia. Splenomegaly was observed in the presence of Cbl mutants. Furthermore, mast cells with variable range of infiltration were noticed in all the vital organs (spleen, liver, bone marrow, lung, kidney, heart) of Cbl (mutant) transplanted mice. Almost all recipients of bone marrow cells transduced with Cbl mutants developed a lethal hematologic disorder with a mean latency of 341 days in the Cbl-R420Q group and 395 days in the Cbl-70Z group. This is the first published report on a hematological disease with Cbl mutants in a mouse model. Co-immunoprecipitation studies indicated that Cbl-70Z binds to Kit, even in the absence of Kit ligand. Cbl-R420Q also bound to Kit in the absence of SCF, albeit to a lesser extent. Association of Cbl mutants to Kit was enhanced in the presence of SCF. Signaling studies demonstrated the constitutive activation of Akt and Erk in the presence of Cbl mutants and Kit. In addition, Cbl mutants enhanced the SCF-dependent Kit, Akt and Erk activation. Cbl-70Z, in association with kinase-dead Kit (Kit-KD) or kinase-dead Flt3 (Flt3-KD), conferred IL3-independent growth and survival to the myeloid 32D cell line. Cbl-R420Q provided only a slight growth advantage in the presence of Kit-KD. As demonstrated by pharmacological inhibition studies, Akt activation was necessary for the transformation mediated by Cbl-70Z and Kit-KD / Flt3-KD. Cbl mutants enhanced the Src family kinases (SFKs) activity. The pharmacological inhibition of SFK activity inhibited the proliferation and colonogenic growth. Interaction was found between Cbl-70Z, SFKs and Kit-KD. The SFK member Fyn was identified to bind to Cbl. In addition, kinase activity of SFKs was necessary for binding to Cbl, since SFKs inhibition by PP-2 abolished the binding between the complex-binding partners. Dasatinib and PP-2, both SFK inhibitors, inhibited the Cbl and Akt phosphorylation indicating that Fyn acts upstream of Akt. Inhibition of Kit with imatinib reduced the proliferation of cells overexpressing Kit WT and Cbl-70Z much stronger compared with cells expressing Kit-KD and Cbl-70Z, but much less than the dual KIT/SFK inhibitor dasatinib. This indicated that Kit kinase activity was required but not essential. The data presented in this thesis work implies that both RTK and SFK inhibition may have to be targeted, in order to effectively prevent transformation. In summary, the present thesis work indicates an important role of Cbl, Kit and SFKs in myeloid transformation and deregulated signal transduction.
In this work we investigate phenomenological aspects of an anisotropic quark-gluon plasma. In the first part of this thesis, we formulate phenomenologicalmodels that take into account the momentumspace anisotropy of the system developed during the expansion of the fireball at early-times. By including the proper-time dependence of the parton hard momentum scale, phard(), and the plasma anisotropy parameter, Xi, the proposed models allow us to interpolate from 0+1 pre-equilibrated expansion at early-times to 0+1 ideal hydrodynamics at late times. We study dilepton production as a valuable observable to experimentally determine the isotropization time of the system as well as the degree of anisotropy developed at early-times. We generalize our interpolating models to include the rapidity dependence of phard and consider its impact on forward dileptons. Next, we discuss how to constrain the onset of hydrodynamics by demanding two requirements of the solutions to the equations of motion of viscous hydrodynamics. We show this explicitly for 0+1 dimensional 2nd-order conformal viscous hydrodynamics and find that the initial conditions are non-trivially constrained. Finally, we demonstrate how to match the initial conditions for 0+1 dimensional viscous hydrodynamics from pre-equilibrated expansion. We analyze the dependence of the entropy production on the pre-equilibrium phase and discuss limitations of the standard definitions of the non-equilibrium entropy in kinetic theory.
The various OPE mixtures were also tested on sSOI material which consists of a thin strained silicon layer on top of an insulator like silicon dioxide. The OPE A, B and F are able to reveal threading dislocations (TD) in the strained silicon film (chapter 5.11). The TD densities determined for the OPE A correspond very well with those obtained with the Secco diluted reference. The tested OPE mixtures are not able to delineate other crystal defects like stacking faults, pile ups or twins, which also appear in the strained silicon. Some Organic Peracid Etches were also tested on wafers with an epitaxial silicon layer and on silicon substrates. Epitaxially produced silicon layers are nearly defect-free. Etching times were chosen such that only a part of the epitaxial layer was removed. Nevertheless, after very long etching times (> 16 h) isolated pits were found, with defect densities ranging from 104/cm3 to 106/cm3 depending on the etching solution used. No etch pits were found in the remaining epitaxial layer when OPE F was used. Longer etching times appear to favour the formation of artefects. These artefacts could be caused by the formation of gas bubbles, particles or micro scratches at the crystal surface. The OPE C and D are able to reveal vacancy agglomerates (D-defects) in silicon substrates (see under 5.5, 5.6 and 5.11in chapter 5). Due to their low removal rates and the long etching times which favour the formation of artifacts, these solutions are less suited to the delineation of defects in silicon substrates. In the second part of this study the different etch formulations have been compared with each other in respect of their physical properties like removal rates, activation energies, standard potentials and selectivities (chapter 6). The selectivity was determined at etch pits caused by dislocations. The depth of the etch pits, determined by atomic force microscopy (AFM), should be dependent on the selectivity of the corresponding etching solution used. The higher the selectivity of the solution the deeper the etch pit should be. It was assumed that a low removal rate and a high activation energy for the etching process should correspond to a high selectivity. However, the experimental results have shown that it is not possible to predict the selectivity of an etching solution from experimental parameters like removal rate or activation energy. One must bear in mind that selectivity was only determined on one particular type of crystal defect, namely on dislocations. Values for selectivity in the etching solutions can differ for other defect types. Besides the etching solutions used in this study differ considerably from each other in respect of their chemical and physical roperties. They can be divided into three completely different etching systems. The original Secco solution and the diluted variations thereof are hydrofluoric acid-dichromate mixtures with the Cr6+ species as the oxidizing agent. The Jeita and MEMC solutions contain nitric acid, hydrofluoric acid and, as diluents, acetic acid and water. Here the oxidizing agents are various N(III) species which are formed autocatalytically during the etching process. The concentration of acetic acid also plays an important role as it lowers the degree of dissociation of HF and of HNO3. This has an influence on the pH and the standard potential of the etching solution. The Organic Peracid Etches are mixtures of hydrogen peroxide and a short-chain alkanoic acid like acetic acid. Such systems are strictly speaking not aqueous solutions, the reactive species is the peracid formed.Within each system, however, a certain relationship is perceived between the selectivity of the etching solution on the one hand, and the and the activation energy or the removal rate on the other. The decreased activation energy for the etching process of silicon at a dislocation can be calculated from experimental data by using the Arrhenius equation (chapter 6.3). It was found that the strain inside the crystal lattice caused by a dislocation loop leads to an increase of the potential energy of ~ 5 % and, hence, a decrease of the activation energy of ~ 5 % and an increase in the removal rate of ~ 100 %.
Enantioselective carbon-carbon bond-forming reactions, particularly, using organocatalysts represent one of the most important areas in modern synthetic chemistry. New concepts and methods in organocatalysis are emerging continuously, allowing more selective, economically more appealing and environmentally friendlier transformations. Chiral Brønsted-acid catalysts have recently emerged as a new class of organocatalysts for a number of enantioselective carbon-carbon bond-forming reactions. The first part of this thesis focused on the new development of new Brønsted acid-catalyzed enantioselective Nazarov cyclizations. The Nazarov reaction belongs to the group of electrocyclic reactions and is one of the most versatile methods for the synthesis of five-membered rings, which are the key structural elements of numerous natural products. In general, the Nazarov cyclization can be catalyzed by Brønsted or Lewis acids. However, only a few asymmetric variations have been described, of which most require the use of large amounts of chiral metal complexes. The reactivities of Nazarov cyclizations are also depending on the substituents of the divinyl ketone substrates as described in the first chapter. The substrates to study Brønsted acid-catalyzed enantioselective Nazarov cyclization were prepared following the known procedures. The dihydropyran was treated with tBuLi in THF at –78 oC and then the α,β-unsaturated aldehydes 1 were added to the reaction mixture to afford the corresponding alcohols 2 in moderate to good yields. The alcohols 2 were oxidized to divinyl ketones 3 employing Dess-Martin periodinane/pyridine (DMP/py) in CH2Cl2 at room temperature to obtain the divinyl ketones 3 in moderate to good yields (Scheme 1). Scheme 1. Preparation of substrates in order to study Brønsted acid-catalyzed enantioselective Nazarov cyclization and subsequent transformations. At the starting point, an evaluation of suitable Brønsted acid catalysts for the enantioselective Nazarov cyclization of divinyl ketone 3a was performed. The initial reactions conducted with various BINOL-phosphoric acids 4a-4e in toluene at 60 oC provided the mixture of cis and trans cyclopentenones 5a with enantioselectivities of up to 82% ee (Table 1, entries 1-5). Eventually, improved reactivity could be achieved by using the corresponding N-triflylphosphoramides 4f and 4g, which even at 0 oC gave complete conversion after ten minutes. Additionally, it was shown that the use of these catalysts significantly enhanced both the diastereoselectivity (cis/trans ratio up to 7:1) and the enantioselectivity (up to 96% ee; Table 1, entries 6 and 7). Table 1. Evaluation of Brønsted acids 4a-4g in the enantioselective Nazarov cyclization. The scope of the Brønsted acid-catalyzed enantioselective Nazarov cyclization of various divinyl ketones 3 was explored under an optimized reaction condition (Scheme 2). Treatment of divinyl ketones 3 in CHCl3 in the presence of 2 mol% chiral BINOL-Ntriflylphosphoramide 4g at 0 oC for 1-6 h provided the corresponding cyclopentenone 5 in good yields (45-92%) with excellent enantioselectivities (up to 93% ee) (Scheme 2). Furthermore, the isomerization of cis-cyclopentenone under basic condition led to the corresponding trans-cyclopentenone without loss of enantiomeric purity. This efficient method introduced here was not only the first example of an organocatalytic electrocyclic reaction but also represented the first enantioselective activation of a carbonyl group catalyzed by a chiral BINOL phosphoric acid. Compared to the metal-catalyzed reaction, special features of this new Brønsted acid-catalyzed electrocyclization are the lower catalyst loadings (2 mol%), higher enantioselectivities, accessibility to all possible stereoisomers, as well as the mild conditions. ....
An eclogite barometer has profound importance in the study of upper mantle processes and potential application to diamond prospecting. Studies on the partitioning of Li between clinopyroxene (cpx) and garnet (grt) in natural samples have shown that this particular element is very sensitive to changes in pressure and could be calibrated as the barometer demanded for bimineralic eclogites. Experiments were performed from 4 to 13 GPa and 1100 to 1400°C in the CMAS (CaO, MgO, Al2O3, SiO2) system with Li added as Li3PO4 to quantify this pressure dependence into a barometer expressed in the following equation: P= (0.00255*T-lnKd)/0.2351 where P is in GPa, T is in °C and Kd is defined as the partition coefficient of Li (in ppm) between clinopyroxene and garnet. The experimental pressures are reproduced to ± 0.38 GPa (1σ) by this equation. This barometer is strictly applicable only to CMAS. Experiments at 1300°C, 8-12 GPa showed that Henry’s Law is fulfilled for Li partitioning between cpx and grt in the concentration range of approximately 0.01 – 1 wt% Li. Direct application of the equation to experiments in natural systems performed at 1300°C from 4 GPa to 13 GPa consistently overestimates pressures by approximately 2 GPa. Our previous experiments in the system CaO-MgO-Al2O3-SiO2 + Li3PO4 showed that the partitioning of Li between garnet and clinopyroxene is pressure dependent in eclogitic bulk compositions. This supports experimentally the hypothesis of Seitz et al. (2003), based on the analysis of Li in eclogitic xenoliths and inclusions in diamond, that the partitioning of this particular element between clinopyroxene and garnet is very sensitive to changes in pressure and could be calibrated as a barometer for bimineralic eclogites. In order to calibrate this pressure dependence into a barometer, experiments were performed in natural systems using starting materials sourced from a well preserved eclogitic xenolith from the Roberts Victor kimberlite pipe (South Africa) to extrapolate our findings in CMAS to natural systems. Sixteen multianvil experiments were performed from 4-13 GPa and 1100-1500°C. Our findings reinforced the general trend we observed in the CMAS system, that KdLi cpx-grt for Li decreases with increasing P, and that at P ≥ 12 GPa, garnet is able to incorporate more Li than clinopyroxene. Multiple linear regression was applied to our experimental results to create the barometer: P = (0.000963*T – ln KdLi cpx-grt + 1.581) / 0.252 Where P is pressure in GPa, T is temperature in °C and KdLi cpx-grt is defined as the partitioning coefficient of Li obtained by dividing the concentration of Li in cpx by the concentration of Li in garnet. This barometer reproduces the experimental conditions to ± 0.2 GPa. It is applicable to eclogitic xenoliths, to garnet pyroxenites and to peridotitic and eclogitic inclusions in diamond. Application of the barometer to diamond bearing xenoliths results in pressures in the diamond stability field. Clinopyroxene is easily corrupted in xenoliths and also preferentially takes in Li during short lived metasomatic processes. Care must be taken therefore to analyse primary, unaltered clinopyroxene. Our preliminary application to natural samples shows that the barometer can be applied beyond the experimental range to pressures down to 3 GPa. Seventeen eclogitic xenoliths were chosen from a sample set of greater than 200 for their fresh microscopic and macroscopic appearance and were analyzed for Li content in coexisting garnet (grt) and clinopyroxene (cpx). These samples can be subdivided into two groups on the basis of Mg in cpx (cpfu: cations per formula unit, based on 6 oxygens): Group 1 with Mg > 0.75, and Group 2 with Mg < 0.75. Group 1 xenoliths show lower Li contents in both grt and cpx compared to Group 2. The Li barom ter calibrated in Hanrahan et al. (2009b)/Chapter 3 was applied to these samples as well as available literature data to obtain pressures of provenance - Group 2 xenoliths often provide pressures that appear unrealistic for eclogitic xenoliths. In light of observed crystal chemical relations in the natural samples, a new fitting procedure was applied to the experimental data presented in Chapter 3. This new fit appears to be more realistic than the previous fit, although a strong relationship with Mg# remains present, suggesting that Li-barometry is, at present, only applicable to Mg-rich eclogites. Inclusions in diamond, with the exception of eclogitic inclusions of coexisting majorite and cpx, often yield pressures that are inconsistent with the pressures required for diamond formation. Although an interesting observation when comparing all of the data is that inclusions in diamond have significantly higher average Li concentrations compared to xenoliths, which suggests that Li is highly present in the fluids from which diamonds form in the mantle, an observation which was previously made for the deep mantle as a result of high Li in ferropericlase inclusions in diamond (Seitz et al. 2003).
This thesis demonstrates the advancement of PELDOR spectroscopy beyond its original design of distance measurements in order to disentangle a maximum amount of information additionally encoded in the PELDOR data. In particular, the successful synthesis of novel polynitroxide radicals is described as well as the extraction of the relative orientation of spin labels, conformational flexibility and the separation of dipolar and exchange coupling via orientation selective PELDOR measurements in combination with PESIM based simulations. Moreover, the method of PELDOR "Spin Counting" was experimentally validated.
The characterization of microscopic properties in correlated low-dimensional materials is a challenging problem due to the effects of dimensionality and the interplay between the many different lattice and electronic degrees of freedom. Competition between these factors gives rise to interesting and exotic magnetic phenomena. An understanding of how these phenomena are driven by these degrees of freedom can be used for rational design of new materials, to control and manipulate these degrees of freedom in order to obtain desired properties. In this work, we study these effects in materials with small exchange interaction between the magnetic ions such as metal-organic and inorganic dilute compounds. We overcome the dfficulties in studying these kind of materials by combining classical and quantum mechanical ab initio methods and many-body theory methods in an effective theoretical approach. To treat metal-organic compounds we elaborate a novel two-step methodology which allows one to include quantum effects while reducing the computational cost. We show that our approach is an effective procedure, leading at each step, to additional insights into the essential features of the phenomena and materials under study. Our investigation is divided into two parts, the first one concerning the exploration of the fundamental physical properties of novel Cu(II) hydroquinone-based compounds. We have studied two representatives of this family, a polymeric system Cu(II)-2,5-bis(pyrazol-1-yl)-1,4-dihydroxybenzene (CuCCP) and a coupled system Cu2S2F6N8O12 (TK91). The second part concerns the study of magnetic phenomena associated with the interplay between different energy scales and dimensionality in zero-, one- and two-dimensional compounds. In the zero-dimensional case, we have performed a comprehensive study of Cu4OCl6L4 with L=diallylcyanamide=NC-N-(CH2-CH=CH2)2 (Cu4OCl6daca4). Interpretations of the magnetic properties for this tetrameric compound have been controversial and inconsistent. From our studies, we conclude that the common models usually applied to this and other representatives in the same family of cluster systems fail to provide a consistent description of their low temperature magnetic properties and we thus postulate that in such systems it is necessary to take into account quantum fluctuations due to possible frustrated behavior. In the one-dimensional case, we studied polymeric Fe(II)-triazole compounds, which are of special relevance due to the possibility of inducing a spin transition between low and high spin state by applying a external perturbation. A long standing problem has been a satisfactory microscopic explanation of this large cooperative phenomenon. A lack of X-ray data has been one mitigating reason for the absence of microscopic studies. In this work, we present a novel approach to the understanding of the microscopic mechanism of spin crossover in such systems and show that in these kind of compounds magnetic exchange between high spin Fe(II) centers plays an important role. The correct description of the underlying physics in many materials is often hindered by the presence of anisotropies. To illustrate this difficulty, we have studied a two dimensional dilute compound K2V3O8 which exhibits an unusual spin reorientation effect when applying magnetic fields. While this effect can be understood when considering anisotropies in the system, it is not sufficient to reproduce experimental observations. Based on our studies of the electronic and magnetic properties in this system, we predict an extra exchange interaction and the presence of an additional magnetic moment at the non-magnetic V site. This sheds a new light into the controversial recent experimental data for the magnetic properties of this material.
Neutron stars are very dense objects. One teaspoon of their material would have a mass of five billion tons. Their gravitational force is so strong that if an object were to fall from just one meter high it would hit the surface of the respective neutron star at two thousand kilometers per second. In such dense bodies, different particles from the ones present in atomic nuclei, the nucleons, can exist. These particles can be hyperons, that contain non-zero strangeness, or broader resonances. There can also be different states of matter inside neutron stars, such as meson condensates and if the density is height enough to deconfine the nucleons, quark matter. As new degrees of freedom appear in the system, different aspects of matter have to be taken into account. The most important of them being the restoration of the chiral symmetry. This symmetry is spontaneously broken, which is a fact related to the presence of a condensate of scalar quark-antiquark pairs, that for this reason is called chiral condensate. This condensate is present at low densities and even in vacuum. It is important to remember at this point that the modern concept of vacuum is far away from emptiness. It is full of virtual particles that are constantly created and annihilated, being their existence allowed by the uncertainty principle. At very high temperature/density, when the composite particles are dissolved into constituents, the chiral consensate vanishes and the chiral symmetry is restored. To explain how and when chiral symmetry is restored in neutron stars we use a model called non-linear sigma model. This is an effective quantum relativistic model that was developed in order to describe systems of hadrons interacting via meson exchange. The model was constructed from symmetry relations, which allow it to be chiral invariant. The first consequence of this invariance is that there are no bare mass terms in the lagrangian density, causing all, or most of the particles masses to come from the interactions with the medium. There are still other interesting features in neutron stars that cannot be found anywhere else in nature. One of them is the high isospin asymmetry. In a normal nucleus, the amount of protons and neutrons is more or less the same. In a neutron star the amount of neutrons is much higher than the protons. The resulting extra energy (called Fermi energy) increases the energy of the system, allowing the star to support more mass against gravitational collapse. As a consequence of that in early stages of the neutron star evolution, when there are still many trapped neutrinos, the proton fraction is higher than in later stages and consequently the maximum mass that the star can support against gravity is smaller. This, between many other features, shows how the microscopic phenomena of the star can reflect into the macroscopic properties. Another important property of neutron stars is charge neutrality. It is a required assumption for stability in neutron stars, but there are others. One example is chemical equilibrium. It means that the number of particles from each kind is not conserved, but they are created and annihilated through specific reactions that happen at the same rate in both directions. Although to calculate microscopic physics of neutron stars the space-time of special relativity, the Minkowski space, can be used, this is not true for the global properties of the star. In this case general relativity has to be used. The solution of Einstein's equations simplified to static, spherical and isotropic stars correspond to the configurations in which the star is in hydrostatic equilibrium. That means that the internal pressure, coming mainly from the Fermi energy of the neutrons, balances the gravity avoiding the collapse. When rotation is included the star becomes more stable, and consequently, can be more massive. The movement also makes it non-spherical, what requires the metric of the star to also be a function of the polar coordinate. Another important feature that has to be taken into account is the dragging of the local inertial frame. It generates centrifugal forces that are not originated in interactions with other bodies, but from the non-rotation of the frame of reference within which observations are made. These modifications are introduced through the Hartle's approximation that solves the problem by applying perturbation theory. In the mean field approximation, the couplings as well as the parameters of the non-linear sigma model are calibrated to reproduce massive neutron stars. The introduction of new degrees of freedom decreases the maximum mass allowed for the neutron star, as they soften the equation of state. In practice, the only baryons present in the star besides the nucleons are the Lambda and Sigma-, in the case in which the baryon octet is included, and Lambda and Delta-,0,+,++, in the case in which the baryon decuplet is included. The leptons are included to ensure charge neutrality. We choose to proceed our calculations including the baryon octet but not the decuplet, in order to avoid uncertainties in the couplings. The couplings of the hyperons were fitted to the depth of their potentials in nuclei. In this case the chiral symmetry restoration can be observed through the behavior of the related order parameter. The symmetry begins to be restored inside neutron stars and the transition is a smooth crossover. Different stages of the neutron star cooling are reproduced taking into account trapped neutrinos, finite temperature and entropy. Finite-temperature calculations include the heat bath of hadronic quasiparticles within the grand canonical potential of the system. Different schemes are considered, with constant temperature, metric dependent temperature and constant entropy. The neutrino chemical potential is introduced by fixing the lepton number in the system, that also controls the amount of electrons and protons (for charge neutrality). The balance between these two features is delicate and influenced mainly by the baryon number conservation. Isolated stars have a fixed number of baryons, which creates a link between different stages of the cooling. The maximum masses allowed in each stage of the cooling process, the one with high entropy and trapped neutrinos, the deleptonized one with high entropy, and the cold one in beta equilibrium. The cooling process is also influenced by constraints related to the rotation of the star. When rotation is included the star becomes more stable, and consequently, can be more massive. The movement also deforms it, requiring the metric of the star to include modifications that are introduced through the use of perturbation theory. The analysis of the first stages of the neutron star, when it is called proto-neutron star, gives certain constraints on the possible rotation frequencies in the colder stages. Instability windows are calculated in which the star can be stable during certain stages but collapses into black holes during the cooling process. In the last part of the work the hadronic SU(3) model is extended to include quark degrees of freedom. A new effective potential to the order parameter for deconfinement, the Polyakov loop, makes the connection between the physics at low chemical potential and hight temperature of the QCD phase diagram with the height chemical potential and low temperature part. This is done through the introduction of a chemical potential dependency on the already temperature dependent potential. Analyzing the effect of both order parameters, the chiral condensate and the Polyakov loop, we can drawn a phase diagram for symmetric as well as for star matter. The diagram contains a crossover region as well as a first order phase transition line. The new couplings and parameters of the model are chosen mainly to fit lattice QCD, including the position of the critical point. Finally, this matter containing different degrees of freedom (depending on which phase of the diagram we are) is used to calculate hybrid star properties.
Many questions regarding gastropod phylogeny have not yet been answered like the molecular confirmation of the Heterobranchia concept based on morphological studies from Haszprunar (1985a; 1988). This taxon contains the “Lower Heterobranchia” with several “primitive” or “basal” members) and the Euthyneura (with the Opisthobranchia and Pulmonata). Phylogenetic relationships of subgroups within the Heterobranchia have not been satisfactorily resolved and monophyly of some taxa within the Heterobranchia (e.g. Opisthobranchia) is questionable. Moreover, most of the “Lower Heterobranchia” have not been included in former molecular studies. In order to resolve phylogenetic relationships within the Heterobranchia, I pursued a molecular systematic approach by sequencing and analysing a variety of genetic markers (including nuclear 28S rDNA + 18S rDNA and mitochondrial 16S rDNA + COI sequences). Maximum likelihood as well as Bayesian inference methods were used for phylogenetic reconstruction. The data were investigated a priori to tree reconstruction in order to find the most appropriate dataset for reconstructing heterobranch phylogeny. A variety of statistical tests (like Chi-Square-Test or Relative-Rate-Test) were applied and the substitution saturation was measured. The Relative-Rate-Test revealed the highest evolution rates within the “Lower Heterobranchia” (Omalogyra sp., Omalogyra fusca, Murchisonella sp., Ebala sp. and Architectonica perspectiva) and Opisthobranchia (Hyalocylis striata). Furthermore, many of the nucleotide positions show a high degree of substitution saturation. Additionally, bipartitions (splits) in the alignment were examined and visualized by split network analyses to estimate data quality. A high level of conflict indicated by many parallel edges of the same lengths could be observed in the neighbournet graphs. Moreover, several taxa with long terminal branches could be identified in all three datasets belonging to the Vetigastropoda, Caenogastropoda, “Lower Heterobranchia” or Opisthobranchia (Nudipleura). All phylogenetic analyses revealed a monophyletic Heterobranchia. Within the Heterobranchia several well supported clades could be resolved. However, the traditional classification based on morphological data could not be confirmed due to paraphyletic Euthyneura (because of the inclusion of the Pyramidellidae and Glacidorboidea) as well as paraphyletic Pulmonata and polyphyletic Opisthobranchia. Based on the phylogenetic inferred evolutionary trends regarding habitat colonisation or character complexes could be deduced. A case study was conducted in order to estimate divergence ages using a “relaxed” molecular clock approach with fossils as minimum age constraints. However, due to large 95% confidence intervals a precise dating of the nodes was not possible. Hence, the results are considered as preliminary. To test the plausibility of the newly obtained hypotheses, the results were evaluated a posteriori using a hypothesis test and secondary structures of the complete 18S rRNA and 28S rRNA. Secondary structure motifs were found within domain 43 and E23 2 &5 of the 18S rRNA as well as within domain E11 and G5_1 of the 28S rRNA, which contain phylogenetic signals to support various groups within the Heterobranchia. In addition, taxon specific motifs were found separating the Vetigastropoda from the Caenogastropoda and Heterobranchia, indicating a possible application of the secondary structure of 18S rRNA and 28S rRNA to reveal phylogenetic relationships at higher taxonomic levels such as Gastropoda or even Mollusca. The utility of the newly invented software RNAsalsa for the reconstruction of secondary structures was tested. The obtained structures were used to adjust evolutionary models specific to rRNA stem (paired basepairs) and loop (unpaired basepairs) regions with the intention of improving phylogenetic results. This approach proved unsuccessful. This molecular phylogenetic investigation provides the most comprehensive molecular study of Heterobranchia relationships to date. Substantial insights into the evolution and phylogeny of this enigmatic taxon have been gained.
In the production of integrated circuits (ICs), photolithography plays a key role in wafer structuring. The basic principle of photolithography is the selective processing of areas (etching, implantation, metallisation etc.) while the others are covered and therefore protected by the resist. After each process step the resist, now modified, has to be removed. In the history of semiconductor manufacturing this has been accomplished with a mixture of H2SO4 and H2O2, H2SO4 and O3 or a plasma etch. As the structure sizes decreased they reached a stage where they had to be exposed to light of shorter wavelengths for the photolithography, going from i-line (365 nm) to DUV (248 nm and 193 nm). This change in wavelength now requires new resists and therewith new stripping methods. Beside the changes in the resist the finer structures are also more sensitive to damages caused by the resist strip. Along with this the demand for cost reduction and environment-friendliness poses a big challenge for modern resist stripping. In this study ozone in deionised water (DI/O3) was the basic chemistry investigated as it is cost efficient in production and disposal as well as environment friendly. Furthermore it is a chemistry known to cause no damage to the wafers. DI/O3 has been successfully applied to strip i-line resists. The challenge now is to find ways and means to make DI/O3 strip even highly implanted DUV resists which currently can only be removed by a plasma etch. To achieve this a detailed understanding of the behaviour of ozone in DI water and the influence of factors both chemical and physical on the stripping efficiency at the different stages in the process is necessary. Along with this, methods which enable the elucidation of resist structures and the changes they undergo during the process of photolithography as well as during the ozone strip have to be developed. This will enable us to understand the mechanisms involved and hence, ideally, develop ozone-based stripping solutions customized for each resist and process step. For this purpose the ozone decomposition in DI water with and without additives was studied via UV-Vis spectroscopy. Radicals generated within the ozone decomposition were trapped and quantified, the resists were studied directly on the wafer with IR and Raman spectroscopy and stripped with DI/O3-mixtures and different setups to find optimum conditions for a complete and damage free resist strip. UV-Vis spectroscopy at 260 nm was used to study ozone decomposition and the factors, both chemical and physical, which influence it. These factors are pH, different additives at the same pH, temperature and mixing of the solution. For the radical determination trapping reactions with MeOH and DMSO both forming CH2O which is further converted to DDL as the detectable species were compared with a variation of the classical iodometric titration acting as an absolute method without the need of calibration. IR spectroscopy proved to be a suitable method for the structural characterisation of the resists and the tracking of the changes undergone during the various processing steps as well as the ozone based stripping. For the stripping with DI/O3 IR spectroscopy delivered well-defined spectra. These displayed significant peak changes which support the assumption of classical ozonolysis as the decomposition mechanism for the unimplanted resist. For the study of the resist crust originating from ion implantation IR was fundamentally unsuitable and was replaced by Raman spectroscopy and microscopy. Raman spectra showed the crust to be of a highly carbon containing structure. Regrettably, the peak assignable to the crust was too broad for the exact composition of the crust to be determined. The wavelength region of the peak corresponds to that of peaks of glassy carbon and highly ordered and conventional graphite. Such a broad peak suggests that the structure of the crust is not uniform but contains more than one carbon modification. As the purpose of all these studies is to enable or improve DI/O3 based resist stripping on unimplanted as well as high-dose implanted resists the removal efficiency of DI/O3 spiked with different additives that alter the pH was studied. For these unimplanted resists the maximum efficiency could be achieved at pH = 5 – 7. Lowering or increasing the pH beyond this range gave poor results. The stripping of highly implanted resists could be achieved only at harsh conditions with a high pH-level of 12 - 13 with a narrow process window showing no stripping at lower pHs and severe damages at higher levels. The principle application of DI/O3 stripping chemistry could be proved but the currently required process time unfortunatelly is too long for commercial application and needs further optimisation.
Based on the commonly used and well-established state-of-the-art DNA sequencing method, i. e. Sanger sequencing, the major target of future research is to develop a fast, cost-effective and gelelectrophoresis-free sequencing method. The aim of the new sequencing technologies is to detect DNA mutations faster and more accurate in order to develop individual therapies for patients (personalized medicine). For this purpose, a lot of novel sequencing techniques like pyrosequencing, mass-spectrometry-assisted sequencing, sequencing by hybridization etc. have been put into practice and already led to commercialized sequencers. The sequencing technology we were mostly interested in is the so-called sequencing-by-synthesis method (SBS). This PhD thesis covers the synthesis of modified nucleosides – the so-called reversible terminators – and their evaluation as reversible terminators. These 3′-modified and dye-labeled nucleotides are incorporated by the polymerase into the DNA-template, then the DNA-synthesis is stopped. After detection of the fluorescent signal, the reversible terminator has to be cleavable in a way (i. e. the polymerase-blocking modification) that the DNA-synthesis can continue. As a result of the polymerase-acceptance tests that have been carried out with the two triphosphates cyanoethoxymethyl(CEM)-dTTP and cyanoethyl(CE)-dTTP as substrates it became clear that the latter one was better incorporated than the first one. Based on this knowledge all four key compounds for the whole reversible terminators possessing the cyanoethyl (CE) group where synthesized within this PhD thesis. Additionally to the synthesis of the modified key compounds, the cleavability of the cyanoethyl function had to be evaluated which is an essential requirement of a reversible terminator for SBS. For addressing this issue, three different CE- and CEM modified monophosphates were created. For each of these three monophosphates an individual synthetic strategy has been developed within this PhD work, each of these strategies and subsequent phosphorylation led to the desired modification. These previously unknown model compounds mimicking the solubility of short oligonucleotides were employed the for qualitative cleavage experiments after their purification and spectroscopical characterization. With these three monophosphates suitable cleavage conditions for a quantitative removal of the CE and the CEM group were examined. In case of the CE function we selectively improved the cleavage conditions while varying the solvent, the reaction temperature as well as the amount of cleaving agent used, in order to make the conditions applicable for an SBS experiment. Due to the fact that the CE function was the most important modification for our SBS experiment, we could even optimize the cleavage efficiency by employing co-solvents like DMSO or DMF. An additional cleavage experiment was carried out by using a short CE-modified oligomer which led to further results that were comparable to the ones obtained from the cleavage experiments of the monomers. One big difference is the required amount of TBAF as cleaving agent for the quantitative removal of the CE-modification from the oligomer. In this case, 7500 equivalents of TBAF are needed for complete CE cleavage at 45 °C compared to the amount of 40 to 80 equivalents TBAF for the monomer (monophosphate). As a conclusion of this result we assume that the amount of cleaving agent and the solubility of the oligomer plays an important role in the CE cleavage efficiency. This assumption was already supported by Saneyoshi et al. who demonstrated for CE-modified RNA oligonucleotides that the CE-cleavage rate is strongly lowered with the increasing of the oligomer length. Thus we could demonstrate that the CE function is quantitatively removable from an oligomer without destroying it. With these results in hands we could prove that the CEM and the CE group are quantitatively cleavable and therefore applicable as blocking groups for reversible terminators. The conditions for the CE cleavage are used for the ArraySBS-“proof-of-principle” which is currently under investigation.
Photosystem (PS) I is a huge membrane protein complex which coordinates around 200 co-factors. Upon light excitation a charge separation at the PS I reaction centre is induced which leads to an electron transport across the thylakoid membrane and the generation of redox equivalents needed for several biochemical reactions, e.g. the synthesis of sugars. For higher plants and cyanobacteria the crystal structure of PS I complexes were resolved to resolutions of 4.4 Å and 2.5 Å. Furthermore, supramolecular structures of PS I of eukaryotic algae, mainly of the green line, were obtained recently. However, up to now, no structure of diatoms is available yet. Diatoms are key players in global primary production and derived from a secondary endosymbiosis event. Their chloroplasts are surrounded by four envelope membranes and their thylakoids are evenly arranged in bands of three, i.e. no separation in grana and stroma regions is apparent. In this thesis a protocol was developed to isolate a functional PS I complex of diatoms which can be used for structural analysis by transmissional electron microscopy (TEM). A photosystem I-fucoxanthin chlorophyll protein (PS I-FCP) complex was isolated from the pennate diatom Phaeodactylum tricornutum by ion exchange chromatography. Spectroscopic analysis proved that bound Fcp polypeptides function as a light-harvesting complex. An active light energy transfer from Fcp associated pigments, Chl c and fucoxanthin, towards the PS I core was proven by fluorescence spectroscopy. Oxidised minus reduced difference spectroscopy evidenced the activity of the PS I reaction centre P700 and yielded a chlorophyll a/P700 ratio of approximately 200:1. These data indicate that the isolated PS I-FCP complex exceeds the PS I cores from cyanobacteria and higher plants in the numbers of chlorophyll a molecules. Because of the strict conservation of PS I cores among organisms the additional 100 chlorophyll a molecules must either be coordinated by Fcps or function as linker molecules between the Fcp antenna and the PS I core as shown for the PS I-LHC I complex of higher plants. To tell something about the structural organisation, the PS I-FCP complex was compared with its cyanobacterial and higher plant counterparts. Whereas cyanobacterial PS I cores aggregate to trimers, usually without associated antennae, higher plant PS I is a monomer and binds additionally two LHC I heterodimers. BN-PAGE and gel filtration experiments showed that also diatoms contain PS I monomers associated with Fcps as light-harvesting antenna. First TEM studies evidenced these observations. Negatively stained PS I-FCP particles had an increased size compared to PS I cores of other organisms. No PS I trimers or higher oligomers have been found. The calculated diameter and shape of the particles correspond to PS I-LHC I particles obtained from green algae, which also comprise of a higher number of LHC I polypeptides compared to the higher plant x-ray structure. Additionally, the analysis of polypeptides indicates that the PS I associated Fcps differ from the free Fcp pool and also from Fcps of a PS II enriched fraction. The assumption that diatoms harbour just one Fcp antenna that serve both Photosystems equally seems to be wrong. To further study the association of Fcps with the two Photosystems, both complexes plus the free FCP complexes were isolated from the centric diatom Cyclotella meneghiniana. Because of the availability of antibodies directed against specific Fcp polypeptides of Cyclotella the PS I-FCP complex of Phaeodactylum could not be used. A trimeric FCP complex, FCPa, and a higher FCP oligomer, FCPb, have already been described for C. meneghiniana. The latter is assumed to be composed of only Fcp5, whereas the FCPa contains Fcp2 and Fcp6. Biochemical and spectroscopical evidences revealed a different subset of associated Fcp polypeptides within the isolated photosystem complexes. Whereas the PS II associated Fcp antenna resembles FCPa, at least three different Fcp polypeptides are associated with PS I. By re-solubilisation of the PS I complex and a further purification step Fcp polypeptides were partially removed from PS I and both fractions were analysed again by biochemical and spectroscopical means, as well as by HPLC. Thereby Fcp4 and a so far undescribed 17 kDa Fcp were found to be strongly coupled to PS I, whereas another Fcp, presumably Fcp5, is only loosely bound to the PS I core. Thus an association of FCPb and PS I is assumed.
In the framework of this thesis the intense low energy ion beam transport was investigated. Especially, the beam transport in toroidal magnetic field configurations was discussed, as it may allow the accumulation of high intensive beams in the future. One of the specific tasks is to design an injection system that can be used for the proposed low energy accumulator ring. This thesis regarding beam transport investigations is related to the larger research fields, storage rings used in accelerator physics and non-neutral plasmas. The proposal of building a storage ring with longitudinal guiding magnetic fields was made. Due to natural transversal focussing in magnetic fields it is possible to accumulate very intense charged particle beams, a subject of interest within the physics community. A simulation code (TBT) was written to describe the particle motion in curved segments. Particle in Cell techniques were utilized to simulate a multi particle dynamics. This code allows the user to generate different particle distributions as input parameter. A possibility of reading an external data file was made available so that a measured distribution can be used to compare simulation results with measured ones. A second order cloud in cell method was used to calculate charge density and in turn to solve Poisson’s equation. The circular toroidal coordinate system was used. The drift motion and gyrating motion was proved to be consistent with analytical values. Further simulations were performed to study the self field effects on beam transport. The experiments with single toroidal segments find niche in the work. The experiments were performed to compare the simulation results and gain practical experience. The toroidal segment has similar dimensions (major axis R = 1:3 m, minor axis r = 0:1 m, arc angle 30°) as for a full scale ring design. The main difference lies in the magnetic field strength. The available segments can be operated at room temperature producing 0:6T on axis maximum magnetic field, while for the storage ring design this value is in the range of 5T. The preparatory experiments consisted of building and characterization of the ion source in a first step. Along with the momentum spectrometer and emittance scanner the beam properties were studied. Low mass ion beams He+ and mixed p, H2+, H3+ beams were analyzed. The proton beam consisting of a 48% H+ fraction was extracted regularly and used for further experiments. A moderate beam energy of 10 keV was chosen as operational energy for which 3.08 mA proton beam current was measured. In the second stage, beams were transported through a solenoid and the phase space distribution was measured as a function of the magnetic field for different beam energies. The phase-space as distributions measured in a first stage were simulated backward and then again forward transported through the solenoid. The simulated results were then compared with the measured distribution. The LINTRA transport program was used. The phase-space distribution was further simulated for transport experiments in a toroidal magnetic field. The experiments with a single toroidal segment give basic results necessary to compare the results between transport code (TBT) and measurements. The optical diagnostic provides measurements which can be well compared with the simulated results. A digital camera with a magnetic shield was used to record images in jpeg file format. A subroutine was written to analyze an image file to give the intensity distribution of a given image file. The integrated profile in vertical and horizontal direction was used to calculate the vertical drift and the beam size. The simulated values were in good agreement with the measured ones. The injection system needs most care. The transport program that was used to simulate the beam in the toroid was also used to design the injection system. The injection system with its special field configurations was designed to perform experiments with room temperature segments. The main point to tackle was to smoothly bring the charged particles generated outside the trap into the acceptance of the ring. The designed system consists of two sources, one representing a ring beam and the other one the injection beam. While simulations showed a clear way, how to inject the particle beam via a well positioned solenoid and in combination with a transverse electric field element causing an ExB drift into the main ring acceptance. After construction of these injection elements it will be very important to measure the robustness of such a system with respect to the beam stability- especially of the injection channel.
The pictorial art of the Church, as a spiritual product of the Christian civilisation, has continually received great influences from its ecclesiastical tradition and it was defined by its formal aesthetical standards and its iconographic preferences. A more nuanced reading of the parallels can be attained by placing the images in their visual context, which would allow a better appreciation of the meanings within. The biblical story of Adam and Eve, which is the theme of the following thesis, reflects the differentiation between the Eastern and the Western understanding of the events of the history of the holy Oikonomia, a point, which is the major ground for the development of the relative pictorial motifs. The protoplasts are the protagonists from their creation and life in paradise, the fall and expulsion until their resurrection through Christ. Their story is visualised in a number of scenes and episodes, having thus their original sin and resurrection for specific reasons centralised. This doctoral thesis attempts to collect as many parallels of the scenes is possible, trying to collate the Eastern with the Western visual approach in a deductive way, in order to reach our constructive conclusions and make available the combination of the art, theology and liturgy in the scenes of Adam and Eve in Genesis and in Resurrection (Anastasis). The reading we tried to perform was based upon the specific iconographical elements, which were worth to be commented. Our aim was to detect the direct bond between the production of art and the relevant patristic and apocryphal writings or even the theological theories, by quoting texts from the ecclesiastical literature, as well as the liturgical praxis.
Macrophages show a remarkable functional plasticity, which enables them to change their phenotype in response to environmental signals. They are key players during infection by initiating inflammation through the release of proinflammatory mediators. Furthermore, macrophages contribute to the resolution of inflammation by phagocytosis of apoptotic granulocytes. Phagocytosis of apoptotic cells (AC) induces an anti-inflammatory phenotype in macrophages and protects them against apoptosis. However, mechanistic details provoking these phenotype alterations are incompletely understood. Therefore, the aim of my Ph.D. thesis was to investigate the molecular basis of anti-inflammatory macrophage polarization. In the first part of my studies, I investigated the expression of heme oxygenase (HO)-1 in macrophages following treatment with supernatants from AC. HO-1 catalyzes the first and rate-limiting step of heme degradation and potentially bears anti-inflammatory as well as anti-apoptotic potential. I was able to show biphasic upregulation of HO-1 by AC supernatants. The first phase of HO-1 induction at 6 h required activation of p38 MAPK and was accomplished by the bioactive lipid sphingosine-1-phosphate (S1P) engaging S1P receptor 1 (S1P1). However, the second wave of HO-1 induction at 24 h was attributed to autocrine signaling of vascular endothelial growth factor (VEGF) A, whose expression was facilitated by S1P. The release of VEGFA from macrophages was STAT1-dependent, whereas VEGFA itself acted on the macrophage HO-1 promoter via STAT1/STAT3 heterodimer binding. Knockdown of HO-1 revealed its relevance in promoting enhanced expression of the anti-apoptotic proteins B cell leukemia/lymphoma-2 (Bcl-2) and B cell leukaemia/lymphoma-x long (Bcl-XL), as well as the anti-inflammatory adenosine receptor A2A. MHC II and indoleamine 2,3-dioxygenase expression were also affected by ACsupernanatants, but were not HO-1 dependent. Unexpectedly, S1P1 was also upregulated following treatment with AC supernatants. Thus, I considered whether S1P1 induction could specifically be mediated by alternative macrophage activating factors. The expression of S1P1 was enhanced in the presence of the alternative activation stimuli IL-4 as well as IL-10, whereas it was unchanged following incubations with LPS, interferon-g or S1P. My next aim was to investigate the expression of the different S1P receptor isoforms in macrophages following treatment with supernatants form AC. While the expressions of S1P1 as well as S1P3 were induced by exposure to supernatants from AC, S1P2 expression was unaffected. As S1P1/3 and S1P2 are conflictively involved in the regulation of cell migration, I asked for a correlation between increased S1P receptor expression and enhanced migration rate. Indeed, macrophages showed enhanced motility following treatment with supernatants form AC, which was inhibited in S1P1 knockout macrophages. In summary, my findings indicate that HO-1, which is induced by AC-derived S1P, is critically involved in macrophage polarization towards an alternatively activated macrophage phenotype. S1P1 seems to represent a central checkpoint during macrophage activation. On the one hand, S1P1 is induced by supernatants form AC and promotes migration of macrophages. On the other hand, it mediates the induction of HO-1, which is accompanied by antiinflammatory as well as anti-apoptotic signaling. Furthermore, my studies provide evidence that upregulation of HO-1 and S1P1 in macrophages may contribute to the resolution of inflammation by establishing an anti-inflammatory macrophage phenotype and provoking macrophage migration along the vascular S1P gradient out of an inflammatory environment into the lymph.
Na+/H+ antiporters are ubiquitous membrane proteins involved in ion homeostasis and pH sensing. The amino acid sequence of one such antiporter, MjNhaP1, from Methanococcus jannaschii, shows a significant homology to eukaryotic sodium proton exchangers like NHE1 from Homo sapiens and SOS1 of Arabidopsis thaliana than to the well-characterized Escherichia coli NhaA or NhaB. MjNhaP1 shows activity at acidic pH unlike NhaA, which is active at basic pH. 13 transmembrane helices have been predicted to be present in NhaP1. A projection map, calculated by Cryo-EM of 2D crystals of MjNhaP1 grown at pH 4, showed it to be a dimer containing elongated densities in the centre of the dimer and a cluster of density peaks on either side of the dimer core (Vinothkumar et al., 2005). Incubation of 2D crystals at pH 8 on the EM grid resulted in well-defined conformational changes, clearly evident in a difference map as a major change in density distribution within the helix bundle (Vinothkumar et al., 2005). The aim of this dissertation is to understand the working mechanism of MjNhaP1 by determining its three-dimensional structure. The aim was initially approached by structure determination by X-ray crystallography. The limitation for this method was the low expression yield, which was 0.5–0.7mg/ml (Vinothkumar et al., 2005). After various optimization trials, the expression yield of the recombinant protein could be elevated to 2-2.5mg of pure protein per litre of culture by the method of autoinduction (Studier et al., 2005). To obtain well diffracting 3D crystals, purification conditions (Vinothkumar et al., 2005) were modified. 3D crystals were obtained under various conditions, which has so far not diffracted X-Ray beyond 8Å. Parallely, optimization of parameters (Vinothkumar et al., 2005) for 2D crystals formation was carried out. A combination of 1% DDM used for lipid solubilization, and 1% OG in the buffer of the purified protein produced 1-2 μm wide tubular 2D crystals of NhaP1. This batch of crystal proved to be the optimal for data collection at higher tilt angle with the electron microscope. A 3D map showed p22121 symmetry and revealed a tight dimer with an oval shape. The region in the central part of the dimer is composed of several tilted helices forming an interface between both monomers. On either side of the dimer interface, a group of six tightly packed helices form a bundle. This bundle contains three straight helices in the centre of the monomer and three helices in the periphery. Comparison of the structures of E.coli NhaA and M. jannaschii NhaP1 show substantial differences in length and slope of corresponding helices between both antiporters. A 3D model of NhaP1 based on the 3D map revealed 13 helices, which has been named as A-M to distinguish it from the NhaA helices. Overlaying the X-ray structure onto the 3D map revealed that the disrupted helices IV and XI of NhaA superimpose two central helices at similar position in the 3D map of NhaP1. The disrupted helices IV and XI in the X-ray structure of NhaA have been proposed as the putative ion-binding and translocation site (Hunte C et al, 2005; Arkin IT et al, 2007; Screpanti & Hunte (2007). This motif appears to be present also in NhaP1, as suggested by the close fit of NhaA helices IV and XI on the putative helices E and L of the NhaP1 model. These two putative helices E and L in NhaP1 contain the highly conserved TDP and GPRVVP motif, which are crucial for antiporter activity (Hellmer et al., 2002, Hellmer et al., 2003). In the overlay, helix V of NhaA containing the two essential, conserved aspartates D163 and D164 fits the density of the putative helix F of NhaP1, which contains the conserved motif FNDP. The homologous D161 in the FNDP motif of NhaP1 is essential for transport activity as show by mutagenesis (Hellmer at al., 2003). Significant differences are visible in the region of the dimer interface of the 3D map of NhaP1 occupied by helices VI, VII, and VIII in NhaA. This region shows an extra helical density (A) in the 3D map of NhaP1. By alignment of MjNhaP1 sequence with the amino acid sequences of several Na+/H+ exchangers, it was evident that the additional helix (A) is located in the N terminus of NhaP1. In our sequence alignment, a putative hydrophobic segment corresponding to this additional helix A is present in other archaeal and eukaryotic antiporters but not in any of the bacterial ones. The N-terminus of the human Na+/H+ exchanger NHE1 has been predicted to contain a highly hydrophobic signal peptide. This indicates the probability of the N-terminal helix A of NhaP1 to be an uncleaved signal peptide. Besides being a signal sequence targeting NhaP1 to the membrane, the map suggests that this helix might be involved in the formation of dimer contacts between both monomers. A gene duplication event is evident in the 3D map of NhaP1, as not only the helices D, E, F and K, L, M are related by an inverted repeat but also the helices B, C and I, J are related. We present here the three-dimensional architecture of a Na+/H+ antiporter from archaea. The presence of the 13th helix suggests the location of the N-terminus to be located in the cytosol and the C-terminus in the periplasm. This would orient NhaP1 in an inverted manner in the membrane in comparison to NhaA. Further structural information at higher resolution and biochemical and biophysical investigations are required to confirm the topology.
1. Fab co-complexes of proton pumping NADH:ubiquinone oxidoreductase (complex I) Fab fragments suitable for co-crystallization with complex I were generated using an immobilized papainbased protocol. The binding of the antibody fragments to complex I was verified using Surface Plasmon Resonance and size exclusion chromatography. The binding constants of the antibodies and their respective Fab fragments were found to be in the nanomolar range. This work presents the first report on successful crystallization of complex I (proton pumping NADH:ubiquinone oxidoreductase) from Yarrowia lipolytica with proteolytic Fab fragments. The quality of the crystals was significantly improved when compared to the initial experiments and the best crystals diffracted X-rays to a resolution of ~7 Å. The activity of complex I remained uninfluenced by antibody fragment binding. The initial diffraction data suggest that the complex I/Fab co-complex crystals represent a space group different to the one observed for the native protein. Ongoing experiments are aimed at further enhancements of the diffraction quality of the crystals. Providing a different space group the CI/Fab co-complexes may become a very useful approach for structure determination of the enzyme. Moreover, the bound Fab offers an additional possibility to generate phase information. The antibody-mediated crystallization represents a valuable tool in structural characterization of the NADH:oxidoreductase subcomplexes or even single subunits. 2. UDP-glucose pyrophosphorylase UDP-glucose pyrophosphorylase from Yarrowia lipolytica displays affinity towards Ni2+ NTA and was first detected in a contaminated sample of complex I. Following, separation from complex I, Ugp1p was purified using anion exchange chromatography. Sequence similarity studies revealed high identity to other known pyrophosphorylases. As indicated by laser-based mass spectrometry method (LILBID) Ugp1p from Y. lipolytica builds octamers similarly to the enzyme from Saccharomyces cerevisiae. The initial crystals grew as thin needles favorably in sitting drop setups. The size of the crystals was increased by employment of a micro batch technique. The improved crystals diffracted X-rays to a resolution of 3.2 Å at the synchrotron beamline. Structural characterization is under way using a molecular replacement approach based on the published structure of baker’s yeast UGPase.
P2X receptors represent the third superfamily of ligand gated ion channels with ATP as their natural ligand. Most of the mammalian P2X receptors are non-selective cation channels, which upon activation, mediate membrane depolarization and have physiological roles ranging from fast excitatory synaptic transmission, modulation of pain-sensation, LTP to apoptosis etc. In spite of them being an attractive drug target, their potential as a drug target is limited by the lack of basic understanding of the structure-function relationship of these receptors. In my thesis, I have investigated the behavior of homomeric P2X receptor subunits with the help of photolabeling and fluorescence techniques coupled to electrophysiological measurements using Xenopus laevis oocytes heterologous expression system. Concurrent photolabeling by BzATP and current recordings from the same set of receptors in real time has revealed that the gating process in homomeric P2X receptors is contributed individually by each subunit in an additive manner. Our study for the first time describes the agonist potency of Alexa-ATP (a fluorescent ATP analog) on P2X1 receptors. The use of Alexa-ATP in our experiments elucidated that receptor subunits are not independent but interacting with each other in a cooperative manner. The type of cooperativity, however, depended on the type and concentrations of allosteric/competing ligands. Based on our results, in my thesis we propose an allosteric model for ligand-receptor interactions in P2X receptors. When simulated, the model could replicate our experimental findings thus, further validating our model. Further, correlation between occupancy of P2X1 receptors (determined using binding curve for Alexa-ATP) with the steady-state desensitization suggests that binding of three agonist molecules per receptor are required to desensitize P2X1 receptors. We further extended the approach of fluorescence with electrophysiological measurement to assign the role for different domains in P2X1 receptors with the help of environmental sensitive, cysteine reactive fluorophore (TMRM). Cysteine rich domain-1 of P2X1 receptors (C117-C165) was found to be involved in structural rearrangements after agonist and antagonist binding. In contrast to the present understanding, that the binding of an antagonist cannot induce desensitization in P2X1 receptors and the receptors need to open first before undergoing desensitization, we propose based on our results that a competitive antagonist can also induce desensitization in P2X1 receptors by bypassing the open state. We have attempted to answer few intriguing questions in the field of P2X receptor research and we think that our answers provide many avenues to the basic understanding of functioning of P2X receptors.